Related papers: Dynamical phase transition of a periodically drive…
We model unzipping of DNA/RNA molecules subject to an external force by a spin-oscillator system. The system comprises a macroscopic degree of freedom, represented by a one-dimensional oscillator, and internal degrees of freedom,…
We propose a dynamical mechanism of the two-way switching between the metastable state and the stable state, which has been found in experiments of photoinduced reversible magnetization and photoinduced structural phase transition. We find…
The nonequilibrium dynamic phase transition, in the two dimensional kinetic Ising model in presence of a randomly varying (in time but uniform in space) magnetic field, has been studied both by Monte Carlo simulation and by solving the mean…
Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting…
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…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
Phase transitions and critical behavior of driven systems are reviewed. Models exhibiting phase transitions, spontaneous symmetry breaking, phase separation and coarsening processes in d=1 dimension are discussed.
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…
Dynamic behaviour of an isotropic Ashkin-Teller model in the presence of a periodically oscillating magnetic field has been analysed by means of the mean field approximation. The dynamic equation of motion has been constructed with the help…
We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude $F$ and frequency $\nu$ and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis…
The majority of dynamical studies in power systems focus on the high voltage transmission grids where models consider large generators interacting with crude aggregations of individual small loads. However, new phenomena have been observed…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
We study the nonequilibrium dynamics of a many-body bosonic system on a lattice, subject to driving and dissipation. The time-evolution is described by a master equation, which we treat within a generalized Gutzwiller mean field…
Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference…
We review the depinning and nonequilibrium phases of collectively interacting particle systems driven over random or periodic substrates. This type of system is relevant to vortices in type-II superconductors, sliding charge density waves,…