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Quasicontinuum representations of atomic-scale mechanics: From proteins to dislocations

Phillips, Rob and Dittrich, ­Markus and Schulten, ­Klaus (2002) Quasicontinuum representations of atomic-scale mechanics: From proteins to dislocations. Annual Review of Materials Research, 32 . pp. 219-233. ISSN 1531-7331. http://resolver.caltech.edu/CaltechAUTHORS:PHIarmr02

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Abstract

Computation is one of the centerpieces of both the physical and biological sciences. A key thrust in computational science is the explicit mechanistic simulation of the spatiotemporal evolution of materials ranging from macromolecules to intermetallic alloys. However, our ability to simulate such systems is in the end always limited in both the spatial extent of the systems that are considered, as well as the duration of the time that can be simulated. As a result, a variety of efforts have been put forth that aim to finesse these challenges in both space and time through new techniques in which constraint is exploited to reduce the overall computational burden. The aim of this review is to describe in general terms some of the key ideas that have been set forth in both the materials and biological setting and to speculate on future developments along these lines. We begin by developing general ideas on the exploitation of constraint as a systematic tool for degree of freedom thinning. These ideas are then applied to case studies ranging from the plastic deformation of solids to the interactions of proteins and DNA.


Item Type:Article
Additional Information:"Reprinted, with permission, from the Annual Review of Materials Research, Volume 32 copyright 2002 by Annual Reviews, www.annualreviews.org" We acknowledge fruitful collaborations and conversations with Michael Ortiz, Art Voter, Niles Pierce, Steve Mayo, Jay Ponder, Richard Lavery, Vivek Shenoy, Vijay Shenoy, Ron Miller, Ellad Tadmor, and David Rodney. The molecular images in this paper were created with the molecular graphics program VMD (8). MD and KS acknowledge support under grants NIH PHS 5 P41RR05969 and NRAC MCA93S028; RP acknowledges support from the NSF. The collaboration of the authors during the project and preparation of this review was greatly facilitated by BioCoRE (3a).
Subject Keywords:proteins; coarse-graining; atomistic simulation
Record Number:CaltechAUTHORS:PHIarmr02
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:PHIarmr02
Alternative URL:http://dx.doi.org/10.1146/annurev.matsci.32.122001.102202
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:3888
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:19 Jul 2006
Last Modified:26 Dec 2012 08:56

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