Related papers: DNA confined in a two-dimensional strip geometry
Two-dimensional materials with hexagonal symmetry such as graphene and transition metal dichalcogenides} are unique materials to study light-field-controlled electron dynamics inside of a solid. Around the $K$-point, the dispersion relation…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
We found solutions of the Bogoliubov-de Gennes equations for the two-dimensional self-consistent model of superconductors with $d_{x^2-y^2}$ symmetry of the order parameter, taking into account spin and charge distributions. Analytical…
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…
Dislocation patterning and self-organization during plastic deformation are associated with work hardening, but the exact mechanisms remain elusive. This is partly because studies of the structure and local strain during the initial stages…
We present results from molecular dynamics simulations of strictly two-dimensional (2D) polymer melts and thin polymer films in a slit geometry of thickness of the order of the radius of gyration. We find that the dynamics of the 2D melt is…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice ($d=3$ dimensions) and square lattice ($d=2$ dimensions), varying chain stiffness by an energy…
We have studied the conformational and scaling behaviors of a flexible dendrimer immersed in athermal or good solvents. A self-consistent field theory combined with a pre-averaged excluded volume potential representing the two-body…
The conformational states of a semiflexible polymer enclosed in a compact domain of typical size $a$ are studied as stochastic realizations of paths defined by the Frenet equations under the assumption that stochastic "curvature" satisfies…
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
The longitudinal response of single semiflexible polymers to sudden changes in externally applied forces is known to be controlled by the propagation and relaxation of backbone tension. Under many experimental circumstances, realized, e.g.,…
We study the dynamical properties of semiflexible polymers with a recently introduced bead-spring model. We focus on double-stranded DNA. The two parameters of the model, $T^*$ and $\nu$, are chosen to match its experimental force-extension…
Motivated by a freely suspended graphene and polymerized membranes in soft and biological matter we present a detailed study of a tensionless elastic sheet in the presence of thermal fluctuations and quenched disorder. The manuscript is…
An end-grafted flexible polymer chain in 3d space between two pistons undergoes an abrupt transition from a confined coil to a flower-like conformation when the number of monomers in the chain, N, reaches a critical value. In 2d geometry,…
We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise…
We study translocation dynamics of a driven compressible semi-flexible chain consisting of alternate blocks of stiff ($S$) and flexible ($F$) segments of size $m$ and $n$ respectively for different chain length $N$ in two dimension (2D).…
We study the effect of intersegment interactions on the effective bending and stretching moduli of a semiflexible polymer chain with a finite stretching modulus. For an interaction potential of a screened Debye-H\" uckel type…
We show striped pattern formation in the large volume limit for a class of generalized antiferromagnetic local/nonlocal interaction functionals in general dimension previously considered Goldman-Runa and Daneri-Runa and in…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…