Related papers: Bubble generation in a twisted and bent DNA-like m…
Curvature in biological membranes can be generated by a variety of different molecular mechanisms such as protein scaffolding, lipid or protein asymmetry, cytoskeletal forces, etc. These mechanisms have the net effect of generating stresses…
We study the dynamics of axions at first-order phase transitions in non-Abelian gauge theories. When the duration of the phase transition is short compared to the timescale of the axion oscillations, the axion dynamics is similar to the…
We investigate the generation of entanglement through a quantum dot molecule under the influence of vibrational phonon modes in a bias voltage junction. The molecular quantum dot system is realized by coupled quantum dots inside a suspended…
Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one…
Bubble nucleation in water induced by boiling, gas supersaturation or cavitation usually originates from pre-existing gas cavities trapped into solid defects. Even though the destabilization of such gas pockets, called nuclei, has been…
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…
Active particles under soft confinement such as droplets or vesicles present intriguing phenomena, as collective motion emerges alongside the deformation of the environment. A model is employed to systematically investigate droplet…
We calculate the spectrum of torsional vibrations of a double-stranded structure that models the double helix of the DNA. We come to the conclusion that within the framework of the model elementary excitations may display an asymmetry as…
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…
DNA toroidal bundles form upon condensation of one or multiple DNA filaments. DNA filaments in toroidal bundles are hexagonally packed, and collectively twist around the center line of the toroid. In a previous study, we and our coworkers…
Bubbles in the interstellar medium are produced by astrophysical sources, which continuously or explosively deposit large amount of energy into the ambient medium. These expanding bubbles can drive shocks in front of them, which dynamics is…
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 study generic aspects of bubble dynamics in DNA under time dependent perturbations, for example temperature change, by mapping the associated Fokker-Planck equation to a quantum time-dependent Schroedinger equation with imaginary time.…
Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a…
Biological information is not only stored in the digital chemical sequence of double helical DNA, but is also encoded in the mechanical properties of the DNA strands, which can influence biochemical processes involving its readout. For…
We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to…
Turbulent radiation flow is commonplace in systems with strong, incoherent, light-matter interactions. In astrophysical contexts, photon bubble turbulence is considered a key mechanism behind enhanced radiation transport, and its importance…
We carry out numerical simulation of the formation of U(1) global vortices in a first order phase transition in 2+1 dimensions in the presence of small explicit symmetry breaking. Bubbles of broken symmetry phase are randomly nucleated,…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
Self-organization of hydrogen bubbles generated by laser-treated areas of an aluminum plate etched in a basic aqueous solution of ammonia is studied experimentally and theoretically. A dynamics of establishment of stationary pattern of gas…