Related papers: DNA toroid condensation as analytic solutions
Nonlinear molecular excitations in DNA have traditionally been modelled using the nonlinear Schr\"odinger equation (NLSE). An alternative approach is based on the plane-base rotator model and the SU(2)/U(1) generalized spin coherent states,…
We develop a theory of non-relativistic bosons in two spatial dimensions with a weak short range attractive interaction. In the limit as the range of the interaction becomes small, there is an ultra-violet divergence in the problem. We…
Many thermodynamic instabilities in one dimension (e.g. DNA thermal denaturation, wetting of interfaces) can be described in terms of simple models involving harmonic coupling between nearest neighbors and an asymmetric on-site potential…
The Gaudin integral equation for the ground state of a one-dimensional delta-function attractive spin-1/2 fermions is solved in the form of power series. The first few terms of the asymptotic expansions for both strong and weak coupling…
The solution of the Dirac equation for an attractive linear potential is considered. The Lorentz nature of the potential (vector or scalar) affects the existence of bound states. For simplicity, and since it is sufficient for the goals of…
Simulations and Mode-Coupling Theory calculations, for a large range of the arm number $f$ and packing fraction $\eta$ have shown that the structural arrest and the dynamics of star polymers in a good solvent are extremely rich: the systems…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
In this paper, we show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation…
In this paper the semi-classical approach to the solution of non-linear evolution equation is developed. We found the solution in the entire kinematic region to the non-linear evolution equation that governs the dynamics in the high parton…
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As…
An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent…
We investigate the evolution of non-linear density perturbations by taking into account the effects of deviations from spherical symmetry of a system. Starting from the standard spherical top hat model in which these effects are ignored, we…
Finite elasticity problems commonly include material and geometric nonlinearities and are solved using various numerical methods. However, for highly nonlinear problems, achieving convergence is relatively difficult and requires small load…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
We present results relevant to the equilibrium organization of DNA strands of arbitrary length interacting with a spherical organizing center, suggestive of DNA-histone complexation in nucleosomes. We obtain a rich phase diagram in which a…
Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it…
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with…
We assess the utility of an optimization-based data assimilation (D.A.) technique for treating the problem of nonlinear neutrino flavor transformation in core collapse supernovae. D.A. uses measurements obtained from a physical system to…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…