• abstract = "Molecular dynamics simulations were performed for an axial-chiral liquid crystalline (LC) monolayer under trans-monolayer gas flow. (elsevierpure.com)
  • Add to Calendar 2023-11-09T16:00:00 0223-11-09T17:00:00 Molecular Simulations of Protein Structure and Dynamics Event Information: Abstract:Molecular dynamics (MD) simulations offer a powerful tool to investigate the structure and dynamics of proteins because they can provide an all-atom view of their complex conformational landscapes. (ubc.ca)
  • http://www.cjmr.org/EN/abstract/abstract9072.shtml. (kingston.ac.uk)
  • Our simulations of a coarse-grained Aβ peptide model predicts 10 different planar β-strand dimer conformations. (psu.edu)
  • We demonstrate the efficacy of SCMD through empirical validations on the complex molecular system (i.e., single-chain coarse-grained polymers in implicit solvent) for long-duration simulation and dynamical property prediction. (openreview.net)
  • Molecular dynamics has a wide range of applications in the life sciences, such as the mechanistic study of protein folding, the mechanistic study of enzyme-catalyzed reactions, the study of the motion of functionally relevant proteins, and the study of large scale conformational changes of biological macromolecules. (iaanalysis.com)
  • Molecular dynamics (MD) simulations offer a powerful tool to investigate the structure and dynamics of proteins because they can provide an all-atom view of their complex conformational landscapes. (ubc.ca)
  • We performed targeted molecular dynamics simulation to obtain trajectory of conformational change from inactive to active form. (intechopen.com)
  • The time series of correlation between residues during the conformational change generated by targeted molecular dynamic simulation. (intechopen.com)
  • Using the built model, a novel compound was proposed, and molecular docking and molecular dynamics simulation were then used to check the conformational stability of the newly proposed compound in the binding site of EGFR. (japsonline.com)
  • Using a series of diverse virology and computational methods, as well as molecular dynamics simulations for conformational mobility, the researchers showed that hypervariable region 1 (HVR1) acts as a "safety catch" that regulates entry. (who.int)
  • We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. (uea.ac.uk)
  • From atomistic molecular dynamics simulations, the many-body electronic polarization effect was found to be important for modeling ILs, especially their dynamics. (uchicago.edu)
  • Nonequilibrium molecular dynamics simulations provide an efficient way of calculating transport coefficients of molecular fluids. (aiche.org)
  • Permeation of water across the membrane/vapor and membrane/liquid-water interfaces of Nafion is studied using nonequilibrium molecular dynamics (NEMD) simulations, providing direct calculations of mass-transfer resistance. (princeton.edu)
  • The conclusions are supported by state-of-the-art molecular dynamics calculations. (osti.gov)
  • We mostly used molecular mechanics (MM) in order to model the protein-ligand interactions, which is more approximate than quantum-mechanical (QM) methods, but necessary to reduce the computational cost when doing calculations on protein-ligand systems, which often contain tens of thousand of atoms. (lu.se)
  • Describe various techniques for Monte Carlo and molecular dynamics calculations of equilibrium properties of complex systems with many degrees of freedom. (lu.se)
  • Molecular dynamics thermodynamic integration (MDTI) method and quantum chemical calculations at the density functional theory B3LYP 6-31+(d,p) level, which included the Tomasi model of the solvent reaction field, were applied to study the tautomeric equilibrium of Mannich base in methanol solution. (cdc.gov)
  • However, the results from quantum mechanical calculations were not as good as the results of MDTI simulations owing to inappropriate treatment of intermolecular hydrogen bonds between the solute molecule and the first shell of solvent molecules in the Tomasi model of the solvent reaction field. (cdc.gov)
  • Molecular Dynamics (MD) is one of the most commonly used methods in molecular simulation. (iaanalysis.com)
  • Currently, molecular dynamics methods have been successfully applied to the modeling of low-energy conformations of macromolecular systems, X-ray crystal diffraction, and the processing of NMR experimental results. (iaanalysis.com)
  • This technique can be seamlessly integrated with molecular simulation methods such as molecular docking and pharmacophore. (iaanalysis.com)
  • Advances in molecular dynamics simulations and enhanced sampling methods for the study of protein systems. (iaanalysis.com)
  • To achieve this, we estimated elastic characteristics of crossbridge components from their known atomic structures by employing molecular dynamic simulations (CHARMM), using three different methods. (solindies.com)
