Modal reduction of mathematical models of biological molecules

DOI10.1016/J.JCP.2005.05.021MaRDI QIDQ2572799zbMATH OpenOpenAlexWikidataFDO

Authors Aiqin Li, E. H. Dowell

Publication date 4 November 2005

Published in Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jcp.2005.05.021

zbMATH Keywords

Biological moleculesComponent modal analysisLinear normal modeModal reductionProper orthogonal decomposition

Mathematics Subject Classification ID

Biophysics (92C05) Biochemistry, molecular biology (92C40)

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Cites work

• A fast algorithm for particle simulations
• Applications of centre manifold theory
• Efficient model reduction in nonlinear dynamics using the Karhunen-Loève expansion and dual-weighted-residual methods
• scientific article; zbMATH DE number 49702 (Why is no real title available?)
• Modelling of fluid-structure interaction
• Multiscale, Multiphenomena Modeling and Simulation at the Nanoscale: On Constructing Reduced-Order Models for Nonlinear Dynamical Systems With Many Degrees-of-Freedom
• NAMD2: Greater scalability for parallel molecular dynamics
• Normal Modes for Non-Linear Vibratory Systems
• Physical interpretation of the proper orthogonal modes using the singular value decomposition
• Reduced order dynamic model for polysaccharides molecule attached to an atomic force microscope
• Structure-preserving model reduction for mechanical systems

Cited in

(7)

• Part 2: Proper orthogonal modal modeling of a fractionally excited beam
• Proper orthogonal decomposition-based model order reduction via radial basis functions for molecular dynamics systems
• Mathematical and numerical results on the sensitivity of the POD approximation relative to the Burgers equation
• Model reduction in classical molecular dynamics
• A geometric method for model reduction of biochemical networks with polynomial rate functions
• Reduced order dynamic model for polysaccharides molecule attached to an atomic force microscope
• Using adaptive proper orthogonal decomposition to solve the reaction-diffusion equation

Describes a project that uses

Uses Software

• CHARMM
• NAMD2

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