Related papers: Nonlinear dynamics of damped DNA systems with long…
Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous…
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 Discrete Nonlinear Schr\"odinger (DNLS) equation is a Hamiltonian model displaying an extremely slow relaxation process when discrete breathers appear in the system. In [Iubini S, Chirondojan L, Oppo G L, Politi A and Politi P 2019…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
We use the helicoidal Peyrard-Bishop model of DNA in the current work. We solve a dynamical equation of motion using a continuum approximation, resulting in kink-solitary waves that travel along the chain. We demonstrate that, whereas…
We study the existence and stability of localized states in the discrete nonlinear Schr{\"o}dinger equation (DNLS) on two-dimensional non-square lattices. The model includes both the nearest-neighbor and long-range interactions. For the…
We study the effects of electron-lattice interaction in the presence of discrete breathers. The lattice is treated classically. We consider two different situations - i) the scattering of an electron by a discrete breather in the…
The dynamics of static and travelling breathers in two-species Bose-Einstein condensates in a one-dimensional optical lattice is modelled within the tight-binding approximation. Two coupled discrete nonlinear Schr\"odinger equations…
We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a…
We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single molecule time series. It is demonstrated that the model recovers the equilibrium properties. We…
We present and discuss the derivation of a nonlinear non-local integro-differential equation for the macroscopic time evolution of the conserved order parameter of a binary alloy undergoing phase segregation. Our model is a d-dimensional…
The equilibrium states of the discrete Peyrard-Bishop Hamiltonian with one end fixed are computed exactly from the two-dimensional nonlinear Morse map. These exact nonlinear structures are interpreted as domain walls (DW), interpolating…
The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot…
Inspired by one--dimensional light--particle systems, the dynamics of a non-Hamiltonian system with long--range forces is investigated. While the molecular dynamics does not reach an equilibrium state, it may be approximated in the…
We propose a lattice model, in both one- and multidimensional versions, which may give rise to matching conditions necessary for the generation of solitons through the second-harmonic generation. The model describes an array of linearly…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
We explore breather propagation in the damped oscillatory chain with essentially nonlinear (non-linearizable) nearest-neighbour coupling. Combination of the damping and the substantially nonlinear coupling leads to rather unusual two-stage…
We study the nonlinear dynamics of a deformed Deoxyribonucleic acid (DNA) molecular chain which is governed by a perturbed sine-Gordon equation coupled with a linear wave equation representing the lattice deformation. The DNA chain…
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for…
We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion…