Related papers: Dynamics of a bubble formed in double stranded DNA
Anomalous dynamics characterized by non-Gaussian probability distributions (PDFs) and/or temporal long-range correlations can cause subtle modifications of conventional fluctuation relations. As prototypes we study three variants of a…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
In the context of fluctuation relations, we study the distribution of energy dissipated by a driven two-level system. Incorporating an energy counting field into the well known spin-boson model enables us to calculate the distribution…
When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
Static nonreciprocal forces between particles generically drive persistent motion reminiscent of self-propulsion. Here, we demonstrate that reciprocity-breaking fluctuations about a reciprocal mean coupling strength are sufficient to…
We analyze the fluctuation-driven escape of particles from a metastable state under the influence of a weak periodic force. We develop an asymptotic method to solve the appropriate Fokker-Planck equation with mixed natural and absorbing…
The stochastic transport of suspended particles through a periodic pattern of obstacles in microfluidic devices is investigated by means of the Fokker-Planck equation. Asymmetric arrays of obstacles have been shown to induce the continuous…
We investigate the universal fluctuations of localized wavefunction in the Fock space of two interacting particles in one-dimensional disordered systems, focusing on the interplay between random potentials and random long-range…
We investigate the stability of stratified fluid layers undergoing homogeneous and periodic tidal deformation. We first introduce a local model which allows to study velocity and buoyancy fluctuations in a Lagrangian domain periodically…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
We study the dynamics of overdamped Brownian particles interacting through soft pairwise potentials on a comb-like structure. Within the linearized Dean-Kawasaki framework, we characterize the particle density fluctuations by computing…
A dynamical mean-field theory is developed to analyze stochastic single-cell dynamics of gene expression. By explicitly taking account of nonequilibrium and nonadiabatic features of the DNA state fluctuation, two-time correlation functions…
Active suspensions, which consist of suspended self-propelling particles such as swimming microorganisms, often exhibit non-trivial transport properties. Continuum models are frequently employed to elucidate phenomena in active suspensions,…
The over-damped motion of a Brownian particle in an asymmetric, bistable, fluctuating potential shows noise induced stability: For intermediate fluctuation rates the mean occupancy of minima with an energy above the absolute minimum is…
We theoretically investigate the effect of random fluctuations on the motion of elongated microswimmers near hydrodynamic transport barriers in externally-driven fluid flows. Focusing on the two-dimensional hyperbolic flow, we consider the…
We consider the motion of an active Brownian particle with speed fluctuations in d-dimensions in the presence of both translational and orientational diffusion. We use an Ornstein-Uhlenbeck process for active speed generation. Using a…
An analytical theory to calculate the dissipatively stable concurrence in the system of two coupled flux superconducting qubits in the strong driving field is developed. The conditions for the entanglement state generation and destruction…