Molecular Dynamics (MD) Simulations
Hydrogen-Deuterium Exchange Mass Spectrometry and Molecular Dynamics Simulations for Studying Protein Structure and Dynamics
... Classical models of allostery envision that effector binding triggers conformational changes that cause distant target binding sites to open or close. 1,2,4 Recent studies have expanded this view by emphasizing the role ...
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Towards Predictive Molecular Dynamics Simulations of DNA: Role of Electrostatics and of the Cell Environment.
... The relationship between DNA sequence and structure is a subject of considerable interest, and its understanding is believed important for essential cellular processes such as replication and transcription. The ...
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The design of high affinity human PD-1 mutants by using molecular dynamics simulations (MD)
... conventional molecular dynamics simulations to observe the structural properties of the PD-1 ...the MD simulations and in silico mutagenesis, we expressed a list of hPD-1 mutants at ...
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Thinking outside the laboratory : analyses of antibody structure and dynamics within different solvent environments in molecular dynamics (MD) simulations
... successes, MD simulations place significant limitations on the time and length scales that can be ...general, MD simulations are performed by considering the solvent molecules explicitly, ...
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Effective mean free path and viscosity of confined gases
... both the direct simulation Monte Carlo (DSMC) and molecular dynamics (MD) simulations. The[r] ...
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Mechanical Properties and Failure Behavior of Hexagonal Boron Nitride–Graphene van der Waals Heterostructures through Molecular Dynamics Simulation
... Molecular dynamics(MD) simulations are carried out to characterize the mechanical properties and failure behavior of van der Waals heterostructures composed of graphene and hexagonal boron ...
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Efficient triple helix formation by oligodeoxyribonucleotides containing alpha- or beta-2-amino-5-(2-deoxy-D-ribofuranosyl) pyridine residues.
... -AP. Molecular modelling studies showed that an α -anomeric AP nucleotide can be accommodated within an otherwise β-anomeric triplex with only minor perturbation of the triplex ...structure. Molecular ...
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Self assembly of decoupled borazines on metal surfaces : the role of the peripheral groups
... of molecular dynamics (MD) simulations suggesting that a very effective decoupling of the central borazine core from the substrate occurs for both molecules, whereas a pro- nounced ...
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Molecular simulation of thin liquid films : thermal fluctuations and instability
... in molecular dynamics (MD) simulations, in contrast to the long-thread profile predicted by the classical lubri- cation equation simplified from NS ...nano-jet dynamics can be remedied ...
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Homology Model and Ligand Binding Interactions of the Extracellular Domain of the Human α4β2 Nicotinic Acetylcholine Receptor
... a molecular framework for understanding ligand-receptor interactions, rendering insights into mechanisms of nicotine addiction and may furnish a tool for efficiently identifying ligands that can bind the nicotine ...
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Electrowetting controls the deposit patterns of evaporated salt water nanodroplets
... Interest in nanodroplets is growing because of their potential applications in manufacturing, such as creating nanostructures through evaporation. The electrowetting properties of nano- droplets are somewhat di ff erent ...
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AN EMPIRICAL STUDY ON GENE PREDICTION TECHNIQUES
... [56] have introduced an ab initio model for gene prediction in prokaryotic genomes on. the basis of physicochemical features of codons computed from molecular dynamics (MD) simulations[r] ...
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Ion – water interaction: Effects and consequences
... and molecular dynamics (MD) simulations 25-31 (that have primarily concentrated on alkali halides) have led to the observation that only water molecules in the first hydration shell are ...
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Effect of Intrinsic Ripples on Elasticity of the Graphene Monolayer
... The effect of intrinsic ripples on the mechanical response of the graphene monolayer is investigated under uniaxial loading using molecular dynamics (MD) simulations with a focus on nonlinear ...
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Molecular Dynamics Studies of Water Flow in Carbon Nanotubes
... Computer simulations such as molecular dynamics (MD) simulations allow an unprece- dented level of fine tuning and observation on short time and length ...these simulations can ...
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1 Computational insight into the effect of natural
... Molecular Dynamics (MD) simulations; 4) preferential binding sites of ligands and their effect on 47.. amyloid structure-dynamics[18] on Aβ fragments and full-length single[r] ...
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Effective mean free path and viscosity of confined gases
... The molecular mean free path (MFP) of gases in confined geometries is numerically eval- uated by means of the direct simulation Monte Carlo (DSMC) method and molecular dynamics (MD) ...
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Schmitz, Matthias (2004): Entwicklung, Anwendung und Vergleich von Methoden zur Berechnung von Infrarotspektren einzelner Moleküle in polaren Lösungsmitteln. Dissertation, LMU München: Fakultät für Physik
... Hybrid molecular dynamics 共 MD 兲 simulations, which combine density functional theory 共 DFT 兲 descriptions of a molecule with a molecular mechanics 共 MM 兲 modeling of its solvent ...
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Investigations of ion channel structure function relationships using molecular modeling and experimental biochemistry
... of MD simulations and circular dichroism studies of multiple channel mutants to probe the curious helical bundle conformation of the MscL C-terminal region seen in the crystal ...different molecular ...
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Different interface orientations of pentacene and PTCDA induce different degrees of disorder
... The molecular dynamic (MD) simulations of the interfaces between PTCDA and pentacene have been performed with the atomistic molecular dynamics package GROMACS (Stockholm Center for ...
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