Data-Driven Langevin Modeling of Nonequilibrium Processes

Multisecond ligand dissociation dynamics from atomistic simulations

(2020) Steffen Wolf et al.   Nature Communications

Real-time observation of ligand-induced allosteric transitions in a PDZ domain

(2020) Olga Bozovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling non-Markovian data using Markov state and Langevin models

(2020) Benjamin Lickert et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of kinetic order parameters for non-equilibrium dynamics

(2019) Fabian Paul et al.   JOURNAL OF CHEMICAL PHYSICS

On the dynamics of reaction coordinates in classical, time-dependent, many-body processes

(2019) Hugues Meyer et al.   JOURNAL OF CHEMICAL PHYSICS

Principal component analysis of nonequilibrium molecular dynamics simulations

(2019) Matthias Post et al.   JOURNAL OF CHEMICAL PHYSICS

MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths

(2018) Alberto Perez et al.   Journal of Chemical Theory and Computation

Metadynamics Enhanced Markov Modeling of Protein Dynamics

(2018) Mithun Biswas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Perspective: Identification of collective variables and metastable states of protein dynamics

(2018) Florian Sittel et al.   JOURNAL OF CHEMICAL PHYSICS

Targeted Molecular Dynamics Calculations of Free Energy Profiles Using a Nonequilibrium Friction Correction

(2018) Steffen Wolf et al.   Journal of Chemical Theory and Computation

On the non-stationary generalized Langevin equation

(2017) Hugues Meyer et al.   JOURNAL OF CHEMICAL PHYSICS

Principal component analysis on a torus: Theory and application to protein dynamics

(2017) Florian Sittel et al.   JOURNAL OF CHEMICAL PHYSICS

Time-resolved observation of protein allosteric communication

(2017) Sebastian Buchenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

External Potential Modifies Friction of Molecular Solutes in Water

(2017) Jan O. Daldrop et al.   Physical Review X

Reaction Coordinates and Mechanistic Hypothesis Tests

(2016) Baron Peters   Annual Review of Physical Chemistry

Global Langevin model of multidimensional biomolecular dynamics

(2016) Norbert Schaudinnus et al.   JOURNAL OF CHEMICAL PHYSICS

Robust Density-Based Clustering To Identify Metastable Conformational States of Proteins

(2016) Florian Sittel et al.   Journal of Chemical Theory and Computation

Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions

(2015) Sebastian Buchenberg et al.   Journal of Chemical Theory and Computation

Multidimensional Langevin Modeling of Nonoverdamped Dynamics

(2015) Norbert Schaudinnus et al.   PHYSICAL REVIEW LETTERS

Accelerating molecular simulations of proteins using Bayesian inference on weak information

(2015) Alberto Perez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Communication: Microsecond peptide dynamics from nanosecond trajectories: A Langevin approach

(2014) Andrzej J. Rzepiela et al.   JOURNAL OF CHEMICAL PHYSICS

Transmission Coefficients, Committors, and Solvent Coordinates in Ion-Pair Dissociation

(2014) Ryan Gotchy Mullen et al.   Journal of Chemical Theory and Computation

Waiting time distribution for continuous stochastic systems

(2014) Robert Gernert et al.   PHYSICAL REVIEW E

Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

(2013) Mary A. Rohrdanz et al.   Annual Review of Physical Chemistry

Data driven Langevin modeling of biomolecular dynamics

(2013) Norbert Schaudinnus et al.   JOURNAL OF CHEMICAL PHYSICS

A simple and effective Verlet-type algorithm for simulating Langevin dynamics

(2013) Niels Grønbech-Jensen et al.   MOLECULAR PHYSICS

Derivation of the generalized Langevin equation in nonstationary environments

(2011) Shinnosuke Kawai et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

How the diffusivity profile reduces the arbitrariness of protein folding free energies

(2010) M. Hinczewski et al.   JOURNAL OF CHEMICAL PHYSICS

Multidimensional Langevin modeling of biomolecular dynamics

(2009) Rainer Hegger et al.   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

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hard spheres: crystallization and glass formation

(2009) P. N. Pusey et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis

(2008) Alexandros Altis et al.   JOURNAL OF CHEMICAL PHYSICS

Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations

(2008) Cristian Micheletti et al.   JOURNAL OF CHEMICAL PHYSICS