相关论文: Self-avoiding worm-like chain model for dsDNA loop…

A likelihood analysis of the observables in deeply virtual exclusive meson production off a proton target is presented. We consider the unpolarized process for which the largest amount of data with all the kinematic dependences are…

We use the worm-like chain model to study supercoiling of DNA under tension and torque. The model reproduces experimental data for a much broader range of forces, salt concentrations and contour lengths than previous approaches. Our theory…

We present a new unbiased algorithm that estimates the expected value of f(U) via Monte Carlo simulation, where U is a vector of d independent random variables, and f is a function of d variables. We assume that f does not depend equally on…

The ground state of the bipartite $t$-$J$ model must satisfy a specific sign structure, based on which the single-hole and two-hole ground state $Ans\ddot{a}tze$ on honeycomb lattice are constructed and studied by a variational Monte Carlo…

Using the pruned-enriched Rosenbluth Monte Carlo algorithm, the scattering functions of semiflexible macromolecules in dilute solution under good solvent conditions are estimated both in $d=2$ and $d=3$ dimensions, considering also the…

An off-lattice Monte Carlo algorithm for solutions of equilibrium polymers (EP) is proposed. At low and moderate densities this is shown to reproduce faithfully the (static) properties found recently for flexible linear EP using a lattice…

Dynamic Programming (DP) suffers from the well-known ``curse of dimensionality'', further exacerbated by the need to compute expectations over process noise in stochastic models. This paper presents a Monte Carlo-based sampling approach for…

We study escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore (DNP) geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical…

We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves…

A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…

Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m…

The purpose of this paper is to introduce a new Markov chain Monte Carlo method and exhibit its efficiency by simulation and high-dimensional asymptotic theory. Key fact is that our algorithm has a reversible proposal transition kernel,…

Two-dimensional semiflexible polymer rings are studied both by imaging circular DNA adsorbed on a mica surface and by Monte Carlo simulations of phantom polymers as well as of polymers with finite thickness. Comparison of size and shape of…

Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using…

Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges…

In the present Comment we show that, contrary to the recent findings of Reisner et al. [Phys. Rev. Lett. 99, 058302 (2007)], the excluded volume effect does not play an important role in determining DNA behavior in nanochannels at low ionic…

Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…

As an important physical quantity to understand the internal structure of polymer chains, the structure factor is being studied both in theory and experiment. Theoretically, the structure factor of Gaussian chains have been solved…

Numerical simulations are performed for isolated cyclic chains with excluded volume. Data are reported for the form factor, S(x), where x is the reduced scattering variable, and also for averages and distributions of the distance between…

Quasiparticle collapsing is a central issue in the study of strongly correlated electron systems. In the one-dimensional case, the quasiparticle collapsing in a form of spin-charge separation has been well established, but the problem…