Faculty of Science Research Report 2005/06 - NUI Maynooth

ForewordContentsIt is my pleasure to introduce theNational University of IrelandMaynooth Faculty of Science ResearchReport for 2005-2006. This reporthighlights the activities of Facultymembers in research and scholarship,representing a record of achievementthat is a testament to the vibrantacademic culture that exists at NUIMaynooth. This is the 18th such reportand is the most extensive in that series.I would like to offer sincere thanksto all the members of the Faculty fortheir efforts in teaching, research andpublic service throughout the past year.Details on all the research activitiesof the Faculty are contained in thepages that follow, creating a cataloguethat is both impressive in scope andfascinating in detail.Dean’s Review 3Biology 11Chemistry 39Computer Science 47Experimental Physics 67Mathematics 79Mathematical Physics 93Psychology 107Research Institutes 127Hamilton Institute 128Institute of Bioengineering and Agroecology 139Institute of Immunology 140National Institute for Cellular Biotechnology 142NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06CONTENTSDr Bernard P. MahonDean, Faculty of ScienceNUI MaynoothTel: 01-7083835Email: science.dean@nuim.ie1

Dean’s ReviewC O N T I N U E DMaynooth Scientsts visit theSpace shuttle flight deck.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 DEAN’S REVIEWNUIM scientists research improved urban transport schemesformation of the Institute of Microelectronics andWireless Systems (IMWS) under the leadership of Dr.Ronan Farrell. The IMWS has secured over€4.5 million from SFI and Enterprise Ireland andhas built strong relations with partner companies.The Institute specialises in combining electronicsand wireless technologies to create new productsand is designing and prototyping new wirelessdevices and silicon microchips.awarded to new scientists was the second highest inthe faculty’s history (Table 1). When one considersthat NUIM does not have an associated Universityhospital or medical school, this figure represents aremarkable success and evidence that once againNUIM is performing well above expectations.Distribution of Current Science Research Funding (Fig. 1)6The flavour of research activity showcased abovereflects an expansion in scale of scientific outputand a rise in scientific quality at NUIM. Theseimpressions are supported by analysis of thescientific activity at Maynooth. In terms of funding,NUIM had secured €49.88 million (Fig. 1). This isa staggering 17% increase on 2004, which wasitself our best year ever. 2005 was also a recordbreaking year in terms of the number of researchstudents studying within the faculty (Table 1). Thenumber research degrees (PhD/research Masters)

Cancer cells studied at NUI MaynoothThis report and indeed this introduction havefocused on research activity, but last year’s reportmade a forceful case that undergraduate educationmust not be neglected. Those comments stillpertain. The quality and integrity of undergraduateprogrammes have to be maintained. Facultiesevolved in the great European Universities toperform that function and they have an importantand continuing role in setting the benchmark ofwhat a scientific education means. The Faculty ofScience at NUIM has undergone and will continueto change and develop. The degrees offered are nowmodularised but a large amount of faculty time hasbeen devoted to assuring the quality of the newofferings and paths available for student learning.There is a temptation to believe that limitless vistasof student choice, the a la carte degree, are somehowthe future of student learning. After all, what couldbe more empowering than letting the “customer”decide what to study? It may seem an attractiveidea, but it is a highly questionable approach. TheRex Waldheim, astronautvisits NUIMweakness is evident when we ask the question ofwhat a Bachelor of Science degree actually means?Few would argue that some opportunity for chemiststo study philosophy or history for example might beuseful, but at what point does choice compromise aprogramme’s integrity? After all, future employerswill expect Chemistry graduates to be competentin at least the basics of organic chemistry as well.These are difficult and complex questions, theanswers should be informed by national strategy,the opinions of external professional bodies andindeed the collected wisdom of faculty. Obviouslystudents should have options and choice, howeverabandoning students to a featureless educationallandscape, which purports to offer unlimitedoptions, is in effect a denial of quality to students. Itignores the experience of the academy, and makesstrategic and integrated education very difficult.There is a danger that Universities create anundergraduate bill of fare that promises unlimitedhorizons, but offers very little support. The pointNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06DEAN’S REVIEW7

Dean’s ReviewC O N T I N U E DScience undergraduates prepare for their research project8NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 DEAN’S REVIEWis that choice must be informed; faculties have acritical role to inform that choice in the modernuniversity and to assure the quality and integrity ofthe learning opportunities for students. The facultyof Science at NUIM has led the country in offeringgenuinely modularised and semesterised programsof undergraduate study, but at Maynooth the facultyhas also played a major role in maintaining theintegrity and quality of the programs. This importantand continuing role is not just setting the benchmarkof scientific education but is also about supportingstudents in rational choices relevant to nationalstrategy.This introduction began by arguing that Irish Sciencewas at a crossroads in 1994. The question then waswhether Ireland would support scientific activityin anything beyond a token way. The decision tofund Science was taken just in time. The economiccompetition now is from China, India, Singapore whoare investing heavily in fundamental research. TheShuttle astronauts prepare for mission.NUIM has collaborations with NASAand the European Space Agency.challenge for Ireland will be to innovate. This surveyof the Faculty of Science research activity in 2005sees Ireland and NUI Maynooth approach anothercrossroads. The challenge has been outlined bynumerous commentators, but can be summarised as“how can a small nation with a successful economybut limited resources, best serve her citizenry?” Thechallenge for Ireland and Maynooth is the same,how do we continue to “punch above our weight”?The answer in both cases is creativity. Ireland aimsto be the creative epicentre of the emerging world,NUI Maynooth has a central role in achievingthat strategy. Just as the HEA PRTLI encourageduniversities to behave strategically, to organise andoperate in new ways. So too in 2006, universitieswill need to act strategically to meet the futurechallenges; to increase the scale and quality ofour scientific output once again. Certainly, this willrequire a further investment in the infrastructurewithin the universities, but also new approaches toresearch and learning. Indeed Maynooth is fortunate

NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 BIOLOGYAcademic StaffProfessor K. Ohlendieck, DipBiol, MSc (Konstanz), PhD, Head of Department (2002-)*Professor A.M. Burnell, BSc, MSc, PhD (1974-)Professor P.J. Dix, BSc, PhD (Leicester), FIBiolI, EurBiol (1980-)Professor M.J. Downes, MAgrSci, PhD, FIBiolI (1973-)Dr. D. Doherty, BA (Mod), MSc, PhD (London) (2000-)Dr. S. Doyle, BSc, PhD (1997-)Dr. M.A. Fares, BSc, PhD (Valencia) (2003-)Dr. C.T. Griffin, BSc, PhD (Dublin) (1992-)Dr. G. Jones, BSc, PhD (Liverpool) (2004-)Dr. K.A. Kavanagh, BSc, PhD (1994-)Dr. B.P. Mahon, BSc (Kent), PhD (Open University) Wellcome Trust Fellow (1998-)Dr. J. McInerney, BSc, PhD (1999-)Dr. N.B. Murphy, BA(Mod), PhD (Dublin) (2005-)Dr. J. Nugent, BSc, MSc, PhD (Michigan) (1995-)Dr. S. O’Dea, BSc, PhD (2001-)Dr. W. Reardon, BSc, PhD (1998-2005)Adjunct ProfessorsProfessor J. Burke, BAgrSci, MSc, PhD (2002-)Professor L. Downey, PhD (Reading), DSc, LLD (2002-)Professor EmeritusProfessor P. Whittaker, BSc (Liverpool), PhD (Leicester), FIBiol, CBiol, FIBiolI, EurBiol (1978-)Principal InvestigatorsDr. P. Johnson, BSc, PhD (QUB) (2000-2005)Dr. C. Meade, BSc, PhD (Dublin) (2000-2005)Part-time Occasional LecturerMs. T. Redmond, BSc (1990-)Senior DemonstratorDr. J. O’Keeffe, BSc, PhD (2005-)12* Unless otherwise stated the higher degrees listed are those of the National University of Ireland.

Research FellowsDr. J. Boyd, BSc, MSc, PhD (Aberdeen) (2003-)Dr. K. Brady, BSc, PhD (2002-)Dr. C. Burns, BSc (Durham), Ph.D. (Bristol) (2003-2005)Dr. P. Corcoran, BSc, PhD (2005-)Dr. C. Creevey, BSc, MSc, PhD (2002-2005)Dr. N. Curran, BSc, PhD (2003-2005)Dr. A. Dillon, BSc, MSc (London), PhD (1998-)Dr. I. Dix, BSc, PhD (Szeged) (1984-2005)Dr. D. Fitzpatrick, BSc, PhD (2000-)Dr. B. Hogg, BSc (Coventry), PhD (Bristol) (2004-)Dr. S. Kahunyoshyeng Jordan, BSc, PhD (King Mongkut Univ) (2003-2005)Dr. M. Klaas, DipBiol, PhD (Kiel) (2004-)Dr. H. Loovers, BSc, MSc (Groningen), PhD (2004-)Dr. L. Madrigal-Estebas, BSc (Madrid), PhD (Dublin) (2002-)Dr. M. McCabe, BSc, PhD (Nottingham) (2000-)Dr. P. Medgyesy, BSc, PhD (Szeged) (2003-)Dr. C. Moore, BSc, PhD (2004-2005)Dr. J.B. Moore, BSc, PhD (Florida) (2005-)Dr. C. Neville, BSc (2000-)Dr. K.H. Nguyen, BSc, PhD (2004-)Dr. T. Nguyen Thi, BSc (Ho Chi Minh Univ), MSc (Freie Univ, Berlin), PhD (2000-)Dr. T. O’Connor, BSc, PhD (2001-)Dr. D. O’Connor, BSc, PhD (2005-)Dr. J. O’Keeffe, BSc, PhD (2000-2005)Dr. K. O’Hanlon, BSc (UU), PhD (Reading) (2004-)Dr. D. Pisiani, BSc, PhD (2004-)Dr. W. Reardon, BSc, PhD (2005-)Dr. E. Reeves, BSc, MSc, PhD (London) (2002-)Dr. K. Reiber, DipBiol ( Wernigerode) PhD(Jena) (2003-)Dr. A. Rolston, BSc (Exeter), PhD (2000-)Dr. D. Schreiber, DipBiol, PhD (Hamburg) (2003-)Dr. S. Travers, BSc, PhD (2001-)Postgraduate Research StudentsMr. M. Alsaiyah, HDip (Libya)(2005-)Mr. D. Bergin, BSc (2002-2005)Ms. L. Byrne, BSc (2005-)Ms. S. Cloney, BA (Mod) (Dublin) (2000-)Ms. J. Commins, BSc (2002-)Ms. M. Conroy, BSc (2005-)Ms. J. Conway, BSc (2005-)Ms. L. Corrigan, BSc (2002-)Ms. M. Corrigan, BSc (2004-)Ms. B. Culleton, BSc (2005-)Ms. C. Davis, BSc (2005-)Ms. P. Donoghue, BSc (2002-)Mr. P. Doran, BSc (2002-)NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06BIOLOGY13

Research Interests Of StaffDr. Philip DoranPost-doctoral fellow in theDepartment of BiologyWhat are your research interests?I am a postdoctoral fellow in the NUI MaynoothMuscle Biology Laboratory investigating thebiochemical effects of fibre aging on muscleperformance. I mostly work on Duchennemuscular dystrophy, the most common inheritedneuromuscular disorder in humans. During myPhD studies I identified several new biomarkers ofthis disease which is caused by genetic mutationsin the dystrophin gene. The most severe form ofmuscular dystrophy affects approximately 1:3500male newborns in Ireland. Dystrophic musclesshow impaired repair mechanisms, increasedfibre damage and the disease process is extremelyprogressive. Most patients are wheelchair-boundin their early teens, and there is currently no curefor this disorder. This gives basic biomedicalstudies into the pathology of muscle diseasesa central importance for the development ofimproved diagnostic procedures and noveltherapeutic strategies. Unlike conventionalbiochemical approaches to identify defectiveproteins in disease processes, which only focuson small numbers of genes or proteins, I used thenovel technique named proteomics. This methodallows for the large-scale analysis of the entireprotein compliment expressed by a given cell,the proteome. With the help of two-dimensionalgel electrophoresis, mass spectrometry anddensitometric scanning it was possible to separateand identify thousands of individual muscleproteins species and to evaluate the differentialexpression levels of these peptides in normalversus diseased muscle tissue.How do you fund your work?I am funded by an SFI award to ProfessorOhlendieckHow did you build your career to date?I completed my honours degree in Biology in2002 and was a PhD student from 2002-2005 inProfessor Ohlendieck’s research group. I wasfortunate to be awarded the Doctoral Prize ofAchievement in Science from NUI Maynooth. Myresearch findings were presented in 2005 to theWorld Muscle Society in Brazil and the MuscularDystrophy Ireland conference in Dublin, which wascovered in an Irish Times and an Irish MedicineWeekly article. Other work was published in theEuropean Journal of Biochemistry, the BiochemicalJournal and the top journal for protein massspectrometric research, Proteomics. The facilitiesand support at NUI Maynooth have been crucial tomy career so far.Bioinformatics and Pharmacogenomics LaboratoryDr. James McInerneyThe principal activities of the Bioinformatics and Pharmacogenomics Laboratory centreon the computational analysis of molecular data. There are four research divisions in theBioinformatics and Pharmacogenomics Laboratory – Software and Algorithms, Human Genome,Bacterial Genomes and Viral Genomes. We have developed software for the analysis of adaptiveevolution in protein-coding genes. Adaptive evolution is said to occur when there has beena rate of amino acid replacement substitutions that is higher than would be expected. Onefrequent result of adaptive evolution is a change in protein structure or function. We havealso developed algorithms and software for phylogenetic supertree construction. In order toconstruct phylogenetic trees from many gene sequences and from complete genomes it isnecessary to develop methods that can deal with missing data – since every genome doesnot have the same complement of genes. We have developed a number of methods that dealwith this issue and we are currently working on large supertree problems. We are workingon a number of bacterial genome sequences including the bacteria that cause meningitis andtuberculosis. The complete genome sequences from multiple strains of these bacteria are knownand we are working on identifying what they have in common, what is different and how thingshave changed in the recent past. Our viral genome work involves the analysis of HIV sequences.HIV is the aetiological agent of the human Acquired Immune Deficiency Syndrome (AIDS), adisease so deadly that unfortunately it needs no introduction. We are trying to identify factorsin the genome sequences that are of vital importance to the virus order for it to survive.Biotechnology LaboratoryDr. Sean DoyleResearch work in the laboratory is funded by the Higher Education Authority (HEA-PRTLI,Cycle 3), The European Union, Enterprise Ireland and The Irish Research Council for Science,Engineering and Technology (IRCSET). Our work, which resulted in a number of peer-reviewedpublications in 2005, is directed towards understanding microbial pathogenicity and is carriedout in close collaboration with Dr Kevin Kavanagh (NUI Maynooth) under the auspices ofthe National Institute for Cellular Biotechnology (NICB). The NICB, under the direction ofProfessor Martin Clynes, is an inter-institutional collaboration between researchers at NUIMaynooth, Dublin City University and IT Tallaght and was established in 2002. The work ofthe NICB group at NUI Maynooth is currently focused on biology, diagnosis and moleculargenetics of the human pathogenic fungus, Aspergillus fumigatus - a major cause of infectionin immunocompromised individuals. Our group has identified a number of potential virulencefactors (proteins) in the organism, which may contribute both to its pathogenicity and emergingresistance to conventional chemotherapies. In particular, we have identified a number ofnonribosomal peptide synthetases and glutathione s-transferases in A. fumigatus. Interestingly,nonribosomal peptide synthetases in fungi represent a novel source of bioactive metabolitesand our published work is at the cutting-edge of this internationally competitive area.Using a well-established recombinant protein expression system we have expressed a numberof A. fumigatus proteins in order to assess their diagnostic potential. In addition, we havedeveloped novel immunoassays to detect fungal metabolites. Proteomic studies of a number oforganisms, using Departmental MALDI-ToF mass spectrometry facilities, are also well underwayand peer-reviewed publications are now emerging from these efforts.BIOLOGYNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-0617

Research Interests Of StaffC O N T I N U E DWith respect to studies on parvovirus B19, a cause of severe disease in immunocompromised patientsand foetal loss, our group has deployed B cell ELISpot technology for the elucidation of the nature ofimmunological memory to the infectious agent in collaboration with Dr Brendan Crowley, St JamesHospital, Dublin, Ireland. Dr. Sean Doyle has recently co-authored a major review of the literature withrespect to parvovirus B19 and this work was published in the Journal of Medical Microbiology in 2004. TheBiotechnology group also has a number of academic and industrial collaborations directed towards theunderstanding and development of novel diagnostic strategies for human and animal infectious agents (e.g.,human metapneumovirus). Moreover, group members have been pro-active in the promotion of the publicunderstanding of science through participation in such activities as the NUI Maynooth Chain Reaction LectureSeries and the National Science Week.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 BIOLOGYEcology LaboratoryProfessor Martin J. DownesThe work of the laboratory has to do mainly with fundamental and applied aspects of biological control of pestand pathogen populations. This includes studies of predatory mites, fungi and entomopathogenic nematodes.The objectives are to understand fundamental aspects of how genetic and geographic biotype boundaries arecreated and maintained, to recognise components of ecological competence, which are important in the successof biological control agents, and to find or build new organisms for better commercial biological control.Environmental Physiology and Behaviour LaboratoryDr. Christine T. GriffinResearch of this laboratory has two related foci: the behaviour and physiology of nematode parasites, and useof insect parasitic nematodes as biological pesticides.A specialised infective juvenile transmits many nematode parasites from host to host. We are interested inthe survival and infection strategies of these infective juveniles, and generally use species of insect parasiticnematode as models in this research. We are currently investigating the complex manner in which severalfactors interact to influence infectivity, including factors operating during development (such as resourceavailability) and those operating during ageing of the infective juveniles. One of our lines of investigation isinto the importance of starvation as a factor modifying the foraging behaviour of infective juveniles, and alsoas a mortality factor for them.The second main strand of our research is the development and utilisation of insect parasitic nematodes asbiological control agents. Pest species currently targeted include pine weevil (Hylobius abietis) in reforestation,black vine weevil (Otiorhynchus sulcatus) in soft fruits, and sciarid and phorid flies in mushroom cultivation.Epithelial Immunobiology GroupDr. Shirley O’DeaAs the principle organs of gas exchange in the body, the lungs are constantly exposed to the vast array ofsubstances present in inhaled air, yet they are lined by just a single layer of epithelial cells. The main functionsof the cells lining the conducting airways involve protection against harmful inhaled substances as well aswarming and humidifying the air before it reaches the delicate alveolar regions where gas exchange takesplace. My team is studying the lung epithelium and the signalling networks that influence its functions inhealth and disease.18The airway epithelium is not merely a passive barrier preventing the entry of harmful substances into the host.The cells within the epithelium carry out a range of specialised functions including detoxification of harmful

substances and active defence against microorganisms as well as communicating directly with the immuneand inflammatory systems. To carry out these essential functions, the epithelium must be intact and containthe appropriate subpopulations of specialised cells. Chronic exposure to harmful substances and underlyinggenetic factors can compromise defence and repair mechanisms in the lungs, leading to long-term damageand disease.My group is interested in interactions between the lung epithelium and its microenvironment and theways in which lung epithelial cells, mesenchymal cells and immune and inflammatory cells modulate eachother’s functions in health and disease. In particular, we are interested in mechanisms of regenerationwithin damaged airways and we are investigating both normal repair processes and the alterations inthese pathways that lead to the development of disease. We are examining the effects of signals emanatingfrom 1. inflammatory and immune cells, 2. underlying mesenchymal cells and extracellular matrices and 3.neighbouring epithelial cells on epithelial cell proliferation and function. Understanding these signallingnetworks should result in the identification of potential areas for intervention strategies to prevent, treatand cure lung disease. In addition, we are examining stem and progenitor cell pathways operating withinthe epithelium in order to identify potential target cells for regeneration therapies, gene therapy and cancertreatments.Gene Flow LaboratoryDr. Conor V. MeadeOur main interest is developing models for the spread of genes through wild and cultivated plantpopulations, and the impact GM crops may have on these patterns. Currently we are investigating gene-flowin Irish populations of Brassica Rapa L. (wild turnip), Lolium perenne L. (perennial ryegrass) and Avenasativa/fatua (cultivated and wild oats).We use a variety of PCR-based fragment analysis techniques including microsatellites (SSRs), AFLPs andRAPDs to investigate genetic diversity, gene-flow, hybridisation and inheritance patterns in these species.Data is being generated from wild and cultivated populations and from controlled experimental crosses.Much of our work is done in collaboration with the Teagasc Crop Research Centre at Oakpark, Co. Carlow.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06BIOLOGYOther research interests include the taxonomy and systematics of the Annonaceae (custard apples) in Southand Southeast Asia, the phytogeography of Asia and phylogenetics.Lymphocyte Biology LaboratoryDr. Derek G. DohertyImmune defence against viruses, bacteria, parasites and tumours involves multiple cell types that mediatethe appropriate effector functions and regulatory mechanisms. The Lymphocyte Biology Group is carryingout fundamental research on subpopulations of human lymphocytes that mediate innate immune responsesand can selectively activate and regulate T cells and B cells of the adaptive immune system. These “innatelymphocytes” include natural killer (NK) cells, natural killer T (NKT) cells and γδ T cells, which recognisecommon structures on target cells that signify danger and initiate immune responses. NK cells, NKT cellsand γδ T cells are found in small numbers in blood but they accumulate at epithelial surfaces, in particularthe liver. We aim to elucidate the mechanisms by which innate lymphocytes from human blood and liverregulate adaptive immune responses and how they can be manipulated for the treatment of disease. We areexamining the receptors and soluble factors that control innate lymphocyte activation, reciprocal interactionsbetween innate lymphocytes and dendritic cells and changes to these cells that occur in disease. We haveevidence that innate lymphocytes play important roles in immunity against hepatitis C virus (HCV). HCVinfects over 170 million people worldwide, and while about 20% of infected individuals successfully clear19

Research Interests Of StaffC O N T I N U E Dthe virus, the majority develop chronic liver disease. The outcome of HCV infection is determined both bydifferences in the amount and nature of the infecting virus and by the host’s immune system. Elucidationof the mechanisms by which NK cells, γδ T cells and NKT cells influence resolution and persistence of HCVinfection may lead to the development of strategies for the treatment of this and other immune-mediateddiseases.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 BIOLOGYMedical Mycology UnitDr. Kevin KavanaghFungal pathogens are recognised as a significant cause of illness and death among patients immunocompromisedas a result of disease (AIDS, cancer) or therapy (immuno-suppressive therapy prior to organtransplantation). Most fungal pathogens are normal components of the body flora but in the event of anunderlying disease they can become invasive and colonise many organs with deleterious consequences.In the Medical Mycology Unit we are concerned with understanding the mechanisms employed by fungito colonise human tissue, with designing novel means of detecting fungal infection and with developingtherapies to complement existing anti-fungal strategies. We are also actively examining the similaritiesbetween the immune system of insects and the mammalian innate immune systems to allow the developmentof in vivo assays that do not require the use of vertebrates.Aspergillus fumigatus is a filamentous fungus, which is associated with a range of pulmonary diseases, anumber of which can disseminate to distant sites in the body and have a mortality rate of 95%. Togetherwith Dr. Sean Doyle we are developing novel diagnostics, which will detect the presence of fungal toxins andenzymes in human blood as an early indicator of fungal infection. Our objective is to make earlier detectionof fungal infection feasible so that anti-fungal therapy can be initiated with a consequent reduction inpatient mortality. In addition, we have embarked on a project to selectively knock-out genes associated withthe production of secondary metabolites that may have a role in tissue invasion. Together with Dr. MalachyMcCann (Department of Chemistry) we are assessing the efficacy of novel metal-based anti-fungal drugs witha view to their possible use in treating a range of superficial fungal infections. To date we have identified themode of action of these drugs and established their potential for controlling the growth of fungi by actingsynergistically with conventional anti-fungal drugs.20Molecular Evolution and Bioinformatics LaboratoryDr. Mario A. FaresThere are four main research areas in the Molecular Evolution and Bioinformatics laboratory. We areinterested in studying adaptive evolution in protein-coding genes, focusing on intracellular pathogensand endosymbiotic bacteria. We are trying to link mathematical analyses of selective constraints withstructural information of the encoded proteins. With this information we are investigating the role ofdifferent proteins in the maintenance of the pathogenesis or symbiotic life-styles of these organisms.This data will allow us to obtain a complete picture of the different evolutionary ways that enable theseorganisms to avoid the host immune system. This information would be extremely valuable in predictingthe different population dynamics in response to a variety of medical treatments. The second main goalof our research is the determination and estimation of the main parameters governing evolution of heatshockproteins. The relationship between heat-shock proteins and maintenance of the intracellular lifestyleforms the core of our research in this area. On the other hand, we would like to test if the evolutionof complexity from archeobacteria to eukaryotes and the stability of key pathways in multi-cellulareukaryotes are heat-shock protein-dependent. Furthermore, we are carrying out studies with completegenomes, including the distribution of selective constraints among genes belonging to different functionalcategories and the co-evolution of functionally and protein expression-based clustered genes. We arealso evaluating the importance of functional innovation and sub-functionalisation after gene duplication

using complete genomes. Within this third area we are interested in coupling information from proteinproteininteraction networks with evolution at the gene sequence level. By using this approach we willbe able to understand the evolution and flexibility of specific cellular pathways, such as those related todevelopment and cellular division with special focus on developmental abnormalities, cancer and aging.Finally, we are designing statistical methods and software to detect selective constraints in protein-codinggenes. We have developed a new sliding-window based method to detect selective constraints in proteincoding genes and the corresponding software (SWAPSC). We are also developing new methods to detectfunctional divergence after gene duplication and to determine to which extent this functional divergence waslinked to sub-functionalisation or neo-functionalisation in each gene copy. Furthermore, we are exploringnew mathematical and statistical ways to correct artefactual phylogenetic trees produced by undesiredphenomena, such as long branch attraction, gene recombination or lateral gene transfer.Molecular Parasitology LaboratoryDr. Noel B. MurphyThe molecular parasitology group undertakes research on the African trypanosomes; protozoan parasitesof both medical and veterinary importance in sub-Saharan Africa. The African trypanosomes also representimportant biological organisms that have been central to discoveries on mechanisms of antigenic variation,mechanisms of adaptation to different host species, gene expression, RNA processing and editing andglycosome biology. With support from Enterprise Ireland (2002-2004) and Science Foundation Ireland(2004-2006) research conducted by the group is directed at gaining insights into trypanosome-host andtrypanosome-trypanosome interactions that contribute to the establishment and maintenance of infectionand the causes of disease. Current funded research is focused on elucidating the molecular processesby which parasites communicate with each other to control their population size, proliferation anddifferentiation status. Communication between strains and species of trypanosomes is achieved througha parasite-produced factor. The process by which this factor arrests proliferation of dividing parasites andinduces differentiation is currently being elucidated. The research group is also interested in mechanismsof host resistance through studies on African wildlife species that do not succumb to disease causedby trypanosomes. Studies have elucidated a mechanism of innate resistance and evidence for acquiredimmunity, and the basis of this acquired immunity is currently being studied through linkages with European,North American and African partners. The overarching aims of the group are to identify new options tocontrol the devastating diseases caused by African trypanosomes by gaining a greater understanding of thebiology of these organisms and their interactions with their host species.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06BIOLOGYMucosal Immunology LaboratoryDr. Bernard MahonOur airways are constantly exposed to foreign material and yet for the most part are maintained as ahealthy, functioning system. The goal of our laboratory is to understand how microbes colonise this mucosalsurface, compromise our health and how the immune system operates to return us to homeostasis. The workfocuses on a fundamental question: how is the local immune response in the airways induced? Recently wehave made significant advances in answering this question by identifying the biochemical signals that areinvolved in recruiting sentinel dendritic cells to the trachea. We have identified three mechanisms wherebyrespiratory pathogens corrupt this process to hinder immunity and prolong infection. The results are alsogiving us unexpected insights into asthma, and new mucosal vaccines. When we understand how immunityis induced, or evaded by microbes, we will be close to understanding a fundamental aspect of human biology.We will also be able to rationally devise new vaccines and medications for both respiratory infections, andindeed other conditions with an immune component such as allergies and asthma.21

Research Interests Of StaffC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 BIOLOGYMuscle Biology LaboratoryProfessor Kay OhlendieckThe functional performance of skeletal muscle is based on refined physiological mechanisms that couplethe electrical depolarisation of the surface membrane to motor protein activation, generally referred to asexcitation-contraction coupling. Our laboratory focuses on the biochemical and physiological characterisationof supramolecular membrane complexes involved in the regulation and stabilisation of this relatively uniquesignal transduction mechanism. In mature fast fibres, direct physical coupling between the voltage-sensingreceptor of the transverse tubules and the calcium release channel complex of the sarcoplasmic reticuluminitiates contraction, while the energy-dependent re-uptake of calcium ions causes muscle relaxation. Usingblot overlay assays with conjugated proteins, two-dimensional gel electrophoresis and chemical cross-linkingand various immunochemical techniques we are characterising the role of protein-protein interactions inion homeostasis. Muscle fibres exhibit enormous plasticity and can adapt efficiently to changes in activity byatrophy, hypertrophy and/or fibre type shifting. Employing chronic low-frequency electro-stimulation to fastfibres, we are studying the effect of the fast-to-slow transition process on isoform expression patterns of keymuscle proteins. Diseases affecting muscle proteins usually have devastating consequences for the organism,i.e. muscular dystrophy or sarcopenia of old age. To elucidate the molecular pathogenesis of these diseases,we are examining naturally occurring animal models, such as the dystrophic mdx mouse. The long-termaim of our laboratory is to make major advances in the understanding of excitation-contraction coupling byfocussing on the elucidation of the molecular architecture of the triad junction, the molecular cell biologyand functional interactions between ion-regulatory elements and on the pathophysiology of neuromusculardiseases arising from abnormalities in calcium handling. In conjunction with research networks fundedby SFI and the European Commission, our laboratory is currently involved in a mass spectrometry-basedproteomics approach to identify all proteins responsible for the assembly and maintenance of the junctionalsarcoplasmic reticulum during myogenesis, transformation and ageing. Recently, we have introducedfluorescence difference gel electrophoresis in our comparative proteomic profiling of muscle fibres, and hopethat the application of this highly sensitive biochemical technique will result in the swift identification ofnovel muscle disease markers.Nematode Genetics LaboratoryProfessor Ann M. BurnellResearch in this laboratory is concentrated mainly on the biology and genetics of nematodes. We work onseveral nematode species, among them Caenorhabditis elegans, which is widely used as a research modelin molecular genetics and whose genome has been fully sequenced; Heterorhabditis bacteriophora andSteinernema carpocapsae, parasites of insects which are commercially produced and marketed for thebiological control of soil dwelling insect pests; and Aphelenchus avenae and Panagrolaimus, nematodeswhich are able to survive desiccation to 0% relative humidity.22Although water is essential for life, a number of organisms can enter a state of suspended animation, whichallows them to survive in a dry state for indefinite periods. This remarkable ability is called anhydrobiosis(“life without water”). In January 2003 we began a second anhydrobiosis project with the nematodePanagrolaimus, which is funded by Science Foundation Ireland. We expect that these project will lead to thediscovery of several novel genes and may ultimately lead to the development of new methods of preservingbiological materials that do not normally survive drying. We are also working on an Enterprise Irelandfunded research project aimed at identifying the genes responsible for the enhanced longevity phenotype ofcertain long-lived mutant strains of the nematode Caenorhabditis elegans. The ultimate aim of this project isto identify homologues of these “enhanced life maintenance genes” in humans.

Plant Biology LaboratoryDr. Jacqueline M. NugentThe research of this laboratory focuses on a number of different aspects of plant molecular biology andevolution. One of our research projects is aimed at understanding the role the plant hormone ethylene playsin regulating plant physiology and development. We are concentrating on cloning ACC synthase genesfrom Antirrhinum majus (snapdragon). Ultimately we will use a PCR-based ‘reverse genetic’ approach toselectively inactivate individual ethylene signalling during plant development. A long-term goal is to focuson the role of ethylene during flower development. We are also interested in understanding how plantdevelopmental processes evolve. Plantago lanceolata (plantain) has regular, wind-pollinated, flowers thathave evolved from irregular, animal pollinated ancestors similar to those of Antirrhinum majus. Three genescycloidea, dichotoma, and divericata play a major role in controlling flower shape in Antirrhinum. We arecurrently investigating what role, if any, the homologues of these genes play in controlling flower shape inPlantago. This study should aid in the elucidation of a general model for how changes in floral shape areachieved as well as providing insight on the associated changes in pollination syndrome. A third project isaimed at characterising the mitochondrial genome of Antirrhinum majus. This study will address how plantorganelle genomes are evolving as well as how organelle/cooperativity in the cell is evolving. The othermain research area in the lab is the development of plants as model systems for the production of human andveterinary oral vaccines. We are developing the plastid as a ‘factory’ for the production of large amounts ofrecombinant antigenic proteins.Plant Cell Biology LaboratoryProfessor Philip J. DixThe research encompasses three main topics:1. Chloroplast transformation technology2. Environmental stress responses in plants3. The function of plant peroxidasesThese themes are connected through the use of transformation methods as a study tool, through the pivotal roleof the chloroplast in responses to environmental stresses, and through the involvement of peroxidases, amongother anti-oxidants, in scavenging reactive oxygen species (ROS) associated with various abiotic stresses.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06BIOLOGYThe laboratory has had a key role in the development of plastid transformation procedures in Europe,having co-ordinated several EU-funded projects in this important emergent area of plant biotechnology. Theprincipal investigator has also been strongly supported through grants from Science Foundation Ireland, andEnterprise Ireland. The emphasis has moved from an understanding of the processes of integration, selection,and expression of foreign genes in the plastid genome (plastome) in the model species (tobacco), throughthe extension of the technology to other crops (potato, tomato, cauliflower), and finally to biotechnologicalapplications. The latter include modification of composition and quality of starch and proteins, and theproduction of oral vaccines (HIV, TB, diabetes).Plastid transformation has also proved a valuable tool for exploring aspects of the response of the chloroplastto environmental stresses, through modification of ROS scavenging systems (superoxide dismutases,glutathione reductase), alteration in fatty acid composition (fatty acid desaturases), and exploration ofstress-related calcium signalling. ROS scavenging is also a component of a project, in collaboration withTeagasc, Carlow, looking at a high light stress induced condition, “physiological leaf spot”, in barley. The roleof peroxidases, in both stress amelioration and plant development (e.g. lignification) is being examined intransgenic tobacco and apple plants.23

Research InterestsOf StaffC O N T I N U E DResearch Grants24NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 BIOLOGYYeast Genetics LaboratoryDr. Gary JonesYeast PrionsIn 1982 the term prion was first coined by StanleyPrusiner to describe the nature of the scrapieinfective agent. A prion is an infectious protein. It isa transmissible amyloid form of a cellular proteinthat replicates by converting the native protein intothe same abnormal prion form. Prion and amyloiddiseases of humans include Creutzfeld-Jacobdisease, Alzheimer’s disease, Huntington diseaseand Type II diabetes. Much research has focusedon understanding the mechanisms by which prionsand amyloid arise and are maintained within anorganism. In 1994 Reed Wickner proposed that thegenetic behaviour of the Saccharomyces cerevisiaenon-mendelian elements [PSI+] and [URE3] couldbe explained if they were prions of the Sup35 andUre2 proteins respectively. Much evidence hasaccumulated to support this proposal. The fact thatprions exist in yeast provides an ideal environmentfor detailed genetic analysis of factors affectingprion propagation.Sup35p is a S. cerevisiae protein involved intermination of translation. In a state referredto as [PSI+], a significant portion of the Sup35protein in the cell coalesces into non-functional,self-propagating, amyloid-like polymers. Thus,yeast strains that are [PSI+] show increasedlevels of nonsense suppression. We can monitorthe presence of the prion in our yeast strains bya simple nutritional assay. Once present, [PSI+]propagates by recruitment of the soluble form ofSup35p into the aggregate in a manner analogousto that of mammalian prions. A search for geneticfactors affecting propagation and maintenance of[PSI+] has identified an essential role for molecularchaperones, namely Hsp70 and Hsp104.Our research aims at deciphering the complexrelationship that exists between protein chaperonesand prion/amyloid maintenance in yeast. The factthat chaperone complexes are extremely wellconserved from yeast to higher eukaryotes meansthat our findings may be directly relevant to ourunderstanding of prion and amyloid diseases inhumans.‘The characterisation of genes expressed bythe nematode Steinernema carpocapsae whenparasitising insects’. Science Foundation IrelandBasic Research Grant 04/BR/B0392, €235,703 (A.M.Burnell, 2004-2007).‘The exploitation of anhydrobiotic genes for thepreservation of intact proteins, cells and tissues ina dry state’. Science Foundation Ireland, €882,000(A.M. Burnell and J. McCaffrey, 2003-2007).‘Equipment supplement: Confocal microscope’.Science Foundation Ireland Equipment SupplementCall, €391,462 (A.M. Burnell and P.J. Dix, 2004-2005).‘The characterization of enhanced life maintenancegenes in the nematode Caenorhabditis elegans’.Enterprise Ireland Basic Research Grants Scheme,€175,108 (A.M. Burnell, 2003-2006).‘Developing efficient and stable biologicalcontainment systems for genetically modified plants(“Transcontainer”)’. EU STREP, €290,000(P. Dix, 2006-2009).‘Recombinant pharmaceuticals from plants forhuman health (PharmaPlanta)’. EU 6th Framework,€260,000 (P.J. Dix, 2004-2009).‘Mechanisms of transgene integration andexpression in crop plant plastids: underpinningtechnology for improving human health(Plastomics)’. EU 6th Framework, STREP, €238,000(P.J. Dix, 2004-2007).‘Macrochloroplasts as a model for the study ofcalcium fluxes in plant cells in response to abioicstress’. Enterprise Ireland Basic Research GrantsScheme, €165,000 (P. Dix, 2002-2006).‘Metabolic engineering of the chloroplast for healthand industry’. Science Foundation Ireland, €638,000(P.J. Dix, 2002-2006).‘Oxidative stress and physiological leaf spot inbarley’. Teagasc, €45,000 (P.J. Dix, 2002-2005).

‘The effect of plastidial expression of reactiveoxygen species-scavenging enzymes on stressresponses in plants’. Enterprise Ireland BasicResearch Grants Scheme, €126,079 (P.J. Dix, 2001-2005).‘The role of CD1d-restricted natural killer T cellsin dendritic cell maturation and differentiation’.Science Foundation Ireland Research FrontiersProgramme, €138,969 (D.G. Doherty, 2005-2008).‘Characterisation and manipulation of human T cellswith early immunomodulatory function’. ScienceFoundation Ireland Basic Research Grant, €214,745(D.G. Doherty, 2004-2006).‘Characterisation of hepatitis C inducedimmunological subversion and its implicationsfor treatment response’. Health Research BoardProgramme Grant for Research on Blood Utilisationand Hepatitis C, €552,000 (€90,000 to NUIMaynooth) (C. O’Farrelly D. Kelleher, K.H.G. Mills,D.G. Doherty, 2003-2006).‘Sex and mortality factors in entomopathogenicnematodes (SEXMORT)’. Irish Research Councilfor Science, Engineering and Technology (IRCSET),Basic Research Grant Programme, €163,709 (M.J.Downes and A.N. Rolston, 2002-2005).‘Control of disease in two integrated strawberryproduction systems (FRAGRA)’. DAFRD ResearchStimulus Fund, €220,000 (M.J. Downes, F.MacNaeidhe and R. Dunne, 2002-2005).‘Maintenance of Departmental DNA sequenceanalysis facilities’. NUI Maynooth EquipmentMaintenance Scheme 2005, €5,000 (M. Downes, C.Meade, S. Doyle, G. Jones, K. Kavanagh, A. Burnell,2005).‘Support for the preparation of a proposal tocoordinate an INCO STREP under FP6’. EnterpriseIreland, €17,203 (M.J. Downes, C.T. Griffin, T. Lola-Luz, A. Dillon, 2005).‘Identification, cloning and expression of A.fumigatus encoded proteases’. Host laboratoryfor Embark Initiative PhD Studentship awardedto Ms Imelda Vickers BSc. Irish Research Councilfor Science Engineering and Technology (IRCSET),€57,150 (S. Doyle, 2002-2005).‘Bioindustry-Led Research Programme’. EnterpriseIreland, €14,400 (S. Doyle, 2005-2006).‘Equipment maintenance grant - Maintenance ofdepartmental mass spectrometry facilities’. NUIMaynooth Equipment Maintenance Scheme, €5,000(S. Doyle, K. Ohlendieck, K. Kavanagh and S. O’Dea,2005).‘Computational and biomedical analysis of heatshock proteins (Hsps): optimisation of proteinfunction and putative drug targets’. President ofIreland Young Researcher Award (PIYRA), ScienceFoundation Ireland, €1,185,365(M. Fares, 2004-2009).‘Correlating LBA, adaptive evolution and expressionat the genome level’. Science Foundation IrelandBasic Research Grant, €111,733(M. Fares, 2004-2007).‘Computational analysis of inter- and intramolecularcovariation in key cellular proteins’.Science Foundation of Ireland UndergraduateResearch Experience and Knowledge Award(UREKA), €5,600 (M. Fares, 2005).‘A new method to detect functionally and structurallyimportant regions in proteins’. Science Foundationof Ireland Undergraduate Research Experience andKnowledge Award (UREKA), €5,600(M. Fares, 2005).‘A multi-disciplinary approach to unravel biologicalfactors responsible for cell viability’. ScienceFoundation of Ireland Science Research AssistantResearcher (STAR), €12,000 (M. Fares, 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06BIOLOGY25

Research GrantsC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 BIOLOGY‘Baseline data, response to pressures, functionsand conservation of keystone micro and macroorganismsin Irish soils’. Environmental ProtectionAgency ERTDI Programme, €132,088 (C.T. Griffin,2006-2009).‘Aggressive competition in nematodes’. IrishResearch Council for Science Engineering andTechnology (IRCSET) Postdoctoral Fellowship to L.Ebssa, €96,300 (C.T. Griffin, 2006-2008).‘Evolution of competitive killing in parasiticnematodes’. Science Foundation Ireland ResearchFrontiers in Science Programme, €145,000 (C.T.Griffin, 2005-2008).‘Molecular and cellular effects of serotonin re-uptakeinhibitors in the nervous system of C. elegans’. EUMarie Curie Outgoing International Fellowship,€262,916 (C.T. Griffin and CM Dempsey, 2004-2007).‘Sustainable management of forest insect pests’.INTERREG 3a, €245,448 (C.T. Griffin and A. Dillon,2004-2007).‘Integrated reduced chemical control of Hylobiusabietis in Sitka spruce’. COFORD, €152,183 (C.T.Griffin and M.J. Downes, 2004-2006).‘Causes and control of the emerging root-knotnematode problem on golf greens’. Teagasc WalshFellowship, €55,000 (C.T. Griffin, 2003-2006).‘Risk assessment for non-indigenous biologicalcontrol agents in forestry’. Environmental SciencesAssociation of Ireland (ESAI) summer studentbursary to A. Maguire, €1,600 (C.T. Griffin, 2005).‘Nematodes for the control of phorid flies inmushroom cultivation’. Teagasc Walsh Fellowship,€55,000 (C.T. Griffin, 2002-2005).‘Pesticide reduction in mushroom cultivation inEurope’. EU Craft, €144,303 (C.T. Griffin, 2002-2005).‘Chaperone effects upon prion propagation’. RIA/SFIIreland-China Collaboration Fund, €11,040(G. Jones, 2005-2007).‘Identification of potential prion proteins in plants’.Marie Curie International Reintegration Fellowship(EU) €80,000 (G. Jones, 2005-2007).‘Hsp70’s Role in Amyloid Propagation’. Irish HealthResearch Board, €189,048 (G. Jones, 2004-2007).‘A genetic approach to investigate the interactionbetween a protein disaggregase and a prion’. ScienceFoundation Ireland, Research Frontiers Award,€68,000 (G. Jones, 2005-2006).‘Characterization of drugs that cure prions’.Enterprise Ireland, Ulysses (Ireland-France) Scheme,€4,200 (G. Jones, 2005-2006).‘Development of a rapid PCR based method for theidentification and characterisation of DermatophyticFungi responsible for ‘Ringworm’ infections in Irishhorses’. Enterprise Ireland Innovation Partnership,€101,800 (K. Kavanagh, 2005-2007).‘Monoclonal antibody development against fungaltoxins’. Enterprise Ireland Feasibility Grant, €9,000(S. Doyle and K. Kavanagh, 2005-2006).‘Biochemical and Immunological Characterisationof the Role of Bacterial Antigens in the Induction ofPapulo-pustular Rosacea’. National Rosacea Society(USA), $25,000 (K. Kavanagh, 2004-2006).‘Use of anti-sense technology to assess the role ofglutathione s-transferase in fungal virulence’.IRCSET Basic Research Grant Programme, €166,000(S. Doyle, K. Kavanagh and E. Reeves, 2003-2006).‘Diseases of the immuno-compromised patient’.National Institute of Cellular Biotechnology (NUIMaynooth) PRTLI 3, €1,700,000 (K. Kavanagh and S.Doyle, 2002-2007).26‘Hsp70 and Hsp104 mutant effects upon [URE3]propagation’. Enterprise Ireland, Ulysses (Ireland-France) Scheme, €4,200 (G. Jones, 2006-2007).‘Design, Synthesis, Purification and Evaluationof Pharmaceuticals as Chemotherapeutics andAnti-microbials’. ITT, DIT & NUI Maynooth (HETAC)€317,000 (K. Kavanagh, 2002-2006).

