Milestoning estimators of dissipation in systems observed at a coarse resolution
Many nonequilibrium, active processes are observed at a coarse-grained level, where
different microscopic configurations are projected onto the same observable state. Such …
different microscopic configurations are projected onto the same observable state. Such …
RNA polymerase drives ribonucleotide excision DNA repair in E. coli
Z Hao, M Gowder, S Proshkin, BK Bharati, V Epshtein… - Cell, 2023 - cell.com
Ribonuclease HII (RNaseHII) is the principal enzyme that removes misincorporated
ribonucleoside monophosphates (rNMPs) from genomic DNA. Here, we present structural …
ribonucleoside monophosphates (rNMPs) from genomic DNA. Here, we present structural …
Inferring entropy production rate from partially observed Langevin dynamics under coarse-graining
The entropy production rate (EPR) measures time-irreversibility in systems operating far
from equilibrium. The challenge in estimating the EPR for a continuous variable system is …
from equilibrium. The challenge in estimating the EPR for a continuous variable system is …
Arrhenius law for interacting diffusive systems
Finding the mean time it takes for a particle to escape from a metastable state due to thermal
fluctuations is a fundamental problem in physics, chemistry, and biology. Here, we consider …
fluctuations is a fundamental problem in physics, chemistry, and biology. Here, we consider …
Compression algorithms reveal memory effects and static disorder in single-molecule trajectories
K Song, DE Makarov, E Vouga - Physical Review Research, 2023 - APS
A key challenge in single-molecule studies is deducing underlying molecular kinetics from
low-dimensional data, as distinct physical scenarios can exhibit similar observable …
low-dimensional data, as distinct physical scenarios can exhibit similar observable …
Uphill drift in the absence of current in single-file diffusion
Single-file diffusion is a paradigmatic model for the transport of Brownian colloidal particles
in narrow one-dimensional channels, such as those found in certain porous media, where …
in narrow one-dimensional channels, such as those found in certain porous media, where …
Milestoning estimators of dissipation in systems observed at a coarse resolution: When ignorance is truly bliss
Many non-equilibrium, active processes are observed at a coarse-grained level, where
different microscopic configurations are projected onto the same observable state. Such" …
different microscopic configurations are projected onto the same observable state. Such" …
Diffusion coefficient expression for asymmetric discrete random walk with unequal jump times, lengths, and probabilities
G Lin, S Zheng - Physica A: Statistical Mechanics and its Applications, 2024 - Elsevier
Random walk has wide applications in many fields, such as generative AI, biology, physics,
and chemistry. Asymmetric random walk could be described by the drift-diffusion equation …
and chemistry. Asymmetric random walk could be described by the drift-diffusion equation …
Asymmetry of forward/backward transition times as a non-equilibrium measure of complexity of microscopic mechanisms
J Shin, AB Kolomeisky - The Journal of Chemical Physics, 2020 - pubs.aip.org
One of the main experimental tools in studying the microscopic mechanisms of complex
phenomena is measuring transition times for individual particles. 1 These observations are …
phenomena is measuring transition times for individual particles. 1 These observations are …
Cycle completion times probe interactions with environment
Recent measurements of the durations of nonequilibrium processes provide valuable
information on microscopic mechanisms and energetics. Theory for corresponding …
information on microscopic mechanisms and energetics. Theory for corresponding …