Related papers: Discrete breathers in protein structures
We analyze the formation and dynamics of bright unstaggered solitons in the disk-shaped dipolar Bose-Einstein condensate, which features the interplay of contact (collisional) and long-range dipole-dipole (DD) interactions between atoms.…
Diffusive motion of regulatory enzymes on biopolymers with eventual capture at a reaction site is a common feature in cell biology. Using a lattice gas model we study the impact of diffusion and capture for a microtubule polymerase and a…
Many systems in biology, physics and engineering can be described by systems of ordinary differential equation containing many parameters. When studying the dynamic behavior of these large, nonlinear systems, it is useful to identify and…
Physical phenomena in the real world are often described by energy-based modeling theories, such as Hamiltonian mechanics or the Landau theory, which yield various physical laws. Recent developments in neural networks have enabled the…
By means of a modified Lugiato-Lefever equation model, we investigate the nonlinear dynamics of dissipative wave structures in coherently-driven Kerr cavities with a parabolic potential. The potential stabilizes system dynamics, leading to…
We provide evidence of an extremely slow thermalization occurring in the Discrete NonLinear Schr\"odinger (DNLS) model. At variance with many similar processes encountered in statistical mechanics - typically ascribed to the presence of…
Combining discrete and continuous data is an important capability for generative models. We present Discrete Flow Models (DFMs), a new flow-based model of discrete data that provides the missing link in enabling flow-based generative models…
Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…
We prove nonexistence of breathers (spatially localized and time-periodic oscillations) for a class of Fermi-Pasta-Ulam lattices representing an uncompressed chain of beads interacting via Hertz's contact forces. We then consider the…
The existence and properties of envelope solitary waves on a periodic, traveling wave background, called traveling breathers, are investigated numerically in representative nonlocal dispersive media. Using a fixed point computational…
We investigate the stability and phase transition of localized modes in Bose-Einstein Condensates (BECs) in an optical lattice with the discrete nonlinear Schr\"{o}dinger model by considering both two- and three-body interactions. We find…
The energy method can be used to identify well-posed initial boundary value problems for quasi-linear, symmetric hyperbolic partial differential equations with maximally dissipative boundary conditions. A similar analysis of the discrete…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
The manipulation of locked intrinsic localized modes/discrete breathers is studied experimentally in nonlinear electric transmission line arrays. Introducing a static lattice impurity in the form of a capacitor, resistor or inductor has…
In this paper we investigate the emergence of time-periodic and and time-quasiperiodic (sometimes infinitely long lived and sometimes very long lived or metastable) solutions of discrete nonlinear wave equations: discrete sine Gordon,…
We study the scattering of a moving discrete breather (DB) on a junction in a Fermi-Pasta-Ulam (FPU) chain consisting of two segments with different masses of the particles. We consider four distinct cases: (i) a light-heavy (abrupt)…
Only about 1,000 qualitatively different protein folds are believed to exist in nature. Here, we review theoretical studies which suggest that some folds are intrinsically more designable than others, {\it i.e.} are lowest energy states of…
Membrane neck formation is essential for scission, which, as recent experiments on tubules have demonstrated, can be location dependent. The diversity of biological machinery that can constrict a neck such as dynamin, actin, ESCRTs and BAR…
Energy-based models (EBMs) offer a flexible framework for probabilistic modelling across various data domains. However, training EBMs on data in discrete or mixed state spaces poses significant challenges due to the lack of robust and fast…