‘Development of technologies to identify signallingpathways involved in lung disease processes’. EUFP6 Marie Curie Transfer of Knowledge Grant,€510,000 (S. O’Dea, B. Mahon, M. Fares, K. Kavanaghand S. Doyle, 2005-2007).‘Centre for Science Engineering and Technology(CSET) in regenerative medicine (REMEDI)Immunology Core’. Science Foundation Ireland,€558,000 (B. Mahon, 2004-2008).‘Use of siRNA as novel immunomodulators’.Enterprise Ireland Basic Research Grants Scheme,€148,000 (B. Mahon, 2002-2004).‘Role of the chemokine CCL28 in respiratory disease’.Health Research Board, €120,000(B. Mahon, 2001-2004).‘Comparison of the nucleotide substitution versusthe gene acquisition paradigms in microbes’. ScienceFoundation Ireland, Research Frontiers Programme,€163,000 (J. McInerney, 2005-2008).‘Irish Centre for High-End Computing: ICHEC (withNUIG, TCD, UCD, DIAS)’. Science Foundation Ireland,€3,400,000 (J. McInerney, 2004-2007).‘Inferring the Universal Tree, or network, of Life:Genomics, Supertrees, and Supernetworks’. MarieCurie post-doctoral fellowship to Dr. Davide Pisani,€166,000 (J. McInerney, 2004-2006).‘Novel Heterogeneous Maximum Likelihood MethodsFor Detecting Adaptive Evolution’. Enterprise IrelandBasic Research Grants Scheme, €75,000(J. McInerney, 2003-2006).‘Programme for Alimentary Health (with UCC andUCD)’. Higher Education Authority Programme forResearch in Third Level Institutes PRTLI Cycle III,€4,000,000 (J. McInerney, 2002-2006).‘Assessing the fitness of GM/non-GM hybrids’.Teagasc Walsh Fellowship, €45,000 (C. Meade andE. Mullins, 2003-2006).‘The origin, distribution and diversity of wild oats(Avena fatua L.) in Irish arable fields’. Department ofAgriculture and Food, €7,500 (C. Meade, 2004-2005).‘Gene flow in cereals and grasses’. DAFRD ResearchStimulus Fund, €180,000 (C. Meade and M.J.Downes, 2002-2005).‘Functional analysis of the African trypanosome ADPribosylation factor 1’. Science Foundation IrelandBasic Research Grant, €177,652(N.B. Murphy, 2004-2006).‘Pharma-Planta’. EU 6th Framework, €260,000(J. Nugent, 2003-2007).‘Developing a plastid-based, multicomponentvaccine against Helicobacter pylori’. Health ResearchBoard, €150,137 (J. Nugent, 2003-2006).‘The development of a model for harvesting andculturing equine bronchial epithelial airway stemcells’. UCD Seed Funding Scheme, €5,000(L Katz, S Carrington and S. O’Dea, 2005).‘Identification of human airway epithelial stemcells and modulation of differentiation pathwaysto treat lung disease’. Science Foundation IrelandCSET Grant in collaboration with the RegenerativeMedicine Institute, NUI Galway, €171,100(S. O’Dea, 2004-2007).‘Combating lung disease: Delivery of therapeuticagents to the airways’. Science Foundation IrelandIndustry/Research supplement, €186,973(S. O’Dea, 2004-2006).‘Determination of Stem Cell and DifferentiationPathways within the Lung Epithelium’. ScienceFoundation Ireland Investigator Programme Grant,€653,000 (S. O’Dea, 2002-2006).‘Evaluation of the HL-60 cell line as a model forhematopoietic-to-lung epithelial cell differentiation’.Science Foundation Ireland Science TeachersAssistant Researchers (STARs) supplement, €10,400(S. O’Dea, 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06BIOLOGY27

Research GrantsC O N T I N U E DPublications inRefereed JournalsNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 BIOLOGY‘Pathobiochemical role of excitation-contractionuncoupling in the age-related decline of skeletalmuscle mass and strength using proteomic,subproteomic and intraproteomic analysis’.Science Foundation Ireland Principal InvestigatorGrant, €704,527 (K. Ohlendieck, 2005-2009).‘Role of the dystrophin-glycoprotein complex andassociated regulatory elements in non-obese type2 diabetic skeletal muscle’. Health Research Board,Basic Research Grant, €168,640(K. Ohlendieck, 2005-2008).‘Excitation-contraction coupling and calciumsignalling in health and disease’. EuropeanCommission, 5th Framework Research and TrainingProgramme, €167,000 (K. Ohlendieck, 2002-2006).‘Identification of novel therapeutic targets indystrophic muscle fibres’. Muscular DystrophyIreland, €22,000 (K. Ohlendieck, 2002-2005).Altpeter, F., N. Baisakh, R. Beachy, R. Bock, T. Capell,P. Christou, H. Daniell, K. Datta, S. Datta, S., P.J. Dix,C. Fauquet, N. Huang, A. Kohli, H. Mooibroek, L.Nicholson, T.T. Nguyen, G. Nugent, K. Raemakers,A. Romano, D.A. Somers, E. Stoger, N. Taylor N.and R. Visser. Particle bombardment and thegenetic enhancement of crops: myths and realities.Molecular Breeding 15, 305-327 (2005).Arnaiz, B., L. Madrigal-Estebas, S. Todryk, T.C. James,D.G. Doherty and U. Bond. A novel method to identifyand characterise peptide mimotopes of heat shockprotein 70-associated antigens. Journal of ImmuneBased Therapies and Vaccines (in press).Barry, F., J.M. Murphy, K. English and B.P. Mahon.Immunogenicity of adult mesenchymal stem cells:lessons from the fetal allograft. Stem Cells andDevelopment 14, 252-65 (2005).Barry, F.P., J.M. Murphy, T. OBrien and B.P. Mahon.Mesenchymal Stem Cell Transplantation for TissueRepair. Seminars in Plastic Surgery 19, 229-240(2005).Bergin, D., E.P. Reeves, J. Renwick, F.B. Wientjes andK. Kavanagh. Superoxide production in haemocytesof Galleria mellonella – identification of proteinshomologous to the NADPH oxidase complex ofhuman neutrophils. Infection and Immunity 73,4161-4173 (2005).Burbridge, E., M. Diamond, P.J. Dix and P.F. McCabe.Use of cell morphology to evaluate the effect of aperoxidase gene on cell death induction thresholdsin tobacco. Plant Science (in press).Burnell, A.M., K. Houthoofd, K. OHanlon and J.R.Vanfleteren. Alternate metabolism during the dauerstage of the nematode Caenorhabditis elegans.Experimental Gerontology 40, 850-856 (2005).Burns C., R. Geraghty, C. Neville, A. Murphy, K.Kavanagh and S. Doyle. Identification, cloning,and functional expression of three glutathionetransferase genes from Aspergillus fumigatus.Fungal Genetics and Biology 42, 319-327 (2005).28

Carberry, S., C.M. Neville, K.A. Kavanagh and S.Doyle. Analysis of major intracellular proteins ofAspergillus fumigatus by MALDI mass spectrometry:Identification and characterisation of an elongationfactor 1B protein with glutathione transferaseactivity. Biochemical Biophysical ResearchCommunications (in press) (2005).Corcoran, A., B. Crowley, C. Dewhurst, B.L. Pizer, andS. Doyle. Establishment of functional B cell memoryagainst parvovirus B19 capsid proteins may beassociated with resolution of persistent infection.Journal of Medical Virology (in press).Corcoran A, S. Doyle, J.P. Allain, D. Candotti and A.Parsyan. Evidence of serological cross-reactivitybetween genotype 1 and genotype 3 erythrovirusinfections. Journal of Virology 79, 5238-5239 (2005).Craig, W., D. Gargano, N. Scotti, T.T. Nguyen, N.T.Lao, T.A. Kavanagh, P.J. Dix and T. Cardi. Directgene transfer in potato: a comparison of particlebombardment of leaf explants and PEG-mediatedtransformation of protoplasts. Plant Cell Reports 24,603-611 (2005).Creaven, B.S., D.A. Egan, K. Kavanagh, M. McCann, MMahon, A. Noble, B. Thati and M. Walsh. Synthesisand Antimicrobial Activity of Copper(II) and Silver(I)Complexes of Hydoxynitrocoumarins: X-ray crystalstructures of [Cu(hnc)2(H2O)2]⋅2H2O and [Ag(hnc)](hncH = 4-hydroxy-3-nitro-2H-chromen-2-one).Polyhedron 24, 949-957 (2005).Creevey, C.J. and J.O. McInerney. CLANN:Investigating phylogenetic information throughsupertree analysis. Bioinformatics 21(3), 390-392(2005).Dean, J., D.D. McCarthy, D.M. Lawler, D.G. Doherty,C. OFarrelly and L. Golden-Mason. Characterizationof NKR+ T-cell subsets in human bone marrow:implications for immunosurveillance of neoplasia.Clinical Immunology 114, 42-51 (2005).Dillon, A., D. Ward, M.J. Downes and C.T.Griffin. Suppression of the large pine weevil,Hylobius abietis Coleoptera: Curculionidae) byentomopathogenic nematodes with differentforaging strategies. Biological Control (in press).Donoghue, P., P. Doran, P. Dowling and K. Ohlendieck.Differential expression of the fast skeletal muscleproteome following chronic low-frequencystimulation. Biochimica et Biophysica Acta– Proteins and Proteomics 1752, 166-176 (2005).English, K., C.M. Brady, P. Corcoran, J.P. Cassidy andB.P. Mahon. Inflammation of the respiratory tractis associated with CCL28 and CCR10 expression ina murine model of allergic asthma. ImmunologyLetters (in press).D.P. Ennis, J.P. Cassidy, and B.P. Mahon. Wholecell pertussis vaccine protects against Bordetellapertussis exacerbation of allergic asthma: Pwimmunization reduces IL-13 and IL-10. Immunologyletters 97, 91-100 (2005).D.P. Ennis, J.P. Cassidy, and B.P. Mahon. Acellularpertussis vaccine protects against Bordetellapertussis exacerbation of allergic asthma but in theabsence of infection potentiates airway IL-10 and IL-13. Clinical and Diagnostic Laboratory Immunology12, 409-17 (2005).Enright, M.R. and C.T. Griffin. Effects of Paenibacillusnematophilus on the entomopathogenic nematodeHeterorhabditis megidis. Journal of InvertebratePathology, 88, 40-48 (2005).Fares, M.A. Computational and statistical methods toexplore the various dimensions of protein evolution.Current Bioinformatics (in press).Fares, M.A., A. Moya and E. Barrio. Convergentadaptive evolution of GroEL in endosymbioticbacteria of insects. Journal of Evolutionary Biology18, 651-660 (2005).Fares, M.A., K.P. Byrne and K.H. Wolfe. Rateasymmetry after genome duplication causessubstantial long branch attraction artifacts in thephylogeny of Saccharomyces species. MolecularBiology and Evolution 23, 245-253 (2006).Fares, M.A. and S.A. Travers. A novel method todetect intra-molecular coevolution: Adding a furtherdimension to selective constraints analyses. Genetics(in press).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06BIOLOGY29

O’Halloran, D.M., D.A. Fitzpatrick, G.P. McCormack,J.O. McInerney and A.M. Burnell. ‘The molecularphylogeny and functional significance of a nematodespecific clade of heterotrimeric G-protein α subunitgenes’. 14 th International C. elegans Conference,University of California, Los Angeles, USA (25-29June).O’Hanlon, K., J.A. Browne, L. Knox and A.M. Burnell.‘Identification and analysis of enhanced lifemaintenance genes in C. elegans’. 14 th InternationalC. elegans Conference, University of California, LosAngeles, USA (25-29 June 2005).Ohlendieck, K. ‘Proteomics screening of x-linkedmuscular dystrophy’. Seminar speaker, EU meeting,Excitation-contraction coupling in health anddisease, Department of Applied Physiology,University of Ulm, Ulm, Germany (11 April 2005).Ohlendieck, K. ‘Calcium handling proteins andmuscular dystrophy’. Invited speaker, MassGeneralInstitute for Neurodegenerative Disease, HarvardMedical School, Boston MA, USA (12 July 2005).Ohlendieck, K. ‘Proteomics of muscular dystrophy’.Invited Speaker, Annual Meeting of MuscularDystrophy Ireland, Dublin, Ireland (15 October 2005).Philip, G.K. and J.O. McInerney. ‘The evolutionaryhistory of the Apicomplexans’. Evolution 2005,Fairbanks, Alaska, USA (10-14 June 2005).Philip, G.K. and J.O. McInerney. ‘Bacterial genes ina eukaryote’. Rocky ’05, Regional Meeting of theInternational Society for Computational Biology,Aspen/Snowmass, Colorado, USA (9-11 December2005).Pisani, D. and J.O. McInerney. ‘Investigatingphylogeny using compatibility based methods’.VIBEmeeting, Dublin City University, Dublin, Ireland (17February 2005).Pisani, D. and J.O. McInerney. ‘Genomics applicationsof compatibility analysis’. The 5 th Biennial Meetingof the Systematics Association, Cardiff, Whales (22-26 August 2005).Rolston, A.N., S. Boyle, T. Kakouli-Duarte, C.T. Griffinand M.J. Downes. ‘Intraspecific variation amongnaturally occurring Steinernema feltiae populationsfrom Bull Island, Republic of Ireland’. COST 850Workshop on Natural occurrence and evolutionof EPNs, Ceské Budejovice, Czech Republic (14-17January 2005).Rolston, A.N., C.T. Griffin and M.J. Downes.‘Emergence patterns, dispersal and host invasionof two Steinernema feltiae isolates’. Society ofNematologists Annual Meeting, Fort Lauderdale,Florida, USA (9-13 July, 2005).Rowan, R, K. Kavanagh and M. McCann. ‘Synthesis,characterisation and microbial testing of metalbaseddrugs’. 10 th Inorganic Chemistry Conference,National University of Ireland, Maynooth, Co.Kildare, Ireland (10-11 September 2005).Rowan, R., M. McCann, K. Kavanagh, M. Devereux, V.McKee, T. Tallon, R. Curran and A. Sheahan. ‘Silverbullets in anti-microbial chemotherapy’. RoyalSociety of Chemistry Biology/Chemistry InterfaceMeeting, Royal College of Surgeons, Dublin, Ireland(12 May 2005).Shannon, A., J. Boyd, J. Browne and A.M. Burnell.‘The anhydrobiotic potential and molecularphylogentics of species and strains of Panagrolaimus(Nematoda, Panagrolainidae)’. Society forIntegrative and Comparative Biology AnnualMeeting, San Diego, CA., USA (4-8 January 2005).Tyson, T. and A.M. Burnell. ‘Genes upregulated inresponse to desiccation in Steinernema carpocapae’.Society for Integrative and Comparative BiologyAnnual Meeting, San Diego, CA., USA (4-8 January2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06BIOLOGY35

External Assignments And Public Service36NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 BIOLOGYProfessor A. M. Burnell• Member of the Management Committee of COST850 Biocontrol Symbioses (A Framework for R&Dcollaboration in Europe).• Member of the Senate of the National Universityof Ireland.• Member Irish Research Council for Science,Engineering and Technology.• Examiner of Ph.D. thesis, Institute ofBiotechnology, University of Cambridge.• Examiner of Ph.D. thesis, Department ofBiochemistry, Queen’s University Belfast.Professor P. J. Dix• External Examiner, PhD, Deakin University,Australia.• Reviewer for the following scientific journals:Nature Biotechnology, Transgenic Research.• Member, Food Safety Authority of IrelandSub-committee on GMOs and Novel Foods.Dr. D. G. Doherty• External examiner, PhD, University of Newcastleupon Tyne, UK.• Reviewer for the following journals:Immunology, Journal of Hepatology, Clinicaland Experimental Immunology, Annals of theRheumatic Diseases.• Committee member, Irish Society forImmunology.Member, Irish Society for Human Genetics,British Society for Immunology, Society forNatural Immunity.Professor M. J. Downes• National Representative on European WorkingGroup on Integrated Pest Management.• Member of Ad Hoc Committee establishingAgri-Food Biotechnology Society.• Member of the Advisory Board of CABInternational Training.• Joint promoter Belderrig Institute Project -Biology.• Convener of COST 850 Working Group 4.• Appointments Boards and Requested StaffMentoring in external third level bodies.• Joint promoter Ceide Fields Project -Biology.• NUI Representative, Second Level BiologyExaminations.• Member of Scientific Advisory Board, ForestProtection Centre of Excellence, Forest ResearchInstitute, Warsaw.• Member of EurSafe.Dr. S. Doyle• Member, Irish Medicines Board (IMB) expertpanel concerning in-vitro Diagnostic MedicalDevices.• Member, Biochemical Society, UK.• Member of the Society for General Microbiology.• Reviewer for International peer-reviewedjournals including: Journal of InfectiousDiseases; Clinical and Diagnostic Virology;Journal of Medical Microbiology; FoodMicrobiology; Journal of Medical Virology;Analytical Biochemistry; Journal of ClinicalInvestigation; Microbiology; ScandinavianJournal of Infectious Diseases; ChemBioChem;FEMS Microbiology Letters; Journal ofHepatology; Clinica Chimica Acta.Dr. C. T. Griffin• Vice chairwoman, COST 850, BiocontrolSymbioses (A framework for R& D collaborationin Europe).• Member of Editorial Board, Biological Control.• Reviewer for granting agency BARD (US-Israel).• Reviewer for the following journals: BiologicalControl, Nematology, Journal of Nematology,Phytoparasitica, Cellular Microbiology, ForestEcology and Management.• Associate specialist (Nematodes) for FaunaEuropaea.Dr. G. Jones• Panel member- HRB Postdoctoral Fellowships.• Panel member- Enterprise Ireland Proof ofConcept Phase.• Council Member- Royal Academy of Medicine inIreland (Biomed Sciences Section).• Reviewer of BBSRC Biochemistry and CellBiology Grants.• Ad hoc reviewer for Journal of Structural Biology,Yeast and Eukaryotic Cell.

Dr. K. Kavanagh• Reviewer for the following journals: Enzymeand Microbial Technology, Cytotechnology, FEMSMicrobiology Letters, Microbiology, British Journalof Biomedical Science, Journal of Pharmacyand Pharmacology, Microbes and Infection,Antimicrobial Agents and Chemotherapy, Journalof Infectious Diseases.• External examiner for MSc, Institute ofTechnology Tallaght, Dublin. August 2005.Dr. B. P. Mahon• Board Member of the Health Research Board.• Irish Representative, European Network ofImmunology Institutes.• EU expert FP6 Life Sciences and Health,(Combatting the diseases of Poverty).• Member of the following Health Research BoardCommittees:• Funding Priorities Committee, Making Knowledge• Work for Health Committee, Ethics Committee.• Chairman of the Health Research Board ReviewPanel on National Imaging Infrastrucure.• Member of the British Society for ImmunologyInfection and Immunity Committee.Member of the Science Foundation IrelandSystems Biology Search Committee.• External reviewer: Wellcome Trust, BritishBiotechnology and Biology Science ResearchCouncil, numerous charities.• External evaluator: Guy’s and St Thomas’Charitable Foundation, Guy’s Hospital, London.• Senior Editorial Board: Journal of Inflammation.• Referee for the following journals: NaturePublishing Group, Journal of Infectious Disease,Infection and Immunity, Immunology, Clinical andExperimental Immunology, Journal of GeneralVirology, Clinical and Experimental Allergy, LifeSciences, Clinical and Diagnostic LaboratoryImmunology.• PhD examiner: University of Dublin (TCD),University of Leeds UK.Dr. J. O. McInerney• Governing Board of The Science FoundationIreland - funded Irish Centre for High-EndComputing (ICHEC).• Expert referee for The Lister Institute ResearchPrizes 2006.• Expert grant reviewer and panel member for TheHealth Research Board Post-doctoral Scheme.• Expert grant reviewer for The Wellcome Trust.• Expert grant project reviewer for BritishBiotechnology and Biological Science ResearchCouncil (UK).• Expert panel member for The Health ResearchBoard Molecular and Cellular Medicine panel2005.• Expert external reviewer for The NetherlandsOrganization for Scientific Research (NWO).• Elected Council Member, Systematics andEvolution Group, Society for General Microbiology.• Panel member for Viruses: The Deadly Enemy, BAFestival of Science, Trinity College Dublin.• Invited speaker for Rocky 05’ BioinformaticsEducation Panel Discussion, Colorado, USA.• Invited lecturer, Imperial College London MSc inAdvanced Methods in Systematics and Evolution.• Member of the Society for Molecular Biology andEvolution.• Member of the International Society forComputational Biology.• Member of the Society for General Microbiology.• Programme Committee member for the EuropeanConference on Computational Biology, Madrid,Spain.• Programme committee member for IntelligentSystems in Molecular Biology, Detroit, Michigan,USA.• Member of the BioPharmaceutical SciencesNetwork.• External examiner, PhD thesis University CollegeLondon.• External examiner, two PhD theses University ofManchester.• External examiner PhD thesis IT Carlow.• External examiner for the BSc Industrial Biologyand Bioinformatics, Institute of Technology,Carlow.• Panel member on The Big Bite, RTE television– Pandemic diseases.• Panel member on The Big Bite, RTE Television– The Evolution of Sex.• Panel Member on Prime Time – Stem CellResearch.• Speaker during Science week opposing theBiology Society/Literary and Debating Societydebate “That this house believes cloning iswrong”.• Speaker during science week for RTÉ radioprogramme, Morning Ireland on the developmentof computational science in Ireland.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06BIOLOGY37

External AssignmentsAnd Public ServiceC O N T I N U E D38NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 BIOLOGY• Referee for the following journals: Science;Nature Reviews Microbiology; Journalof Bacteriology; BMC Genomics, BMCBioinformatics, BMC Evolutionary Biology;Bioinformatics; Genome Biology; GenomeResearch; Nucleic Acids Research; Gene;Molecular Biology and Evolution; Heredity;Proceedings of the Royal Society of London(Biology Series); Journal of Molecular Evolution.Dr. N. B. Murphy• Reviewer for the following scientific journals:Experimental Parasitology and KinetoplastidBiology and Disease.• Member of Editorial Board of KinetoplastidBiology and Disease.• Member of Advisory Panel of the DoyleFoundation, UK.Dr. J. Nugent• Committee member, Irish Research Scientists’Association.• Convener of the Chain Reaction Lecture Series- NUIM for Leaving Cert Biology and PhysicsStudents and Teachers.• Lecturer in the Chain Reaction Lecture Series- NUIM - “Plant Biotechnology”.Dr. S. O’Dea• Chair, Science Foundation Ireland ResearchFrontiers Programme, Biochemistry Panel.• Treasurer (2005-2007), Irish Society for Gene andCell Therapy.Professor K. Ohlendieck• Member, Life Science Panel, Royal Irish Academy.• Committee member of the Irish Area Section ofthe Biochemical Society.• Committee member, Molecular and CellularMedicine panel of the Health Research Board.• Member, Editorial Advisory Board: Basic andApplied Myology (Unipress, Pavia, Italy).• Member, Review Board, HETAC Delegation ofAuthority, Institute of Technology, Limerick, (15-18 May 2005).• Member, Promotions Board to the Gradeof Senior Lecturer, School of Life Sciences,University College Dublin.• Reviewer of the following scientific journals:Analytical Biochemistry, Proteomics, Basicand Applied Myology, Cellular and MolecularLife Sciences, Physiological Genomics,Neuromuscular Disorders, Journal ofChromatography, Trends in Cell Biology, Journalof Neurochemistry, Journal of Gerontology.• Project reviewer for the following foundations:Biotechnology and Biological Sciences ResearchCouncil UK, Enterprise Ireland, French MuscularDystrophy Association, Italian Telethon, HealthResearch Board.• Member, Biochemical Society, UK.• Member, British Society for Cell Biology.• Member, German Society for Cell Biology.ConferencesHostedDr. K. Kavanagh. Institute of Biology of IrelandBiology Today Conference, NUI Maynooth (Attendedby 110 students from 7 local schools) (27 January2005).Professor Martin Downes. CRC Oakpark/IBAMaynooth Joint Meeting, (1 September 2005).Dr. K. Kavanagh. Microbiology Research Conference,National Institute for Cellular Biotechnology, NUIMaynooth (12 September 2005).Prof. Kay Ohlendieck. Predoctoral Symposium of theIrish Area Section of the Biochemical Society,(7 October 2005).

Faculty of ScienceResearch Report 2005-06Chemistry

40NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 CHEMISTRYAcademic StaffDr. J.M. Briody BSc (London), PhD (London) (1978-), Acting Head of Dept, 2005-06.Dr. G.M. McCann BSc (UUC), PhD (QUB) (1983-)Dr. C.B. Breslin BSc (NUIG), PhD (NUIG) (1990-)Dr. M.F. Heaney BSc (QUB), PhD (QUB) (1999-)Dr. J.G. McCaffrey BSc (NUIG), PhD (Toronto) (1991-)Dr. A.D. Rooney BSc (QUB), PhD (QUB) (1994-)Dr. J. McGinley BSc (NUIG), PhD (NUIG) (2004-)Dr. S.O. Dunne, BSc, PhD (2004-)Dr. M. Sheridan, BSc (DCU), PhD (DCU) (2004-)Dr. J.C. Stephens, BSc (NUIG), PhD (NUIG) (2005-)Research FellowsDr. S. Earley, BSc, PhD (2001-)Dr. B. Alcock, BSc, PhD (2002-)Technical StaffMs. A. Cleary BSc (UCC) (1990-)Ms. R.G. Collery-Walsh, MIOSH (1978-)Dr. K. Maddock BSc, PhD (1994-)Mr. N. Williams BSc (DCU), M Eng (DCU) (1997-)Ms. B. Woods BSc (QUB), GradDip (ITT) (2001-)Ms. O. Fenelon BSc, MSc (TCD) (2004-)Full-Time Postgraduate Research StudentsMs. M. Gallagher, BSc (2000-)Ms. S. Reilly, BSc (2000-)Ms. E. Sheridan, BSc (2001-)Ms. M. Ryan, BSc (2003-)Mr. P. Lall, BSc (2003-)Ms. T. Tallon, BSc (Open University) (2003-)Mr. R. Rowan, BSc (2004-)Ms. C. Harley, BSc (2005-)Ms. G. Hendy, BSc (2005-)Mr. O. Byrne, BSc (2005-)Mr. C. Murray, BSc (2005-)Mr. R. Curran, BSc (2005-)Mr. J. Walsh, BSc (2005-)Ms. L. Doyle, BSc (2005-)Part-Time Postgraduate Research StudentsMr. R. Clarke, BEdSc (Portsmouth University) BSc (Open University), AMRSC (2004-)Ms. S. Crawley, BSc (2005-)Executive AssistantMs. N. Kelly BA (2004-)Emeritus ProfessorProfessor C.M. Quinn, BSc (QUB), MA (Oxford), PhD (QUB), DSc (Birmingham), MRIA* Unless otherwise stated the higher degrees listed are those of the National University of Ireland.

Head Of Department’s Review Of The YearIn June 2005 the Department hosted the 57 th Irish Universities Research Colloquium. This was a verysuccessful event and one of our students, Ms Elaine Lawless won the prize for the best lecture in OrganicChemistry. In September the Department hosted the 9 th Irish Inorganic Chemistry Conference. In Novemberwe were honoured with the presence of Professor Judith K. Howard FRS who gave the 5 th Lonsdale Lecture.During the year the successor to Professor Martin Quinn as Professor and Head of the Department ofChemistry was announced. Dr. John Lowry will return to the Department as Professor and Head in 2006. Inthe meantime, Dr. Mairéad Sheridan and Dr. Simon Dunne were reappointed as lecturers on contract for asecond year.Ms. B. Alcock, Mr. A. Algawari, Mr. S. Earley, Ms. E. Lawless, Mr. T. McCarthy and Mr. I. McColgan successfullycompleted their postgraduate courses and we wish them well with their future careers.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06CHEMISTRY41

Research Interests Of StaffNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 CHEMISTRYDr. Carmel BreslinDr. Breslin’s research interests lie in the field of Electrochemistry and herwork ranges from fundamental studies of electron-transfer reactions to theapplication of electrochemistry in the formation and characterisation ofnew materials. Current projects are centred on the development of a noveldrug delivery system using the redox chemistry of conducting polymers, theincorporation of functionalised cyclodextrin derivatives within conductingpolypyrrole films to form new materials that can be used for the selectivedetection of neurotransmitters and in environmental remediation, theelectrosynthesis of chiral surfaces and their application as sensors fordiscriminating between the enantiomers of drugs, electrodeposition of metalnanoparticles and metal nanowires in oxide templates and electrodepositionreactions in room temperature ionic liquids.Dr. John BriodyThe development of synthetic pathways for the production of combinatoriallibraries of substituted imidazoles for evaluation as drug precursors. The useof derivatives of imidazole as chiral auxiliaries in asymmetric synthesis andanalytical chemistry. The synthesis and application of novel ionic liquids.Dr. Frances HeaneyDr. Heaney’s research interests lie in the field of synthetic and mechanisticorganic chemistry; she is especially interested in heterocyclic chemistry. Shehas been studying the generation of new 1,3-dipoles and their cycloadditionreactions for the synthesis of novel and unusual ring systems containingnitrogen and oxygen atoms. The mechanistic aspects of this chemistry forman important aspect of ongoing research.Dr. Malachy McCannResearch is conducted on the design, synthesis and biological testing ofnew transition metal complexes. Emphasis is placed on complexes that mayexhibit bioactivity and, thus, are potential candidates for new pharmaceuticaldrugs. The activities of complexes are assessed for their ability to inhibitthe growth of pathogenic microbes, such as the yeast Candida albicans andbacteria such as E.coli and MRSA. New compounds are required in this areain order to combat problems where the microbes are acquiring increasedresistance to the current prescription drugs. In vitro testing has revealedthat a number of our new complexes have marked antimicrobial activity.In addition, several of the new metal complexes have also demonstratedmarked activity, in vitro, against a number of cancer cell lines.Dr. Carmel BreslinSenior Lecturer in the Departmentof ChemistryWhat are your research interests?My laboratory focuses on the applicationof electrochemistry in the formation andcharacterisation of new materials.We havedeveloped new polymeric materials that can beprogrammed to bind and release drugs. Thesematerials provide a technology platform for a drugdelivery system. We have also produced a novelmaterial that is capable of sensing dopamine in thepresence of large concentrations of ascorbic acid.The selective sensing of dopamine is a particularchallenge because it co-exists in the body with anumber of interfering species, such as ascorbicacid. This selective sensing offers the potential forthe real-time monitoring of dopamine. I also workon problems of environmental Chemistry and indeveloping materials that can be used to bind andextract pollutants from water and soil samples.How do you fund your work?This research work is funded by theHealth Research Board, Enterprise Ireland(Commercialisation Fund), IRCSET, SFI andthrough collaborations with Industry. The successof the research is a tribute to the hard work andcommitment of the former and current membersof the research group and the expertise of othermembers of the department, particularly, Dr.Denise Rooney, Dr. John Stephens and ProfessorJohn Lowry who collaborate on different aspects ofthe research work.How did you build your career to date?I joined the staff of NUI Maynooth in 1990 aftercompleting a PhD degree in Physical Chemistryand Electrochemistry at NUI Galway. I wasfortunate, in my early career, to work with someleading researchers in the field of Electrochemistryat Penn State University, USA and the Universityof Southern California, Los Angeles, USA, while onsabbatical leave from NUI Maynooth.42Dr. John McCaffreyThe dissociation of organometallic molecules, such as dimethylzinc, usingvacuum ultraviolet radiation. This research was conducted by Maynoothpost-graduate students, using the vacuum ultraviolet beamline HIGITI, at theSynchrotron Radiation Facility HASYLAB/DESY in Hamburg.

Time-resolved, luminescence spectroscopy using pulsed lasers of atoms and simple molecules isolated in thesolid rare gases as model systems to examine the solvation of these elementary systems under solid stateconditions. Tuneable laser radiation is also used to examine forbidden transitions of d- and f-block elements(atomic Mn and Eu) that become enhanced in the solid state. Theoretical work done on the luminescence ofthese “matrix-isolated” atomic species (M/RG), based on the use of sums of diatomic pair-potentials for aMRG 18cluster, has allowed identification of the vibrational modes dominating atomic emission in the solidstate. A current collaboration with Dr. Claudine Crepin at the CNRS, Orsay France uses molecular dynamicscalculations to simulate the isolation of atomic guest species in the solid rare gases and the evolution ofelectronically excited states prior to emission.The spectroscopic techniques of Circular dichroism, Fourier Transform infra-red (FTIR) and Fluorescenceresonant energy transfer (FRET) are being utilised in studies of the secondary structure of late embryonicabundant (LEA) proteins in sugar glasses to probe their anhydrobiotic characteristics, i.e., their stability withrespect to loss of water. This work is being done in collaboration with Prof. A. Burnell, Dept. of Biology.Work being developed involves time-resolved “step-scan” FTIR spectroscopy of excited state metal atomreactions with hydrocarbons and silanes in low-temperature solids. The objective is to analyse energydisposal in the newly formed products and identify intermediates prior to cage recombination.Dr. Denise RooneyResearch continues into time-resolved spectroscopic and low-temperature matrix isolation studies ontransient intermediates involved in the reaction mechanisms of organometallic complexes. In order toutilise the synthetic capabilities of organometallics to an even greater extent it is essential to gain a betterunderstanding of how they act as catalysts or synthetic reagents. To achieve this it is necessary to determinewhat intermediates occur along the reaction pathway. Ongoing research projects can be divided into threesections; (1) the study of charge-transfer interactions between Lewis acids and organometallic complexes,(2) the study of the photochemical reactions of metal carbenes with respect to their ability to act as reagentsfor the formation of cyclic organic compounds and (3) the development of ‘push-pull’ complexes with thepotential to act as nonlinear optical materials.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06CHEMISTRYDr. John McGinleyTransition metal complexes containing polypyridyl ligands have received and continue to receiveconsiderable attention because of their potential applications to the fields of photoinitiated energy transfer,redox catalysis and bioinorganic chemistry. Dr. McGinley’s research interests lie in the development ofligands containing nitrogen donors (but not necessarily pyridyls only) into new materials.The research areas which he envisages these new materials to impact on are (i) catalysts: transition metalorganometallics based on phosphine, pyridyl and pyridylphosphine ligands, using calixarenes (or similarcompounds) as scaffolds; and (ii) bioinorganic chemistry: neuroprotective Agents involving thiol-calixarenesand their derivatives as potential copper chelators, to reduce oxidative damage in the central nervous system,and anti-tumour agents involving organotin/transition metal complexes and calixarenes as potential modelsystems for biological systems.All of the work combines both organic and inorganic synthesis as well as NMR ( 1 H, 13 C and multi-nuclear)spectroscopy. Some of this work is being carried out in collaboration with Professor Hans Toftlund in theUniversity of Southern Denmark, Odense, Denmark and Dr. Bernie Creaven in the Institute of TechnologyTallaght, Dublin.43

Research Interests Of StaffC O N T I N U E DDr. John StephensResearch in the Stephens group focuses onsynthetic organic chemistry and methodology. Dr.Stephens’s research interests lie in the developmentof new routes to novel heterocyclic anti-microbialagents, evaluating their biological activities andinvestigating their mode of action.(J.G. McCaffrey in collaboration with A. Burnell,Biology, 2002-2007).‘A time-resolved, infra-red spectroscopic study of theactivation of silane by electronically excited metalatoms’. Science Foundation Ireland Basic Research,€227,114, (J.G. McCaffrey, 2004-2007).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 CHEMISTRYDue to the chiral nature of many prescription drugsthe pharmaceutical industry is driving the demandfor new and economical asymmetric reactions.Dr. Stephens is interested in the efficient controlof selectivity (enantio-, diastereo, regio- andchemo-) in bond making reactions, particularlyC-C bond making processes. Research involves theinvestigation of these processes and the generationof new asymmetric catalytic systems and novelligand libraries.Research Grants‘Conducting Polymers as a Novel Drug DeliverySystem’. Health Research Board, €206,600 (C.B.Breslin and J.P. Lowry, 2005-2008).‘Electrodeposition reactions in Ionic Liquids’.Enterprise Ireland, Proof of Concept Scheme,€76,600 (C.B. Breslin, 2005-2006).‘Title Confidential’. Henkel Loctite, €80,000 (C.B.Breslin and J.M. Briody, 2005-2006).‘Title Confidential’. Hewlett Packard, €30,100, (C.B.Breslin, 2005).‘Controlling Copper Redox Activity – Possible Routeto New Therapies for Neurodegenerative Diseases.’Post-Graduate R&D Skills Programme TechnologicalSector Research: Strand I, €34,000 (J. McGinley andB. Creaven, ITT Dublin, 2005-2007).‘Controllable synthesis, characterisation andproperties of low-dimensional semiconductornanomaterials’. SFI/MOST China / Ireland Scienceand Technology Research Collaboration Fund,€24,381 (J.G. McCaffrey, 2005-2007).‘Recording NIR emission of solvated electrons andatomic anions stabilised in the solid rare gases’SFI UREKA Supplement, €5,500 (J.G. McCaffrey,summer 2005).Embark Postgraduate Scholarship. Irish Council forScience Engineering and Technology, €57,150(G. Hendy, 2005-2008).Embark Postgraduate Scholarship. Irish Council forScience Engineering and Technology, €57,150(C. Harley, 2005-2008)Embark Postgraduate Scholarship. Irish Council forScience Engineering and Technology, €57,150(L. Doyle, 2005-2008).Embark Postgraduate Scholarship. Irish Council forScience Engineering and Technology, €57,150(R. Curran, 2005-2008).Embark Postgraduate Scholarship. Irish Council forScience Engineering and Technology, €57,150(O. Byrne, 2005-2008).Embark Postgraduate Scholarship. Irish Council forScience Engineering and Technology, €57,150(M. Ryan, 2003-2006).44‘Life without water - gene discovery and functionalanalysis of anhydrobiosis in nematodes’. ScienceFoundation Ireland, Investigator Grant, €382,050,

Publications inRefereed JournalsBreslin, C.B., A.M. Fenelon and K.G. Conroy. Surfaceengineering: corrosion protection using conductingpolymers. Materials and Design, 26, 237-244 (2005).Collier, M.A. and J.G. McCaffrey. The absorption andexcitation spectroscopy of matrix-isolated atomicmanganese: Sites of isolation in the solid rare gases.Journal of Chemical Physics, 122, 054503 1-9 (2005).Collier, M.A.and J.G. McCaffrey. Luminescencespectroscopy of matrix-isolated z 6 P state atomicmanganese. Journal of Chemical Physics, 122,184507 1-15 (2005).Collier, M.A, M.A. Ryan and J.G. McCaffrey.Luminescence spectroscopy of matrix-isolated atomicmanganese; Excitation spectroscopy of the forbiddena 6 D ¬ a 6 S transitions. Journal of Chemical Physics,123, 044508 1-11 (2005).Creaven B.S., D.A. Egan, K. Kavanagh, M. McCann, M.Mahon, A. Noble, B. Thati and M. Walsh. Synthesisand Antimicrobial Activity of Copper(II) and Silver(I)Complexes of Hydoxynitrocoumarins: X-ray crystalstructures of [Cu(hnc) 2(H2O) 2]⋅ 2H 2O and [Ag(hnc)](hncH = 4-hydroxy-3-nitro-2H-chromen-2-one).Polyhedron in press.Creaven B. S., D. A. Egan, K. Kavanagh, M. McCann,A. Noble, B. Thati and M. Walsh. Synthesis,Charaterization and Antimicrobial Activity of a Seriesof Substituted Coumarin-3-carboxylatosilver(I)Complexes. Inorganica Chimica Acta 2006, in press.Deegan C., M. McCann, M. Devereux, B. Coyle andD.A. Egan. In vitro chemotherapeutic potential andmechanism of action of 1,10-Phenanthroline (phen),[Ag 2(phen) 3(mal)]⋅2H 2O, [Cu(phen) 2(mal)]⋅2H 2O and[Mn(phen) 2(mal)]⋅2H 2O (malH 2= malonic acid),using human cancer cells. Cancer Letters in press.Devereux M., M. McCann, D. O Shea, M. OConnor, E.Kiely, V. McKee, D. Naughton, A. Fisher, A. Kellett, M.Walsh, D. Egan and C. Deegan. Synthesis, superoxidedismutase mimetic and anticancer activities ofmetal complexes of 2,2-dimethylpentanedioic acid(2dmepdaH 2) and 3,3-dimethylpentanedioic acid(3dmepdaH 2): X-ray crystal structures of [Cu(3dmepda)(bipy)] 2·6H 2O and [Cu(2dmepda)(bipy)(EtOH)]2·4EtOH (bipy = 2,2bipyridine). Main Group MetalChemistry in press.Earley, S.T., D.P. Dowling, J.P. Lowry and C.B. Breslin.Formation of Adherent Polypyrrole Coatings onTi and AlTiV Alloy. Synthetic Metals 148, 111-118(2005).Fenelon, A.M. and C.B. Breslin. Polyaniline-CoatedIron: Studies on the Dissolution and ElectrochemicalActivity as a function of pH. Surface and CoatingsTechnology 190, 264-270 (2005).Fenelon, A.M. and C.B. Breslin. The formation ofpolypyrrole at iron from the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate. Journal ofthe Electrochemical Society, 152, D6-D11 (2005).Heaney, F. T. McCarthy, M.Mahon and V. McKee.Bridgehead nitrogen heterocycles which contain thequinazoline moiety - synthesis and cycloadditionof 1,2-dihydroquinazoline 3-oxides. Organic &Biomolecular Chemistry 3(24), 4351-4361 (2005).McGinley, J., B.S. Creaven, M.F. Mahon and A-M.Moore. Copper(II) complex of a tridentate N-donorligand with unexpected Cu-H interaction. Inorg.Chem. Commun., 9, 231-234 (2006).McGinley, J., A. Fleming, F. Kelleher, M.F. Mahon andV. Prajapati. Reactions of bis(tetrazole)phenylenes.Surprising formation of vinyl compounds from alkylhalides. Tetrahedron, 61, 7002-7011 (2005).McGinley, J., B.S. Creaven, T.L. Gernon, T. McCormac,A-M. Moore and H. Toftlund. Unusual reactivity ofcopper(I) complexes of functionalised calix[4]arenas.Inorg. Chim. Acta, 358, 2661-2670 (2005).R. Rowan, T. Tallon, A.M. Sheahan, R. Curran, M.McCann, K. Kavanagh, M. Devereux and V. McKee.Silver bullets in antimicrobial chemotherapy:synthesis, characterisation and biological screeningof some new Ag(I)-containing imidazole complexes.Polyhedron in press.Sheridan, E.M. and C.B. Breslin. EnantioselectiveDetection of D and L-Phenylalanine using OpticallyActive Polyaniline. Electroanalysis 17, 532-537 (2005).Timofte, R.S., J.J. Titman, L. Shao, J. C. Stephens andS. Woodward. Investigations into the Utility of High-Surface Area Silica Pellets as Potential Solid-PhaseSynthesis Supports. Tetrahedron, 61, 51-59, (2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06CHEMISTRY45

External Assignmentsand Public ServiceNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 CHEMISTRYDr. C.B. Breslin• Secretary and Treasurer of the European Sectionof the Electrochemical Society (US).• NCEA External Examiner for Diploma and Degreecourses in Chemistry at Athlone Institute ofTechnology.• Reviewer for the following ScientificJournals: Electrochimica Acta, Journal ofthe Electrochemical Society, Journal ofApplied Electrochemistry, ElectrochemistryCommunications, Journal of Physical ChemistryB, Phys Rev Letters, Materials Chemistry,Journal of Materials Research, MaterialsScience Forum, Materials Research Bulletin,Surface and Coatings Technology, CorrosionScience, Corrosion, Surface Science, AppliedSurface Science, Synthetic Metals, Langmuir,Water Research, Environmental Science andTechnology, Journal of Polymer Research,Materials Chemistry and Physics, CanadianJournal of Chemistry, Australian Journal ofChemistry.• Grant reviewer for Commercialisation Fund- Technology Development (CFTD) Programme,Enterprise Ireland.• Member of the Organising Committee for theInternational Conference on Materials-EnergyDesign (MED06), Dublin, 14 th –17 th March (2006).• Member of the Organising Committee forthe International Conference on Science andTechnology of Synthetic Metals (ICSM), Dublin,2 nd - 7 th July (2006).Dr. M.F. Heaney• Member of the Royal Society of Chemistry• External Examiner for undergraduate sciencecourses in Athlone Institute of Technology.• External Examiner for Fiona Catherine LynchPh.D. Thesis, DCU, December 2005.• Member of The American Chemical Society.• Founding Member of the Pharma Research &Development Team centered in the Instituteof Technology Tallaght and founded in 2002(funding Euro 317,000).Dr. J. McGinley• Referee for the ‘Polyhedron’• Referee for ‘Inorganica Chimica Acta’.Dr. A.D. Rooney• Reviewer of Organometallics.• Member of the Royal Society of Chemistry.Dr. J.C. Stephens• Member of the Royal Society of ChemistryConferences Hosted57 th Irish Universities Chemistry ResearchColloquium. Dr. K. Maddock (22-24 June 2005)10 th Irish Inorganic Chemistry Conference. Drs. J.McGinley & K. Maddock (10-11 September 2005)Dr. J.G. McCaffrey• Reviewer for the ‘Journal of Physical Chemistry A.’• Reviewer for the ‘Journal of Physical Chemistry B.’• Reviewer for the ‘Journal of Chemical Physics.’46Dr. G.M. McCann• Reviewer for the ‘Polyhedron’• Reviewer for the ‘Journal of InorganicBiochemistry’• Reviewer for the ‘Inorganic ChemistryCommunications’• Reviewer for the ‘Inorganic Chemistry (ACS)’

Faculty of ScienceResearch Report 2005-06Computer Science

48NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 COMPUTER SCIENCEAcademic Staff *Professor R. Reilly, BSc, PhD Head of Department (2002-)Professor B. Pearlmutter, BSc (CWRU, USA) PhD (Carnegie Mellon, USA) (2002-)Mr. S. Brown, BA (Dublin), BAI, MSc (Dublin), MIEI, CEng (1995-)Dr. T. Dowling, BSc (Dublin), MSc, PhD (1998-)Dr. J.P. Gibson, BSc (Stirling), PhD (Stirling) (1998-)Mr. J.G. Harpur, BSc, MA (1990 -)Dr. J.G. Keating, BSc, PhD, CPhys, MInstP (1990-)Mr. D. Kelly, BSc, MSc (1991-)Mr. T. Lysaght, BA, BD, HDipEd, MCompSci (1998-)Dr. C. Markham, BSc (DCU), PhD (DCU), CPhys, MInstP (1999-)Ms. R. Monahan, BSc, MSc (1999-)Mr. J. McDonald, BSc (1998-)Mr. T. Naughton, BSc (1998-)Dr. D. O’Donoghue, BSc, MSc, PhD (1991-)Dr. J. Power, BSc, MSc, PhD (DCU) (1998-)Dr. J. Timoney, BA (Dublin), BAI (Dublin), MSc (Dublin), PhD (Dublin) (1999-)Dr. A.C. Winstanley, BA (Cantab), MSc (QUB), PhD (QUB) (1995-)Postgraduate Research StudentsMs. B. Annam, BSc, MSc (Osmania University, India) (2002-)Ms. S. Bergin, BSc Mgmt (Dublin), HDipIT, MCompSci (1999 -)Mr. A. Burnett, BSc (2002-)Mr. S. Butler, BSc (2004- )Mr. B. Busschots, BSc (2001-)Mr. P. Corcoran, BSc (2005-)Mr. A. Duffy, BSc (2002-)Ms. P. Eslambolchilar, BEng (University of Tehran, Iran) (2003-)Mr. J. Foody, BSc (2004-)Mr. H. Gannud, BSc (Al Fateh University, Tripoli, Libya) (2003-)Mr. P. Gaughran, BSc (1999-)Mr. M. Hennessy, BSc (2002- )Ms. S. Jyothi, BEng (Osmania University, India) (2003-)Mr. J. Lambert, BSc (2004-)Mr. P. Lewis, BSc (2005-)Mr. F. Matthews, BSc (2004-)Mr. J. Maycock, BSc (2004-)Mr. K. Maycock, BSc (2004-)Mr. S. McCann, BSc (2003-)Mr. C. McElhinney, BSc (2004-)Ms. M. McGaley, BSc (2003-)Mr. S. McLoughlin, BSc (2000-)Ms. J. McQuillan, BSc (2000-)Ms. E-C. Mullally, BSc (2004-)Mr. N. Murphy, BSc (2005-)Mr. U. T. Neary, BSc (2003-)* Unless otherwise stated the higher degrees listed are those of the National University of Ireland.

