Related papers: Non-exponential relaxation and hierarchically cons…
1. Role of inter-domain water clusters in large-scale dynamics of proteins; 2. Description of large-scale dynamics of proteins based on generalized Stokes-Einstein and Eyring-Polany equation; 3. Dynamic model of protein-ligand complexes…
A key feature of non-equilibrium thermodynamics is the Markovian, deterministic relaxation of coarse observables such as, for example, the temperature difference between two macroscopic objects which evolves independently of almost all…
The hysteretic behavior exhibited by collagen fibrils, when subjected to cyclic loading, is known to result in both dissipation as well as accumulation of residual strain. On subsequent relaxation, partial recovery has also been reported.…
Non-reciprocal systems exhibit diverse dynamical phases whose character depends on the type and degree of non-reciprocity. In this study, we theoretically investigate dynamical structures in a mixture of non-reciprocally aligning polar…
We investigate the emergence of universal dynamical scaling in quantum critical spin systems adiabatically driven out of equilibrium, with emphasis on quench dynamics which involves non-isolated critical points (i.e., critical regions) and…
In this work a new non-minimally coupled model is presented, where a generic function $f(R)$ of the scalar curvature factors the usual Einstein-Hilbert action functional, motivated by relevant results obtained from similar models. Its…
We present a machine learning framework for modeling protein dynamics. Our approach uses L1-regularized, reversible hidden Markov models to understand large protein datasets generated via molecular dynamics simulations. Our model is…
Experience collected in mesoscopic dynamic modeling of externally driven systems indicates absence of potentials that could play role of equilibrium or nonequilibrium thermodynamic potentials yet their thermo-dynamics-like modeling is often…
We establish new scaling properties for the universality class of Model C, which describes relaxational critical dynamics of a nonconserved order parameter coupled to a conserved scalar density. We find an anomalous diffusion phase, which…
We present a dynamical model of lipoprotein metabolism derived by combining a cascading process in the blood stream and cellular level regulatory dynamics. We analyse the existence and stability of equilibria and show that this…
The Discrete NonLinear Schr\"odinger (DNLS) equation displays a parameter region characterized by the presence of localized excitations (breathers). While their formation is well understood and it is expected that the asymptotic…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
Derivation of reduced order representations of dynamical systems requires the modeling of the truncated dynamics on the retained dynamics. In its most general form, this so-called closure model has to account for memory effects. In this…
The structural relaxation of amorphous materials is described as arising from the superposition of elementary processes with varying activation energies. We show that it is possible to obtain the kinetic parameters of these processes from…
We consider the non--equilibrium dynamics of a chain of classical rotators coupled at its edges to an external reservoir at zero temperature. We find that the energy is released in a strongly discontinuous fashion, with sudden jumps…
[Abridged] Recently we have found that a family of models of partially relaxed, anisotropic stellar systems, inspired earlier by studies of incomplete violent relaxation, exhibits some interesting thermodynamic properties. Here we present a…
We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…
A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable.…
The Kramers' survival probability has been generalized by using nonextensive formalism. This nonextensive survival probability is studied in detail and associated Kramers' rate has been calculated in the high and low viscosity limit. It has…
The response of many materials to applied forces and boundary constraints depends upon internal geometric changes at multiple submacroscopic levels. Hierarchical structured deformations provide a mathematical setting for the description of…