85 citations · 440 across the 18 of their papers we have counts for
18 papers
Accurate estimation of the normalized mutual information of multidimensional data
Daniel Nagel, Georg Diez, Gerhard Stock
While the linear Pearson correlation coefficient represents a well-established normalized measure to quantify the interrelation of two stochastic variables and , it fails fo…
Nonadiabatic Dynamics of Molecules Interacting with Metal Surfaces: A Quantum-Classical Approach Based on Langevin Dynamics and the Hierarchical Equations of Motion
Samuel L. Rudge, Christoph Kaspar, Robin L. Grether +3
A novel mixed quantum-classical approach to simulating nonadiabatic dynamics of molecules at metal surfaces is presented. The method combines the numerically exact hierarchical equ…
Log-periodic oscillations as real-time signatures of hierarchical dynamics in proteins
Emanuel Dorbath, Adnan Gulzar, Gerhard Stock
The time-dependent relaxation of a dynamical system may exhibit a power-law behavior that is superimposed by log-periodic oscillations. Sornette [Phys. Rep. 297, 239 (1998)] showed…
Investigation of rare protein conformational transitions via dissipation-corrected targeted molecular dynamics
Matthias Post, Steffen Wolf, Gerhard Stock
To sample rare events, dissipation-corrected targeted molecular dynamics (dcTMD) applies a constant velocity constraint along a one-dimensional reaction coordinate , which drive…
Towards a Benchmark for Markov State Models: The Folding of HP35
Daniel Nagel, Sofia Sartore, Gerhard Stock
Adopting a s-long molecular dynamics (MD) trajectory of the reversible folding of villin headpiece (HP35) published by D. E. Shaw Research, we recently constructed a Mark…
Selecting Features for Markov Modeling: A Case Study on HP35
Daniel Nagel, Sofia Sartore, Gerhard Stock
Markov state models represent a popular means to interpret molecular dynamics trajectories in terms of memoryless transitions between metastable conformational states. To provide a…
Path separation of dissipation-corrected targeted molecular dynamics simulations of protein-ligand unbinding
Steffen Wolf, Matthias Post, Gerhard Stock
Protein-ligand (un)binding simulations are a recent focus of biased molecular dynamics simulations. Such binding and unbinding can occur via different pathways in and out of a bind…
Nonequilibrium Modeling of the Elementary Step in PDZ3 Allosteric Communication
Ahmed A. A. I. Ali, Adnan Gulzar, Steffen Wolf +1
While allostery is of paramount importance for protein signaling and regulation, the underlying dynamical process of allosteric communication is not well understood. PDZ3 domain re…
Energy Transport and its Function in Heptahelical Transmembrane Proteins
Nadja Helmer, Steffen Wolf, Gerhard Stock
Photoproteins such as bacteriorhodopsin (bR) and rhodopsin (Rho) need to effectively dissipate photoinduced excess energy to prevent their damage. Another well-studied G protein-co…
Correlation-based feature selection to identify functional dynamics in proteins
Georg Diez, Daniel Nagel, Gerhard Stock
To interpret molecular dynamics simulations of biomolecular systems, systematic dimensionality reduction methods are commonly employed. Among others, this includes principal compon…
Molecular origin of driving-dependent friction in fluids
Matthias Post, Steffen Wolf, Gerhard Stock
The friction coefficient of fluids may become a function of the velocity at increased external driving. This non-Newtonian behavior is of general theoretical interest as well as of…
Data-driven Langevin modeling of nonequilibrium processes
Benjamin Lickert, Steffen Wolf, Gerhard Stock
Given nonstationary data from molecular dynamics simulations, a Markovian Langevin model is constructed that aims to reproduce the time evolution of the underlying process. While a…
Real-time observation of ligand-induced allosteric transitions in a PDZ domain
Olga Bozovic, Claudio Zanobini, Adnan Gulzar +6
While allostery is of paramount importance for protein regulation, the underlying dynamical process of ligand (un)binding at one site, resulting time evolution of the protein struc…
Multisecond ligand dissociation dynamics from atomistic simulations
Steffen Wolf, Benjamin Lickert, Simon Bray +1
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescal…
Principal component analysis of nonequilibrium molecular dynamics simulations
Matthias Post, Steffen Wolf, Gerhard Stock
Principal component analysis (PCA) represents a standard approach to identify collective variables , which can be used to construct the free energy land…
Inferring transition rates on networks with incomplete knowledge
Purushottam D. Dixit, Abhinav Jain, Gerhard Stock +1
Across many fields, a problem of interest is to predict the transition rates between nodes of a network, given limited stationary state and dynamical information. We give a solutio…
Dynamic treatment of vibrational energy relaxation in a heterogeneous and fluctuating environment
Hiroshi Fujisaki, Gerhard Stock
A computational approach to describe the energy relaxation of a high-frequency vibrational mode in a fluctuating heterogeneous environment is outlined. Extending previous work [H.…
Quantum and classical vibrational relaxation dynamics of N-methylacetamide on ab initio potential energy surfaces
Hiroshi Fujisaki, Kiyoshi Yagi, Kimihiko Hirao +2
Employing extensive quantum-chemical calculations at the DFT/B3LYP and MP2 level, a quartic force field of isolated N-methylacetamide is constructed. Taking into account 24 vibrati…