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CH412:Advanced Biophysical Chemistry 3

This class was created by Brainscape user Tim Lafosse. Visit their profile to learn more about the creator.

By: Tim Lafosse
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Decks in this class (7)

Topic 1
-Outline molecular dynamics method for sampling the configurational states of a system of particles -Write down an approximate expression for the total potential energy and use it to -Describe the terms in a typical molecular mechanics force field for biomolecules -Explain the length and time scale problems in molecular simulation.
27  cards
Topic 2
-Describe the similarities and differences between all-atom and coarse-grained force fields. -Explain how coarse-graining attempts to address the length and timescale problems in molecular dynamics -Compare three different methods for developing coarse-grained interaction potentials/force fields -Evaluate a coarse-grained simulation study of a biological system
31  cards
Topic 3
-Explain the challenge with calculating free energies from molecular simulations. -Outline the thermodynamic perturbation approach. -Calculate the free energy difference of two states of a simple model system by thermodynamic perturbation. -Explain how you might evaluate the results of a free energy calculation.
20  cards
Topic 4
-Give examples of reaction coordinates commonly used to study free energy changes in biophysical systems -Explain why the use of biased potential could offer a strategy for dealing with the timescale problem in MD. -Give a basic overview of the umbrella sampling and metadynamics methods. -Describe the pros and cons of umbrella sampling with each other and with other methods covered in this course -Be aware of how these techniques may be used to study biophysical systems.
24  cards
Topic 5
Learning objectives -Outline the Monte Carlo methods for sampling configurational states of a system of particles. -Briefly describe the REMD method -Explain the advantages and disadvantages of REMD compared to regular MD and other advanced sampling methods. -Discuss the practical aspects of setting up and running a REMD calculation.
26  cards
Key notes
Give examples of biological syste...,
Discuss changes in binding and st...,
Experimentally we can find the fr...
44  cards
Key notes final
What do computer simulations do a...,
Why bother using comupter simulat...,
What is an md simulation and how ...
78  cards

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CH412:Advanced Biophysical Chemistry 3

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