Topological localization in out-of-equilibrium dissipative systems

In this paper we report that notions of topological protection can be applied to stationary configurations that are driven far from equilibrium by active, dissipative processes. We show this for physically two disparate cases : stochastic networks governed by microscopic single particle dynamics as well as collections of driven, interacting particles described by coarse-grained hydrodynamic theory. In both cases, the presence of dissipative couplings to the environment that break time reversal symmetry are crucial to ensuring topologically protection. These examples constitute proof of principle that notions of topological protection, established in the context of electronic and mechanical systems, do indeed extend generically to processes that operate out of equilibrium. Such topologically robust boundary modes have implications for both biological and synthetic systems.Comment: 11 pages, 4 figures (SI: 8 pages 3 figures

Equilibria, Fixed Points, and Complexity Classes

Many models from a variety of areas involve the computation of an equilibrium or fixed point of some kind. Examples include Nash equilibria in games; market equilibria; computing optimal strategies and the values of competitive games (stochastic and other games); stable configurations of neural networks; analysing basic stochastic models for evolution like branching processes and for language like stochastic context-free grammars; and models that incorporate the basic primitives of probability and recursion like recursive Markov chains. It is not known whether these problems can be solved in polynomial time. There are certain common computational principles underlying different types of equilibria, which are captured by the complexity classes PLS, PPAD, and FIXP. Representative complete problems for these classes are respectively, pure Nash equilibria in games where they are guaranteed to exist, (mixed) Nash equilibria in 2-player normal form games, and (mixed) Nash equilibria in normal form games with 3 (or more) players. This paper reviews the underlying computational principles and the corresponding classes

Erratum: Signal propagation in proteins and relation to equilibrium fluctuations (PLoS Computational Biology (2007) 3, 9, (e172) DOI: 10.1371/journal.pcbi.0030172))

Elastic network (EN) models have been widely used in recent years for describing protein dynamics, based on the premise that the motions naturally accessible to native structures are relevant to biological function. We posit that equilibrium motions also determine communication mechanisms inherent to the network architecture. To this end, we explore the stochastics of a discrete-time, discrete-state Markov process of information transfer across the network of residues. We measure the communication abilities of residue pairs in terms of hit and commute times, i.e., the number of steps it takes on an average to send and receive signals. Functionally active residues are found to possess enhanced communication propensities, evidenced by their short hit times. Furthermore, secondary structural elements emerge as efficient mediators of communication. The present findings provide us with insights on the topological basis of communication in proteins and design principles for efficient signal transduction. While hit/commute times are information-theoretic concepts, a central contribution of this work is to rigorously show that they have physical origins directly relevant to the equilibrium fluctuations of residues predicted by EN models

A Coevolutionary Particle Swarm Algorithm for Bi-Level Variational Inequalities: Applications to Competition in Highway Transportation Networks

A climate of increasing deregulation in traditional highway transportation, where the private sector has an expanded role in the provision of traditional transportation services, provides a background for practical policy issues to be investigated. One of the key issues of interest, and the focus of this chapter, would be the equilibrium decision variables offered by participants in this market. By assuming that the private sector participants play a Nash game, the above problem can be described as a Bi-Level Variational Inequality (BLVI). Our problem differs from the classical Cournot-Nash game because each and every player’s actions is constrained by another variational inequality describing the equilibrium route choice of users on the network. In this chapter, we discuss this BLVI and suggest a heuristic coevolutionary particle swarm algorithm for its resolution. Our proposed algorithm is subsequently tested on example problems drawn from the literature. The numerical experiments suggest that the proposed algorithm is a viable solution method for this problem