Related papers: Non-exponential relaxation and hierarchically cons…
Collagen fibrils, when subjected to cyclic loading, are known to exhibit hysteretic behaviour with energy dissipation that is partially recovered on relaxation. In this paper, we develop a kinetic model for a collagen fibril incorporating…
Dynamic relaxation of the XY model and fully frustrated XY model quenched from an initial ordered state to the critical temperature or below is investigated with Monte Carlo methods. Universal power law scaling behaviour is observed. The…
We explore the long-time dynamics of a system of identical charged particles trapped on a closed helix. This system has recently been found to exhibit an unconventional deformation of the linear spectrum when tuning the helix radius. Here…
Hierarchical granular piles composed of aggregates are key structural features in both geoscience and planetary science, from fault gouge in seismic zones to the internal structures of comets. Although experimental studies have suggested a…
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…
We study the growth of a periodic pattern in one dimension for a model of spinodal decomposition, the Cahn-Hilliard equation. We particularly focus on the intermediate region, where the non-linearity cannot be negected anymore, and before…
We present a general formalism able to derive the kinetic equations of polymer dynamics. It is based on the application of nonequilibrium thermodynamics to analyze the irreversible processes taking place in the conformational space of the…
Understanding the slowest relaxations of complex systems, such as relaxation of glass-forming materials, diffusion in nanoclusters, and folding of biomolecules, is important for physics, chemistry, and biology. For a kinetic system, the…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
This paper describes new results linking constrained optimization theory and nonlinear contraction analysis. Generalizations of Lagrange parameters are derived based on projecting system dynamics on the tangent space of possibly…
The structure of hadronic form factors at high energies and their deviations from perturbative quantum chromodynamics provide insight on nonperturbative dynamics. Using an approach that is consistent with dispersion relations, we construct…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
A methodology is presented for investigating the dynamics of heterogeneous media using the nonlocal continuum model given by the peridynamic formulation. The approach presented here provides the ability to model the macroscopic dynamics…
The conformational dynamics of a single protein molecule in a shear flow is investigated using Brownian dynamics simulations. A structure-based coarse grained model of a protein is used. We consider two proteins, ubiquitin and integrin, and…
The non-equilibrium thermodynamics of a gas inside a piston is a conceptually simple problem where analytic results are rare. For example, it is hard to find in the literature analytic formulas that describe the heat exchanged with the…
Models of adhesion of extended particles on linear and planar substrates are of interest in interpreting surface deposition in colloid, polymer, and certain biological systems. An introduction is presented to recent theoretical advances in…
Exactly solvable models provide an opportunity to study different aspects of reduced quantum dynamics in detail. We consider the reduced dynamics of a single spin in finite XX and XY spin 1/2 chains. First we introduce a general expression…