Institute of Technology, Resource and Energy-efficient Engineering (TREE)
TREE-Kolloquium - Andreas Krämer: "MD Simulations"
Date
Tuesday, 18 December 2018
Time
15:00 - 16:30
Andreas Krämer berichtet seinem Vortrag von seinen ersten Projekten als Postdoc am Laboratory of Computational Biology der National Institutes of Health (NIH) in Bethesda, MD, das in der Nähe von Washington D.C. angesiedelt ist.
Titel des Vortrags ist: "Membrane Permeability from Conventional MD Simulations: Counting Transitions vs. Bayesian Analysis"
Abstract:
The permeation of small molecules through membranes can presently be observed in conventional (i.e., non-enhanced) molecular dynamics simulations. This contribution focuses on three important aspects of such calculations. (1) The advantages and disadvantages of calculating permeability by direct counting of transition events versus Bayesian analysis based on the inhomogeneous solubility diffusion model. (2) A new Python/C++ tool that speeds up a previous implementation of the Bayesian analysis by two orders of magnitude and allows permeabilities to be extracted in a matter of seconds from a previously generated trajectory. (3) Simulated permeabilities of water, oxygen, and ethanol through various homogeneous bilayers. The results fall short of the experimental values, clearly demonstrating the requirement for accurate polarizable force fields.
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Dirk Reith
Computational Science and Engineering , Managing Director of the TREE Institute, Presidential commissioner for institutional research co-operations, Faculty Advisor BRS Motorsport
Research fields
Location
Sankt Augustin
Room
B 223
Address
Grantham-Allee 20
53757 Sankt Augustin
Telephone
+49 2241 865 9678