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Neural noise sets a limit to information transmission in sensory systems. In several areas, the spiking response (to a repeated stimulus) has shown a higher degree of regularity than predicted by a Poisson process. However, a simple model…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
We study the elasticity of random fiber networks. Starting from a microscopic picture of the non-affine deformation fields we calculate the macroscopic elastic moduli both in a scaling theory and a self-consistent effective medium theory.…
Collisions and contacts of elastic materials are numerically and theoretically investigated. Using a two-dimensional spring-mass model with defect particles under the free boundary condition, we reproduce the Hertzian contact theory at…
Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology,…
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…
Hierarchical structures are very common in Nature, but only recently have they been systematically studied in materials physics, in order to understand the specific effects they can have on the mechanical properties of various systems.…
We study correlation properties of the generalized elastic model which accounts for the dynamics of polymers, membranes, surfaces and fluctuating interfaces, among others. We develop a theoretical framework which leads to the emergence of…
We present a minimal non-Hermitian model where a topologically nontrivial complex energy spectrum is induced by inter-particle interactions. Our model consists of a one-dimensional chain with a dynamical non-Hermitian gauge field with…
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character,…
We simulate the evolution of model protein sequences subject to mutations. A mutation is considered neutral if it conserves 1) the structure of the ground state, 2) its thermodynamic stability and 3) its kinetic accessibility. All other…
The problem of characterizing the structure of an elastic network constrained to lie on a frozen curved surface appears in many areas of science and has been addressed by many different approaches, most notably, extending linear elasticity…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Network science provides a universal framework for modeling complex systems, contrasting the reductionist approach generally adopted in physics. In a prototypical study, we utilize network models created from spectroscopic data of atoms to…
We develop a thermodynamic framework for closed and open chemical networks applicable to non-elementary reactions that do not need to obey mass action kinetics. It only requires the knowledge of the kinetics and of the standard chemical…
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…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Real networks are complex dynamical systems, evolving over time with the addition and deletion of nodes and links. Currently, there exists no principled mathematical theory for their dynamics -- a grand-challenge open problem. Here, we show…
We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the…
Disordered spring networks can exhibit rigidity transitions, due to either the removal of materials in over-constrained networks or the application of strain in under-constrained ones. While an effective medium theory (EMT) exists for the…