Related papers: DNA confined in a two-dimensional strip geometry
We consider closed subschemes in the affine grassmannian obtained by degenerating $e$-fold products of flag varieties, embedded via a tuple of dominant cocharacters. For $G= \operatorname{GL}_2$, and cocharacters small relative to the…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
Using the delta correction to the standard free energy \cite{bc} in the elastic setting with a quadratic foundation term and some parameters, we introduce a one dimension only model for strong segregation in diblock copolymers, whose sharp…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
We numerically study the wetting (adsorption) transition of a polymer chain on a disordered substrate in 1+1 dimension.Following the Poland-Scheraga model of DNA denaturation, we use a Fixman-Freire scheme for the entropy of loops. This…
In a recent paper, Chan, \L aba, and Pramanik investigated geometric configurations inside thin subsets of the Euclidean set possessing measures with Fourier decay properties. In this paper we ask which configurations can be found inside…
We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $\beta-$sheets in protein, by…
The de Gennes extrapolation length is a direction dependent measure of the spatial evolution of the pairing gap near the boundary of a superconductor, and thus provides a viable means to probe its symmetry. It is expected to be infinite and…
We consider the $N$-components 3-dimensional massive Gross-Neveu model compactified in one spatial direction, the system being constrained to a slab of thickness $L$. We derive a closed formula for the effective renormalized $L$-dependent…
We study the scaling properties of polymers in a d-dimensional medium with quenched defects that have power law correlations ~r^{-a} for large separations r. This type of disorder is known to be relevant for magnetic phase transitions. We…
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible…
We performed molecular dynamics simulations to study equilibrium and flow properties of a liquid in a nano-channel with confining surfaces coated with a layer of grafted semiflexible polymers. The coverage spans a wide range of grafting…
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…
The statistical mechanics of nearly parallel vortex filaments confined in the unbounded plane by angular momentum, first studied by Lions and Majda (2000), is investigated using a mean-field approximation to interaction and a spherical…
Using nanoparticles to impart extrinsic rippling in graphene is a relatively new method to induce strain and to tailor the properties of graphene. Here we study the structure and elastic properties of graphene grown by chemical vapour…
When compressed in a slit of width $D$, a $\Theta$-chain that displays the scaling of size $R_0$ (diameter) with respect to the number of monomers $N$, $R_0\sim aN^{1/2}$, expands in the lateral direction as $R_{\parallel}\sim a…
Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living…
We study the effects of intrinsic sequence-dependent curvature for a two dimensional semiflexible biopolymer with short-range correlation in intrinsic curvatures. We show exactly that when not subjected to any external force, such a system…
The local deformation of two-dimensional Lennard-Jones glasses under imposed shear strain is studied via computer simulations. Both the mean squared displacement and mean squared strain rise linearly with the length of the strain interval…