Related papers: Discrete breathers in protein structures
The formation of protein patterns inside cells is generically described by reaction-diffusion models. The study of such systems goes back to Turing, who showed how patterns can emerge from a homogenous steady state when two reactive…
Phase separation of intrinsically disordered proteins is important for the formation of membraneless organelles, or biomolecular condensates, which play key roles in the regulation of biochemical processes within cells. In this work, we…
In different nonlinear mediums, the wave trains carry energy and expose many amazing features. To describe a nonlinear phenomenon, a soliton is one that preserves its shape and amplitude even after the collision. Breather is one kind of…
The interaction of discrete breathers with the primary lattice defects in transition metals such as vacancy, dislocation, and surface is analyzed on the example of bcc iron employing atomistic simulations. Scattering of discrete breathers…
It is demonstrated that the breather solutions recently discovered in the weakly coupled topological discrete sine-Gordon system are spectrally unstable. This is in contrast with more conventional spatially discrete systems, whose breathers…
We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the…
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
We investigate the long-time evolution of weakly perturbed single-site breathers (localized stationary states) in the discrete nonlinear Schroedinger (DNLS) equation. The perturbations we consider correspond to time-periodic solutions of…
We present a theoretical study of linear wave scattering in one-dimensional nonlinear lattices by intrinsic spatially localized dynamic excitations or discrete breathers. These states appear in various nonlinear systems and present a…
We study the properties of moving breathers in a bent DNA-related model with short range interaction, due to the stacking of the base pairs, and long range interaction, due to the finite dipole moment of the bonds within each base pair. We…
The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide…
A novel discrete model (D-model) is presented describing nonlinear wave interactions in systems with small and moderate nonlinearity under narrow frequency band excitation. It integrates in a single theoretical frame two mechanisms of…
Nonlinear interaction between normal modes dramatically affects energy equipartition, heat conduction and other fundamental processes in extended systems. In their celebrated experiment Fermi, Pasta and Ulam (FPU, 1955) observed that in…
For a one-dimensional linear lattice, earlier work has shown how to systematically construct a slowly-decaying linear potential bearing a localized eigenmode embedded in the continuous spectrum. Here, we extend this idea in two directions:…
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…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Deflation is an efficient numerical technique for identifying new branches of steady state solutions to nonlinear partial differential equations. Here, we demonstrate how to extend deflation to discover new periodic orbits in nonlinear…
We investigate the nonlinear dynamics of a damped Peyrard-Bishop DNA model taking into account long-range interactions with distance dependence |l|^-s on the elastic coupling constant between different DNA base pairs. Considering both…
The existence of breather type solutions, i.e., periodic in time, exponentially localized in space solutions, is a very unusual feature for continuum, nonlinear wave type equations. Following an earlier work [Comm. Math. Phys. {\bf 302},…