Physical CUME Materials May 2018

CUME Topic for PHYSICAL Chemistry

Released: May 4, 2018
Exam date: May 14, 2018

UPDATE: The CUME is now released (attached below as PDF)

Continuous- and Discrete-time chemical master equation kinetics 
Vincent Voelz

DESCRIPTION

The subject of this exam is the chemical master equation, and its relation to discrete-time (Markov) models of molecular kinetics.  This is a very broad topic (!) and the exam is by no means comprehensive.    That said, hopefully after studying the material you will gain some familiarity with these methods, enabling you to (1) analytically solve some simple problems with a bit of linear algebra, and (2) be familiar with some of the benefits and challenges of building these models from simulation data.

NOTE:  To do well on the exam, you must be able to calculate eigenvalues and eigenvectors for a 2 x 2 matrix. 

The first three references are REQUIRED reading. They discuss the application of the master equation approach to building models of biomolecular dynamics.   PDFs of all the references can be found at:


REFERENCES

Vincent Voelz (2018). Notes on continuous- and discrete-time chemical master equation kinetics (PDF)

Noé, F., & Fischer, S. (2008). Transition networks for modeling the kinetics of conformational change in macromolecules. Current Opinion in Structural Biology, 18(2), 154–162. http://doi.org/10.1016/j.sbi.2008.01.008

Chodera, J. D., & Noé, F. (2014). Markov state models of biomolecular conformational dynamics. Current Opinion in Structural Biology, 25, 135–144. http://doi.org/10.1016/j.sbi.2014.04.002

Buchete, N.-V., & Hummer, G. (2008). Coarse Master Equations for Peptide Folding Dynamics. The Journal of Physical Chemistry B, 112(19), 6057–6069. http://doi.org/10.1021/jp0761665

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Vincent Voelz,
May 4, 2018, 7:33 AM
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Vincent Voelz,
May 4, 2018, 7:37 AM
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Vincent Voelz,
May 4, 2018, 7:35 AM
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Vincent Voelz,
May 4, 2018, 7:28 AM
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Vincent Voelz,
May 14, 2018, 2:36 PM
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