Keywords: پتانسیل نیروی متوسط; Graphene; Mixed surfactants; Dispersion; Molecular dynamics simulations; Potential of mean force;
مقالات ISI پتانسیل نیروی متوسط (ترجمه نشده)
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Keywords: پتانسیل نیروی متوسط; Multiscale simulations; Drug-membrane systems; Potential of mean force; Enhanced sampling; DMPC; 1,2-dimyristoyl-sn-glycero-3-phosphocholine; DOPC; 1,2-dioleoyl-sn-glycero-3-phosphocholine; POPC; 1-palmitoyl-2-oleoylphosphatidylcholine; MD; molecular dyna
Keywords: پتانسیل نیروی متوسط; Ionic liquid; Potential of mean force; Energy and entropy; Colloidal particles; Nano particles; Integral equation theory;
Keywords: پتانسیل نیروی متوسط; Electric fields; Hofmeister effects; Molecular dynamics; Polarization effects; Potential of mean force;
Keywords: پتانسیل نیروی متوسط; Molecular dynamics; Drug delivery; Non-covalent interactions; Potential of mean force;
Keywords: پتانسیل نیروی متوسط; Integral membrane proteins; Molecular dynamics simulations; Protein-ligand interactions; Markov State Models; Kinetic cell models; AP; action potential; EM; electron microscopy; HH; Hodgkin and Huxley model; hERG; human ether-a-go-go channel; HCN; hyperpo
The role of metal substitution in the promiscuity of natural and artificial carbonic anhydrases
Keywords: پتانسیل نیروی متوسط; B3LYP; Becke 3 parameter Lee - Yang - Parr functional; CA; carbonic anhydrase; CHARMM; Chemistry at HARvard Molecular Mechanics; DFT; density functional theory; FF; force field; MD; Molecular Dynamics; NAMD; Nanoscale Molecular Dynamics; NBO; Natural
Selective ion binding and transport by membrane proteins - A computational perspective
Keywords: پتانسیل نیروی متوسط; ABF; Adaptive Biasing Force; ADP; Adenosine Diphosphate; aHL; alpha-Hemolysin; AMBER; Assisted Model Building with Energy Refinement; AMP; Adenosine Monophosphate; AMOEBA; Atomic Multipole Optimized Energetics for Biomolecular Simulation; ATP; Adenosine T
Keywords: پتانسیل نیروی متوسط; AMA; amantadine; BFM; bond fluctuation method; BST-2; bone marrow stromal cell antigen 2; CD; circular dichroism; CGMD; coarse-grained molecular dynamics; ClyA; cytolysin A; DHPC; dihexanoylphosphocholine; DPC; dodecylphosphocholine; E. coli; Escherichia
Keywords: پتانسیل نیروی متوسط; MD; molecular dynamics; PMF; potential of mean force; RDF; radial distribution function; SAXS; small-angle X-ray scattering; SANS; small-angle neutron scattering; EINS; elastic incoherent neutron scattering; QENS; quasi-elastic neutron scattering; NMR; nu
Keywords: پتانسیل نیروی متوسط; Review; Membrane; Lipid bilayer; Permeation; Non-facilitated; Solubility-diffusion model; Molecular dynamics; Diffusion; PMF; Potential of mean force; Polarizable; Coarse grain;
Keywords: پتانسیل نیروی متوسط; Smoluchowski equation; Homogenization; Stochastic two-scale convergence in the mean; Hard-sphere potential; Potential of mean force; Random materials; Composites
Keywords: پتانسیل نیروی متوسط; Graphene; Boron nitride nanosheet; Potential of mean force; Heavy metal; Nanostructured membrane
Keywords: پتانسیل نیروی متوسط; Membrane microdomain; Membrane dipole potential; DLVO theory; Membrane electrostatic surface potential; Membrane functional imaging; Potential of mean force;
Keywords: پتانسیل نیروی متوسط; Structure-based drug discovery; Homology modeling; Ligand docking; Virtual screening; Protein flexibility; Active site water molecules; GPCR; G Protein-coupled receptor; HM; homology modeling; HTD; high-throughput docking; LSHM; Ligand-steered homology mo
Keywords: پتانسیل نیروی متوسط; Potential of mean force; Liquid-liquid interface; Intrinsic surface; Intrinsic PMF;
Keywords: پتانسیل نیروی متوسط; Nanostructured membrane; Graphene; Potential of mean force; Molecular dynamics simulation; Desalination
Keywords: پتانسیل نیروی متوسط; HNC-OZ theory; Reentrant behavior; Potential of mean force; Actin; DNA; Charged colloidal particle;
Keywords: پتانسیل نیروی متوسط; Potential of mean force; Contact ion pair; Solvent assisted ion pair; Solvent separated ion pair; Solvation structure of ion pair;
Keywords: پتانسیل نیروی متوسط; MD; molecular dynamics; CG; coarse-grained; DPD; dissipative particle dynamics; DAPC; diarachidonyl-PC; DMPC; dimyristoyl-PC; DOPC; dioleoyl-PC; DPPC; dipalmitoyl-PC; POPC; palmitoyl-oleoyl-PC; PSM; palmitoyl-sphingomyelin; PMF; potential of mean force; L
