Kinetochores are nano-structures that mechanically couple chromosomesto dynamic microtubules to generate the forces necessary for properchromosome segregation during mitosis. Recent studies reveal newdetails of the kinetochore's molecular composition and structure,demonstrating the mechanically compliant nature of the kinetochorelinkage to the m...
Creator:
Odde, David J. (University of Minnesota, Twin Cities)
Created:
2013-05-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
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.
Several phenomena take place at the interface between liquid water and the gold (111) surface. For example, it is a widespread system for controlled electrochemical investigations, for the study of molecular conduction and of the interaction between proteins and the solid surfaces in water. Despite this great and interdisciplinary importance, th...
Creator:
Corni, Stefano (Consiglio Nazionale delle Ricerche (CNR))
Created:
2008-12-10
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Joint work with Marat Valiev, Niri Govind, Peng-Dong Fan,W.A. de Jong(William R Wiley Environmental Molecular Sciences Laboratory andChemical Sciences Division,Pacific Northwest National LaboratoryP.O. Box 999, MS K1-96, Richland, WA 99352) and Jeff R. Hammond(The University of Chicago).The coupled-cluster (CC) methodology has become a leadingfo...
Creator:
Kowalski, Karol (Battelle Pacific Northwest National Laboratory)
Created:
2008-09-29
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Recent studies have questioned the consistency and applicability of the existing implicit-solvent models in which solvent accessible surfaces (SAS) or solvent excluded surfaces (SES) are pre-defined, and used for the calculation of solvation free energies. As an emerging concept and theory, the variational implicit solvation determines equilibri...
Creator:
Li, Bo (University of California, San Diego)
Created:
2008-12-09
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
First-principles molecular dynamics (FPMD) is a simulation method that combines molecular dynamics with the accuracy of a quantum mechanical description of electronic structure. It is increasingly used to address problems of structure determination, statistical mechanics, and electronic structure of solids, liquids and nanoparticles. The high co...
Creator:
Gygi, François (University of California, Davis)
Created:
2008-10-03
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
For molecular dynamics to be useful for recovering macroscopically-relevant information (e.g. thermodynamic averages), it must be regulated by auxiliary control laws. Typically these would represent thermal or pressure controls. In this talk I will discuss a general family of stochastic-dynamic methods, including gentle thermostats which mildly ...
Creator:
Leimkuhler, Benedict (University of Edinburgh)
Created:
2009-05-22
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Few years ago, we have succeeded to "probe" water molecules bound in a cavity of a protein by means of the statistical mechanics of molecular liquids, or the RISM/3D-RISM theory. This is the first finding in the history of the statistical mechanics to show that the theory is applicable to such fluids in an extremely inhomogeneous field in atomic...
Creator:
Hirata, Fumio (National Institutes of Natural Sciences)
Created:
2008-12-11
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Molecular phylogenetics is concerned with inferring evolutionaryrelationships (phylogenetic trees) from biological sequences (such asaligned DNA sequences for a gene shared by a collection of species).The probabilistic models of sequence evolution that underly statisticalapproaches in this field exhibit a rich algebraic structure.After an introd...
Creator:
Allman, Elizabeth S. (University of Alaska)
Created:
2007-03-06
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
The efficient determination of reliable rare event statistics is one of the grand challenges in molecular dynamics. For example, direct accurate computation of folding rates requires very long simulations, in many cases infeasibly long ones. The question of how the exploration of such transition statistics can be sped up has attracted much atten...
Creator:
Schütte, Christof (Freie Universität Berlin)
Created:
2009-01-13
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Conformation dynamics aims at an identification of dynamically metastable subsets of the position space of molecular systems.A time-discretized molecular simulation of such a system leads to a Markov operator. A space discretization of this operator leads to a stochastic transition matrix. In the talk, a cluster algorithm is presented which iden...
Creator:
Weber, Marcus (Konrad-Zuse-Zentrum für Informationstechnik (ZIB))
Created:
2009-01-13
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Joint work with Sophya Garashchuk (Universit of South Carolina).Semiclassical implementation of the quantum trajectory formalism [J. Chem. Phys. 120, 1181 (2004)] is further developed to give stable long-time description of zero-point energy in anharmonic systems of high dimensionality. The method is based on a numerically cheap linearized quant...
Creator:
Rassolov, Vitaly (University of South Carolina)
Created:
2009-01-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Intracellular transport is driven primarily by molecular motorproteins, such as kinesin and dynein, which convert chemical energy(stored in ATP) to directed motion along microtubules. Mathematicalmodels of this process typically involve stochastic elements todescribe the progress of binding and other chemical steps in themolecular motor stepping...
Creator:
Kramer, Peter R. (Rensselaer Polytechnic Institute)
Created:
2013-05-13
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Molecular dynamics simulation has become a powerful tool for studying biochemical properties. At the heart of these calculations is the potential energy function that describes intermolecular interactions in the system, and often it is the accuracy of the potential energy surface that determines the reliability of simulation results. The current...
Creator:
Gao, Jiali (University of Minnesota, Twin Cities)
Created:
2009-01-15
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Knowledge of uncertainties is a key requirement for the acceptance of molecular simulation as part of an engineering toolkit. One of the main sources of uncertainty in a molecular simulation is the force field (interatomic potential) used to model the material. We will discuss our efforts to provide researchers with useful information to help th...
Creator:
Becker, Chandler (National Institute of Standards and Technology)
Created:
2013-12-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
This talk will highlight recent work in our group in which we use Diffusion Monte Carlo approaches to study molecular vibrations of several fluxional systems. The molecular systems that will be the focus of the talk will be CH5+ and ion-water complexes. For these studies, we focus on two approaches. The first involves a fixed-node treatment of r...
Creator:
McCoy, Anne B. (The Ohio State University)
Created:
2009-01-12
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.