Mr. P. O’Grady, BEng, MEng (2003-)Ms J. O’Kelly, BA Mgmt. (NCEA) (2004-)Mr. A. Page, BSc (2003-)Mr. L. Raeside, BSc (2003-)Ms. J. Reilly, BSc (AIT) MSc (AIT) (2005-)Mr. S. Sheridan, BSc (2004-)Mr. C. Soraghan, BSc (2005-)Mr. S. Strachan, BSc (2003-)Mr. D. Traynor, BSc (2003-)Mr. V. Vatsa, BSc (2003-)Research AssistantsDr. J. Ghent, BSc, PhD (2005-)Dr. B. Hennelly, BSc, PhD (2005-)Dr. H. Koesling, MSc, PhD (Bielefeld University, Germany) (2004-)Dr. P. Mooney, BSc, PhD (2004-)Ms. A. Shortt, BSc (2005-)TechniciansMr. J. Cotter, BSc, Dip. SoftEng (1990-)Mr. P. Marshall, BSc, Dip. Strategic Management (DIT) (2001-)Mr. M. Monaghan, (1999-)Dr. V. Paturyan, Dip. Phys. (Yerevan State University, Armenia) PhD (2002-)Departmental AdministratorMr. D. Noonan, BSc, MSc (UUJ) (2002-)Executive AssistantsMs. A. Murphy, (1983-)Ms. L. Donohoe, HDipIT (1999-)Ms. L. Cannon, (2000-)NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06COMPUTER SCIENCEIndustrial Placement OfficerMs. P. Murray, BSc (2000-)49

Head Of Department’s Review Of The YearThis past academic year has been a somewhat turbulent one for the Department. The undergraduate intakehas remained steady, helped in part by the Music Department’s new BA in Music Technology, to which theDepartment of Computer Science is making a significant contribution. This course received the highestnumber of first preferences of any NUIM course on its CAO debut.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 COMPUTER SCIENCEThe Departmental strategy of increasing both undergraduate and postgraduate intake by broadening courseofferings has resulted in the development of a number of new courses. At the undergraduate level, a courseentitled BSc in Applied Computing has been submitted for approval to the University’s New ProgrammesCommittee. This course is aimed primarily at international students who wish to take the final year of theirfour-year Computer Science BSc at NUIM. An agreement was signed at the end of 2005 between JiangsuPolytechnical University (JPU) and NUIM to facilitate the transfer of students from JPU to such a programme.On the outreach front, the Department of Computer Science was involved with the Hamilton Institute inrunning the successful NUIM Grand Challenge which started in January 2006. This challenge consisted of 20puzzles spread over 10 weeks. It was aimed at secondary school pupils with the aim of promoting interest inmathematical thinking and related subjects.At the postgraduate level, the Department has introduced two new specialisations to the taught MScprogramme: signal processing and robotics, and cryptography and security. We are also the coordinatingdepartment for a submission to the EU’s Erasmus Mundus programme applying for support for an interinstitutionalMSc with a software engineering specialisation. The proposed degree will involve studentstaking course modules in two of either NUI Maynooth, St Andrew’s University in Scotland, or Université HenriPoincaré in Nancy.The past academic year has seen a steady increase in the number of PhD graduations. Congratulations aredue to our most recent crop of graduates: Eva Belso-Burlo, John Ghent, Áine Mitchell, Aidan Mooney, AlisonShortt, and Damien Woods. We should take some pride in the fact that one of our students was offered apost-doctoral position by their Cornell-based external examiner. Clearly, our research PhDs are of the highestinternational standard.This year the Department made progress in further fostering links with industrial partners. The mostrecent collaborations are in the areas of cryptography (Dr. Tom Dowling) and the provision of a passengerinformation system for trams (Dr. Adam Winstanley). On a related note, congratulations are due to FiachraMatthews who won the HP Invent Award for his final year project. His project involved the development of aUSB-based orientation sensor and was supervised by Dr Charles Markham.A long-serving member of the Department, Dr. Fred Lunnon, retired at the end of 2005. We will miss hiscontribution to the social and academic life of the Department.This year also saw the departure of three contract members of staff: Dr. Declan Delaney, Mr. George Mitchell,and Ms. Jackie O’Kelly. All three have made an important contribution to the Department, particularly in thearea of teaching innovation. Indeed, Dr. Delaney and Mr. Mitchell were joint recipients of the NUIM BiennialPresidential Prize for Distinguished Teaching in 2004. Ms. O’Kelly pioneered the introduction of problembasedlearning to the teaching of first-year programming.Finally, I would like to thank Dr. Paul Gibson and Mr. John Harpur who took turns as Acting Head while I wason away sabbatical.50

Research Interests Of StaffMs. Susan BerginPostgraduate student in theDepartment of Computer ScienceWhat are your research interests?My PhD thesis is based on a longitudinalstudy of factors that influence introductoryprogramming success by students andon the development of machine learningmodels to predict incoming studentperformance. Although numerous studieshave previously developed models toattempt this, the models have failedto achieve high levels of accuracy. Myapproach overcomes this by providing amachine learning technique, using a set ofthree significant factors that can classifystudents as ‘weak’ or `strong’ programmerswith ~80% accuracy after only three weeksof programming experience. Consequently,timely interventions can be put in place toprevent struggling students from failing.How do you fund your work?My research is funded by the HigherEducation AuthorityHow did you build your career to date?I received an honours primary degree inBusiness from the University of Dublinin 1996 before securing a scholarship tocomplete a Masters in Computer Sciencein 2001 at the Department of ComputerScience, NUI Maynooth. I received thehighest results ever recorded on theMasters program and my research waspublished in one of the top journalsin the field. In addition, my work wasinstrumental in the modification oftelecommunications legislation obligingmobile phone operators to providetransparent pricing information, in theRepublic of Ireland. In 2002 I began mydoctorate in Computer Science at Maynoothwhich is now being completed, and I hopeto continue as a postdoctoral fellow inthis field.Mr. Stephen BrownPrimary research interest is in embedded networking systems: Sensor Networks, SoftwareEngineering Education; Design and Analysis of routers/bridges for Performance and Stability,especially under overload; Engineering for Software Systems (Software Engineering);Embedded Operating Systems (especially support for latency, throughput, & buffering).Dr. Tom DowlingTheory and practice of cryptography and cryptanalysis. Information warfare. Java and perlbased implementation of cryptographic protocol and systems. Smart card development andintegration. Numerical computing. Developing computer based simulations of algebraicconstructs. Theory and application of Elliptic curves over finite fields and extension fields.Performance analysis of elliptic curve algorithms. Computer forensics and network securityprotocols and tools.Dr. J. Paul GibsonDr. J. Paul Gibson is the TASS (Theoretical Aspects of Software Systems) research groupco-ordinator. He has experience in rigorous software engineering for secure systems, objectoriented formal methods and models, telecommunication service specification, simulation andverification, transfer of formal methods to industry, electronic voting, and CS education research.Mr. John HarpurModelling features of autism; social competence enhancement through computer game basedlearning; human computer interaction; assistive technology development.Dr. John KeatingJohn Keating is interested in Information Processing using Artificial Neural Networks, ChaoticbasedWatermarking and Image Processing. He has also recently been working on VirtualLearning and Collaborative Environments and manages the Virtual Telescopes in Educationproject which will provide a VLE for science education to second-level schools. He is also aVisiting Scientist at IBM’s Centre for Advances Studies at Dublin, where he is working oneLearning and on-demand mechanisms.Mr. Dermot KellyDistributed Systems, the Internet and its application to the emergence of virtual societies, gridcomputing, e-commerce and database backed services, mobile internet services, multimediadelivery, collaborative applications, network centric games, virtual reality environments andremote monitoring and control. Entertainment Technology Systems for sound and lightingresources, analyzing and synthesising, visualising and controlling these resources.Mr. Tom LysaghtDigital signal processing with application to real-time audio. Sound synthesis. Computer vision.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06COMPUTER SCIENCE51

Research Interests Of StaffC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 COMPUTER SCIENCEDr. Charles MarkhamCharles Markham is currently collaborating with the Engineering Department at NUIM to develop abrain computer interface based on optical tomography. The work involves developing accurate methodsof photometry to allow blood oxygen levels to be measured and so infer brain activity. In collaborationwith the Vision Groups, Institute for Technology. Blanchardstown and NUIM Dr. Markham is developinga mobile computer vision system. This project has created interest from the National Roads Authority forroad infrastructure management. The Vision Group (NUIM) is also investigating the use of sensor fusion toimprove performance of pedestrian detection systems. Initial work has been carried out using a combinedLIDAR and Vision System as part of the autotram project. Dr Markham has special interest in the design ofnovel imaging sensors. He has developed techniques for Infrared imaging using coded apertures and widebaselinestereo imaging methods to achieve a visual radar system.Ms. Rosemary MonahanRosemary Monahan’s research is concerned with the development of reliable software systems. In particularshe is interested in the development of a mathematical model for object-oriented specifications and acorresponding program construction theory that will ensure that object-oriented software is designedin a precise unambiguous manner. Her main interests include formal methods for program construction(Refinement, the Z specification language, Weakest Precondition Calculus) as well as the exploration of thetheoretical foundations of programming languages, with a particular emphasis on type systems and theirimpact on reliable software development.Mr. John McDonaldJohn McDonald’s primary research interests lie in the areas of computer vision, image processing, andpattern recognition. In the past he has worked on topics such as face recognition systems, 3-dimensionalsurface registration and analysis, and intelligent vehicle systems. More recently he has been involved in thedevelopment a novel computational model of facial expression and techniques for 3-dimensional holgraphicimage processing. He is a member of the Computer Vision and Imaging Laboratory in the Department ofComputer Science (vision.cs.may.ie).Mr. Thomas NaughtonThomas Naughton has research interests at intersections of computer science, optics, and biology. In thefield of optical information processing, he has developed tools for the processing and analysis of threedimensionalscenes encoded in digital holograms, has built matrix-algebra optical computers that utilisean optical Fourier transform, and has applied computational complexity theory to the analysis of analogoptical computing architectures. At the intersection of computer science and biology, he is interested inbiologically-inspired computation (genetic algorithms, neural networks), biocomputation (computing withmolecules), and bioinformatics (for example,applying distributed computing to phylogenetic tree constructionand genome database searching). In computer science, he is working on dynamic scheduling for distributedcomputing, and provably reliable operating systems.52

Dr. Hendrik KoeslingPost-doctoral fellow in theDepartment of Computer ScienceWhat are your research interests?My research interests are in visual perceptionand attention in humans. I investigate howvisual information is processed in the humanbrain and develop cortical computational modelsand cognitive models of language. I collect eyemovementdata with a sophisticated eye-trackingapparatus and compute where a person is lookingand how the focus of attention moves about. Such“gaze paths” indicate how people solve certaintasks and which problem-solving strategies areapplied. Computer models are then implementedto reproduce the empirical eye-movement patternsand to simulate human visual behaviour. Usingsuch models in artificial vision systems makes themmore “humanoid” and leads to more intuitive manmachineinterfaces. I have recently investigateddecision-making processes in computer games.My findings could help to improve the anticipatoryabilities of such games and thus enhance their“intelligence”. I have also studied the interactionbetween language and visual attention during thepresentation of navigation messages while driving.The results of this study suggest that it wouldbe beneficial for in-car navigations systems todynamically generate navigation messages guidedby the current traffic situation. This would optimisethe processing of concurrent tasks - steering, trafficobservation and message comprehension haveto be accomplished in parallel - and thus improvedriving safety.How do you fund your work?I was awarded a prestigious research grant fromthe German Science Foundation DFG to carry outwork in the Computational Cognitive ModelingResearch Group, led by Professor Ronan Reilly.I currently run the “eye-tracking” laboratory atNUIM.How did you build your career to date?I studied Computer Science and Physics atBielefeld University, Germany graduating in 1997.I received a PhD from the same institution in2003. I worked as a lecturer and researcher in theNeuroinformatics Group at Bielefeld Universityfrom 1998-2004. During this time, I was also amember of the Collaborative Research CentreSFB360 “Situated Artificial Communicators”. Ijoined the Department of Computer Science atNUI Maynooth as a postdoctoral associate inNovember 2004.Dr. Diarmuid O’DonoghueDiarmuid O’Donoghue’s research is φοχυσεδ on computational models of how people reasonwith analogical comparisons. He has been focusing on geometric proportional analogies,typified by those problems found in IQ tests. These analogies take the form A:B as C:D (read as,A is to B as C is to D), with the objective being to generate D from the given information (A, Band C).We consider analogies where each of the objects include attributes, such as colour and shading.Solutions being developed combine (isomorphic) structure mapping between parts A and C ofthe analogy, with an attribute matching process - resulting in a family of structure matchingalgorithms. These algorithms are also being applied to the domain of qualitative spatialreasoning, particularly to interpreting and enhancing topographic maps. Other areas of interestinclude mathematical models of the web, genetic algorithms and simulated genetic-repairoperators.Professor Barak PearlmutterProf. Pearlmutter’s primary technical interest is in systems that adapt: how to analyze them,how to understand them, how to build them. Because the most flexible and competent adaptivesystems available is the nervous system, he is interested in artificial neural networks andcomputational neuroscience. He is most φοχυσεδ on the construction of novel architecturesand algorithms that enable us to understand and attack previously unassailable problems, andto understand previously mysterious aspects of nervous system function.A secondary interest of Prof. Pearlmutter’s is in programming systems, especially advancedprogramming language design and implementation. One of his projects is to build a newefficient advanced programming language with novel constructs that allow many numericalgorithms and scientific computations to be expressed very clearly and succinctly.Dr. James PowerJames Power’s research is focused on the application of techniques and tools from complierdesign to software engineering problems, particularly program comprehension, reverseengineering and software visualisation. One thread of this research involves studyingworkloads and profiles of Java programs in order to provide a quantitative foundation for thedesign of intermediate representations, such as Java bytecode, as well as the virtual machinesthat execute them. Another thread of the research is the development of an open source reverseengineering and analysis framework for ISO C++, a syntactically complex and heavily contextsensitivelanguage. Common to both the Java and C++ threads of the research is an emphasis onapplying the results to software testing and verification.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06COMPUTER SCIENCE53

Research Interests Of StaffC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 COMPUTER SCIENCEProfessor Ronan ReillyRonan Reilly’s main research interests are in the areas of visual perception and language understanding.His interest in vision research primarily relates to eye movement control in reading, which also convenientlycombines a language dimension. His research in this area involves data collection using an eye trackingsystem, and the computational modeling of these data. More recently he has started to look at the applicationof my reading model to web usability analysis. Within the language area, he has a specific interest inalternatives to the currently dominant nativist accounts of language acquisition. Again, this work isunderpinned by computational modelling.Prof. Reilly has also been working on a theoretical approach to modelling cortical computation, which herefers to as “Cortical Software Re-Use”. The goal of this theory is to try to account for the construction ofcognitive capabilities within a developmental and evolutionary framework. The main assumption of this lineof research is that cognitive and linguistic capabilities are incrementally constructed from sensory-motorfunctions. These act as a repertoire of neural functionality that get exploited in the development of morecomplex neural capacities.Dr. Joseph TimoneyDigital audio signal processing with an emphasis towards multimedia applications. Specifically, in the areaof speech signal processing current projects include the development of a diphone speech synthesiser forIrish gaelic and the investigation of post-processing methods to improve the synthesised speech. Theseare being carried out in collaboration with the members of the Department of Electronic Engineering.Additionally, a research group consisting of staff from the computer science department with researchersfrom DIT is creating new methods for the analysis of the partial envelopes of musical sounds. Another projectin collaboration with researchers from DIT is the development of ASIC technology to implement an adaptivefiltering approach for speech enhancement.Dr. Adam Winstanley1. A.I. and statistical approaches of graphical data including using shape, context, and statistical LanguageModelling for recognition and validation of graphical objects. Applications include:- (re-)structuring topographic data for GIS- Validation and Quality assessment of Geographic Data- Recognition of complex objects within graphical data- Structuring data for multi-media systems2. Electric vehicle control systems- Control systems for electric rail vehicles- Development of sensory algorithms to control autonomous public-transport vehicles in unsegregatedenvironments3. Transport information systems- Journey planners optimised on multiple criteria- In-vehicle passenger information systems using global positioning systems54

Research Grants‘Lifetime support for wireless sensor networks’.Science Foundation Ireland, Tyndall NationalInstitute National Access Program, €25,000 (S.Brown, 2005-2006).‘E-Learning Innovation Fund’. Quality PromotionsOffice, NUIM, €2,696.84 (S. Brown, 2005-2006).‘Problem-Based-Learning (PBL) - from theoryto practice’. Enterprise Ireland InternationalCollaboration Research Grant 2005 EI/IC/2005/49between Clemson University, USA and NUIM, 2005,€4500 (J.P. Gibson, R. Monahan and J. O’Kelly).‘Virtual Telescopes in Education’. National Centrefor Technology in Education, €101,600 (J.G. Keating,2003-2005).‘Embedding and Detection Algorithms for ChaosbasedWatermarking Schemes’. Enterprise Ireland,International Collaboration Grant, €6,000 (J.G.Keating, 2005-2006).‘Bringing e-learning into an on-demand framework’.IRCSET, €63,960 (K. Maycock and J.G. Keating, 2005-2007).‘Explanation-Based Information Retrieval (EBiR)’.EI Research Innovation Fund, €126,000 (T. Veale, D.O’Donoghue and F. Costello, 2002-2005).‘Development of a computational model for thedescription of the shape, texture and dynamicsof facial expression’. Science Foundation IrelandResearch Frontiers Grants Scheme, €145,000 (J.B.McDonald and P.F. Whelan, 2005-2008).‘Designing computers from biomolecules’. IRCSET,€57,150 (N. Murphy, T.J. Naughton and D. Woods,2005-2008).‘Real-time segmentation of 3D objects fromholographic video’. IRCSET, €57,150 (C. McElhinneyand T.J. Naughton, 2004-2007).‘Distributed computing and high throughputphylogenomics’. IRCSET, €47,625 (T. Keane and T.J.Naughton, 2004-2007).‘Encryption and decryption of digital hologramsof three-dimensional objects’. Science FoundationIreland, €170,000 (J.T. Sheridan and T.J. Naughton,2004-2007).‘Three-dimensional holographic image processing’.Science Foundation Ireland, €160,400 (J.B.McDonald, T.J. Naughton and J.T. Sheridan, 2004-2007).‘Holographic image encryption’. IRCSET, €76,000 (N.Nishchal and T.J. Naughton, 2004-2006).‘Self optimising distributed systems’. IRCSET,€57,150 (A. Page and T.J. Naughton, 2003-2006).‘Compression of digital holograms of threedimensionalobjects’. Enterprise Ireland, €119,830(T.J. Naughton, 2003-2006).‘Specification of an abstract operating systemrunning on a single stack pushdown automaton’.IRCSET, €57,150 (A. Delaney, T.J. Naughton and J.P.Gibson, 2002-2005).‘Wearable kinematic and physiological biofeedbacksystem for movement-based relaxation’. HEA/MLECollaboration Grant, €250,000 (T. Ward, C. Markhamand G. McDarby, 2004-2007).‘NIRS Brain Computer Interface’. HEA/MLECollaboration Grant, €180,000 (T. Ward and C.Markham, 2002-2005).‘Integration of an INS into a mobile machine visionsystem’. Strand 1 Grant, Council of Directors of theInstitute of Technology, €24,000 (C. Deegan and C.Markham, 2005-2006).‘IT needs analysis in the community and voluntarysector’. Grant funded by the Information SocietyFund, €180,000 (R.G. Reilly, 2005).‘Climate Change IT Systems Development’. PostdoctoralFellowship, Environmental ProtectionAgency, Environmental Research Developmentand Innovation Programme, €169,499.95 (A.C.Winstanley and P. Mooney, 2004-2007).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06COMPUTER SCIENCE55

Research GrantsC O N T I N U E DPublications inRefereed JournalsNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 COMPUTER SCIENCE‘Texture Based Classification of Objects usingComputer Vision’. Government Of Ireland ResearchScholarships In Science, Engineering AndTechnology, Irish Research Council For Science,Engineering And Technology, €57,150 (A.C.Winstanley and P. Corcoran, 2004-2007).‘Spatial Video Data Analysis and Access overrestricted Networks’. Government Of IrelandResearch Scholarships In Science, Engineering AndTechnology, Irish Research Council For Science,Engineering And Technology, €57,150 (P. Lewis, A.C.Winstanley and S. Fotheringham, 2005-2008).Centre for Geocomputation, Science FoundationIreland Research Professorships Scheme,€2,500,000 (S. Fotheringham, R. Kitchin and A.C.Winstanley, 2004-2009).‘Statistical Language Modelling for Graphical ObjectRecognition’. HEA Technological Sector Research:Strand I Post-Graduate R&D Skills Programme,€34,000 (L. Keyes and A.C. Winstanley, 2004-2006).‘Graphics Recognition using Structural Descriptors’.Science Foundation Ireland China / Ireland Scienceand Technology Collaboration Research Fund, €26,500 (A.C. Winstanley and S. Fotheringham, 2005-2007).Brown, S., A. Mitchell and J.F. Power. ‘A CoverageAnalysis of Java Benchmark Suites’. The IASTEDInternational Conference on Software Engineering,Innsbruck, Austria, (15-17 February, 2005).O’Kelly, J. and J.P. Gibson. ‘Software engineering asa model of understanding for learning and problemsolving’. Proceedings of the First InternationalComputing Education Research Workshop (ICER2005), ACM PRESS, ISBN 1-59593-043-4, Seattle,USA, pp 87-97 (1-2 October 2005).Woods, D. and J.P. Gibson. ‘Lower bounds onthe computational power of an optical model ofcomputation’. Fourth International Conference onUnconventional Computation (UC’05), Lecture Notesin Computer Science volume (3699), edited by C.S.Calude, M.J. Dinneen, G.Paun’ M.d.J. Pérez-Jiménezand G. Rozenberg, Springer Verlag, ISBN 3-540-29100-8, Sevilla, Spain, pp 237–251 (3-7 October2005).Carew, D., C. Exton, J. Buckley, M. McGaley andJ.P. Gibson. ‘Preliminary Study to EmpiricallyInvestigate the Comprehensibility of RequirementsSpecifications’. Proceedings of the Psychology ofProgramming Interest Group 17 th annual workshop(PPIG 2005), edited by Romero, P., Good, J., AcostaChaparro, E., and S. Bryant, pp 182-202. Universityof Sussex, Brighton, UK, pp 540-551 (28 June - 1 July2005).Woods, D. and J.P. Gibson. ‘Complexity of continuousspace machine operations’. First Conference onComputability in Europe: New ComputationalParadigms. (CiE2005), Lecture Notes in ComputerScience volume (3526), edited by Barry Cooper, S.,Cooper, Löwe, B., Torenvliet, L., Springer Verlag,ISBN 3540261796, Amsterdam, The Netherlands, pp540-551 (8-12 June 2005).56Hallinan, S. and J.P. Gibson. ‘A Graduate’s Role InTechology Transfer: From Requirements to Designwith UML’. IASTED International Conference onSOFTWARE ENGINEERING 2005 (SE 2005),IASTED (ACTA PRESS), editor P. Kokol, ISBN 0-88986-464-0, Innsbruck, Austria, pp 94-99, (15-17February 2005).

Traynor, D. and J.P. Gibson. ‘Synthesis and Analysis ofAutomatic Assessment Methods in CS1: Generatingintelligent MCQs’. Special Interest Group onComputer Science Education (SIGCSE05) TechnicalSymposium, ACM International ConferenceProceedings Series, edited by Dann, W., Naps, T.,Tymann, P. and D. Baldwin, ISBN 1-58113-997-7, St.Louis, Missouri, USA, pp 495–499 (23-27 February2005).Harpur, J. ‘Philosophical Implications of Autism forArtificial Intelligence’, Track on Cognitive Science,Proceedings E-CAP 05, European Conference onComputing and Philosophy, Vasteras, Sweden (2-4June, 2005).Harpur, J. ‘Rediscovering small talk’, Track onComputational Linguistics, Proceedings E-CAP 05,European Conference on Computing and Philosophy,Vasteras, Sweden (June 2-4, 2005).Harpur, J., Bengtsson, L. and Lawlor , M.‘Maladaptive discourse constraints’, In Constraintsin Discourse 06, Sassen, C., Benz, A. and Kuhnlein, P.(Eds), pp.122-128, Universitat Dortmund (2005).Harpur, J., D. Madden and M. Lawlor. ‘Attachmenttheory and affective user models’In Proceedings of Workshop on Adapting theInteraction Style to Affective Factors in conjunctionwith User Modeling and IJCAI, Edinburgh, Scotland(30 July 2005).Maycock, K. and J.G. Keating. ‘Building IntelligentLearning Management Systems to implement theteacher student dialogue’. IEEE LTTC LearningTechnology Newsletter, 7, 1, 16-20 (2005).Mooney, A. and J.G. Keating. ‘Generation andDetection of Watermarks Derived from ChaoticFunction’. Proceedings of Opto-Ireland, ProceedingsSPIE, 5823, 58-69, (2005).Busschots, B., N. Kelly, V. Vatsa, E. O’Cinneideand J.G. Keating. ‘The VTIE collaborative writingenvironment for school projects’. Proceedings SPIE,5827, 579-590 (2005).Busschots, B. and J.G. Keating. ‘The VTIE telescoperesource management system’. Proceedings SPIE5827, 660-668 (2005).Raeside, L., B. Busschots, E. O’Cinneide, S. Foy andJ.G. Keating. ‘Empowering schoolchildren to doastronomical science with images’. ProceedingsSPIE, 5827, 669-678 (2005).Maycock, K. and J.G. Keating. ‘Bridging the gapbetween Adaptive Hypermedia Systems and theSharable Content Object Reference Model’. 4 thWSEAS Int. Conf. on E-ACTIVITIES, Miami, Florida,U.S.A., pp 69-73 (17-19 November 2005).Ghent, J. and J. McDonald. ‘Photo-Realistic FacialExpression Synthesis’. Image and Vision Computing,23(12), 1029-1144 (2005).Ghent, J. and J. McDonald. ‘Facial ExpressionClassification using a One-Against-All SupportVector Machine’. In Proceedings of Irish MachineVision and Image Processing Conference, edited byAmira, A., A. Bouridane and F. Kurugollu, pp 219-226(2005).Ghent, J. and J. McDonald. ‘Holistic Facial ExpressionClassification’. In Imaging and Vision, edited byMurtagh, F. D., Proceedings of SPIE, SPIE Press,Bellingham, 5823, 143-153 (2005).Carter G., R. Monahan and J. Morris. ‘SoftwareRefinement with Perfect Developer’. SoftwareEngineering and Formal Methods, (September2005).Page, A. J. and T.J. Naughton. ‘Framework for taskscheduling in heterogeneous distributed computingusing genetic algorithms’. Artificial IntelligenceReview, 24, 415-429 (2005).Woods, D. and T.J. Naughton. ‘An optical model ofcomputation’. Theoretical Computer Science, 334,227-258 (2005).Keane, T. M. and T.J. Naughton. ‘DSEARCH: sensitivedatabase searching using distributed computing’.Bioinformatics, 21, 1705-1706 (2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06COMPUTER SCIENCE57

Publications in Refereed JournalsC O N T I N U E D58NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 COMPUTER SCIENCEKeane, T. M., T.J. Naughton, S. A. A. Travers, J. O.McInerney and G. P. McCormack. ‘DPRml: distributedphylogeny reconstruction by maximum likelihood’.Bioinformatics, 21, 969-974 (2005).Shortt, A. E., T. J. Naughton and B. Javidi.‘Compression of encrypted digital holograms usingartificial neural networks (Invited Article)’. Optics inInformation Systems, 16, 1-8 (2005).Naughton, T.J. and J. T. Sheridan. Editors. Opticsin Information Systems, Special issue on OpticalEncryption, vol. 16, no. 1, SPIE Press, Bellingham,Washington (2005).Naughton, T.J. and B. Javidi. ‘Compression of digitalholograms for secure three-dimensional imagestorage and transmission (Invited)’. In Optical andDigital Techniques for Information Security, editedby Javidi, B., Springer-Verlag, Berlin, pp 173-191(2005).Gopinathan, U., D. S. Monaghan, T.J. Naughton, J. T.Sheridan and B. Javidi. ‘Strengths and weaknessesof optical encryption algorithms (Invited Paper)’. In18 th Annual Meeting of the IEEE Lasers and Electro-Optics Society, edited by Delfyett, P. J., Golovchenko,E. and Amann, M., IEEE Press, New York, pp 951-952(2005).Maycock, J., C.P. McElhinney, A.E. Shortt, T.J.Naughton, J.B. McDonald, B.M. Hennelly, U.Gopinathan, D.S. Monaghan, J.T. Sheridan and B.Javidi. ‘Holographic image processing of threedimensionalobjects (Invited Paper)’. In Three-Dimensional TV, Video, and Display IV, edited byJavidi, B., Okano, F. and Son J., Proceedings of SPIE,SPIE Press, Bellingham, 6016, 190-204 (2005).Javidi, B., E. Tajahuerce, M. Martínez-Corral, T.J.Naughton and Y. Frauel. ‘New developments in activeand passive 3D image sensing, visualization, andprocessing (Invited Keynote Paper)’. In Unmanned/Unattended Sensors and Sensor Networks II, editedby Carapezza, E. M., Proceedings of SPIE, SPIE Press,Bellingham, 5986, 1-11 (2005).Frauel, Y., A. Castro, T.J. Naughton and B. Javidi.‘Security analysis of optical encryption (InvitedPaper)’. In Unmanned/Unattended Sensors andSensor Networks II, edited by Carapezza, E. M.,Proceedings of SPIE, SPIE Press, Bellingham, 5986,25-34 (2005).Javidi, B., E. Tajahuerce, T.J. Naughton, Y. Frauel andO. Matoba. ‘Three-dimensional image encryption,transmission, and processing by using digitalholography (Invited Keynote Paper)’. In Systems ofOptical Security, edited by Jaroszewicz, Z., Popov, S.Y. and Wyrowski, F., Proceedings of SPIE, SPIE Press,Bellingham, 5954, 16-29 (2005).Monaghan, D.S., U. Gopinathan, B.M. Hennelly, T.J.Naughton and J. T. Sheridan. ‘Digital optics, digitalholography, and optical encryption (Invited Paper)’.In Optical Information Systems III, edited by JavidiB. and Psaltis, D., Proceedings of SPIE, SPIE Press,Bellingham, 5908, 209-223 (2005).Shortt, A.E., T.J. Naughton and B. Javidi. ‘Compressionof digital holograms of three-dimensional objectsusing the wavelet transform (Invited Paper)’. InOptical Information Systems III, edited by JavidiB. and Psaltis, D., Proceedings of SPIE, SPIE Press,Bellingham, 5908, 17-29 (2005).Maycock, J., C.P. Mc Elhinney, T.J. Naughton, J.B.McDonald and B. Javidi. ‘Independent componentanalysis applied to digital holograms of threedimensionalobjects’. In Optical Information SystemsIII, edited by Javidi B. and Psaltis, D., Proceedings ofSPIE, SPIE Press, Bellingham, 5908, 42-50 (2005).McElhinney, C.P., J. Maycock, T.J. Naughton, J.B.McDonald and B. Javidi. ‘Extraction of threedimensionalshape information from a digitalhologram’. In Optical Information Systems III, editedby Javidi B. and Psaltis, D., Proceedings of SPIE, SPIEPress, Bellingham, 5908, 30-41 (2005).Shortt, A.E., T.J. Naughton and B. Javidi. ‘Nonuniformquantization for compression of encrypted digitalholograms’. In Optical Information Systems III, editedby Javidi B. and Psaltis, D., Proceedings of SPIE, SPIEPress, Bellingham, 5908, 416-426 (2005).Keane, T.M., A.J. Page, J.O. McInerney and T.J.Naughton. ‘A high throughput bioinformaticsdistributed computing platform’. In 18 th IEEEInternational Symposium on Computer-Based

Medical Systems, edited by Cunningham, P., TsymbalA. and Bolshakova, N., IEEE Press, New York, pp377-382 (2005).Gopinathan, U., D.S. Monaghan, A.E. Shortt, T.J.Naughton, J.T. Sheridan and B. Javidi. ‘Capture,encryption, compression, and display of digitalholograms of three-dimensional objects’. InHolography 2005 - International Conference onHolography, Optical Recording and Processing ofInformation, edited by Denisyuk, Y. N., Sainov, V. C.and Stoykova, E. V., SPIE Press, Bellingham, pp 21-25(2005).Naughton, T.J. and B. Javidi. ‘Compression ofencrypted three-dimensional objects using digitalholography’. In Photon Management Research inIreland, edited by Sheridan, J. T., O’Dowd, R. F. andO’Sullivan, G. D., Proceedings of SPIE, SPIE Press,Bellingham, 5827, 399-409 (2005).Shortt, A.E., T.J. Naughton and B. Javidi. ‘Optimalquantization applied to digital holographic data’In Photon Management Research in Ireland, editedby J.T. Sheridan, R.F. O’Dowd and G.D. O’Sullivan,Proceedings of SPIE, SPIE Press, Bellingham, 5827,58-68 (2005).Shortt, A. E., T. J. Naughton and B. Javidi. ‘Vectorquantization compression of digital holograms ofthree-dimensional objects’ In Photon ManagementResearch in Ireland, edited by J.T. Sheridan, R.F.O’Dowd and G.D. O’Sullivan, Proceedings of SPIE,SPIE Press, Bellingham, 5827, 265-273 (2005).Monaghan, D.S., U. Gopinathan, B.M. Hennelly, D.P.Kelly, T.J. Naughton and J.T. Sheridan. ‘Applications ofspatial light modulators in optical signal processingsystems’. In Photon Management Research inIreland, edited by J.T. Sheridan, R.F. O’Dowd andG.D. O’Sullivan, Proceedings of SPIE, SPIE Press,Bellingham, 5827, 358-368 (2005).McElhinney, C., J. Maycock, J.B. McDonald, T.J.Naughton and B. Javidi. ‘Three-dimensional scenereconstruction using digital holograms’. In Imagingand Vision, edited by Murtagh, F. D., Proceedings ofSPIE, SPIE Press, Bellingham, 5823, 48-57 (2005).Page, A.J. and T.J. Naughton. ‘Dynamic taskscheduling using genetic algorithms forheterogeneous distributed computing’. In 19 th IEEEInternational Parallel and Distributed ProcessingSymposium, IEEE Press, New York, pp 189a.1-189a.8(2005).Page, A.J., T.M. Keane and T.J. Naughton.‘Bioinformatics on a heterogeneous Java distributedsystem’. In 19 th IEEE International Parallel andDistributed Processing Symposium, IEEE Press, NewYork, pp 184a.1-184a.4 (2005).Gopinathan, U., D.S. Monaghan, T.J. Naughton andJ.T. Sheridan. ‘An optical encryption scheme thatuses polarization of coherent light’. In OSA Frontiersin Optics/Laser Science Conference, OSA Press,Washington (2005).Mullally, E.C. and D. O’Donoghue. ‘GeometricProportional Analogies In Topographic Maps:Theory and Application’. Proceedings of 25 th SGAIInternational Conference on Innovative Techniquesand Applications of Artificial Intelligence,Cambridge, UK. Ann Macintosh, Richard Ellis, TonyAllen (Eds.) ISBN: 978-1-84628-223-2, pp 95-108,UK (12-14 December 2005).O’Donoghue, D., A. Loughlin, A. Bohan and M.T.Keane. ‘Geometric Analogies and Topographic Maps’.Computational Creativity Workshop 2005, at IJCAI,(Eds.) P. Gervais, T. Veale, and A. Pease, Edinburgh,Scotland, pp 30-37, (30July 2005).Cleary, D., B. Danev and D. O’Donoghue. ‘UsingOntologies to Simplify Wireless NetworkConfiguration’. Formal Ontologies Meet Industry,Verona, Italy (9-10 June 2005).Paturyan, V., E. Radu and D.H. Tchrakian. ‘Rotatingregular solutions in Einstein-Yang-Mills-Higgstheory’. Physics Letters B, 609, 360-366 (March2005).O’Grady P.D., B.A. Pearlmutter and S.T. Rickard.‘Survey of Sparse and Non-Sparse Methods inSource Separation’. International Journal of ImagingSystems and Technology (IJIST), special issueon blind source separation and deconvolution inimaging and image processing, 15, 18-33, (2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06COMPUTER SCIENCE59

Publications in Refereed JournalsC O N T I N U E DJun, S.C. and B.A. Pearlmutter. ‘Fast Robust Subject-Independent Magnetoencephalographic SourceLocalization using an Artificial Neural Network’.Human Brain Mapping, 24(1), 21-34, (2005).Sinclair D. and J.F. Power. ‘Specifying and VerifyingCommunications Protocols using Mixed IntuitionisticLinear Logic’. Electronic Notes in TheoreticalComputer Science, 133, 255-273 (31 May 2005).60NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 COMPUTER SCIENCEHalchenko, Y.O., S J. Hanson and B.A. Pearlmutter.‘Multimodal Integration: fMRI, MRI, EEG, MEG’ InAdvanced Image Processing in Magnetic ResonanceImaging (Eds.) Luigi Landini, Vincenzo Positano andMaria Filomena Santarelli, ISBN 0824725425 pp223-265, Dekker, book series on Signal Processingand Communications, (2005).Siskind, J.M. and B.A. Pearlmutter. ‘PerturbationConfusion and Referential Transparency: CorrectFunctional Implementation of Forward-Mode AD’.Proceedings of the 17 th International Workshopon Implementation and Application of FunctionalLanguages (IFL2005), Dublin, Ireland (19-21September 2005).Murray-Smith, R. and B.A. Pearlmutter.‘Transformations of Gaussian Process Priors’. InMachine Learning Workshop (Eds.) J. Winkler, N.Lawrence, and M. Niranjan pp 110-125, Springer-Verlag LNAI 3635 (2005).Kraft, N.A., B.A. Malloy and J.F. Power. ‘Toward anInfrastructure to Support Interoperability in ReverseEngineering’. 12 th IEEE Working Conference onReverse Engineering, Pittsburgh, Pennsylvania, USA,pp 196-205 (8-11 November 2005).Hennessy, M. and J.F. Power. ‘An Analysis of RuleCoverage as a Criterion in Generating Minimal TestSuites for Grammar-Based Software’. 20 th IEEE/ACMInternational Conference on Automated SoftwareEngineering, Long Beach, California, USA, p. 104-113(7-11 November 2005).Malloy, B.A. and J.F. Power. ‘Using a MolecularMetaphor to Facilitate Comprehension of 3D ObjectDiagrams’. IEEE Symposium on Visual Languagesand Human-Centric Computing, Dallas, Texas, USA,p. 233-240 (20-24 September 2005).Gregg, D., J.F. Power and J.T. Waldron. ‘A methodlevelcomparison of the Java Grande and SPEC JVM98benchmark suites’. Concurrency and Computation:Practice and Experience, 17(7-8), 757-773 (June-July2005).Malloy, B.A. and J.F. Power. ‘Exploiting UMLdynamic object modeling for the visualizationof C++ programs’. ACM Symposium on SoftwareVisualization, St. Louis, Missouri, USA, pp 105-114(15-16 May 2005).Mitchell, Á. and J.F. Power. ‘Using Object-Level Run-Time Metrics to Study Coupling Between Objects’20th Annual ACM Symposium on AppliedComputing, Santa Fe, New Mexico, pp 1456-1462(13-17 March 2005).Power, J.F. and J.T. Waldron. ‘Editorial: Special Issueon the Principles and Practice of Programming inJava’. Science of Computer Programming, 54(1), 1-2(January 2005).Lehtimaki, T. and R.G. Reilly. ‘Improving eyemovement control in young readers’. AritificalIntelligence Review, 24, 477-488 (2005).Setola, P. and R.G. Reilly. ‘Words in the brain’slanguage: An experimental investigation’. Brain andLanguage, 94, 251-259 (2005).Reilly, R.G., R. Radach, D. Corbic and S.Luksaneeyanawin. ‘Comparing reading in Englishand Thai - The role of spatial word unit segmentationin distributed processing and eye movement control’.In Proceedings of the 13 th European Conference onEye Movements, University of Bern, Switzerland,August (14-18 August 2005).Bergin. S. and R.G. Reilly. ‘Programming: Factorsthat influence success’ In Proceedings of the 36 thSIGCSE technical symposium on Computer ScienceEducation, 27(1), 120-126 (February 2005).Bergin. S., R.G. Reilly and D. Traynor. ‘Examiningthe role of Self-Regulated Learning on IntroductoryProgramming Performance’ In Proceedings of theFirst International Computing Education ResearchWorkshop, ICER 2005, Seattle, WA, U.S.A. (1-2October 2005).

