SEMINAR @ SISSA, SBP, dr. S. Bottaro - March 19, at 11.00 hrs.

[Barbara Corzani]

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STATISTICAL AND BIOLOGICAL PHYSICS SEMINAR
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Dott. Sandro Bottaro

Technical University of Denmark (DTU)



Title:

"Conducting Monte Carlo simulations of dense molecular systems”

 

Mon March 19, 2012 @ 11.00 a.m.

 

SISSA – First floor – room 132
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Abstract:

 

Although Markov chain Monte Carlo simulation is a potentially powerful
approach for exploring
conformational space of biomolecules, it has been unable to compete
with molecular dynamics
in the analysis of high density structural states, such as the native
state of globular proteins.
Here, we introduce a novel Monte Carlo move, CRISP, that greatly
enhances the sampling efficiency in
all-atom MC simulations of dense systems. The algorithm is based on an
exact analytical solution
to the classic chain-closure problem,  making it possible to express
the interdependencies among
degrees of freedom in the molecule as correlations in a multivariate
Gaussian distribution.
We demonstrate that our method reproduces  structural variation in
proteins with greater efficiency
than current state-of-the-art Monte Carlo methods,  and has real-time
simulation performance on par
with molecular dynamics simulations. The presented  results suggest
our method as a valuable tool
in the study of molecules in atomic detail, offering a potential
alternative to molecular dynamics for
probing long time-scale conformational transitions.



 

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Barbara Corzani - FA and SBP Secretariat
SISSA - Via Bonomea 265, 34136 Trieste
Santorio A Building, fourth floor, room 402
Tel: 0403787424
Fax: 0403787466
E-mail:  <mailto:corzani at sissa.it> corzani at sissa.it
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