Catalogue of Courses & Student Handbook - SUPA

Physics and Life Sciences
Introducing Biology to Physicists (SUPAIBP)
Lecturer: Timothy Newman
Institution: Dundee
Hours Equivalent Credit: 20
Assessment: Attendance, quizzes and short research project
Course Description
An overview of fundamental areas of biology for students with little
biology background, emphasizing evolution, connections between
length and time scales in biology, and the potential role of physics to
inform biology at all of these different scales. Introduction: what is life?,
Darwin’s theory of evolution, Mendelian genetics, tree of life, basics
of prokaryotic cells, basics of eukaryotic cells. Biochemistry and
molecular biology: structure and functions of proteins, structure of
DNA, DNA replication, transcription, translation, protein folding.
Cell biology: membrane structure, membrane transport, metabolism
and mitochondria, cytoskeleton, cell cycle. Multicellular organisms:
germ cells, fertilisation, development. Populations: introduction to
ecology, population genetics and evolution.
The Theme of Physics and Life Sciences (PaLS) covers a large breadth
of both physical and life sciences. As students come from a wide
range of backgrounds and experiences, and are pursuing diverse
PhD projects, the exact courses to be taken should be discussed with
the student’s individual supervisor. Students are also invited to select
relevant courses from any of the themes and or to take appropriate and
relevant non-SUPA courses within their home institution, but it is essential
that the appropriate assessment (in the form of examination, written
assignment or oral assignment) be discussed and agreed with the
PaLS Theme Leader (Kishan Dholakia) in advance.
Semester 1
Biophotonics (SUPABIP)
Lecturer: Kishan Dholakia and Carlos Penedo-Esteiro
Institution: St Andrews
Hours Equivalent Credit: 33
Assessment: Attendance, news and views article.
This is a final year undergraduate course organised by University
of St Andrews.
Course Description
The module will expose students to the exciting opportunities offered
by applying photonics methods and technology to biomedical sensing
and detection. A rudimentary biological background will be provided
where needed. Topics include fluorescence microscopy and assays
including time-resolved applications, super-resolution imaging, optical
tweezers for cell sorting and DNA manipulation, single molecule studies,
photodynamic therapy, lab-on-a-chip concepts and bio-MEMS. Two
thirds of the module will be taught as lectures, including guest lectures
by specialists, with the remaining third consisting of problem-solving
exercises, such as writing a specific news piece on a research paper,
assessed tutorial sheets and a presentation. A visit to a biomedical
research laboratory at St Andrews using various photonics methods
will also be arranged.
Collective Dynamics in Biophysical Systems (SUPACDB)
Lecturer: Antonio Politi and Francesco Ginelli
Institution: Aberdeen
Hours Equivalent Credit: 12
Assessment: Oral Presentation
Course Description
The spontaneous emergence of collective behaviour is a universal
property of biological systems that requires a proper theoretical and
modelling framework to be fully understood. Our approach aims
at showing that minimal models may capture many properties of
collective biological phenomena. Minimal model are based on the
essential features of the system at hand, such as conservation laws
and symmetries, and allow for a deeper understanding of the universal
mechanisms lying behind many biological problems. We plan to
introduce the basic concepts and tools – both analytical and numerical --
of this approach by analysing two different classes of systems exhibiting
non-trivial collective dynamics, both at the forefront of current research:
Neural networks – Brain can be described as a network of mathematical
models of single neurons, suitably coupled through various kinds of
synaptic connections. Various issues must be considered: single neuron
dynamics (above/below threshold, number of local variables); synaptic
connections (excitatory vs. inhibitory, synaptic own dynamics); network
structures (random, scale free, sparse coupling, etc.). The various
classes of collective dynamics are discussed.
(ii) Active matter -- Active matter is composed of particles able to self
propel themselves in a systematic way by extracting and dissipating
energy from their surroundings. Systems of interacting active particles
describe the collective motion observed in systems as diverse as
animal groups (bird flocks, fish school, etc.), bacteria, molecular
motors, as well as driven granular matter.
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