68,718 Hits in 7.6 sec

Network visualization of conformational sampling during molecular dynamics simulation

Logan S. Ahlstrom, Joseph Lee Baker, Kent Ehrlich, Zachary T. Campbell, Sunita Patel, Ivan I. Vorontsov, Florence Tama, Osamu Miyashita
2013 Journal of Molecular Graphics and Modelling  
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

Alexander Kaiser, Oksana Ismailova, Antti Koskela, Stefan E. Huber, Marcel Ritter, Biagio Cosenza, Werner Benger, Renat Nazmutdinov, Michael Probst
2014 Journal of Molecular Liquids  
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

Robert Patro, Cheuk Yiu Ip, Sujal Bista, D. Thirumalai, Samuel S. Cho, Amitabh Varshney
2011 2011 IEEE Symposium on Biological Data Visualization (BioVis).  
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

Hagen Eckert, Maria Montagna, Arezoo Dianat, Rafael Gutierrez, Manfred Bobeth, Gianaurelio Cuniberti
2020 BMC Materials  
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

Smruti R. Panigrahi, Sankar Jayaram, Uma Jayaram, Hussein M. Zbib, Sinisa Dj. Mesarovic
2014 Modeling and Numerical Simulation of Material Science  
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

Bao-Yu Guo, Paul Zulli, Daniel Maldonado, Ai-Bing Yu
2010 Metallurgical and materials transactions. B, process metallurgy and materials processing science  
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

Randall T. Cygan, Jeffery A. Greathouse, Hendrik Heinz, Andrey G. Kalinichev
2009 Journal of Materials Chemistry  
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

Joao Francisco Ventrici de Souza, Maria Elisabete Darbello aniquelli
2012 Biophysical Journal  
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

Mica Grujicic, Subrahmanian Ramaswami, Jennifer Snipes, Ramin Yavari, Gary Lickfield, Chian-Fong Yen, Bryan Cheeseman
2013 Multidiscipline Modeling in Materials and Structures  
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

Md Shahriar K. Khandaker, Daniel M. Dudek, Eric P. Beers, David A. Dillard, David R. Bevan
2016 Journal of The Mechanical Behavior of Biomedical Materials  
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

Eric Behle, Adélaïde Raguin, Megan L. Matthews
2021 PLoS Computational Biology  
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

Marian Bulla, Stefan Kolling, Elham Sahraei
2021 Energies  
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

Abdelwahed Barkaoui, Ridha Hambli
2011 Journal of Applied Biomaterials & Functional Materials  
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

Daniela Ribeiro, Gabriel Yuto, Silvia Lenyra M. Campos Titotto
2019 Journal of Materials Science and Chemical Engineering  
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

Varshika Singh, Santanu Patra, Natarajan Arul Murugan, Dana-Cristina Toncu, Ashutosh Tiwari
2022 Materials Advances  
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
« Previous Showing results 1 — 15 out of 68,718 results