molecular dynamics
Alloy by Molecular Dynamics Simulation
... This paper presents the results of Molecular Dynamics (MD) simulations of Cu 60.0 Zr 32.5 Ti 7.5 alloy through the open source code LAMMPS. Amorphous samples were produced by quenching the molten metal from ...
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Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations
... [13], molecular dynamics (MD) [14–16] or Monte Carlo simulations [17] have provided not only successful data validation but also accurate fitting of the scattering profile be- cause of the potential to ...
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Local sharing as a predominant determinant of synaptic matrix molecular dynamics.
... remarkable molecular dynamics exhibited by synaptic cytomatrix molecules studied so far, it may be fair to conclude that the ability of synapses to maintain some level of structural and functional stability ...
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Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
... the molecular dynamics (MD) simulation methods, which have been successfully applied to many similar researches [28–30], were used to explore the binding pathway of NAM to two PncA enzymes from two ...
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Insight into the intermolecular recognition mechanism between Keap1 and IKKβ combining homology modelling, protein-protein docking, molecular dynamics simulations and virtual alanine mutation.
... Degradation of certain proteins through the ubiquitin-proteasome pathway is a common strategy taken by the key modulators responsible for stress responses. Kelch-like ECH-associated protein-1(Keap1), a substrate adaptor ...
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Successful application of virtual screening and molecular dynamics simulations against antimalarial molecular targets
... drugs. Molecular modelling techniques have been used as tools to develop new ...to molecular dynamics simulations in vacuum implemented on an NAMD ...
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Effects of single nucleotide polymorphisms on human N-acetyltransferase 2 structure and dynamics by molecular dynamics simulation.
... of polymorphisms [9,47,48,49]. Because of the important role of NAT2 in the metabolism of arylamine, hydrazine drugs and many arylamine procarcinogens, understanding the structural basis of acetylation polymorphism is of ...
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The Study on the Nanocutting by Rigid Body Tool and Elastic Body Tool Using Molecular Dynamics Simulations
... uses molecular dynamics to simulate the nanoscale cutting of a Cu single crystal by a conical diamond ...combines molecular dynamics with finite element deformation model (MDFM) to calculate ...
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Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations and binding free energy calculations: AIRE-PHD1, a comparative study.
... the molecular details at the basis of H3K4me0 read-out by PHD fingers, it is of primary importance to investigate the dynamic events characterizing histone recognition and to define the energetic parameters ...
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Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations.
... detailed molecular mechanism remains unclear. In this study, molecular dynamics (MD) simulations and free energy calculations were used to elucidate the mechanism about the effect of chirality of ...
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Molecular determinants of epidermal growth factor binding: a molecular dynamics study.
... Each EGFR ligand shares a common EGF-like motif (or fold). This fold is characterized by three intramolecular disulfide bonds constraining three solvent-accessible loops [19]. In addition to the conserved cysteines, ...
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Dynamics of the contact between a ruthenium surface with a single nanoasperity and a flat ruthenium surface: Molecular dynamics simulations
... (Received 24 March 2010; revised manuscript received 7 December 2010; published 4 April 2011) We study the dynamics of the contact between a pair of surfaces (with properties designed to mimic ruthenium) via ...
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IDENTIFICATION OF PHARMACOLOGICAL TARGETS COMBINING DOCKING AND MOLECULAR DYNAMICS SIMULATIONS
... Studies that include both experimental data and computational simulations (in silico) have increased in number because the techniques are complementary. In silico methodologies are currently an essential component of ...
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Correction: Exploration of Novel Inhibitors for Class I Histone Deacetylase Isoforms by QSAR Modeling and Molecular Dynamics Simulation Assays.
... Citation: Noor Z, Afzal N, Rashid S (2015) Correction: Exploration of Novel Inhibitors for Class I Histone Deacetylase Isoforms by QSAR Modeling and Molecular Dynamics Simulation Assays.[r] ...
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Vibrational G peak splitting in laterally functionalized single wall carbon nanotubes: Theory and molecular dynamics simulations
... In order to test the hypothesis described above, we employed molecular dynamics simulations to investigate the effects of lateral functionalization in vibrational modes of SWCNTs. Our calculations show that ...
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Effects of radiation on the molecular dynamics of Pseudomonas aeruginosa
... An insertion mutagenesis approach using a reporter gene both directed at genes of protein with expression differences and at random, followed by a variety of phenotypic assays directed [r] ...
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Molecular dynamics simulation in hybrid systems
... Usually the most time consuming task is the calculation of forces, especially the computation of non-bonded interactions. In bonded interactions the number of bonds terms is proportional to the number of atoms in the ...
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An interaction potential for materials and molecular dynamics simulations.
... quando tratamos de materiais onde a distribuição eletrônica ou a ligação química em torno do átomo muda significativamente durante os movimentos dos átomos que são de interesse na simulação. Por outro lado, uma grande ...
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Closure of the human TKFC active site: comparison of the apoenzyme and the complexes formed with either triokinase or FMN cyclase substrates
... The normal mode analysis of the systems apo-hTKFC, hTKFC:2DHA:2ATP and hTKFC:2FAD indicated that there could be subtle differences in their harmonic movements perhaps due to the absence or presence of different ligands. ...
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Explicit and implicit modeling of nanobubbles in hydrophobic confinement
... water molecular dynamics (MD) computer simulations of hydrophobic solutes, for instance, give evidence of capil- lary evaporation on nanometer scales, ...
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