Bergin. S. and R.G. Reilly. ‘The influence ofmotivation and comfort level on learning toprogram’. In Proceedings of the 17 th Workshop of thePsychology of Programming Interest Group, PPIG05, University of Sussex, Brighton, UK (28 June – 1July 2005).Lazzarini, V., J. Timoney and T. Lysaght. ‘AlternativeAnalysis Synthesis Approaches for Time-Scale,Frequency and Other Transformations of MusicalSignals’. In Proceedings Of 8 th InternationalConference on Digital Audio Effects (DAFX-05),Madrid, Spain, pp 18-23 (20-22 September 2005).Timoney, J., T. Lysaght, V. Lazzarini and L. MacManus. ‘Comparing synthetic and real templates fordynamic time warping to locate partial envelopefeatures’. In Proceedings Of 8th InternationalConference on Digital Audio Effects (DAFX-05),Madrid, Spain, pp 226-231 (20-22 September 2005).Matthias J., A. Schwarzbacher and J. Timoney.‘CMOS Implementation of an Adaptive NoiseCanceller into a Subband Filter’. In ProceedingsOf 8th International Conference on Digital AudioEffects (DAFX-05), Madrid, Spain, pp 61-64 (20-22September 2005).Timoney, J., T. Lysaght, L. MacManus and V. Lazzarini.‘An Evaluation of Warping Techniques appliedto Partial Envelope Analysis’. In Proceedings OfInternational Computer Music Conference (ICMC-05),Barcelona, Spain (5-9 September 2005).Lysaght, T., V. Lazzarini and J. Timoney. ‘A StreamingObject Oriented Implementation of the ModalDistribution’. In Proceedings Of InternationalComputer Music Conference (ICMC-05), Barcelona,Spain (5-9 September 2005).Lazzarini, V., J. Timoney and T. Lysaght. ‘Time-Stretching using the Instantaneous FrequencyDistribution and Partial Tracking’. In Proceedings OfInternational Computer Music Conference (ICMC-05),Barcelona, Spain (5-9 September 2005).Timoney, J., B. Brichta, F. Mathias, A. Schwarzbacherand B. Hoppe. ‘VLSI implementation of the SIFTalgorithm for pitch detection’. In Proceedings ofthe Irish Systems and Signals Conference, Dublin,Ireland, pp 24-28 (September 2005).Winstanley, A.C., L. Keyes and A. O’Sullivan.‘Statistical Language Models for Graphical ObjectRecognition’. ITB Journal, 10, 25-36 (2005).Winstanley, A.C. and P. Corcoran. ‘Large RobustTexture Separability within Aerial Photography’In Proceedings of GIS Research UK, edited by Billen,R., Drummond, J., Forest, D. and Jaoa E., University ofGlasgow, pp 93-98, (2005).Winstanley, A.C., P. Mooney, C. McDonagh andG. O’Hare. ‘Data Quality Issues in EnvironmentalResearch Data Management’. In Proceedings ofGIS Research UK, edited by Billen, R., Drummond,J., Forest, D. and Jaoa E., University of Glasgow, pp104-109, (2005).Winstanley, A.C., P. Lewis, and M. O’Brien. ‘WebTools for Accessing Irish Census Data’In Proceedings of GIS Research UK, edited by Billen,R., Drummond, J., Forest, D. and Jaoa E., University ofGlasgow, pp 194-202, (2005).Winstanley, A.C., A. O’Sullivan and L. Keyes. ‘AnExtended System for Labelling Graphical DocumentsUsing Statistical Language Models’. In Proceedingsof IAPR Workshop on Graphics Recognition (GREC2005), edited by Wenyin L. and Llados, J. CityUniversity of Hong Kong, pp 77-86 (2005).Winstanley, A.C. and P. Corcoran. ‘A Novel Approachto the evaluation of Gabor and Wavelet TextureFeatures for the Segmentation of Aerial Scenes’.IMVIP 2005 Proceedings of the Irish Machine Visionand Image Processing Conference, edited by Amira,A. Bouridane, A. and Kurugollu, F., 79-86, QueensUniversity of Belfast (2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06COMPUTER SCIENCE61

Conference ProceedingsNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 COMPUTER SCIENCEO’Kelly, J. and J.P. Gibson. ‘PBL: year One Analysis- Interpretation and Validation’. Presented at the 3rdInternational Conference on Problem Based Learning(PBL 2005), Lahti, Finland (9-11 June 2005).J. Harpur. ‘The embodied mind and intersubjectivity’,Science and Process Philosophy Conference, NUIMaynooth, Co. Kildare, Ireland (10-13 May 2005).Maycock, K. and J.G. Keating. ‘Building IntelligentLearning Management Systems to Implement theteacher student dialogue’. IBM CASCON, Dublin,Ireland (February 2005).Lebid, S., T. Ward, R. O’Neill, C. Markham and S.Coyle, ‘Towards dual modality nerve assessmentusing electrical and optical techniques’. 17thInternational Conference on Optical Fibre Sensors,Bruges, Belgium (23-27 May 2005).Lebid, S., R. O’Neill, C. Markham, T. Ward and S.Coyle. ‘Multi-timescale measurements of brainresponses in visual cortex during functionalstimulation using time-resolved spectroscopy’.SPIE Opto Ireland Conference, Royal Dublin Society,Dublin, Ireland (4-6 April 2005).Coyle, S., C. Markham, W. Lanigan and T. Ward.‘A Mechanical Mounting System for FunctionalNear-Infrared Spectroscopy Brain Imaging Studies’.SPIE Opto Ireland Conference, Royal Dublin Society,Dublin, Ireland (4-6 April 2005).Humphreys, K., C. Markham and T. Ward.‘A CMOS camera-based system for clinicalphotoplethysmographic applications’. SPIE OptoIreland Conference, Royal Dublin Society, Dublin,Ireland (4-6 April 2005).Humphreys, K., T. Ward and C. Markham. ‘A CMOSCamera-Based System For Non-Contact PulseOximetry Imaging’. 3rd European Medical andBiological Engineering Conference EMBEC’05and IFMBE European Conference on BiomedicalEngineering, Prague, Czech Republic, (20-25November 2005).McLoughlin, S., N. Murphy, J. Hanley, B. Lanigan andC. Markham. ‘Measuring Biaxial Strain in Rubberusing Stereo Vision’. Irish Machine Vision and ImageProcessing Conference, Belfast, Northern Ireland(30-31 August 2005).Mulvihill, C., C. Deegan, C. Fitzgerald, C. Markhamand S. McLoughlin. ‘Mobile Stereo Vision for theIdentification of Defective Road Studs’. Irish MachineVision and Image Processing Conference, Belfast,Northern Ireland(30-31 August 2005).Foody, J., F. Mathews, D. Kumar, B. Caulfield, T. Wardand C. Markham. ‘A USB Interfaced Motion CaptureSensor, using Tri-axis Magnetic/Inertial Sensors foruse in Kinematic Studies’. 3rd European Medicaland Biological Engineering Conference EMBEC’05and IFMBE European Conference on BiomedicalEngineering, Prague, Czech Republic, (20-25November 2005).Kumar, D., J. Foody, B. Caulfield, T. Ward and C.Markham. ‘Wearable kinematic and biofeedbacksystem for movement based relaxation’.Cybertherapy 2005, Basel, Switzerland (7th-10thJune 2005).Shakya, K., C. Deegan, F. Hegarty and C. Markham.‘Dynamic Response Measurement of Clinical GasAnalysers’. IEEE International Symposium onComputer-Based Medical Systems, PP165-170, TCDIRELAND (22-24 JUNE 2005).Ghent, J. and J. McDonald. ‘Facial ExpressionClassification using a One-Against-All SupportVector Machine’. Irish Machine Vision and ImageProcessing Conference, Belfast, Northern Ireland(30-31 August 2005).Ghent, J. and J. McDonald. ‘Holistic Facial ExpressionClassification’. Imaging and Vision, Dublin, Ireland(4-6 April 2005).Monahan, R. ‘Software Refinement with PerfectDeveloper’. Software and Systems EngineeringSeminar Series, NUI Maynooth, Co. Kildare, Co.Kildare, Ireland (December 2005).62

Monahan, R. ‘Problem-Based Learning: A HybridModel’. Department of Computer Science, ClemsonUniversity, South Carolina, USA (June 2005).Gopinathan, U., D.S. Monaghan, T.J. Naughton, J.T.Sheridan and B. Javidi. ‘Strengths and weaknessesof optical encryption algorithms’. Invited paper, 18thAnnual Meeting of the IEEE Lasers and Electro-Optics Society (IEEE LEOS 2005), Sydney, Australia(23-27 October 2005).Maycock, J., C.P. McElhinney, A.E. Shortt, T.J.Naughton, J.B. McDonald, B. M. Hennelly, U.Gopinathan, D. S. Monaghan, J. T. Sheridan andB. Javidi. ‘Holographic image processing ofthree-dimensional objects’. Invited paper, Three-Dimensional TV, Video, and Display IV, Part of theSPIE Optics East Symposium, Boston, USA (23-26October 2005).Javidi, B., E. Tajahuerce, M. Martínez-Corral, T.J.Naughton and Y. Frauel. ‘New developments inactive and passive 3D image sensing, visualization,and processing’. Invited keynote paper, Unmanned/Unattended Sensors and Sensor Networks II, Partof the SPIE European Symposium on Optics andPhotonics for Defence and Security, Brugge, Belgium(26-28 September 2005).Frauel, Y., A. Castro, T.J. Naughton and B. Javidi.‘Security analysis of optical encryption’. Invitedpaper, Unmanned/Unattended Sensors and SensorNetworks II, Part of the SPIE European Symposiumon Optics and Photonics for Defence and Security,Brugge, Belgium (26-28 September 2005).Javidi, B., E. Tajahuerce, T.J. Naughton, Y. Frauel andO. Matoba. ‘Three-dimensional image encryption,transmission, and processing by using digitalholography’. Invited keynote paper, Systems ofOptical Security, Part of the SPIE Symposium onOptics and Optoelectronics, Warsaw, Poland (28August - 2 September 2005).Monaghan, D.S., U. Gopinathan, B. M. Hennelly, T.J.Naughton and J.T. Sheridan. ‘Digital optics, digitalholography, and optical encryption’. Invited paper,Optical Information Systems III, San Diego, USA (31July - 4 August 2005).Shortt, A.E., T.J. Naughton and B. Javidi. ‘Compressionof digital holograms of three-dimensional objectsusing the wavelet transform’. Invited paper, OpticalInformation Systems III, San Diego, USA (31 July - 4August 2005).Maycock, J., C.P. Mc Elhinney, T.J. Naughton, J.B.McDonald and B. Javidi. ‘Independent componentanalysis applied to digital holograms of threedimensionalobjects’. Optical Information SystemsIII, San Diego, USA (31 July - 4 August 2005).Mc Elhinney, C.P., J. Maycock, T.J. Naughton, J.B.McDonald and B. Javidi. ‘Extraction Of Three-Dimensional Shape Information From A DigitalHologram’. Optical Information Systems III, SanDiego, USA (31 July - 4 August 2005).Shortt, A.E., T.J. Naughton and B. Javidi. ‘Nonuniformquantization for compression of encrypted digitalholograms’. Optical Information Systems III, SanDiego, USA (31 July - 4 August 2005).Keane, T.M., A.J. Page, J.O. McInerney and T.J.Naughton. ‘A high throughput bioinformaticsdistributed computing platform’. 18th IEEEInternational Symposium on Computer-BasedMedical Systems, Special track on Bioinformaticsand its Medical Applications, Dublin, Ireland (23-24June 2005).Gopinathan, U., D.S. Monaghan, A.E. Shortt, T.J.Naughton, J.T. Sheridan and B. Javidi.‘Capture, encryption, compression, and display ofdigital holograms of three-dimensional objects’.Holography 2005 - International Conference onHolography, Optical Recording and Processing ofInformation, Varna, Bulgaria (21-25 May 2005).Naughton, T.J. and B. Javidi. ‘Compression ofencrypted three-dimensional objects using digitalholography’. Photon Management Research inIreland, Dublin, Ireland (4-6 April 2005).Shortt, A.E., T.J. Naughton and B. Javidi. ‘Optimalquantization applied to digital holographic data’.Photon Management Research in Ireland, Dublin,Ireland (4-6 April 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06COMPUTER SCIENCE63

Conference ProceedingsC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 COMPUTER SCIENCEShortt, A.E., T.J. Naughton and B. Javidi. ‘Vectorquantization compression of digital holograms ofthree-dimensional objects’. Photon ManagementResearch in Ireland, Dublin, Ireland (4-6 April 2005).Monaghan, D.S., U. Gopinathan, B.M. Hennelly, D.P.Kelly, T.J. Naughton and J.T. Sheridan. ‘Applications ofspatial light modulators in optical signal processingsystems’. Photon Management Research in Ireland,Dublin, Ireland (4-6 April 2005).McElhinney, C., J. Maycock, J.B. McDonald, T.J.Naughton and B. Javidi. ‘Three-dimensional scenereconstruction using digital holograms’. Imaging andVision, Dublin, Ireland (4-6 April 2005).Page A.J. and T.J. Naughton. ‘Dynamic task schedulingusing genetic algorithms for heterogeneousdistributed computing’. 19th IEEE InternationalParallel and Distributed Processing Symposium,Denver, USA (4-8 April 2005).Page, A. J., T. M. Keane and T.J. Naughton.‘Bioinformatics on a heterogeneous Java distributedsystem’. 19th IEEE International Parallel andDistributed Processing Symposium, Denver, USA (4-8April 2005).Gopinathan, U., D.S. Monaghan, T.J. Naughton andJ. T. Sheridan. ‘An optical encryption scheme thatuses polarization of coherent light’. OSA Frontiers inOptics/Laser Science Conference, Tucson, USA (16-20October 2005).O’Donoghue, D. ‘Topographic Analogies’. InformationTechnology Society, NUI Galway, Ireland (10 March2005).O’Donoghue, D. A. Loughlin, A. Bohan, M. T. Keane.‘Geometric Analogies and Topographic Maps’.Computational Creativity Workshop at IJCAI,Edinburgh, Scotland, (30 July 2005).Pearlmutter, B.A., H. Asari and A.M. Zador. ‘NeuronalPredictions of Sparse Linear Representations’. ForumAcusticum 2005, Budapest, Hungary, (29 August –2Sep 2005).Power, J.F. ‘Using a Molecular Metaphor to FacilitateComprehension of 3D Object Diagrams’.Software Engineering Seminar, Clemson University,South Carolina, U.S.A. (30 June, 2005).Kraft, N.A., B.A. Malloy and J.F. Power. ‘g4re:Harnessing GCC to Reverse Engineer C++Applications’.Transformation Techniques in Software Engineering:Dagstuhl Seminar No. 05161, Schloss Dagstuhl,Germany (17-22 April 2005).Reilly, R.G. ‘Computational Cognitive Modelling’.Department of Psychology, Florida State University,U.S.A. (13 September 2005).Reilly, R.G. ‘Reading Without Spaces: Eye movementcontrol issues in reading Thai’. Florida Centre forReading Research, Florida, U.S.A. (14 September2005).Reilly, R.G. ‘Glenmore: A computational model ofinformation processing and reading’. Departmentof Psychology Colloquim Series, Florida StateUniversity, U.S.A. (16 September 2005).Bergin. S. and R.G. Reilly. ‘Assessing the executivefunctions of students on a third level introductoryprogramming course’. The 37th Annual GeneralMeeting of the European Brain and BehaviourSociety, Trinity College Dublin, Dublin, Ireland(September 2005).Timoney, J., T. Lysaght, V. Lazzarini and R. Gao.‘A Reinvestigation of the Extended Kalman Filterapplied to Formant Tracking’. Electronic Circuitsand Systems Conference 2005, Bratislava, Slovakia(September 2005).Timoney, J., T. Lysaght, V. Lazzarini and L. MacManus.‘Partial Envelope Analysis with Nonnegative MatrixFactorization’, Electronic Circuits and SystemsConference 2005, Bratislava, Slovakia (September2005).64

External Assignmentsand Public ServiceWinstanley, A.C. ‘Graphics Recognition usingStructural Descriptors’ Invited speaker, China /Ireland Collaboration Review Meeting, Royal IrishAcademy, Dublin, Ireland (18 November 2005).Corcoran, P and A.C. Winstanley. ‘Large RobustTexture Separability within Aerial Photography’, GISResearch UK, Glasgow, Scotland 93-98 (6-8 April2005).Mooney, P., C. McDonagh, A.C. Winstanley andG. O’Hare, ‘Data Quality Issues in EnvironmentalResearch Data Management’, GIS Research UK,Glasgow, Scotland 93-98 (6-8 April 2005).Lewis, P, M. O’Brien and A.C. Winstanley, ‘Web Toolsfor Accessing Irish Census Data’, GIS Research UK,Glasgow, Scotland 93-98 (6-8 April 2005).O’Sullivan, A., L. Keyes and A.C. Winstanley. ‘AnExtended System for Labeling Graphical DocumentsUsing Statistical Language Models’, IAPR Workshopon Graphics Recognition (GREC 2005), 77-86, HongKong (25-26 August 2005).Corcoran, P. and A.C. Winstanley. ‘A Novel Approachto the evaluation of Gabor and Wavelet TextureFeatures for the Segmentation of Aerial Scenes’.IMVIP 2005 Irish Machine Vision and ImageProcessing Conference, Belfast, Northern Ireland(30-31 August 2005).Mr. S. Brown• Reviewer for IEEE Transactions on Education.Reviewer for IEEE 14th Workshop on Local andMetropolitan Area Networks.• School judge in IEI/STEPS K’Nex Competition,and host and judge for the Kildare RegionalFinals at the Department of Computer Science,NUI Maynooth (May 24th 2005).Dr. J.P. Gibson• External examiner for the BSc in ComputerApplications (Information Systems/SoftwareEngineering) at DCU - school of computing.• MPhil Thesis examiner for DIT.• EU Expert evaluator - European funding (FP6,IST priority 2 call 5: 2.5.5 Software and Services).• EU Expert reviewer – RODIN project (FP6IST priority 2 call 2: IST-2002-2.3.2.3) - Opendevelopment platforms for software and serviceDr. J.G. Keating• External Examiner, Institute of Technology,Carlow.• External Examiner, Dundalk Institute ofTechnology.• IBM Centre for Advanced Studies, Faculty Fellow.• Member, RDS Science and TechnologyCommittee.Markham, C.• HP Invent Award December 1st 2005 FiachraMatthews, project supervisor Charles Markham.• ‘Rise of the Robots’, Demonstration Lecture forScience Day, 14th March 2005.Ms. R. Monahan• Independent Reviewer of projects funded underthe sixth framework programme of the EU.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06COMPUTER SCIENCE65

External Assignments and Public ServiceC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 COMPUTER SCIENCEMr. T.J. Naughton• Reviewer for Optics Letters (OSA).• Reviewer for Applied Optics (OSA).• Reviewer for Optics Communications (Elsevier).• Reviewer for Optical Engineering (SPIE).• Reviewer for Journal of Optics A: Pure andApplied Optics (IOP).• Reviewer for Measurement Science andTechnology (IOP), and ETRI Journal (ETRI) in thearea of optical information processing.• Reviewer for Bioinformatics (OUP) andComputers & Operations Research in the area ofalgorithms.• Program committee member, Electro-OpticalSensors and Systems, 18th Annual Meeting ofthe IEEE Lasers and Electro-Optics Society (IEEELEOS 2005), Sydney, Australia, 23-27 October2005.• Program committee member, Optical InformationSystems III, 50th Annual Meeting of SPIE - TheInternational Society for Optical Engineering,San Diego, USA, 31 July - 4 August 2005.• Program committee member, PhotonManagement in Ireland, SPIE Opto-IrelandSymposium 2005, Dublin, Ireland, 4-6 April 2005.• Co-chair (with F. Wirth), Complexity Workshop,NUI Maynooth, 16 September 2005, funded byIRCSET and Hamilton Institute, 45 participants.Dr. D. O’Donoghue• Reviewer for Artificial Intelligence Review.• Program Committee Member for theComputational Creativity Workshop, held duringthe International Joint Conferences on ArtificialIntelligence (IJCAI-2005), July 30th University ofEdinburgh, Scotland.• Program Committee Member for the 16th IrishConference on Artificial Intelligence & CognitiveScience AICS-2005 - University of Ulster, 7th- 9th, September 2005.• External Examiner for M.Sc. by Research in I. T.Tallaght.• Program Reviewer - B.Sc. in Computing,Department of Computing, I.T. Tallaght.• Executive Committee Member, ArtificialIntelligence Association of Ireland.Dr. J.F. Power• External Examiner for the National Certificate inCommercial Computing and the BSc. in AppliedComputing at Waterford Institute of Technology.• PhD. thesis external examiner, Dept. of ComputerScience, Trinity College, Dublin.• Professor R.G. Reilly• PhD External examiner, University of Limerick.• Reviewer for the EU INTAS programme.• Member of Editorial Board for ConnectionScience, Neural Processing Letters, and ArtificialIntelligence Review.• Tenure Assessor, Department of Psychology,University of Pittsburgh.• Manuscript reviewer, John Benjamins.Dr. J. Timoney• Member of external course approval committeefor a new degree in Music Technology andProduction at Limerick Institute of Technology,November 2005.• Proposal reviewer for the InternationalAssociation for the Promotion of Co-operationwith Scientists from the New Independent States(NIS) of the Former Soviet Union (INTAS).• Visiting Lecturer at the Polish-Japanese Instituteof Information Technology, Warsaw, Poland (June2005).66

Faculty of ScienceResearch Report 2005-06Experimental Physics

NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 EXPERIMENTAL PHYSICSAcademic Staff*Professor J.A. Murphy, MSc, MS (Caltech), PhD (Cantab), CPhys, FInstP, FRAS, MIEEE (1988-)Dr. M.F. Cawley, MSc, PhD, CPhys, MInstP (1987-)Mr. W. Lanigan, BSc (Open Univ), MSc, MIEE, CEng (1986-)Dr. F. McGroarty, BSc(DCU), PhD (DCU) (2004-)Mr. G. McMahon, MSc (2000-)Dr. F.J. Mulligan, BSc, PhD, CPhys, MInstP (1984-)Dr. R.W. O’Neill, BSc (QUB), PhD (QUB), CPhys, MInstP (1996-)Dr. C. O’Sullivan, BSc, PhD (Cantab) (1998-)Dr. N. Trappe, BSc (UL), PhD (2003-)Dr. P.J.M. van der Burgt, MS (Utrecht), PhD (Utrecht), CPhys, MInstP (1993-)Technical StaffDr. N.E. McKeith, BSc (QUB), PhD (QUB) (1978-)Mr. D. Gleeson, (1976-)Ms. M. Galligan, BSc, DipIndInstr (NCEA) (1991-)Mr. J. Kelly, BSc, HDipAppPh (1999-)Mr. I. McAuley, MSc (2000-)Mr. P. Seery, BA, DipEl (Dundalk IT)Mr. D. Watson, DipMechEng, (2000-)Senior Executive AssistantMs. G. Roche, BA (1997-)Research FellowsDr. M. Gradziel, BSc (Torun), PhD (2000-)Dr. E. Gleeson, BSc, PhD (2001-2005)Mr. T. Peacocke, BSc (Edin) (2004-)Dr. V. Yurchenko, MSc, PhD (Kharkov Polytech), DSc (NAS, Ukraine) (2000-)68* Unless otherwise stated the higher degrees listed are those of the National University of Ireland.

Postgraduate Research StudentsMr. G. Barrett, BSc (2005-)Mr. G. Cahill, BSc (2001-)Mr. M. Candotti, MSc (Padova), (2003-)Mr. E. Cartwright, BSc (2003-)Ms. A. Cuddihy, BSc (2004-)Mr. G. Curran, BSc, MSc (2005-)Ms. E. Duffy, BSc, HDipAppPh (2003-2005)Mr. T. Finn, BSc (2002-)Ms. K. Foley, BSc (Aberystwyth), (2002-)Mr. J. Lavelle, BEng (Edinburgh) (2002-)Mr. P. Leavey, BSc, HDipAppPh (2004-)Mr. J. Loughran, B.A.Mod (TCD), MB (TCD), HDipEd (TCD), BSc (2003-2005)Mr. D. McGlynn, BSc (2003-2005)Mr. R. Mahon, BSc (2002-)Mr. R. May, BSc (2002-)Ms. P. Mooney, BSc (2004-)Mr. F. Noviello, Italian Laurea (Rome, La Sapienza) (2004-)Mr. P. O’Connor, BSc (2004-)Mr. C. Soraghan, BSc (2004-)Mr. D. White, MSc (2003-)Mr. M. Whale, BSc (2005-)Ms. L. Young, BSc (2005-)Mr. E. Yurchenko, MSc (NTU,Ukraine) (2004-2005)Emeritus ProfessorsProfessor S. McKenna-Lawlor, MSc, PhD, FRAS, FIBA, CPhys, MInstP, Academician (IAA)Professor J. A. Slevin, M.Sc.(QUB), Ph.D.(CUNY), C.Phys., F.Inst.P., M.R.I.A.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06EXPERIMENTAL PHYSICS69

Head Of Department’s Review Of The YearNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 EXPERIMENTAL PHYSICSThe Department of Experimental Physics is strongly committed to academic research and we regard thetraining of postgraduate research students as one of our core missions. The department continues to behighly active in astrophysics and astronomical instrumentation, terahertz optics, atomic and cluster physics,quantum entanglement, biophysics and experimental fluid dynamics. It is noteworthy that 2005 wascelebrated by physicists throughout the world as the centenary year of Einstein’s famous papers on relativity,Brownian motion and the quantum theory of light.A feature of the research in the department is our strong international collaboration work with laboratoriesabroad, including very close links with the Cavendish Laboratory Cambridge, Cardiff University, StanfordUniversity, the Space Research Organisation of the Netherlands (SRON) and the Institut d’AstrophysiqueSpatiale (Paris). Research students have opportunities to spend some time at these institutions as part oftheir research projects. A new research collaboration was initiated in 2005 with the University of Wisconsinand Brown University on a NASA funded project known as the Millimeter-wave Bolometric Interferometer,which is concerned with faint polarization measurements of the Cosmic Microwave Background. Our researchis funded through grants from a range of agencies including Science Foundation Ireland, Enterprise Ireland,the Irish Research Council for Science Engineering and Technology, the NUIM Research Enhancement Fund,European Office of Aerospace Research and Development and the European Space Agency. Also, in 2005,the research work of 4 students in the Experimental Physics Department was funded under the EMBARKScholarship scheme.As well as collaboration meetings and scientific visits abroad, both staff and students attended severalinternational conferences and workshops in Europe, North America and Australia during 2005 andpresentations were made on research being carried out in the department. These conferences included the2005 Joint 30 th International Conference on Infrared and Millimeter Waves and 13 th International Conferenceon Terahertz Electronics, in Williamsburg, Virginia, the SPIE Defense and Security Symposium, in Orlando,Florida, the 28 th ESA Antenna Workshop on Space Antenna Systems and Technologies, at the EuropeanSpace Agency Technology Centre, Netherlands, the 16 th International Symposium on Space TerahertzTechnology, in Gothenburg, Sweden, the 8 th Australasian Heat and Mass Transfer Conference, in Perth,Australia, the 37 th Conference of the European Group of Atomic Systems, at DCU, Dublin and the XXXV YoungEuropean Radio Astronomers’ Conference, Cagliari, Italy.The regular seminar series hosted by the department continued during 2005 with a number of invited guestspeakers visiting the department. A high point was the colloquium in April 2005 given by the ProfessorPhilip Diamond of Jodrell Bank Radio Astronomy Observatory and the University of Manchester, as part ofthe Institute of Physics in Ireland Lecture Programme series. Professor Diamond, who is also Director ofthe Merlin Radio Interferometer UK National Facility, spoke on the latest advances in radio astronomy. Weare delighted that Professor Diamond could come at this time as it highlights the full rolling out of our newdenominated degree programme in Physics with Astrophysics. September 2005 saw the graduation of ourfirst astrophysics class. Most of the class have now gone on to undertake research degrees including at NUIM,Cardiff and Oxford.The department continues to have a strong commitment to the promotion of physics in schools with thevery popular and successful laboratory initiative for senior cycle students. The programme is based aroundcompulsory Leaving Certificate experiments, which are difficult for schools to mount, and a large number ofschools visited the department in 2005. This creates an extremely positive impression of science at Maynooth,building a close relationship with physics teachers in schools and by extension with career guidance teachers,parents and the wider community.70

Research Interests Of StaffProfessor J. Anthony MurphyIn 2005 the terahertz optics group continued participation in a number of international collaborative projectsin far-infrared astronomical instrumentation. We are involved with the development of two European SpaceAgency satellite systems due to be launched in early 2008: the PLANCK Surveryor, which will make detailedmaps of the cosmic microwave background radiation, and the Herschel Space Observatory, which will enablewide-ranging astronomical observations of far-infrared sources in the sky. Our main contribution to bothprojects is in the optical design, detailed system analysis and calibration performance of these exquisitelysensitive satellite systems. This research work is undertaken in particularly close working collaboration withthe Institute d’Astrophysique Spatiale (Paris), the Space Research Organisation of the Netherlands (SRON)and Cardiff University.During 2005 we also continued our role in the QUAD millimeter-wave telescope development in collaborationwith Stanford, Cardiff and Chicago Universities, along with Caltech and JPL in Pasadena. The QUAD telescope,optimized for mapping the polarization characteristics of the cosmic microwave background, is located atthe South Pole, a superb site from which to make these kinds of observations. This experiment has its firstsuccessful season taking data during the austral winter of 2005. The goal is to unambiguously determinefundamental cosmological parameters and distinguish between theories of the early universe. At Maynoothwe are playing a key role as experts in the optical analysis of the system.Terahertz optics is a fast developing field of applied physics. Funded by significant grant under the ScienceFoundation Ireland Investigator Award scheme we are developing CAD software tools for terahertz optics incollaboration with the Computing Department of Tallaght Institute of Technology. We have extended noveltheoretical frameworks and implemented sophisticated optical analysis software. As part of this grant weare also constructing a prototype dual-band medical imager in collaboration with Computer Science andElectronic Engineering at NUIM. This will combine the fields of millimeter-wave imaging with the nearinfrared and promises important applications in medicine, particularly to skin disorders.Dr. Michael CawleyWork continued during 2005 on the study of various aspects of the density anomaly in water. A convectiveflow technique was developed and used to measure the shift in the temperature of the density maximum as afunction of solute nature and concentration. This work was extended to encompass the behaviour of stratifiedfluids. The influence of the density maximum on the rate of heat transfer through water was studied bothexperimentally and through the use of computational fluid dynamics. The possibility of asymmetrical heattransfer through bodies of water in the vicinity of the density maximum was explored.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06EXPERIMENTAL PHYSICSMr. William LaniganBill Lanigan’s research interests are in the field of Terahertz instrumentation for astronomy and medicalimaging. As part of the NUIM Far-Infrared and Submillimetre Space Astrophysics group he carries outmeasurement and verification of quasi-optical components for space based astronomical instruments. Hisother area of research is in the field of using Terahertz radiation for medical imaging. Terahertz radiationis much less damaging to biological tissue than conventional x-rays and while it does not provide the samepenetration or resolution as X-rays there are many potential applications where it will be well suited.Dr. Fiona McGroartyFiona McGroarty’s research is in the area of optical observations of star formation. Ongoing studies involvelarge scale observations to determine the extent of outflows from various different types of young, formingstars. The properties of these outflows can in turn be used to extrapolate the accretion history of the star71

Research Interests Of StaffC O N T I N U E D72NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 EXPERIMENTAL PHYSICSallowing us to track its evolution at a time when it is surrounded by cloudsof dust and gas and hence optically obscured. The optical observationsfor this work were carried out at the Isaac Newton Telescope in La Palma,Canary Islands by Dr. McGroarty and done in collaboration with groups atthe Dublin Institute for Advanced Studies and the University of Colorado,USA. Current research expands these results to determine the extent towhich forming stars influence their surroundings. Further observations at LaPalma are planned.Dr. Raymond O’NeillIn 2005 we continued with a new research programme into applications ofnear-infrared (NIR) light for biomedical diagnostics. This is in collaborationwith Dr. Tomas Ward of Electronic Engineering and Dr. Charles Markham ofComputer Science. The interrogation of biological tissue with NIR light (600-1000 nm) allows non-invasive monitoring of biochemical processes. Opticaltechniques are based on measuring intrinsic activity-related changes intissue reflectance and scattering which arise from functional physiologicalchanges; for example, changes in the absorption of compounds such asoxy- and deoxyhaemoglobin and cytochrome oxidase allow measures ofmetabolic activity to be made. This is the basis of in vivo near-infraredspectroscopy (ivNIRS). We are currently working on techniques to measureoptical analogues of electrical signals that are commonly used in brainimaging and nerve conduction studies. Interest in these techniques hasrapidly expanded over the last decade as increasingly non-invasive, nonionising,safe techniques have been sought for clinical applications.We have also been investigating the fundamental physics of ‘quantumentanglement’, the curious quantum state in which the properties of twoparticles separated by arbitrarily large distances are mutually dependentbut undefined until the instant a measurement is performed. Non-linearoptical techniques are used to produce pairs of photons whose polarisationstates are entangled and we have succeeded in producing a polarisationentangledtwo-photon state, confirmed by a measured violation of theClauser-Horne-Shimony–Holt inequality.Dr. Créidhe O’SullivanCréidhe O’Sullivan’s research interests are in the fields of astrophysicsand astronomical instrumentation. As part of the NUIM Far-Infrared andSubmillimetre Space Astrophysics group Dr. O’Sullivan works on a numberof international research programmes. These include QUaD, one of the newgeneration of submillimetre telescopes designed to search for the extremelyfaint polarisation anisotropies of the Cosmic Microwave Background,the relic radiation left over from the Big Bang. A measurement of thispolarisation will allow cosmologists to distinguish between competingmodels of the early Universe. QUaD was deployed to the South Pole, anexcellent site for submillimetre observations, in the 2004/2005 summerseason and began observing in March 2005. The first season’s observing wassuccessfully completed by October and the data is currently being analysed.A new collaboration was begun with researchers from Brown Universityand the University of Wisconsin-Madison on a NASA project to developDr. Créidhe O’SullivanLecturer in the Department ofExperimental PhysicsWhat are your research interests?My research interests are in the fields ofastrophysics and astronomical instrumentation. Aspart of the NUIM Far-Infrared and SubmillimetreSpace Astrophysics group I work on a numberof international research programmes includingQUaD, one of the new generation of sub-millimetretelescopes designed to measure the extremelyfaint polarisation fluctuations in the CosmicMicrowave Background, the relic radiation left overfrom the Big Bang. Measuring the CMB allowscosmologists to distinguish between competingmodels of the early Universe. QUaD was deployedto the South Pole, an excellent site for submillimetreobservations, in the 2004/2005 Australsummer and began observing in March 2005.I also work with researchers from BrownUniversity and the University of Wisconsin-Madison on a NASA project to develop MBI, thefirst bolometric interferometer. MBI will become aprototype for a new generation of instruments withthe capability of measuring the faint polarisationsignatures of the Microwave BackgroundHow do you fund your work?Currently I have an Engineering and TechnologyBasic Research Award from the Irish ResearchCouncil for Science with J.A. Murphy for 3 years,an Enterprise Ireland Basic Research Award, incollaboration with V. Yurchenko, an InvestigatorAward, Science Foundation Ireland along withJ.A. Murphy, W. Lanigan, D. White, V. Yurchenko,T. Ward and C. Markham and finally a Grant fromPRODEX Fund (European Space Agency along withJ.A. Murphy and Neil Trappe.How did you build your career to date?I received my B.Sc. in Experimental Physics fromUniversity College Dublin in 1992 and my PhD inPhysics, Observations of Anisotropies in the CMBRat 15GHz with CAT from University of Cambridge(1992-1995) after which I spent a year as aResearch Scientist in the National MicroelectronicsResearch Centre, UCC. I was a Post-DoctoralResearch Fellow in NUI Galway from 1996-1998and then came as a Lecturer, to the Department ofExperimental Physics, NUI Maynooth in 1998.

MBI, the first bolometric interferometer. MBI will combine the advantages of bolometers and interferometry tobecome a prototype for a new generation of instruments with the capability of measuring the polarisation ofthe Microwave Background.Dr. Neil TrappeNeil Trappe’s research is in the area of terahertz optics and the design and analysis of long wavelengthastronomical instrumentation. This work is carried out as part of the NUIM Far Infrared and Submillimetre SpaceAstrophysics group. In particular Dr. Trappe is involved in a number of international research collaborationsincluding the HIFI instrument for the Herschel Space Observatory and also ALMA (Atacama Large MillimeterArray). In the case HIFI, a full optical analysis of the front-end optical train is underway to fully characterise thesystem performance. This work is carried out in collaboration with SRON (Space Research Organisation of theNetherlands) and is funded a PRODEX contract from ESA. He is also involved in optical analysis on a specificfrequency channel (Band 9) for the ALMA receiver. This collaborative project to verify, model and optimisethe ALMA Channel 9 receiver system began in early 2004. A variety of specialised techniques developed atMaynooth utilising Gaussian Beam Mode analysis and Physical Optics are employed to analyse the opticalsystem and verify its functionality. Another SRON space mission ‘ESPRIT’ is currently being proposed by SRONand Dr. Trappe has been invited to participate in the initial design concept and analysis of this exciting project,which will utilise six submillimetre wave satellites working together as an interferometer to observe, withunprecedented resolution, the exciting processes of star birth, formation and death.Dr. Peter van der BurgtResearch is focussing on electron- and photon-impact fragmentation processes of molecules and clusters thatare of interest to plasma physics, atmospheric physics and other fields. The focus is on small noble gas andmolecular clusters, with the goal to study metal-embedded rare-gas clusters and water clusters containingbiomolecules. The experiment consists of a differentially pumped vacuum system, with an expansion chamberto generate a pulsed supersonic beam of molecules or clusters, and a collision chamber where the moleculesor clusters are fragmented. In the collision chamber the supersonic beam is crossed with an electron beam ora laser beam and the reaction products are detected. Ions are detected with a reflectron time-of-flight massspectrometer, and neutral metastable atoms are detected with a metastable detector.Mass spectra have been measured for argon, methanol, carbondioxide and air. Small clusters have beenobserved for alcohol, and further work is in progress to optimise the pulsed valve and the generation ofclusters in the supersonic expansion. A LabView program to measure spectra as a function of electron impacthas been developed and tested. The program controls the data acquisition with the multichannel scaler andthe programmable power supply used to set the electron impact energy. A metastable atom detector has beenconstructed and is about to be tested. Time-of-flight detection of neutral metastable fragments will be usedto obtain kinetic energy distributions of neutral fragments. Ms. Elaine Duffy completed her MSc thesis on thiswork.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06EXPERIMENTAL PHYSICSDr. Volodymir YurchenkoOne of Dr. Yurchenko’s lines of research lies in the theory and simulations of nonlinear time-delay couplingof arrays of active devices – Gunn diodes, resonant tunneling diodes, Josephson junctions, semiconductorsuper-lattices, arrays of quantum dots etc – in microwave systems with power combining, phase locking,spectrum modification and emerging dynamical chaos, as needed for the development of new kinds of compactsolid-state oscillators and chaotic signal generators for THz applications (such as ultra-wideband noise radars,tuneable THz lasers etc). A second major line focuses on fast physical optics simulations of large-aperturebroadband beams and optimization of incoherent bolometric detectors for the High-Frequency Instrumentof the ESA Planck deep-space submillimeter-wave telescope being designed for measuring the temperatureanisotropies and polarization characteristics of the Cosmic Microwave Background.73

Research GrantsNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 EXPERIMENTAL PHYSICS‘Optical Design of the QUEST telescope to map thepolarisation properties of the Cosmic MicrowaveBackground’, Engineering and Technology BasicResearch Award, Irish Research Council for Science,€152,800 (J.A. Murphy and C. O’Sullivan 2002–2005)‘Qualification of the HFI Instrument on the PLANCKSurveyor, an ESA deep space project in observationalcosmology, Enterprise Ireland Basic ResearchAward, €166,400 (J.A. Murphy, V. Yurchenko, 2003- 2006).‘The development of an integrated quasi-opticaland electromagnetic numerical simulator forthe computer aided design and analysis of novelterahertz systems’. Investigator Award, ScienceFoundation Ireland, €786,000 (J.A. Murphy, W.Lanigan, C. O’Sullivan, D. White, V. Yurchenko, T.Ward and C. Markham, 2003 - 2006,).‘Verification of the optical design of HIFI for theHerschel Space Telescope and detailed modellingof the instrument.’ Grant from PRODEX Fund(European Space Agency) €141,000 (J.A. Murphy,Neil Trappe and C. O’Sullivan 2003 - 2005).‘Characterisation and verification of the opticalsystem for the Atacama Large Millimeter ArrayChannel 9’, Research Frontiers Grant, ScienceFoundation Ireland, €146,000 (N. Trappe, 2005- 2008).‘Applications of CAD software tools for the terahertzwaveband being developed at NUI Maynooth’,Science Foundation Ireland UREKA Award, €5,000(J.A. Murphy, 2005).‘Modelling of Power Combining in Microstrips withArrays of Active Devices – Josephson Junctions andGunn Diodes – for THz Applications’, European Officeof Aerospace, R&D, U.S. Airforce, $25,800 Oct 2005– Oct 2006 (V.B. Yurchenko and J.A. Murphy 2005– 2006).‘The optical analysis and verification of ALMA(Atacama Large Millimetre Array), a revolutionarysubmillimetre interferometer’, Enterprise Ireland,International Collaboration Travel Support, €7,000(N. Trappe, 2005 - 2006).Embark Postgraduate Scholarships, Irish Council forScience, Engineering and Technology, €57,000(P. Mooney, 2004 - 2007).Embark Postgraduate Scholarships, Irish Council forScience, Engineering and Technology, €57,000(T. Finn, 2002 -2006).Embark Postgraduate Scholarships, Irish Council forScience, Engineering and Technology, €57,000,Oct 2002 – Mar 2006 (R. Mahon).Embark Postgraduate Scholarships, Irish Council forScience, Engineering and Technology, €57,000,Oct 2005 – Sept 2007 (A. Cuddihy).74‘The QUAD project to map the polarization propertiesof the Cosmic Microwave Background’, EnterpriseIreland International Collaboration, €4,950(J. A. Murphy, 2005 –2006).

