期刊
VACCINE
卷 33, 期 44, 页码 5890-5896出版社
ELSEVIER SCI LTD
DOI: 10.1016/j.vaccine.2015.05.099
关键词
Virus-like particle; Molecular dynamics; Multiscale factorization; Computer-aided vaccine design
资金
- NSF INSPIRE program [ECCS-1344263]
- Indiana University College of Arts and Science via the Center for Theoretical and Computational Nanoscience
- Lilly Endowment, Inc.
- Indiana METACyt Initiative
Simulations of virus-like particles needed for computer-aided vaccine design highlight the need for new algorithms that accelerate molecular dynamics. Such simulations via conventional molecular dynamics present a practical challenge due to the millions of atoms involved and the long timescales of the phenomena of interest. These phenomena include structural transitions, self-assembly, and interaction with a cell surface. A promising approach for addressing this challenge is multiscale factorization. The approach is distinct from coarse-graining techniques in that it (1) avoids the need for conjecturing phenomenological governing equations for coarse-grained variables, (2) provides simulations with atomic resolution, (3) captures the cross-talk between disturbances at the atomic and the whole virus-like particle scale, and (4) achieves significant speedup over molecular dynamics. A brief review of multiscale factorization method is provided, as is a prospective on its development. (C) 2015 Elsevier Ltd. All rights reserved.
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