Related papers: Stability analysis of kinked DNA in $\mathcal{F}(K…
We study the stability of the one electron atom Schr\"odinger model with self-generated magnetic field in two dimensions. The magnetic energy is taken of the general form $K\int_{\mathbb{R}^2} |B|^p$ and we study the stability of the model…
The extended Hubbard Hamiltonian is a widely accepted model for uncovering the effects of strong correlations on the phase diagram of low-dimensional systems, and a variety of theoretical techniques have been applied to it. In this paper…
The robust statistical description of dynamical systems under perturbations is a central problem in ergodic theory. In this paper, we investigate the statistical properties of skew-product maps driven by a subshift of finite type with…
The spontaneous nucleation and dynamics of topological kink defects have been studied in trapped arrays of 41-43 Yb ions. The number of kinks formed as a function of quench rate across the linear-zigzag transition is measured in the…
The wide deployment of renewable generation and the gradual decrease in the overall system inertia make modern power grids more vulnerable to transient instabilities and unacceptable frequency fluctuations. Time-domain simulation-based…
Genetic systems with multiple loci can have complex dynamics. For example, mean fitness need not always increase and stable cycling is possible. Here, we study the dynamics of a genetic system inspired by the molecular biology of…
Prestrained elastic networks arise in a number of biological and technological systems ranging from the cytoskeleton of cells to tensegrity structures. To understand the response of such a network as a function of the prestrain, we consider…
From the per unit length free energy for DNA under tension, we have calculated an effective contour length dependent persistence length for short DNA. This effective persistence length results from the enhanced fluctuations in short DNA. It…
We report the counter-intuitive instability of charged elastic rings, and the persistence of sinusoidal deformations in the lowest-energy configurations by the combination of high-precision numerical simulations and analytical perturbation…
The electrostatic contribution to twist rigidity of DNA is studied, and it is shown that the Coulomb self-energy of the double-helical sugar-phosphate backbone contributes considerably to twist rigidity of DNA--the electrostatic twist…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
In the stability analysis of an equilibrium, given by a stationary point of a functional F[n] (free energy functional, e.g.), the second derivative of F[n] plays the essential role. If the system in equilibrium is subject to the…
In order to study a one-dimensional analogue of the spontaneous curvature model for two-component lipid bilayer membranes we consider planar curves that are made of a material with two phases. Each phase induces a preferred curvature to the…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
It was first suggested by Englander et al to model the nonlinear dynamics of DNA relevant to the transcription process in terms of a chain of coupled pendulums. In a related paper [q-bio.BM/0604014] we argued for the advantages of an…
We numerically solve the equations of motion (EOM) for two models of circular cosmic string loops with windings in a simply connected internal space. Since the windings cannot be topologically stabilized, stability must be achieved (if at…
We add to a kink, which is a 1 dimensional structure, two transversal directions. We then check its asymptotic stability with respect to compactly supported perturbations in 3D and a time evolution under a Nonlinear Wave Equation (NLW). The…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the…