Keywords: پتانسیل نیروی متوسط; CV; collective variable; d-AFED; driven adiabatic free energy dynamics; DLPC; dilinoleoyl-phosphatidylcholine; GUV; giant unilamellar vesicle; MD; molecular dynamics; PMF; potential of mean force; UFED; unified free energy dynamics; Electroporation; Oxidi
A molecular dynamics simulation scenario for studying solvent-mediated interactions of polymers and application to thermoresponse of poly(N-isopropylacrylamide) in water
Keywords: پتانسیل نیروی متوسط; Polymer aggregation; Thermoresponsive polymers; Hydrogels; Umbrella sampling; Potential of mean force; Molecular dynamics simulations; Simulation method;
Identification of small-molecule ligands that bind to MiR-21 as potential therapeutics for endometriosis by screening ZINC database and in-vitro assays
Keywords: پتانسیل نیروی متوسط; miR-21; MicroRNA-21; GO; gene ontology; PDB; protein data bank; PMF; potential of mean force; 2AP; analog 2-aminopurine; microRNA-21; Small-molecule ligand; Drug design; Endometriosis;
Biobetters From an Integrated Computational/Experimental Approach
Keywords: پتانسیل نیروی متوسط; Rational drug design; Molecular dynamics; Docking; Potential of mean force; Free energy perturbation;
Investigation of α-conotoxin unbinding using umbrella sampling
Keywords: پتانسیل نیروی متوسط; α-Conotoxin; Nicotinic acetylcholine receptor; Umbrella sampling; Potential of mean force
Mechanism of pyrophosphate ion release in T7 RNA polymerase revealed by free energy simulations
Keywords: پتانسیل نیروی متوسط; Molecular dynamics simulation; T7 RNA polymerase; PPi release; Potential of mean force;
Distribution and dynamics of quinones in the lipid bilayer mimicking the inner membrane of mitochondria
Keywords: پتانسیل نیروی متوسط; MD; molecular dynamics; US; umbrella sampling; WHAM; weighted histogram analysis method; PMF; potential of mean force; Q; quinone or its analogue; PC; phosphatidylcholine; PE; phosphatidylethanolamine; CL; cardiolipin; Electron transport chain; Molecular
Multi-ion free energy landscapes underscore the microscopic mechanism of ion selectivity in the KcsA channel
Keywords: پتانسیل نیروی متوسط; Free energy profile; Potential of mean force; Umbrella sampling;
Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin
Keywords: پتانسیل نیروی متوسط; Binding pathway; Potential of mean force; Protein-ligand interaction; Michaelis-menten kinetics; Steered molecular dynamics; Jarzynski equality;
Structural perturbation of a dipalmitoylphosphatidylcholine (DPPC) bilayer by warfarin and its bolaamphiphilic analogue: A molecular dynamics study
Keywords: پتانسیل نیروی متوسط; Bolaamphiphile; Bilayer; Anticoagulant; Toxicity; Permeation; Phospholipid; Warfarin; Brodifacoum; Defect; Hydroxycoumarin; DPPC; dipalmitoylphosphatidylcholine; VKOR; vitamin K epoxide reductase; NPT; isobaric, isothermal ensemble, constant number of par
Aminoglycoside binding and catalysis specificity of aminoglycoside 2â³-phosphotransferase IVa: A thermodynamic, structural and kinetic study
Keywords: پتانسیل نیروی متوسط; APH(2â³); aminoglycoside 2â³-phosphotransferases; APH(3â²); aminoglycoside 3â²,5â³-phosphotransferases; LE; ligand efficiency; NCNO; number of non-hydrogen atoms of the ligand; PMF; potential of mean force; Aminoglycoside modifying enzymes; Transient
The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans
Keywords: پتانسیل نیروی متوسط; Intrinsically disordered protein; cis–trans isomerization; Binding affinity; Molecular dynamics; Potential of mean force
Optical laser-induced CO desorption from Ru(0001) monitored with a free-electron X-ray laser: DFT prediction and X-ray confirmation of a precursor state
Keywords: پتانسیل نیروی متوسط; CO desorption; Potential of mean force; Two-temperature model; Pump-probe; X-ray spectroscopy; Density functional theory;
Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes
Keywords: پتانسیل نیروی متوسط; Reaction path; Free energy; QM/MM; Potential of mean force; Bennett's acceptance ratio; BAR; Reweighting; QM-Non-Boltzmann Bennett; QM-NBB;
Recent advances in QM/MM free energy calculations using reference potentials
Keywords: پتانسیل نیروی متوسط; ABF; adaptive biasing force; CG; coarse-grained; EVB; empirical valence bond; FEP; free energy perturbation; LRA; linear response approximation; MD; molecular dynamics; PD; paradynamics; PMF; potential of mean force; QM/MM; quantum mechanics/molecular mec
