A geometric initial guess for localized electronic orbitals in modular biological systems
Abstract
Recent firstprinciples molecular dynamics algorithms using localized electronic orbitals have achieved O(N) complexity and controlled accuracy in simulating systems with finite band gaps. However, accurately deter mining the centers of these localized orbitals during simulation setup may require O(N ^{3}) operations, which is computationally infeasible for many biological systems. We present an O(N) approach for approximating orbital centers in proteins, DNA, and RNA which uses nonlocalized solutions for a set of fixedsize subproblems to create a set of geometric maps applicable to larger systems. This scalable approach, used as an initial guess in the O(N) firstprinciples molecular dynamics code MGmol, facilitates firstprinciples simulations in biological systems of sizes which were previously impossible.
 Authors:
 Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Univ. of Chicago, IL (United States)
 Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
 Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
 Publication Date:
 Research Org.:
 Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
 Sponsoring Org.:
 USDOE
 OSTI Identifier:
 1393357
 Report Number(s):
 LLNLTR738503
 DOE Contract Number:
 AC5207NA27344
 Resource Type:
 Technical Report
 Country of Publication:
 United States
 Language:
 English
 Subject:
 59 BASIC BIOLOGICAL SCIENCES; 74 ATOMIC AND MOLECULAR PHYSICS; 97 MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
Citation Formats
Beckman, P. G., Fattebert, J. L., Lau, E. Y., and OseiKuffuor, D. A geometric initial guess for localized electronic orbitals in modular biological systems. United States: N. p., 2017.
Web. doi:10.2172/1393357.
Beckman, P. G., Fattebert, J. L., Lau, E. Y., & OseiKuffuor, D. A geometric initial guess for localized electronic orbitals in modular biological systems. United States. doi:10.2172/1393357.
Beckman, P. G., Fattebert, J. L., Lau, E. Y., and OseiKuffuor, D. 2017.
"A geometric initial guess for localized electronic orbitals in modular biological systems". United States.
doi:10.2172/1393357. https://www.osti.gov/servlets/purl/1393357.
@article{osti_1393357,
title = {A geometric initial guess for localized electronic orbitals in modular biological systems},
author = {Beckman, P. G. and Fattebert, J. L. and Lau, E. Y. and OseiKuffuor, D.},
abstractNote = {Recent firstprinciples molecular dynamics algorithms using localized electronic orbitals have achieved O(N) complexity and controlled accuracy in simulating systems with finite band gaps. However, accurately deter mining the centers of these localized orbitals during simulation setup may require O(N3) operations, which is computationally infeasible for many biological systems. We present an O(N) approach for approximating orbital centers in proteins, DNA, and RNA which uses nonlocalized solutions for a set of fixedsize subproblems to create a set of geometric maps applicable to larger systems. This scalable approach, used as an initial guess in the O(N) firstprinciples molecular dynamics code MGmol, facilitates firstprinciples simulations in biological systems of sizes which were previously impossible.},
doi = {10.2172/1393357},
journal = {},
number = ,
volume = ,
place = {United States},
year = 2017,
month = 9
}

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