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

Direct sampling from a Slater determinant is combined with an autoregressive deep neural network as a Jastrow factor into a fully autoregressive Slater-Jastrow ansatz for variational quantum Monte Carlo, which allows for uncorrelated…

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.…

A number of recent experiments have provided detailed observations of the configurations of long DNA strands under nano-to-micrometer sized confinement. We therefore revisit the problem of an excluded volume polymer chain confined between…

We implement a scale-free version of the pivot algorithm and use it to sample pairs of three-dimensional self-avoiding walks, for the purpose of efficiently calculating an observable that corresponds to the probability that pairs of…

The efficiency of Monte Carlo samplers is dictated not only by energetic effects, such as large barriers, but also by entropic effects that are due to the sheer volume that is sampled. The latter effects appear in the form of an entropic…

We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the…

We study the distribution of lengths and other statistical properties of worms constructed by Monte Carlo worm algorithms in the power-law three-sublattice ordered phase of frustrated triangular and kagome lattice Ising antiferromagnets.…

We calculate the entropic part of partition function of a bubble embedded in a double stranded DNA (dsDNA) by considering the total weights of possible configurations of a system of two single stranded DNA (ssDNA) of given length which…

To examine the relationship between sidechain geometry and sidechain packing, we use an all-atom Monte Carlo simulation to sample the large space of sidechain conformations. We study three models of excluded volume and use umbrella sampling…

We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…

Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for…

The work addresses the analogy between trivial knotting and excluded volume in looped polymer chains of moderate length, $N<N_0$, where the effects of knotting are small. A simple expression for the swelling seen in trivially knotted loops…

We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…

The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As…

We study the large-scale dynamics of event chain Monte Carlo algorithms in one dimension, and their relation to the true self-avoiding walk. In particular, we study the influence of stress, and different forms of interaction on the…

Effects of randomness on the spin-1/2 and 1 antiferromagnetic Heisenberg chains are studied using the quantum Monte Carlo method with the continuous-time loop algorithm. We precisely calculated the uniform susceptibility, string order…

Unusually high bending flexibility has been recently reported for DNA on short length scales. We use atomic force microscopy (AFM) in solution to obtain a direct estimate of DNA bending statistics for scales down to one helical turn. It…

We study the dynamics of one-dimensional (1D) interacting particles simulated with the event-chain Monte Carlo algorithm (ECMC). We argue that previous versions of the algorithm suffer from a mismatch in the factor potential between…

Some recent work pointed out the usefulness of taking a large-deviation perspective when trying to extract anything resembling a macroscopic order parameter from a computer simulation. In this paper we note that the end-to-end distance of…

We present a Markov-chain Monte Carlo algorithm of "worm"type that correctly simulates the O(n) loop model on any (finite and connected) bipartite cubic graph, for any real n>0, and any edge weight, including the fully-packed limit of…