Related papers: Protein viscoelastic dynamics: a model system
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
A general model covering a large variety of the so-called adhesive or cohesive, possibly also frictional, contact interfaces between visco-elastic bodies with inertia considered in a thermodynamical context is presented. A semi-implicit…
An experimental arrangement and a set of experiments are developed to generate empirical evidence of the effect of noise on a rotating, macro-scale cantilever structure. The experiment is a controlled representation of a rotating machinery…
Osmosis plays a central role in the function of living and soft matter systems. While the thermodynamics of osmosis is well understood, the underlying microscopic dynamical mechanisms remain the subject of discussion. Unraveling these…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
Recent experimental results on the static or quasistatic response of granular materials have been interpreted to suggest the inapplicability of the traditional engineering approaches, which are based on elasto-plastic models (which are…
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…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
A system consisting of a doubly clamped beam with an attached body (slider) free to move along the beam has been studied recently by multiple research groups. Under harmonic base excitation, the system has the capacity to passively adapt…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations…
We study the dynamics of a simple adaptive system in the presence of noise and periodic damping. The system is composed by two paths connecting a source and a sink, the dynamics is governed by equations that usually describe food search of…
The response to a localized force provides a sensitive test for different models of stress transmission in granular solids. The elasto-plastic models traditionally used by engineers have been challenged by theoretical and experimental…
Small mechanical forces play important functional roles in many crucial cellular processes, including in the dynamical behavior of the cytoskeleton and in the regulation of osmotic pressure through membrane-bound proteins. Molecular…
The effects of intrinsic noise on stochastic delay systems is studied within an expansion in the inverse system size. We show that the stochastic nature of the underlying dynamics may induce oscillatory behaviour in parameter ranges where…
We describe a model of cytoskeletal mechanics based on the force-induced conformational change of protein cross-links in a stressed polymer network. Slow deformation of simulated networks containing cross-links that undergo repeated, serial…
Amorphous elastomers exhibit significant rate-stiffening and unique viscous flow characteristics across a wide range of strain rates, often undergoing glass transition above a strain rate threshold. We have developed a…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
A dynamical model is proposed for isotropic turbulence driven by steady forcing that yields a viscosity independent dynamics for the small-scale (inertial) regime. This reproduces the Kolmogorov spectrum for the two-point velocity…