Related papers: Manipulating a single adsorbed DNA for a critical …
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…
We show that when a self-avoiding polymer chain is pulled off a sticky surface by force applied to the end segment, it undergoes a first-order thermodynamic phase transition albeit without phase coexistence. This unusual feature is…
Using Brownian Dynamics, we study the dynamical behavior of a polymer grafted onto an adhesive surface close to the mechanically induced adsorption-stretching transition. Even though the transition is first order, (in the infinite chain…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
Using previous results from boundary conformal field theory and integrability, a phase diagram is derived for the 2 dimensional Ising model at its bulk tri-critical point as a function of boundary magnetic field and boundary spin-coupling…
The distance-resolved effective interaction potential between two parallel DNA molecules is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. Adding counterions first yields an attractive minimum…
Two-step crystallization via a metastable intermediate phase is often regarded as a non-classical process that lies beyond the framework of classical nucleation theory (CNT). In this work, we investigate two-step crystallization in…
We discuss the appropriate techniques for modelling the geometry of open ended elastic polymer molecules. The molecule is assumed to have fixed endpoints on a boundary surface. In particular we discuss the concept of the winding number, a…
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…
Monte Carlo simulations and finite-size scaling theory have been used to study the critical behavior of repulsive dimers on square lattices at 2/3 monolayer coverage. A "zig-zag" (ZZ) ordered phase, characterized by domains of parallel ZZ…
Some proteins can find their targets on DNA faster than by pure diffusion in the three-dimensional cytoplasm, through the process of facilitated diffusion: They can loosely bind to DNA and temporarily slide along it, thus being guided by…
When double stranded DNA is turned in experiments it undergoes a transition. We use an interacting self-avoiding walk on a three-dimensional fcc lattice weighted by writhe to relate to these experiments and treat this problem via…
We study the mechanics of a reversible decohesion (unzipping) of an elastic layer subjected to quasi-static end-point loading. At the micro level the system is simulated by an elastic chain of particles interacting with a rigid foundation…
The analytical approach developed by us for the calculation of the phase diagram for the Anderson localization via disorder [J.Phys.: Condens. Matter 14, 13777 (2002)] is generalized here to the case of a strong magnetic field when $q$…
We analyze the phase diagrams of self-avoiding walk models of uniform branched polymers adsorbed at a surface and subject to an externally applied vertical pulling force which, at critical values, desorbs the polymer. In particular, models…
We consider a self-avoiding walk model of polymer adsorption where the adsorbed polymer can be desorbed by the application of a force. In this paper the force is applied normal to the surface at the last vertex of the walk. We prove that…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…