Related papers: Topological interactions in DNA catenanes
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
We numerically examine the nonlinear rubber elasticity of topologically constrained polymer networks. We propose a simple and effective model based on Graessley and Pearson's topological model (GP model) for describing the topological…
We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius…
Molecular ecology uses molecular genetic data to answer traditional ecological questions in biogeography and biodiversity among others. Several ecological principles, such as the niche hypothesis and the competitive exclusions, are based on…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
The interaction between an electron and an elastic wave is investigated for HgTe and InAs-GaSb quantum wells. The well-known Bernevig-Hughes-Zhang model, i.e., the $4\times 4$ model for a two-dimensional (2D) topological insulator (TI), is…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…
Entangled ring polymers, along with blends of ring and linear polymers, continue to be a topic of great interest and debate due to the conflicting experimental results in the literature as well as the difficulty of producing entangled…
At low temperatures, dynamics in amorphous silicon occurs through a sequence of discrete activated events that locally reorganize the topological network. Using the activation-relaxation technique, a data base containing over 8000 such…
We derive formulae for the electrostatic interaction between two long, rigid macromolecules that may have arbitrary surface charge patterns and cross at an arbitrary interaxial angle. We calculate the dependence of the interaction energy on…
Motivated by recent experiments, we extend the Joanny-deGennes calculation of the elasticity of a contact line to an arbitrary contact angle and an arbitrary plate inclination in presence of gravity. This requires a diagonalization of the…
We investigate experimentally the distribution of configurations of a ring with an elementary topological constraint, a ``figure-8'' twist. Using vibrated granular chains, which permit controlled preparation and direct observation of such a…
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…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype. Here we discuss probabilistic models of…
Resonant electron interaction with whistler-mode chorus waves is recognized as one of the main drivers of radiation belt dynamics. For moderate wave intensity, this interaction is well described by quasi-linear theory. However, recent…
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…
Using the recently-proposed ``activation-relaxation technique'' for optimizing complex structures, we develop a structural model appropriate to a-GaAs which is almost free of odd-membered rings, i.e., wrong bonds, and possesses an almost…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…