Algorithms in MacroMolecular Modeling Conference November 11 – 15, 2009

The next AM³ conference Algorithms in MacroMolecular Modeling will be held in Austin Texas November 11-15, 2009.

Location

Austin is the capital of Texas and home to the University of Texas at Austin with about 50,000 students. Also called the "live music captial of the world," it offers a variety of entertainment options far superior to reading this web page. It is easily accessed by air by most major airlines and public transportation to and in the city is exceptional.

Scope of the Meeting

With advances in multi-core systems, special purpose hardware and software, and in algorithms and physics-based theory, molecular modeling and simulation has become a standard partner to experiment. Computer simulations help to create plausible atomic structures from low-resolution images of large biomolecular complexes, and link the static experimental structures of proteins and nucleic acids with their dynamic behavior in aqueous solution and realistic environment of the cell. Molecular dynamics (MD) and other modeling and simulation techniques can offer an effective tool for refining experimental models and for probing systematically how molecules fold and reshape and perform the basic functions of life. Modeling provides comprehensive atomically detailed picture of the process that supplement the average and more limited experimental information. Yet many fundamental and practical limitations face biomolecular modelers. They include the approximate nature of the governing force fields as well as simulation protocols, the limited range of configurational sampling and relatively short trajectory times, the neglect of quantum effects in classical molecular dynamics, and the enormous computational requirements (needed to simulate a solvated macro-molecular system with full details of the environment). New algorithmic approaches, hierarchical spatial representations, and improved computing platforms are thus continuously in demand to enhance the reliability of macromolecular simulations, enhance the scope of theoretical work, and address biological problems with great specificity. In light of the highly multidisciplinary nature of macromolecular modeling, educational efforts are also crucial for training the current generation of young biomolecular modelers.

Purpose of the meeting

This meeting brings together both the developers of computational and theoretical tools for biomolecular simulations and those biological and chemical scientists interested in modeling applications. The meeting will be genuinely cross-disciplinary, with representation from most relevant areas on the organizing committee and in the invited speaker lists. Applied mathematicians and computer scientists will benefit from close interaction with the modelers — to direct their formulation of numerical and algorithmic problems and their focus on the most critical open problems. Biochemical modelers will, in turn, be exposed to recent developments in theory numerical analysis and algorithms from which their studies can benefit. Consistently, a lag has occurred between developments in the mathematical community and their transfer, implementation, and application to biological and chemical areas. An example is the development of algorithms to compute rate and extend the time scale of simulations.