Elasticity-based polymer sorting in active fluids: A Brownian dynamics study

J Shin, AG Cherstvy, WK Kim… - Physical Chemistry …, 2017 - pubs.rsc.org
While the dynamics of polymer chains in equilibrium media is well understood by now, the
polymer dynamics in active non-equilibrium environments can be very different. Here we …

Fluctuations in the ensemble of reaction pathways

G Mazzola, S Beccara, P Faccioli… - The Journal of chemical …, 2011 - pubs.aip.org
The dominant reaction pathway is a rigorous framework to microscopically compute the most
probable trajectories, in nonequilibrium transitions. In the low-temperature regime, such …

Transition state theory approach to polymer escape from a one dimensional potential well

H Mökkönen, T Ikonen, T Ala-Nissila… - The Journal of Chemical …, 2015 - pubs.aip.org
The rate of escape of an ideal bead-spring polymer in a symmetric double-well potential is
calculated using transition state theory (TST) and the results compared with direct dynamical …

Predicting the unobserved: A statistical mechanics framework for non-equilibrium material response with quantified uncertainty

S Huang, IR Graham, RA Riggleman, PE Arratia… - Journal of the …, 2022 - Elsevier
Can far-from-equilibrium material response under arbitrary loading be inferred from
equilibrium data and vice versa? Can the effect of element transmutation on mechanical …

Diffusion in periodic potentials with path integral hyperdynamics

T Ikonen, MD Khandkar, LY Chen, SC Ying… - Physical Review E …, 2011 - APS
We consider the diffusion of Brownian particles in one-dimensional periodic potentials as a
test bench for the recently proposed stochastic path integral hyperdynamics (PIHD) scheme …

Effects of static and temporally fluctuating tensions on semiflexible polymer looping

J Shin, W Sung - The Journal of Chemical Physics, 2012 - pubs.aip.org
Biopolymer looping is a dynamic process that occurs ubiquitously in cells for gene
regulation, protein folding, etc. In cellular environments, biopolymers are often subject to …

Polymer escape from a confining potential

H Mökkönen, T Ikonen, H Jonsson… - The Journal of Chemical …, 2014 - pubs.aip.org
The rate of escape of polymers from a two-dimensionally confining potential well has been
evaluated using self-avoiding as well as ideal chain representations of varying length, up to …

Atomistic simulation methods for long-time dynamics in materials for nuclear energy systems

BP Uberuaga, D Perez, AF Voter - 2018 - osti.gov
Many important processes in materials systems are intrinsically atomistic in nature but
involve time scales that span many orders of magnitude, thus exceeding what can be …

Escape Rates of Externally Confined Polymers

H Mökkönen - 2016 - opinvisindi.is
A polymer escaping from a confining external potential represents a generic description of
long macromolecules crossing an energy barrier. This type of barrier crossing problems are …