Publications in Refereed JournalsCawley, M.F., D. McGlynn and P.A. Mooney.Measurement of the temperature of densitymaximum of water solutions using a convective flowtechnique. In Int. J. Heat and Mass Transfer(in press).Gleeson E., J. A. Murphy, B. Maffei, W. Lanigan, J.Brossard, G. Cahill, E. Cartwright, S. E. Church, J.Hinderks, E. Kirby and C. OSullivan. Corrugatedwaveguide band edge filters for CMB experimentsin the far infrared. Infrared Physics and Technology,46, 493-505 (2005).Mahon, R. J., J. A. Murphy and W. Lanigan. Digitalholography at millimetre wavelengths.Optics Communications (in press).Martín-Jiménez, F., E. García, C. OSullivan, L. DeHaro, J. A. López Fernández, F. Tercero, M. Sierra-Castañer and J. Martín-Pintado. Convergence ofGaussian-beam modes in corrugated conical horns.Microwave and Optical Technology Letters, 45,199-203 (2005).Murphy, J.A., E. Gleeson, G. Cahill, W. Lanigan, C.OSullivan, E. Cartwright, S.E. Church, J. Hinderks, E.Kirby, K. Thompson, B. Rusholme, B. Maffei, P.A.R.Ade, C. Tucker and B. Jones. Millimeter-Wave ProfiledCorrugated Horns for the QUaD Cosmic BackgroundPolarization Experiment. International Journal ofInfrared and Millimeter Waves, 26, 4, 505–523(2005).Rosset, C., V. B. Yurchenko, J. Delabrouille, J. Kaplan,Y. Giraud-Heraud, J.-M. Lamarre and J. A. Murphy.Beam Mismatch Effects in Cosmic MicrowaveBackground Polarization Measurements. Astronomyand Astrophysics, (in press).Trappe, N., J.A. Murphy, S. Withington, and W.Jellama. Gaussian Beam Mode Analysis of StandingWaves Between Two Coupled Corrugated Horns.IEEE Transactions on Antennas and Propagation,53, 1755-1761, (2005).Trappe, N., R. Mahon, W. Lanigan, J.A. Murphyand S. Withington. The quasi-optical analysis ofBessel beams in the far infrared. Infrared Physics &Technology, 46, 233-247 (2005).Yurchenko, L.V. and V.B. Yurchenko. Chaos in aCavity with Active Microwave Devices. Applied RadioElectronics, 4, 80-84 (2005).Yurchenko, L.V. and V.B. Yurchenko. Generationof Ultra-Short Pulses in a Cavity with an ActiveLayer and a Dielectric Mirror. PrikladnayaRadioelektronika (Applied Radio Electronics), 4,195-200 (2005).Yurchenko, L.V. and V.B. Yurchenko. NonlinearDynamics of Semiquantal Ballistic Electronsin Superlattices under the Strong MicrowaveExcitation. Radioelektronika i informatika (RadioElectronics and Informatics), 23-28 (2005).Yurchenko, V.B. and J.-M. Lamarre. EfficientComputation of the Broadband Beam SidelobesExemplified by the Planck High-FrequencyInstrument. Journal of the Optical Society of AmericaA, 22, 2838-2846, (2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06EXPERIMENTAL PHYSICS75

Conference ProceedingsNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 EXPERIMENTAL PHYSICSCandotti, M. A.M. Barishev, N. Trappe, R. Hesper, J.A.Murphy and J. Barkhof. ‘Quasi-Optical Verificationof the Band 9 ALMA Front-End’. 16 th InternationalSymposium on Space Terahertz Technology,Chalmers, Göteborg, Sweden (May 2-4, 2005).Coyle, S., C. E. Markham, T. E. Ward and W.P. Lanigan.‘A mechanical mounting system for functionalnear-infrared spectroscopy brain imaging studies’.SPIE OPTO Ireland Conference, Dublin, Ireland (April2005).Duffy, E. and P. J. M. van der Burgt. ‘A New Apparatusfor the Study of Electron-Impact Fragmentation ofClusters’. 37 th Conference of the European Group forAtomic Systems (EGAS 37), Europhysics ConferenceAbstracts 29I, p. 250, (August, 2005).Finn, T., N. Trappe, W. Jellema, J.A. Murphy andS. Withington. ‘Gaussian Beam Mode Analysisof Standing Waves in Optical Systems’. 28 th ESAAntenna Workshop on Space Antenna Systems andTechnologies, Noordwijk, The Netherlands (2005).Gradziel, M.L., D. White and J. A. Murphy. ‘Analysisand design of millimetre-wave and terahertz opticalsystems using Gaussian Beam Modes’. Optics andPhotonics Network Meeting (OPN), TCD, Dublin,Ireland (August 2005).Gradziel, M. L., D. White, S. Withington and J.A. Murphy. ‘Fast CAD Software For The OpticalDesign Of Long Wavelength Systems’. Joint 30 thInternational Conference on Infrared and MillimeterWaves and 13 th International Conference onTerahertz Electronics, Williamsburg, Virginia, USA(September 2005).Lanigan, W.P., N. Murphy, J. Hanley, J. McCartin,S. McLoughlin, S. Jerrams, G. Clauss and R.Johannknecht. ‘Determining multiaxial fatigue inelastomers using bubble inflation’. ConstitutiveModels for Rubber (Proceedings of the 4 th EuropeanConference), Stockholm, Sweden (June 2005).Leavey, P. ‘Quasioptical analysis of long wavelengthreceivers’. XXXV Young European RadioAstronomer’s Conference, Cagliari, Italy (12- 16October 2005).Mahon, R. J., W. P. Lanigan, J. A. Murphy, N. A. Trappeand S. Withington. ‘Novel techniques for a millimeterwave imaging systems operating at 100GHz’, SPIEDefense and Security Symposium. Orlando, Florida,USA (28 March – 1 April 2005).McLoughlin, S.D., N. Murphy, J. Hanley, W. P. Laniganand C. E. Markham. ‘Measuring Biaxial Strain inRubber Using Stereo Vision’. IMVIP 2005, QueensUniversity Belfast, Northern Ireland (August 2005).McGlynn, D. and M.F. Cawley. ‘A study of the changein the temperature of the density maximum of wateras a function of solute nature and concentration’.Institute of Physics in Ireland, Kildare, Ireland (18-20March 2005).Mooney, P.A. and M.F. Cawley. ‘Free Convection inWater in the vicinity of the Density Maximum’. 8 thAustralasian Heat and Mass Transfer Conference,Curtin University of Technology, Perth, Australia(26-29 July, 2005).Murphy, J.A. and E. Yurchenko. ‘Simulations ofa quasi-optical bench with a dielectric lens forPLANCK-HFI horn testing’. Proceedings of the28 th ESA Antenna Workshop on Space AntennaSystems and Technologies, ESTEC, Noordwijk, theNetherlands, pp.887-894, (2005).O’Sullivan, C. ‘New Views of the Early Universe’. IrishAstronomical Society, Dublin, Ireland (April 2005).O’Sullivan, C., G. Cahill, J. A. Murphy, E. Gleeson,W. Lanigan, W. Gear and S. Church. ‘The Quasi-Optical Design and Analysis of the QUaD Telescope’.Proceedings of the 28 th ESA Antenna Workshop onSpace Systems & Technologies, ESTEC, Noordwijk,the Netherlands, pp.681-688 (2005).76Lanigan, W.P., J.A. Murphy, R. May, R. Mahon, I.McAuley, C. Markham, K. Humphries, T. Ward and S.Withington. ‘Quasi-Optical millimetre-wave imagingwith bio-medical applications’. IRMMW-THz 2005,Williamsburg, Virginia, USA (September 2005).O’Sullivan, C., N. Trappe and J.A. Murphy. ‘Studyingthe Origins of Structure in the Universe’. The IrishScientist 2005, p.82, (2005).

External Assignmentsand Public ServicePeacocke, T., M. Candotti, T. Finn, J.A. Murphy, N.Trappe and J. Lavelle. ‘HIFI beam pattern predictions,Part 1: simulations’. HIFI Consortium Meeting,Groningen, Netherlands (Sept. 2005).Whale, M. ‘The commissioning and calibration ofa small radio telescope for NUI Maynooth’. XXXVYoung European Radio Astronomer’s Conference,Cagliari, Italy (12- 16 October 2005).White, D., Gradziel, M. L., S. Withington, J. A.Murphy, T. Peacocke and W. Jellema. ‘EfficientQuasi-optical Analysis and Design on Space AntennaSystems and Technologies’. In Proceeedings of the28 th ESA Antenna Workshop on Space AntennaSystems and Technologies, ESTEC, Noordwijk, theNetherlands, pp. 643-650, (2005).Yurchenko, E. and V. Yurchenko. ‘Reciprocityin the Modelling of Bolometric Detectors inTransmitting Mode’. Proceedings of the 28 th ESAAntenna Workshop on Space Antenna Systemsand Technologies, ESTEC, Noordwijk, pp. 879-886,(2005).Yurchenko, V.B. ‘Power Combining of Gunn Diodes inMicrostrip Structures’ (Invited Paper). Proceedingsof the 2 nd Int. Radio Electronics Forum (IREF’2005),Kharkov, Ukraine, 5, pp. 13-16, (2005).Yurchenko, V.B. and E.V. Yurchenko. ‘ReciprocalFormulation of the Bolometer-Transmitter Problemin the ESA Planck HFI Modeling for Radio-Astronomical Observations’. Proceedings of the 2 ndInt. Radio Electronics Forum (IREF’2005), Kharkov,Ukraine, 1, pp. 203-206, (2005).Yurchenko, V.B. and J. A. Murphy, ‘Multi-GaussianFitting Parameters of Multi-Mode ESA Planck HFIBeams’. Proceeedings of the 28 th ESA AntennaWorkshop on Space Antenna Systems andTechnologies, ESTEC, Noordwijk, the Netherlands,pp. 643-650, (2005).Dr. M.F. Cawley• External examiner, M.Phil., University ofStrathclyde.• Examiner, NUI Travelling Studentships, July2005.Mr. G. McMahon• Trainer for Discover Primary Science & EngineeringProject Workshops.Dr. F.J. Mulligan• Vice-President, NUIM• Chairman, Radiological Protection Institute ofIreland.Professor J.A. Murphy• Member, National Committee for Astronomy andSpace Science, Royal Irish Academy.• NUI Representative in consultations with theState Examinations Commission on the LeavingCertificate Examination in Physics 2005.• Programme Committee for the SPIE Terahertzand Gigahertz Electronics and PhotonicsConference at the Photonics West 2006, San Jose,California.• Referee for the Journal of the Optical Society ofAmerica A.• Reviewer for the SFI Frontiers ResearchProgramme.• Reviewer for the Swiss National Science Foundationresearch grants scheme.• Member of Preliminary Design Review Panel forPPARC-funded CLOVER project, Oxford.Dr. R.W. O’Neill• Management Committee member EU COST P9Programme ‘Radiation Damage in Biomolecularsystems’.• Dean, Research & Postgraduate Studies, NUIM• Dean, Faculty of Science, NUIMDr. C. O’Sullivan• Member, Royal Irish Academy Physical SciencesCommittee.• Member, Royal Irish Academy Astronomy &Space Research.• Secretary & Treasurer, Astronomical ScienceGroup of Ireland.• Referee for ‘Journal of the Optical Society ofAmerica’.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06EXPERIMENTAL PHYSICS77

NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 EXPERIMENTAL PHYSICSExternal Assignmentsand Public ServiceC O N T I N U E DDr. N. Trappe• Secretary, Faculty of Science, NUIMDr. P.J.M. van der Burgt• Committee Member, Institute of Physics inIreland.• Secretary, 37 th International Conference of theEuropean Group for Atomic Systems (EGAS 37),Dublin City University, 3 rd – 6 th August 2005.• Referee for Journal of Physics B: Atomic,Molecular and Optical Physics.University Representative, Maynooth FairtradeSteering Committee.ConferencesHostedQUAD Consortium Meeting, NUI Maynooth,October 6-7, 2005.78

Faculty of ScienceResearch Report 2005-06Mathematics

NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICSAcademic StaffProfessor A.G. O’Farrell, MSc, PhD (Brown), MRIA, FIMA, CMath (1975- )*Professor S. M. Buckley, MSc, PhD (Chicago) (1993- )Dr. C. M. Comiskey, BA (Mod), MSc, PhD (DCU), FIMA, CMath (1998- )Dr. D. Dickinson, BSc, DPhil (York) (2001- )Dr. C. B. Hurley, BSc, PhD (Washington) (1995- )Dr. P. McCarthy, MSc, PhD (1994- )Dr. G. McGuire, MSc, PhD (Caltech) (1998- )Dr. J. Murray, BEng, DipMathSc, MSc, PhD (Illinois) (2001- )Dr. F. Ó Cairbre, MSc, PhD (Berkeley) (1990- )Dr. A. O’Shea, MA, MS (Notre Dame), PhD (Notre Dame) (1992- )Dr. D. Redmond, MSc, PhD (Illinois) (1977- )Dr. A. Small, BA (Warwick), PhD (Warwick) (1995- )Dr. D. Walsh, MSc, PhD (Swansea) (1972- )Dr. R. O. Watson, MSc, BD, MPhil (Warwick), PhD (1973- )Dr. D. Wraith, BA (Cambridge), PhD (Notre Dame) (1997- )Contract LecturersMr. P. Kelly, HDip StatsDr. J. Ramón Mari, BSc, MSc (Uni de Barcelona), PhD (University of Durham)Visiting LecturerDr. V. Chrastinová, BA, MA, PhD (Masaryk University Brno)Post-Doctoral FellowsDr. N. Budarina, PhD (Vladimir)Dr. K. Falk, Dipl Math, PhD (St Andrews)Dr. S. Kokkendorff, MSc (Aarhus), PhD (TU Denmark) (2003-)Dr. I. Short, PhD (Cambridge)80* Unless otherwise stated the higher degrees listed are those of the National University of Ireland.

Postgraduate Research StudentsMs. C. Bergin, BSc (2003- )Mr. C. List, Dipl Math (Tübingen), MA (1996- )Mr. C. Mac an Bhaird, BA, MSc, MLitt (1998- )Ms. S. MacDonald, BA, MA, PD Comp Sc (Keele) (2002- )Mr. P. Mulligan, BSc (2004- )Ms. E. Murphy, BSc (2004- )Mr. L. Pforte, Dipl Math (Friedrich-Schiller) (2005)Ms. E. White, BSc (DCU) (2004- )Technical StaffMs. J. Love, Senior Technician, MSc (1994 - )Administrative StaffMs. D. Keenan, (1999- )Ms. G. O’Rourke, BA (2000- )Rosie Project:Principal Investigators:Dr. C. Comiskey, BA (Mod), MSc, PhD (DCU), FIMA, CMath (1998- )Project Manager:Dr. G. Cox, MSc (Wales), PhD (Manchester), DiplStat (TCD) (2003 - )Research Assistants:Ms J. Cronly, BA (TCD) (2005 - )Mr P. Kelly, HDip Stats (2005 - )Ms E. Murphy, BSc (2005 - )Ms. E. White, BSc, (DCU) (2003 -)NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICSProject Administrator:Ms A. Kemp, BA Mod (TCD) (2005)81

Head Of Department’s Review Of The YearDavid Redmond continued as University Registrar. Stephen Buckley was released from his teaching duties inorder to prepare the launch of a Mathematics course through Irish for our final year students, and José Ramonreplaced him. José works in Algebraic Geometry.The Department did well in the competition for SFI awards under the Research Frontiers Programme, and wewelcomed three new post-doctoral researchers: Ian Short, Kurt Falk and Natalia Budarina. We also welcomedlong-term visits from Veronika Chrastinová and Josef Dallik, of TU Brno.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICSJohn Murray and Detta Dickinson were the Seminar Organisers for the two academic years, and arranged anexceptionally fine slate of visitors.Catherine Comiskey’s ROSIE project moved into its final stage, and a further project has now been funded.Members of the Department played an active part at national level, with Richard Watson chairing the newRIA National Committee for Mathematical Sciences, and Ann O’Shea acting as Secretary.Mathematicians here and elsewhere were much encouraged by the SFI Mathematics Initiative, and ourpeople took an active part in the consultation process; and participated in applications when the call came.The funding environment for Mathematics, including fundamental areas, has never been so benign, and weare hopeful that the country is ready to move to a new level.The Department (principally Stephen Buckley and David Wraith) hosted the Third Irish Geometry Conferencein May.82

Research Interests Of StaffDr. Stephen BuckleyStephen Buckley is interested in several areas of analysis and geometry, including hyperbolic geometry,quasiconformal mappings, potential theory, partial differential equations, and harmonic analysis. This yearhe finished work with David Herron (Cincinnati) on uniform domains, and with Dragan VukotiÐ (Madrid) onnonlinear superposition operators. He also continued projects with Simon Kokkendorff on sphericalization,and with Alex Stanoyevitch (Guam) and André Diatta (Liverpool) on weak slice conditions. He beganwork with David Herron and Xiangdong Xie (also Cincinnati) on inversion in metric spaces. He gave fivemathematical talks during the year, including one at the Franco-Nordic congress in Reykjavik. He also maderesearch trips to Cincinnati, Lausanne, and El Escorial.Dr. Veronika ChrastinováIn general the geometrical (alternatively: formal) theory of systems of differential equations and the classicalCalculus of variations. In more detail, symmetries and infinitesimal symmetries of differential equations andLagrange variational problems. Investigation of the invertible higher-order generalizations of the classicalpoint and contact transformations which destroy the structure of finite-order jets. Distinction between thedegenerate and nondegenerate variational problems in connection to the extremality properties in terms ofgeneralized Poincaré-Cartan forms without the use of Lagrange multipliers.Dr. Catherine ComiskeyCatherine Comiskey holds a B.A.(Mod) degree in Mathematics from Trinity College, Dublin University, Irelandand M.Sc. and Ph.D. degrees in applied mathematics with statistics and epidemiology from Dublin CityUniversity, Ireland. She has been working in the area of the dynamics of epidemic modelling since 1985 andhas published in Ireland, Europe and Australia on HIV and AIDS in drug users. Dr. Comiskeys current worklooks at models for prevalence and treatment of opiate use. She is the Principal Investigator of the ROSIEproject, this is the first national longitudinal study evaluating treatment for opiate use in Ireland.( www.nuim.ie/rosie)Dr. Detta DickinsonDetta Dickinson’s research interests lie in the areas of measure theory and metric Diophantineapproximation, in particular, Diophantine approximation on manifolds. Classically, Diophantineapproximation is the study of how well real numbers can be approximated by rationals. This can be extendedto higher dimensions by asking how well real points in n-dimensional Euclidean space can be approximatedby rational points or by rational hyperplanes. Results in this area are very delicate as shown in Khintchine’stheorem, where the set of well approximable points has either zero or full measure depending on theconvergence or divergence of a certain volume sum. This leads to further questions - those of Hausdorffdimension in the case of measure zero and those of asymptotic number of solutions in the case of fullmeasure. Both of the above questions become more difficult when the set under investigation is restricted toa manifold embedded in Euclidean space, and this is Detta’s current area of interest.Dr. Catherine HurleyCatherine Hurley’s research interests are in statistical computing, graphics and data analysis. At present, sheis interested in the use of combinatorial methods for improved data visualisation. She has recently submitteda software package in R called “gclus” to the online repository at www.r-project.org, for enhanced scatterplotmatrix and parallel coordinate displays. This software incorporates algorithms for generating improvedarrangements of their component displays leading to improved data visualisations.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICS83

Research Interests Of StaffC O N T I N U E DDr. Kurt FalkKurt Falk’s main area of interest is Hyperbolic Geometry and Kleinian Groups. At present he works with ProfStephen Buckley on related topics such as Gromov hyperbolic spaces and groups, boundaries at infinity ofgroups and metric spaces, measure theory on such boundaries and generalised notions of hyperbolicity.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICSHe has written his PhD thesis on Mostow rigidity and dynamics in hyperbolic manifolds. He continuedworking on the latter, with emphasis on transient dynamical phenomena occurring in geometrically infinitehyperbolic manifolds, and in particular so called Patterson-Sullivan measures on limit sets of Kleiniangroups. His expertise in these classical areas of mathematics will benefit the common research project withProf Stephen Buckley on boundaries at infinity and notions of hyperbolicity for metric spaces and groups.Dr. Simon KokkendorffSimon Kokkendorff is interested in geometry and analysis on metric spaces ranging from combinatoricalanalysis on finite metric spaces to Riemannian geometry. His current research is focused on metric spacesthat are Gromov hyperbolic. Simon also has an interest in semi-Riemannian geometry and applications torelativity.Mr. Christoph ListChristoph List’s interest is in interactive tools for statistical graphics and data visualisation (PhD Project,Supervisor: Dr. Catherine Hurley).Dr. Pat McCarthyPat McCarthy is interested in the interplay between real and complex analysis and in particular in the studyof interpolation operators and maximal summation operators. He is also interested in analytic and algebraicnumber theory, especially in cyclotomic number fields and Gaussian sums. His current M.Sc. student ShaneBrannick, is working on symbolic integration and differential fields.Dr. Gary McGuireGary McGuire’s research area is algebra and discrete mathematics, usually involving error-correcting codes,combinatorial designs, finite geometries, algebraic geometry and algebraic number theory. Recently he hasbeen working on connections between combinatorial objects known as quasi-3 designs, and objects arisingfrom statistical mechanics known as spin models. Another recent research topic concerns types of functionson finite fields known as crooked functions. Using algebraic geometry results towards a classification of suchfunctions have been proved. Using the algebraic geometry of genus 2 curves the weights appearing in somecyclic codes have been determined.84Dr. John MurrayJohn Murray works on topics in the representation theory of groups, particularly those of finite groups overfields of positive characteristic. During the summer John collaborated with Dr. Harald Ellers, of NIU - DeKalbon the representation theory of symmetric groups. They are studying the effect of Murphy operators on theirreducible modules of such groups. John attended “Group representation theory”, EPFL, Switzerland andtalked at the “Special sessions on representation theory”, AMS/DMV/OMG joint meeting at the Universityof Mainz, Germany in June and also “6th century conference in representation theory” at the University ofAberdeen, Scotland in October. John has continued his work on the SFI funded project “Involutions in therepresentation theory of finite groups”.

Dr. Fiacre Ó CairbreFiacre Ó Cairbre’s main research interests lie in the general area of Dynamical Systems and in applicationsto electronic engineering. He is currently working on problems related to the stability of certain types ofswitching systems of differential equations.Professor Anthony G. O’FarrellAnthony O’Farrell φοχυσεδ principally on the problem of understanding the nature of reversible maps.He worked with his post-doctoral assistant Ian Short, with Roman Lavicka of Charles University, with MariaRoginskaya of Chalmers University, with colleagues in the Department, and he initiated contacts with otherexperts abroad who have relevant expertise. He is making rapid progress in this exciting field. He organisedthe One-Day Function Theory Meeting in London in September, funded by the London Mathematical Society.He was a joint organiser of a two-day meeting in honour of Hamilton at the RIA at the end of September.Dr. Ann O’SheaAnn O’Shea’s research interests lie in the areas of Value Distribution Theory and Mathematics Education. Shewas invited to speak at the HELM Mathematics Education Conference held at the University of Loughboroughin September 2005. She is currently secretary of the Royal Irish Academy’s Committee for the MathematicalSciences as well as the subcommittee for Mathematics Education. In this role, she drafted the Royal IrishAcademy’s response to the NCCA’s review of mathematics in post-primary education.Dr. Adam RalphAdam Ralph’s research interests are in X-ray crystallography is a technique to determine the atomic structureof materials. Of particular interest to me are proteins, atomic structures can help in determining the functionand mode of action of these molecules. Even though most of the human genome has been mapped, thefunction of most cellular proteins is undetermined. Crystallography experiments produce information onthe Fourier coefficients of the protein’s electron density, atomic positions are then inferred. However onlythe magnitudes of these coefficients are measured but not the arguments or phases. The image needs to bereconstructed on computer with additional information. Can information about the properties of the electrondensity lead to information about the phases? The eigenvalue spectrum of a specially formulated matrix,called a Karle-Hauptman matrix, is influenced by the properties of the electron density. Currently I amresearching into whether these matrices can be used in the structure solution pathway.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICSDr. David RedmondDavid Redmond’s area of specialisation is Group Theory and Permutation Groups. He has been working withProfessor Quinn (Maynooth) and Dr. P.W. Fowler (Exeter) on the application of group theory in Chemistry andin particular on the recent developments in the chemistry and geometry of Fullerenes.Dr. Ian ShortIan Short is currently working on a project with Professor Anthony O’Farrell to classify and manipulate thereversible maps within different groups. This is a broad project covering many areas of mathematics. He alsointerested in the analytic and geometric aspects of continued fraction theory, and various topics involvinghyperbolic geometry.85

Research Interests Of StaffC O N T I N U E DDr. Anthony SmallAnthony Small is working on problems in algebraic/differential geometry, in particular, the construction andstudy of differential geometric objects of variational origin, via ‘transforms’ that convert the data into moretractable algebro-geometric objects, e.g., minimal surfaces (soap films), constant mean curvature surfaces(soap bubbles) and monopoles.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICSDr. David WalshDavid Walsh’s research interests are in the area of Classical and Functional Analysis especially in the theoryof function spaces (analytic and otherwise) and in Hankel Operators. There is a close interplay between thesetopics. Currently he is working on the radial variation of functions in Besov spaces and related spaces. Thecollaborative work he has been engaged in about test functions for Hankel Operators in the Schatten classeshas been successfully completed recently.Dr. Richard O. WatsonRichard Watson is interested in algebraic number theory, algebraic K-theory, and algebras of smoothfunctions. He continues to work with Susan MacDonald (Waterford Institute of Technology) on mattersrelated to Irish secondary school geometry syllabi.Dr. David WraithDavid Wraith’s research interests encompass Differential Geometry and Algebraic Topology and focusprimarily on the topological implications of positive curvature. Most of his work to date explores the effects ofsurgery on Ricci positive manifolds.86

Research GrantsPublications inRefereed Journals‘Gromov Hyperbolicity and QuasihyperbolicGeodesics.’ Enterprise Ireland Basic ResearchAward, €125,850 (S. Buckley, 2003-2007)‘Aspectos Modernos de la Teoria de FuncionesAnaliticas y la Teoria de Operadores.’ External expertmember of the UA Madrid Node of the Network,Grant from Ministerio de Ciencia y Tecnologia, Spain,€21,670 (S. Buckley, 2003-2006).‘Three year follow up of the National LongitudinalStudy to Evaluate Treatment for Opiate Use.’National Advisory Committee on Drug, Departmentof Gealtacht Rural and Community Affairs, €500,000(C. Comiskey, 2005-2007).‘Modelling the Drug Using Career with a view toAssisting and Informing Health Policy and Planning.’Health Research Board, Health Services Fellowship,€160,000 (C. Comiskey and E. White, 2005-2008).‘Prevalence and Incidence of Drug Use in Ireland.’Health Research Board, General Research Grant,€60,000 (C. Comiskey, 2005-2008).‘Extension of the National Longitudinal Studyto Evaluate Treatment for Opiate Use.’ NationalAdvisory Committee on Drug, Department ofGealtacht Rural and Community Affairs, €80,000 (C.Comiskey, Sept 2005 - Dec 2005).‘Simultaneous Diophantine Approximation onManifolds.’ Science Foundation Ireland, €160,000(D. Dickinson, 2005-2008).‘P-adic Diophantine Approximation.’ EnterpriseIreland, €3,800 (D. Dickinson, August 2005).‘Involutions in the Representation Theory of Group.’Science Foundation Ireland, Research FrontiersProgramme 2005, €85,000 (J. Murray, 2005-2008).International Collaboration Grant 2005, EnterpriseIreland, €2,200 (J. Murray, July-August 2005).International Collaboration Programme 2005Enterprise Ireland, €1,250. (D. Wraith, 2005).Buckley, S. and Z. Balogh. ‘Sphericalization andFlattening ‘ Conformal Geometry and Dynamics, 9,76-101 (2005).Budarina, N. ‘Deformations of Diophantine Systemsfor Quadratic Forms of the Checkerboard Lattices D n ’(Russian) Chebyshevski ˘ı Sb., 5, 4(12), 65-74 (2005).Falk, K. ‘A Note on Myrberg Points and Ergodicity.’Mathematica Scandinavica, 96, 107-116 (2005).Falk, K. and B. Stratmann. ‘Constructing RestrictedPatterson Measures for Geometrically InfiniteKleinian Groups.’ Acta Mathematica Sinica,published online http://www.ActaMath.com (2005).Hurley, C., A. Buja, D. Cook and D. Asimov .‘Computational Methods for High-DimensionalRotations in Data Visualization.’ Handbook ofStatistics, Eds. C. R. Rao, E. Wegman, J. Solka,Elsevier, North-Holland, 14, 391-413, (2005).McGuire, G. and J. Voloch. ‘Weights in Codes andGenus 2 Curves.’ Proceedings of the AmericanMathematical Society, 133(8), 2429-2437 (2005).McGuire, G. and C. Bracken. ‘Characterization of SDPDesigns that Yield Certain Spin Models’Designs Codes and Cryptography, 36, 45-52 (2005).‘On Quasi-3 Designs and Spin Models’. DiscreteMathematics, 294, 21-24 (2005).Murray, J., L. Héthelyi, E. Horváth and B.Külshammer.’Central Ideals and Cartan Invariantsof Symmetric Algebras’ Journal of Algebra, 293, 243-260 (2005).Murray, J., T. Breuer, L. Héthelyi, E. Horváth and B.Külshammer.’ Central Ideals and Cartan Invariantsof Group Algebras.’ Journal of Algebra, 16 pages,published online (8 June 2005).Murray, J. ‘Projective Modules and Involutions.’Journal of Algebra, 7 pages, published online(5 July 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICS87

NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICSPublications inRefereed JournalsC O N T I N U E DÓ Cairbre, F. ‘William Rowan Hamilton (1805-1865):Ireland’s Greatest Mathematician.’ Astronomy andSpace, pp 10-13 (January 2005).O’Shea, A. ‘Helping Students Make the Transitionfrom School to University.’ Proceedings of the HELMConference, Loughborough University, publishedonline http://www.engsc.ac.uk/downloads/helm/proceedings/session7a_oshea.doc, (15 September2005).Small, A. ‘On Algebraic Minimal Surfaces in |R 3Deriving from Charge 2 Monopole Spectral Curves’International Journal of Mathematics, 16(2),pp 173-180 (February 2005).Conference ProceedingsBergin, C. ‘On Brieskorn 5-Manifolds.’ Seminar,NUIM (20 April 2005).Buckley, S. ’Ends of Metric Measure Spaces andSobolev Inequalities.’ Franco-Nordic Congress,Reykjavik (7 January 2005).Buckley, S. ‘Uniform Domains and RelatedConditions’. Colloquium, TCD (29 April 2005).Buckley, S. ’The Boundary at Infinity of a MetricSpace.’ Colloquium, UCC (13 October 2005).Buckley, S. ’The Floyd Boundary of a Metric Space.’Colloquium, DCU (20 October 2005).Buckley, S. ‘Uniform spaces.’ Seminar, NUIM(23 November 2005).Budarina, N. ‘Deformations of Diophantine Systemsfor Quadratic Forms of the Checkerboard Lattices D n ’Analytical Methods In Number Theory, ProbabilityTheory And Statistics (dedicated to the 90 thanniversary of academician Yu.V.Linnik’s birth)St Petersburg, Russia (25-29 April 2005).Budarina, N. ‘Deformations of Diophantine Systemsfor Quadratic Watson Forms.’ V InternationalAlgebraic Conference, Odessa (Ukraine) (20-27 July2005).Comiskey, C. ‘Characteristics of the ROSIE DrugTreatment Cohort.’ Presentation to the TreatmentSub-Committee of the National Advisory Committeeon Drugs, Ballsbridge, Dublin (14 July 2005).Comiskey, C. ‘Outcomes at 12 months, Results fromthe ROSIE National Drug Treatment Study.’Presentation to the National Advisory Committeeon Drugs, Government Buildings, Leinster House,Dublin (15 December 2005).Dickinson, D. ‘Metric Diophantine Approximation.’Northwest University, Xi’an, PR China (10 August2005).88Falk, K. ‘Patterson-Sullivan Measures.’ HyperbolicGeometry Workshop, TCD (7-8 October 2005).

Kokkendorff, S. ‘Polar Duality and the GeneralizedLaw of Sines.’ Seminar, NUIM (16 February 2005).Kokkendorff, S. ‘Mean Distance and Curvature.’Seminar, NUIM (30 March 2005).McGuire, G. and E. Byrne, ‘Results on NonlinearFunctions Arising in Cryptography and CodingTheory.’ Workshop on Coding and Cryptography,Boole Centre for Research in Informatics, UCC (23May 2005).McGuire, G. and E. Byrne, ‘On the Non-Existence ofAPN Functions.’ International Workshop on Codingand Cryptography, Bergen, Norway (15 March 2005).Murray, J. ‘Carter Payne Homomorphisms andBranching Rules for Specht Modules.’ Seminar at theRényi Institute of Mathematics, Budapest, Hungary(1 March 2005).Murray, J. ‘Involutions, Projective Modulesand the Frobenius-Schur Indicator.’ AlgebraSeminar, Budapest University of Technology andEconomics,Budapest, Hungary (2 March 2005).Murray, J. ‘Applications of the Frobenius-SchurIndicator in Characteristic 2.’ Special Session on‘Representations and Cohomology of Groups andAlgebras. ‘AMS/DMV/OMG 2nd Joint Meeting Mainz,Germany (19 June 2005).Ó Cairbre, F. ‘William Rowan Hamilton (1805-1865): Ireland’s Greatest Mathematician.’ Seminar,Astronomy Ireland New Year, Dunsink Observatory(10 January 2005).Ó Cairbre, F. ‘William Rowan Hamilton (1805-1865):Ireland’s Greatest Mathematician.’ Seminar, OldDrogheda Society, Drogheda (9 February 2005).Ó Cairbre, F. ‘William Rowan Hamilton.’ MaynoothAstronomy Society, NUIM (26 April 2005).O’Shea, A. ‘Helping Students Make the Transitionfrom School to University.’ HELM Conference,Loughborough University (15 September 2005).Short I. ‘Continued Fractions, MoebiusTransformations and Hyperbolic Geometry.’ Seminar,University of Warwick (UK) (13 January 2005). ‘VanVleck Continued Fractions.’Seminar, University ofSouthampton (UK) (11 February 2005).Short I. ‘Magic Letter Groups.’ Seminar, NationalUniversity of Ireland, Maynooth (5 October 2005).Short I. and E. Crane. ‘Conical Limit Sets.’ Seminar,University of Cambridge (UK) (2 March 2005).Short I. and E. Crane. ‘Continued Fractions,Hyperbolic Geometry and Quaternions.’ Seminar,University College Cork (17 November 2005).Short I. and E. Crane. ‘Continued Fractions,Hyperbolic Geometry and Quaternions.’ Seminar,University College Dublin (22 November 2005).Small, A. ‘Klein’s Correspondence.’ Third IrishGeometry Conference, NUIM (24 May 2005).Small, A. ‘Geometry of Monopoles.’ Maths MeetingCiregynogg, National University of Wales (2 June2005).Wraith, D. ‘Surgery Techniques in RiemannianGeometry.’ Seminar, University of Warwick, England(21 February 2005).Wraith, D. ‘Curvature and Contact Surgery. Seminar,University of Cologne, Germany (4 July 2005).Wraith, D. ‘New Connected Sums with Positive RicciCurvature.’ Curvature and Global Shape Workshop,University of Münster, Germany (5 August 2005).Wraith, D. ‘New Connected Sums with PositiveRicci Curvature.’ Dublin Area Colloquium, TCD (21October 2005).Wraith, D. ‘Stable Bundles with Positive RicciCurvature.’ Winter Symposium, Dublin Institute forAdvanced Studies (15 December 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICS89

Visiting & Guest LecturersNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICSDr. Dmitri Zaitsev. TCD. ‘Nonresonant Vector Fieldsand Extension of Local Automorphisms’ (9 February2005).Dr. Juergen Mueller. Friedrich-Schiller University,Jena, Germany. ‘On Modular Representations of theSymmetric Group.’ (23 February 2005).Dr. Shane F. Whelan. UCD ‘Modelling the Risk inRisky Investments’ (2 March 2005).Dr. Veronika Chrastinová. Brno University ofTechnology. ‘The Mystery of Degenerate VariationalProblems.’ (9 March 2005).Professor Geoffrey Robinson. University of Aberdeen‘Local Structure and Conjugacy Classes.’ (16 March2005).Professor Vaughan Jones. Fields Medallist Berkeley‘Supertransitivity.’ (16 March 2005).Dr. Josef Dalik. Brno University of Technology.‘Quadratic Interpolation in Vertices of PlanarTriangulations and an Application.’ (6 April 2005).Dr. Michele Intermont. Kalamazoo College MI, USA.‘The A-Complexity of Spaces’ (11 April 2005).Professor John Haslett. TCD ‘Bayesian Palaeo ClimateReconstruction.’ (13 April 2005).Dr. Maria Roginskaya. Chalmers University ofTechnology, Göteborg, Sweden. ‘Energy and RieszProducts.’ (27 April 2005).Professor Chris Brunsdon. School of Computing,University of Glamorgan. ‘Geographically WeightedLocal Statistics Applied to Binary Data.’ (4 May2005).Mr. Oliver Mason. Hamilton Institute, NUIM. ‘PositiveDynamical Systems: Some Recent Results and NovelApplications.’ (11 May 2005).Dr. Ben McKay. UCC. ‘Projective Planes.’ (21September 2005).Dr. Bryan Rynne. Heriot-Watt University. ‘SomeRecent Results on Periodic, Jumping NonlinearityProblems.’ (28 September 2005).Dr. Marcus Greferath. UCD.’The Projective Geometryof Modules’ (12 October 2005).Dr. Michael Scott. DCU. ‘Pairings for Dummies.’(19October 2005).Dr. Peter Collins. St Edmund Hall, Oxford. ‘TheMetrisation of Topological Spaces.’ (26 October2005).Dr. Kurt Falk. NUIM.’Kleinian Groups and Patterson-Sullivan Measures.’ (9 November 2005).Dr. Marc Troyanov. EPFL, Lausanne, Switzerland.‘Axiomatic Sobolev Spaces on Metric Spaces.’ (16November 2005).Dr. Maria Meehan. UCD. ‘Towards AdvancedMathematical Thinking - A Second Year Course inAnalysis.’ (23 November 2005).Dr. Maria Roginskaya. Chalmers University ofTechnology, Göteborg, Sweden. ‘Point Spectra ofPartially Power-bounded Operators’ (30 November2005).Professor Burkhard Wilking. WestfälischeWilhelms-Universität, Münster. ‘FundamentalGroups of Manifolds with Ricci Curvature BoundedBelow.’ (5 December 2005).Dr. Grant Walker. Manchester University. ‘AlgebraicCombinatorics’(7 December 2005).90

External Assignments and Public ServiceDr. S. Buckley• Reviewer for Mathematical Reviews.• Referee for the following internationalmathematics journals:• Proceedings of the Edinburgh MathematicalSociety; Pacific Journal of Mathematics;Publicacions Matematiques; ContemporaryMathematics.• Member of the Training Team for the IrishMathematical Olympiad, NUIM.Dr. C. Comiskey• External Interviewer, Mathematics Department,Dublin Institute of Technology.Dr. D. Dickinson• Reviewer for Mathematical Reviews.• Referee for international journals.Dr. C. Hurley• Associate Editor for the journal Statistics andComputing.• Maintain Irish Statistical Association website.Dr. S. Kokkendorff• Reviewer for Zentralblatt MATH.Dr. G. McGuire• Cryptography/Coding session for NationalUniversity of Ireland, Maynooth Science Camp.• Member of the Training Team for the IrishMathematical Olympiad, NUIM.• Served as a referee for the journals Designs,Codes and Cryptography, Finite Fields and theirApplications, IEEE Transactions on InformationTheory.Dr. P. McCarthy• Member of the Training Team for the IrishMathematical Olympiad, NUIM.Dr. J. Murray• Referee for the Journal of Algebra.• Referee for the Journal of AlgebraicCombinatorics.• Participated in ‘Algebraic Groups And FiniteReductive Groups’,• Bernouilli Centre, Ecole Polytechnique Federalede Lausanne (EPFL), Switzerland.• Participated in ‘Sixth Century Conference inRepresentation Theory’, University of Aberdeen.• Participated in ‘Groups in Galway 2005’, NUIG.• Member of the Training Team for the IrishMathematical Olympiad, NUIM.Dr. F. Ó Cairbre• School presentations on Mathematics.• Participation in TV documentary on Hamilton.Dr. A. O’Shea• Secretary of the Irish Mathematical Society2004-2008.• Secretary of Royal Irish Academy Committee forMathematical Sciences 2004-2008.• Secretary of Royal Irish Academy Subcommitteefor Mathematics Education 2004-2008.• Reviewer for Zentralblatt Math.Dr. D. Walsh• Referee for Glasgow Mathematical Journal.• External Examiner for Travelling Studentships inMathematics, National University of Ireland.Dr. R. Watson• Chair of the Royal Irish Academy Committee forMathematical Sciences.• Member of the Training Team for the Irish MathematicalOlympiad, NUIM.• Member of the Board for Science of the RoyalIrish Academy.• President, North Kildare Maths Problem Club.• Member of IMS and IMTA.Dr. D. Wraith• Treasurer of Irish Mathematical Society.• Reviewer for Mathematical Reviews.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICS91

Conferences HostedD. Wraith and Prof. S. Buckley. Third Irish GeometryConference. (20-21 May 2005).D. Wraith. ‘The Legacy of William Rowan Hamilton:Symplectic and Contact Geometry and HamiltonianSystems’ (30 September-1 October 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICS92

Faculty of ScienceResearch Report 2005-06Mathematical Physics

NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICAL PHYSICSAcademic StaffProfessor D. M. Heffernan, MA (TCD), MS, PhD (Cornell) (1993-)*Professor D. H. Tchrakian, BSc.(Lond.), ARCS, PhD (Edin.) (1971-)Professor C. Nash, BA (Mod.) (TCD), PhD (Cantab.) (1979-)Dr. B.P. Dolan, BSc (Edin.), PhD (Durham) (1986-)Dr. J.A. Twamley, BA (Mod.) (TCD), PhD (Alberta) (1997-)Adjunct ProfessorProfessor V. Bužek, MSc, PhD (Moscow)Contract LecturerDr. D. Grigoriev, MSc, PhD (Moscow) (2003-)Part-time LecturersMr. W. Hanan, BSc (DCU) (2001-)Mr. D. Stynes, BA.(Mod) (Dublin), MSc (DCU) (2001-)Dr. G. Kells, BSc (DCU), PhD (2005-)Sfi Research FellowDr. J. Vala, MSc (Bratislava), PhD (Jerusalem) (2005-)Research FellowsDr. D. McHugh, BA (Mod) (Dublin) MSc, PhD (2005-)Dr. E. Radu, PhD (Freiburg) (2004-)Dr. A. Chefles, BSc, PhD (Strathclyde) (2004-)Postgraduate Research StudentsMr. G. Kells, BSc (2001-2005)Mr. D. McHugh, BA (Mod) (Dublin) MSc (DCU) (2001-2005)Mr. A. Rogers, BE Meng (2001-)Mr. M. Howard, BSc (2003-)Mr. J. Fitzsimons, BSc (2004-)Ms. A. Ghesquire, Bsc (2005-)TutorsMs T. Hughes, (2005-)Executive AssistantMs. M. Harte (1993-)94* Unless otherwise stated the higher degrees listed are those of the National University of Ireland.

