Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape
出版年份 2015 全文链接
标题
Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape
作者
关键词
-
出版物
JOURNAL OF CHEMICAL PHYSICS
Volume 142, Issue 13, Pages 130901
出版商
AIP Publishing
发表日期
2015-04-02
DOI
10.1063/1.4916307
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Communication: Optimal parameters for basin-hopping global optimization based on Tsallis statistics
- (2014) C. Shang et al. JOURNAL OF CHEMICAL PHYSICS
- Communication: Analysing kinetic transition networks for rare events
- (2014) Jacob D. Stevenson et al. JOURNAL OF CHEMICAL PHYSICS
- Phase behavior of the 38-atom Lennard-Jones cluster
- (2014) Ray M. Sehgal et al. JOURNAL OF CHEMICAL PHYSICS
- Benchmarks for Characterization of Minima, Transition States, and Pathways in Atomic, Molecular, and Condensed Matter Systems
- (2014) Samuel T. Chill et al. Journal of Chemical Theory and Computation
- Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics
- (2014) Peng Tao et al. Journal of Chemical Theory and Computation
- Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins
- (2014) Ignacia Echeverria et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Structure Prediction for Multicomponent Materials Using Biminima
- (2014) D. Schebarchov et al. PHYSICAL REVIEW LETTERS
- Molecular origins of internal friction effects on protein-folding rates
- (2014) David de Sancho et al. Nature Communications
- Superposition Enhanced Nested Sampling
- (2014) Stefano Martiniani et al. Physical Review X
- Surveying a complex potential energy landscape: Overcoming broken ergodicity using basin-sampling
- (2013) David J. Wales CHEMICAL PHYSICS LETTERS
- Communication: A new paradigm for structure prediction in multicomponent systems
- (2013) D. Schebarchov et al. JOURNAL OF CHEMICAL PHYSICS
- High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant
- (2013) Polina V. Banushkina et al. Journal of Chemical Theory and Computation
- Exploring Energy Landscapes: Metrics, Pathways, and Normal-Mode Analysis for Rigid-Body Molecules
- (2013) Victor Rühle et al. Journal of Chemical Theory and Computation
- Visualizing Basins of Attraction for Different Minimization Algorithms
- (2013) Daniel Asenjo et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Single-molecule fluorescence probes dynamics of barrier crossing
- (2013) Hoi Sung Chung et al. NATURE
- Symmetrisation schemes for global optimisation of atomic clusters
- (2013) Mark T. Oakley et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Exploring energy landscapes: from molecular to mesoscopic systems
- (2013) Dwaipayan Chakrabarti et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- A conformational factorisation approach for estimating the binding free energies of macromolecules
- (2013) Kenji Mochizuki et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations
- (2013) E. R. Henry et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Quasi-Continuous Interpolation Scheme for Pathways between Distant Configurations
- (2012) David J. Wales et al. Journal of Chemical Theory and Computation
- A Local Rigid Body Framework for Global Optimization of Biomolecules
- (2012) Halim Kusumaatmaja et al. Journal of Chemical Theory and Computation
- Replica Exchange Statistical Temperature Molecular Dynamics Algorithm
- (2012) Jaegil Kim et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Macromolecular Systems Understood through Multiscale and Enhanced Sampling Techniques
- (2012) Peter J. Ortoleva et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Computing Free Energy of a Large-Scale Allosteric Transition in Adenylate Kinase Using All Atom Explicit Solvent Simulations
- (2012) Davit A. Potoyan et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Peptide Chain Dynamics in Light and Heavy Water: Zooming in on Internal Friction
- (2012) Julius C. F. Schulz et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables
- (2011) Jaegil Kim et al. JOURNAL OF CHEMICAL PHYSICS
- Simulating structural transitions by direct transition current sampling: The example of LJ38
- (2011) Massimiliano Picciani et al. JOURNAL OF CHEMICAL PHYSICS
- Markov models of molecular kinetics: Generation and validation
- (2011) Jan-Hendrik Prinz et al. JOURNAL OF CHEMICAL PHYSICS
- Revisiting and Computing Reaction Coordinates with Directional Milestoning
- (2011) Serdal Kirmizialtin et al. JOURNAL OF PHYSICAL CHEMISTRY A
- Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories
- (2011) Thomas J. Lane et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Diffusion models of protein folding
- (2011) Robert B. Best et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Energy landscapes: some new horizons
- (2010) David J Wales CURRENT OPINION IN STRUCTURAL BIOLOGY
- Solvent Viscosity and Friction in Protein Folding Dynamics
- (2010) Stephen J. Hagen CURRENT PROTEIN & PEPTIDE SCIENCE
- Nonlinear reaction coordinate analysis in the reweighted path ensemble
- (2010) Wolfgang Lechner et al. JOURNAL OF CHEMICAL PHYSICS
- Steady-state simulations using weighted ensemble path sampling
- (2010) Divesh Bhatt et al. JOURNAL OF CHEMICAL PHYSICS
- Milestoning without a Reaction Coordinate
- (2010) Peter Májek et al. Journal of Chemical Theory and Computation
- Extracting Physically Intuitive Reaction Coordinates from Transition Networks of a β-Sheet Miniprotein
- (2010) Bo Qi et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Computing free energies of protein conformations from explicit solvent simulations
- (2010) Pavel I. Zhuravlev et al. METHODS
- Free-energy landscapes from adaptively biased methods: Application to quantum systems
- (2010) F. Calvo PHYSICAL REVIEW E
- Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol
- (2009) Camilo Velez-Vega et al. JOURNAL OF CHEMICAL PHYSICS
- Calculating rate constants and committor probabilities for transition networks by graph transformation
- (2009) David J. Wales JOURNAL OF CHEMICAL PHYSICS
- Progress and challenges in the automated construction of Markov state models for full protein systems
- (2009) Gregory R. Bowman et al. JOURNAL OF CHEMICAL PHYSICS
- Markovian milestoning with Voronoi tessellations
- (2009) Eric Vanden-Eijnden et al. JOURNAL OF CHEMICAL PHYSICS
- Transition Path Theory for Markov Jump Processes
- (2009) Philipp Metzner et al. MULTISCALE MODELING & SIMULATION
- Refined kinetic transition networks for the GB1 hairpin peptide
- (2009) Joanne M. Carr et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Simulations of rigid bodies in an angle-axis framework
- (2009) Dwaipayan Chakrabarti et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Coordinate-dependent diffusion in protein folding
- (2009) R. B. Best et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Exploring the Free Energy Landscape: From Dynamics to Networks and Back
- (2009) Diego Prada-Gracia et al. PLoS Computational Biology
- Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water
- (2008) Jarek Juraszek et al. BIOPHYSICAL JOURNAL
- Reaction Coordinates for the Flipping of Genetic Switches
- (2008) Marco J. Morelli et al. BIOPHYSICAL JOURNAL
- Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide
- (2008) Birgit Strodel et al. CHEMICAL PHYSICS LETTERS
- Transition networks for modeling the kinetics of conformational change in macromolecules
- (2008) Frank Noé et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Energy landscapes for diffusion: Analysis of cage-breaking processes
- (2008) Vanessa K. de Souza et al. JOURNAL OF CHEMICAL PHYSICS
- Folding Pathways and Rates for the Three-Stranded β-Sheet Peptide Beta3s using Discrete Path Sampling
- (2008) Joanne M. Carr et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Measuring internal friction of an ultrafast-folding protein
- (2008) T. Cellmer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Diffusive reaction dynamics on invariant free energy profiles
- (2008) S. V. Krivov et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload NowAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started