85 citations · 440 across the 18 of their papers we have counts for
4 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…
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…