相关论文: Effect of interaction shape on the condensed DNA t…
A single semiflexible polymer chain folds into a toroidal object under poor solvent conditions. In this study, we examined the morphological change in such a toroidal state as a function of the width and stiffness of the chain together with…
It now becomes apparent that condensed DNA toroid which emerges in a poor solvent condition can be realised in the framework of the non-linear sigma model on a line segment. In fact, the classical solutions of the model, i.e., of the…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
We introduce a novel model for DNA condensation (whip-toroid transition) using the path integral method in the framework of the non-linear sigma model on a line segment. We show that some of its classical configurations exhibit toroidal…
We update a previous study of the effects of vector interactions in the Nambu--Jona-Lasinio model on the formation of inhomogeneous chiral symmetry breaking condensates. In particular, by properly considering a spatially modulated vector…
DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical…
The one dimension interacting Kitaev chain at half filling is studied. The symmetry of the Hamiltonian is examined by dual transformations and various physical quantities as functions of the fermion-fermion interaction $U$ are calculated…
DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global…
We present an approach for computing long-range van der Waals (vdW) interactions between complex molecular systems and arbitrarily shaped macroscopic bodies, melding atomistic treatments of electronic fluctuations based on density…
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…
Over the last decade, the field of programmable self-assembly has seen an explosion in the diversity of crystal lattices that can be synthesized from DNA-coated colloidal nanometer- and micrometer-scale particles. The prevailing wisdom has…
Interplay between structure and function in atomically thin crystalline nanoribbons is sensitive to their conformations yet the ability to prescribe them is a formidable challenge. Here, we report a novel paradigm for controlled nucleation…
Based on our previous paper [cond-mat/0507477], we establish a general model for the whip-toroid transitions of a semiflexible homopolymer chain using the path integral method and the O(3) nonlinear sigma model on a line segment with the…
The finite size behavior of the susceptibility, Binder cumulant and some even moments of the magnetization of a fully finite O(n) cubic system of size L are analyzed and the corresponding scaling functions are derived within a…
In the paper we investigate statistical and topological properties of fractional Brownian polymer chains, equipped with the short-range volume interactions. The attention is paid to statistical properties of collapsed conformations with the…
The stability of the Majorana modes in the presence of a repulsive interaction is studied in the standard semiconductor wire - metallic superconductor configuration. The effects of short-range Coulomb interaction, which is incorporated…
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 introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
Experiments on quasi-one-dimensional systems such as quantum wires and metallic chains on surfaces suggest the existence of electron-electron interactions of substantial range and hence physics beyond the Hubbard model. We therefore…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…