19 citations · 80 across the 30 of their papers we have counts for
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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…
Intrinsic cell-to-cell variance from experimental single-cell motility data
Anton Klimek, Johannes C. J. Heyn, Debasmita Mondal +5
When analyzing the individual positional dynamics of an ensemble of moving objects, the extracted parameters that characterize the motion of individual objects, such as the mean-sq…
Predictability Analysis and Prediction of Discrete Weather and Financial Time-Series Data with a Hamiltonian-Based Filter-Projection Approach
Henrik Kiefer, Denis Furtel, Cihan Ayaz +3
The generalized Langevin equation (GLE), derived by projection from a general many-body Hamiltonian, exactly describes the dynamics of an arbitrary coarse-grained variable in a com…
Temporal coarse-graining and elimination of slow dynamics with the generalized Langevin equation for time-filtered observables
Roland R. Netz
By exact projection in phase space we derive the generalized Langevin equation (GLE) for time-filtered observables. We employ a general convolution filter that directly acts on arb…
Quantitative Prediction of Protein-Polyelectrolyte Binding Thermodynamics: Adsorption of Heparin-Analog Polysulfates to the SARS-CoV-2 Spike Protein RBD
Lenard Neander, Cedric Hannemann, Roland R. Netz +1
Interactions of polyelectrolytes (PEs) with proteins play a crucial role in numerous biological processes, such as the internalization of virus particles into host cells. Although…
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…
How Thick is the Air-Water Interface? -- A Direct Experimental Measurement of the Decay Length of the Interfacial Structural Anisotropy
Alexander P. Fellows, Álvaro Díaz Duque, Vasileios Balos +4
The air-water interface is a highly prevalent phase boundary with a far-reaching impact on natural and industrial processes. Water molecules behave differently at the interface com…
Quantifying the efficiency of principal signal transmission modes in proteins
Anil Kumar Sahoo, Richard Schwarzl, Markus S. Miettinen +1
On the microscopic level, biological signal transmission relies on coordinated structural changes in allosteric proteins that involve sensor and effector modules. The timescales an…
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…