Molecular structure

Wednesday, September 30, 2015 - 1:30pm - 2:30pm
Domitilla Del Vecchio (Massachusetts Institute of Technology)
Control systems theory has laid out a powerful framework for modularly analyzing and designing the dynamics of interconnected input/output dynamical systems, wherein an interconnection is traditionally viewed as a one-way interaction. Whether biomolecular networks can be modularly analyzed and designed is one of the most vexing questions in systems biology and is also critical for the advancement of synthetic biology.
Friday, September 18, 2009 - 9:00am - 9:45am
Paul Callaghan (Victoria University of Wellington)
In the study of shear banding phenomena in wormlike micelles, Rheo-NMR has
proven of especial value, not only indicating the clear existence of shear
bands, but also that they are associated with fluctuations, and sometimes,
with molecular alignment. The subtlety of the correspondence (or lack of
correspondence) between birefringence effects and shear banded flow has also
been revealed. Recent measurements of shear-banded flow under Couette flow
of the micellar system cetylpyridinium chloride and sodium salicylate
Thursday, May 21, 2009 - 10:00am - 10:40am
Peter Bolhuis (Universiteit van Amsterdam)
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 Metadynamics can overcome these free energy barriers, and give thermodynamic equilibrium properties. However, they do not preserve the dynamical pathways needed to gain insight into kinetics and mechanism of conformational change.
Wednesday, May 20, 2009 - 2:00pm - 2:40pm
Christof Schütte (Freie Universität Berlin)
The talk will center around conformation dynamics and rare
Thursday, May 21, 2009 - 2:00pm - 2:40pm
Eric Darve (Stanford University)
Joint work with Amirali Kia and Jose Solomon.
Friday, May 22, 2009 - 9:00am - 9:40am
Ron Elber (The University of Texas at Austin)
Milestoning is a theory for stochastic coarse graining in space and time and an algorithm to compute kinetics and reaction dynamics of complex molecular systems. I will discuss the theory and algorithm properties, implementation, and an application to the folding of a helix and to the recovery stroke of the protein myosin. I will review the difficulties of simulating functions of biological molecules on relevant time scales and suggest that Milestoning addresses some of these problems.
Monday, December 8, 2008 - 11:10am - 11:50am
Florin Despa (University of California)
Hydration shells of normal proteins display both structured and bulk-
like waters. Isomers with considerable bulk-like hydration tend to
aggregate. In my talk, I will present both theoretical and experimental
data showing that different morphological states of aggregated isomers
differ by hydration distribution profiles and water magnetic resonance
(MR) signals. The results help explain the MR contrast patterns of
amyloids, a subject of long controversy, and suggest a new approach for
Thursday, January 17, 2008 - 2:00pm - 2:30pm
Alan Cheng (Amgen Cambridge Research Center)
Lead generation is a major hurdle in small-molecule drug discovery, with an estimated 60% of projects failing from lack of lead matter or difficulty in optimizing leads for drug-like properties. It would be valuable to identify these less-druggable targets before incurring substantial expenditure and effort. We discovered that a model-based approach using basic biophysical principles yields good prediction of druggability based solely on the crystal structure of the target binding site.
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