Head Of Department’s Review Of The YearThe study of Mathematical Physics at Maynooth has a long and distinguished tradition. Modern theoreticalphysics and applied mathematics are exciting and dynamic and that excitement is reflected in the researchprojects which are pursued in the Department. Each permanent member of the Department holds a ResearchAssociateship at the School of Theoretical Physics of the Dublin Institute of Advanced Studies, in whosescientific work they participate actively. In addition, the Department maintains strong, international contactswith major academic centres abroad.The main areas of research are nonlinear physics, at both the macroscopic and microscopic level, and thestudy of the fundamental forces of nature. Detailed studies are undertaken to understand the dynamicalbehaviour of fundamental physical systems far from equilibrium, in quantum computing and informationprocessing, nonlinear dynamics, condensed matter physics, classical and quantum chaos and the topologicalphases of matter. A major research effort within the Department is to develop a better understanding of thefundamental forces of nature. There are four basic forces: Gravity, Electromagnetism and the two nuclearforces, the Strong and the Weak nuclear forces. The last three are believed to be well described by themathematical framework of Relativistic Quantum Field Theory, while Gravity is so far understood only atthe level of classical physics. Both the gravitational force and the other three forces are described in termsof Gauge Field Models. Most prominent amongst these is the Yang-Mills model with its rich geometrical andtopological features, and plays a central role in current understanding of these forces. Detailed informationon the Department’s research activities is given below.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICAL PHYSICS95

Research Interests Of StaffNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICAL PHYSICSProf. Vladimír BužekThe research interests of Prof. V. Buzek can be divided into several mutually related groups:(1) quantum information processing -- universal optimal manipulations with quantum information (e.g.universal quantum machines such as quantum cloners, or universal NOT gates)(2) quantum state reconstruction -- reconstruction of states of quantum systems from incomplete data (e.g.application of the principle of maximum entropy and the Bayesian quantum inference)(3) dynamics of open quantum systems -- stochastic quantization, quantum decoherence, nonclassical effectsin quantum optics, reconstruction of Liouvillian superoperators, description of dynamics of open systemsfrom the point of view of quantum information theory.(4) quantum entanglement in multi-partite systems -- generation of entanglement (non-classical correlations)in many body systems, utilization of multi-partite entanglement to communication protocols (e.g.quantum secret sharing).(5) theoretical quantum optics -- various aspects of matter-light interactions and generation of non-classicalstates of light.Dr. Anthony CheflesDr. Chefles’s work is in the field of quantum information science. His specific interests are the kind ofmanipulations which must be carried out on quantum states in order to store and process information inthem. These include discrimination among and copying quantum states. He studies the general propertiesof the processes that quantum states can undergo, especially the determination of whether or not a givenprocess which may be useful in applications is physically realisable. Current research includes:1) Quantum voting protocols: can quantum states be used to guarantee the anonymity of voters participatingin a secret ballot?2) Distinguishability of quantum states and quantum operations.3) Noise properties and entanglement generating capabilities of quantum channels.Dr. Brian DolanResearch interests: relativistic quantum field theory, general relativity, quantum gravity and condensedmatter.From a theoretical point of view geometry has always provided an immensely fertile bridge between physicsand mathematics, many mathematical concepts being motivated by physical considerations and vice versa.All four of the fundamental forces of Nature (Gravity, Electro-magnetism and two nuclear forces-the Strongand Weak nuclear forces) fit nicely into the mathematical framework of the geometry of curved spaces andgauge field theories. A quantum mechanical analysis of these theories however reveals profound differences,in particular between gravity and the three forces studied in modern particle physics-the electro-magnetic,the strong and the weak forces. The aim of my research programme is to develop a deeper understandingof these fundamental physical theories and of the unifying role played by geometry and symmetry, bothin classical and in quantum physics but especially in the latter. The physical and mathematical techniquesinvolved are applicable to many other areas of physics too, such as solid state, low temperature physics andthe theory of condensed matter.96

Current research includes:i) Duality symmetries. Physical phenomena change under variations in scale (the renormalisation group),for example the parameters that determine the strength of the fundamental forces change with theenergy scale at which they are measured. Discrete symmetries, sometimes called duality, can play a veryimportant role here, for example they can be used to obtain information on the different possible phasesof supersymmetric YangMills theories and in the quantum Hall effect - two apparently very differentphenomena which show a remarkable similarity in terms of the structure of their different phases andtheir renormalisation group flow. Symmetries can be used to gain deep insights into the way in whichparameters change under changes in energy scale and this is one aspect of research.ii) Non-commutative geometry. A new technique for analysing quantum field theories is under investigation,that of non-commutative geometry in which the space-time continuum is replaced by a discrete setof points in an abstract ‘fuzzy’ space-in a way specially designed to preserve all of the symmetries of thetheory. This has applications in renormalisation group theory and to the problem of quantum gravity.iii) Chaotic renormalisation group flow. In some circumstances the parameters of a physical theory changein a chaotic manner when the length scale or the energy scale is changed and this phenomenon is alsocurrently under investigation.Dr. Dmitri GrigorievScientific interests of Dr. Grigoriev include quantum field theory, particle cosmology and computationalphysics. The key areas of research in 2005 were electroweak baryogenesis, quark-gluon plasma instabilitiesand proton decay.Baryogenesis is essentially a way to explain the total lack of antimatter in the current Universe. Thereare good reasons to believe that the very early Universe was matter-antimatter symmetric, with a smallbaryon excess developing dynamically at later stages, but before the annihilation of remaining antimatterinto photons now observed as the cosmic microwave background (CMB). The actual dynamical scenariofor baryogenesis is yet to be found, with the electroweak baryogenesis being the only possibility based onexperimentally proven physical effects. A promising idea being currently investigated is to incorporate thephysics of strong interactions, including quark-gluon plasma instabilities, into electroweak baryogenesis,and, in particular, into recently proposed baryogenesis in hadronic jets.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICAL PHYSICSThe latter are actively being discussed lately as a way to explain the rapid thermalisation of quark-gluonplasma, experimentally observed in the last few years in high-energy collisions of heavy atomic nuclei. Theinstabilities can rapidly transfer the energy from the hard colliding particles to the soft infrared plasmamodes which rapidly thermalise. The rapid growth of infrared modes can also result in intense nonthermalbaryon number violation which is an essential component of electroweak baryogenesis. The current studyis concentrated on analysis of instabilities within hadronic jets and their contribution to the baryon numberviolation rate.Monopole catalysis of proton decay is another example of anomalous baryon number violation, relatedto baryogenesis by the common topological background, but different virtually in any dynamical andobservational aspect. The detailed numerical study of proton decay within the framework of Skyrmemonopolesystem is being continued.97

Research Interests Of StaffC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICAL PHYSICSProfessor Daniel M. HeffernanThe main area of research is nonlinear science. Detailed work is being undertaken to quantify andcharacterize the fractal structures that occur in nature and in the phase space of dynamical systems. Theproblem is a fundamental and universal one underlying many areas of physics, such as diffusion limitedaggregation, percolating clusters, neural networks and turbulence in fluids. The question of the existence ofa quantum analogue of classical chaos is fundamental and is a major preoccupation of our research group.Computational and theoretical techniques have been developed and applied to obtain an understanding ofthe physics of these systems. Some of the projects under study by the group in 2005 were:The development and utilization of generalised dimensional and f(alpha) spectral techniques for the studyof the dynamics of physical systems. Detailed studies were completed of the formation and evolution ofmultifractal structures in some simple nonlinear dynamical systems. This is part of a major programme todevelop a statistical-thermodynamic approach to the characterization and elucidation of the structural anddynamical properties of nonlinear systems, particularly spatio-temporal chaos.The detailed study of the classical and quantum chaos. In particular a fundamental and detailed programmeis underway to study the nonlinear dynamics of low dimensional mesoscopic systems and the study of chaosin atomic spectra and structure. The application of chaos theory for nonlinear control and pattern recognitionwas systematically investigated.The physics, both classical and quantum, of external cavity lasers and low dimensional systems.Dr. Derek McHughDr. McHugh’s research interests are in quantum information theory. My PhD was φοχυσεδ on practicalaspects of constructing and operating a scalable ion trap quantum computer. Now I’m working on moretheoretical issues regarding entanglement in quantum systems, particularly continuous variable quantumsystems.Professor Charles NashProfessor Nash’s research is in quantum field theories using both analytical and topological techniques.Of interest on the analytical side is the renormalisation of quantum field theories and the relation of thisto quark confinement and QCD. The topological investigations centre on the properties of Yang-Millsgauge theories and the relation of these to quantum field theories in dimensions 2, 3 and 4. These involveinvestigations of classical solutions representing instantons, solitons and monopoles and relate to chiralanomalies, Donaldson invariants and Witten-Turaev-Viro invariants. The analytical and topological aspectscan be combined in a geometric study of the renormalisation group and this is also under study.A key recent topic of mine is an investigation of quantum field theory models on the lattice in order to shedinsight into suitable approximation methods which may be tractable for basic calculations. This has resultedso far in results relating the topology of the continuum quantum field situation with the lattice combinatorialone. This rather like the relation between the combinatorial formulation of cohomology and the continuum deRham formulation using calculus (i.e. differential forms). There are interesting new, and calculable, featuresof the energy momentum tensors of such models and links with the modular invariance of string theory.98A development closely related to the above is that of the discovery by Witten of an Abelian monopoledescription of the 4-manifold polynomial invariants of Donaldson. This is also related to the new equationsof Seiberg and Witten and this is under study at present. In particular some new results on the threedimensional Seiberg-Witten equations have been derived recently and are under active development. Other

separate work is a new project on non-commutative matrix models of Quantum field theories.Dr. Eugen RaduResearch activity – main area of interest:Einstein Gravity: Regular and black hole solutions with nonabelian fields: numerical solutions withcosmological constant, new hairy black holes, rotating configurations.Black holes: topological black holes; solutions in non-asymptotically flat background, black holethermodynamics.Rotating universes: new rotating solutions, field quantization.Scientific VisitsInstitut fur Physik, Universitat Oldenburg, Germany, October 2005.Professor T. TchrakianResearch activity: Main area: Higher dimensional field theories, including dimensional descent. Abelian andnon Abelian gauged Higgs and Skyrme field theories, including their gravitating cases. Special emphasison higher curvature gravitational terms, as well as inclusion of (negative) cosmological constant. Specificproblems tacked are listed:Construction of a U(1) (Maxwell) gauged Skyrmion in 3+1 dimensions. This is a stable soliton when theelectric potential vanishes, and is quasistable otherwise. In the second case we succeeded in finding a staticspinning finite energy lump. This is the only such example that does not involve stationary fields.Continued our study of the systems consisting of two distinct gravitating members of the Yang--Millshierarchy, going beyond the first two members of the Yang--Mills hierarchies in dimensions d=6,..,12,extending our previous results restricted to the first two members of this hierarchy, and to dimensionsd=6,..,8. Using fixed point analysis combined with numerical techniques, we established that the varioussolutions are characterised by three types of fixed points, at zero and infinity, Reissner--NordstrØm type, andwhat we called a ‘conical’, this last one being a feature exclusively in dimensions 5,9,.. etc. In this study, werestricted to Einstein--Hilbert gravity, and to regular solutions only.Again in this area, and restricting to Einstein--Hilbert gravity, we studied such systems in the presence of anegative cosmological constant. The results are qualitatively similar to those of the usual $3+1$dimensional case, except that the peculiar accident in the latter case allowing finite mass solution withmonopole like rather than sphaleron like asymptotic behaviour. Here, only the latter type exist, except indiemsnions where a Pontryagin charge is defined, when their asymptotic behaviour is instanton like.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICAL PHYSICSFinally, again in this area, we studied higher diemensional gravitating Yang--Mills systems, but with thegravitational term being a member of the gravitational hierarchy (e.g. Gauss--Bonnet). It was shown that thequalitative properties of the usual 4 dimensional case repeated modulo4p dimensions.Constructed ‘monopoles’ in 4p-1 dimensions, employing the 2p-th members of the Yang--Mills hierarchy. Thecorresponding dyons were also discussed, and in a subclass of these models its existence is guaranteed.This project is ongoing and at present we are gravitating these systems. It is planned also to apply theseobjects to brane theories.Started on the construction of axially symmetric instantons in all even Euclidean dimensions, and of axiallysymmetric monopoles in all odd Euclidean dimensions. In the latter case we have also considered monopole99

Research Interests Of StaffC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICAL PHYSICSantimonopoles, and monopole antimonopole chains.Started the construction of axially symmetric instantons of the 4dimensional Yang-Mills system, which unlike Witten’s axially symmetricinstantons are labeled by a voertex like charge n. This project is ongoing.Scientific Visits for research collaborationsWerner-Heisenberg-Institut fur Physik,Max-Planck-Institut, Munich, 2005.Yerevan Physics Institute (UerPhI), Yerevan, 2005.Dr. Jason TwamleyDr. Twamley is primarily interested in the whole area of QuantumTechnology and Information Science.This is a new emerging area of science which examines the issues relatingto the control of quantum systems and the use of controlled quantumsystems to perform certain tasks such as quantum information processing.The field is highly multi-disciplinary and encompasses quantum theory,computer science, atomic physics, condensed matter physics, chemistry,photonics etc. Issues that are of particular interest to me are: new quantumcomputer architectures, decoherence and decoherence repair techniques,new uses for quantum computers such as simulating other quantumsystems. He has pioneered the potential use of doped Buckyballs (C EMBEDEquation.3 ), molecules as ingredients in a solid-state quantum computerand also have interests in trapped-ion quantum computer designs.Dr. Jiri ValaDr. Vala’s iterests are: topological phases of matter, topological quantumcomputation, theory of decoherence, quantum error correction andsuppression and fault-tolerant quantum computation.Dr Jiri ValaThe President of Ireland YoungResearcherWhat are your research interests?My interests are in topologicalphases of matter and in topologicalquantum computation and quantumerror correction. These are topicsessential for fault-tolerant quantumcomputations which could reliablyprovide solution to computationalproblems that are not known to besolvable on a classical computer.These problems are relevant tostrategically important fieldsincluding for example informationsecurity and nanotechnologyresearch and development.How do you fund your work?I joined the Department ofMathematical Physics as a recipientof the President of Ireland YoungResearcher Award Fellow sponsoredby the Science Foundation Ireland.It is a competitive and highlyprestigious award which runs for fiveyears. Its total value is Ð880,976 andincludes funding for postdoctoralfellows and Ph.D. students.How did you build your career todate?I received my Ph.D. from the HebrewUniversity of Jerusalem in 2001.I spent the next four years as aResearch Scholar at the Universityof California at Berkeley where Iworked on quantum informationscience before joining theMathematical Physics Department inNovember 2005.100

Research GrantsPublications inRefereed Journals‘Effects of Gravitational and Yang-Mills Hierarchiesin the low energy effective action of string theory:i) Particle like and black hole solutions, and ii)Compactification to the brane’. Enterprise IrelandBasic Research Grants Scheme, €131,600 (D.H.Tchrakian, 2004-2007).‘Contractor in INTAS Project’. INTAS, €9,000 (D.H.Tchrakian, 2000-2005).‘Quantum Field Theory from Matrix models, analternative to lattice field theory’. Enterprise IrelandBasic Research Grants Scheme, €190,000 (B.P. Dolanand D. O’Connor, 2003-2005).‘Chaos Based System Identification and PatternRecognition.’ Enterprise Ireland Basic ResearchAward, €44,440 (D.M. Heffernan, R. Shorten and J.G.Keating, 2000-2005).‘Effects of Gravitational and Yang-Mills Hierarchiesin the low energy effective action of string theory:i) Particle like and black hole solutions, and ii)Compactification to the brane.’ Enterprise IrelandBasic Science Research Project, €167,132 (T.Tchrakian, 2004-2007).‘Einstein--Yang-Mills systems in higher dimensions.’Enterprise Ireland International CollaborationProject, €5,100 (T. Tchrakian, 2004-2007).‘Topological Phases and Topological QuantumComputation.’ President of Ireland Young ResearcherAward, Science Foundation Ireland, €880,976 (J.Vala, 2005-2010).Agop, M., E. Radu and R. Slagter. ‘On Ernst blackholes with a dilaton potential.’ Mod. Phys. Lett. A 20,1077 (2005)Brihaye, Y., B. Hartmann and E. Radu. ‘Deformedvortices in (4+1)-dimensional Einstein-Yang-Millstheory.’ Phys. Rev. D 71, 085002 (2005)Brihaye, Y., B. Hartmann and E. Radu. ‘Black stringsin (4+1)-dimensional Einstein-Yang-Mills theory.’Phys. Rev. D 72 104008 (2005)Brihaye, Y. and E. Radu. ‘Nutty dyons.’ Phys. Lett.B 615 1 (2005)Breitenlohner, P., D. Maison and D.H. Tchrakian.‘Regular solutions to higher order curvatureEinstein-Yang-Mills systems in higher dimensions.’Class. Quant. Grav. 22, 5201-5222 (2005)Brihaye, Y. and D.H. Tchrakian. ‘Yang--Millssphalerons in all even spacetime dimensions d=2k,k>2 : k=3,4.’ J. Phys. A 38, 3679-3694 (2005)Brazier, A., V. Buzek, and P. L. Knight. ‘Probabilisticprogrammable quantum processors with multiplecopies of program state.’ Phys. Rev. A 71, 032306-1-7(2005)Buzek, V., M. Orszag, and M. Rosko. ‘Instabilityand entanglement of the ground state of the Dickemodel.’ Phys. Rev. Lett. 94, 163601 (2005).Dolan, B. ‘Quantum Black Holes: the Event Horizonas a Fuzzy Sphere.’ JHEP 02, 008 0409299 (2005)Dolan, B. ‘Meromorphic Scaling Flow of N=2Supersymmetric SU(2) Yang-Mills with Matter.’NPB (in press)Feng. M., and J. Twamley. ‘Single-spin detectionby qubit SWAP to a molecular nanomagnet.’Europhysics Letters 69, 699-705 (2005)Fitzsimons, J. and J. Twamley. ‘Superballisticdiffusion of entanglement in disordered spin chains.’Physical Review A 72, 050301 (2005)NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICAL PHYSICS101

Publications in Refereed JournalsC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICAL PHYSICSGrigoriev, D. ‘Real-time dynamics of proton decay.’Procs. of Science (PoS), LAT2005, 313 pp.6 (2005)Hillery, M., L. Mlodinow and V. Buzek. ‘Quantuminterference with molecules: The role of internalstates.’ Phys. Rev. A 71, 062103 (2005)Kilbane, D., A. Cummings, D.M. Heffernan and G.O’Sullivan. ‘Characterization of the structure andeigenvalue spectra of the compound states of Sm IX.’Physica Scripta (in press)Kilbane, D., A. Cummings, G. O’Sullivan and D.M.Heffernan. ‘The classical-quantum correspondenceof a kicked particle in an infinite potential well.’Chaos, Solitons and Fractals (in press)Kilbane, D., A. Cummings, G. O’Sullivan and D. M.Heffernan. ‘Quantum statistics of a kicked particlein an infinite potential well.’ Chaos, Solitons andFractals (in press)Koniorczyk, M. and V. Buzek. ‘Non-maximallyentangled bases and their application inentanglement purification via swapping.’ Phys. Rev.A 71, 032331-1-10 (2005)Koniorczyk, Matyas, Peter Rapcan, and VladimırBuzek. ‘Direct versus measurement assisted bipartiteentanglement in multi-qubit systems and theirdynamical generation in spin systems.’ Phys. Rev. A72, 022321 (2005)Kosık, J. and V. Buzek. ‘Scattering model for quantumrandom walk on hypercube.’ Phys. Rev. A 71, 012306(2005).Mc Hugh, D. and J. Twamley. ‘Trapped-ion qutritspin molecule quantum computer.’ New Journal ofPhysics 7, 174 (2005)Mooney, A., J. G. Keating and D. M. Heffernan.‘A detailed study of the generation of opticallydetectable watermarks using the logistic map.’Chaos, Solitons and Fractals (in press)Nash, C. ‘Four manifold invariants and physics.’Encyclopedia of Mathematical Physics, Elsevier(in press)Paturyan, V., E. Radu and D.H. Tchrakian. ‘Rotatingregular solutions in Einstein-Yang-Mills-Higgstheory.’ Phys. Lett. B 609, 360-366 (2005)Paturyan, V., E. Radu and D.H. Tchrakian. ‘Solitonsand soliton antisoliton pairs of a Goldstone model in3+1 dimensions.’ J. Phys. A. (in press)Radu, E. ‘On a Petrov-type D homogeneous solution.’Int. J. Mod. Phys. A (in press)Radu, E. and E. Winstanley. ‘Conformally coupledscalar solitons and black holes with negativecosmological constant.’ Phys.Rev. D 72 024017(2005)Radu, E. and D.H. Tchrakian ‘New hairy black holesolutions with dilaton potential.’ Class. QuantumGrav. 22, 879-892 (2005)Radu, E. and D.H. Tchrakian. ‘New axially symmetricYang-Mills-Higgs solutions with negativecosmological constant.’ Phys. Rev. D 71, 0411084(2005)Radu, E. and D.H. Tchrakian. ‘Static BPS ‘monopoles’in all even spacetime dimensions.’ Phys. Rev. D 71,125013 (2005)Radu, E. and D.H. Tchrakian. ‘No hair conjecture,nonabelian hierarchies and anti-de Sitter spacetime.’Phys. Rev. D 73 0508033 (2005)102Mc Hugh, D. and J. Twamley. ‘Sixth-order robustgates for quantum control.’ Physical Review A 71,012327 (2005)Mc Hugh, D. and J. Twamley. ‘Quantum computerusing a trapped-ion spin molecule and microwaveradiation.’ Physical Review A 71, 012315 (2005)Rogers, A., R. Shorten and D. M. Heffernan. ‘Anovel matrix approach for controlling the invariantdensities of chaotic maps.’ Chaos, Solitons andFractals (in press)Sen, A. De, U. Sen, C. Brukner, V. Buzek, and M.Zukowski. ‘Entanglement swapping of noisy states: Akind of superadditivity in nonclassicality.’ Phys. Rev.A 72, 042310-1-10 (2005)

Stelmachovic, P. and V. Buzek. ‘Bounds on action oflocal channels on entangled states.’ J. Phys. A 38,6051 - 6064 (2005)Storcz, M.J., F.K. Wilhelm, J. Vala, K. R. Brown,J. Kempe and K. B. Whaley. ‘Full Protection ofSuperconducting Qubit Systems from CouplingErrors.’ Phys. Rev. B. 72, 064511 (2005)Vala, J., D.S. Weiss and K.B. Whaley. ‘Quantum ErrorCorrection of Qubit Loss in Addressable OpticalLattice.’ Phys. Rev. A 72, 052318 (2005)Vala, J., A.V. Thapliyal, S. Myrgren, U. Vazirani, D. S.Weiss, and K. B. Whaley. ‘Perfect Pattern Formationof Neutral Atoms in an Addressable Optical Lattice.’Phys. Rev. A 71, 032324 (2005)Wright, M.J., S.D. Gensemer, J. Vala, R. Kosloff and P.L.Gould. ‘Ultracold Collisions with Frequency-ChirpedLight.’ Phys. Rev. Lett. 95, 063001 (2005)Ziman, M., P. Stelmachovic, and V. Buzek.‘Description of quantum dynamics of open systemsbased on collision-like models.’ Open Sys. & Inf.Dynamics 12, 81-91 (2005)Ziman, M., M. Plesch, and V. Buzek. ‘Processreconstruction from incomplete and/or inconsistentdata.’ European Physics Journal D 32, 215 (2005)Ziman, M. and V. Buzek. ‘Realization of POVMs usingmeasurement-assisted programmable quantumprocessors.’ Phys. Rev. A 72, 022343 (2005)Ziman, M., M. Plesch, V. Buzek and P. Stelmachovic.‘Process reconstruction: From unphysical to physicalmaps via maximum likelihood.’ Phys. Rev. A 72,022106 (2005)Ziman, M. and V. Buzek. ‘All (qubit) decoherences:Complete characterization and physicalimplementation.’ Phys. Rev. A 72, 022110 (2005)Ziman, M. and V. Buzek. ‘Concurrence vs purity:Influence of local channels on Bell states of twoqubits.’ Phys. Rev. A 72, 052325–1-9 (2005)Zoller, P., T. Beth, D. Binosi, R. Blatt, H. Briegel, D.Bruss, T. Calarco, JI. Cirac, D. Deutsch, J. Eisert, A.Ekert, C. Fabre, N, Gisin, P. Grangiere, M. Grassl,S. Haroche, A. Imamoglu, A. Karlson, J. Kempe, L.Kouwenhoven, S. Kroll, G. Leuchs, M. Lewenstein,D. Loss, N. Lutkenhaus, S. Massar, J.E. Mooij, M.B.Plenio, E. Polzik, S. Popescu, G. Rempe, A. Sergienko,D. Suter, J. Twamley, G. Wendin, R. Werner, A. Winter,J. Wrachtrup, A. Zeilinger. ‘Quantum informationprocessing and communication - Strategic reporton current status, visions and goals for research inEurope.’ European Physical Journal D 36, 203-228(2005)Book ChaptersBuzek, V., R. Derka, and S. Massar. ‘Optimal quantumclocks’ in Asymptotic Theory of Quantum StatisticalInference, edited by Masahito Hayashi WorldScientific, Singapore, (2005)Editor of aSpecial IssueBuzek, V., P. Grangier and P. Tombesi, eds.:‘QuantumInformation with Atoms, Ions and Photons’ Specialissue of The European Physical Journal D, n.2, 32(2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICAL PHYSICS103

TalksNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICAL PHYSICSBuzek, V. ‘Quantum information processing withthree qubits.’ QUPON, Wien (26 May 2005).Buzek, V. ‘Optimal manipulations with quantuminformation: Programmable quantum processors.’Science and Art in Europe - meeting of the MaxPlanck Society, Dresden (25 May 2005).Buzek, V. ‘Physics of qubit applications.’ QISTmeeting, Innsbruck (14 February 2005).Buzek, V. ‘Dynamics of open quantum systems:Quantum information theory approach.’ ObergurglQuantum Optics Meeting 2005, Obergurgl (3 March2005).Buzek, V. ‘Optimal manipulations with quantuminformation: Programmable quantum processors.’Annual meeting of the Slovak Physical Society,Košice, Slovakia (7 September 2005).Buzek, V. ‘Visions and challenges.’ Slovakgovernment conference devoted to the projectMINERVA, Bratislava, Slovakia (10 February 2005).Buzek, V. ‘Is there anything new we can still learnfrom the Dicke model’? University of Ulm, Germany(10 June 2005).Buzek, V. ‘Pros and cons of European projects.’Faculty of Natural Sciences, Comenius University,Bratislava, Slovakia (12 October 2005).Buzek, V. ‘Physics of information.’ Scientific councilof the Slovak Academy of Sciences, Bratislava,Slovakia (15 December 2005).Buzek, V. ‘Can a scientific career be attractive.’ Publiclecture, Bratislava, Slovakia (11 November 2005).Buzek, V. ‘Think different: Quantum information.’INTAS Review meeting, Brussels (3 June 2005).Buzek, V. ‘Dynamics of open quantum systemsfrom a perspective of quantum information theory.’Colloquium Nielse Bohr Institute, Copenhagen (14September 2005).Buzek, V. ‘Entanglement and quantum phasetransitions in the Dicke model.’ Colloquium Instituteof Physics, Slovak Academy of Sciences, Bratislava,Slovakia (7 February 2005).Buzek, V. ‘Optimal manipulations with quantuminformation: From flipping spins to quantumprogramming.’ Lecture at the editorial boardmeeting of J. Phys. B, London (27 October 2005).Buzek, V. and I. Zeljenka. ‘Public discussion: Timein Physics and Music.’ Academy of Arts, Bratislava,Slovakia (16 Dec 2005).Dolan, B. ‘Duality Symmetries in N=2Supersymmetric Yang-Mills and the Quantum HallEffect.’Mathematics Dept., Heriot-Watt University,Edinburgh, Scotland (2 February 2005).Dolan, B. ‘Quantum Black Holes: the Event Horizonas a Fuzzy Sphere.’ Invited talk at the 11th Meetingof the North British Mathematical Physics Seminar,International Centre for Mathematical Sciences,Edinburgh, Scotland (16 February 2005).Dolan, B. ‘Duality Symmetries in N=2Supersymmetric Yang-Mills and the QuantumHall Effect.’ Invited talk at Conference on HigherDimensional Quantum Hall Effect, Chern SimonsTheory and Non-Commutative Geometry inCondensed Matter Physics and Field TheoryInternational Centre for Theoretical Physics (ICTP),Trieste, Italy (2 March 2005).Dolan, B. ‘Non-commutative Geometry, Fuzzy Spacesand Event Horizons.’ Physics. Department, Universityof Winnipeg, Winnipeg, Canada (19 April 2005).Dolan, B. ‘Duality Symmetries in N=2Supersymmetric Yang-Mills and the QuantumHall Effect.’ Department of Physics, University ofManitoba, Winnipeg, Canada (20 April 2005).Dolan, B. ‘Duality Symmetries in N=2Supersymmetric Yang-Mills and the QuantumHall Effect.’ Department of Physics, University ofSwansea, Swansea, Wales (2 December 2005).104

Grigoriev, D. ‘Dynamics of proton decay in Skyrmemonopolesystem.’ Talk at 12 th Irish Quantum FieldTheory Meeting, TCD, Dublin (20-21 May 2005).Grigoriev, D. ‘Real-time dynamics of proton decay.’Talk at 23 rd International Symposium on Lattice FieldTheory: Lattice 2005, TCD, Dublin (25-30 July 2005).McHugh, D. Contributed talk, ‘Trapped-Ion QutritSpin Molecule Quantum Computer.’ Young EuropeanPhysicists conference in Budmerice, Slovakia (14October 2005).McHugh, D. Contributed talk, ‘Trapped-Ion SpinMolecule Quantum Information Processors.’ NATOAdvanced Study Institute, Quantum Information inCrete (11 May 2005).Radu, E. ‘On NUT-charged solutions in anti-de Sitterspace-time.’ Talk given at 12th Irish Quantum FieldTheory Meeting, Trinity College Dublin (20-21 May2005).Radu, E. ‘On rotating solitons in general relativity.’Talk given at International Conference onFundamental and Applied Research in Physics, Iasi,Romania (28 October 2005).Vala, J. ‘Topological Quantum Computation.’Department of Mathematical Physics Seminar,NUIM (2 December 2005).Vala, J. ‘Topological Quantum Computation.’ PYIRAInterview Presentation, Science Foundation Ireland,Dublin (19 July 2005).Vala, J. ‘Topological Phases for QuantumComputation: Their Properties and PhysicalRealization.’ Institute for Quantum InformationSeminar Caltech, Pasadena, California, USA (19 April2005).Poster PresentationsVala, J. ‘Spectral Properties of Topological Phases forNaturally Fault Tolerant Quantum Computation’DARPA (Defense Advanced Research ProjectAdministration), Program Review Meeting, St.Augustine, Florida, USA (6 August 2005).Vala, J. ‘Ultracold Collisions Induced by Frequency-Chirped Light: the Influence of Chirp Direction.’ 36 thAnnual Meeting of DAMOP (Division of Atomic,Molecular and Optical Physics of American PhysicalSociety), University of Nebraska, Lincoln, Nebraska,USA; abstract published in Bull. Am. Phys. Soc. (18May 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06MATHEMATICAL PHYSICS105

External Assignments and Public ServiceNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 MATHEMATICAL PHYSICSProf. V. Buzek• Expert and reviewer for the INTAS• Member of the IST committee of the EC in the6th FP• Board member of the Quantum Electronics andOptics Division of the European Physical Society• Expert and reviewer for the 6th FrameworkProgram of the EU• Member of the Scientific Board of the ARC Seibersdorfresearch GmbH , Austria• Member of the EPSRC (Engineering and PhysicalSciences Research Council) Peer Review College,UK.• Member of the Board of governors of the Scienceand Development Agency of the Slovak republic.• Member of editorial boards:- Journal of Modern Optics, published by Taylor& Francis Ltd. (London )- Journal of Optics B: Quantum andSemiclassical Optics- Central European Journal of Physics- Acta Physica Hungarica: Quantum Electronics- Physical Review A- European Journal of Physics D- Journal of Physics B: Atomic, Molecular andOptical PhysicsDr. B. Dolan• Referee for Physical Review Letters• Referee Physical Review B• Referee Physical Review D• Referee Journal of Physics A• Referee Physics Letters A• Member of the Institute of PhysicsProf. D.M. Heffernan• Advisor to Science Foundation Ireland• Advisor to Department of Education and Science• External Examiner, University of Limerick, B.Sc.(Applied Physics), Grad Diploma and Master ofScience in Industrial Physics• External examiner, Ph.D., University of Limerick• Reviewer for Journal of Physics B• Reviewer for Physics Letters AProf. C .Nash• External examiner MSc thesis Supervisor andinternal examiner MSc thesis The Atiyah-SingerIndex Theorem• Elected to the commission of the InternationalUnion of Pure and Applied Physics.Prof. T. Tchrakian• Research Associate at the School of TheoreticalPhysics, Dublin Institute for Advanced Studies.Dr. J. Vala• Reviewer for Physical Review Letters• Reviewer for Physical Review A• Organizer of Berkeley Quantum Information andComputation Seminar, University of California,Berkeley, California, USA.• Irish node leader of CONQUEST (ControlledQuantum Coherence and Entanglement in Setsof Trapped Particles) Marie Curie Research andTraining Network, EC Marie Curie Project.• Representing Ireland in ERA Pilot QIST(Quantum Information Science and Technology).• Participating in the ERA Pilot QIST WP3Workshop in Bratislava, Slovak Republic.• Contributing to the ERA Pilot QIST document“Analysis of Network Structures for Future Collaboration”,in collaboration with Dr. Twamley,Macquarie University and Dr. Dodd, SFI.Dr. J.A. Twamley• PhD Thesis examiner for Queen’s UniversityBelfast and University of Queensland• Journal reviewer for Physical Review, PhysicalReview A• Expert Reviewer for the European Commission• Member of the Scientific Advisory Committee forthe International Society for Nanoscale Science.106

Faculty of ScienceResearch Report 2005-06Psychology

NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 PSYCHOLOGYAcademic StaffProfessor D. Barnes-Holmes, BSc, CertEd, D Phil (Ulster), CPsychol (Head of Department 1999-)Dr. Y. Barnes-Holmes, BSc, PhD, CPsychol (2003-)Dr. S. Commins, BSc, HDipStat, PhD (Dub) (2001-)Dr. D. Desmond, BA, HDipStat, PhD (Dub) (2004-)Dr. F. Lyddy, BA, PhD, CPsychol, AFBPsS, AFPsSI (2001-)Dr. S. McGilloway, BSocSc, PhD (QUB), CPsychol (2000-)Dr. B. Roche, BA, PhD, CPsychol (2000-)Dr. R. Roche, BA (Sch.), HDipStat, PhD (Dub) (2004-)Technical StaffMr. D. Walsh, BSc (2001-)Administrative StaffMs. A. Dooley, BA, DipSocAdmin (2000-)Ms. V. Thompson, (2003-)108* Unless otherwise stated the higher degrees listed are those of the National University of Ireland.

Postgraduate Research StudentsMs. C. Campbell, BA (2004-)Ms. G. Chan, BA (University of British Columbia), MA (Columbia University) (2004-)Ms. A. Cochrane, BA (2004-)Ms. F. Coogan, BA (2004-)Ms. L. Cunningham, BA (2003-)Ms. S. Craig, BSc (TCD) (2002-)Ms. K. Deasy, BA (Saint Louis University) (2002-)Ms. C. Egan, BA (Simon Fraser University) MA (Columbia University) (2003-)Ms. D. Harvey, BA (2004-)Ms. S. Gallagher, BA (2002-)Ms. A. Gavin, BA (2004-)Ms. M. Gorham, BA (2005-)Ms. A. Kehoe, BA (2004-)Ms. C. Kelleher, BA (2004-)Ms. C. Keogh, BA (2004-)Mr. N. Kenny, BA (2002-)Mr. C. Linehan, BA (2005-)Ms. A.M. McGauran, BA (2003-)Ms. J. Moore, BA (2005-)Ms. C. Murphy, BA (2003-)Mr. J. Murphy, BA (2005-)Ms. S. O’Connor, BS (Loyola University Chicago) (2004-)Ms. C. O’Toole, BA (2005-)Ms. C. Parsons, BA (2005-)Ms. A. Roberts, BA (2004-)Ms. C. Roche-Dwyer, BA (DCU) (2004-)Mr. T. Saeed, BA (University of Peshawar-Pak) MPhil (University of Peshawar-Pak) MA (2005-)Ms. G. Scanlon, BA (2004-)Mr. P. Scanlon, BA (2005-)Ms. S. Smyth, BA (2003-)Ms. C. Sweeney, BA (2002-)Mr. C. Wilson, BA (2005-)NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06PSYCHOLOGY109

Head Of Department’s Review Of The YearThe first cohort of MH209 students commenced their third year of the BSc in Psychology, taking all psychologymodules. The CAO points also remained high at approximately 480 this year. The BSc in Psychology is theonly denominated science degree in the discipline in country and is clearly a popular choice among students.The basic training that these students receive in the sciences will prepare them well for pursuing behaviouraland cognitive neuroscience, and other areas of experimental psychology. This year also saw an ‘open entry’policy introduced with our first year BA psychology degree allowing all first year students to take psychologyas one of their choice subjects. In addition, 15 extra places are being made available for these students insecond year BA psychology.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 PSYCHOLOGYThe addition of two extra staff members last year (Dr. Deirdre Desmond and Dr. Richard Roche (see profile))has strengthened the research streams within the Department particularly the areas of Mental Health andHealth Care, and Cognitive Science and Neuroscience. The strength and growth of the Department is reflectedin an increase in the number of postgraduate students registered, currently standing at 32, an increase incompetitively secured funding from a number of national and international funding agencies includingthe two Irish research councils (IRCHSS and IRCSET), the Spanish Ministry of Education and Science(collaborating partner), An Chomhairle um Oideachas Gaeltachta & Gaelscolaíochta, the Health ResearchBoard and the Irish Hospice Foundation and the NHS National R&D Programme on Forensic Mental Health(UK, collaborating partner) and in a general increase in research productivity.The Department underwent a quality review in May 2005. At the start of this academic year we received verypositive feedback from this process and we were encouraged to maintain the excellent standard of teachingand research that already exists within the Department. In addition, the Department received support for theimplementation of its strategic plan for the next five years.Later this year both the BA and BSc degrees will again be subject to review, for the purposes of accreditation,by the Psychological Society of Ireland.110

Research Interests Of StaffDr. Richard RocheDepartment of PsychologyWhat are your research interests?My current research is concerned with theways in which a cognitive map of the worldis generated, the operation of the processesinvolved and the anatomical substratesthat underpin these processes and mentalrepresentations.I am also investigating the mechanismswhereby new memories are laid down in thebrain, the anatomical structures involved inthis process and the neural mechanisms thatcarry out this important cognitive operation.I have maintained strong links with severalDublin hospitals to allow for patient work,and have initiated both domestic and overseascollaborations with research institutions (e.g.the Trinity College Institute of Neuroscience,Dublin; Nathan Kline Institute, NY), whichl facilitates the production of high-impactresearch into the future.How do you fund your work?I am currently supervising three PhD studentsunder funding from IRCSET. This has resultedin the formation of the Memory ResearchLaboratory (MRL), which I co-founded withDr. Seán Commins; this group represents avertically-integrated approach to the questionsof memory and spatial representation,incorporating neurophysiology andneuropharmacology (Dr. Commins) and humanbehaviour and electrophysiology (Dr. Roche).The MRL has already been responsible for thefirst 128-channel EEG recordings ever to becarried out in IrelandHow did you build your career to date?I received my PhD in Cognitive Neurosciencefrom Trinity College, Dublin in 2002, afterwhich I spent two years as a Research Fellowin the Trinity College Institute of Neuroscience(TCIN), working with Profs Shane O’Maraand Ian Robertson. I was appointed to theDepartment of Psychology, NUI Maynooth inFebruary 2005.Language and Cognition:Professor Dermot Barnes-HolmesThe experimental analysis of human behaviour. Relational frame theory. Behaviouralneuroscience focusing on language and cognition. Clinical behaviour analysis. Appliedbehaviour analysis. Conceptual issues in behaviour analysis.Dr. Yvonne Barnes-HolmesThe experimental analysis of human behaviour. Relational frame theory and the analysisof human language and cognition. Clinical behaviour analysis, with a special interest inacceptance and change therapies. Experimental analyses of clinical phenomena, includingexperiential avoidance and psychological acceptance. Applied behaviour analysis and specialeducation.Dr. Bryan RocheExperimental social psychology. Relational frame theory. Experimental psychopathology.Human sexuality and psycho-physiology. Social Constructionism and BehaviouralHermeneutics.Cognitive Science and Neuroscience:Dr. Seán ComminsThe area of neuroscience that is concerned with the function of brain areas and their relation tobehaviour. Consolidation of long-term memories. Neuroanatomical projections of brain areas.Investigation of neuroimmune and neuroendocrine interactions. Spatial navigation.Dr. Fiona LyddyThe psychology of language and memory. Connectionist models of language processing.Development of working memory and language. Reading and biliteracy. Bilingualism andphonological awareness.Dr. Richard RocheNeuroscience of Learning and Memory. Spatial Memory and Navigation. Consolidationand Reconsolidation. Memory and Ageing. Human Electrophysiology. Response Inhibition.Sustained Attention. Traumatic Brain Injury. Visual Search.Mental Health and Health Care:Dr. Deirdre DesmondPsychosocial adjustment to illness and disability. Rehabilitation. Stress, coping and positivemeaning in chronic illness. Pain (in particular, post-amputation). Body image and disfigurement.Dr. Sinéad McGillowayThe psychological aspects and community context of health care and social problems. Childand adult mental health. Research evaluation. The health and social care needs of sociallyexcluded people. Employment and social integration for people with mental health problemsand learning disabilities.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06PSYCHOLOGY111

Research GrantsNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 PSYCHOLOGY‘Contextual control in conditional discriminations.’Spanish Ministry of Science and Technology,€16,000 (D. Barnes-Holmes and L. Perez-Gonzalez,2003-2006).‘The acquisition and maintenance of laboratoryinducedhuman fear: Developing a relational framemodel.’ Irish Research Council for the Humanitiesand Social Sciences (IRCHSS), €38,100 (S. Smythand D. Barnes-Holmes, 2003-2006).‘Behavioural and psycho-physiological responses toinduced emotional arousal: Acceptance and controlbasedstrategies.’Irish Research Council for theHumanities and Social Sciences (IRCHSS), €38,100(A. Cochrane and D. Barnes-Holmes, 2004-2007).‘Cognitive Defusion as a Coping Strategyfor Negative Self-Referential Thoughts: AnExperimental Analysis.’ Irish Research Councilfor the Humanities and Social Sciences (IRCHSS),€25,400.00 (not including university fees) (C. Keogh,D. Barnes-Holmes and Y. Barnes-Holmes, 2005-2007)‘Derived Stimulus Relations versus ClassicalConditioning: Developing a Model of Fear Acquisitionand Maintenance using the Implicit Association Testand Event Related Potentials.’ NUI, Maynooth, Johnand Pat Hume Postgraduate Scholarship €15,000.00(C O’Toole and D. Barnes-Holmes, 2005-2008,).‘Psychological Acceptance and Relaxation as CopingStrategies: An Experimental Analysis.’ Irish ResearchCouncil for the Humanities and Social Sciences(IRCHSS), €38,100.00 (C. Wilson, D. Barnes-Holmesand Y. Barnes-Holmes, 2005-2008).‘Analysing Verbal Relations in Forming DestructiveExperiential Avoidance and in Altering it ThroughACT Methods.’ Spanish Ministry of Education andScience, Programme I+D (SEJ-05-05845/PSY),€33,677.00 (D. Barnes-Holmes and Y. Barnes-Holmes, Collaborating Partner, 2005-2008).‘Behavioural and electrophysiological examinationof cue-based associations acquired during thelearning phase of a spatial navigation task.’ IrishResearch Council for Science, Engineering andTechnology (IRCSET) Postgraduate ResearchScholarship, €57,150 (D. Harvey and S. Commins,2004-2007).‘Behavioural examination of cue-based associationsduring long-term retention of a spatial navigationtask.’ Irish Research Council for the Humanities andSocial Sciences (IRCHSS) Postgraduate ResearchScholarship, €57,000 (A-M.T. McGauran and S.Commins, 2004-2007).‘Neural bases of spatial learning and memoryin humans.’ Irish Research Council for Science,Engineering and Technology (IRCSET) PostgraduateResearch Scholarship, €57,150 (J. Murphy, R.A.P.Roche and S. Commins, 2005-2008).‘Irish-English Bi-literacy.’ An Chomhairle umOideachas Gaeltachta & Gaelscolaíochta, €36,000 (F.Lyddy, 2005-2008).‘Health promotion in palliative care: identifying andresponding to attitudinal barriers to service use.’The Health Research Board and the Irish HospiceFoundation under the Building Partnerships for aHealthier Society Research Awards 2005, €117,000(S. McGilloway, J. Fleming, P. Doorley and M.Donnelly, 2006-2007).‘Identifying and connecting detainees with a mentalillness to appropriate health and social services.’ TheNHS National R&D Programme on Forensic MentalHealth (UK), €222,400 (M. Donnelly, S. McGilloway,R. McClelland, F. Browne and D. Scott, 2004-2007).The ‘hidden costs’ of sexual violence: A multidimensionalapproach to the impact and experienceof trauma.’ Irish Research Council for the Humanitiesand Social Sciences (IRCHSS), €12,700 (C. Kelleherand S. McGilloway, 2005-2006).112

Publications inRefereed Journals‘An evaluation of bereavement support services inhospice.’ The Irish Hospice Foundation, €26,000 (A.Roberts and S. Mc Gilloway, 2004-2006).‘A pilot evaluation of the ‘Incredible Years’ programin Ireland.’ The Clondalkin Partnership, €4,650 (S.McGilloway and C. Kelleher, 2005).‘Behavioural and electrophysiological sequelae ofstress during memory encoding, consolidation andreconsolidation.’ Irish Research Council for Science,Engineering and Technology (IRCSET) PostgraduateResearch Scholarship, €57,150 (J. Moore and R.A.P.Roche, 2005-2008)Murphy, C., D. Barnes-Holmes and Y. Barnes-Holmes. ‘Derived manding in children with autism:Synthesizing Skinner’s Verbal Behavior withrelational frame theory.’ Journal of Applied BehaviorAnalysis, 38, 445-462 (2005).O’Hora, D., D. Barnes-Holmes and D. Pelaez. ‘Derivedrelational responding and performance on theverbal subtests of the WAIS III.’ The PsychologicalRecord, 55, 155-175 (2005).Smeets, P.M. and D. Barnes-Holmes. ‘Establishingequivalence classes in preschool children withone-to-many and many-to-one training protocols.’Behavioural Processes, 69, 281-293 (2005).Smeets, P.M. and D. Barnes-Holmes. ‘Auditory-visualand visual-visual equivalence relations in children.’The Psychological Record, 55, 483-503 (2005).Reilly, T., D. Barnes-Holmes and R. Whelan.‘The effects of training structure on the latencyof responses to a five-term linear chain.’ ThePsychological Record, 55, 233-249 (2005).Barnes-Holmes, D., M. Rodriguez Valverde andR. Whelan. ‘Relational frame theory and theexperimental analysis of human language andcognition.’ Latin American Journal of Psychology(Special Issue on Behavior Analysis of Languageand Cognition), 37, 255-276 (2005).Carpentier, F., D. Barnes-Holmes and P.M. Smeets.‘Matching compound samples with unitarycomparisons: The interchangeability of stimulusterms.’ Latin American Journal of Psychology(Special Issue on Behavior Analysis of Languageand Cognition), 37, 317-332 (2005).Barnes-Holmes, D. ‘Behavioral pragmatism isa-ontological not antirealist: A reply to Tonneau.’Behavior and Philosophy, 33, 67-79 (2005).Barnes-Holmes, D., Y. Barnes-Holmes, S. Commins,S. Dymond, P.M. Smeets, C. Staunton, I. Stewart, D.Walsh and R. Whelan. ‘Derived stimulus relations,semantic priming, and event-related potentials:Testing a behavioral theory of semantic networks.’Journal of the Experimental Analysis of Behavior,84, 417-434 (2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06PSYCHOLOGY113

Publications in Refereed JournalsC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 PSYCHOLOGYBarnes-Holmes, D., Y. Barnes-Holmes, S. Commins,S. Dymond, D. Regan, P. M. Smeets, I. Stewart, D.Walsh and R. Whelan. ‘Relating derived relations asa model of analogical reasoning: Reaction times andevent related potentials.’ Journal of the ExperimentalAnalysis of Behavior, 84, 435-452 (2005).Roche, R.A.P., S. Commins, M.A. Mangaoangand S.M. O’Mara. ‘Hippocampal contributions toneurocognitive mapping in humans: A new model.’Hippocampus, 15, 622-641 (2005).Craig, S. and S. Commins. ‘Interaction betweenpaired-pulse facilitation and long-term potentiationin the projection from hippocampal area CA1 to theentorhinal cortex.’ Neuroscience Research, 53, 140-146 (2005).Shaw, K.N., S. Commins and S.M. O’Mara.‘Cyclooxygenase Inhibition Attenuates Endotoxin-Induced Spatial Learning Deficits, But Not anEndotoxin-Induced Blockade Of Long-TermPotentiation.’ Brain Research, 1038, 231-237 (2005).Craig, S., L. Cunningham, L. Kelly and S. Commins.‘Long-term retention and overshadowing of proximaland distal cues following habituation in an objectexploration task.’ Behavioural Processes, 68 (2),117-128 (2005).McGauran, A-M.T., S. Commins and S.M. O’Mara.‘Vestibular influence on water maze retention:transient whole body rotations improve the accuracyof the cue-based retention strategy.’ BehaviouralBrain Research, 158, 183-187 (2005).Roche, R.A.P., S. Commins, M.A. Mangaoangand S.M. O’Mara. ‘Hippocampal contributions toneurocognitive mapping in humans: A new model.’Acta Neurobiologiae Experimentalis, 65, 83 (2005).Desmond, D.M. and M. MacLachlan. ‘Copingstrategies as predictors of psychosocial adaptation tolower limb amputation.’ Social Science & Medicine,(Epub ahead of print; Jun 27 2005).Desmond, D.M. and M. MacLachlan. ‘The factorstructure of the Hospital Anxiety and DepressionScale in older individuals with acquiredamputations: A comparison of 4 models usingconfirmatory factor analysis.’ International Journalof Geriatric Psychiatry, 20, 344-349 (2005).Desmond, D.M. and M. MacLachlan. ‘The factorstructure of the Trinity Amputation and ProsthesisExperience Scales (TAPES) with individuals withacquired upper limb amputations.’ American Journalof Physical Medicine & Rehabilitation, 84,506-513(2005).Lyddy, F., B. O’Loinsigh and C. Parsons. ‘The Stroopinterference effect: Its use in the study of biliteracy.’The Irish Psychologist, 31 (10), 294 (2005).Munro, S., M.J. Ball, M. Duckworth, F. Lyddy andN. Muller. ‘Phonological acquisition in Welsh-English bilingual children.’ Journal of MultilingualCommunication Disorders, 3, (1), 24-49 (2005).Lyddy, F. ‘Social values, science and technology inEurope.’ The Irish Psychologist, 32 (2), 36-41 (2005).114Harvey, D. and S. Commins. ‘Acquisition of spatialrelations between the distal cues and the platform’slocation occurs during locomotion in the Morriswater maze.’ Acta Neurobiologiae Experimentalis,65, 52 (2005).McGauran, A-M.T. and S. Commins. ‘The cue-platformassociation in the water maze task builds upgradually during locomotion and not whilst on theplatform.’ Acta Neurobiologiae Experimentalis, 65,64 (2005).Lyddy, F. ‘Celtic biliteracy.’ Literacy Today, 12,(June 2005).Lyddy, F., B. O’Loinsigh and C. Parsons. ‘Readingprocesses in Irish-English bilinguals: Evidence fromthe Stroop interference effect.’ In Learning to Read:Reading to Learn, edited by Kennedy, E. and Hickey,T.M., Reading Association of Ireland, Dublin, 90-99(2005).Lyddy, F. ‘Dyslexia, reading and the brain.’ The IrishPsychologist, 32 (5-60), 145-146 (2005).

