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The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulation. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which…
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…
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…
Metastable `false' vacuum states are an important feature of the Standard Model of particle physics and many theories beyond it. Describing the dynamics of a phase transition out of a false vacuum via the nucleation of bubbles is essential…
We study the influence of a THz field on thermal properties of DNA molecules. A Peyrard- Bishop-Dauxois model with the inclusion of a solvent interaction term is considered. The THz field is included as a sinusoidal driven force in the…
We investigate kinetic pathways of the DNA melting transition using variable-range versions of the Poland-Scheraga (PS) and Peyrard-Dauxois-Bishop (PDB) models of DNA. In the PS model, we construct a phi^4-field theory to calculate the…
Starting from the QCD Lagrangian and the surface tension of QCD bubbles we derive the critical size of bubbles, the nucleation probability and the nucleation site separation distance. We find the separation of sites is more than an order of…
We investigate DNA breathing dynamics by suggesting and examining several different Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base…
Eukaryotic transcription generally occurs in bursts of activity lasting minutes to hours; however, state-of-the-art measurements have revealed that many of the molecular processes that underlie bursting, such as transcription factor binding…
We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our…
We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local…
We report on the nucleation of bubbles on solids that are gently rubbed against each other in a liquid. The phenomenon is found to depend strongly on the material and roughness of the solid surfaces. For a given surface, temperature, and…
Micro-bubbles and bubbly flows are widely observed and applied in chemical engineering, medicine, involves deformation, rupture, and collision of bubbles, phase mixture, etc. We study bubble dynamics by setting up two numerical simulation…
The formation of bubble defects of the double stranded DNA is treated according to the Lifshits theory of disordered chains. A molecule of the DNA is modelled on a harmonic lattice with nearest neighbour interaction, elastic constants being…
A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores…
Thermal oscillations of base pairs in the Peyrard-Bishop-Holstein model are simulated by stochastic fluctuations of base overlap integrals. Numerical investigation of the model is carried out for a hole transfer in $G_1A_2G_3G_4$ sequence…
Single-particle tracking allows to infer the motion of single molecules in living cells. When we observe a long trajectory (more than 100 points), it is possible that the particle switches mode of motion over time. Then, fitting a single…
This study seeks to understand the origins of intermittency in quantities of interest in pool boiling, such as bubble departure diameter and departure time. The intermittency of nucleation site activity due to nonuniform and unsteady…
This review focuses on Direct numerical simulations (DNS) of turbulent flows laden with droplets or bubbles. DNS of these flows are more challenging than those of flows laden with solid particles due to the surface deformation in the…