17 citations · 20 across the 12 of their papers we have counts for
13 papers
Reaction dynamics in non-Markovian systems with non-monotonically decaying memory
Artur Bakaev, Otto Geburtig, Benjamin A. Dalton +1
Whereas the effect of monotonically decaying memory kernels on reaction dynamics has been studied extensively, the effect of oscillatory memory, observed for widely different syste…
Reaction-Coordinate-Dependent Non-Markovian Friction Governs Protein-Folding Dynamics
Lucas Tepper, Benjamin J. A. Héry, Cihan Ayaz +4
It is common to project the full atomic-resolution representation of a protein onto a one-dimensionalreaction coordinate (RC) to capture the protein-folding kinetics. As a direct c…
Hierarchical friction memory leads to subdiffusive configurational dynamics of fast-folding proteins
Anton Klimek, Benjamin A. Dalton, Lucas Tepper +1
Proteins often exhibit subdiffusive configurational dynamics. The origins of this subdiffusion are still unresolved. We investigate the impact of non-Markovian friction and the fre…
The influence of multi-dimensionality and off-diagonal non-Markovian friction coupling on coarse-grained dynamics
Henrik Kiefer, Cihan Ayaz, Benjamin A. Dalton +1
Coarse-graining complex molecular systems to lower-dimensional reaction coordinates is a powerful approach for capturing their effective dynamics. The generalized Langevin equation…
Subdiffusion from competition between multi-exponential friction memory and energy barriers
Anton Klimek, Benjamin A. Dalton, Roland R. Netz
Subdiffusion is a hallmark of complex systems, ranging from protein folding to transport in viscoelastic media. However, despite its pervasiveness, the mechanistic origins of subdi…
Analysis and Simulation of Generalized Langevin Equations with Non-Gaussian Orthogonal Forces
Henrik Kiefer, Benjamin J. A. Héry, Lucas Tepper +3
The generalized Langevin equation (GLE) is a useful framework for analyzing and modeling the dynamics of many-body systems in terms of low-dimensional reaction coordinates, with it…
Non-Markovianity increases transition path probability
Florian N. Brünig, Benjamin A. Dalton, Jan O. Daldrop +1
Defining low-dimensional reaction coordinates is crucial for analyzing the dynamics of complex systems and for comparison with experiments. The maximal value of the transition-path…
Memory and Friction: From the Nanoscale to the Macroscale
Benjamin A. Dalton, Anton Klimek, Henrik Kiefer +5
Friction is a phenomenon that manifests across all spatial and temporal scales, from the molecular to the macroscopic scale. It describes the dissipation of energy from the motion…
Effect of Frequency-Dependent Viscosity on Molecular Friction in Liquids
Henrik Kiefer, Domenico Vitali, Benjamin A. Dalton +2
The relation between the frequency-dependent friction of a molecule in a liquid and the hydrodynamic properties of the liquid is fundamental for molecular dynamics. We investigate…
Rapid state-recrossing kinetics in non-Markovian systems
Qingyuan Zhou, Roland R. Netz, Benjamin A. Dalton
The mean first-passage time (MFPT) is one standard measure for the reaction time in thermally activated barrier-crossing processes. While the relationship between MFPTs and phenome…
pH modulates friction memory effects in protein folding
Benjamin A. Dalton, Roland R. Netz
We study the non-Markovian folding dynamics of the 3D protein under low- and neutral-pH conditions. Recently published all-atom simulations of 3D by the Shaw group reveal tha…
Accurate Memory Kernel Extraction from Discretized Time Series Data
Lucas Tepper, Benjamin Dalton, Roland R. Netz
Memory effects emerge as a fundamental consequence of dimensionality reduction when low-dimensional observables are used to describe the dynamics of complex many-body systems. In t…
Conformational isomerization dynamics in solvent violates both the Stokes-Einstein relation and Kramers' theory
Benjamin A. Dalton, Henrik Kiefer, Roland R. Netz
Molecular isomerization kinetics in liquid solvents are determined by a complex interplay between the friction acting on a rotating dihedral due to interactions with the solvent, i…