Molecular Dynamics Simulations
Molecular dynamics simulations: advances and applications
... Dovepress Molecular dynamics simulations out these procedures using a set of helper ...biomolecular simulations among the bioinformatics or the biochemical ...launch simulations with ...
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Molecular dynamics simulations and drug discovery
... a molecular dynamics simulation be run in which the bound ligand vanishes? What about the ligand in solu- tion? To address these questions, alchemical transfor- mations are selected based on the ...
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Salient Frame Detection for Molecular Dynamics Simulations
... 4 Results We have compared our detected salient frames with the ones identified independently by our collaborators (biology scientists) for molecular dynamics simulations. Figure 5 shows the five ...
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New ways to boost molecular dynamics simulations
... accuracy Molecular dynamics simulations can be very sensitive to the pro- tocol and algorithms used, especially when events that occur on longer time scales are investigated, like protein folding or ...
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Adaptive Multilevel Splitting in Molecular Dynamics Simulations*
... stochastic simulations to identify trajectories across a high potential barrier separating one metastable state from another, and to estimate the probability of observing such a ...Carlo simulations. In ...
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Atomistic molecular dynamics simulations of shock compressed quartz
... non-equilibrium molecular dynamics simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer, and van Santen ...
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Machine learning for performance enhancement of molecular dynamics simulations
... with simulations to enhance the performance of the simulation and improve its usability for research and ...parallelized molecular dynamics simulations designed to extract the distribution of ...
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Event-driven molecular dynamics simulations of protein mixtures
... event-driven Molecular Dynamics simulations, we set up a model that will be suitable for studying how the interactions of mixtures of protein molecules at high concentrations affect key thermodynamic ...
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Enhanced Sampling Methods for Molecular Dynamics Simulations of Proteins
... all-atom simulations with a physics-based force field that could successfully derive the difference between the two ...of molecular dynamics simulations with physical force fields results from ...
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Molecular Dynamics Simulations
... • Force fields are constructed by parameterising the potential functions using either experimental data (X- ray and electron diffraction, NMR and IR spectroscopy) or ab initio and semi-e[r] ...
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Introduction to Molecular Dynamics Simulations
... • Mutant protein maintains some structure • Binding to nucleic acids is less strong. Structural determinants for the specificity of NC for DNA[r] ...
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Thermostat Algorithms for Molecular Dynamics Simulations
... atomistic simulations, and in particular molecular dynamics (MD) simu- lations, have nowadays become a common tool for investigating the properties of polymer [1] and (bio-)molecular systems ...
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Molecular Dynamics Simulations of Charged Nanodroplets
... 1.7 Water Models Choosing a proper water model for computer simulations of charged droplets plays a significant role in the final results. The literature serves as a vast repository of various water models ...
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Molecular dynamics simulations of nanofriction and wear
... model was employed to study the behaviour of the friction coefficient, contact pressure and scratch hardness of a silver surface as a function of depth.. The effec[r] ...
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Molecular Dynamics Simulations of Metallic Nanoglasses
... We also showed that in case of the covalent Ge glass the excess free volume localized in the interfaces is much higher in comparison with CuZr metallic glasses.. Thermal stability of int[r] ...
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On the Conformational Dynamics of DNA: A Perspective from Molecular Dynamics Simulations
... addition, simulations were performed on double stranded DNA molecules of the same sequence, but in which base 6 and 7 of the main strand were replaced by CPD, and Z corresponded to ...
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Molecular dynamics simulations of conjugated semiconducting molecules
... using their version of this MD ensemble technique for thiophene 32mers gives better quantitative agreement with the peak of their experimental result. Their results give a spectrum peaked at 2.9 eV with a band edge at ...
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Modeling of Uranium Mononitride with Molecular Dynamics Simulations
... 1.4 Computational Techniques In general, computational simulations of atomic behavior fall under stochastic methods (e.g. Monte Carlo), deterministic methods (e.g. MD), or a mixture of both. Traditionally, ...
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Molecular dynamics simulations in graphite and carbon materials
... cascade simulations in Chapters 4 and ...cade simulations as wrapped atoms could enter from the opposite side of the cell resulting in cascades being formed in a new part of the ...
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The modelling of electronic effects in molecular dynamics simulations
... 8.3. Future outlook great practical implications, as these will serve as input to other modelling strategies, which are higher up in the multi-scale radiation damage modelling hierarchy. In chapter 6 we have investigated ...
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