Campuses:

Molecular

Friday, January 16, 2009 - 12:20pm - 1:20pm
David Coker (Boston University)
No Abstract
Tuesday, January 13, 2009 - 4:30pm - 5:00pm
Christof Schütte (Freie Universität Berlin)
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 attention recently. The talk will
present some new approaches to this problem. In these approaches the energy landscape of
Monday, January 12, 2009 - 2:00pm - 2:45pm
Anne McCoy (The Ohio State University)
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 rotationally and vibrationally excited states. This approach enables us to evaluate the zero-order bright state associated with a particular molecular vibration.
Tuesday, December 9, 2008 - 3:00pm - 3:40pm
Bo Li (University of California, San Diego)
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 equilibrium solute-solvent interfaces and solvation free energies by minimizing a mean-field free-energy functional. This free energy couples the surface energy, dispersive interaction, and electrostatic contribution.
Thursday, December 11, 2008 - 11:30am - 12:10pm
Fumio Hirata (National Institutes of Natural Sciences)
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 scale. On the other hand, the finding implies that we got a powerful machinery in our hand to clarify the “molecular recognition” which is the most fundamental process in living cells.
Wednesday, December 10, 2008 - 11:30am - 12:10pm
Stefano Corni (Consiglio Nazionale delle Ricerche (CNR))
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, the wettability properties of the gold surface are microscopically not well understood. For example, the contact angle between water and clean gold is zero, thus the gold surface is considered hydrophilic [1].
Monday, September 29, 2008 - 1:30pm - 2:20pm
Karol Kowalski (Pacific Northwest National Laboratories)
Joint work with Marat Valiev, Niri Govind, Peng-Dong Fan,
W.A. de Jong
(William R Wiley Environmental Molecular Sciences Laboratory and
Chemical Sciences Division,
Pacific Northwest National Laboratory
P.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 leading
formalism not only in gas-phase calculations but also in
modeling systems for which the inclusion of the surrounding
Tuesday, March 6, 2007 - 9:00am - 9:50am
Elizabeth Allman (University of Alaska)
Molecular phylogenetics is concerned with inferring evolutionary
relationships (phylogenetic trees) from biological sequences (such as
aligned DNA sequences for a gene shared by a collection of species).
The probabilistic models of sequence evolution that underly statistical
approaches in this field exhibit a rich algebraic structure.

After an introduction to the inference problem and phylogenetic
models, this talk will survey some of the highlights of current
Monday, December 16, 2013 - 3:55pm - 4:25pm
Chandler Becker (National Institute of Standards and Technology)
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 them make informed selections of these models in a timely manner.
Thursday, May 16, 2013 - 10:15am - 11:05am
David Odde (University of Minnesota, Twin Cities)
Kinetochores are nano-structures that mechanically couple chromosomes
to dynamic microtubules to generate the forces necessary for proper
chromosome segregation during mitosis. Recent studies reveal new
details of the kinetochore’s molecular composition and structure,
demonstrating the mechanically compliant nature of the kinetochore
linkage to the microtubule. This finding stands in contrast to
previous theoretical models of kinetochore motility (Hill, 1985;
Molodtsov et al., 2005), which assumed an infinitely stiff linkage.

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