相关论文: Base Pair Openings and Temperature Dependence of D…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in…
The influence of finite temperatures and pairing correlations on the ground state properties of multi $\Lambda$- Ca, Sn and Pb hypernuclei is explored using finite temperature Hartree Fock Bogoliubov approach and contact pairing…
We obtain, using transfer matrix methods, the distribution function $P(R)$ of the end-to-end distance, the loop formation probability and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the…
We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…
We study the tautomeric transitions in base pairs of DNA considering elastic properties of DNA as classical and tunneling of protons as quantum, and show that the dynamics of the transitions admits of soliton like solutions whose shape and…
The temperature increase in the contact regions between solids in sliding contact has a huge influence on friction and wear. Here we test an analytical theory for the flash temperature, valid for randomly rough surface with multiscale…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
Folding of RNA is subject to a competition between entropy, relevant at high temperatures, and the random, or random looking, sequence, determining the low- temperature phase. It is known from numerical simulations that for random as well…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
The properties of crystals consisting of several components can be widely tuned. Often solid solutions are produced, where substitutional or interstitional disorder determines the crystal thermodynamic and mechanical properties. The…
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…
From the crystal structure data and using the concept of equilbrium statistical mechanics we show how to calculate the thermodynamics of protein/DNA complexes. We apply the method to the TATA-box binding protein (TBP)/TATA sequence complex.…
The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine-cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard-Bishop-Dauxois model at 310 K. An analytical description…
In this paper, we investigate the open tight-binding model with $N$ sites coupled to two reservoirs on its edges with the nonequilibrium Green function method to understand effects of open boundaries. As a result, we obtain an analytical…
The metallicity dependence of the wide binary fraction (WBF) is critical for studying the formation of wide binaries. While controversial results have been found in recent years. Here we combine the wide binary catalog recognized from Gaia…
The simplest approximation of interaction potential between amino-acids in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation.…
The dynamic properties of fluid, including density, surface tension, diffusivity and viscosity, are temperature-dependent and can significantly influence the flow dynamics of mesoscopic non-isothermal systems. To capture the correct…