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PHY2707 F SPECIALIZED
Cellular and Molecular Biophysics I

Official description

This course investigates the physical properties of biomolecules with emphasis on principles of equilibrium and non-equilibrium thermodynamics and statistical mechanics that can be used to describe quantitatively biological structure and function. Through rigorously introduced new concepts and theories, and an extensive use of examples from literature, students will gain an understanding of the general importance and broad applicability of Physical Laws to life sciences. Student participation includes reading and preparing papers assigned for discussion in each lecture.

Specific topics will vary and may include:

Molecular associations: statistical mechanics of associations, ligand binding, allosteric interactions; MWC, KNF and SK models; hemoglobin, GPCRs, allosteric enzymes [CG]

Fundamental rate processes: exponential relaxations, activation energy, Kramers’ theory  for barrier crossing, single-molecule kinetics [CG]

Association kinetics: diffusion limit, ligand-binding to proteins, DNA and membrane receptors, reduction of dimensionality [CG]

Multi-state kinetics: 3-state model, separation of time-scales, pathway counting, multi-subunit kinetics [AH]

Random walks: diffusion, “stretched kinetics”, detailed balance, fluctuation-dissipation theorem [AH]

Fluctuations in biology: breaking of thermodynamic equilibrium, linear noise approximation, models of gene expression noise, fundamental limits on stochastic control [AH]

Prerequisite
There are no particular prerequisites other than basic undergraduate physics, chemistry and mathematics courses.
Co-requisite
n.a.
Exclusion
n.a.
Recommended preparation
n.a.
Textbook
                            ['"Molecular and Cellular Biophysics" by Meyer Jackson']
                        
Breadth requirement
BR=5
Distribution requirement
DR=SCI

Additional information

Grading scheme:

Class participation: 10% (Students are required to read assigned papers to be discussed in lectures. Submitting a critical 1-page discussion of the respective paper will be required 24h before each class.)

Assignments: 60% (Four equally weighted homework assignments.) Research Paper Report & Presentation: 30%

course title
PHY2707 F SPECIALIZED
session
fall
group
specialized course
time and location
R 1:30 - 3:30, MP606, in person & online PHY2707 intro meeting Time: Sep 10, 2020 01:30 PM Eastern Time (US and Canada) https://utoronto.zoom.us/j/93461285799
instructors

Delivery Methods

In Person

A course is considered In Person if it requires attendance at a specific location and time for some or all course activities.*.

* Subject to adjustments imposed by public health requirements for physical distancing.

Online - Synchronous
A course is considered Online Synchronous if online attendance is expected at a specific time for some or all course activities, and attendance at a specific location is not expected for any activities or exams.
Asynchronous
A course is considered Asynchronous if it has no requirement for attendance at a specific time or location for any activities or exams.