  • MD offers a useful tool to elucidate the molecular basis for effects observed using experimental methods, and to quantitatively describe differences in protein ensembles. (ubc.ca)
  • These methods are multi-scale in nature, direct comparisons between high fidelity density functional the- ory (DFT) and linear-scaling MSD simulations is done throughout this work, with advancements made to MSD allowing for electronic structure changes being reflected in classical dynamics. (sandia.gov)
  • Recognise problems that can be approached with Monte Carlo or molecular dynamics methods. (lu.se)
  • The course begins with a brief introduction to methods for Monte Carlo and molecular dynamics simulations. (lu.se)
  • apply numerical methods, such as Molecular Dynamics Metropolis Monte Carlo simulations · use Statistical Mechanical tools with, as well as without, the aid of computer programs to calculate various properties of macroscopic systems. (lu.se)
  • Here we elucidate the molecular mechanism of these drugs by combining experiments and simulations. (rsc.org)
  • The essential dynamics analysis of GlnBP also revealed a third class of motion which suggests a mechanism for signal transmission in GluRs. (ox.ac.uk)
  • Molecular dynamics simulations were performed for highlighting the mechanism of cross resistance displayed by the Gly407Ser mutation. (cdc.gov)
  • The investigation provides novel insight into the dynamics of an intramolecular excitation energy transfer mechanism that can be used to activate long-lived metal centered excited states of importance for emerging photocatalytic and sustainable solar energy conversion applications. (lu.se)
  • The molecular mechanism of entry remains largely undefined and presents a challenge both in the understanding of fundamental molecular aspects of HCV and in the potential design of new therapeutics beyond the current direct-acting antivirals. (who.int)
  • The implemented routines analyze the protein environment of water molecules in molecular dynamics (MD) simulations and can differentiate between hydrogen bonded waters as well as waters in a protein environment of hydrophobic, charged, or aromatic atom groups. (acs.org)
  • PyRod adds a new perspective to structure-based screening campaigns by providing easy-to-interpret dMIFs and purely protein-based pharmacophores that are solely based on tracing water molecules in MD simulations. (acs.org)
  • We present molecular-dynamics (MD) simulations of surface tension of aqueous ionic solutions of different concentrations for two different salts with different anion size: NaCl and NaF at 300 K in explicit water molecules. (rti.org)
  • There were many challenges to overcome in designing and implementing QMPFF3-based molecular dynamics simulations especially to study the behavior of water molecules next to hydrophobic surfaces at atomic detail and subpicosecond time resolution. (phys.org)
  • Unlike most molecular viewers that show static structures, molecular dynamics models show functions of molecules, primarily through visualizing the cause-effect relationships set up by properly-chosen initial conditions or directed by user operations in the middle of a simulation. (concord.org)
  • At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules. (uea.ac.uk)
  • Based on molecular force fields, this method is able to dynamically describe the motion of molecules and subsequently the dynamic processes of life. (iaanalysis.com)
  • We studied the deposition dynamics of C 2 H 2 molecules on diamond reconstructed (001)-(2×1) surface by molecular dynamics method using semi-empirical many-body Brenner potential (#2). (epj.org)
  • Ring penetrations occur when two or more molecules overlap, which leads to unrealistic and unphysical behavior in the simulations of a molecule. (cbirt.net)
  • From large language models (LLMs) that generate de novo proteins, small molecules, and the 3D structure of a protein to molecular dynamic simulations, novel deep learning techniques are changing the way that scientists explore the ever-expanding chemical and biological research space. (nvidia.com)
  • The radial distribution functions between solute atoms and solvent atoms confirmed the formation of hydrogen bonds between the solute molecule and surrounding methanol molecules and indicated that the zwitterionic form is associated more with an organized solvent structure at the level of the first solvation shell than is the molecular form. (cdc.gov)
  • All human download introduction to practice of molecular simulation molecular dynamics monte carlo brownian dynamics landscapes should turn brought by a heavy adhesive still to spring. (kendewaard.com)
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  • basics of Monte Carlo, basics of Molecular Dynamics. (lu.se)
  • Additionally, we compared how MD and grand-canonical Monte Carlo (GCMC) can be used to assess dynamics and thermodynamics of protein-ligand binding for both buried and solvent-exposed binding sites. (lu.se)
  • Describe various techniques for Monte Carlo simulations of naturally stochastic processes, such as scattering processes. (lu.se)
