Related papers: The evaluation of directionally writhing polymers
A coarse grained model for flexible polymers end-grafted to repulsive spherical nanoparticles is studied for various chain lengths and grafting densities under good solvent conditions, by Molecular Dynamics methods and density functional…
Twisted cylindrical tubes are important model systems for nanostructures, heterostructures, and curved quantum devices. In this work, we investigate the quantum behavior of an electron confined to a twisted cylindrical surface. By first…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
Simple theoretical concepts and models have been helpful to understand the folding rates and routes of single-domain proteins. As reviewed in this article, a physical principle that appears to underly these models is loop closure.
We define winding numbers of regular closed curves on surfaces with a nice euclidean or hyperbolic geometry. We prove that two regular closed curves are regularly homotopic if and only if they are freely homotopic and have the same winding…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
The conventional topological description given by the fundamental group of nematic order parameter does not adequately explain the entangled defect line structures that have been observed in nematic colloids. We introduce a new topological…
In this paper we show that certain trigonometric polynomial shearlets which are special cases of directional de la Vall\'{e}e Poussin type wavelets are able to detect singularities along boundary curves of periodic characteristic functions.…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
We obtain a formula for the density of the winding number of planar Brownian motion around the origin, and deduce from it asymptotic expansions in inverse powers of the logarithm of the squared time, explicit in the angular variable. In…
Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here we investigate…
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…
The cage model for polymer reptation, proposed by Evans and Edwards, and its recent extension to model DNA electrophoresis, are studied by numerically exact computation of the drift velocities for polymers with a length L of up to 15…
A directed polymer is allowed to branch, with configurations determined by global energy optimization and disorder. A finite size scaling analysis in 2D shows that, if disorder makes branching more and more favorable, a critical transition…
We consider the continuum directed random polymer (CDRP) model that arises as a scaling limit from $1+1$ dimensional directed polymers in the intermediate disorder regime. We show that for a point-to-point polymer of length $t$ and any…
We derive reduced finite dimensional ODE models starting from one dimensional lubrication equations describing coarsening dynamics of droplets in nanometric polymer film interacting on a hydrophobically coated solid substrate in the…
The existing kinetic theory of gases is based on an analytical approach that becomes intractable for all but the simplest molecules. Here we propose a simple numerical scheme to compute the transport properties of molecular gases in the…
Despite their considerable practical and biological applications, the link between molecular properties, assembly conditions and self-organized structure in confined polymer solutions remains elusive. Here, we explore the lyotropic nematic…
We explore the elastic behavior of a wormlike chain under compression in terms of exact solutions for the associated probability densities. Strikingly, the probability density for the end-to-end distance projected along the applied force…
Elastic scattering of a twisted (Bessel) electron beam by CO$_2$ molecules is studied theoretically at high energies. The molecule's structure is optimized using coupled cluster theory and density functional theory with…