Optimization problem in biomolecular simulations with DCA-based modeling of transition from a coarse to a fine fidelity

Kurt S. Anderson, Mohammad Poursina

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Scopus citations

Abstract

In multiscale modeling of highly complex biomolecular systems, it is desirable to switch the system model either to coarser, or higher fidelity models to achieve the appropriate accuracy and speed. These transitions are achieved by effectively imposing (or releasing) certain systems constraints from a fine scale model to a reduced order model (or vice versa). The transition from a coarse model to a fine one may not result in a unique solution. Therefore, a knowledge-based or physics-based optimization procedure may be used to arrive at the finite number of solutions. In this paper, it is shown that traditional approaches to address and solve the optimization problem such as Lagrange multipliers or changing the constrained optimization problem to an unconstrained one based on coordinate partitioning or basic linear algebra methods are computationally expensive for biomolecular systems. It is demonstrated that using a DCA based approach in modeling the transition can reduce dramatically the computational expense associated with the manipulations performed as part of optimization as well as the ones performed to derive the dynamics of the transition.

Original languageEnglish (US)
Title of host publicationProceedings of the ASME International Design Engineering Technical Conferences and Computers and Information in Engineering Conference 2009, DETC2009
Pages1467-1475
Number of pages9
EditionPART C
DOIs
StatePublished - Jun 25 2010
Event2009 ASME International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, DETC2009 - San Diego, CA, United States
Duration: Aug 30 2009Sep 2 2009

Publication series

NameProceedings of the ASME International Design Engineering Technical Conferences and Computers and Information in Engineering Conference 2009, DETC2009
NumberPART C
Volume4

Conference

Conference2009 ASME International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, DETC2009
CountryUnited States
CitySan Diego, CA
Period8/30/099/2/09

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Hardware and Architecture
  • Electrical and Electronic Engineering

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    Anderson, K. S., & Poursina, M. (2010). Optimization problem in biomolecular simulations with DCA-based modeling of transition from a coarse to a fine fidelity. In Proceedings of the ASME International Design Engineering Technical Conferences and Computers and Information in Engineering Conference 2009, DETC2009 (PART C ed., pp. 1467-1475). (Proceedings of the ASME International Design Engineering Technical Conferences and Computers and Information in Engineering Conference 2009, DETC2009; Vol. 4, No. PART C). https://doi.org/10.1115/DETC2009-87319