相关论文: Effect of Sequence-Dependent Rigidity on Plectonem…

We study weak localization effects in the ballistic regime as induced by man-made scatterers. Specular reflection of the electrons off these scatterers results into backscattered trajectories which interfere with their time-reversed path…

We look at the magnetic field induced weak localisation peak of graphene samples with different mobilities. At very low temperatures, low mobility samples exhibit a very broad peak as a function of the magnetic field, in contrast to higher…

DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater…

DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…

Hints on the possible localization of fermions on double thick D-branes (Domain Walls) are found by analyzing the moduli space of parameters. Deeper analysis toward this direction might help to select phenomenologically plausible models. A…

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…

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…

Spontaneous strain localization occurs during mechanical tests of a model amorphous solid simulated using molecular dynamics. The degree of localization depends upon the extent of structural relaxation prior to mechanical testing. In the…

Side chain flexibility is an important factor in ligand binding. In order to determine the extent to which side chain flexibility is involved in ligand binding, a knowledge-based approach was taken. A database composed of examples of…

We investigate the phase ordering (pattern formation) of systems of two-dimensional core-shell particles using Monte-Carlo (MC) computer simulations and classical density functional theory (DFT). The particles interact via a pair potential…

We have studied the conformational properties of a flexible end-grafted chain (length $N$) with a rigid side chain (length $S$) by means of Monte Carlo simulations. Depending on the lengths $N$ and $S$ and the branching site, $b$, we…

Cells move differently on substrates with different elasticities. In particular, the persistence time of their motion is higher on stiffer substrates. We show that this behavior will result in a net transport of cells directed up a…

Local chain structure and local environment play an important role in the dynamics of polymer chains in miscible blends. In general, the friction coefficients that describe the segmental dynamics of the two components in a blend differ from…

Certain bacteria form filamentous colonies when the cells fail to separate after dividing. In Bacillus subtilis, Bacillus thermus, and cyanobacteria, the filaments can wrap into complex supercoiled structures as the cells grow. The…

Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we…

We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of…

Presented here, is a technical manuscript that may form the basis of later published work. In it, we develop a statistical mechanical model to describe a closed loop plectoneme, applicable for when the closed loop is sufficiently…

We report on progress towards constructing string models incorporating both realistic D-brane matter content and moduli stabilisation with dynamical low-scale supersymmetry breaking. The general framework is that of local D-brane models…

In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are…

The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…