Related papers: Deconvolution of dynamic mechanical networks
Real-world networks in technology, engineering and biology often exhibit dynamics that cannot be adequately reproduced using network models given by smooth dynamical systems and a fixed network topology. Asynchronous networks give a…
The relaxation of an elastic network, constructed by a contact map of a fractal (crumpled) polymer globule is investigated. We found that: i) the slowest mode of the network is separated from the rest of the spectrum by a wide gap, and ii)…
Inspired by experiments on dynamic extensile gels of biofilaments and motors, we propose a model of a network of linear springs with a kinetics consisting of growth at a prescribed rate, death after a lifetime drawn from a distribution, and…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
Real-world networks are composed of diverse interacting and evolving entities, while most of existing researches simply characterize them as particular static networks, without consideration of the evolution trend in dynamic networks.…
The dynamics of swollen fractal networks (Rouse model) has been studied through computer simulations. The fluctuation-relaxation theorem was used instead of the usual Langevin approach to Brownian dynamics. We measured the equivalent of the…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The distribution of entanglement between the nodes of a quantum network plays a fundamental role in quantum information applications. In this work, we investigate the dynamics of a network of qubits where each edge corresponds to an…
This paper uses dynamical invariants to describe the evolution of collisionless systems subject to time-dependent gravitational forces without resorting to maximum-entropy probabilities. We show that collisionless relaxation can be viewed…
In this paper we present a network model to study the impact of spatial distribution of constituents, coupling between them and diffusive processes in the context of biological situations. The model is in terms of network of mobile elements…
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force…
We describe a phase transition that gives rise to structurally non-trivial states in a two-dimensional ordered network of particles connected by harmonic bonds. Monte Carlo simulations reveal that the network supports, apart from the…
Elastic deformation due to embedded fluidic networks is currently studied in the context of soft-actuators and soft-robotic applications. In this work, we analyze interaction between the elastic deflection of a slender beam and viscous flow…
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…
In this work, we study in detail the distribution of stochastic forces generated by the molecular motors activity, in the actin cortex of pre-muscular cells. By combining active and passive rheology experiments, performed on the same…
In living cells, proteins involved in specialized biochemical functions are often spatially organized within biomolecular condensates. Increasing evidence suggests that some of these condensates, including DNA repair condensates, emerge…
Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…
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…
A novel approach to moment closure problem is used to derive low dimensional laws for the dynamics of the moments of the membrane potential distribution in a population of spiking neurons. Using spectral expansion of the density equation we…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…