相关论文: Force induced stretched state: Effects of temperat…
When double stranded DNA is turned in experiments it undergoes a transition. We use an interacting self-avoiding walk on a three-dimensional fcc lattice weighted by writhe to relate to these experiments and treat this problem via…
Thermal conduction force plays a crucial role in manipulating the local thermal conductivity of crystals. However, due to the diffusive nature of thermal conduction, investigating the force effect is challenging. Recently, researchers have…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
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…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
We investigate the effects excluded volume on the stretching of a single DNA in solution. We find that for small force F, the extension h is not linear in F but proportion to F^{\chi}, with \chi=(1-\nu)/\nu, where \nu is the well-known…
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…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
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…
We consider the phase transition induced by compressing a self-avoiding walk in a slab where the walk is attached to both walls of the slab in two and three dimensions, and the resulting phase once the polymer is compressed. The process of…
Considering screeening of electron scattering interactions in terms of the finite-temperature STLS theory and solving the linearized Boltzmann equation (with no appeal to a relaxation time approximation), we present a theoretical analysis…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent…
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…
We present a phenomenological dynamical model able to describe the stretching features of the curve of DNA length vs applied force. As concerns the chain, the model is based on the discrete wormlike chain model with elastic modifications,…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
The hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based mechanobiology assays. While strong tension accelerates DNA melting and decelerates DNA annealing,…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Many seemingly different macroscopic systems (magnets, ferroelectrics, CDW, vortices,..) can be described as generic disordered elastic systems. Understanding their static and dynamics thus poses challenging problems both from the point of…
From the per unit length free energy for DNA under tension, we have calculated an effective contour length dependent persistence length for short DNA. This effective persistence length results from the enhanced fluctuations in short DNA. It…