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Record 30 of 5617
Better, Cheaper, Faster Molecular Dynamics
Author and Affiliation:
Pohorille, Andrew(NASA Ames Research Center, Moffett Field, CA United States)
DeVincenzi, Donald L. [Technical Monitor]
Abstract: Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.
Publication Date: Feb 28, 2001
Document ID:
20010095453
(Acquired Oct 19, 2001)
Subject Category: AEROSPACE MEDICINE
Document Type: Preprint
Meeting Information: Numerical Methods Seminar; 21 Feb. 2001; Unknown
Contract/Grant/Task Num: RTOP 344-38-22-06
Financial Sponsor: NASA Ames Research Center; Moffett Field, CA United States
Organization Source: NASA Ames Research Center; Moffett Field, CA United States
Description: 1p; In English
Distribution Limits: Unclassified; Publicly available; Unlimited
Rights: No Copyright
NASA Terms: MOLECULAR DYNAMICS; ALGORITHMS; COMPUTERIZED SIMULATION; EQUATIONS OF MOTION; MOLECULAR BIOLOGY; PARALLEL PROCESSING (COMPUTERS); ARCHITECTURE (COMPUTERS); COMPUTER AIDED DESIGN; DRUGS; ELECTROSTATICS; FOLDING; FREE ENERGY; MASSIVELY PARALLEL PROCESSORS; PARALLEL COMPUTERS; SPACE EXPLORATION
Availability Source: Other Sources
Availability Notes: Abstract Only
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