Estimating Constitutive Law of a Filament From its Deformed Shapes Using Input Reconstruction

2015 ◽  
Author(s):  
Roshan Chavan ◽  
Harish Palanthandalam-Madapusi ◽  
Sachin Goyal
Keyword(s):  
Molecular Dynamics ◽  
Constitutive Law ◽  
Structure Identification ◽  
Elastic Rod ◽  
Efficient Tool ◽  
Pair Sequence ◽  
Dynamics Simulations ◽  
Input Reconstruction ◽  
Elastic Rod Model ◽  
Atomistic Structure

Twisting and bending dynamics of biological filaments such as DNA play a central role in their biological activity including gene expression. The elastic rod model is an efficient tool to simulate such deformations. However, the accuracy of elastic rod predictions depend strongly on the constitutive law, which follows from the atomistic structure of the DNA molecule and is known to be nonlinear and to vary along the length according to the base pair sequence of the DNA. Unfortunately, it is impractical to derive the constitutive law analytically from the atomistic structure. Identification of the nonlinear sequence-dependent constitutive law from experimental data and feasible molecular dynamics simulations remains a significant challenge. In this paper, we extend earlier work by employing techniques based on input reconstruction and state estimation filters to estimate the constitutive law using molecular dynamics data of deformations in bio-filaments.

Atomistic structure of (Ba,Sr)TiO3: Comparing molecular-dynamics simulations with structural measurements

2013 ◽  
Vol 103 (2) ◽  
pp. 022909 ◽  
Author(s):  
M. J. Noordhoek ◽  
V. Krayzman ◽  
A. Chernatynskiy ◽  
S. R. Phillpot ◽  
I. Levin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Atomistic Structure

A Method for Identification of the Constitutive Law of Biological Filaments From Their Dynamic Equilibria

2015 ◽  
Author(s):  
Soheil Fatehiboroujeni ◽  
Sachin Goyal ◽  
Apostol Gramada
Keyword(s):  
Conformational Changes ◽  
Inverse Method ◽  
Vital Role ◽  
Constitutive Law ◽  
Cellular Processes ◽  
Inverse Approach ◽  
Double Stranded Dna ◽  
Dynamics Simulations ◽  
Dynamic Equilibria ◽  
Atomistic Structure

There are several biological filaments that play vital role in cellular processes via twisting and bending deformations. From the double-stranded DNA molecule containing genetic information to the cytoskeletal fibers that provide shape to the cell, biological filaments undergo conformational changes as they perform their biological tasks. Therefore the ability of a filament to deform, which depends on their atomistic structure, is a characteristic property that governs its biological functions. Since there is no direct analytic method to derive the deformability or constitutive law of such filaments from their atomistic structure, the constitutive law has to be identified from their actual deformations. An inverse approach based on a continuum rod model was developed recently that uses deformations in static equilibrium to estimate the constitutive law in bending and torsion. We extend the inverse method to use dynamic states of deformations, and consequently expand its scope to leverage a wide variety of choices in molecular dynamics simulations for identifying the constitutive law. This paper presents and validates the technique applying it to filaments with artificial atomistic structure.

Atomistic Structure of Calcium Silicate Intergranular Films Between Prism and Basal Planes in Silicon Nitride: A Molecular Dynamics Study

2004 ◽  
Vol 19 (3) ◽  
pp. 752-758 ◽  
Author(s):  
Xiaotao Su ◽  
Stephen H. Garofalini
Keyword(s):  
Molecular Dynamics ◽  
Interatomic Potential ◽  
Intergranular Films ◽  
Ca Ions ◽  
The Difference ◽  
Dynamics Simulations ◽  
Experimental Findings ◽  
Bonding Characteristics ◽  
Atomistic Structure ◽  
Crystal Interface

Molecular dynamics simulations of approximately 15 Å thick intergranular films (IGFs) containing SiO2 and CaO in contact with two surface terminations of the prism (10¯10) and basal planes (0001) of Si3N4 were performed using a multibody interatomic potential. Samples with the same composition (1.5 mol% CaO) and number of atoms but different crystal planes (i.e., the prism and basal planes of Si3N4) were studied. In both the prism and basal cases, the IGF in the final configuration is well-ordered in the interface region. A small number of N ions from the crystal moved into the IGF near the interface, and O ions moved into the N sites in the crystal, indicating the formation of a Si–O–N interface. In addition, Ca ions do not segregate to the IGF–crystal interface. The bonding characteristics of the O ions at the interface with neighbor Si ions are different in the prism and basal cases. Such difference may be explained by the difference in the two crystal Si3N4 surfaces. The Si–O bond length of the IGF has a range from 1.62 Å to 1.64 Å, consistent with recent experimental findings.

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