Related papers: Protein viscoelastic dynamics: a model system
Based on the wormlike chain model, a coarse-grained description of the nonlinear dynamics of a weakly bending semiflexible polymer is developed. By means of a multiple scale perturbation analysis, a length-scale separation inherent to the…
We use particle dynamics simulations to probe the correlations between noise and dynamics in a variety of disordered systems, including superconducting vortices, 2D electron liquid crystals, colloids, domain walls, and granular media. The…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
On the microscopic level, biological signal transmission relies on coordinated structural changes in allosteric proteins that involve sensor and effector modules. The timescales and microscopic details of signal transmission in proteins are…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
Live cells have ambiguous mechanical properties. They were often described as either elastic solids or viscoelastic fluids and have recently been classified as soft glassy materials characterized by weak power-law rheology. Nonlinear…
The dynamics of an ensemble of bistable elements with global time-delayed coupling under the influence of noise is studied analytically and numerically. Depending on the noise level the system undergoes ordering transitions and demonstrates…
The paper presents a model for low friction made up of a self-excited oscillator sliding along a periodic potential. It is shown that if the self-excitation affects a body sliding tangentially to a surface, than stick-slip modification and…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
We study the thermodynamic properties of a microscopic model of coupled oscillators that exhibits a dynamical phase transition from a desynchronized to a synchronized phase. We consider two different configurations for the thermodynamic…
The hydrodynamics of viscoelastic materials (for example polymer melts and solutions) presents interesting and complex phenomena, for example instabilities and turbulent flow at very low Reynolds numbers due to normal stress effects and the…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Presented here is a study of well-posedness and asymptotic stability of a "degenerately damped" PDE modeling a vibrating elastic string. The coefficient of the damping may vanish at small amplitudes thus weakening the effect of the…
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…
Adaptation to environmental change is a common property of biological systems. Cells initially respond to external changes in the environment, but after some time, they regain their original state. By considering an element consisting of…
We use linear stability analysis and hybrid lattice Boltzmann simulations to study the dynamical behaviour of an active nematic confined in a channel made of viscoelastic material. We find that the quiescent, ordered active nematic is…
We consider the dynamics of a rigid filament in a motor protein assay under external loading. The motor proteins are modeled as active harmonic linkers with tail ends immobilized on a substrate. Their heads attach to the filament…
The influence of out-of-plane oscillations on friction is a well-known phenomenon that has been studied extensively with various experimental methods, e.g. pin-on-disk tribometers. However, existing theoretical models have yet achieved only…
With the invent of nanoindentation technology capable of greater frequency of oscillation the full resonant behaviour can be observed. Here we lay out a proposed mathematical basis to interpret the measured dynamic compliance of a system to…
We explore the joint effect of the intrinsic noise and time delay on the spatial pattern formation within a multi-scale mobile lattice model of the epithelium. The protein fluctuations are driven by transcription/translation processes in…