Related papers: Dynamics and energetics of a molecular zipper unde…
We investigate a simple model corresponding to particles driven in opposite directions and interacting via a repulsive potential. The particles move off-lattice on a periodic strip and are subject to random forces as well. We show that this…
Nonequilibrium energetics of single molecule translational motor kinesin was investigated by measuring heat dissipation from the violation of the fluctuation-response relation of a probe attached to the motor using optical tweezers. The sum…
We propose a two-dimensional model for the organization of stabilized microtubules driven by molecular motors in an unconfined geometry. In this model two kinds of dynamics are competing. The first one is purely diffusive, with an…
We describe some general results that constrain the dynamical fluctuations that can occur in non-equilibrium steady states, with a focus on molecular dynamics. That is, we consider Hamiltonian systems, coupled to external heat baths, and…
A discrete-state model of the F1-ATPase molecular motor is developed which describes not only the dependences of the rotation and ATP consumption rates on the chemical concentrations of ATP, ADP, and inorganic phosphate, but also on…
Motivated by recent experiments [Lee et al. Nature 498, 209 (2013)], we present here a detailed theoretical analysis of the Joule heating in current-carrying single-molecule junctions. By combining the Landauer approach for quantum…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
The relaxation rate of a Maxwellian velocity distribution function that has an initially anisotropic temperature $(T_\parallel \neq T_\perp)$ is an important physical process in space and laboratory plasmas. It is also a canonical example…
This study aims to address the nature of state change, measurement, and probabilistic outcomes in non-relativistic quantum mechanics. We consider a pair of particles that interact in a one-dimensional setting via a delta-function potential.…
We discuss a nonlinear model for the relaxation by energy redistribution within an isolated, closed system composed of non-interacting identical particles with energy levels e_i with i=1,2,...,N. The time-dependent occupation probabilities…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
The dynamics of active matter driven by interacting molecular motors has a non-potential structure at the local scale. However, we show that there exists a quasi-potential effectively describing the collective self-organization of the…
We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the…
A simple zipper model is introduced, representing in a simplified way, e.g., the folded DNA double helix or hairpin structures in RNA. The double stranded hairpin is connected to a heat bath at temperature $T$ and subject to an external…
We consider a model of a dynamical Lorentz gaz : a single particle is moving in $\mathbb{R}^d$ through an array of fixed an soft scatterers each possessing an internal degree of freedom coupled to the particle. Assuming the initial velocity…
The motion of molecular motor is essential to the biophysical functioning of living cells. In principle, this motion can be regraded as a multiple chemical states process. In which, the molecular motor can jump between different chemical…
In this work, we investigate the dynamics of a non-local model describing spontaneous cell polarisation. It consists in a drift-diffusion equation set in the half-space, with the coupling involving the trace value on the boundary. We…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
We propose a model with a quantized degree of freedom to study the heat transport in quasi-one dimensional system. Our simulations reveal three distinct temperature regimes. In particular, the intermediate regime is characterized by heat…