Related papers: Collective behaviours: from biochemical kinetics t…

The simple algorithm for the simulation and visualization of non relativistic quantum dynamics is proposed that is based on a collective behavior of classical particles. Any quantum particle is represented as the swarm of its classical…

We address the many-atom emission of a dilute cloud of two-level atoms through a renormalized perturbation theory. An analytical solution for the truncated coupled-dipole equations is derived, which contains an effective spectrum associated…

The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a…

Cooperative task execution, a hallmark of eusociality, is enabled by local interactions between the agents and the environment through a dynamically evolving communication signal. Inspired by the collective behavior of social insects whose…

Classical theories of chemical kinetics assume independent reactions in dilute solutions, whose rates are determined by mean concentrations. In condensed matter, strong interactions alter chemical activities and create inhomogeneities that…

The statistical mechanics of Gibbs is a juxtaposition of subjective, probabilistic ideas on the one hand and objective, mechanical ideas on the other. In this paper, we follow the path set out by Jaynes, including elements added…

Statistical mechanics provides the foundation for describing complex materials using only a few thermodynamic variables. No such framework currently exists far from equilibrium. In this Letter, we demonstrate how thermodynamics emerges far…

In this paper, one of the major shortcomings of the conventional numerical approaches is alleviated by introducing the probabilistic nature of molecular transitions into the framework of classical computational electrodynamics. The main aim…

The phenomena of synchronization and nontrivial collective behavior are studied in a model of coupled chaotic maps with random global coupling. The mean field of the system is coupled to a fraction of elements randomly chosen at any given…

Distinctive features in the sub-dynamics of an interacting bipartite system are explored. The sub-dynamic Heisenberg operators are introduced in a novel way leading to the quasi-particle-like concept in the respective subsystems. This…

In this paper, we propose a new method to identify biochemical reaction networks (i.e. both reactions and kinetic parameters) from heterogeneous datasets. Such datasets can contain (a) data from several replicates of an experiment performed…

Based on our experience in kinetic modeling of coupled multiple metabolic pathways we propose a generic rate equation for the dynamical modeling of metabolic kinetics. Its symmetric form makes the kinetic parameters (or functions) easy to…

An understanding of the precise nature of a chemical reactivity descriptor is of utmost interest to quantum chemists. In the present investigation an attempt has been made to analyze whether the electrophilicity index is a reliable…

We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We contrast the dynamics after excitation of a quantum mechanical system with that of a classical system. We demonstrate…

We present a mean field model for the phase diagram of a community of micro-organisms, interacting through their metabolism so that they are, in effect, engaging in a cooperative social game. We show that as a function of the concentration…

Many physical, chemical and biological systems exhibit a cooperative or sigmoidal response with respect to the input. In biochemistry, such behavior is called an allosteric effect. Here we demonstrate that a system with such properties can…

Starting from a quantum kinetic equation including the mean field and a conserving relaxation-time approximation we derive an analytic formula which describes the time dependence of the dielectric function in a plasma created by a short…

Swarm robotics has potential for a wide variety of applications, but real-world deployments remain rare due to the difficulty of predicting emergent behaviors arising from simple local interactions. Traditional engineering approaches design…

The experimental study of neural networks requires simultaneous measurements of a massive number of neurons, while monitoring properties of the connectivity, synaptic strengths and delays. Current technological barriers make such a mission…

In the first part of this paper we give a short review of the hierarchy of stochastic models, related to physical chemistry. In the basement of this hierarchy there are two models --- stochastic chemical kinetics and the Kac model for…