Related papers: Protein viscoelastic dynamics: a model system
Analysis is presented of a system whose dynamics are dramatically simplified by tiny amounts of additive noise. The dynamics divide naturally into two phases. In the slower phase, trajectories are close to an invariant manifold; this allows…
The dynamics of many macromolecular machines is characterized by chemically-mediated structural changes that achieve large scale functional deployment through local rearrangements of constitutive protein sub-units. Motivated by recent high…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
A dynamic model for failures in biological organisms is proposed and studied both analytically and numerically. Each cell in the organism becomes dead under sufficiently strong stress, and is then allowed to be healed with some probability.…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
Physical experiments can characterize the elastic response of granular materials in terms of macroscopic state-variables, namely volume (packing) fraction and stress, while the microstructure is not accessible and thus neglected. Here, by…
We study single-variable approaches for describing stochastic dynamics with small inertia. The basic models we deal with describe passive Brownian particles and phase elements (phase oscillators, rotators, superconducting Josephson…
Polycrystalline materials have a viscoelastic rheology where the strains produced by stresses depend on the timescale of deformation. Energy can be stored elastically within grain interiors and dissipated by a variety of different…
The aim of this paper is to calculate the time dependence of the mean position (and orientation) of a fluid particle when a fluid system at thermodynamic equilibrium is submitted to a mechanical action. The starting point of this novel…
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…
When an oscillator switches abruptly between different frequencies, there is some ambiguity in deciding how the system should be modelled at the switch. Here we describe two seemingly natural models of a switch in a simple…
The unjamming transition of granular systems is investigated in a seismic fault model via three dimensional Molecular Dynamics simulations. A two--time force--force correlation function, and a susceptibility related to the system response…
It has been claimed that quasistatic granular materials, as well as nanoscale materials, exhibit departures from elasticity even at small loadings. It is demonstrated, using 2D and 3D models with interparticle harmonic interactions, that…
The social force model belongs to a class of microscopic force-based pedestrian model for which the interaction with the neighbors solely depends on the distance spacings. Yet, distance based models can lead to unrealistic oscillating…
The dynamics of filaments in flow are central to understanding a wide range of biological and soft-matter systems, yet their behavior under time-dependent forcing remains poorly understood. Here, we investigate the long-time dynamics of…
We develop an effective description of noise-induced oscillations based on deterministic phase dynamics. The phase equation is constructed to exhibit correct frequency and distribution density of noise-induced oscillations. In the simplest…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
A realistic continuous-time dynamics for fiber bundles is introduced and studied both analytically and numerically. The equation of motion reproduces known stationary-state results in the deterministic limit while the system under…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
Model order reduction in high-dimensional, nonlinear dynamical systems if often enabled through fast-slow timescale separation. One such approach involves identifying a low-dimensional slow manifold to which the state rapidly converges and…