Related papers: Discrete breathers in protein structures
Proteins and nucleic acids can spontaneously self-assemble into membraneless droplet-like compartments, both in vitro and in vivo. A key component of these droplets are multi-valent proteins that possess several adhesive domains with…
Nonequilibrium, quasi-stationary states of a one-dimensional "hard" $\phi^4$ deterministic lattice, initially thermalized to a particular temperature, are investigated when brought into contact with a stochastic thermal bath at lower…
The onset of life is often framed around membrane bound compartments and encoded metabolism, leaving unresolved how spatial organization arose before stable boundaries. In this context, environmental gradients are usually treated as…
We consider the localized nonlinear breathing modes that emerge in heterogeneous granular configurations of two materials with a periodicity of three and four beads. We examine as characteristic examples chains with 1 steel and 2 alumnium…
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…
We describe Structured Random Binding (SRB), a minimal model of protein-protein interactions rooted in the statistical physics of disordered systems. In this model, nonspecific binding is a generic consequence of the interaction between…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
In the aerospace industry the trend for light-weight structures and the resulting complex dynamic behaviours currently challenge vibration engineers. In many cases, these light-weight structures deviate from linear behaviour, and complex…
We uncover subtle and previously unexplored phenomena arising from the interplay of nonlinearity and nonreciprocity in topological mechanical metamaterials. We study a nonreciprocal topological Klein-Gordon chain of asymmetrically coupled…
In this paper we consider a 2D hexagonal crystal lattice model first proposed by Marin, Eilbeck and Russell in 1998. We perform a detailed numerical study of nonlinear propagating localized modes, that is, propagating discrete breathers and…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…
The dynamics of a system composed of elastic hard particles confined by an isotropic harmonic potential are studied. In the low-density limit, the Boltzmann equation provides an excellent description, and the system does not reach…
Nonlinear networks can host spatially compact time periodic solutions called compact breathers. Such solutions can exist accidentally (i.e. for specific nonlinear strength values) or parametrically (i.e. for any nonlinear strength). In this…
The Fermi-Pasta-Ulam (FPU) paradox was observed fifty years ago. The surprising finding was a localization of energy in the reciprocal q-space of a model with discrete translational invariance, despite the presence of interaction between…
In many crystals with sufficient anharmonicity, a special kind of lattice vibrations, namely, discrete breathers (DBs) can be excited either thermally or by external triggering, in which the amplitude of atomic oscillations greatly exceeds…
We explore a recently proposed locally resonant granular system bearing harmonic internal resonators in a chain of beads interacting via Hertzian elastic contacts. In this system, we propose the existence of two types of configurations: (a)…
Bound states of solitons (molecules) occur in various settings, playing an important role in the operation of fiber lasers, optical emulations, encoding, and communications. Soliton interactions are generally related to breathing dynamics…
Many functional units in biology, such as enzymes or molecular motors, are composed of several subunits that can reversibly assemble and disassemble. This includes oligomeric proteins composed of several smaller monomers, as well as protein…