McGilloway, S. and C. Kelleher. ‘Work-related stressamong flight attendants.’ Flight Safety Foundation(Cabin Crew Safety), 40 (6) (2005).McGilloway, S. and C. Kelleher. ‘IncredibleYears in Ireland: a pilot evaluation of the ParentTraining (BASIC) program.’ Dublin: The ClondalkinPartnership (2005).McGilloway, S. and S. Gallagher. ‘Experience ofCritical Incidents and their impact on health andwell-being.’ Psychology and Health, 20 (1), 88(2005).McGilloway, S. and M. O’Donoghue. ‘The mentalhealth consequences of spontaneous miscarriage.’Proceedings of the British Psychological Society,13 (2), 230 (2005).McGilloway, S. and B. Aylward. ‘Mental health andpsychosocial well-being in a student population.’Proceedings of the British Psychological Society,13 (2), 230 (2005).McGilloway, S., C. Kelleher and S. McDonnell.‘They don’t come with a handbook”: Irish parents’experience of an innovative parent trainingprogram.’ The Irish Psychologist, 32 (4), 107 (2005).McGilloway, S. and M. O’Donoghue. ‘Losing ababy: The psychological impact and experienceof miscarriage.’ The Irish Psychologist, 32 (4), 110(2005).McGilloway, S. and G. Scanlon. ‘Special educationalprovision for children with special needs inmainstream education: A Professional Perspective.’The Irish Psychologist, 32 (4), 116-117 (2005).Roche, B., K. Hand, M. O’Riordan and M. Ruiz. ‘Arelational frame approach to the psychologicalassessment of sex offenders.’ In Viewing ChildPornography on the Internet: Understanding theOffence, managing the Offender, and Helping theVictims, edited by Taylor, M. and Quayle, E., Dorset:Russell House Publishing, pp109-125 (2005).Dymond, S., R. Rhefeldt and B. Roche. ‘RelationalFrame Theory and the transformation of stimulusfunctions.’ Revista Latinamericana De Psicologia,37(2), 291-303 (2005).Roche, B., S. Coyle, C. Markham, G. McDarby and T.Ward. ‘Near-infrared Spectroscopy as an instrumentfor the measurement of general autonomic arousal.’The Behavior Analyst Today, 6, 121-127 (2005).Roche, R.A.P., J. J. Foxe, H. Garavan and S.M. O’Mara.‘Individual differences discriminate event-relatedpotentials but not performance during responseinhibition.’ Experimental Brain Research, 160, 60-70(2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06PSYCHOLOGY115

Conference ProceedingsNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 PSYCHOLOGYWhelan, R., D. Barnes-Holmes and D. Walsh.‘Interfacing Visual Basic with peripheral devices:EEG acquisition equipment, square wavestimulators, and eye-trackers.’ Paper presentedduring the symposium, Expanding the Boundariesof Behavior Analysis with Advances in ComputerTechnology, at the 31 st Annual Convention of theAssociation for Behavior Analysis, Chicago, USA(27-31 May 2005).Gutierrez, O., D. Barnes-Holmes, Y. Barnes-Holmesand C. Luciano-Soriano. ‘Paradoxical effectsof thought suppression through equivalenceclasses.’ Paper presented during the symposium,Investigating Acceptance and Control, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA (27-31 May 2005).Cochrane, A., D. Barnes-Holmes, Y. Barnes-Holmesand I. Stewart. ‘Developing a behavioral approachtask to examine acceptance- versus control-basedstrategies.’ Paper presented during the symposium,Investigating Acceptance and Control, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA (27-31 May, 2005).Kehoe, A., Y. Barnes-Holmes, D. Barnes-Holmes andI. Stewart. ‘The effects of acceptance- and controlbasedcoping strategies on tolerance for radiantheat pain.’ Paper presented during the symposium,Investigating Acceptance and Control, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA. (27-31 May, 2005).McMullen, J., D. Barnes-Holmes, Y. Barnes-Holmesand I. Stewart. ‘Acceptance-based strategies and paintolerance: The role of rule-following and relationalcoherence.’ Paper presented during the symposium,Investigating Acceptance and Control, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA (27-31 May, 2005).Chan, G.G., D. Barnes-Holmes and Y. Barnes-Holmes. ‘The implicit association test and relationalframe theory: A behavioral approach to socialbehavior.’ Paper presented during the symposium,Methodologies for Exploring Derived StimulusRelations, at the 31 st Annual Convention of theAssociation for Behavior Analysis, Chicago, USA(27-31 May, 2005).Van Wijnen, Y., D. Barnes-Holmes, Y. Barnes-Holmesand I. Stewart. ‘The implicit association test as ameasure of implicit parental attitudes towardstheir children with autism versus siblings.’ Paperpresented during the symposium, Methodologiesfor Exploring Derived Stimulus Relations, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA (27-31 May, 2005).Milne, R., D. Barnes-Holmes, Y. Barnes-Holmesand I. Stewart. ‘Measures of attitudes using the IATand IREP.’ Paper presented during the symposium,Methodologies for Exploring Derived StimulusRelations, at the 31 st Annual Convention of theAssociation for Behavior Analysis, Chicago, USA(27-31 May, 2005).Ninness, C., D. Barnes-Holmes, S. Ninness andR. Rumph. ‘Transformation of mathematical andstimulus functions: The value of elegance.’ Paperpresented during the symposium, Conceptual andEmpirical Analysis of Complex Verbal Behavior, atthe 31 st Annual Convention of the Association forBehavior Analysis, Chicago, USA (27-31 May, 2005).Hayden, E., D. Barnes-Holmes, Y. Barnes-Holmesand I. Stewart. ‘The implicit relational evaluationprocedures (IREP) and event related potentials:Developing a methodology for assessing previouslyestablished relational frames.’ Paper presentedduring the symposium, Derived RelationalResponding and the Implicit Association Test, atthe 31 st Annual Convention of the Association forBehavior Analysis, Chicago, USA (27-31 May, 2005).116

Barnes-Holmes, D, Y. Barnes-Holmes, S. Dymond, I.Stewart and R. Whelan. ‘A derived relations modelof the implicit association test: Reaction times andevent related potentials.’ Paper presented duringthe symposium, Derived Relational Respondingand the Implicit Association Test, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).O’Toole,C., D. Barnes-Holmes, Y. Barnes-Holmes, S.Smyth and I. Stewart. ‘Derived relational responding,the implicit association test, and event relatedpotentials: A possible model of the verbal processesinvolved in the IAT effect.’ Paper presented duringthe symposium, Derived Relational Respondingand the Implicit Association Test, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).Smyth, S. and D. Barnes-Holmes. ‘A behavioranalyticinvestigation of expectancy bias:Developing a relational frame exploration of“expectancy” functions model of irrational fears.’Paper presented during the symposium, DerivedRelations and Psychopathology, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).Coogan, F., D. Barnes-Holmes and Y. Barnes-Holmes. ‘Exploring experiential avoidance throughderived stimulus relations.’ Paper presentedduring the symposium, Derived Relations andPsychopathology, at the 31 st Annual Convention ofthe Association for Behavior Analysis, Chicago, USA(27-31 May, 2005).Cunningham, L., D. Barnes-Holmes and Y. Barnes-Holmes. ‘Experiential avoidance and deficitsin autobiographical memory.’ Paper presentedduring the symposium, Derived Relations andPsychopathology, at the 31 st Annual Convention ofthe Association for Behavior Analysis, Chicago, USA(27-31 May, 2005).Smyth, S. and D. Barnes-Holmes. ‘Implicitassociations and self-reports: The roleof instructions.’ Paper presented duringthe symposium, Derived Relations andPsychopathology, at the 31 st Annual Convention ofthe Association for Behavior Analysis, Chicago, USA(27-31 May, 2005).Smyth, S., D. Barnes-Holmes, Y. Barnes-Holmes,L. Harvey and F. O’Neill. ‘Assessing emotive andnon-emotive A-B transfer effects using respondentand matching-to-sample training procedures.’ Paperpresented during the symposium, What Exactly Arethe Associations in the Implicit Association Test?,at the 31 st Annual Convention of the Association forBehavior Analysis, Chicago, USA (27-31 May, 2005).Smyth, S., D. Barnes-Holmes, Y. Barnes-Holmes,M. Dillon and S. Doran. ‘Assessing emotive andnon-emotive B-A symmetry transfer effectsusing respondent and matching-to-sampletraining procedures.’ Paper presented during thesymposium, What Exactly Are the Associations inthe Implicit Association Test?, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).Smyth, S., D. Barnes-Holmes, Y. Barnes-Holmes,G. O’Malley and L. Woods. ‘Assessing emotiveand non-emotive A-C transitivity transfer effectsusing respondent and matching-to-sampletraining procedures.’ Paper presented during thesymposium, What Exactly Are the Associations inthe Implicit Association Test?, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).Smyth, S., D. Barnes-Holmes, Y. Barnes-Holmes andS. Furney. ‘Assessing emotive and non-emotive C-Aequivalence transfer effects using respondent andmatching-to-sample training procedures.’ Paperpresented during the symposium, What Exactly Arethe Associations in the Implicit Association Test?,at the 31 st Annual Convention of the Association forBehavior Analysis, Chicago, USA (27-31 May, 2005).Moore, H., D. Barnes-Holmes, Y. Barnes-Holmes andI. Stewart. ‘Acceptance and personal values in thecontext of aversive stimulation.’ Paper presentedduring the symposium, Analysis of Verbal Processesin Clinical Values Methods, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06PSYCHOLOGY117

Conference ProceedingsC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 PSYCHOLOGYLuciano-Soriano, C., D. Barnes-Holmes, Y. Barnes-Holmes, O. Gutierrez, Y. Molina, M. Rodriguez-Valverde and K. Wilson. ‘Coordination andopposition relations between aversive private eventsand evaluated actions: An experimental preparation.’Paper presented during the symposium, Analysisof Verbal Processes in Clinical Values Methods, atthe 31 st Annual Convention of the Association forBehavior Analysis, Chicago, USA (27-31 May, 2005).Barnes-Holmes, D., Y. Barnes-Holmes, S. Commins,S. Dymond, P.M. Smeets, C. Staunton, D. Walsh andR. Whelan. ‘Equivalence relations and semanticpriming: A preliminary behavior-analytic modelof semantic networks.’ Paper presented duringthe symposium, Behavior Analysis and theNeuroscience of Language and Cognition: SemanticPriming and Derived Stimulus Relations, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA (27-31 May, 2005).Ryan, E.J., D. Barnes-Holmes, S. Dymond andR.Whelan. ‘Visual-visual equivalence relationsand semantic priming: A behavioral and eventrelated potentials study.’ Paper presented duringthe symposium, Behavior Analysis and theNeuroscience of Language and Cognition: SemanticPriming and Derived Stimulus Relations, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA (27-31 May, 2005).Garner, K., D. Barnes-Holmes, S. Dymond, E. J.Ryan and R. Whelan. ‘Auditory-visual equivalencerelations and semantic priming.’ Paper presentedduring the symposium, Behavior Analysis and theNeuroscience of Language and Cognition: SemanticPriming and Derived Stimulus Relations, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA (27-31 May, 2005).Power, L., D. Barnes-Holmes and I. Stewart. ‘Stimulusequivalence, transitivity and non-arbitrary relations.’Paper presented during the symposium, DerivedRelational Responding and Non-Arbitrary Relations,at the 31 st Annual Convention of the Association forBehavior Analysis, Chicago, USA (27-31 May, 2005).Casserly, M., D. Barnes-Holmes and I. Stewart.‘Stimulus equivalence, non-arbitrary relations andnon-arbitrary training.’ Paper presented duringthe symposium, Derived Relational Respondingand Non-Arbitrary Relations, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).Kenny, N., D. Barnes-Holmes and I. Stewart.‘Exploring the interfering effects of non-arbitraryrelations on derived relational responding inchildren with a diagnosis of autism: A possiblebehavioral methodology for assessing executivefunction.’ Paper presented during the symposium,Derived Relational Responding and Non-ArbitraryRelations, at the 31 st Annual Convention of theAssociation for Behavior Analysis, Chicago, USA(27-31 May, 2005).Kelly, G., D. Barnes-Holmes and I. Stewart. ‘Anempirical investigation of contextual controlover non-arbitrary relational responding.’ Paperpresented during the symposium, Derived RelationalResponding and Non-Arbitrary Relations, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA (27-31 May, 2005).Lyons, M., D. Barnes-Holmes and Y. Barnes-Holmes.‘Comparing the IAT and MTS as methods formeasuring pre-experimentally established verbalrelations.’ Paper presented during the symposium,Derived Relations, Implicit Associations, andClinically-Relevant Stimuli, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).Ward, M., D. Barnes-Holmes and Y. Barnes-Holmes.‘Implicit associations and food-related stimuli.’Paper presented during the symposium, DerivedRelations, Implicit Associations, and Clinically-Relevant Stimuli, at the 31 st Annual Convention ofthe Association for Behavior Analysis, Chicago, USA(27-31 May, 2005).118

Quinlan, J., D. Barnes-Holmes and Y. Barnes-Holmes.‘Equivalence relations, self-evaluations and selfesteem.’Paper presented during the symposium,Derived Relations, Implicit Associations, andClinically-Relevant Stimuli, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).Rodriguez-Valverde, M., D. Barnes-Holmes and C.Luciano-Soriano. ‘Transfer of respondent elicitationestablished through aversive conditioning.’ Paperpresented during the symposium, Derived Relations,Implicit Associations, and Clinically-RelevantStimuli, at the 31 st Annual Convention of theAssociation for Behavior Analysis, Chicago, USA(27-31 May, 2005).Mesa Manjon, H., D. Barnes-Holmes and S.Gomez Martin. ‘Analogy between multiplestimulusrelations, respondent-type training andtransformation of functions: New paths in RFTresearch on analogy.’ Paper presented during thesymposium, Relational Frame Theory Research onAnalogical Reasoning and Coherence, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA (27-31 May, 2005).Coyne, S., D. Barnes-Holmes and I. Stewart.Equivalence-equivalence and transfer of function:Further investigations. Paper presented during thesymposium, Relational Frame Theory Research onAnalogical Reasoning and Coherence, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA (27-31 May, 2005).Lopez Rios, F., D. Barnes-Holmes, S. Gomez Martinand H. Mesa Manjon. ‘A transformation of aversiveand reinforcing functions based on analogy.’ Paperpresented during the symposium, Relational FrameTheory Research on Analogical Reasoning andCoherence, at the 31 st Annual Convention of theAssociation for Behavior Analysis, Chicago, USA(27-31 May, 2005).Garro Espin, M.J., D. Barnes-Holmes and S. GomezMartin. ‘Relational frame theory and coherence: Anexperimental approach.’ Paper presented during thesymposium, Relational Frame Theory Research onAnalogical Reasoning and Coherence, at the 31 stAnnual Convention of the Association for BehaviorAnalysis, Chicago, USA (27-31 May, 2005).McHugh, L., D. Barnes-Holmes, Y. Barnes-Holmes, S.Dymond, I. Stewart and R. Whelan. ‘An event relatedpotentials measure of false belief understandingas generalized operant behavior.’ Paper presentedduring the symposium, Overcoming Core Deficits inAutism Spectrum Disorders: Stimulus Overselectivityand Perspective-Taking, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).Murphy-Ball, C., D. Barnes-Holmes and Y. Barnes-Holmes. ‘Derived transfer of more/less relationalmand functions in three children diagnosed withautism.’ Paper presented during the symposium,Relational Frame Theory and Education for Childrenwith Autism, at the 31 st Annual Convention of theAssociation for Behavior Analysis, Chicago, USA(27-31 May, 2005).Egan, C.E. and D. Barnes-Holmes. ‘Comparing theacquisition of mands and tacts with generalizedreinforcement, and tacts with differentialreinforcement.’ Paper presented during thesymposium, Relational Frame Theory and Educationfor Children with Autism, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).Sweeney, C. and D. Barnes-Holmes. ‘Teachingnegotiation skills to young children.’ Paperpresented during the symposium, Relational FrameTheory and Education for Children with Autism, atthe 31 st Annual Convention of the Association forBehavior Analysis, Chicago, USA (27-31 May, 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06PSYCHOLOGY119

Conference ProceedingsC O N T I N U E D120NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 PSYCHOLOGYBarnes-Holmes D., Y. Barnes-Holmes, S. Dymond,I. Stewart and R. Whelan. ‘Electrophysiologicalmeasures of derived stimulus relations: What canthey tell us about behavior that we did not alreadyknow?’ Paper presented during the symposium,Studying the Neural Substrates of EquivalenceClasses and Derived Relations, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).Dickens, D., D. Barnes-Holmes, Y. Barnes-Holmes,A. Mayes, D. Montaldi and N. Roberts. ‘Onneuroimaging derived relations.’ Paper presentedduring the symposium, Studying the NeuralSubstrates of Equivalence Classes and DerivedRelations, at the 31 st Annual Convention of theAssociation for Behavior Analysis, Chicago, USA(27-31 May, 2005).Barnes-Holmes, Y. and D. Barnes-Holmes.‘Investigating the role of perspective-takingin human psychopathology: A relational frameanalysis.’ Paper presented during the symposium,Relational Frame Theory and Perspective-Takingin Human Psychopathology, at the 31 st AnnualConvention of the Association for Behavior Analysis,Chicago, USA (27-31 May, 2005).Luciano-Soriano, C., D. Barnes-Holmes, Y. Barnes-Holmes, O. Gutierrez, F. Molina, M. Paez, M.Rodriguez-Valverde and M.S. Valdivia Salas. ‘Verbalprocesses underlying some defusion/perspectivetakingmethods: Clinical-experimental preparations.’Paper presented during the symposium, RelationalFrame Theory and Perspective-Taking in HumanPsychopathology, at the 31 st Annual Convention ofthe Association for Behavior Analysis, Chicago, USA(27-31 May, 2005).O’Connor, J., D. Barnes-Holmes and Y. Barnes-Holmes. ‘Establishing flexibility in responding tocontextually controlled symmetry and asymmetrytasks in young children with autism’. Paperpresented during the symposium, DerivedRelational Responding: Implications for ClinicallyRelevant Behavior, at the 31 st Annual Convention ofthe Association for Behavior Analysis, Chicago, USA(27-31 May, 2005).McGuinness, R., D. Barnes-Holmes and Y. Barnes-Holmes. ‘Using protocols of relational respondingto analyze perspective-taking and relatedrepertoires in children with Asperger’s syndrome.’Paper presented during the symposium, DerivedRelational Responding: Implications for ClinicallyRelevant Behavior, at the 31 st Annual Convention ofthe Association for Behavior Analysis, Chicago, USA(27-31 May, 2005).Roche, B., D. Barnes-Holmes, Y. Barnes-Holmesand I. Stewart. ‘The implicit relational evaluationprocedure as a methodology for examiningself-related terms.’ Paper presented during thesymposium, Derived Relational Responding:Implications for Clinically Relevant Behavior, atthe 31 st Annual Convention of the Association forBehavior Analysis, Chicago, USA (27-31 May, 2005).Power, L., D. Barnes-Holmes and I. Stewart. ‘Theeffect of transitivity testing on the emergenceof stimulus equivalence in a context involvingcompetition between arbitrarily applicable andnon-arbitrary relational control.’ Paper presentedduring the Symposium, Derived Relations, atthe 2 nd Conference of the European Associationfor Behaviour Analysis, Gdansk, Poland (6 - 9September, 2005)Kelly, G., D. Barnes-Holmes and I. Stewart.‘Demonstrating complex contextual control overnon-arbitrary relational responding.’ Paperpresented during the Symposium, Derived Relations,at the 2 nd Conference of the European Associationfor Behaviour Analysis, Gdansk, Poland (6 - 9September, 2005)Ryan, E., D. Barnes-Holmes, S. Dymond and R.Whelan. ‘Equivalence relations and semanticpriming: A behavioural and event related potentialsstudy.’ Paper presented during the Symposium,Behaviour Analysis and the Neuroscience ofLanguage and Cognition: Derived StimulusRelations, Semantic Priming, and Perspective-Taking, at the 2 nd Conference of the EuropeanAssociation for Behaviour Analysis, Gdansk, Poland(6 - 9 September, 2005)

McHugh, L., D. Barnes-Holmes, Y. Barnes-Holmes, S. Dymond, I. Stewart and R. Whelan. ‘Aneurophysiological investigation of perspectivetakingas derived relational responding.’ Paperpresented during the Symposium, BehaviourAnalysis and the Neuroscience of Languageand Cognition: Derived Stimulus Relations,Semantic Priming, and Perspective-Taking, atthe 2 nd Conference of the European Associationfor Behaviour Analysis, Gdansk, Poland (6 - 9September, 2005)Dymond ,S., D. Barnes-Holmes, B. Roche andR. Whelan. ‘The transformation of respondenteliciting and extinction functions in accordancewith sameness and opposition.’ Paper presentedduring the Symposium, Further advances inresearch on derived relational responding andthe transformation of stimulus functions, atthe 2 nd Conference of the European Associationfor Behaviour Analysis, Gdansk, Poland (6 - 9September, 2005)Arntzen, E., D. Barnes-Holmes and Y. Barnes-Holmes.‘Behaviour-analytic and cognitive approachesto concept formation: From concepts to conceptlearning.’ Paper presented during the Symposium,Conceptual Issues, at the 2 nd Conference of theEuropean Association for Behaviour Analysis,Gdansk, Poland (6 - 9 September, 2005)Barnes-Holmes, D., Y. Barnes-Holmes, C. O’Toole, S.Smyth and I. Stewart. ‘Derived relational responding,the implicit association test, and event relatedpotentials.’ Paper presented during the symposium,Behavioural Analyses of Human Language andCognition, at the 36 th Annual Conference of thePsychological Society of Ireland, Derry, NorthernIreland (17-20 November, 2005).Stewart, I., D. Barnes-Holmes and L. Power. ‘Theeffect of transitivity testing on the emergence ofstimulus equivalence.’ Paper presented duringthe symposium, Behavioural Analyses of HumanLanguage and Cognition, at the 36 th AnnualConference of the Psychological Society of Ireland,Derry, Northern Ireland (17-20 November, 2005).Stewart, I., D. Barnes-Holmes and G. Kelly.‘Demonstrating complex contextual control overnon-arbitrary relational responding.’ Paperpresented during the symposium, DerivedRelational Responding and Complex HumanBehavior, at the 36 th Annual Conference of thePsychological Society of Ireland, Derry, NorthernIreland (17-20 November, 2005).Smyth, S., D. Barnes-Holmes and Y. Barnes-Holmes.‘Associations or derived relations: Testing anassociative account of generative human learning.’Paper presented during the symposium, DerivedRelational Responding and Complex HumanBehavior, at the 36 th Annual Conference of thePsychological Society of Ireland, Derry, NorthernIreland (17-20 November, 2005).Barnes-Holmes, D., Y. Barnes-Holmes, R. Milneand I. Stewart. ‘The implicit relational assessmentprocedure (IRAP): Measuring attitudes to autismamong professionals with differing levels ofexperience working with autistic spectrum disorder.’Paper presented during the symposium, DerivedRelational Responding and Complex HumanBehavior, at the 36 th Annual Conference of thePsychological Society of Ireland, Derry, NorthernIreland (17-20 November, 2005).Cochrane, A., D. Barnes-Holmes, Y. Barnes-Holmes and I. Stewart. ‘A behavioral approachtask to examine acceptance- versus control-basedstrategies.’ Paper presented during the symposium,Derived Relational Responding and ComplexHuman Behavior, at the 36 th Annual Conference ofthe Psychological Society of Ireland, Derry, NorthernIreland (17-20 Novemeber, 2005).Keogh, C., D. Barnes-Holmes and Y. Barnes-Holmes.‘Analyzing the impact of cognitive defusion asa coping intervention for negative self-relevantthoughts.’ Paper presented during the symposium,Counselling Research Papers, at the 36 th AnnualConference of the Psychological Society of Ireland,Derry, Northern Ireland (17-20 November, 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06PSYCHOLOGY121

Conference ProceedingsC O N T I N U E D122NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 PSYCHOLOGYBarnes-Holmes, D. ‘Relational Frame Theory: Amodern behavioral approach to human languageand cognition.’ A two and a half day workshopdelivered to Trainee Clinical Psychologists inthe Department of Personality, Assessment andTreatment Psychology, University of Almeria,Almeria, Spain (4-6 April, 2005).Barnes-Holmes, D., Y. Barnes-Holmes and I. Stewart.‘An introduction to RFT for clinicians.’ A half-dayworkshop delivered during the ACT SummerInstitute II, La Salle University, Philadelphia, USA(18-22 July, 2005).Barnes-Holmes, D., Y. Barnes-Holmes, E.J. Fox, J.McElwee and I. Stewart. ‘Early intensive behavioralintervention and relational frame theory.’ A halfdayworkshop delivered during the ACT SummerInstitute II, La Salle University, Philadelphia, USA(18-22 July, 2005).Barnes-Holmes, D., Y. Barnes-Holmes and C.Luciano-Soriano. ‘ACT methods and possibleprocesses involved in the transformation offunction.’ A half-day workshop delivered duringthe ACT Summer Institute II, La Salle University,Philadelphia, USA (18-22 July, 2005).Barnes-Holmes, D., Y. Barnes-Holmes, R. Merwinand K. Wilson. ‘ACT and “Self”: From basic scienceto case conceptualization and treatment.’ A halfdayworkshop delivered during the ACT SummerInstitute II, La Salle University, Philadelphia, USA(18-22 July, 2005).Barnes-Holmes, D. and S.C. Hayes. ‘Consultation ondeveloping ACT/RFT protocols/research.’ A halfdayworkshop delivered during the ACT SummerInstitute II, La Salle University, Philadelphia, USA(18-22 July, 2005).Barnes-Holmes, D., Y. Barnes-Holmes and I.Stewart. ‘Using RFT to construct new metaphorsand exercises for therapy.’ A half-day workshopdelivered during the ACT Summer Institute II, LaSalle University, Philadelphia, USA (18-22 July,2005).Barnes-Holmes, D. ‘Analogical reasoning in childrenand adults: What does behavioral psychologyhave to offer?’ Invited guest lecture delivered tothe Department of Personality, Assessment andTreatment Psychology, University of Almeria,Almeria, Spain (6 April, 2005).Barnes-Holmes, D. ‘Relational frame theory andanalogical reasoning in children and adults: Canbehavior analysis make an important contribution tothe study of higher cognition?’ Invited annual guestspeaker for the University of Wisconsin-MilwaukeeLecture Series on Behavior Analysis, USA (24 April,2005).Barnes-Holmes, D. ‘Relational frame theory andanalogical reasoning in children and adults: Whatcan behavior analysis teach cognitive psychologistsabout cognition?’ International invited addressdelivered at the 31 st Annual Convention of theAssociation for Behavior Analysis, Chicago, USA(27-31 May, 2005).Barnes-Holmes, D. ‘Developing behavioral models ofhuman language and cognition based on relationalframe theory.’ International invited paper deliveredat the 31 st Annual Convention of the Association forBehavior Analysis, Chicago, USA (27-31 May, 2005).Barnes-Holmes, D. and S.C. Hayes. ‘State of theevidence in ACT and RFT.’ Invited address deliveredduring the ACT Summer Institute II, La SalleUniversity, Philadelphia, USA (18-22 July, 2005).Barnes-Holmes, Y., F. Bond and M. Webster. InvitedPlenary Discussion Leader at the First European ACTInstitute, Bournemouth, U.K (2005).Barnes-Holmes, Y., S. Batten, J. Dahl, C. Luciano-Soriano and R. Walser. Invited Plenary DiscussionLeader at ACT Summer Institute, Philadelphia, USA(2005).Barnes-Holmes, Y. ‘Acceptance and CommitmentTherapy: An Advanced Sills and ExperientialWorkshop’. Workshop presented at the NationalUniversity of Ireland Maynooth, Maynooth, Co.Kildare (2005).

Barnes-Holmes, Y. and M. Webster. ‘An Introductionto Acceptance and Commitment Therapy (ACT)for clinicians.’ Two-day experiential workshoppresented at the First European ACT Institute,Bournemouth, U.K (2005).Barnes-Holmes, Y. ‘An Introduction to RelationalFrame Theory (RFT) for clinicians.’ One-dayworkshop presented at the First European ACTInstitute, Bournemouth, U.K (2005).Barnes-Holmes, Y. ‘Empirical analyses of acceptanceand willingness.’ One-day workshop presented atthe First European ACT Institute, Bournemouth, U.K(2005).Barnes-Holmes, Y. and R. Walser. ‘Live Clients/RolePlays.’ Workshop presented at the ACT SummerInstitute, Philadelphia, USA (2005).Barnes-Holmes, Y. ‘Acceptance and CommitmentTherapy.’ Workshop for the M.A. Behaviour andCognitive Therapies, National University of Ireland,Maynooth (2005).Barnes-Holmes, Y. ‘Case conceptualization andtreatment.’ Workshop for the M.A. Behaviour andCognitive Therapies, National University of Ireland,Maynooth (2005).Barnes-Holmes, Y. ‘Case formulation and diagnosis.’Workshop for the M.A. Behaviour and CognitiveTherapies, National University of Ireland, Maynooth(2005).Barnes-Holmes, Y. ‘Acceptance and CommitmentTherapy: An Introduction.’ Workshop for the BelgianAssociation for Behaviour Therapy, Leuven, Belgium(January 2005).Barnes-Holmes, Y. ‘Acceptance and CommitmentTherapy: An Advanced Workshop.’ Workshop for theBelgian Association for Behaviour Therapy, Leuven,Belgium (January 2005).Roche, R.A.P., S. Commins, M. A. Mangaoangand S. M. O’Mara. ‘Hippocampal contributions toneurocognitive mapping in humans: A new model.’The 37 th Annual General Meeting of the EuropeanBrain and Behaviour Society (EBBS), Dublin, Ireland(September 2005).Harvey, D. and S. Commins. ‘Acquisition of spatialrelations between the distal cues and the platform’slocation occurs during locomotion in the Morriswater maze.’ The 37 th Annual General Meeting ofthe European Brain and Behaviour Society (EBBS),Dublin, Ireland (September 2005).McGauran, A-M.T. and S. Commins. ‘The cueplatformassociation in the water maze task buildsup gradually during locomotion and not whilst onthe platform.’ The 37 th Annual General Meeting ofthe European Brain and Behaviour Society (EBBS),Dublin, Ireland. (September 2005).Desmond, D.M. and M. MacLachlan. ‘Copingstrategies as predictors of psychosocial adaptationto lower limb amputation.’ 19 th Annual Conference ofthe European Health Psychology Society, Galway (31August – 3 September, 2005).Desmond, D.M. and P. Gallagher. ‘Quality ofLife Measures: Generic, condition-specific andindividualised measures of quality of life.’ Invitedpresentation, The Myocelectric Controls Conference:Integrating Prosthetics & Medicine, Fredericton,Canada (15-19 August 2005).Desmond, D.M. and P. Gallagher. ‘The TrinityAmputation and Prosthesis Experience Scales(TAPES).’ Invited presentation, The MyocelectricControls Conference: Integrating Prosthetics &Medicine, Fredericton, Canada (15-19 August 2005).Lyddy, F., H. Ambrose and B. Roche. ‘The effect oflanguage background and task context on wordrecognition in an Irish-English homograph task.’Presented at the Reading Association of IrelandAnnual Conference, Rathmines, Dublin (1 October2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06PSYCHOLOGY123

Conference ProceedingsC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 PSYCHOLOGYLyddy, F., H. Ambrose and B. Roche. ‘Languagecontact and reading skills: The effect of languagebackground and task context on word recognitionin an Irish-English homograph task.’ Presented atLinguistic Diversity: A Joint IRCHSS-CNRS Workshop,University College Cork (5 November 2005).Byrne, S., T. Kelley and F. Lyddy. ‘PhilosophicalPresuppositions in Recent Cognitive Theories ofConcepts within Cognitive Psychology.’ Presentedat the 36 th Annual Conference of the PsychologicalSociety of Ireland, Derry (7 November 2005).Deasy, K. and F. Lyddy. ‘Conversations with acongenitally deafblind individual: A Case Study.’Presented at the 36 th Annual Conference of thePsychological Society of Ireland, Derry (7 November2005).C. Roche-Dwyer and F. Lyddy. ‘Bilingual StroopEffects: Evidence of Stroop Interference in English/Irish Bilinguals.’ Presented at the 36 th AnnualConference of the Psychological Society of Ireland,Derry (7 November 2005).McGilloway, S. ‘Caring for young minds: The role ofHealth Psychology.’ Guest lecture to the Departmentof Psychology, NUI Galway (9 November 2005).McGilloway, S. and S. Gallagher. ‘The impact ofCritical Incident Stress on ambulance personnel- A qualitative perspective.’ The Health PsychologyDivision (PSI) Conference, Trinity College Centre forHealth Sciences, Tallaght Hospital, Dublin (22 April2005).McGilloway, S. and B. Aylward. ‘Mental health andpsychosocial well-being in a student population.’Paper presented at the Annual Conference of theBritish Psychological Society (NI Branch), Portrush,N.Ireland (23-24 April 2005).McGilloway, S. and M. O’Donoghue. ‘The mentalhealth consequences of spontaneous miscarriage.’Paper presented at the Annual Conference of theBritish Psychological Society (NI Branch), Portrush,N.Ireland (23-24 April 2005).McGilloway, S. and S. Gallagher. ‘Experience ofCritical Incidents and their impact on the healthand well-being of Irish ambulance workers.’ Posterpresentation to the 19 th Annual Conference of theEuropean Health Psychology Society, NUI Galway (2September 2005).McGilloway, S., C. Kelleher and S. McDonnell.‘“They don’t come with a handbook”: Irish parents’experience of an innovative parent trainingprogram.’ Paper presented at the 36 th AnnualConference of the Psychological Society of Ireland,Derry, (17-20 November 2005).McGilloway, S. and M. O’Donoghue. ‘Losing ababy: The psychological impact and experience ofmiscarriage.’ Paper presented at the 36 th AnnualConference of the Psychological Society of Ireland,Derry, N. Ireland (17-20 November 2005).McGilloway, S. and G. Scanlon. ‘Special educationalprovision for children with special needs inmainstream education: A Professional Perspective.’Paper presented at the 36 th Annual Conferenceof the Psychological Society of Ireland, Derry, N.Ireland (17-20 November 2005).Roche, B., M. O’Riordan, E. Quayle, M. Ruiz and M.Taylor. ‘A Derived Relations Approach to Screeningtests for Sex-Offenders: An Update.’ Paper presentedat the Annual Conference of the Association forBehavior Analysis, Chicago, USA (May 27-31, 2005)Gavin, A., C. Gormley, B. Roche and M. Ruiz. ‘TheIAT: A Measure of Relational History or Attitudes?’Paper presented at the Annual Conference of theAssociation for Behavior Analysis, Chicago, USA(27-31 May 2005).Brown, K., D. E. Baruch, J. Kanter and B. Roche.‘Talk Therapy or Exposure for Avoidance? Anexperimental comparison of derived versus directresurgence and extinction of laboratory inducedavoidance.’ Paper presented at the AnnualConference of the Association for Behavior Analysis,Chicago, USA (27-31 May 2005).124

Doyle, M., T. O’Donohue and B. Roche. ‘Acceptanceand Pain Tolerance: The role of trait anxiety levels inthe effectiveness of Acceptance-based interventionsfor pain.’ Paper presented at the Annual Conferenceof the Association for Behavior Analysis, Chicago,USA (27-31 May 2005).Melia, R., S. O’Connor and B. Roche. ‘Flex ThoseEmotions! An Emotional Flexibility Interventionfor Experiential Avoidance.’ Paper presented at theAnnual Conference of the Association for BehaviorAnalysis, Chicago, USA (27-31 May 2005).Tyndall, I., J. James and B. Roche. ‘Effects ofEmotional and Neutral Stimulus Functions onthe Emergence of Derived Stimulus Relations.’Paper presented at the Annual Conference of theAssociation for Behavior Analysis, Chicago, USA(27-31 May 2005).O’Connor, S., D. O’Hora and B. Roche. ‘The Questto Raise IQ: Finding Hope in Multiple ExemplarRelational Training.’ Paper presented at the AnnualConference of the Association for Behavior Analysis,Chicago, USA (27-31 May 2005).Ruiz, M., A. Florio, K. Hand and B. Roche.‘Unconscious prejudice: Verbal histories as tools forsensitivity training.’ Paper presented at the thirtiethAnnual Meeting of the Association for Women inPsychology, Florida, USA (February 2005).Linehan,C., D. Delaney, S. McLoone, B. Roche and T.Ward. ‘Behavioural modelling of complexity in onlinecomputer gaming: A derived relations analysis.’Paper presented at the European Association forBehaviour Analysis Convention, Gdansk, Poland (6-9September 2005).Gavin, A., B. Roche and M. Ruiz. ‘What typesof associations are measured by the ImplicitAssociation Test?’ Paper presented at the EuropeanAssociation for Behaviour Analysis Convention,Gdansk, Poland (6-9 September 2005).O’Connor, S., D. O’Hora and B. Roche. ‘Developing apsychological intervention to raise IQ: Contributionsfrom Relational Frame Theory.’ Paper presented atthe European Association for Behaviour AnalysisConvention, Gdansk, Poland (6-9 September 2005).Dymond, S., D. Barnes-Holmes, B. Roche andR. Whelan. ‘The transformation of respondenteliciting and extinction functions in accordancewith sameness and opposition.’ Paper presented atthe European Association for Behaviour AnalysisConvention, Gdansk, Poland (6-9 September 2005).Mullally, S.M., J. Laing, S.M. O’Mara, I.H. Robertsonand R.A.P. Roche. ‘A virtual lesion of the HumanHippocampus: Anteceding n-Back performanceinhibits subsequent hippocampal-dependentmemory function.’ Cognitive Neuroscience SocietyAnnual Meeting, New York, USA (April 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06PSYCHOLOGY125

External Assignments and Public ServiceNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 PSYCHOLOGYProfessor Dermot Barnes-Holmes• Served on the editorial board of The EuropeanJournal of Behavior Analysis.• Served on the editorial board of ThePsychological Record.• Served on the editorial board of TheInternational Journal of Psychology andPsychological Therapy (Associate Editor)• Served on the editorial board of The EuropeanJournal of Psychology.• Served as a Guest Co-Editor for a special issue ofthe Journal of Organizational BehaviorManagement.• Served on the Council of the PsychologicalSociety of Ireland.• Served as Chairperson of the Diploma ReviewGroup for the Psychological Society of Ireland.• Member of the Foundation Committee for theAssociation of Contextual Behavioral Science.Dr. Sean Commins• Reviewer of grant application for the NewZealand Health Research Council 2005.• Reviewer for the journal Neuroscience andPharmacological Research.• Co-ordinator of The 37th Annual GeneralMeeting of the European Brain and BehaviourSociety (24-27 September 2005).• Associate Member, Trinity College Institute ofNeuroscienceDr. Deirdre Desmond• Co-director of the Dublin PsychoprostheticsGroup.• Reviewer of research papers for Disability andRehabilitation, and Archives of Physical Medicineand Rehabilitation.Dr. Sinead McGilloway• Reviewer for Health and Social Care in theCommunity.• External assessor for the Health Research Board(Information Systems to underpin R&D forHealth awards, 2005).• Interviewed on miscarriage and mental health,South East Radio, 24 November 2005.• ‘Study reveals trauma of women who miscarry’.Interview for the Irish Times(Health Supplement), 22 November 2005.• Member of the Irish Forum for Global Health.• Interviewed for the Derry Journal (Sunday issue)on the psychological impact of miscarriage, 19November 2005.Dr. Bryan Roche• Served on the Editorial Board of the EuropeanJournal of Behavior Analysis.Dr. Richard Roche• Manuscript reviewer for the European Journal ofNeuroscience (EJN), Acta Pharmacologica Sinica,Dementia & Geriatric Cognitive Disorders.• Honorary Secretary on the Interim Committee ofNeuroscience Ireland, 2005-2006.126Dr. Fiona Lyddy• Member of the Psychological Society of IrelandCouncil.• Member of the European Federation ofPsychologists’ Associations Standing Committeeon Scientific Affairs.• Editor, The Irish Psychologist.• Review Consultant, The Psychologist.• External examiner for PhD at the University ofWales.

