57 citations · 101 across the 7 of their papers we have counts for
5 papers · 1 filter
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…
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…