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 the finite spatiotemporal resolution and the limited accessibility to all of the nonequilibrium degrees of freedom. Here, we estimate the irreversibility in partially observed systems following oscillatory dynamics governed by coupled overdamped Langevin equations.

Statistics of Reaction Flux and Dynamical Activity Associated with a Diffusion-Influenced Ligand-Binding Reaction.

In this paper, we consider a macromolecule with two competitive binding sites where a ligand can bind to and gives rise to a unicyclic reaction network consisting of four states-(i) a single state with both binding sites vacant, (ii) two states with one bound site and one free binding site, and (iii) an another single state with both sites occupied. We obtain probability densities of the time-integrated current along the clockwise direction and the dynamical activity or mean number of jumps between different states for finite times at a fast diffusion limit. On the other hand, in the diffusion-limited case, ligand diffusion between the two binding sites directly connects the mono-ligated states-changing the reaction scheme.

The effects of slit-like confinement on flow-induced polymer deformation.

This paper is broadly concerned with the dynamics of a polymer confined to a rectangular slit of width D and deformed by a planar elongational flow of strength γ̇. It is interested, more specifically, in the nature of the coil-stretch transition that such polymers undergo when the flow strength γ̇ is varied, and in the degree to which this transition is affected by the presence of restrictive boundaries. These issues are explored within the framework of a finitely extensible Rouse model that includes pre-averaged surface-mediated hydrodynamic interactions.

Polymer extension under flow: Some statistical properties of the work distribution function.

In an extension of earlier studies from this group on the application of the Jarzynski equality to the determination of the elastic properties of a finitely extensible Rouse model of polymers under flow [A. Ghosal and B. J.

Polymer extension under flow: A path integral evaluation of the free energy change using the Jarzynski relation.

The Jarzynski relation (and its variants) has provided a route to the experimental evaluation of equilibrium free energy changes based on measurements conducted under arbitrary non-equilibrium conditions. Schroeder and co-workers [Soft Matter 10, 2178 (2014) and J. Chem.