Related papers: Manipulating a single adsorbed DNA for a critical …
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
We consider a model for a polymer interacting with an attractive wall through a random sequence of charges. We focus on the so-called diluted limit, when the charges are very rare but have strong intensity. In this regime, we determine the…
We consider the properties of a self-avoiding polymer chain, adsorbed on a solid attractive substrate which is attached with one end to a pulling force. The conformational properties of such chain and its phase behavior are treated within a…
The adsorption of a single multi-block $AB$-copolymer on a solid planar substrate is investigated by means of computer simulations and scaling analysis. It is shown that the problem can be mapped onto an effective homopolymer adsorption…
The process of adsorption on a planar repulsive, "marginal" and attractive wall of long-flexible polymer chains with excluded volume interactions is investigated. The performed scaling analysis is based on formal analogy between the polymer…
The onset of an "eye-phase" and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
Fluctuations can drive continuous phase transitions between two distinct ordered phases -- so-called deconfined quantum critical points (DQCPs) -- which lie beyond the Landau-Ginzburg-Wilson paradigm. Despite several theoretical predictions…
We start with a discussion of a phase diagram and three special collision energies: (i) the first touching of the mixed phase; (ii) the softest point; (iii) the critical point. We then proceed to more details about the role a massless…
We consider two complementary polymer strands of length $L$ attached by a common end monomer. The two strands bind through complementary monomers and at low temperatures form a double stranded conformation (zipping), while at high…
The critical behavior of many physical systems involves two competing $n^{}_1-$ and $n^{}_2-$component order-parameters, ${\bf S}^{}_1$ and ${\bf S}^{}_2$, respectively, with $n=n^{}_1+n^{}_2$. Varying an external control parameter $g$,…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
We have studied the separation of a double stranded DNA (dsDNA), which is driven either by the temperature or force. By monitoring the probability of opening of entire base pairs along the chain, we show that the opening of a dsDNA depends…
Continuous phase transitions are studied in a two dimensional nonequilibrium model with an infinite number of absorbing configurations. Spreading from a localized source is characterized by nonuniversal critical exponents, which vary…
A class of nucleosome remodeling motors translocate nucleosomes, to which they are attached, toward the middle of DNA chain in the presence of ATP during in vitro experiments. Such a biological activity is likely based on a physical…
The deconfined quantum critical point (DQCP) was originally proposed as a continuous transition between two spontaneous symmetry breaking phases in 2D spin-1/2 systems. While great efforts have been spent on the DQCP for 2D systems, both…
We show the existence of a force induced triple point in an interacting polymer problem that allows two zero-force thermal phase transitions. The phase diagrams for three different models of mutually attracting but self avoiding polymers…
Advanced chain-growth computer simulation methodologies have been employed for a systematic statistical analysis of the critical behavior of a polymer adsorbing at a substrate. We use finitesize scaling techniques to investigate the…