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Description:: All-atom explicit solvent molecular dynamics simulations of (un)folding and other conformational changes in proteins remain a great challenge because of the long time scales involved. These long times are due to high free energy barriers between metastable states. Rare event simulation methodology, such as Replica Exchange (REMD) and Metadynamic...
Creator:: Bolhuis, Peter (Universiteit van Amsterdam)
Created:: 2009-05-21
Contributed By:: University of Minnesota, Institute for Mathematics and its Applications.
Last Updated:: 2018-06-19

Description:: Conformational changes in proteins are intrinsic to almost every function, but sampling such changes remains one of the most difficult bio-computational problems. The challenge lies on two levels. First, algorithms which can efficiently focus computer time on the correct path ensemble are necessary. Second, even if perfect path-sampling algorith...
Creator:: Zuckerman, Daniel M. (University of Pittsburgh)
Created:: 2009-05-21
Contributed By:: University of Minnesota, Institute for Mathematics and its Applications.
Last Updated:: 2018-06-19

Description:: The behavior of supercooled polymer melt composed of shortchains with ten beads between rapidly oscillating plates issimulated by using a hybrid simulation of molecular dynamicsand computational fluid dynamics.The flow profiles of polymer melt near an oscillating plate arequite different from those of Newtonian fluid.The viscous boundary layer o...
Creator:: Yamamoto, Ryoichi (Kyoto University)
Created:: 2009-05-21
Contributed By:: University of Minnesota, Institute for Mathematics and its Applications.
Last Updated:: 2018-06-19

Description:: In the first part of the talk, I will explain why we may need to go beyond the standard framework of transition state theory (TST) to describe activated processes and reactive events, and I will present another framework, termed transition path theory (TPT), that permits to do that. Unlike TST, which gives mainly an expression for the rate of th...
Creator:: Vanden-Eijnden, Eric (New York University)
Created:: 2009-05-21
Contributed By:: University of Minnesota, Institute for Mathematics and its Applications.
Last Updated:: 2018-06-19

Description:: In this talk I shall describe two kinds of soft matter system in whichthe interfacial behaviour is of interest. Firstly, the adsorption ofpolymers and peptides on solid surfaces is of growing interest becauseof the possible applications in biotechnology. We have recently improveda Monte Carlo simulation method for studying lattice polymers near ...
Creator:: Allen, Michael Philip (University of Warwick)
Created:: 2009-05-20
Contributed By:: University of Minnesota, Institute for Mathematics and its Applications.
Last Updated:: 2018-06-19

Description:: The sequence dependent folding landscapes of nucleic acidhairpins reflect much of the complexity of biomolecularfolding. Recently, mechanical folding trajectories, generatedusing single molecule force clamp experiments by attachingsemiflexible polymers to the ends of hairpins have been used toinfer their folding landscapes. Using simulations and...
Creator:: Thirumalai, Devarajan (University of Maryland)
Created:: 2009-05-20
Contributed By:: University of Minnesota, Institute for Mathematics and its Applications.
Last Updated:: 2018-06-19

Description:: We discuss theoretical and computational methodologies for quantitativelydescribing how cell-membrane topologies are actively mediated andmanipulated by intracellular protein assemblies. Such scenarios areubiquitous in intracellular trafficking mechanisms, i.e., active transportmechanisms characterized by vesicle nucleation and budding of the ce...
Creator:: Radhakrishnan, Ravi (University of Pennsylvania)
Created:: 2009-05-20
Contributed By:: University of Minnesota, Institute for Mathematics and its Applications.
Last Updated:: 2018-06-19

Description:: The talk will center around 'conformation dynamics' and 'rareevents.'
Creator:: Schütte, Christof (Freie Universität Berlin)
Created:: 2009-05-20
Contributed By:: University of Minnesota, Institute for Mathematics and its Applications.
Last Updated:: 2018-06-19

Description:: We present the need (especially critical for multiscale simulations) of extending standard equilibrium Molecular Dynamics to nonequilibrium situations. We show how this is possible in full rigor by use of the nonlinear Kubo-Onsager relation, connecting dynamical nonequilibrium averages to equilibrium (more genarally, initial distribution) averag...
Creator:: Ciccotti, Giovanni (Università di Roma 'La Sapienza')
Created:: 2009-05-19
Contributed By:: University of Minnesota, Institute for Mathematics and its Applications.
Last Updated:: 2018-06-19

Description:: 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.
Last Updated:: 2018-06-19