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 Citations (Scopus)

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 Design Engineering Technical Conference
Pages1467-1475
Number of pages9
Volume4
EditionPARTS A, B AND C
DOIs
StatePublished - 2009
Externally publishedYes
EventASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE2009 - San Diego, CA, United States
Duration: Aug 30 2009Sep 2 2009

Other

OtherASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE2009
CountryUnited States
CitySan Diego, CA
Period8/30/099/2/09

Fingerprint

Fidelity
Optimization Problem
Modeling
Simulation
Multiscale Modeling
Reduced Order Model
Optimization
Number of Solutions
Constrained Optimization Problem
Knowledge-based
Lagrange multipliers
Linear algebra
Model
Unique Solution
Constrained optimization
Manipulation
Partitioning
Complex Systems
Switch
Physics

ASJC Scopus subject areas

  • Mechanical Engineering
  • Computer Graphics and Computer-Aided Design
  • Computer Science Applications
  • Modeling and Simulation

Cite this

Anderson, K. S., & Poursina, M. (2009). Optimization problem in biomolecular simulations with DCA-based modeling of transition from a coarse to a fine fidelity. In Proceedings of the ASME Design Engineering Technical Conference (PARTS A, B AND C ed., Vol. 4, pp. 1467-1475) https://doi.org/10.1115/DETC2009-87319

Optimization problem in biomolecular simulations with DCA-based modeling of transition from a coarse to a fine fidelity. / Anderson, Kurt S.; Poursina, Mohammad.

Proceedings of the ASME Design Engineering Technical Conference. Vol. 4 PARTS A, B AND C. ed. 2009. p. 1467-1475.

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

Anderson, KS & Poursina, M 2009, Optimization problem in biomolecular simulations with DCA-based modeling of transition from a coarse to a fine fidelity. in Proceedings of the ASME Design Engineering Technical Conference. PARTS A, B AND C edn, vol. 4, pp. 1467-1475, ASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE2009, San Diego, CA, United States, 8/30/09. https://doi.org/10.1115/DETC2009-87319
Anderson KS, Poursina M. Optimization problem in biomolecular simulations with DCA-based modeling of transition from a coarse to a fine fidelity. In Proceedings of the ASME Design Engineering Technical Conference. PARTS A, B AND C ed. Vol. 4. 2009. p. 1467-1475 https://doi.org/10.1115/DETC2009-87319
Anderson, Kurt S. ; Poursina, Mohammad. / Optimization problem in biomolecular simulations with DCA-based modeling of transition from a coarse to a fine fidelity. Proceedings of the ASME Design Engineering Technical Conference. Vol. 4 PARTS A, B AND C. ed. 2009. pp. 1467-1475
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