相关论文: Base Pair Openings and Temperature Dependence of D…

A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…

A previously established multiscale population genetics model states that fitness can be inferred from the physical properties of proteins under the physiological assumption that a loss of stability by any protein confers the lethal…

The infinite-dimensional Hubbard model is studied by means of a modified perturbation theory. The approach reduces to the iterative perturbation theory for weak coupling. It is exact in the atomic limit and correctly reproduces the…

We propose a new strategy to improve the self-assembly properties of DNA-functionalised colloids. The problem that we address is that DNA-functionalised colloids typically crystallize in a narrow temperature window, if at all. The…

We investigate the one-dimensional Hubbard model with an additional bond-charge interaction, recently considered in the description of compounds that exhibit strong 1D features above the temperature of ordered phases. The partition function…

We compute the dynamical charge susceptibility in the two-dimensional Hubbard model within the dynamical cluster approximation. In order to understand the connection between charge susceptibility and pseudogap, we investigate the momentum,…

Among the outstanding problems in the theory of supercooled liquids are the reasons for the rapid increase in their viscosity and relaxation times as the temperature is lowered towards the glass transition temperature, the non-exponential…

It has long been puzzling regarding the mechanism behind the nonlinearity of lattice thermal expansion at low temperatures despite modeling considerations from various perspectives in classical or quantum approximations. An analytical…

We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects…

A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…

The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…

We study the spectrum of light baryons and hyperons as a function of temperature using lattice gauge theory methods. We find that masses of positive parity states are temperature independent, within errors, in the hadronic phase. The…

The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…

We study the thermodynamics of open superstrings in the presence of $p$-dimensional D-branes. We get some finite temperature dualities relating the one-loop canonical free energy of open strings to the self-energy of D-branes at dual…

A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…

Collective response of DNA to THz electric fields is studied in a simple pair bond model. We confirm, with some caveats, a previous observation of destabilising DNA breather modes and explore the parameter-dependence of these modes. It is…

The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide…

We present a quantitative finite temperature analysis of a recent experiment with Bose-Fermi mixtures in optical lattices, in which the dependence of the coherence of bosons on the inter-species interaction was analyzed. Our theory…

The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a…

Many structures inside the cell such as nucleosomes and protein-mediated DNA loops contain sharply bent double-stranded (ds) DNA. Therefore, the energetics of strong dsDNA bending constitutes an essential part of cellular thermodynamics.…