Related papers: Dynamical phase transition of a periodically drive…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. The worm-like chain model provides a good description of small to moderate bending fluctuations, but some experiments on strongly-bent shorter molecules…
A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the dependence of the unzipping forces on…
Properties of the two dimensional Ising model with fixed magnetization are deduced from known exact results on the two dimensional Ising model. The existence of a continuous phase transition is shown for arbitrary values of the fixed…
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…
We introduce a driven diffusive model involving poly-dispersed hard k-mers on a one dimensional periodic ring and investigate the possibility of phase separation transition in such systems. The dynamics consists of a size dependent…
The nonequilibrium dynamic phase transition in ferromagnetic systems is reviewed. Very recent results of dynamic transition in kinetic Ising model and that in Heisenberg ferromagnet is discussed.
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
We investigate the driven states of a two-dimensional crystal whose ground state can be tuned through a square-triangular transition. The depinning of such a system from a quenched random background potential occurs via a complex sequence…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
The formation of polarized signaling domains on cell membranes is a fundamental example of biological pattern formation. While such patterns resemble structures from equilibrium phase separation, they are intrinsically non-equilibrium,…
A mathematical model for a two-gene regulatory network is derived and several of their properties analyzed. Due to the presence of mixed continuous/discrete dynamics and hysteresis, we employ a hybrid systems model to capture the dynamics…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
We study a 1D-Quantum Ising Model in transverse field driven out of equilibrium by performing a composite quantum quench to deduce the asymptotic properties of the transverse magnetization stationary state via the analysis of the spectral…
We study numerically the phase diagram and the response under a driving force of the phase field crystal model for pinned lattice systems introduced recently for both one and two dimensional systems. The model describes the lattice system…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
We propose a periodically driven system whose dimensionality is an emergent property that can be tunable, thus enables us to realize not only many-body phases with arbitrary dimensions, but also phase transitions, instead of crossovers,…
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…