Related papers: Healing Length and Bubble Formation in DNA
From the theory of topological defect formation proposed for the early universe, the so called Kibble mechanism, it follows that the density correlation functions of defects and anti-defects in a given system should be completely determined…
We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well…
We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed…
The glass-forming ability is an important material property for manufacturing glasses and understanding the long-standing glass transition problem. Because of the nonequilibrium nature, it is difficult to develop the theory for it. Here we…
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…
Short DNA linkers are increasingly being exploited for driving specific self-assembly of Brownian objects. DNA-functionalised colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach…
Dynamical quantities such as the diffusion coefficient and relaxation times for some glass-formers may depend on density and temperature through a specific combination, rather than independently, allowing the representation of data over…
Bubble-nucleation processes of a Lennard-Jones liquid are studied by molecular dynamics simulations. Waiting time, which is the lifetime of a superheated liquid, is determined for several system sizes, and the apparent finite-size effect of…
In this paper we study the formation of microbubbles upon the irradiation of an array of plasmonic Au nanoparticles with a laser in n-alkanes ($C_{n}H_{2n+2}$, with n = 5-10). Two different phases in the evolution of the bubbles can be…
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA…
The phase transition of $(PolyA/PolyT)_{100}$ duplex into the denaturated state is studied in the Peyrard-Bishop-Dauxois model by the method of direct molecular-dynamical modeling. The temperature dependencies of the total energy and heat…
We numerically investigate turbulent Rayleigh-B\'enard convection with gas bubbles attached to the hot plate, mimicking a core feature in electrolysis, catalysis, or boiling. The existence of bubbles on the plate reduces the global heat…
We analyse those objects in the Brightest 55 sample of clusters of galaxies which have a short central cooling time and a central temperature drop. Such clusters are likely to require some form of heating. Where clear radio bubbles are…
One possible way in which phase transitions in the early universe may have ocurred is via nucleation of bubbles of the new phase (true vacuum) in the old phase (false vacuum). The technique most widely used to compute the probability of…
The melting curves of short heterogeneous DNA chains in solution are calculated on the basis of statistical thermodynamics and compared to experiments. The computation of the partition function is based on the Peyrard-Bishop hamiltonian,…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
Here we derive and experimentally test a free energy functional that captures the adhesion of DNA-coated emulsion droplets. Generalizing previous approaches, the theory combines important energetic and entropic effects of microscopic DNA…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
In this paper we investigate bubble nucleation in a disordered Landau-Ginzburg model. First we adopt the standard procedure to average over the disordered free energy. This quantity is represented as a series of the replica partition…
We propose a new strategy to improve the self-assembly properties of DNA-functionalised colloids. The problem that we address is that DNA-functionalised colloids typically crystallize in a narrow temperature window, if at all. The…