Related papers: Bubble generation in a twisted and bent DNA-like m…
Low-energy hydrogen irradiation is known to induce bubble formation in tungsten, while its atomistic mechanisms remain little understood. Using first-principles calculations and statistical models, we studied the self-clustering behavior of…
The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the…
We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the…
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…
We carry out high resolution two-dimensional radiation-hydrodynamic numerical simulations to study the formation and evolution of hot bubbles inside planetary nebulae (PNe). We take into account the evolution of the stellar parameters, wind…
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…
The liquid-liquid phase separation of biomolecules is an important process for intracellular organization. Biomolecular sequence combinatorics leads to a large variety of proteins and nucleic acids which can interact to form a diversity of…
The assembly of banana-shaped rodlike proteins on membranes, and the associated membrane shape transformations, are investigated by analytical theory and coarse-grained simulations. The membrane-mediated interactions between two…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
The expansion and collision of two wind-blown superbubbles is investigated numerically. Our models go beyond previous simulations of molecular cloud formation from converging gas flows by exploring this process with realistic flow…
The spherical dynamics of a bubble in a compressible liquid has been studied extensively since the early work of Gilmore. Numerical codes to study the behavior, including when large non-spherical deformations are involved, have since been…
We analyze the properties of naturally formed nano-bubbles in Lennard-Jones molecular dynamics simulations of liquid-to-vapor nucleation in the boiling and the cavitation regimes. The large computational volumes provide a realistic…
The damping effect to the DNA bubble is investigated within the Peyrard-Bishop model. In the continuum limit, the dynamics of the bubble of DNA is described by the damped nonlinear Schrodinger equation and studied by means of variational…
Motivated by recent experiments on biomimetic membranes exposed to several aqueous phases, we theoretically study the morphology of a membrane in contact with a liquid droplet formed via aqueous phase separation. We concentrate on membranes…
Backward terahertz radiation can be produced by a high-intensity laser normally incident upon an underdense plasma. It is found that terahertz radiation is generated by electrons refluxing along the bubble shell. These shell electrons have…
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…
Cold atomic gases offer the prospect of simulating the physics of the very early universe in the laboratory. In the condensate phase, the gas is described by a field theory with key features of high energy particle theory. This paper…
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can…
In this study, we present an experimental work on bubble nucleation and growth using a model system comprised of viscoelastic polyvinyl butyral confined in a Hele-Shaw cell geometry that is decompressed at elevated temperatures. The…
Membrane tubulation is a ubiquitous process that occurs both at the plasma membrane and on the membranes of intracellular organelles. These tubulation events are known to be mediated by forces applied on the membrane either due to motor…