Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations
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The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling correctionsPolymer uncrossing and knotting in protein folding, and their role in minimal folding pathwaysA growing string method for determining transition states: comparison to the nudged elastic band and string methodsExploring the free energy landscape: from dynamics to networks and backpH replica-exchange method based on discrete protonation statesSystematic determination of order parameters for chain dynamics using diffusion maps.Inherent structure versus geometric metric for state space discretization.Rapid equilibrium sampling initiated from nonequilibrium dataEstimating diffusivity along a reaction coordinate in the high friction limit: Insights on pulse times in laser-induced nucleation.Mechanistic insight into ligand binding to G-quadruplex DNAMolecular basis of cyclooxygenase enzymes (COXs) selective inhibitionReaction coordinates and rates from transition paths.Network models for molecular kinetics and their initial applications to human healthFree energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.Coarse-grained analysis of stochasticity-induced switching between collective motion states.Sampling protein motion and solvent effect during ligand bindingWater pulls the strings in hydrophobic polymer collapse.BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method.Rate theories for biologistsGyration-radius dynamics in structural transitions of atomic clusters.Building Markov state models along pathways to determine free energies and rates of transitionsExploration of effective potential landscapes using coarse reverse integration.Communication: Microsecond peptide dynamics from nanosecond trajectories: a Langevin approach.Analyzing single-molecule manipulation experiments.On the assumptions underlying milestoning.On coarse projective integration for atomic deposition in amorphous systems.Intramolecular energy transfer and the driving mechanisms for large-amplitude collective motions of clusters.Markovian milestoning with Voronoi tessellations.Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency.Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters.Intrinsic map dynamics exploration for uncharted effective free-energy landscapes.A Bayesian method for construction of Markov models to describe dynamics on various time-scales.Effective stochastic dynamics on a protein folding energy landscape.Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.Adaptive biasing force method for scalar and vector free energy calculations.Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation.Coarse molecular-dynamics analysis of an order-to-disorder transformation of a krypton monolayer on graphite.A multiscale model for kinetics of formation and disintegration of spherical micelles.Apparent hysteresis in a driven system with self-organized drag.Effective dynamics along given reaction coordinates, and reaction rate theory.
P2860
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P2860
Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations
description
article
@en
im Juni 2003 veröffentlichter wissenschaftlicher Artikel
@de
wetenschappelijk artikel
@nl
наукова стаття, опублікована в червні 2003
@uk
name
Coarse molecular dynamics of a ...... ong-time dynamics computations
@en
Coarse molecular dynamics of a ...... ong-time dynamics computations
@nl
type
label
Coarse molecular dynamics of a ...... ong-time dynamics computations
@en
Coarse molecular dynamics of a ...... ong-time dynamics computations
@nl
prefLabel
Coarse molecular dynamics of a ...... ong-time dynamics computations
@en
Coarse molecular dynamics of a ...... ong-time dynamics computations
@nl
P2860
P356
P1476
Coarse molecular dynamics of a ...... ong-time dynamics computations
@en
P2093
Ioannis G. Kevrekidis
P2860
P304
10762-10773
P356
10.1063/1.1574777
P407
P577
2003-06-15T00:00:00Z
P818
physics/0212108