Related papers: Dynamics and energetics of a molecular zipper unde…
We study heat conduction in a one-dimensional chain of particles with longitudinal as well as transverse motions. The particles are connected by two-dimensional harmonic springs together with bending angle interactions. The problem is…
Dynamics of molecular motor dimers, consisting of rigidly bound particles that move along two parallel lattices and interact with underlying molecular tracks, is investigated theoretically by analyzing discrete-state stochastic…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
We study the stationary state of a one-dimensional kinetic model where a probe particle is driven by an external field E and collides, elastically or inelastically, with a bath of particles at temperature T. We focus on the stationary…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
We describe the dynamics of a bound state of an attractive $\delta$-well under displacement of the potential. Exact analytical results are presented for the suddenly moved potential. Since this is a quantum system, only a fraction of the…
Chemically active droplets provide simple models for cell-like systems that can grow and divide. Such active droplet systems are driven away from thermodynamic equilibrium and turn over chemically, which corresponds to a simple metabolism.…
We consider a heat conduction model introduced in \cite{Collet-Eckmann 2009}. This is an open system in which particles exchange momentum with a row of (fixed) scatterers. We assume simplified bath conditions throughout, and give a…
The inhomogeneous cooling state describing the hydrodynamic behavior of a freely evolving granular gas strongly confined between two parallel plates is studied, using a Boltzmann kinetic equation derived recently. By extending the idea of…
A molecular dynamics study of a two dimensional system of particles interacting through a Lennard-Jones pairwise potential is performed at fixed temperature and vanishing external pressure. As the temperature is increased, a solid-to-liquid…
Non-Hermitian dynamics in open systems can give rise to a variety of fascinating non-equilibrium phenomena, ranging from symmetry-breaking transitions to directional energy flow. Parity-time (PT) symmetry breaking determines the occurrence…
A kinetic model is proposed for rarefied flows of molecular gas with rotational and temperature-dependent vibrational degrees of freedom. The model reduces to the Boltzmann equation for monatomic gas when the energy exchange between the…
Recently proposed non-adiabatic ring polymer molecular dynamics (NRPMD) approach has shown to provide accurate quantum dynamics by incorporating explicit electronic state descriptions and nuclear quantizations. Here, we present a rigorous…
We study the model of a molecular switch comprised of a molecule with a soft vibrational degree of freedom coupled to metallic leads. In the presence of strong electron-ion interaction, different charge states of the molecule correspond to…
We study the trajectories of a single colloidal particle as it hops between two energy wells A and B, which are sculpted using adjacent optical traps by controlling their respective power levels and separation. Whereas the dynamical…
Dynamics of inelastic gases are studied within the framework of random collision processes. The corresponding Boltzmann equation with uniform collision rates is solved analytically for gases, impurities, and mixtures. Generally, the energy…
This paper presents a molecular dynamics simulation of an inelastic gas, where collisions between molecules are characterized by a coefficient of restitution less than unity. The simulation employs an event-driven algorithm to efficiently…
General discrete one-dimensional stochastic models to describe the transport of single molecules along coupled parallel lattices with period $N$ are developed. Theoretical analysis that allows to calculate explicitly the steady-state…
We present a theoretical investigation of thermal fluctuation statistics in a molecular motor. Energy transfer in the motor is described using a multidimensional discrete master equation with nearest-neighbor hopping. In this theory, energy…