Related papers: Protein viscoelastic dynamics: a model system
A thin flat rectangular plate supported on its edges and subjected to in-plane loading exhibits stable post-buckling behaviour. However, the introduction of a nonlinear (softening) elastic foundation may cause the response to become…
Understanding cellular response to mechanical forces is immensely important for a plethora of biological processes. Focal adhesions are multi-molecular protein assemblies that connect the cell to the extracellular matrix and play a pivotal…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
A model for harmonic oscillator damping due to the internal friction of solids has been developed, based on considerations of a long period pendulum. The assumption of a complex elastic modulus to describe stress-strain hysteresis in the…
The short-term memory effects recently observed in vibration-induced compaction of granular materials are studied. It is shown that they can be explained by means of quite plausible hypothesis about the mesoscopic description of the…
We report a surprising hysteretic behavior in the dynamics of a simple one-dimensional nonlinear model inspired by the tribological problem of two sliding surfaces with a thin solid lubricant layer in between. In particular, we consider the…
We have investigated the mean field dynamics of an overdamped viscoelastic medium driven through quenched disorder. The model introduced incorporates coexistence of pinned and sliding degrees of freedom and can exhibit continuous elastic…
The dynamical properties of entangled polymers originate from the dynamic constraints due to the uncrossability between polymer chains. We propose a highly coarse-grained simulation model with transient bonds for such dynamically…
To produce sounds, we adjust the tension of our vocal folds to shape their properties and control the pitch. This efficient mechanism offers inspiration for designing reconfigurable materials and adaptable soft robots. However,…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
We propose a dissipative electro-elastic network model (DENM) to describe the dynamics and statistics of electrostatic fluctuations at active sites of proteins. The model combines the harmonic network of residue beads with overdamped…
A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected…
The hysteretic behavior exhibited by collagen fibrils, when subjected to cyclic loading, is known to result in both dissipation as well as accumulation of residual strain. On subsequent relaxation, partial recovery has also been reported.…
Constructing numerical models of noisy partial differential equations is very delicate. Our long term aim is to use modern dynamical systems theory to derive discretisations of dissipative stochastic partial differential equations. As a…
We investigate theoretically how the stress propagation characteristics of granular materials evolve as they are subjected to increasing pressures, comparing the results of a two-dimensional scalar lattice model to those of a molecular…
In this paper we prove the existence of solutions for a class of viscoelastic dynamic systems on time--dependent cracked domains, with possibly degenerate viscosity coefficients. Under stronger regularity assumptions we also show a…
Networks of filamentous proteins play a crucial role in cell mechanics. These cytoskeletal networks, together with various crosslinking and other associated proteins largely determine the (visco)elastic response of cells. In this letter we…
High-quality nanomechanical oscillators can sensitively probe force, mass, or displacement in experiments bridging the gap between the classical and quantum domain. Dynamics of these stochastic systems is inherently determined by the…