dc.contributor.authorXia, Kelin
dc.contributor.authorOpron, Kristopher
dc.contributor.authorWei, Guo-Wei
dc.date.accessioned2016-08-10T04:14:15Z
dc.date.available2016-08-10T04:14:15Z
dc.date.issued2013
dc.identifier.citationXia, K., Opron, K., & Wei, G.-W. (2013). Multiscale multiphysics and multidomain models—Flexibility and rigidity. The Journal of Chemical Physics, 139(19), 194109-.en_US
dc.identifier.issn0021-9606en_US
dc.identifier.urihttp://hdl.handle.net/10220/41111
dc.description.abstractThe emerging complexity of large macromolecules has led to challenges in their full scale theoretical description and computer simulation. Multiscale multiphysics and multidomain models have been introduced to reduce the number of degrees of freedom while maintaining modeling accuracy and achieving computational efficiency. A total energy functional is constructed to put energies for polar and nonpolar solvation, chemical potential, fluid flow, molecular mechanics, and elastic dynamics on an equal footing. The variational principle is utilized to derive coupled governing equations for the above mentioned multiphysical descriptions. Among these governing equations is the Poisson-Boltzmann equation which describes continuum electrostatics with atomic charges. The present work introduces the theory of continuum elasticity with atomic rigidity (CEWAR). The essence of CEWAR is to formulate the shear modulus as a continuous function of atomic rigidity. As a result, the dynamics complexity of a macromolecular system is separated from its static complexity so that the more time-consuming dynamics is handled with continuum elasticity theory, while the less time-consuming static analysis is pursued with atomic approaches. We propose a simple method, flexibility-rigidity index (FRI), to analyze macromolecular flexibility and rigidity in atomic detail. The construction of FRI relies on the fundamental assumption that protein functions, such as flexibility, rigidity, and energy, are entirely determined by the structure of the protein and its environment, although the structure is in turn determined by all the interactions. As such, the FRI measures the topological connectivity of protein atoms or residues and characterizes the geometric compactness of the protein structure. As a consequence, the FRI does not resort to the interaction Hamiltonian and bypasses matrix diagonalization, which underpins most other flexibility analysis methods. FRI's computational complexity is of at most, where N is the number of atoms or residues, in contrast to for Hamiltonian based methods. We demonstrate that the proposed FRI gives rise to accurate prediction of protein B-Factor for a set of 263 proteins. We show that a parameter free FRI is able to achieve about 95% accuracy of the parameter optimized FRI. An interpolation algorithm is developed to construct continuous atomic flexibility functions for visualization and use with CEWAR.en_US
dc.format.extent16 p.en_US
dc.language.isoenen_US
dc.relation.ispartofseriesThe Journal of Chemical Physicsen_US
dc.rights© 2013 American Institute of Physics. This paper was published in The Journal of Chemical Physics and is made available as an electronic reprint (preprint) with permission of American Institute of Physics. The published version is available at: [http://dx.doi.org/10.1063/1.4830404]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law.en_US
dc.subjectProteinsen_US
dc.subjectElasticityen_US
dc.titleMultiscale multiphysics and multidomain models—Flexibility and rigidityen_US
dc.typeJournal Article
dc.contributor.schoolSchool of Physical and Mathematical Sciencesen_US
dc.identifier.doihttp://dx.doi.org/10.1063/1.4830404
dc.description.versionPublished versionen_US


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