  • Conduct Monte Carlo simulations of naturally stochastic processes. (lu.se)
  • Conduct Monte Carlo and molecular dynamics simulations of equilibrium properties of complex systems. (lu.se)
  • The gathered information is further processed to generate dynamic molecular interaction fields (dMIFs) for visualization and pharmacophoric features for virtual screening. (acs.org)
  • Molecular dynamics models can be used as a complementary tool to molecular visualization tools widely used in classrooms, such as Jmol. (concord.org)
  • LongBondEliminator is a tool designed to detect and fix ring penetrations in simulation systems and can be used as a plugin for the molecular visualization program Visual Molecular Dynamics (VMD). (cbirt.net)
  • Then doing the required parameters molecular dynamic from trajectory and extraction simulation and analyzing of results were done. (journalcra.com)
  • Trajectory analysis and molecular dynamics simulations of the Gly407Ser variant. (cdc.gov)
  • Moreover, we systematically investigate changes of dynamical behavior by varying the molecular weight of the polymers and investigate the interpretation of experimental results, in particular of nuclear magnetic resonance data. (tu-darmstadt.de)
  • Ring penetrations is a prevalent problem that leads to unrealistic physical behavior in simulations, and LongBondEliminator provides a powerful solution and has the potential to enhance the accuracy of simulations for a number of applications. (cbirt.net)
  • The multiscale coarse-graining methodology has also been employed to increase the simulation speed by a factor of 100 or more, thereby making it possible to study the mesoscopic behavior of ILs by computer simulations. (uchicago.edu)
  • LongBondEliminator (LBE) is a plugin for the molecular simulation engine NAMD that can identify and correct ring-piercing errors caused by the addition of new entities to the system. (cbirt.net)
  • Clara for Drug Discovery includes a variety of tools and frameworks for molecular simulation, including GROMACS , NAMD , Tinker-HP , VMD , TorchANI , and DeePMD-Kit . (nvidia.com)
  • Simulations were performed with the NAMD 2.12b1 ( 2 ) software using the CHARMM36m force field, TIP3P waters, a time step of 2 femtoseconds, and periodic boundary conditions. (cdc.gov)
  • Scalable molecular dynamics with NAMD. (cdc.gov)
  • In collaboration with BioExcel, ENCCS is offering an online workshop on advanced GROMACS simulations taught by Dr Mark Abraham, Dr Christian Blau, and Dr Artem Zhmurov. (lu.se)
  • International journal of molecular sciences 2023 0 0. (cdc.gov)
  • Human molecular genetics 2023 0 0. (cdc.gov)
  • Dr. Gaurav Chopra and Professor Michael Levitt in the Department of Structural Biology used molecular dynamics simulations involving a state-of-the-art Quantum Mechanical Polarizable Force Field (QMPFF3) to study the hydration of buckminsterfullerene, the smallest hydrophobic nanosphere widely referred to as a buckyball or C 60 . (phys.org)
  • In this paper, we propose a structural causal molecular dynamics model (SCMD), the first causality-based framework to model interatomic and dynamical interactions in molecular systems by inferring causal relationships among atoms from observational data. (openreview.net)
  • Using ideas from computer vision, we adapt a specific type of neural network called a PointNet to identify local structural environments in molecular simulations. (osti.gov)
  • Visual Molecular Dynamics (to view and analyze the molecular dynamics trajectories). (msu.ru)
  • With increasing computational power, it is now possible to generate very long and complex simulations, which are cumbersome to explore using traditional 3D animations of protein movements. (eg.org)
  • Molecular computational were simulated and were studied. (journalcra.com)
  • Dr. Sarah Rauscher is a computational biophysicist whose research addresses the challenging problem of understanding the structure and dynamics of intrinsically disordered proteins. (ubc.ca)
  • Markov state models have become popular in the computational biochemistry and biophysics communities as a technique for identifying stationary and kinetic information of protein dynamics from molecular dynamics simulation data. (aip.org)
  • The toolbox can address a wide set of tasks in computational biology struggling to account for protein flexibility, and supports the full-atom model building, optimization/equilibration of the molecular system, classical/conventional and accelerated molecular dynamics simulations. (msu.ru)
  • We have assessed and used computational tools for this aim, most of them based on molecular dynamics (MD) simulations. (lu.se)
  • A computational investigation of a rhodium-based light-harvesting complex based on ab initio molecular dynamics simulations carried out by members of the Computational Chemistry Division is highlighted on the Cover of the latest issue of Chemical Science - the flagship journal of the Royal Society of Chemistry (RSC). (lu.se)
