Related papers: A two-state kinetic model for the unfolding of sin…
We propose a dynamical model for state symmetrization of two identical particles produced in spacelike-separated events by independent sources. We adopt the hypothesis that the pair of non-interacting particles can initially be described by…
When two macromolecules come very near in a fluid, the surrounding molecules, having finite volume, are less likely to get in between. This leads to a pressure difference manifesting as an entropic attraction, called depletion force. Here…
We show that the rare events present in dissipated work that enters Jarzynski equality, when mapped appropriately to the phenomenon of large deviations found in a biased coin toss, are enough to yield a quantitative work probability…
Brownian dynamics simulations are used to study the detachment of a particle from a substrate. Although the model is simple and generic, we attempt to map its energy, length and time scales onto a specific experimental system, namely a bead…
We investigate a microscopic motor based on an externally controlled two-level system. One cycle of the motor operation consists of two strokes. Within each stroke, the two-level system is in contact with a given thermal bath and its energy…
Analysis of bond rupture data from single-molecule force spectroscopy experiments commonly relies on the strong assumption that the bond dissociation process is irreversible. However, with increased spatiotemporal resolution of instruments…
Propagation of a particle accelerated by an external field through a scattering medium is studied within the generalized Lorentz model allowing inelastic collisions. Energy losses at collisions are proportional to $(1-\alpha^{2})$, where…
A single bit memory system is made with a brownian particle held by an optical tweezer in a double-well potential and the work necessary to erase the memory is measured. We show that the minimum of this work is close to the Landauer's bound…
We consider the relation between the microscopic and effective descriptions of the unfolding experiment on a model polypeptide. We evaluate the probability distribution function of the performed work by Monte Carlo simulations and compare…
A two-electron one-dimensional model of a heteroatomic molecule composed of two open-shell atoms is considered. Including only two electrons isolates and examines the effect that the highest occupied molecular orbital has on the Kohn-Sham…
We consider the paradigm of an overdamped Brownian particle in a potential well, which is modulated through an external protocol, in the presence of stochastic resetting. Thus, in addition to the short range diffusive motion, the particle…
We introduce a discrete time microscopic single particle model for kinetic transport. The kinetics is modeled by a two-state Markov chain, the transport by deterministic advection plus a random space step. The position of the particle after…
Collections of self-propelled particles that move persistently by continuously consuming free energy are a paradigmatic example of active matter. In these systems, unlike Brownian "hot colloids", the breakdown of detailed balance yields a…
The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is…
We consider in this paper, a few important issues in non-equilibrium work fluctuations and their relations to equilibrium free energies. First we show that Jarzynski identity can be viewed as a cumulant expansion of work. For a switching…
We relate the breakdown of equations of states for the mechanical pressure of generic dry active systems to the lack of momentum conservation in such systems. We show how sources and sinks of momentum arise generically close to confining…
A model multilevel molecule described by two sets of rotational internal energy levels of different parity and degenerate ground states, coupled by a constant interaction, is considered, by assuming that the random collisions in a gas of…
A collisional model of a confined quasi-two-dimensional granular mixture is considered to analyze homogeneous steady states. The model includes an effective mechanism to transfer the kinetic energy injected by vibration in the vertical…
We consider mechanically generated molecular braids composed of two molecules where long range interactions between them can be considered to be very weak. We describe a model that takes account of the thermal fluctuations of the braid,…
We study a model of active particles that perform a simple random walk and on top of that have a preferred direction determined by an internal state which is modelled by a stationary Markov process. First we calculate the limiting diffusion…