Overview talk:<br/><br/>Advanced computing platforms offer a microscope<br/><br/>for [simulating] conformational changes
Tuesday, January 13, 2009 - 2:00pm - 2:45pm
Solving challenging conformational dynamics problems requires advanced tools from chemistry, mathematics, physics, biology, engineering and scientific computing. In recent years, an enormous range of methods has been proposed for exploring conformational space, deducing mechanistic information, computing free energy profiles, and estimating reaction rates. Methods range from simple stochastic approaches to various spectral-based methods, to coarse-graining approaches, to rigorous mathematical approaches that manipulate by divide and conquer strategies the energy function an simulation protocol. A flavor of this enormous range of innovative approaches will be presented through selected examples and applications. Applications to DNA polymerases fidelity mechanisms by transition path sampling, molecular dynamics, and quantum/classical hybrid simulations will also be described.