  • As no experimental structure is available, we provide a model of the TMPRSS2 equilibrium structure and its fluctuations by relaxing an initial homology structure with extensive 330 microseconds of all-atom molecular dynamics (MD) and Markov modeling. (rsc.org)
  • and 2), we employ all-atom molecular mechanics simulations to estimate thermodynamic stability of all dimer conformations. (psu.edu)
  • We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. (psu.edu)
  • The COMPASS force field was used as the molecular mechanics force field in the simulations. (pku.edu.cn)
  • Nearly, 100 ns MD simulation indicated the stability of the designed compounds at 100 ns, while molecular mechanics-Poisson Boltzmann surface area calculation showed that the designed compound had a higher affinity than that of the parent compound. (japsonline.com)
  • We expect the easyAmber will contribute to a wide-spread implementation of the molecular dynamics at a daily laboratory routine, supporting a recent trend away from inefficient "static" approaches in protein sciences towards a deeper understanding of the dynamics in protein structures. (msu.ru)
  • Molecular Workbench offers 2D and 3D interactive molecular dynamics simulations for teaching physics, chemistry, and biology. (concord.org)
  • In this molecular dynamics simulation study we ascertain the dynamics of the glass transition for polymer melts and ionic liquids. (tu-darmstadt.de)
  • We find that various scaling approaches, which incorporate different control parameters, e.g., temperature, volume and entropy, describe the dramatic slowdown of dynamics approaching the glass transition for an ionic liquid and four polymer systems. (tu-darmstadt.de)
  • Understanding the physical properties of ionic liquids (ILs) via computer simulation is important for their potential technological applications. (uchicago.edu)
  • Using simulations, we study biomolecular systems consisting of hundreds of thousands to millions of atoms on a nanosecond to microsecond timescale. (ubc.ca)
  • The extended discrete element method (XDEM) is a numerical technique that extends the dynamics of granular material or particles as described through the classical discrete element method (DEM) (Cundall and Allen) by additional properties such as the thermodynamic state, stress/strain or electro-magnetic field for each particle. (wikipedia.org)
  • 79.20.Rf - Atomic, molecular, and ion beam impact and interactions with surfaces / 61.20.Ja - Computer simulation of liquid structure / 81.15.Gh - Chemical vapor deposition (including plasma-enhanced CVD, MOCVD, etc. (epj.org)
  • Together they represent a potential energy surface from which the mechanical forces on the atoms and the precession dynamics of the atomic spins are computed. (sandia.gov)
  • In contrast, our approach is a generic framework that requires no system-specific feature engineering and operates on the raw output of the simulations, i.e., atomic positions. (osti.gov)
  • Furthermore, we provide a detailed analysis on the origin of deviations between the theoretic framework of polymer dynamics and experimental results. (tu-darmstadt.de)
  • Moreover, the glass transition temperature range of the molecular asphalt model was computed from the relationship between the specific volumes and temperatures after the molecular dynamics experimental simulation. (mtu.edu)
  • Diffusion coefficients were determined from long NVT simulation times (up to 3 or 1.5 ns) in the temperature range of 278-378 K. The diffusion coefficients calculated fromthe Einstein relationship agree well with available experimental data. (pku.edu.cn)
  • Numerical simulation of fluid injection into a gaseous environment nowadays is adopted by a large number of CFD-codes such as Simcenter STAR-CCM+, Ansys and AVL-Fire. (wikipedia.org)
  • Explain the different sources of errors in numerical simulations and how the choice of algorithm may influence the convergence of simulations. (lu.se)
  • Significantly, the influence of the ligand on GlnBP dynamics is similar to that previously observed in simulations of rat glutamate receptor (GluR2) ligand-binding domain. (ox.ac.uk)
  • Through molecular dynamics we have analysed the stability of the ISCA1-cryptochrome complex and characterized the interaction at the binding sites between individual cryptochrome and ISCA1. (nature.com)
  • Our goal is to provide customers from all over the world with professional and reliable molecular interaction research assistance, and to reduce the time and cost of project research for customers. (iaanalysis.com)
  • Note: This article is part of the Special Topic "Markov Models of Molecular Kinetics" in J. Chem. (aip.org)
  • For this purpose we study poly(propyleneoxide) in a neutral confinement of four geometries and find length scales, which describe the evolution of bulk dynamics approaching the glass transition. (tu-darmstadt.de)
