Related papers: Discrete breathers in protein secondary structure
Rigidity analysis using the "pebble game" has been applied to protein crystal structures to obtain information on protein folding, assembly and t he structure-function relationship. However, previous work using this technique has not made…
We present analytical and numerical studies of phase-coherent dynamics of intrinsically localized excitations (breathers) in a system of two weakly coupled nonlinear oscillator chains. We show that there are two qualitatively different…
Suspensions of Active Brownian Particles (ABP) undergo motility induced phase separation (MIPS) over a wide range of mean density and activity strength [1], even in the absence of an explicit attraction. Negative values of the mechanical…
The impact of confinement on self-assembly of particles interacting with short-range attraction and long-range repulsion (SALR) potential is studied for thermodynamic states corresponding to local ordering of clusters or layers in the bulk.…
Abridged abstract: Inert interactions between randomly moving entities and spatial disorder play a crucial role in quantifying the diffusive properties of a system. These interactions affect only the movement of the entities, and examples…
Nonlinear classical Hamiltonian lattices exhibit generic solutions in the form of discrete breathers. These solutions are time-periodic and (typically exponentially) localized in space. The lattices exhibit discrete translational symmetry.…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
Discrete breathers are time-periodic, spatially localized solutions of the equations of motion for a system of classical degrees of freedom interacting on a lattice. Such solutions are investigated for a diatomic Fermi-Pasta-Ulam chain, i.…
Adhesion interactions mediated by multiple bond types are relevant for many biological and soft matter systems, including the adhesion of biological cells and functionalized colloidal particles to various substrates. To elucidate advantages…
Homogeneous active Brownian particle (ABP) systems with purely repulsive interactions are considered to have simple phase behavior, but various physical attributes of active entities can lead to variation in the collective dynamics. Recent…
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
We study discrete surface breathers in two-dimensional lattices of inductively-coupled split-ring resonators with capacitive nonlinearity. We consider both Hamiltonian and dissipative systems and analyze the properties of the modes…
The electronic properties of one- and two-dimensional biphenylene-based systems, such as nanoribbons and bilayers, are studied within a unified approach. Besides the bilayer with direct (AA) stacking, we present two additional symmetric…
Discrete bright breathers are well known phenomena. They are localized excitations that consist of a few excited oscillators in a lattice and the rest of them having very small amplitude or none. In this paper we are interested in the…
Associative polymer networks have shown a major promise in fabrication of self-healing and responsive materials. The can also serve as simple models to study more complex biological systems where transient interactions play an important…
A new mechanism of LENR in solids is proposed, which is based on the large amplitude anharmonic lattice vibrations, a.k.a. intrinsic localized modes or discrete breathers (DBs). In particular, so called gap DBs, which can arise in diatomic…
We explore the dynamics of strongly localized periodic solutions (discrete solitons, or discrete breathers) in a finite one-dimensional chain of asymmetric vibro-impact oscillators. The model involves a parabolic on-site potential with…
The mechanism of electron pairing in high-temperature superconductors is still the subject of intense debate. Here, we provide direct evidence of the role of structural dynamics, with selective atomic motions (buckling of copper-oxygen…
The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of…
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…