Related papers: Protein viscoelastic dynamics: a model system
We study a class of elastic systems described by a (hyperbolic) partial differential equation. Our working example is the equation of a vibrating string subject to linear disturbance. The main goal is to establish conditions for…
We propose a general hybrid physics-informed machine learning framework for modeling nonlinear, history-dependent viscoelastic behavior under multiaxial cyclic loading. The approach is built on a generalized internal state variable-based…
A model of saturated hyperelastic porous solids at large strains is formulated and analysed. The material response is assumed to be of a viscoelastic Kelvin-Voigt type and inertial effects are considered, too. The flow of the diffusant is…
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…
It is shown that the dynamics of a two-dimensional crystal with a finite concentration of dislocations, as well as vacancy and interstitial defects, is governed by the hydrodynamic equations of a viscoelastic medium. At the longest length…
The sliding friction of a dimer moving over a periodic substrate and subjected to an external force is studied in the steady state for arbitrary temperatures within a one-dimensional model. Nonlinear phenomena that emerge include dynamic…
The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule…
Stochastic oscillations in individual cells are usually characterized by a non-monotonic power spectrum with an oscillatory autocorrelation function. Here we develop an analytical approach of stochastic oscillations in a minimal hybrid…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
In this paper we report, clarify and broaden various recent efforts to complement the chemistry-centered models of force generation in muscles by mechanics-centered models. The physical mechanisms of interest can be grouped into two…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
We consider an explicit model of a semiflexible filament moving in two dimensions on a gliding assay of motor proteins, which attach to and detach from filament segments stochastically, with a detachment rate that depends on the local load…
We study two closely related, nonlinear models of a viscoplastic solid. These models capture essential features of plasticity over a wide range of strain rates and applied stresses. They exhibit inelastic strain relaxation and steady flow…
We consider an active, stochastic microscopic model of particles suspended in a fluid and show that the coarse-grained description of this model renders odd viscoelasticity. The particles are odd dumbbells, each featuring a robotic device…
Multisite protein modification is a ubiquitous mechanism utilized by cells to control protein functions. We have recently proposed a dynamical description of multisite protein modification which embodies all the essential features of the…