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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
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44  cards
Key notes final
No deck description has yet been added by the author.
78  cards

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ch412:advanced biophysical chemistry 3

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