Related papers: Dynamical phase transition of a periodically drive…
Hysteresis and the non-equilibrium dynamic phase transition in thin magnetic films subject to an oscillatory external field have been studied by Monte Carlo simulation. The model under investigation is a classical Heisenberg spin system…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
Hysteresis can be found in driven many-body systems such as magnets and superfluids. Rate-dependent hysteresis arises when a system is driven periodically while relaxing towards equilibrium. A two-state paramagnet driven by an oscillating…
We study various dynamical aspects of systems possessing a first order phase transition in their phase diagram. We isolate three qualitatively distinct types of theories depending on the structure of instabilities and the nature of the low…
We investigate the mechanisms of histone sliding and detachment with a stochastic model that couples thermally-induced, passive histone sliding with active motor-driven histone unwrapping. Analysis of a passive loop or twist defect-mediated…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
The phase transition between the intermediate and normal states in type-I superconducting films is investigated using magneto-optical imaging. Magnetic hysteresis with different transition fields for collapse and nucleation of…
We study theoretically the unzipping of a double stranded DNA from a condensed globule state by an external force. At constant force, we find that the double stranded DNA unzips an at critical force Fc and the number of unzipped monomers M…
The experiment that the high spin selectivity and the length-dependent spin polarization are observed in double-stranded DNA [Science ${\bf 331}$, 894 (2011)], is elucidated by considering the combination of the spin-orbit coupling, the…
We study three different lattice models in which two species of diffusing particles are driven in opposite directions by an electric field. We focus on dynamical phase transitions that involve phase separation into domains that may be…
Dynamical equations that are valid in the vicinity of the phase transition into the superconducting state are given. Probable effects of the field of charge carriers' magnetic interactions and the field of temperature fluctuations were…
We consider a binary system of particles with repulsive interactions that move in opposite or perpendicular directions to each other under an applied external drive. For opposite driving, at higher drives a phase-separated laned state forms…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
We study the large deviations of additive quantities, such as energy or current, in stochastic processes with intermittent reset. Via a mapping from a discrete-time reset process to the Poland-Scheraga model for DNA denaturation, we derive…
Cells can often choose among several stably heritable phenotypes. Examples are the expression of genes in eukaryotic cells where long chromosomal regions can adopt persistent and heritable silenced or active states, that may be associated…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
We investigate the depinning transition in a dirty periodic medium considering a model of layered charge density waves as a prototype system. We find that depinning from strong disorder occurs via a two stage process, where, first, the…
Polymerization of RNA from a template DNA is carried out by a molecular machine called RNA polymerase (RNAP). It also uses the template as a track on which it moves as a motor utilizing chemical energy input. The time it spends at each…