Faculty of ScienceResearch Report 2005-06Research Institutes

Hamilton InstituteNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 RESEARCH INSTITUTESInstitute PersonnelFacultyProf. Jens KalkkuhlProf. Douglas Leith (Director)Prof. William LeitheadDr. Roderick Murray-SmithProf. Barak PearlmutterProf. Robert ShortenProf. Peter WellsteadDr. Fabian WirthResearch FellowsDr. Mehmet AkarDr. Eric BullingerDr. Peter CliffordDr. Ken DuffyDr. John FoyDr. Dimitris KalamatianosDr. Chris KellettDr. David MaloneDr. Oliver MasonDr. Qiang NiDr. Zhendong SunDr. Mark VerwoerdDr. Yunong ZhangResearch StudentsMr. Ian DangerfieldMs. Parisa EslambolchilarMr. Baruch EvenMr. Santiago JaramilloMr. TianJi LiMr. Fiachra MatthewsMr. Simon McCannMr. Keith NeoMr. Anthony NgMr. Paul O’GradyMr. Ross O’NeillMr. Emanuele RagnoliMr. Selim SolmazMr. Rade StanojevichMr. Steven StrachanMr. Carlos VillegasScientific AdvisorsProf. Kumpati Narendra(Yale Univ.)Prof. Abraham Berman (Technion)Prof. Frank Kelly, FRS (Cambridge)Prof. Debasis Mitra(Bell Laboratories)Associate MembersProf. Daniel HeffernanProf. Anthony O’FarrellProf. Ronan ReillyProf. John RingwoodLonger-term VisitorsProf. Abraham Berman (Technion)Prof. Rick Middleton(Newcastle, Australia)Prof. Uriel Rothblum (Technion)AdministratorsMs. Rosemary HuntMs. Kate MoriartyInformation & Enquiries:Prof. Doug LeithDirectorHamilton Institute,National University of IrelandMaynooth,MaynoothCo. Kildare.Tel: +353 1 7086100Fax: +353 1 7086269Email: hamilton@nuim.ieWebsite: http://www.hamilton.ie128

Research OverviewHamilton Institute researchers work at the interfacebetween mathematics and its applications in ICT andBiology. Applications inform the direction of muchof our mathematical work while new understandinggained from theoretical developments feed backinto applications and technology transfer. Theinstitute has strong international links and the seniorstaff have a track record in industry collaboration,technology transfer and company start-up based onscientific IP. Current areas of research include:Communication NetworksCollaborating Organisations: Intel CommunicationsEurope, Cisco Systems, Eircom, University of Limerick,Dublin Institute of TechnologyInternational collaborators: Caltech, Stanford, UCL,Yale, Technion, Intel Research Cambridge.Hybrid Systems: Complex systems involvingdynamics and logicCollaborating Organisations: EU MAC network,Enterprise Ireland, DaimlerChrysler Research,University College DublinInternational Collaborators: Yale University, Technion,NTNU Trondheim, Northeastern University, Universityof Bremen.Systems biology: Systems Understanding ofNeurodegenerative DiseasesCollaborating Organisations: ACImetricsInternational collaborators: University of Rostock,UVM South Korea, Manchester University.Dynamic interaction in human-computer interfacesCollaborating Organisations: Nokia, Samsung,Enterprise Ireland.International collaborators: MIT, Max PlanckTubingen, University of Glasgow, Nokia ResearchMachine Learning & Computational NeuroscienceCollaborating Organisations: Trinity College Dublin,University College Dublin.International collaborators: Cold Spring Harbor,Columbia, Rutgers, University of New Mexico.Research Grants‘Centre for Computer Controlled Systems’. ScienceFoundation Ireland, €7,500,000. (D. Leith and R.Shorten, 2001-2006).‘National Communications Network Research Centre’.Science Foundation Ireland, €5,488,114(D. Leith, M. Davis, DIT and J. Nelson, UL, 2004-2008).‘Continuous Gestural Interaction with MobileDevices’. IRCSET/Enterprise Ireland Basic ResearchGrant, €77,300 (R. Murray-Smith, 2003-2006).‘Body Space: Feedback for Closed-Loop Control ofGesture Input’. HEA/Media Lab Europe, €45,500(R. Murray-Smith, 2004-2005).‘Audioclouds: Three-Dimensional Audio and GesturalInterfaces for Mobile and Wearable Computers’.EPSRC funded research project, £237,000 (R. Murray-Smith, 2002-2005).‘Tongue-Based Electrode Array for SensorySubstitution and Computer I/O’. HEA/Media LabEurope, €100,000 (B. Pearlmutter, 2004-2005).‘Complex Embedded Automotive Control Systems’. EUSTREP, €220,000 (R. Shorten and D. Leith, 2004-2008).‘Systems Biology’. Science Foundation IrelandResearch Professorship, €2.630,000 (P. Wellstead,2004-2009).‘Modelling and Design of Future CommunicationNetworks: A Hybrid Systems Approach’. ScienceFoundation Ireland Investigator Programme,€883,201 (R. Shorten, 2004-2008).‘Equipment Grant’. Science Foundation Ireland,€75,585 (D. Leith and R. Shorten, 2004-2005).‘International Collaboration Programme’. EnterpriseIreland, €3,000 (R. Shorten, 2005-2006).‘1 st Systems Biology Workshop’. Science FoundationIreland Conference & Workshop Grant, €3,321(P. Wellstead, 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06RESEARCH INSTITUTES‘2 nd Systems Biology Workshop’. Science FoundationIreland Conference & Workshop Grant, €8,140 (P.Wellstead, 2005).129

Hamilton InstituteC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 RESEARCH INSTITUTESPublications In Refereed JournalsPaul, A., M. Akar, M.G. Safonov and U. Mitra. Adaptivepower control for wireless networks using multiplecontrollers and switching. IEEE Transactionson Neural Networks (special issue on AdaptiveLearning Systems in Communication Networks),16(5), 1212-1218 (2005).Bullinger, E. System analysis of a programmed celldeath model. Proc. of the 44 th IEEE Conf. on Decisionand Control and European Control Conference,ECC’05, pp 7994–7999 (2005).Bullinger, E. and Allgöwer, F. Adaptive λ-trackingfor nonlinear higher relative degree systems.Automatica, 41(7), pp 1191-2000 (2005).Eißing, T., F. Allgöwer and E. Bullinger. Robustnessproperties of apoptosis models with respect toparameter variations and intrinsic noise. IEEProceedings - Systems Biology, 152(4), 221-228(2005).Ofiteru, I.R., V. Lavric, F. Allgöwer and E. Bullinger.Sensitivity analysis of Escherichia coli’s TricarboxilicAcid Cycle under anaerobic conditions. Foundationsof Systems Biology FOSBE 2005, pp 337–340 (2005).Cimatoribus, C., T. Eißing, N. Elvassore, F. Allgöwerand E. Bullinger. Model discrimination tools inapoptosis. Foundations of Systems Biology FOSBE2005, pp 197–200 (2005).Duffy, K. and A. Metcalfe. The large deviationsof estimating rate-functions. Journal of AppliedProbability, 42(1), 267-274 (2005).Duffy, K., D. Malone and D.J. Leith. Modelling the802.11 Disributed Coordination Function in NonsaturatedConditions. IEEE Communications Letters,9(8), 715-717 (2005).Kalamatianos, D., P. Liatsis and P.E. Wellstead.Classification of Urea Data from a Novel NearinfraredSpectrometer. Proceedings of SPIE, 5969,379-387 (2005).Kellett, C.M. and A.R. Teel. On the robustness of KLstabilityfor difference inclusions: smooth discretetimeLyapunov functions. SIAM Journal on Controland Optimization, 44(3), 777-800 (2005).Kellett, C.M., I.M.Y. Mareels and D. Nesic. Stabilityresults for networked control systems subject topacket dropouts. Proceedings of the 16 th IFAC WorldCongress, paper Mo-A11-TO/2 (2005).Vilaplana, M.A., D.J. Leith, W.E. Leithead andJ. Kalkkuhl. Modification of vehicle handlingcharacteristics using 4-wheel steer-by-wire.Transactions SAE: Journal of Passenger Cars,July (2005).Leith, D. and R. Shorten. Analysis and Design ofSynchronised Communication Networks. Automatica,41, 725-730 (2005).Leith, D.J., P. Clifford and D.W. Malone. Ng, A. TCPFairness in 802.11e WLANs. IEEE CommunicationsLetters, 9(11), 964-966 (2005).Malone, D. Misbehaving name servers and whatthey’re missing. Cisco Internet Protocol Journal, 8(1),2-5 (2005).Malone, D. A Sinister View of Dilation Equations.International Journal of Wavelets, Multiresolutionand Information Processing, 3(1), 67—77(2005).Vilaplana, M., O. Mason, D. Leith and W. Leithead.Control of yaw rate and sideslip in 4-wheel steeringcars with actuator constraints. LNCS 3355 Switchingand Learning in Feedback Systems, pp 201-222(2205).Williamson, J. and R. Murray-Smith. Sonification ofProbabilistic Feedback through Granular Synthesis.IEEE Multimedia, 12(2), 45-52 (2005).Williamson, J. and R. Murray-Smith. Dynamics andprobabilistic text entry. Proceedings of the HamiltonSummer School on Switching and Learning inFeedback systems, Lecture Notes in ComputingScience, 3355, 333-342 (2005).130

Girard, A. and R. Murray-Smith. Gaussian Processes:Prediction at a noisy input and application toiterative multiple-step ahead forecasting of timeseries.Proceedings of the Hamilton Summer Schoolon Switching and Learning in Feedback systems,Lecture Notes in Computing Science, 3355, 158-184(2005).Sbarbaro, D. and R. Murray-Smith. Self-tuningcontrol of non-linear systems using Gaussianprocess prior models. Proceedings of the HamiltonSummer School on Switching and Learning inFeedback systems, Lecture Notes in ComputingScience, 3355, 140-157 (2005).Kamnik, R., J.Q. Shi, R. Murray-Smith and T. Bajd.Nonlinear modelling of FES-supported standing upin paraplegia for selection of feedback sensors. IEEETransactions on Neural Systems & RehabilitationEngineering, 13(1), 40-52 (2005).Shi, J.Q., R. Murray-Smith and D.M. Titterington,Hierarchical Gaussian process mixtures forregression. Statistics and Computing, 15, 31-41(2005).Kocijan, J., A. Girard, B. Banko and R. Murray-Smith.Dynamic systems identification with Gaussianprocesses. Mathematical and Computer Modellingof Dynamical Systems, 11(4), 411-424 (2005).Kocijan, J. and R. Murray-Smith. Nonlinear PredictiveControl with Gaussian Process Model. Proceedingsof the Hamilton Summer School on Switching andLearning in Feedback systems, Lecture Notes inComputing Science, 3355, 185-200 (2005).Shi, J.Q., R. Murray-Smith, D.M. Titterington and B.Pearlmutter. Learning with large data sets usingfiltered Gaussian Process priors. Proceedings ofthe Hamilton Summer School on Switching andLearning in Feedback systems, Lecture Notes inComputing Science, 3355, 128-139 (2005).Murray-Smith, R. and B.A. Pearlmutter.Transformations of Gaussian Process priors. MachineLearning Workshop, LNAI 3635, 110–123 (2005).Ni, Q. Performance Analysis and Enhancements forIEEE 802.11e Wireless Networks. IEEE Network,19(4), 21-27 (2005).Ni, Q., G.R. Cantieni, C. Barakat and T. Turletti.Performance Analysis under Finite Load andImprovements for Multirate 802.11. ComputerCommunications, 28(4), 1095-1109 (2005).Ni, Q., T. Li, T. Turletti and Y. Xiao. SaturationThroughput Analysis of Error-Prone 802.11Wireless Networks. Wiley Journal of WirelessCommunications and Mobile Computing (JWCMC),5(8), 945-956 (2005).O’Grady, P.D., B.A. Pearlmutter and S.T. Rickard.Survey of Sparse and Non-Sparse Methods inSource Separation. International Journal of ImagingSystems and Technology (IJIST), special issue onblind source separation and deconvolution inimaging and image processing, 15, 18-33 (2005).Jun, S.C. and B. A. Pearlmutter. Fast Robust Subject-Independent Magnetoencephalographic SourceLocalization using an Artificial Neural Network.Human Brain Mapping, 24(1), 21-34 (2005).Halchenko, Y.O., S.J. Hanson and B.A. Pearlmutter.Multimodal Integration: fMRI, MRI, EEG, MEG.Advanced Image Processing in Magnetic ResonanceImaging, edited by Luigi Landini, Vincenzo Positanoand Maria Filomena Santarelli, pp 223-265 (2005).Shorten, R., D. Leith, J. Foy and R. Kilduff. Analysisand design of synchronised communicationnetworks. Automatica, 41, 725-730 (2005).Shorten, R.N., D.J. Leith, F. Wirth and C.M. Kellett.Switched linear systems and Internet congestioncontrol. Proceedings of the 13th Yale Workshop onAdaptive and Learning Systems, pp 135-156 (2005).Shorten, R. and O. Mason. The geometry of convexcones associated with the Lyapunov inequalityand common Lyapunov functions. Electronic LinearAlgebra, 12, 42-63 (2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06RESEARCH INSTITUTES131

Hamilton InstituteC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 RESEARCH INSTITUTESShorten, R., O. Mason and K. Wulff. Convex cones,Lyapunov functions and the stability of switchedlinear systems. LNCS 3355 Switching and Learning inFeedback Systems, pp 31-46 (2005).Sun, Z. and S.S. Ge. Analysis and synthesis of switchedlinear control systems. Automatica, 41(2), 181-195(2005).Sun, Z. and R. Shorten. On convergence rates ofswitched linear systems. IEEE Transactions onAutomatic Control, 50(8), 1224-1228 (2005).Wolkenhauer, O., M. Ullah, P. Wellstead and K.H.Cho. The Dynamic Systems Approach to Control andRegulation of Intracellular Networks. FEBS Letters,579, 1846-1853 (2005).Wolkenhauer, O., S.N. Sreenath, Wellstead, P.,Ullah, M., Cho, K. H. A Systems and Signal OrientedApproach to Intracellular Dynamics. BiochemicalSociety Transactions, 33(3), 507-515 (2005).Wellstead, P., O. Mason, W.T. O’Connor, K-H. Cho,Bullinger, E., O. Wolkenhauer and S. Duncan. Towardsa systems understanding of the cerebral motor circuit.Foundations of Systems Biology FOSBE 2005, pp185–188 (2005).Wirth, F. The generalized spectral radius is strictlyincreasing. Linear Algebra and its Applications, 395,141-153 (2005).Wirth, F. A converse Lyapunov theorem for linearparameter varying and linear switching systems.SIAM Journal on Control and Optimization, 44, 210-239 (2005).Plischke, E., F. Wirth and N. Barabanov. Duality resultsfor the joint spectral radius and transient behavior.Proc. of the 44 th IEEE Conf. on Decision and Controland European Control Conference, ECC’05, pp 2344-2349 (2005).Wirth, F. A converse Lyapunov theorem for switchedlinear systems with dwell times. Proc. of the 44 th IEEEConf. on Decision and Control and European ControlConference, ECC’05, pp 4572-4577 (2005).Dashkovskiy, S., B.S. Rüffer and F.R. Wirth. Asmall-gain type stability criterion for large scalenetworks of ISS systems. Proc. of the 44 th IEEE Conf.on Decision and Control and European ControlConference, ECC’05, pp 5633-5638 (2005).Zhang, Y. and S.S. Ge. HYPERLINK “http://ieeexplore.ieee.org/iel5/72/32643/01528525.pdf?tp=&arnumber=1528525&isnumber=32643” Design and analysisof a general recurrent neural network model fortime-varying matrix inversion. IEEE Transactions onNeural Networks, 16(6), 1477-1490 (2005).Books, Book Chapters and ReviewsMurphy, N. and D. Malone. IPv6 NetworkAdministration, (eds M. Loukides, Sebastopol), CA,(2005).Murray-Smith, R., and R. Shorten. LNCS 3355Switching and Learning in Feedback Systems:European Summer School on Multi-Agent Control,Maynooth, Ireland, September 8-10, 2003, RevisedLectures and Selected Papers, (eds R. Murray-Smithand R. Shorten), Springer-Verlag, Berlin, (2005).Sun, Z. and S.S. Ge. Switched Linear Systems Controland Design, (eds E.D. Sontag, M. Thoma, A. Isidoriand J.H. van Schuppen), London (2005).132Wirth, F. On the structure of the set of extremalnorms of a linear inclusion. Proc. of the 44 th IEEEConf. on Decision and Control and European ControlConference, ECC’05, pp 3019-3024 (2005).

Conference ProceedingsAkar, M. ‘Robust tracking for a class of nonlinearsystems using multiple models and switching’.American Control Conference, Portland, USA (8-10June 2005).Akar, M., A. Paul, M. Stefanovic and M.G. Safonov.‘Multiple controller adaptive control for a trackingproblem using an unfalsification approach’. IEEEConference on Decision and Control, Seville, Spain(12-15 December 2005).Bullinger, E. ‘A Systems Biology Approach toApoptosis’. Invited speaker, Department ofPhysiology, RCSI, Dublin, Ireland (20 July 2005).Bullinger, E. ‘Modelling of Cellular Dynamics’. 2ndSystems Biology Workshop, NUI Maynooth, Co.Kildare, Ireland (1 September 2005).Bullinger, E. ‘Dynamic Modelling, Simulation &Analysis – Useful for Understanding Biology?’.Invited speaker, Department of Biochemistry, NUIGalway, Ireland (11 November 2005).Bullinger, E. ‘System analysis of a programmed celldeath model’. IEEE Conference on Decision andControl, Seville, Spain (12-15 December 2005).Clifford, P. and D. Leith. ‘Modelling TCP Dynamicsin Wireless Networks’. IEEE Wirelesscom 2005,Hawaii, USA (13-16 June 2005).Clifford, P. and D. Leith. ‘TCP Fairness in 802.11eWLANs’. IEEE Wirelesscom 2005, Hawaii, USA(13-16 June 2005).Kalamatianos, D. ‘Classification of Urea Data froma Novel Near-infrared Spectrometer’. Photonics inMedicine, Toronto, Canada (12-14 September 2005).Kellett, C. ‘TCP: Systems Analysis and Design’. Invitedspeaker, University of Melbourne, Australia (1 June2005).Kellett, C. ‘TCP: Systems Analysis and Design’. Invitedspeaker, University of Newcastle, Australia (8 June2005).Kellett, C. ‘TCP: Systems Analysis and Design’. Invitedspeaker, University of California at Santa Barbara,USA (15 June 2005).Leith, D.J., R. Shorten and Y. Lee. ‘Evaluating TCPCongestion Control’. PFLDnet, Lyon, France (3-4February 2005).Leith, D. ‘Evaluating TCP Congestion Control’.PLDNet, Lyon, France (3-4 February 2005).Leith, D.J., K. Duffy and D. Malone. ‘Modelling the802.11 DCF under heterogenous finite load’. WiOpt05, Trentino, Italy (3-7 April 2005).Leith, D.J. and P.Clifford. ‘Using the 802.11e EDCFto Achieve TCP Upload Fairness over WLAN Links’ .WiOpt 05, Trentino, Italy (3-7 April 2005).Leith, D.J., and R. Shorten. ‘TCP Dynamics, Fairnessand Efficiency’. 13 th Yale Workshop on Adaptive &Learning Systems, New Haven, USA (30 May–1 June2005).Leith, D.J. ‘Fair & useful comparisons: how should weevaluate new TCP proposals?’. Terena NetworkingConference, Poznan, Poland (6-9 June 2005).Leith, D.J., A. Ng and D. Malone. ‘ExperimentalEvaluation of TCP Performance and Fairness inan 802.11e Test-bed’. SIGCOMM Workshop onExperimental Approaches to Wireless NetworkDesign & Analysis, Philadelphia, USA (22-26 August2005).Leith, D.J., K. Duffy and D. Malone. ‘Modelling 802.11Wireless Links’. 44 th IEEE Conference on Decisionand Control, Seville, Spain (12-15 December 2005).Leith, D.J., W.E. Leithead and M. Vilaplana. ‘Robustlateral controller for 4-wheel steer cars with actuatorconstraints’. 44 th IEEE Conference on Decision andControl, Seville, Spain (12-15 December 2005).Leithead, W., E. Ragnoli and J. O’Reilly. ‘Open-loopUnstable Feedback Systems with Double-SidedInputs: an Explicit Demostration of Self-Consistence’.44 th IEEE Conference on Decision and Control,Seville, Spain (12-15 December 2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06RESEARCH INSTITUTES133

Hamilton InstituteC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 RESEARCH INSTITUTESMalone, D.W., P. Clifford, K. Duffy and D. Leith. ‘OnImproving Voice Capacity in 802.11 InfrastructureNetworks’. IEEE Wirelesscom 2005, Hawaii, USA(13-16 June 2005).Malone, D. and O. McGann . ‘Flow Label FilteringFeasibility’. 1st European Conference on ComputerNetwork Defence (EC2ND), School of Computing,University of Glamorgan, UK (15-16 December 2005).Mason, O. ‘Some results on the stability of positiveswitched linear systems’. Invited speaker, Institute ofTechnology, Tallaght, Dublin, Ireland (6 April 2005).Mason, O. ‘Positive dynamical systems: some recentresults and novel applications’. Invited speaker,Mathematics Department, NUI Maynooth, Co.Kildare, Ireland (11 May 2005).Mason, O., E. Zeheb, S. Solmaz and R. Shorten. ‘Onthe quadratic stability of switched interval systems:preliminary results’. 20th IEEE InternationalSymposium on Intelligent Control and the 13thMediterranean Conference on Control andAutomation, Limassol, Cyprus (27-29 June 2005).Mason, O. ‘Switched linear systems and CQLF’s’.Invited speaker, University of Limerick, Limerick,Ireland (21 October 2005).Murray-Smith. R. ‘Dynamics and interaction: gesturalinteraction with mobile devices’. InternationalWorkshop on Processes of Communication, Centerfor Interdisciplinary Research (ZiF), BielefeldUniversity, Germany (10-11 February 2005).Murray-Smith, R., A. Crossan, S. Brewster, J. Kelly andB. Musizza. ‘Gait Phase Effects in Mobile Interaction’.CHI 2005, Portland, USA (2-7 April 2005).Murray-Smith, R., R. Kamnik, T. Bajd and J.Williamson. ‘Rehabilitation Robot Cell forMultimodal Standing-Up Motion Augmentation’.International Conference on Robotics andAutomation (ICRA 2005), Barcelona, Spain (18-22April 2005).Murray-Smith. R. ‘Dynamics and interaction’. Invitedspeaker, Nokia Mobile Phones, Copenhagen,Denmark (2 June 2005).Murray-Smith. R. ‘Dynamics and interaction’. Invitedspeaker, Dept. of Informatics and MathematicalModelling, Denmarks Tekniske Universitet, Lyngby,Denmark (3 June 2005).Murray-Smith, R., S. Gentry and E. Feron. ‘Humanhumanhaptic collaboration in cyclical Fitts’ tasks’IEEE/RSJ International Conference on IntelligentRobots and System, Alberta, Canada (2-6 August2005).Murray-Smith. R. ‘Sensors & gestures in interaction’.Invited speaker, Nokia Mobile Phones, Copenhagen,Denmark (30 September 2005).Murray-Smith. R. ‘Sensitive computers...?’. Invitedspeaker, IT Wales ICT forum, (24 November 2005).Murray-Smith, R., J. Hansen and T.A. Johansen.‘Nonparametric Identification of Linearizationsand Uncertainty using Gaussian Process Models- Application to Robust Wheel Slip Control’. 44 th IEEEConference on Decision and Control (CDC-ECC’05),Seville, Spain (12-15 December 2005).Ni, Q., T. Li, T. Turletti and Y. Xiao. ‘PerformanceAnalysis of the IEEE 802.11e Block ACK Schemein a Noisy Channel’. IEEE BroadNets WirelessNetworking Symposium, Boston, MA, USA (3-7October 2005).Pearlmutter, B.A., H.i Asari and A. M. Zador.‘Neuronal Predictions of Sparse LinearRepresentations’. Forum Acusticum 2005, Budapest,Hungary (29 31 August 2005).Pearlmutter, B.A. and J. M. Siskind. ‘PerturbationConfusion and Referential Transparency: CorrectFunctional Implementation of Forward-Mode AD’.17th International Workshop on Implementationand Application of Functional Languages (IFL2005),Dublin, Ireland (19-21 September 2005).134Shorten, R. ‘Positive matrices and the internet’.Invited speaker, University of Limerick, Limerick,Ireland (29 April 2005).

Shorten, R., D. Leith and C. Kellett. ‘Switched LinearSystems and Internet Congestion Control’. 13th YaleWorkshop on Adaptive and Learning Systems, NewHaven, USA (30 May–1 June 2005).Shorten, R. and D. Leith. ‘TCP Dynamics, Fairness andEfficiency’. 13th Yale Workshop on Adaptive andLearning Systems, New Haven, USA (30 May–1 June2005).Shorten, R. ‘Stability of Switched Systems’. AmericanControl Conference, Portland, Oregan, USA (8-10June 2005).Shorten, R. ‘Spectral Conditions for SPR’. AmericanControl Conference, Portland, Oregan, USA (8-10June 2005).Shorten, R. ‘On Common quadratic Lyapunovfunctions’. Invited speaker, University of Californiaat San Diego, USA (10 June 2005).Shorten, R. ’Positive systems and the internet’.Invited speaker, Purdue University, USA (13 June2005).Shorten, R. ‘On the quadratic stability of switchedinterval systems’. IEEE International Symposium onIntelligent Control, Cyprus (27-29 June 2005).Shorten, R. ‘On the stability of state dependentswitching laws’. Joint Conference on Decision andControl and European Control Conference, Seville,Spain (12-15 December 2005).Shorten, R. ‘On the stabilisation of a class ofSISO switched linear systems’. Joint Conferenceon Decision and Control and European ControlConference, Seville, Spain (12-15 December 2005).Shorten, R. ‘AIMD congestion control and consensus’.Invited speaker, Max Planck Institute, Magdeburg,Germany (20 December 2005).Smigoc, H. ‘Necessary conditions for the existenceof CQLF’s’. Linear Algebra Workshop, Bled, Slovenia(16-24 May 2005).Strachan, S. ‘gpsTunes - Controlling Navigation ViaAudio Feedback’. Mobile HCI 2005, Salzburg, Austria(19-22 September 2005).Sun, Z. ‘A general robustness theorem for switchedlinear systems’. IEEE International Symposium onIntelligent Control, Cyprus (27-29 June 2005).Sun, Z. ‘Reachability of switched linear systemswith switching/input constraints’. 16th IFAC WorldCongress, Prague, Czech Republic (4-8 July 2005).Sun, Z. and S. S. Ge. ‘Switched stabilization ofhigher-order switched linear systems’. 44 th IEEEConference on Decision and Control, Seville, Spain(12-15 December 2005).Wellstead, P. ‘Schrodinger’s Legacy: Systems andLife’. E.T.S. Walton Lecture, Royal Irish Academy,Dublin, Ireland (21 April 2005).Wellstead, P., O. Mason, W. O’ Connor, K-H. Cho,E. Bullinger, O. Wolkenhauer and S. Duncan.‘Towards a Systems Understanding of the CerebralMotor Circuit’. Foundations of Systems Biology inEngineering (FOSBE), University of California, SantaBarbara Campus (7-10 August 2005).Wirth, F. ‘A Markov Chain Model of InternetCongestion: Fairness and Responsiveness’. InvitedSpeaker, University of Frankfurt, Germany (March2005).Wirth, F., F. Camilli and L. Grüne. ‘Calculatingthe domain of attraction: Zubov’s method andextensions’. Stability and Control Processes 2005,dedicated to the 75th birthday of V.I. Zubov, St.Petersburg, Russia (29-30 June 2005).Wirth, F., F. Camilli and L. Grüne. ‘Zubov’s methodfor stochastic control systems’. 16 th IFAC WorldCongress, Prague, Czech Republic (4-8 July 2005).Wirth, F. ‘The Gelfand formula for linear parametervarying and linear switching systems’. 16 th IFACWorld Congress, Prague, Czech Republic (4-8 July2005).NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06RESEARCH INSTITUTES135

Hamilton InstituteC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 RESEARCH INSTITUTESWirth, F. ‘On the Dynamics of AIMD CongestionControl’. Hamilton Workshop on Congestion Control,Maynooth, Co. Kildare, Ireland (27-29 September2005).Wirth, F. ‘Some results on a class of positive dynamicsystems’. Invited speaker, University of Bremen,Germany (November 2005).Wirth, F., E. Plischke and N. Barabanov. ‘Dualityresults for the joint spectral radius and transientbehavior’. Joint Conference on Decision and Controland European Control Conference CDC/ECC 2005,Seville, Spain (12-15 December 2005).Wirth, F. ‘On the structure of the set of extremalnorms of a linear inclusion’. Joint Conferenceon Decision and Control and European ControlConference CDC/ECC 2005, Seville, Spain (12-15December 2005).Wirth, F., R. Shorten and K. Wulff. ‘On thestabilisation of a class of SISO switched linearsystems’. Joint Conference on Decision and Controland European Control Conference CDC/ECC 2005,Seville, Spain (12-15 December 2005).Wirth, F. ‘A converse Lyapunov theorem for switchedlinear systems with dwell times’ . Joint Conferenceon Decision and Control and European ControlConference CDC/ECC 2005, Seville, Spain (12-15December 2005).Wirth, F., S. Dashkovskiy and B.S. Rüffer. ‘A smallgaintype stability criterion for large scale networksof ISS systems’. Joint Conference on Decision andControl and European Control Conference CDC/ECC2005, Seville, Spain (12-15 December 2005).Zhang, Y. ‘On the LVI-based primal-dual neuralnetwork for solving online linear and quadraticprogramming problems’. 2005 American ControlConference, Portland, Oregon, USA (8-10 June 2005).Zhang, Y. and W.E. Leithead. ‘Efficient Gaussianprocess based on BFGS updating and logdetapproximation’. 16 th IFAC World Congress, Prague,Czech Republic (4-8 July 2005).Zhang, Y., W.E. Leithead and K. Neo. ‘Wind turbinerotor acceleration: identification using Gaussianregression’. 2 nd International Conference onInformatics in Control, Automation and Robotics,Barcelona, Spain (14-17 September 2005).Zhang, Y. ‘Minimum-Energy RedundancyResolution Unified by Quadratic Programming’.15 th International Symposium on Measurementand Control in Robotics, Brussels, Belgium (8-10November 2005).Zhang, Y., W.E. Leithead and D.J. Leith. ‘Time-seriesGaussian process regression based on Toeplitzcomputation of O(N^2) operations & O(N)-levelstorage’. 44 th IEEE Conference on Decision andControl, Seville, Spain (12-15 December 2005).Conferences HostedP. Wellstead, First Systems Biology Workshop,Hamilton Institute, Maynooth (14 June 2005).P. Wellstead, Second Systems Biology Workshop,Hamilton Institute, Maynooth (1-2 September 2005).F. Wirth, Complexity Workshop, Hamilton Institute,Maynooth (16 September 2005).D. Malone, Congestion Control Workshop, HamiltonInstitute, Maynooth (27-28 September 2005).136Zhang, Y. ‘Revisit the analog computer and gradientbasedneural system for matrix inversion’. IEEEInternational Symposium on Intelligent Control,Cyprus (27-29 June 2005).

External Assignments& Public ServiceDr. E. Bullinger• Program Committee member of PFLDnet 2005and 2006.• Reviewer for University of Applied Sciences,Osnabrück; Biosystems; IEEE Transactions onAutomatic Control; IEE Proceedings SystemsBiology.Dr. K. Duffy• Reviewer for Mathematical Reviews; IEEE/ACMJournal on Selected Areas of Communications;IEEE Communications Letters; American Journalof Mathematical and Management Sciences.• Conference organizing: J.T. Lewis Memorial Conference,4 days, 41 international speakers, withT. Dorlas (DIAS) and B. Goldsmith (DIT). ScienceFoundation Ireland funded 50k Euro.Dr. C.M. Kellett• Referee for the following: Systems and ControlLetters; International Journal of Control;Automatica.Prof. D.J. Leith• Expert evaluator for: Enterprise-Ireland; ScienceFoundation Ireland; UK EPSRC; EuropeanCommission.• Reviewer for IEEE Transaction on AutomaticControl; IEEE Communications Letters;Automatica.• Member of Science Foundation Ireland ICTadvisory panel.• Program Committee member of PFLDnet 2005and 2006.Prof. W.E. Leithead• Project reviewer for UK Engineering & PhysicalSciences Research Council.• Reviewer for: Automatica, International Journalof Control, IEE Proceedings, and ControlEngineering Practice.• Consultant to Renew4able Energy Systems Ltd.,UK; BAE Systems, UK; Neg-Micon, Denmark.• External Examiner for Dept. of Electronic andElectrical Eng. at Loughborough UniversityDr. O. Mason• Reviewer for IEEE Transactions on AutomaticControl; IEEE Transactions on Circuits andSystems; Linear Algebra and its Applications;European Journal of Control; IEE Proceedings,Control Theory and Applications.• Reviewer for IEEE Conference on Decision andControl.• Conference organisation: the first and secondSystems Biology Workshops in June andSeptember 2005.Dr. R. Murray-Smith• IEEE transactions on Automatic Control;International Journal of Machine Learning;Automatica; Virtual Reality.• Reviewer for SIGACM CHI 2005; Mobile HCI2005; Neural Information Processing Systems2005; UIST 2005.• Reviewer for the Finnish Academy.• Expert Evaluator for the European CommissionResearch Directorate.Prof. B. Pearlmutter• Co-Chair of NIPS*2003 Workshops, “ ICA: SparseRepresentations in Signal Processing”,Organizing body: The NIPS Foundation, Dates:Dec 12-13, 2003, Venue: Whistler Village, B.C.,Canada.• Reviewer/panel member for US NSF, ResearchGrants Council of Hong Kong.Dr. R. Shorten• Reviewer for European Control Conference.• Reviewer for American Control Conference.• Reviewer for IEEE Conference on Decision andControl.• Reviewer for IEEE Transactions on Circuits andSystem.• Reviewer for IEEE Transactions on AutomaticControl.• Reviewer for Systems & Control Letters.• Reviewer for IEE Proceedings on Control Theory& Applications.• Scientific reviewer for European Union.• Conference Chair for MAC Summer School.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06RESEARCH INSTITUTES137

Hamilton InstituteC O N T I N U E DNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 RESEARCH INSTITUTESProf. P. Wellstead• External D.Phil/PhD Examinations Oxford Universityand Cambridge University.• Member of Organising Group for the ComplexSystems Session for the International SystemsBiology Conference, Japan, 2006.• Member of International Planning Committeefor IFAC Systems Identification Conference,Australia, 2006.• Visiting Professor City University, London.• Reviewer IEE Journal of Systems Biology; IEEProceedings on Control Theory andApplications; American Control Conference;Conference Decision and Control (CDC); IFACConference on Systems Identification.Dr. F. Wirth• Conference Organisation: Complexity Workshopat the Hamilton Institute, September 16, 2005;The Joint Spectral Radius – Theory, Numerics andApplications, Invited session at the Joint IEEEConference on Decision and Control – EuropeanControl Conference 2005.• Reviewer for Joint IEEE Conference on Decisionand Control – European Control Conference 2005.• Reviewer for Automatica; Dynamical Systems;IEE Proceedings Control Theory & Applications;International Journal of Control; InternationalJournal of Systems Science; Linear Algebra andits Applications; Nonlinearity; NonlinearAnalysis Series A: Theory Methods andApplications; Systems & Control Letters; SIAMJournal on Control and Optimization.• Reviewer for Belgian National Fund for ScientificResearch; Council of Physical Sciences of theNetherlands Organization for Scientific Research(NWO).• External PhD Examinations Universität Bremen,Germany; Université Catholique de Louvain-La-Neuve, Belgium.• Associate editor of SIAM Journal of Control andOptimization and of Systems and Control Letters.• Associate Editor of Systems & Control Letters;SIAM Journal on Control and Optimization.138

Institute of Bioengineering and AgroecologyResearch OverviewThe Institute for Bioengineering and Agroecology (IBA) was set up with public and private support underCycle 1 of the Irish Higher Education Authority PRTL initiative, building on a pre-existing consortium ofacademic laboratories at NUl Maynooth. Its overall concern is the benign manipulation of organisms for fielduse in pursuit of food security, human health, environmental enhancement, and novel materials.The IBA conducts research in the following areas: genetics, development, behaviour and ecology of biologicalcontrol organisms, developmental biology, stress physiology and genetic modification of plants, and themanagement requirements of genes inserted in plants or biocontrol organisms.Institute PersonnelPrincipal InvestigatorsProfessor P. Dix, DirectorDr. C. Griffin, Deputy DirectorProfessor A. BurnellProfessor M. DownesDr. J. NugentDr. C. MeadeAdjunct ProfessorsProfessor J. BurkeProfessor L. DowneyResearch FellowsDr. J. BoydDr. K. BradyDr. J. BrowneDr. C. DempseyDr. A. DillonDr. I. DixDr. M.R. EnrightDr. S. Khunyoshyeng JordanDr. M. KlaasDr. M. McCabeDr. P. MedgyesyDr. C. MooreDr. T.T. NguyenDr. K. O’HanlonDr. W. ReardonDr. A. RolstonPostgraduateMs. S. CloneyMs. L. CorriganMr. D. DowneyMr. D. EnnisMs. E. FitzgibbonMs. T. Lola-LuzMr. H. McWeeneyMs. M. MoranMs. K. MorrisMs. Z. Mulroy HehirMs. K. O’CallaghanMr. D. O’HalloranMs. S. Omar RegeaiMr. C. PettiMs. M. PoageMs. E. RyanMr. A. SalvetaMr. A. ShannonMr. T. TysonProject ManagersMs. N. TraversPublications, research grantsand external assignments of theNICB personnel are listed in theBiology Department entry.Information and enquiries:Professor P. Dix, Director,Institute for Bioengineering andAgroecology,Department of Biology,National University of IrelandMaynooth, Maynooth,Co. Kildare.Tel: +353-1-7083836Email: phil.dix@nuim. ieWebsite: http://www.nuim.ie/academic/biology/iba.shtmlNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06RESEARCH INSTITUTES139

Institute of ImmunologyNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 RESEARCH INSTITUTESDirector’s Review of the YearImmunology is a scientific field that has changed the modern world. The discovery of different vaccines has ledto the eradication of smallpox and the near disappearance of many childhood illnesses. Immunology is also acore discipline to the emerging technologies that are revolutionising biology. The science is central to Ireland’sbiomedical sector and to the clinical diagnostic industry in particular. The overriding aim of the Institute forImmunology at NUl Maynooth is to conduct internationally competitive research of the highest standard in thediscipline and to prepare individuals at undergraduate, postgraduate and postdoctoral level to become futureleaders in this area.2005 has seen major advances originate from the Institute. Using the core facilities ideally suited to advancedimmunological research such as advanced flow cytometry, digital imaging facilities, real-time quantitative PCRequipment, and the specialist histology laboratory, Institute scientists have advanced our understanding ofhuman health. For example the Mahon team published three landmark studies examining the links betweenasthma and infant immunization. The work confirmed the safety and efficacy of certain infant vaccines andallayed public misconceptions about asthma and immunization. In fact the team, in collaboration with cliniciansin Tallaght hospital, showed evidence of a new mechanism by which airway damage caused by infection canexacerbate respiratory diseases such as asthma. The Mahon team also collaborated with scientists in NUIGalway as part of the SFI REMEDI team to examine how adult stem cells can be safely used in transplantation.The first results from this major collaboration appeared this year. The Doherty group continued to probe theunique immunological environment of the Liver and the specific role of the NT cell. This work is of fundamentalvalue in uncovering immunological mechanisms and of clinical importance for understanding the impact ofHepatitis C infection. 2005 also saw two P.I.s join the permanent staff of the university, Dr. Shirley O’Dea, andDr. Noel Murphy. The O’Dea team were already based in the Institute and funded by SFI to examine questionsof lung repair. That team was joined by Dr. Bernadette Moore from the NIH who brings advanced proteomicskills to the Institute, and enhances the EU Marie Curie Transfer of Knowledge award, pioneered by theO’Dea team and others. Dr. Noel Murphy joins NUIM after a brief period in TCD following 15 years researchinto African Trypanosomiasis based in Kenya. Noel’s insights into global health and development shouldprovide a solid platform for future research to combat the infectious diseases linked to poverty. Infectiousdisease disproportionately affects the world’s poorest. The work of the Murphy team, builds on Maynooth’slong tradition of service to the developing world. Other staff moved to pastures new during 2005; Dr. PatriciaJohnston, took a permanent lectureship in DCU, but retains collaborative links to Maynooth, Ms. Caroline Wilson,our technician also made the same journey, postdoctoral fellows such as David Casey moved on to lucrativecareers in forensic science, and graduating students such as Darren Ennis made the transition to postdoctorallife in academia. To all, we wish continued success.The educational role of the Institute continues to be developed, with Institute scientists developing new coursesfor undergraduates and guiding the studies of a number of postgraduate and postdoctoral fellows. 2005saw all undergraduate taught modules associated with the institute supported by Moodle, a virtual learningenvironment. 2005 also saw the first Maynooth Immunology Masterclass, during which the renowned Prof.Polly Matzinger from the NIH, lead a group of Irish and British postgraduates through a day that gave practicaladvice in basic science, career portfolios and grant writing, supported by speakers from the Wellcome Trust, andScience Next Wave. The day finished with a Bar-B-Q, a game of rounders and some very late night discussions!At second level, the Institute continues to provide support for teachers of Biology through a web based service,and through hosting specific schemes such as the SFI STAR programme. The Institute’s website also allowedleaving Cert. students to ask research scientists questions on science and careers, in time for the leaving Certexams.1402006 will see major advances in the educational offerings from the Institute and 2005 required significantpreparatory work for this. The Institute in conjunction with the Department of Biology will collaborate withother departments in NUIM to offer a new M.Sc Immunology and Global Health. This course will provide

students with a thorough knowledge in fundamental Immunology combined with an understandingof development issues required for implementation (details: http://immunology.nuim.ie). The Instituteacknowledges all the support from the Biology and other departments that made this course possible, inparticular Prof. Ohlendieck.NUl Maynooth has built a solid foundation in immunological research over the past ten years and currentlyhas several internationally recognised Investigators, with substantial research funding from SFI, The EuropeanCommission, The Health Research Board, Enterprise Ireland and industry. Further recognition of excellencein research can be judged by a large number of peer-reviewed papers in high impact research journals thatachieve the widest possible dissemination. International recognition of expertise in the field of Immunology isalso recognised through inclusion on grant review boards, working groups, invitations to speak at internationalscientific conferences, and serving on editorial board and peer review panels for international scientificjournals. However the most significant advance of 2005 is the hardest to measure. 2005 saw a step up in theintellectual life of the Institute. This was made possible through the Institute’s business plan, which has seenthe Institute move from dependence on HEA PRTLI funding in 2001, to independent financial sustainability by2005. The product of that transformation is a vibrant intellectual atmosphere, with lively journal clubs and anoutstanding seminar series. Highlights of 2005 included visits from Alan Perleson from Los Alamos in the USand Phil Hodgkin from WEHI Australia who delivered outstanding papers, and both commented on the qualityof our student contributions to debate. This is perhaps the indicator of which we are most proud-the fact thatthe institute is creating the sort of intellectual vibrancy that is a feature of the best international centres.Current And Future Research Areas Include:• Is it possible or safe to transplant adult stem cells into mismatched donors?• Are there links between immunizations, infections and asthma?• Can we combat diseases relevant to global health: Trypanosomiasis, Hepatitis C and HIV ?• Can we design better vaccines and mucosal adjuvants against diseases of infancy?• How does the lung repair after damage? And what is the lung stem cell?• Why do we understand so little about inflammation?• Can we use systems approaches to investigate immunology?(details of specific projects and PhD vacancies can be found on http://immunology.nuim.ie)NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06RESEARCH INSTITUTESInstitute PersonnelPrincipal InvestigatorsDr. B.P. Mahon, Scientific DirectorDr. S. O’DeaDr. D. DohertyDr. N. MurphyDr. S. Miggin (from 2006)Postgraduate FellowsMs. M. O’GormanMs. M. FlynnMr. D. EnnisMs. J. Kelly RogersMs. K. EnglishMs. J. RyanMs. C. NoonanMs. H. AstrafelMr. O. ZachariadisMs. J. MastersonMr. D. MadsenMs. C. Field CorbettMr. A. HoganMr. J. PurcellMs. E. MolloyPostdoctral FellowsDr. T. O’ConnorDr. L. Madrigal-EstebasDr. P. CorcorranResearch AssistantsMs. M. KilleenMs. A. AdamsMr. L. BacilieriResearch TechnicianMs. D. DalyAdministratorMs. L.M. JenningsInformation and enquires:Ms. Loretta M. Jennings,Institute for Immunology,National University of IrelandMaynooth, Co. KildareTel: +353-1-708 6480,email: Loretta.m.Jennings@nuim.ieWebsite: http://immunology.nuim.iePublications, research grantsand external assignments of theInstitute’s personnel are listed inthe Biology Department entry.141

National Institute of Cellular BiotechnologyNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 RESEARCH INSTITUTESNICB Personnel at NUI MaynoothDirector:Dr. Kevin Kavanagh,Department of Biology,NUI Maynooth.Deputy Director:Dr. Sean Doyle,Department of Biology,NUI Maynooth.Post-doctoral ResearchersDr. E. ReevesDr. K. Reiber.Dr. J. O’KeeffeDr. C. BurnsDr. C. NevillePost-graduate StudentsMs. N. LaceyMr. L. O’ShaughnessyMr. S. CarberryMs. M. CorriganMs. N. LaceyMr. D. BerginMs. C. EganMs. B. ThattiMr. P. MowldsMs. I. Vickers.Ms D. StackMs. J. KelllyMs. J. RenwickMr. R. RowanExecutive AssistantMs. C. BatchelorFurther information:Dr. Kevin Kavanagh, NationalInstitute for CellularBiotechnology, Department ofBiology, NUI Maynooth,Co. Kildare, Ireland.Tel: +353-1 - 708 3859Fax: +353-1- 708 3845Email: kevin.kavanagh@nuim.ieWebsite: http://www.nuim.ie/academic/biology/NICB/shtmlPublications, research grantsand external assignments of theNICB personnel are listed in theBiology Department entry.142

Director’s Review of the YearThe NATIONAL INSTITUTE FOR CELLULAR BIOTECHNOLOGY (NICB) was awarded €33 Million in researchfunding by the Higher Education Authority under Cycle 3 of the Programme for Research in Third LevelInstitutes (PRTLI). Dr. Kevin Kavanagh and Dr. Sean Doyle of the Department of Biology are the PrincipalInvestigators of the NICB at NUI Maynooth.The NICB is a multi-disciplinary research institute, which consists of researchers at Dublin City University,the Institute of Technology Tallaght and NUI Maynooth. The Director of the NUI Maynooth component ofthe NICB proposal is Dr. Kavanagh who, together with Prof. Martin Clynes of DCU and Dr. Ken Carroll of ITT,is responsible for the implementation of the research plan. In addition, Dr. Doyle has been central to theformation and operation of the NUI Maynooth research institute.The work of the researchers at NUI Maynooth entails the development of novel means of detecting andtreating fungal diseases (e.g., Candida and Aspergillus spp.) in those patients immuno-compromised as aresult of disease (e.g., cancer, AIDS, diabetes) or therapy (e.g., organ transplantation). Fungal infection isinternationally recognised as an emerging threat to the health of specific groups of vulnerable patients andthe work at NUI Maynooth will lead to the development of improved diagnostic and therapeutic procedures.Both Dr. Kavanagh and Dr. Doyle have strong track records in attracting funding and publishing in the area offungal pathogenicity, molecular biology and human disease diagnosis and this grant allows them to developthis expertise to the point of producing novel diagnostic and therapeutic strategies for fungal disease.The allocation of funding from the HEA is for a 5 year period (2002 - 2007) and will allow the employmentof an additional 10 - 12 researchers at post-doctoral, post-graduate and research assistant levels in thelaboratories of the NICB at NUI Maynooth bringing the total staff number to 20. In addition, as part of theirmembership of the NICB, researchers will have access to state of the art equipment and other researchfacilities that will be housed in a new Biotechnology building to be constructed at Dublin City University.NUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06RESEARCH INSTITUTES143

NotesNUI MAYNOOTH FACULTY OF SCIENCE RESEARCH REPORT 2005-06 NOTES144