相关论文: DNA loop statistics and torsional modulus

DNA looping is important in DNA condensation and regulation. One method for forming a DNA loop, thought to be used by the condensing agent protamine, is bind-and-bend. In bind-and-bend, molecules bind all along the DNA, each creating a bend…

Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of…

The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…

We calculate the equation of state of DNA under tension for the case that the DNA features loops. Such loops occur transiently during DNA condensation in the presence of multivalent ions or sliding cationic protein linkers. The…

The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…

The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…

Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…

The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…

It is well-established that many physical properties of DNA at sufficiently long length scales can be understood by means of simple polymer models. One of the most widely used elasticity models for DNA is the twistable worm-like chain…

The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…

The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…

Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA -- subject to the earlier found unusual, frustrated…

In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…

We show how rate-distortion theory provides a mechanism for automated theory building by naturally distinguishing between regularity and randomness. We start from the simple principle that model variables should, as much as possible, render…

The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of the unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that…

We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…

The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the…

Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…

A model for the motion of ring-shaped DNA in a gel is introduced and studied by numerical simulations and a mean-field approximation. The ring motion is mediated by finger-shaped loops (hernias) that move in an amoeba-like fashion around…

Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long…