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Network visualization of conformational sampling during molecular dynamics simulation
2013
Journal of Molecular Graphics and Modelling
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Effective data reduction methods are necessary for uncovering the inherent conformational relationships present in large molecular dynamics (MD) trajectories. ...
We compare the results of network visualization against 11 clustering algorithms and principal component conformer plots. ...
Acknowledgments L.S.A. gratefully appreciates funding from the NIH training grant GM084905 and from Achievement Rewards for College Scientists (Phoenix chapter). ...
doi:10.1016/j.jmgm.2013.10.003
pmid:24211466
pmcid:PMC3893665
fatcat:sfipbz73rzbetbgxb5jk7e3w2m
Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network
2014
Journal of Molecular Liquids
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Molecular dynamics simulations of liquid ethylene glycol described by the OPLS-AA force field were performed to gain insight into its hydrogen-bond structure. ...
In an attempt to understand the complicated hydrogen-bonding, we developed new molecular visualization tools within the Vish Visualization shell and used it to visualize the life of each individual hydrogen-bond ...
Acknowledgments This work was supported by the Austrian Science Fund (FWF) under the project I200-N29 and the DK+ Project on Computational Interdisciplinary Modeling, W1227-N16. ...
doi:10.1016/j.molliq.2013.05.033
pmid:24748697
pmcid:PMC3990454
fatcat:4ve2k4osufgi3nx5pgk636iy4e
MDMap: A system for data-driven layout and exploration of molecular dynamics simulations
2011
2011 IEEE Symposium on Biological Data Visualization (BioVis).
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Contemporary molecular dynamics simulations result in a glut of simulation data, making analysis and discovery a difficult and burdensome task. ...
We represent a molecular dynamics simulation as a state transition graph over a set of intermediate (stable and semi-stable) states. ...
Any opinions, findings, conclusions, or recommendations expressed in this article are those of the authors and do not necessarily reflect the views of the research sponsors. ...
doi:10.1109/biovis.2011.6094055
dblp:conf/biovis/PatroIBTCV11
fatcat:o22gdmswbndvtjijjdgmvdre2m
Exploring the organic–inorganic interface in biosilica: atomistic modeling of polyamine and silica precursors aggregation behavior
2020
BMC Materials
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In this work, we use all-atom Molecular Dynamics simulations to investigate the aggregation behavior of polysilicic acid and silica nanoparticles in solution in the presence of protonated long-chain polyamines ...
Our main simulation results are in qualitative agreement with in vitro experiments, so that we expect they can contribute to shedding light on the initial stages of biosilica mineralization in diatoms. ...
Kröger (BCube Dresden, Germany), Armin Geyer (Philipps University of Marburg, Germany), and Miguel Jorge (University of Strathclyde, UK) for very fruitful and interesting discussions. ...
doi:10.1186/s42833-020-00012-z
fatcat:2ehp2n5vbzeijn7vaapmecdpai
Immersive 3D Visualization of the Collective Behavior of Particles and Crystal Dislocations Using Virtual Reality Technology
2014
Modeling and Numerical Simulation of Material Science
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Understanding of such behaviors and developments of coarse-scale theories, often requires insight into collective behavior that can only be obtained through immersive visualization. ...
In this article, we present a three-dimensional visualization technique that has been developed in order to establish an interactive immersive environment to visualize the particles in granular materials ...
Ok Joon Kim in helping setup the Virtual Reality Devices for the demonstrations in the VRCIM Lab at WSU and Dr. Jagan Padbidri for sharing his expertise in contact mechanics. ...
doi:10.4236/mnsms.2014.43010
fatcat:j5hnzfogknbhlpj4zc62zfkcd4
A Model to Simulate Titanium Behavior in the Iron Blast Furnace Hearth
2010
Metallurgical and materials transactions. B, process metallurgy and materials processing science
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In the current article, a mathematical model based on computational fluid dynamics is proposed to simulate the behavior of solid particles in the liquid iron. ...
The model provides an insight into the fundamental mechanism of solid particle formation, and it may form a basic model for subsequent development to study the formation of titanium scaffold in the blast ...
In the current article, a mathematical model based on computational fluid dynamics is proposed to simulate the behavior of solid particles in the liquid iron. ...
doi:10.1007/s11663-010-9384-2
fatcat:5y464kfscvfy5doqoosfckrk7u
Molecular models and simulations of layered materials
2009
Journal of Materials Chemistry
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The low symmetry, multicomponent compositions, defects, and disorder phenomena of clays and related phases necessitate the use of molecular models and modern simulation methods. ...
Combined with classical energy minimization, molecular dynamics, and Monte Carlo techniques, quantum methods provide accurate models of layered materials such as clay minerals, layered double hydroxides ...
Department of Energy, Office of Basic Energy Sciences, Geosciences Research received through the Sandia contract and university grants DE-FG02-00ER-15028 and DE-FG02-08ER-15929. ...
doi:10.1039/b819076c
fatcat:k2fwre7o4jhf3hm733cn35adxa
Particulate Material Effects on Pulmonary Surfactant Models
2012
Biophysical Journal
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These studies show that both the size and morphology of membrane rafts can be controlled by adjusting the composition and the type of low-melting lipid in mixtures with high-melting lipid and cholesterol ...
liquid-ordered and liquid-disordered coexistence region in DSPC/DOPC/ POPC/Chol mixtures. ...
