Related papers: Solvated dissipative electro-elastic network model…
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…
Many organisms have an elastic skeleton that consists of a closed shell of epithelial cells that is filled with fluid, and can actively regulate both elastic forces in the shell and hydrostatic pressure inside it. In this work we introduce…
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
The thermodynamics and dynamics of supercooled liquids correlate with their elasticity. In particular for covalent networks, the jump of specific heat is small and the liquid is {\it strong} near the threshold valence where the network…
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…
Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent…
The elastic response of mechanical, chemical, and biological systems is often modeled using a discrete arrangement of Hookean springs, either representing finite material elements or even the molecular bonds of a system. However, to date,…
Disordered soft materials, such as fibrous networks in biological contexts exhibit a nonlinear elastic response. We study such nonlinear behavior with a minimal model for networks on lattice geometries with simple Hookian elements with…
Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well-defined internal mechanical motions to various initial deformations and that these…
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…
An exactly solvable model for the rewiring dynamics of weighted, directed networks is introduced. Simulations indicate that the model exhibits two types of condensation: (i) a phase in which, for each node, a finite fraction of its total…
We present an extension of the Poisson-Boltzmann model in which the solute of interest is immersed in an assembly of self-orienting Langevin water dipoles, anions, cations, and hydrophobic molecules, all of variable densities. Interactions…
The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching…
The design of hydrogels that combine mechanical robustness with dynamic reconfigurability remains a fundamental challenge, as increasing crosslink dissociation rates compromise network integrity. This limitation is addressed through the…
Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric cluster with a large magnitude of its average dipole moment. The emergence of this new mesophase dramatically alters the…
We study the dynamical rheology of spring networks with a percolation model constructed by bond dilution in a two-dimensional triangular lattice. Hydrodynamic interactions are implemented by a Stokesian viscous coupling between the network…
A novel field theoretical approach towards modelling dynamic networking in complex systems is presented. An equilibrium networking formalism which utilises Gaussian fields is adapted to model the dynamics of particles that can bind and…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
Using an Ising-like model of protein mechanical unfolding, we introduce a diffusive dynamics on its exactly known free energy profile, reducing the nonequilibrium dynamics of the model to a biased random walk. As an illustration, the model…