Related papers: Elastic Network Models: Theoretical and Empirical …
We report a detailed computational study by Brownian Dynamics simulations of the structure and dynamics of a liquid of patchy particles which develops an amorphous tetrahedral network upon decreasing temperature. The highly directional…
In many physical systems, degrees of freedom are coupled \emph{via} hydrodynamic forces, even in the absence of Hamiltonian interactions. A particularly important and widespread example concerns the transport of microscopic particles in…
Most social, technological and biological networks are embedded in a finite dimensional space, and the distance between two nodes influences the likelihood that they link to each other. Indeed, in social systems, the chance that two…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…
The spring network model constitutes the backbone in the representations of a host of physical systems. In this work, we report the disturbance-driven microscopic dynamics of an isolated, closed spring network of spherical topology in…
Quasiperiodic models are important physical platforms to explore Anderson transitions in low dimensional systems, yet the exact mobility edges (MEs) are generally hard to be determined analytically. To date, the MEs in only a few models can…
Elasticity theory provides an accurate description of the long-wavelength vibrational dynamics of homogeneous crystalline solids, and with supplemental boundary conditions on the displacement field can also be applied to abrupt…
We propose a general framework for modelling network data that is designed to describe aspects of non-exchangeable networks. Conditional on latent (unobserved) variables, the edges of the network are generated by their finite growth history…
We provide a detailed multiscale analysis of a system of particles interacting through a dynamical network of links. Starting from a microscopic model, via the mean field limit, we formally derive coupled kinetic equations for the particle…
We study the dynamics of the contact-process, one of the simplest nonequilibrium stochastic processes, taking place on a scale-free network. We consider the network topology as annealed, i.e. all links are rewired at each microscopic time…
Across all scales of the physical world, dynamical systems can often be usefully represented as abstract networks that encode the system's units and inter-unit interactions. Understanding how physical rules shape the topological structure…
Dynamic graphs are rife with higher-order interactions, such as co-authorship relationships and protein-protein interactions in biological networks, that naturally arise between more than two nodes at once. In spite of the ubiquitous…
Understanding the relationship between the microscopic structure and topology of a material and its macroscopic properties is a fundamental challenge across a wide range of systems. Here, we investigate the viscoelasticity of DNA nanostar…
We propose a three dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue…
The elastic moduli of four numerical random isotropic packings of Hertzian spheres are studied. The four samples are assembled with different preparation procedures, two of which aim to reproduce experimental compaction by vibration and…
The connection between network topology and stability remains unclear. General approaches that clarify this relationship and allow for more efficient stability analysis would be desirable. Inspired by chemical reaction networks, I…
An elastic spring network is an example of evolvable matter. It can be pruned to couple separated pairs of nodes so that when a strain is applied to one of them, the other responds either in-phase or out-of-phase. This produces two pruned…