Related papers: Deconvolution of dynamic mechanical networks
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
The cytoskeleton is an inhomogeneous network of semi-flexible filaments, which are involved in a wide variety of active biological processes. Although the cytoskeletal filaments can be very stiff and embedded in a dense and cross-linked…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active…
Classical network embeddings create a low dimensional representation of the learned relationships between features across nodes. Such embeddings are important for tasks such as link prediction and node classification. In the current paper,…
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
We use a minimal model for a dense suspension undergoing thickening and thinning to investigate microstructural changes in 2d simulations. Our simulations show that in steady flow the contact network contains distinct building blocks which…
Plastic deformation of metals involves the complex evolution of dislocations forming strongly connected dislocation networks. These dislocation networks are based on dislocation reactions, which can form junctions during the interactions of…
Capturing the dynamics of granular flows at intermediate length scales can often be difficult. We propose studying the dynamics of contact networks as a new tool to study fracture at intermediate scales. Using experimental three-dimensional…
We investigate recurrent neural networks with asymmetric interactions and demonstrate that the inclusion of self-couplings or sparse excitatory inter-module connections leads to the emergence of a densely connected manifold of dynamically…
A physics-informed neural network is presented for poroelastic problems with coupled flow and deformation processes. The governing equilibrium and mass balance equations are discussed and specific derivations for two-dimensional cases are…
A coarse-grained molecular simulation approach originally developed for entangled polymeric liquids is extended to model the mechanical behavior of long-fiber networks. The model, based on the slip-link picture of chain entanglements,…
Collagen networks provide the main structural component of most tissues and represent an important ingredient for bio-mimetic materials for bio-medical applications. Here we study the mechanical properties of stiff collagen networks derived…
In this paper, we develop a blended dynamics framework for open quantum networks with diffusive couplings. The network consists of qubits interconnected through Hamiltonian couplings, environmental dissipation, and consensus-like diffusive…
We present a diagrammatic formulation of a theory for the time dependence of density fluctuations in equilibrium systems of interacting Brownian particles. To facilitate derivation of the diagrammatic expansion we introduce a basis that…
In many complex systems, the dynamical evolution of the different components can result in adaptation of the connections between them. We consider the problem of how a fully connected network of discrete-state dynamical elements which can…
Novel method of reconstructing dynamical networks from empirically measured time series is proposed. By examining the variable--derivative correlation of network node pairs, we derive a simple equation that directly yields the adjacency…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…