Related papers: Self-avoiding worm-like chain model for dsDNA loop…
A scaling analysis is presented of the statistics of long DNA confined in nanochannels and nanoslits. It is argued that there are several regimes in between the de Gennes and Odijk limits introduced long ago. The DNA chain folds back on…
Nonreversible Markov chains can outperform reversible chains in the Markov chain Monte Carlo method. Lifting is a versatile approach to introducing net stochastic flow in state space and constructing a nonreversible Markov chain. We present…
We study the statistics of branching polymers with excluded-volume interactions, by modeling them as single self-avoiding trees on a generic regular periodic lattice with coordination number $q$. Each lattice site can be occupied at most by…
For the $t$-$J$ model, variational wave functions can generally be constructed based on an accurate description of antiferromagnetism (AFM) at half-filling and an exact phase-string sign structure under doping. The single-hole-doped and…
We show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance…
A lattice model of the directed self-avoiding walk is used to estimate the possibility on the formation of an infinitely long linear semi-flexible copolymer chain. The copolymer chain is assumed to composed of four different types of the…
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…
We consider an one-dimensional conservation law with random space-time forcing and calculate using large deviations the exponentially small probabilities of anomalous shock profile displacements. Under suitable hypotheses on the spatial…
Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…
Single molecule magnets (SMMs) with single-ion anisotropies $\mathbf d$, comparable to exchange interactions J, between spins have recently been synthesized. In this paper, we provide theoretical insights into the magnetism of such systems.…
Based on three general guiding principles, i.e., no double occupancy constraint, accurate description of antiferromagnetism at half-filling, and the precise sign structure of the $t$-$J$ model, a new ground state wave function has been…
Force extension curves (FECs), which quantify the response of a variety of biomolecules subject to mechanical force ($f$), are often quantitatively fit using worm-like chain (WLC) or freely-jointed chain (FJC) models. These models predict…
Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computational models cannot reconcile recent in vitro observations…
We introduce an efficient, scalable Monte Carlo algorithm to simulate cross-linked architectures of freely-jointed and discrete worm-like chains. Bond movement is based on the discrete tractrix construction, which effects conformational…
For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…
The angular distribution of the phase space arising in two-particle emission reactions induced by electrons and neutrinos is computed in the laboratory (Lab) system by boosting the isotropic distribution in the center of mass (CM) system…
We have investigated two-electron bound state formation in a square two-dimensional t-J-U model with hopping anisotropies for zero electron density; these anisotropies are introduced to mimic the hopping energies similar to those expected…
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation…
We analyze the probability of a single loop formation in a long flexible polymer chain in disordered environment in $d$ dimensions. The structural defects are considered to be correlated on large distances $r$ according to a power law $\sim…