Related papers: Deconvolution of dynamic mechanical networks
Dimension reduction is a common strategy to study non-linear dynamical systems composed by a large number of variables. The goal is to find a smaller version of the system whose time evolution is easier to predict while preserving some of…
Dynamic force spectroscopy of single molecules is described by a model which predicts a distribution of rupture forces, the corresponding mean rupture force and variance, all amenable to experimental tests. The distribution has a pronounced…
Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fluctuations in their expression can affect the levels of…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
Link prediction is an important network science problem in many domains such as social networks, chem/bio-informatics, etc. Most of these networks are dynamic in nature with patterns evolving over time. In such cases, it is necessary to…
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…
A modeling framework for the internal conformational dynamics and external mechanical movement of single biological macromolecules in aqueous solution at constant temperature is developed. Both the internal dynamics and external movement…
In quasi-two-dimensional experiments with photoelastic particles confined to an annular region, an intruder constrained to move in a circular path halfway between the annular walls experiences stick-slip dynamics. We discuss the response of…
We study the mechanical stiffening behavior in two-dimensional (2D) cross-linked networks of semiflexible biopolymer filaments under simple shear. Filamental constituents immersed in a fluid undergo thermally excited bending motions.…
The dynamics of fluctuations is considered for electrons near a positive ion or for charges in a confining trap. The stationary nonuniform equilibrium densities are discussed and contrasted. The linear response function for small…
Living cells exhibit an important out-of-equilibrium mechanical activity, mainly due to the forces generated by molecular motors. These motor proteins, acting individually or collectively on the cytoskeleton, contribute to the violation of…
The linear response of non-equilibrium systems with Markovian dynamics satisfies a generalized fluctuation-dissipation relation derived from time symmetry and antisymmetry properties of the fluctuations. The relation involves the sum of two…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
The analysis of single particle trajectories plays an important role in elucidating dynamics within complex environments such as those found in living cells. However, the characterization of intracellular particle motion is often confounded…
We theoretically investigate the extractable work in single molecule unfolding-folding experiments with applied feedback. Using a simple two-state model, we obtain a description of the full work distribution, from discrete to continuous…
To mimic the mechanical response of passive biological cilia in complex fluids, we study the bending dynamics of an anchored elastic fiber submitted to a dilute granular suspension under shear. We show that the bending fluctuations of the…
In single molecule laser optical tweezer (LOT) pulling experiments a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent…
Many of the biological, social and man-made networks around us are inherently dynamic, with their links switching on and off over time. The evolution of these networks is often non-Markovian, and the dynamics of their links correlated.…
The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as for instance the fluctuations in ribsome copy numbers for a gene regulatory network. While several…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…