Related papers: Protein viscoelastic dynamics: a model system
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…
The dynamics of biological systems, from proteins to cells to organisms, is complex and stochastic. To decipher their physical laws, we need to bridge between experimental observations and theoretical modeling. Thanks to progress in…
Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
It is well known that energy dissipation and finite size can deeply affect the dynamics of granular matter, often making usual hydrodynamic approaches problematic. Here we report on the experi-mental investigation of a small model system,…
Mechanically induced folding of passive cross-linkers is a fundamental biological phenomenon. A typical example is a conformational change in myosin II responsible for the power-stroke in skeletal muscles. In this paper we present an…
We model and simulate the stepping dynamics of the kinesin motor including electric and mechanical forces, environmental noise, and the complicated potentials produced by tracking and neighboring protofilaments. Our dynamical model supports…
Elastomers are viscoelastic materials and their properties significantly depend on the loading rate. The actual stress experienced by these materials is the sum of equilibrium and dissipative (inelastic) terms. At very low loading rates we…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
We study forced oscillations of a rod with a body attached to its free end so that the motion of a system is described by two sets of equations, one of integer and the other of the fractional order. To the constitutive equation we associate…
Recent experimental and computational studies of vibrated thin layers of identical spheres have shown transitions to ordered phases similar to those seen in equilibrium systems. Motivated by these results, we carry out simulations of hard…
We consider an immersed elastic body that is actively driven through a structured fluid by a motor or an external force. The behavior of such a system generally cannot be solved analytically, necessitating the use of numerical methods.…
We have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains. Our simulation results show that mean protein folding…
We present two simplified models of protein dynamics based on Langevin's equation of motion in a viscous medium. We explore the effect of the potential energy function's symmetry on the kinetics and thermodynamics of simulated folding. We…
We propose a model for motor proteins based on a hierarchical Hamiltonian that we have previously introduced to describe protein folding. The proposed motor model has high efficiency and is consistent with a linear load-velocity response.…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
We study the dynamical response of a single semiflexible polymer chain based on the theory developed by Hallatschek et al. for the wormlike-chain model. The linear viscoelastic response under oscillatory forces acting at the two chain ends…
A generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues, reproduces the energy probability distribution of real proteins over a very large range…