Coarse-graining the potential energy surface into the basins ofattraction of local minima, provides a computational framework forinvestigating structure, dynamics and thermodynamics in molecularscience. Steps between local minima form the basis for globaloptimisation via basin-hopping and for calculating thermodynamicproperties using the superpo...
Creator:
Wales, David John (University of Cambridge)
Created:
2009-05-19
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Large scale conformational rearrangements represent both achallenge and an opportunity for rational drug design.Exploring the conformational space of a target protein with sufficient detail is computationally very demanding and most current docking programs are very limited in this respect.If it were possible, however, it could open the avenue t...
Creator:
Gervasio, Francesco Luigi (Eidgenössische TH Zürich)
Created:
2009-05-19
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
The study of the interaction between (large) molecules and inorganic (metal) surfaces is a typical multiscale problem. In fact while the specific chemistry emergesat the quantum scale with the interaction of the electrons of the surface with the valenceelectrons of the molecule, the molecular conformations are instead the expression of a large s...
Creator:
Delle Site, Luigi (Max-Planck Institut für Polymerforschung)
Created:
2009-05-19
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
I will present a computational method for simulating the dynamics of atomic systems on time scales much longer than can be accessed with classical dynamics. Possible reaction mechanisms available to the system are found by exploring the potential energy surface from minima to find nearby saddle points. Reaction rates are then calculated using ha...
Creator:
Henkelman, Graeme (The University of Texas at Austin)
Created:
2009-05-18
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
I will discuss a coarse-grained model of molecular dynamics incrystalline solids. Such system usually has an underlying latticestructure, and the empirical potentials are of quite simple forms.Thus it provides a nice setting in which coarse-graining (CG) methodscan be considered. The goal of the CG method is to reduce theatomic degrees of freedo...
Creator:
Li, Xiantao (The Pennsylvania State University)
Created:
2009-05-18
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
I will present a seamless multiscale method for the study of fluid systems with unknown constitutive relationsand/or unknown boundary conditions. The multiscale method aims at capturing the macroscale behaviorof the fluid system; this is done by combining the conservation laws for the mass and momentum (the macro model)and the molecular dynamics...
Created:
2009-05-18
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
In this talk I will discuss some of the problems arising in connection with the dynamics of polymers under confinement (such as proteins traversing transmembrane pores). Confinement often partitions a polymer's configuration space into distinct basins of attraction separated by large free energy barriers. Because of the predominantly entropic na...
Creator:
Makarov, Dmitrii E. (The University of Texas at Austin)
Created:
2009-05-18
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.