Related papers: Force induced stretched state: Effects of temperat…
The temperature in the transient climate response is lower than the equilibrium temperature for the same amount of forcing. The degree of disequilibrium is not constant in time and depends on various climate parameters. We derive intuition…
A discrete nonlinear Schrodinger (NLS) model with long-range dispersive interactions describing the dynamical structure of DNA is proposed. Dispersive interactions of two types: the power dependence $r^{-s}$ and the exponential dependence…
We investigate the role of bubble positioning in the force-induced melting of double-stranded DNA using two distinct approaches: Brownian Dynamics simulations and the Gaussian Network Model. We isolate the effect of bubble positioning by…
Most bacteriophages are known to inject their double-stranded DNA into bacteria upon receptor binding in an essentially spontaneous way. This downhill thermodynamic process from the intact virion toward the empty viral capsid plus released…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
We study theoretically the unzipping of a double stranded DNA from a condensed globule state by an external force. At constant force, we find that the double stranded DNA unzips an at critical force Fc and the number of unzipped monomers M…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…
The freely jointed chain is often applied to model the thermodynamics of single polymer chains, but the traditional formulation of the model lacks internal energy changes due to bond stretching. For this reason, the extensible freely…
The magnetic properties of Cu97Co3 and Cu90Co10 granular alloys were measured over a wide temperature range (2 to 300K). The measurements show an unusual temperature dependence of the coercive field. A generalized model is proposed and…
First-order phase transition in a highly correlated electron system can manifest as a dynamic phenomenon. The presence of multiple domains of the coexisting phases average out the dynamical effects making it nearly impossible to predict the…
Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and…
Active polymers possess numerous unique properties that are quite different from those observed in the system of small active molecule due to the intricate interplay between their activity and topological constraints. This study focuses on…
We study the effect of random forces on a double stranded DNA in unzipping the two strands, analogous to the problem of an adsorbed polymer under a random force. The ground state develops bubbles of various lengths as the random force…
We consider force-induced unzipping transition for a heterogeneous DNA model with a long-range correlated base-sequence. It is shown that as compared to the uncorrelated situation, long-range correlations smear the unzipping…
The thermal fluctuations that exist at very low temperature in disordered systems are often attributed to the existence of some two-level excitations. In this paper, we revisit this question via the explicit studies of the following 1D…
We study the effect of crowders on the melting profile of homogeneous and heterogeneous DNA molecules. We find out the melting profile of short DNA molecules and compare our findings with the experiments. We consider some random…
Phase-separated magnetic fluids provide a very strong magnetic response ($\mu>25$) in a liquid state material. Even small fields can cause a notable material response, but this depends on its properties, which are often difficult to…
We investigate thermalization in a tight-binding chain with an on-site defect subject to local dephasing noise implemented as random phase kicks. For a single linear defect of strength $\epsilon$, we obtain an exact analytical description…
We study the thermophoretic motion of a micron sized single colloidal particle in front of a flat wall by evanescent light scattering. To quantify thermophoretic effects we analyse the nonequilibrium steady state (NESS) of the particle in a…