Revealing networks from dynamics: an introduction

What can we learn from the collective dynamics of a complex network about its interaction topology? Taking the perspective from nonlinear dynamics, we briefly review recent progress on how to infer structural connectivity (direct interactions) from accessing the dynamics of the units. Potential applications range from interaction networks in physics, to chemical and metabolic reactions, protein and gene regulatory networks as well as neural circuits in biology and electric power grids or wireless sensor networks in engineering. Moreover, we briefly mention some standard ways of inferring effective or functional connectivity.Comment: Topical review, 48 pages, 7 figure

Optimized auxiliary oscillators for the simulation of general open quantum systems

A method for the systematic construction of few-body damped harmonic oscillator networks accurately reproducing the effect of general bosonic environments in open quantum systems is presented. Under the sole assumptions of a Gaussian environment and regardless of the system coupled to it, an algorithm to determine the parameters of an equivalent set of interacting damped oscillators obeying a Markovian quantum master equation is introduced. By choosing a suitable coupling to the system and minimizing an appropriate distance between the two-time correlation function of this effective bath and that of the target environment, the error induced in the reduced dynamics of the system is brought under rigorous control. The interactions among the effective modes provide remarkable flexibility in replicating non-Markovian effects on the system even with a small number of oscillators, and the resulting Lindblad equation may therefore be integrated at a very reasonable computational cost using standard methods for Markovian problems, even in strongly non-perturbative coupling regimes and at arbitrary temperatures including zero. We apply the method to an exactly solvable problem in order to demonstrate its accuracy, and present a study based on current research in the context of coherent transport in biological aggregates as a more realistic example of its use; performance and versatility are highlighted, and theoretical and numerical advantages over existing methods, as well as possible future improvements, are discussed.Comment: 23 + 9 pages, 11 + 2 figures. No changes from previous version except publication info and updated author affiliation

Relaxation, thermalization and Markovian dynamics of two spins coupled to a spin bath

It is shown that by fitting a Markovian quantum master equation to the numerical solution of the time-dependent Schr\"odinger equation of a system of two spin-1/2 particles interacting with a bath of up to 34 spin-1/2 particles, the former can describe the dynamics of the two-spin system rather well. The fitting procedure that yields this Markovian quantum master equation accounts for all non-Markovian effects in as much the general structure of this equation allows and yields a description that is incompatible with the Lindblad equation.Comment: arXiv admin note: text overlap with arXiv:1605.0660