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Energy landscapes #9

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maxentile opened this issue May 16, 2015 · 2 comments
Open

Energy landscapes #9

maxentile opened this issue May 16, 2015 · 2 comments

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@maxentile
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How can we inspect them? How are they structured in general?

How to inspect:

  1. Sampling -- Collect a large number of conformations
  2. Analytical -- Inspect simple models (e.g. Geometry of Random Fields book)

Previous work:
"Dynamics of hierarchical folding on energy landscapes of hexapeptides" http://wws.weizmann.ac.il/sb/faculty_pages/Levy/sites/weizmann.ac.il.sb.faculty_pages.Levy/files/ma_jcp.pdf
@maxentile
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How much insight can generalize across different protein systems?

@maxentile
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Nice slides by David Wales: https://www.icts.res.in/media/uploads/Old_Talks_Lectures/Document/1267764052David-Wales-Jan7.pdf

  • Visualizing energy landscapes in terms of disconnectivity graphs / trees: each leaf is a potential energy minimum, and two leaves are merged in the tree at the minimum energy required to reach one from another
  • Describing energy landscapes in terms of the potential energy function, Hessian of the potential energy function, etc.
  • Basin-hopping algorithm
  • Coverage of elastic band algorithm and nudge-elastic band algorithm

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@maxentile