Revisiting and computing reaction coordinates with Directional Milestoning.
about
Bridging scales through multiscale modeling: a case study on protein kinase AEnzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy PartitionUnassisted transport of N-acetyl-L-tryptophanamide through membrane: experiment and simulation of kinetics.Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE ParallelizationModeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation.Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations.Characterization of a dynamic string method for the construction of transition pathways in molecular reactionsEarly events in helix unfolding under external forces: a milestoning analysis.Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning.Perspective: Computer simulations of long time dynamicsIntegrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.Coiled-coil response to mechanical force: global stability and local crackingTwo Relations to Estimate Membrane Permeability Using MilestoningAnalyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples.Simulation-Based Approaches for Determining Membrane Permeability of Small CompoundsCatch bond-like kinetics of helix cracking: network analysis by molecular dynamics and milestoning.Computational study of peptide permeation through membrane: Searching for hidden slow variables.Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning.Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with MilestoningThermodynamic Cycle Without Turning Off Self-Interactions: Formal Discussion and a Numerical Example.Experiments and comprehensive simulations of the formation of a helical turnAn adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates.Exact milestoning.A MATHEMATICAL FRAMEWORK FOR EXACT MILESTONING.Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.Milestoning with coarse memory.Computation of transit times using the milestoning method with applications to polymer translocation.A new paradigm for atomically detailed simulations of kinetics in biophysical systems.SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.Milestoning with transition memory.Robust and efficient configurational molecular sampling via Langevin dynamics.Microscopically computing free-energy profiles and transition path time of rare macromolecular transitions.
P2860
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P2860
Revisiting and computing reaction coordinates with Directional Milestoning.
description
2011 nî lūn-bûn
@nan
2011年の論文
@ja
2011年論文
@yue
2011年論文
@zh-hant
2011年論文
@zh-hk
2011年論文
@zh-mo
2011年論文
@zh-tw
2011年论文
@wuu
2011年论文
@zh
2011年论文
@zh-cn
name
Revisiting and computing reaction coordinates with Directional Milestoning.
@en
type
label
Revisiting and computing reaction coordinates with Directional Milestoning.
@en
prefLabel
Revisiting and computing reaction coordinates with Directional Milestoning.
@en
P2860
P356
P1476
Revisiting and computing reaction coordinates with Directional Milestoning.
@en
P2093
Serdal Kirmizialtin
P2860
P304
P356
10.1021/JP111093C
P407
P577
2011-04-18T00:00:00Z