相关论文: Energy Localization in the Peyrard-Bishop DNA mode…
We present a new mechanism for generating exponential hierarchies in four-dimensional field theories inspired by Anderson localization in one dimension, exploiting an analogy between the localization of electron energy eigenstates along a…
Thermal oscillations of base pairs in the Peyrard-Bishop-Holstein model are simulated by stochastic fluctuations of base overlap integrals. Numerical investigation of the model is carried out for a hole transfer in $G_1A_2G_3G_4$ sequence…
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…
Nearest-neighbor(NN) free energy parameters for DNA are well studied and reliable values of these parameters exist in the literature. They have been found to be very useful in studying DNA melting and DNA stabilization studies. In this…
We propose an approach to position measurements based on the hypothesis that the action of a position detector on a quantum system can be effectively described by a dissipative disordered potential. We show that such kind of potential is…
Using the method of energy-level statistics, the localization properties of electrons moving in two dimensions in the presence of a perpendicular random magnetic field and additional random disorder potentials are investigated. For this…
The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other…
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…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
Genetic oscillators, such as circadian clocks, are constantly perturbed by molecular noise arising from the small number of molecules involved in gene regulation. One of the strongest sources of stochasticity is the binary noise that arises…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
The effect of defects on the melting profile of short heterogeneous DNA chains are calculated using the Peyrard-Bishop Hamiltonian. The on-site potential on a defect site is represented by a potential which has only the short-range…
We establish spectral and dynamical localization for several Anderson models on metric and discrete radial trees. The localization results are obtained on compact intervals contained in the complement of discrete sets of exceptional…
We study the internal resonance, energy transfer, activation mechanism, and control of a model of DNA division via parametric resonance. While the system is robust to noise, this study shows that it is sensitive to specific fine scale modes…
We study the large amplitude response of classical molecules to electromagnetic radiation, showing the universality of the transition from the linear to nonlinear response and brakeup at sufficiently large amplitudes. A range of models,…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
We investigate the dynamics of highly polydispersed finite granular chains. From the spatio-spectral properties of small vibrations, we identify which particular single-particle displacements lead to energy localization. Then, we address a…
We introduce two time-delay models of metabolic oscillations in yeast cells. Our model tests a hypothesis that the oscillations occur as multiple pathways share a limited resource which we equate to the number of available ribosomes. We…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the…