We study lipid phase behavior using giant unilamellar vesicles to model cell membrane dynamics. ...
doi:10.1016/j.bpj.2011.11.1597
fatcat:ltmkwk4gpveg5hdpyrjri6yfsa
Molecular-level computational investigation of mechanical transverse behavior of p-phenylene terephthalamide (PPTA) fibers
2013
Multidiscipline Modeling in Materials and Structures
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Figure 3 shows several examples of the computational models used. The models used were all constructed using Visualizer [I] and Amorphous Cell [II] molecular-microstructure pre-processing tools. ...
material constitutive models capable of describing the behavior of fibers and structures under high-rate loading conditions. ...
doi:10.1108/mmms-11-2012-0018
fatcat:32245dfcvzfxfkxgfpaytkjnoi
Molecular modeling of the elastomeric properties of repeating units and building blocks of resilin, a disordered elastic protein
2016
Journal of The Mechanical Behavior of Biomedical Materials
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Using molecular dynamics (MD) simulations, we studied the relative roles of SYGAP, and its less common variants SYSAP and TYGAP, on the elastomeric properties of resilin. ...
What we learned from simulating the repetitive motifs of resilin may be applicable to the biology and mechanics of other elastomeric biomaterials, and may provide us the deeper understanding of their unique ...
Brown and former ESM graduate student Albert L. Kwansa, for their help with the use of GROMACS and NAMD. ...
doi:10.1016/j.jmbbm.2016.01.017
pmid:26851528
fatcat:e6xivrethzd6db5cl4rr2u4ddi
Stochastic model of lignocellulosic material saccharification
2021
PLoS Computational Biology
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The saccharification dynamics is simulated in silico using a stochastic procedure based on a Gillespie algorithm. ...
We model a cell wall microfibril composed of cellulose and surrounded by hemicellulose and lignin, with various relative abundances and arrangements. ...
Besides, Charlier and Mazeau [19] proposed a molecular dynamics model including cellulose, xylan, water, and lignin. ...
doi:10.1371/journal.pcbi.1009262
pmid:34516546
pmcid:PMC8460048
fatcat:smvuyeklsjau5jmxhoc5fws5xm
A Material Model for the Orthotropic and Viscous Behavior of Separators in Lithium-Ion Batteries under High Mechanical Loads
2021
Energies
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For the safety and crashworthiness investigations, a deeper understanding of the mechanical behavior under high and dynamic loads is needed. ...
The purpose is to predict the anisotropic, rate-dependent stiffness behavior of separator materials in order to improve FE simulations of the mechanical behavior of batteries and therefore reduce the development ...
Acknowledgments: The authors would like to thank to Boston Powers for providing the isolator materials.
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/en14154585
fatcat:yb3yjtdkmnewxc2vgmoc75xdz4
Finite element 3D modeling of mechanical behavior of mineralized collagen microfibrils
2011
Journal of Applied Biomaterials & Functional Materials
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In the present paper an equivalent homogenised model was developed to assess the whole microfibril mechanical properties (Young's modulus and Poisson's ratio) under varying mechanical properties of each ...
The aim of this work is to develop a 3D finite elements model to study the nanomechanical behaviour of mineralized collagen microfibrils, which consists of three phases, (i) collagen phase formed by five ...
and the 3D simulation using the multiphase model. ...
doi:10.5301/jabb.2011.8876
pmid:22139755
fatcat:wowwsn4cc5gtvkuxpqal2orr7m
Analysis about the Behavior and Modeling of pH-Sensitive Hydrogels with Different Ratios of Chitosan and Polyvinylpyrrolidone
2019
Journal of Materials Science and Chemical Engineering
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After the collection of results and in order to understand the phenomena in a visual way, models of the molecules were also elaborated using the Avogadro software. ...
Smart material can be defined as a material that can dock or convert energy between physical domains or as a material that can generate a response, in their characteristics, properties or geometries, when ...
Acknowledgements Thank FAPESP, CNPq, the chemistry didactic laboratory at UFABC and the research group "4D Printing and Biomimetics" for the support. ...
doi:10.4236/msce.2019.78008
fatcat:axzax2gqs5eznhcjc5prrpurou
Recent trends in computational tools and data-driven modeling for advanced materials
2022
Materials Advances
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The paradigm of advanced materials has grown exponentially over the last decade, with their new dimensions including digital design, dynamics, and functions. ...
Acknowledgements The authors gratefully acknowledge the financial support from the International Association of Advanced Materials. ...
CHARMM QM/MM Modeling and simulation OpenMM Molecular dynamics Simulation YASARA Molecular dynamics Molecular graphics, modeling, and simulation TINKER Molecular mechanics Molecular dynamics Modeling ...
doi:10.1039/d2ma00067a
fatcat:2ww2zqtj6vf2ta7djtkbqyc7hm
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