Related papers: A first principle (3+1) dimensional model for micr…
We study the dynamics of emission of radiation (small-amplitude waves) in fast collisions between two solitons of the nonlinear Schr\"odinger (NLS) equation in the presence of weak cubic loss. We calculate the radiation dynamics by a…
In many intracellular processes, the length distribution of microtubules is controlled by depolymerizing motor proteins. Experiments have shown that, following non-specific binding to the surface of a microtubule, depolymerizers are…
Microtubule dynamics is largely influenced by nucleotide hydrolysis and the resultant tubulin configuration changes. The GTP cap model has been proposed to interpret the stabilizing mechanism of microtubule growth from the view of…
Very narrow spatial bright solitons in (1+1)D and (2+1)D versions of cubic-quintic and full saturable models are studied, starting from the full system of the Maxwell's equations, rather than from the paraxial (NLS) approximation. For the…
Molecular communication (MC), one of the emerging techniques in the field of communication, is entering a new phase following several decades of foundational research. Recently, attention has shifted toward MC in liquid media, particularly…
We study numerically the integrable turbulence in the framework of the one-dimensional nonlinear Schrodinger equation (1D-NLSE) of the focusing type using a new approach called the "growing of turbulence". In this approach, we add a small…
We investigate the mechanical origin of polymorphic structures in two-dimensional tubulin assemblies, of which microtubules are the best known example. These structures feature twisted ribbons, flat tubulin sheets, macrotubules, and hoops,…
We consider the nonlinear Schrodinger equation with cubic (focusing or defocusing) nonlinearity on the multidimensional torus. For special small initial data containing only five modes, we exhibit a countable set of time layers in which…
The question of collapse (blow-up) in finite time is investigated for the two-dimensional (non-integrable) space-time nonlocal nonlinear Schrodinger equations. Starting from the two-dimensional extension of the well known AKNS q,r system,…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
In the lyotropic phase of lipids with excess water, multilamellar tubules (MLTs) grow from defects. A phenomenological model for the stability of MLTs is developed that is universal and independent of the underlying growth mechanisms of…
Solitons are typically stable objects in 1D models, but their straightforward extensions to 2D and 3D settings tend to be unstable. In particular, the ubiquitous nonlinear Schroedinger (NLS) equation with the cubic self-focusing, creates…
Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T=3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to…
This paper presents a novel methodology for the direct numerical modeling and simulation of turbulent flows. The kinetic model equation is firstly extended to turbulent flow with the account of coupled evolution of kinetic, thermal, and…
In weakly magnetized, dilute plasmas in which thermal conduction along magnetic field lines is important, the usual convective stability criterion is modified. Instead of depending on entropy gradients, instability occurs for small…
We examine statistical properties of integrable turbulence in the defocusing and focusing regimes of one-dimensional small-dispersion nonlinear Schrodinger equation (1D-NLSE). Specifically, we study the 1D-NLSE evolution of partially…
Based on a novel concept of multiplicative multiscale decomposition, we have derived a multiscale micromorphic molecular dynamics (MMMD)to extent the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and macroscale. The…
In this paper, we present a spatio-temporal mathematical model for simulating the formation and growth of a thrombus. Blood is treated as a multi-constituent mixture comprised of a linear fluid phase and a thrombus (solid) phase. The…
We have developed a simulation technique of multiscale Lagrangian fluid dynamics to tackle hierarchical problems relating to historical dependency of polymeric fluid. We investigate flow dynamics of dilute polymeric fluid by using the…
We use three-dimensional simulations to study the statistics of supersonic turbulence in molecular clouds. Our numerical experiments describe driven turbulent flows with an isothermal equation of state, Mach numbers around 10, and various…