  • Molecular dynamics (MD) simulations describe the mechanical behaviors of molecular systems through empirical approximations of interatomic potentials. (openreview.net)
  • The simulation approach enables us to identify contributions unaccounted for in common interpretation and theoretic consideration and quantify them. (tu-darmstadt.de)
  • In case studies with different MD simulation data sets and research questions, we found that the proposed visual analysis approach facilitates exploratory analysis to generate, confirm, or reject hypotheses about causalities. (eg.org)
  • We introduce a molecular dynamics approach to study Aβ dimer formation. (psu.edu)
  • Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. (uea.ac.uk)
  • Our results suggest the approach will be broadly applicable to many types of local structure in simulations. (osti.gov)
  • article{osti_1542673, title = {A generalized deep learning approach for local structure identification in molecular simulations}, author = {DeFever, Ryan S. and Targonski, Colin and Hall, Steven W. and Smith, Melissa C. and Sarupria, Sapna}, abstractNote = {Identifying local structure in molecular simulations is of utmost importance. (osti.gov)
  • The molecular dynamics is a very complex approach, and the general-purpose protocols implemented in our toolbox may require further customization to fit the particular research objective. (msu.ru)
  • In a previous simulation study of the M.janaschii dimer it was found that the monomer-monomer contacts in the GDP bound dimer is lower which results in the high curvature of the GDP bound protofilaments. (biorxiv.org)
  • The present study provides new insight into differences and similarities between a wide range of glass formers, the application of theoretic models of the glass transition, application of confinements to investigate the glass transition, methodical understanding of NMR observables, and deviations from predicted regimes in polymer dynamics. (tu-darmstadt.de)
  • The objectives of this molecular dynamics study are to simulate the asphalt model using the common components from the references, and to predict the physical properties of asphalt material. (mtu.edu)
  • Molecular dynamics (MD) simulations were performed to study the transport properties of gases (oxygen, nitrogen, and methane) in amorphous cis -1,4-polyisoprene over a wide range of temperatures. (pku.edu.cn)
  • The goal of this study was to identify the epidemiological and molecular characteristics of TBEV associated with fatal meningoencephalitis in Mongolia. (who.int)
  • Molecular dynamics is a computer simulation technique widely used in academic research to assist scientists to discover new materials, new chemicals, and increasingly important, new drugs. (concord.org)
  • LiGaMD and LiGaMD2 simulations could capture repetitive ligand binding and unbinding events within microsecond simulations, allowing to simultaneously characterize ligand binding thermodynamics and kinetics , which is expected to greatly facilitate drug design . (bvsalud.org)
  • In this work, the effect of hydrostatic compression on dehydrogenation of crumpled graphene is investigated using molecular dynamics simulation. (lettersonmaterials.com)
  • GPU-powered molecular dynamics frameworks can simulate the fundamental mechanisms of cells and calculate how strongly a candidate drug will bind to its intended protein target. (nvidia.com)
  • Exploration of the Shared Molecular Mechanisms between COVID-19 and Neurodegenerative Diseases through Bioinformatic Analysis. (cdc.gov)
  • Molecular dynamics simulations can help you understand the motion and biological functions of biological macromolecules and protein-small molecule interactions at the molecular level. (iaanalysis.com)
  • In this paper, we extend the applicability of automated Markov state modeling to simulation data of molecular self-assembly and aggregation by constructing collective coordinates from molecular descriptors that are invariant to permutations of molecular indexing. (aip.org)
  • As a proof of principle, we demonstrate our Markov state model technique on simulations of the KFFE peptide, a subsequence of Alzheimer's amyloid-β peptide and one of the smallest peptides known to aggregate into amyloid fibrils in vitro . (aip.org)
  • Machine-learned potentials, which show promise for quantum mechanical-level accuracy, energies, and forces, are fundamentally changing molecular simulation. (nvidia.com)
  • Here we use microsecond molecular dynamics simulations to explore the effect of stalk deletion on enzymatic activity, contrasting NA proteins from the A/swine/Shandong/N1/2009 strain both with and without a stalk deletion. (nih.gov)
  • I will present recent and ongoing simulation studies of proteins across the continuum of protein disorder, from ordered states of proteins in crystals to intrinsically disordered regions. (ubc.ca)
  • Understanding molecular self-assembly is of critical importance if we want to deepen our understanding of neurodegenerative diseases where the aggregation of misfolded or disordered proteins is thought to be the main culprit. (aip.org)