Molecular dynamics methods to predict peptide locations in membranes: LAH4 as a stringent test case
Keywords: پتانسیل نیروی متوسط; PMF; potential of mean force; AA; all-atom; CG; coarse-grained; MD; molecular dynamics; CPP; cell-penetrating peptide; FF; force-field; ATR-FTIR; attenuated total reflection Fourier-transform IR; OCD; oriented circular dichroism; TM; transmembrane; LAH4-c
Computational and experimental analysis of drug binding to the Influenza M2 channel
Keywords: پتانسیل نیروی متوسط; Channel blocker; Cell based assay; Anti-flu agent; Potential of mean force
Free energy analysis of conductivity and charge selectivity of M2GlyR-derived synthetic channels
Keywords: پتانسیل نیروی متوسط; Cystic fibrosis; Molecular dynamics; Potential of mean force; Anion selectivity; Ion channels; Peptide design
Distinct interactions of Na+ and Ca2+ ions with the selectivity filter of the bacterial sodium channel NaVAb
Keywords: پتانسیل نیروی متوسط; NaVAb; bacterial sodium channel (Arcobacter butzleri); NaVRh; bacterial sodium channel (Rickettsiales sp. HIMB114); MD simulation; molecular dynamics simulation; PMF; potential of mean force; SF; selectivity filter; DOPC; dioleoylphospathidylcholine; PDB;
Monte Carlo simulation of the static properties of Hg solution in (O2, N2) gassed water
Keywords: پتانسیل نیروی متوسط; Metal mercury solution in water; Nitrogen oxygen gassed water; Structural correlation; Interaction with mercury; Monte Carlo simulation; Radial distribution function; Potential of mean force;
Temporal multiscale approach for nanocarrier motion with simultaneous adhesion and hydrodynamic interactions in targeted drug delivery
Keywords: پتانسیل نیروی متوسط; Multiscale; Nanocarrier; Potential of mean force; Hydrodynamics; Adhesion; Fluctuating Hydrodynamics; Finite element method
A general acid-general base reaction mechanism for human brain aspartoacylase: A QM/MM study
Keywords: پتانسیل نیروی متوسط; Human brain aspartoacylase; QM/MM; Reaction path; Potential of mean force; Electrostatic interaction;
Outer membrane phospholipase A in phospholipid bilayers: A model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers
Keywords: پتانسیل نیروی متوسط; DLPC; dilaurylphosphatidylcholine; MF; refers to the Moon & Fleming hydrophobicity scale [24]; OmpLA; outer membrane phospholipase A; PMF; potential of mean force; POPC; palmitoyl-oleoyl-phosphatidylcholine; WW; refers to the Wimley & White octanol scale
Molecular dynamics simulations of carbon nanotube dispersions in water: Effects of nanotube length, diameter, chirality and surfactant structures
Keywords: پتانسیل نیروی متوسط; Carbon nanotubes; Molecular dynamics simulations; Dispersion; Potential of mean force; Surfactant;
Potential of mean force for separation of the repeating units in cellulose and hemicellulose
Keywords: پتانسیل نیروی متوسط; Cellobiose; Xylobiose; Disaccharides; Potential of mean force; Umbrella sampling; Molecular dynamics simulations;
Self-assembly of graphenes
Keywords: پتانسیل نیروی متوسط; Graphene; Self-assembly; Water; Molecular dynamics simulation; Potential of mean force; Hydrogen bond;
The dielectric continuum solvent model adapted for treating preferential solvation effects
Keywords: پتانسیل نیروی متوسط; Solvation theory; Dielectric continuum model; Non-local electrostatics; Preferential solvation; Potential of mean force;
Molecular dynamics simulations of the interactions and dispersion of carbon nanotubes in polyethylene oxide/water systems
Keywords: پتانسیل نیروی متوسط; Carbon nanotube; Molecular dynamics simulations; Potential of mean force;
Phase-transfer energetics of small-molecule alcohols across the water–hexane interface: Molecular dynamics simulations using charge equilibration models
Keywords: پتانسیل نیروی متوسط; Charge equilibration; Water; Hexane; Interface; Potential of mean force; Alcohols; Methanol; Ethanol; Propanol; Molecular dynamics; Polarizable force fields
Selectivity and Permeation of Alkali Metal Ions in K+-channels
Keywords: پتانسیل نیروی متوسط; SF, selectivity filter; MD, molecular dynamics; PMF, potential of mean forcemolecular dynamics; potassium channels; umbrella sampling; potential of mean force; free energy