[Colloquium] Seminar Announcement: Orientational Accuracy for Coarse Graining Gained from Multidimensional Free Energy Volumes -TODAY!

[Ninfa Mayorga]

CI/CCI Seminar

Speaker: Kevin J. Naidoo, Scientific Computing Research Unit and Department of Chemistry , University of Cape Town, Rondebosch, Cape Town, 7701, South Africa 
Host: Karl Freed 
Date: April 5, 2012
Time: 2:30 PM - 3:30 PM
Location: University of Chicago, Searle 240A, 5735 S. Ellis Avenue

Orientational Accuracy for Coarse Graining Gained from Multidimensional Free Energy Volumes 

Abstract: 
Our recently generalized adaptive reaction coordinate force biasing method termed the Free Energies from Adaptive Reaction Coordinate Forces (FEARCF) method1-3 will be described. I will show its ability to produce multidimensional free energy volumes. The effective searching and sampling of configurational space using the FEARCF approach is illustrated by calculating the thermodynamics of benzene-benzene association in vacuum and water as a function of the molecules' relative orientation. We find that while the potential energy and enthalpy play an important role in the association of benzene dimers they do not determine their orientation on close contact in solution. 4 

Using the free energy volume derived from all atom simulations we are able to produce orientationally accurate coarse-grain simulations, by parameterizing a suitable effective coarse-grain intermolecular potential (viz., the Gay-Berne potential). The structure and dynamics of the benzene solvent observed from these coarse-grain simulations show excellent correlation with that of the all atom simulations and experimental observations. 

Finally, we hint at the possibility of parameterizing coarse grain potentials from QM/MM simulations. We do this with reference to our developmental work on the acceleration of the general electronic structure package GAMESS-UK.5 on General purpose Graphical Processing Units (GPGPUs).5 These initiatives point to an era where highly accurate long time scale dynamic simulations of biophysical systems are possible. 

References: 
(1) Barnett, C. B.; Naidoo, K. J. Mol. Phys. 2009, 107, 1243. 
(2) Strümpfer, J.; Naidoo, K. J. J. Comp. Chem. 2010, 31, 308. 
(3) Naidoo, K. J. SCIENCE CHINA Chemistry 2011, 54, 1962. 
(4) Gamieldien, M. R.; Strümpfer, J.; Naidoo, K. J. The Journal of Physical Chemistry B 2012, 116, 324. 
(5) Wilkinson, K.; Sherwood, P.; Guest, M. F.; Naidoo, K. J. J. Comp. Chem. 2011, 32, 2313. 




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