  • While many studies have been focused on the membrane structure, the dynamics of such systems are crucial for the function of the membrane including membrane bound proteins. (lu.se)
  • Accelerating Molecular Dynamics Simulations for Drug Discovery. (bvsalud.org)
  • Compared with explicit water MD simulations, SPM gives qualitatively incorrect results for the dependence of surface tension on the type of salt. (rti.org)
  • Although much has been learned about reaction dynamics involving one hydrogen atom, less is known about those processes where two or more hydrogen atoms participate. (osti.gov)
  • A data-driven framework is presented for building magneto-elastic machine-learning interatomic potentials (ML-IAPs) for large-scale spin-lattice dynamics simulations. (sandia.gov)
  • Having a precise description of water s structure is critical to constructing accurate simulations of molecular events, including protein folding, substrate binding, macromolecular recognition, and complex formation. (phys.org)
  • We also use these simulations to predict previously unrecognized druggable "hotspots" on the neuraminidase surface that may prove useful for future efforts aimed at structure-based drug design. (nih.gov)
  • The toxicity of Aβ oligomers depends on their structure, which is governed by assembly dynamics. (psu.edu)
  • In the SC-VAE, the encoder and decoder infer the causal structure and temporal dynamics. (openreview.net)
  • Furthermore, by concerning the underlying data generation process, inducing the causal structure and temporal dynamics of the system, one can enjoy a robust and flexible MD simulation model to explicitly capture the long-range and time-dependent movement dynamics. (openreview.net)
  • An exemplar is a fer- romagnetic material like iron, while familiar and widely used, we lack a simulation capability to characterize the interplay of structure and magnetic effects that govern material strength, ki- netics of phase transitions and other transport properties. (sandia.gov)
  • Identifying local structure in molecular simulations is of utmost importance. (osti.gov)
  • The goal of our IL research is to obtain a unified understanding of the properties of ILs with respect to their underlying molecular structure. (uchicago.edu)
  • We evaluated consequences of 12 intragenic variants by protein modelling and molecular dynamic studies. (springer.com)
  • Herein we construct and demonstrate the Molecular-Spin Dynamics (MSD) simulation capability for iron from ambient to earth core conditions, all software advances are open source and presently available for broad usage. (sandia.gov)
  • With recent advances in both simulation and experiment, it is now possible to make direct comparisons between data obtained in silico and in vitro. (ubc.ca)
  • Simulations of the dimer were performed with GTP, GDP and ATP. (biorxiv.org)
  • However, it remains challenging for conventional molecular dynamics (MD) simulations due to sampling issues. (bvsalud.org)
  • These simulation results are useful to understand the temperature dependence of diffusion coefficients, and provide a basis for the determination of diffusion coefficients at high temperatures and the modeling of thermo-oxidative degradation of polyisoprene. (pku.edu.cn)
  • First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. (uea.ac.uk)
  • Multi-nanosecond molecular dynamics simulations have been used to explore motions about the hinge region and how they are altered by ligand binding. (ox.ac.uk)
  • Essential dynamics analysis of inter-domain motion revealed the presence of both hinge-bending and twisting motions, as has been reported for a related sugar-binding protein. (ox.ac.uk)
  • To check the limits of applicability of the solvent primitive model (SPM), we solve exactly the system with the approximation that the solvent (water) is a background dielectric continuum using MD simulations. (rti.org)
  • As a beginner, what you need to do is to launch the software, open a page with a model, push the "run" button to start a simulation, and watch it unfolding on the computer screen. (concord.org)
  • The geometry and energy optimizations of the molecular components were used to establish the stable asphalt model system. (mtu.edu)
  • The viscosity data of the molecular asphalt model was calculated using the Muller-Plathe algorithm. (mtu.edu)
  • In addition, the bulk modulus of the molecular asphalt model was determined and obtained by applying the infinitesimal strain in the model boundaries. (mtu.edu)
  • The rotational direction exactly corresponded to what was expected in the proposed chiral molecular propeller model (Tabe, Y. (elsevierpure.com)
  • These data were analyzed within the framework of a simple, analytical model that was motivated by a first-principles molecular dynamics investigation into the release response of aluminum, as well as by a survey of the release response determined from several tabular equations of state for aluminum. (sandia.gov)