Related papers: Localization of Denaturation Bubbles in Random DNA…
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…
We study the dynamics of solutions of infinitely thin needles up to densities deep in the semidilute regime by Brownian dynamics simulations. For high densities, these solutions become strongly entangled and the motion of a needle is…
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles respectively, when the strands of the DNA are subjected to a force along the same…
By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately $100$ base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an…
A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular…
Cavitation is a ubiquitous phenomenon in nature and bubble dynamics in open spaces have been widely studied, but the effects of the wall on the dynamics of cavitation bubbles in confined spaces are still unclear. Here, the dynamics of…
Large-deviations theory deals with tails of probability distributions and the rare events of random processes, for example spreading packets of particles. Mathematically, it concerns the exponential fall-of of the density of thin-tailed…
Motivated by the constrained many-body dynamics, the stability of the localization-delocalization properties to the inclusion of the soft constraints is addressed in random matrix models. These constraints are modeled by correlations in…
We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
Detecting many-body localization (MBL) typically requires the calculation of high-energy eigenstates using numerical approaches. This study investigates methods that assume the use of a quantum device to detect disorder-induced…
We consider Bose-Einstein condensed atoms confined in a toroidal trap. We demonstrate that under conditions of one-dimensional behavior, the density distribution of the atoms may be exponentially localized/delocalized, even for very small…
We investigate the coalescence of two DNA-bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
Bubbles in complex fluids are often desirable, and sometimes simply inevitable, in the processing of formulated products. Bubbles can rise by buoyancy, grow or dissolve by mass transfer, and readily respond to changes in pressure, thereby…
Light propagation through turbulence produces speckles, whose ensemble behavior is typically characterized by snapshot intensity statistics. Here, we track the spatiotemporal evolution of individual speckles and quantify fragmentation,…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…