Related papers: Nonlinear waves in double-stranded DNA
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…
Non-linear equations of radial motion of a gas bubble in a compressible viscous liquid have been modified considering effects of viscosity and compressibility more complete than all previous works. A new set of equations has been derived…
We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and…
We present a data-driven pipeline for model building that combines interpretable machine learning, hydrodynamic theories, and microscopic models. The goal is to uncover the underlying processes governing nonlinear dynamics experiments. We…
Reaction-diffusion equations appear in biology and chemistry, and combine linear diffusion with different kind of reaction terms. Some of them are remarkable from the mathematical point of view, since they admit families of travelling waves…
We study pattern-forming nonlinear dynamics starting from a continuous wave state of quasi-one-dimensional two-component Bose-Einstein condensates with synthetic spin-orbit coupling induced by Raman lasers. Modulation instability can occur…
Strongly nonlinear models of internal wave propagation for incompressible stratified Euler fluids are investigated numerically and analytically to determine the evolution of a class of initial conditions of interest in laboratory…
We study nonlinear resonance of coupled modes in nano-mechanical systems. To reveal the qualitative features of the dynamics, we consider the limiting cases, where the results can be obtained analytically. For 1:3 resonance, we find the…
We demonstrate the application of the efficient semi-inverse asymptotic method to resonant interaction of the nonlinear normal modes belonging to different branches of the CNT vibration spectrum. Under condition of the 1:1 resonance of the…
We present initial results regarding the existence, stability and interaction of linear and nonlinear vibrational modes in a system of two coupled, one dimensional lattices with unequal numbers of masses. The effects on these nonlinear…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic…
Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work we employ…
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.…
We present an experimentally realizable, simple mechanical system with linear interactions whose geometric nature leads to nontrivial, nonlinear dynamical equations. The equations of motion are derived and their ground state structures are…
This thesis is concerned with dynamics of conservative nonlinear waves on bounded domains. In general, there are two scenarios of evolution. Either the solution behaves in an oscillatory, quasiperiodic manner or the nonlinear effects cause…
We investigate the dissipative dynamics of linear and nonlinear waves in harmonic traps by means of engineered complex non-Hermitian potentials. By combining an analytical mapping between real and complex Schr\"odinger equations with direct…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
The results of Brownian dynamics simulations of a single DNA molecule in shear flow are presented taking into account the effect of internal viscosity. The dissipative mechanism of internal viscosity is proved necessary in the research of…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
The interplay of nuclear and electronic dynamics characterizes the multi-dimensional electronic spectra of various molecular and solid-state systems. Theoretically, the observable effect of such interplay can be accounted for by response…