Interplay of non-Markov and internal friction effects in the barrier crossing kinetics of biopolymers: Insights from an analytically solvable model

Configuration-Dependent Diffusion Dynamics of Downhill and Two-State Protein Folding

(2012) Weixin Xu 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

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy

(2012) A. Soranno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Molecule Fluorescence Experiments Determine Protein Folding Transition Path Times

(2012) H. S. Chung et al.   SCIENCE

Polymer reversal rate calculated via locally scaled diffusion map

(2011) Wenwei Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Failure of one-dimensional Smoluchowski diffusion models to describe the duration of conformational rearrangements in floppy, diffusive molecular systems: A case study of polymer cyclization

(2011) Ryan R. Cheng et al.   JOURNAL OF CHEMICAL PHYSICS

Numerical Construction of thepfold(Committor) Reaction Coordinate for a Markov Process

(2011) Sergei V. Krivov   JOURNAL OF PHYSICAL CHEMISTRY B

The Free Energy Landscape Analysis of Protein (FIP35) Folding Dynamics

(2011) Sergei V. Krivov   JOURNAL OF PHYSICAL CHEMISTRY B

Optimal dimensionality reduction of complex dynamics: The chess game as diffusion on a free-energy landscape

(2011) Sergei V. Krivov   PHYSICAL REVIEW E

Kinetics and Reaction Coordinates of the Reassembly of Protein Fragments Via Forward Flux Sampling

(2010) Ernesto E. Borrero et al.   BIOPHYSICAL JOURNAL

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

A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements

(2010) Srabanti Chaudhury et al.   JOURNAL OF CHEMICAL PHYSICS

End-to-Surface Reaction Dynamics of a Single Surface-Attached DNA or Polypeptide

(2010) Ryan R. Cheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Generalized Langevin equation formulation for anomalous polymer dynamics

(2010) Debabrata Panja   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Unfolded-State Dynamics and Structure of Protein L Characterized by Simulation and Experiment

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Mechanistic Study of Electron Transfer from the Distal Termini of Electrode-Bound, Single-Stranded DNAs

(2010) Takanori Uzawa et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Recent advances in transition path sampling: accurate reaction coordinates, likelihood maximisation and diffusive barrier-crossing dynamics

(2010) Baron Peters   MOLECULAR SIMULATION

An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain

(2010) A. Reiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extremely slow intramolecular diffusion in unfolded protein L

(2010) S. A. Waldauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

(2010) Isabella Daidone et al.   PLoS Computational Biology

The Length and Viscosity Dependence of End-to-End Collision Rates in Single-Stranded DNA

(2009) Takanori Uzawa et al.   BIOPHYSICAL JOURNAL

Dynamic pathways to mediate reactions buried in thermal fluctuations. I. Time-dependent normal form theory for multidimensional Langevin equation

(2009) Shinnosuke Kawai et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamic pathways to mediate reactions buried in thermal fluctuations. II. Numerical illustrations using a model system

(2009) Shinnosuke Kawai et al.   JOURNAL OF CHEMICAL PHYSICS

Protein dynamics from single-molecule fluorescence intensity correlation functions

(2009) Irina V. Gopich et al.   JOURNAL OF CHEMICAL PHYSICS

Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories

(2009) H. S. Chung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computer Simulations and Theory of Protein Translocation

(2008) Dmitrii E. Makarov   ACCOUNTS OF CHEMICAL RESEARCH

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

Protein folding studied by single-molecule FRET

(2008) Benjamin Schuler et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The rate constant of polymer reversal inside a pore

(2008) Lei Huang et al.   JOURNAL OF CHEMICAL PHYSICS

On the assumptions underlying milestoning

(2008) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Kinetics of Loop Formation in Polymer Chains†

(2008) Ngo Minh Toan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unfolded Protein and Peptide Dynamics Investigated with Single-Molecule FRET and Correlation Spectroscopy from Picoseconds to Seconds†

(2008) Daniel Nettels et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Pulling Direction as a Reaction Coordinate for the Mechanical Unfolding of Single Molecules†

(2008) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Theory, analysis, and interpretation of single-molecule force spectroscopy experiments

(2008) O. K. Dudko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA