Related papers: Energy transfer in nonlinear network models of pro…

We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a…

Protein machines often exhibit long range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the non--linear energy localization and the basic mechanisms of energy transfer in…

Proteins are large and complex molecular machines. In order to perform their function, most of them need energy, e.g. either in the form of a photon, like in the case of the visual pigment rhodopsin, or through the breaking of a chemical…

Topological defects in low-dimensional non-linear systems feature a sliding-to-pinning transition of relevance for a variety of research fields, ranging from biophysics to nano- and solid-state physics. We find that the dynamics after a…

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as…

While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior…

During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local,…

Collective protein modes are expected to be important for facilitating energy transfer in the Fenna-Matthews-Olson (FMO) complex, however to date little work has focussed on the microscopic details of these vibrations. The nonlinear network…

Recently, using a numerical surface cooling approach, we have shown that highly energetic discrete breathers (DB) can form in the stiffest parts of nonlinear network models of large protein structures. In the present study, using an…

We discuss the process by which energy, initially evenly distributed in a nonlinear lattice, can localize itself into large amplitude excitations. We show that, the standard modulational instability mechanism, which can initiate the process…

The study of energy transport properties in heterogeneous materials has attracted scientific interest for more than a century, and it continues to offer fundamental and rich questions. One of the unanswered challenges is to extend Anderson…

By using a Generalized Hubbard model for bosons, the energy transfer in a nonlinear quantum lattice is studied, with special emphasis on the interplay between local and nonlocal nonlinearity. For a strong local nonlinearity, it is shown…

We investigate the dynamics of highly polydispersed finite granular chains. From the spatio-spectral properties of small vibrations, we identify which particular single-particle displacements lead to energy localization. Then, we address a…

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…

Recent experimental findings on a protein showed the diffusion of vibrational energy does not occur along the backbone interaction,as it might be expected, but prevalently on non-bonded contacts. These results are explained presenting a…

In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins…

We investigate the energy transport in one-dimensional disordered granular solids by extensive numerical simulations. In particular, we consider the case of a polydisperse granular chain composed of spherical beads of the same material and…

One-dimensional chain of pointwise particles harmonically coupled with nearest neighbors and placed in six-order polynomial on-site potentials is considered. Power of the energy source in the form of single ac driven particles is calculated…

By employing a nonlinear quantum kicked rotor model, we investigate the transport of energy in multidimensional quantum chaos. Parallel numerical simulations and analytic theory demonstrate that the interplay between nonlinearity and…

This work targets the influence of disorder on the relaxed structure and macroscopic mechanical properties of elastic networks. We construct network classes of different types of disorder (length, topology and stiffness), which are…