An Estimation Method of a Constitutive-law for the Rod Model of DNA using Discrete-Structure Simulations - Physics > Biological PhysicsReport as inadecuate




An Estimation Method of a Constitutive-law for the Rod Model of DNA using Discrete-Structure Simulations - Physics > Biological Physics - Download this document for free, or read online. Document in PDF available to download.

Abstract: The continuum-rod model has emerged as an efficient tool to describe thelong-length-scale structural-deformations of DNA which are critical tounderstanding the nature of many biological processes such as gene expression.However, a significant challenge in continuum-mechanics-based modeling of DNAis to estimate its constitutive law, which follows from its interatomicbond-stiffness. Experiments and all-atom molecular dynamics MD simulationshave suggested that the constitutive law is nonlinear and non-homogeneoussequence-dependent along the length of DNA. In this paper, we present anestimation method and a validation study using discrete-structure simulations.We consider a simple cantilever-rod with an artificially constructed, discretelattice-structure which gives rise to a constitutive law. Large deformationsare then simulated. An effective constitutive-law is estimated from thesedeformations using inverse methods. Finally, we test the estimated law byemploying it in the continuum rod-model and comparing the simulation resultswith those of discrete-structure simulations under a different cantileverloading-conditions.



Author: Adam R. Hinkle, Sachin Goyal, Harish J. Palanthandalam-Madapusi

Source: https://arxiv.org/







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