Related papers: DNA unzipping via stopped birth and death processe…
We consider force-induced unzipping transition for a heterogeneous DNA model with a long-range correlated base-sequence. It is shown that as compared to the uncorrelated situation, long-range correlations smear the unzipping…
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
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…
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…
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…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
We analyze the dynamics of structural transitions between normal right-handed B form and unusual left-handed Z form for a linear DNA molecule. The dynamics under the external torque in physiological buffer is modeled by a Langevin equation,…
An 1d model with time-dependent random hopping is proposed to describe charge transport in DNA. It admits to investigate both diffusion of electrons and their tunneling between different sites in DNA. The tunneling appears to be strongly…
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…
It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the…
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…
We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…
We consider the unbinding of a directed polymer in a random media from a wall in $d=1+1$ dimensions and a simple one-dimensional model for DNA unzipping. Using the replica trick we show that the restricted partition functions of these…
Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al.,…
We study the statistical properties of a simple genetic regulatory network that provides heterogeneity within a population of cells. This network consists of a binary genetic switch in which stochastic flipping between the two switch states…