PHY2707 F specialized: Cellular and Molecular Biophysics I
Course Title  PHY2707 F specialized 

Session  fall 
Year of Study  1st year 
Time and Location 
Lectures: Thursday 1:30pm – 3:30pm MP505 Office hours: Thursday, 3:30pm4:30pm, MP313 
Andreas
Hilfinger 

Joshua
Milstein 
Official Description
This course investigates the physical properties of biomolecules with emphasis on principles of equilibrium and nonequilibrium 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, singlemolecule kinetics [CG]

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

Multistate kinetics: 3state model, separation of timescales, pathway counting, multisubunit kinetics [AH]

Random walks: diffusion, “stretched kinetics”, detailed balance, fluctuationdissipation 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. 

Corequisite:  n.a. 
Exclusion:  n.a. 
Recommended preparation:  n.a. 
BR=5 , DR=SCI  
Textbook 
"Molecular and Cellular Biophysics" by Meyer Jackson 
Additional Notes
Grading scheme:
Class
participation: 10% (Students are required to read assigned papers
to be discussed in lectures. Submitting a critical 1page discussion of the
respective paper will be required 24h before each class.)
Assignments: 30% (Three equally weighted homework assignments.)
Research Paper Report & Presentation: 20%
Final Exam: 40%