Related papers: Solitons in alpha-helical proteins
We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…
We study the dynamics of soliton solutions to the perturbed mKdV equation $\partial_t u = \partial_x(-\partial_x^2 u -2u^3) + \epsilon V u$, where $V\in \mathcal{C}^1_b(\mathbb{R})$, $0<\epsilon\ll 1$. This type of perturbation is…
The dynamics of dark-bright solitons beyond the mean-field approximation is investigated. We first examine the case of a single dark-bright soliton and its oscillations within a parabolic trap. Subsequently, we move to the setting of…
We present a detailed numerical study of solutions to the Zakharov-Kuznetsov equation in three spatial dimensions. The equation is a three-dimensional generalization of the Korteweg-de Vries equation, though, not completely integrable. This…
We describe wave propagation and soliton localization in photonic lattices which are induced in a nonlinear medium by an optical interference pattern, taking into account the inherent lattice deformations at the soliton location. We obtain…
We study the statics and dynamics of a binary dipolar Bose-Einstein condensate soliton for repulsive inter- and intraspecies contact interactions with the two components subject to different spatial symmetries $-$ distinct…
Transport processes in crowded periodic structures are often mediated by cooperative movements of particles forming clusters. Recent theoretical and experimental studies of driven Brownian motion of hard spheres showed that cluster-mediated…
Symmetry breaking is reported for continuous families of solitons in the nonlinear Schr\"odinger equation with a two-dimensional complex potential. This symmetry-breaking bifurcation is forbidden in generic complex potentials. However, for…
We study nonlinear dynamics of a periodic inhomogeneous DNA double helical chain under dynamic plane-base rotator model by considering angular rotation of bases in a plane normal to the helical axis. The dynamics is governed by a perturbed…
Motivated by the observation of localized circular excitations (`oscillons') in vertically vibrated granular layers (P.B. Umbanhowar, F. Melo and H.L. Swinney, Nature 382 (1996) 793), we numerically investigate an extension of a…
We consider shapes and dynamics of semi-discrete solitons (SDSs) in the known model of the set of linearly-coupled waveguides with the intrinsic cubic nonlinearity. The model applies to the description of a planar array of optical fibers,…
We introduce multi-soliton sets in the two-dimensional medium with the second-harmonic-generating nonlinearity subject to spatial modulation in the form of a triangle of singular peaks. Various families of symmetric and asymmetric sets are…
3D topological solitons are marvels of mathematical physics that arise in theoretical models in elementary particle and nuclear physics, condensed matter, and cosmology. A particularly interesting type of them is described by the…
We perform full three-dimensional numerical relaxations of isospinning Hopf solitons with Hopf charge up to 8 in the Skyrme-Faddeev model with mass terms included. We explicitly allow the soliton solution to deform and to break the…
We consider a PT-symmetric ladder-shaped optical array consisting of a chain of waveguides with gain coupled to a parallel chain of waveguides with loss. All waveguides have the focusing Kerr nonlinearity. The array supports two co-existing…
Periodic potentials with flat bands in their spectra support strongly localized nonlinear excitations. Although a perfectly flat band cannot exist in a continuous system, a spin-orbit-coupled Bose-Einstein condensate loaded in a Zeeman…
Particles whose shapes couple translation to rotation display a rich array of behaviors as they sediment at low Reynolds number. We introduce a unifying perspective in which the possible dynamical regimes and bifurcations between them can…
Orbital and asymptotic stability for 1-soliton solutions to the Toda lattice equations as well as small solitary waves to the FPU lattice equations are established in the energy space. Unlike analogous Hamiltonian PDEs, the lattice…
This article offers a review of results for solitons in 2D and 3D models of nonlinear dissipative media. The existence of such solitons requires to maintain two balances: between nonlinear self-focusing and linear diffraction and/or…
We report on a novel behavior of solitary localized structures in a real Swift-Hohenberg equation subjected to a delayed feedback. We shall show that variation in the product of the delay time and the feedback strength leads to nontrivial…