Related papers: Bethe approximation for a DNA-like self-avoiding w…
The interplay of quantum statistics, interactions and temperature is studied within the framework of the bosonic two-component theory with repulsive delta-function interaction in one dimension. We numerically solve the thermodynamic Bethe…
We set up a hydrodynamic description of the non-equilibrium dynamics of sine-Gordon quantum field theory for generic coupling. It is built upon an explicit form of the Bethe Ansatz description of general thermodynamic states, with the…
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles respectively, when the strands of the DNA are subjected to a force along the same…
We derive the Bethe ansatz equations describing the complete spectrum of the transition matrix of the partially asymmetric exclusion process with the most general open boundary conditions. For totally asymmetric diffusion we calculate the…
Thermodynamic Bethe ansatz equations for XXZ model at $|\Delta|\ge 1$ is simplified to an integral equation which has one unknown function. This equation is analytically continued to $|\Delta|<1$.
We investigate the influence of a dissipative environment which effectively comprises the effects of counterions and hydration shells, on the transport properties of short \DNA wires. Their electronic structure is captured by a…
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…
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
We consider the Ising model on the Bethe lattice with aperiodic modulation of the couplings, which has been studied numerically in Phys. Rev. E 77, 041113 (2008). Here we present a relevance-irrelevance criterion and solve the critical…
Conformal field theory and Bethe ansatz are used to investigate the low energy features of the spectral function in one dimensional models which exhibit a gap in the spin or in the charge excitation spectrum. Exotic behavior is found in the…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
Quantum walks provide a versatile framework for probing the structural and dynamical properties of complex systems ranging from biological networks to synthetic materials. However, their realization on current noisy pre-fault-tolerant…
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…
We show experimentally that a cheap glass microcapillary can accumulate {\lambda}-phage DNA at its tip and deliver the DNA into the capillary using a combination of electro-osmotic flow, pressure-driven flow, and electrophoresis. We develop…
In simulating continuum model fluids that undergo phase separation and criticality, significant gains in computational efficiency may be had by confining the particles to the sites of a lattice of sufficiently fine spacing, $a_{0}$…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
The dynamics of loops at the DNA denaturation transition is studied. A scaling argument is used to evaluate the asymptotic behavior of the autocorrelation function of the state of complementary bases (either open or closed). The long-time…
The inverse Ising problem consists in inferring the coupling constants of an Ising model given the correlation matrix. The fastest methods for solving this problem are based on mean-field approximations, but which one performs better in the…
A toy model is proposed for four dimensional non-abelian gauge theories coupled to a large number of fermionic degrees of freedom. As the number of flavors is varied the gauge theory may be confining, walking or conformal. The toy model…