Related papers: Dynamics of DNA Bubble in Viscous Medium
The presence of a thermodynamic phase of a three-stranded DNA, namely, a mixed phase of bubbles of two bound strands and a single one, is established for large dimensions ($d\geq 5$) by using exact real space renormalization group (RG)…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
The nonlinear dynamics of a warped accretion disc is investigated in the important case of a thin Keplerian disc with negligible viscosity and self-gravity. A one-dimensional evolutionary equation is formally derived that describes the…
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…
Unlike Newtonian fluids, viscoelastic fluids may break time-reversal symmetry at low Reynolds numbers resulting in elastic turbulence. Furthermore, under some conditions, instead of the chaotic turbulence, large-scale regular waves form, as…
We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein…
The deformation and break-up of Newtonian/viscoelastic droplets are studied in confined shear flow. Our numerical approach is based on a combination of Lattice-Boltzmann models (LBM) and finite difference schemes, the former used to model…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
Intermolecular forces are modeled by means of a modified Lennard-Jones potential, introducing a distance of minimum approach, and the effect of intermolecular interactions is accounted for with a self consistent field of the Vlasov type. A…
Biological membranes are host to proteins and molecules which may form domain-like structures resulting in spatially-varying material properties. Vesicles with such heterogeneous membranes can exhibit intricate shapes at equilibrium and…
A droplet bouncing on the surface of a vertically vibrating liquid bath can walk horizontally, guided by the waves it generates on each impact. This results in a self-propelled classical particle-wave entity. By using a one-dimensional…
Dynamic buckling is addressed for complete elastic spherical shells subject to a rapidly applied step in external pressure. Insights from the perspective of nonlinear dynamics reveal essential mathematical features of the buckling…
The linear instability of Faraday waves in Hele-Shaw cells is investigated with consideration of the viscosity of fluids after gap-averaging the governing equations due to the damping from two lateral walls and the dynamic behavior of…
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…
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 electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the…
We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are…
Hysteretic damping is often modeled by means of linear viscoelastic approaches such as "nearly constant Attenuation (NCQ)" models. These models do not take into account nonlinear effects either on the stiffness or on the damping, which are…
The duality between deformations of elastic bodies and non-inertial flows in viscous liquids has been a guiding principle in decades of research. However, this duality is broken when a spheroidal or other doubly-curved liquid film is…
The nonlinear theory of Landau damping of electrostatic wave envelopes (WEs) is revisited in a quantum electron-positron (EP) pair plasma. Starting from a Wigner-Moyal equation coupled to the Poisson equation and applying the multiple scale…