Efficient Energy Transport in Photosynthesis: Roles of Coherence and Entanglement

Recently it has been discovered---contrary to expectations of physicists as well as biologists---that the energy transport during photosynthesis, from the chlorophyll pigment that captures the photon to the reaction centre where glucose is synthesised from carbon dioxide and water, is highly coherent even at ambient temperature and in the cellular environment. This process and the key molecular ingredients that it depends on are described. By looking at the process from the computer science view-point, we can study what has been optimised and how. A spatial search algorithmic model based on robust features of wave dynamics is presented.Comment: 6 pages, 3 figures, to appear in the proceedings of the Symposium "75 Years of Quantum Entanglement: Foundations and Information Theoretic Applications", January 2011, Kolkata, Indi

A path integral for classical dynamics, entanglement, and Jaynes-Cummings model at the quantum-classical divide

The Liouville equation differs from the von Neumann equation 'only' by a characteristic superoperator. We demonstrate this for Hamiltonian dynamics, in general, and for the Jaynes-Cummings model, in particular. -- Employing superspace (instead of Hilbert space), we describe time evolution of density matrices in terms of path integrals which are formally identical for quantum and classical mechanics. They only differ by the interaction contributing to the action. This allows to import tools developed for Feynman path integrals, in order to deal with superoperators instead of quantum mechanical commutators in real time evolution. Perturbation theory is derived. Besides applications in classical statistical physics, the "classical path integral" and the parallel study of classical and quantum evolution indicate new aspects of (dynamically assisted) entanglement (generation). Our findings suggest to distinguish 'intra'- from 'inter-space' entanglement.Comment: 22 pages; based on invited talk at Quantum 2010 - Advances in Foundations of Quantum mechanics and Quantum Information with Atoms and Photons (Torino, May 2010). To appear in Int. J. Qu. Inf

An information theoretic approach for knowledge representation using Petri nets

A new hybrid approach for Petri nets (PNs) is proposed in this paper by combining the PNs principles with the foundations of information theory for knowledge representation. The resulting PNs have been named Plausible Petri nets (PPNs) mainly because they can handle the evolution of a discrete event system together with uncertain (plausible) information about the system using states of information. This paper overviews the main concepts of classical PNs and presents a method to allow uncertain information exchange about a state variable within the system dynamics. The resulting methodology is exemplified using an idealized expert system, which illustrates some of the challenges faced in real-world applications of PPNs

Permutation entropy and its main biomedical and econophysics applications: a review

Entropy is a powerful tool for the analysis of time series, as it allows describing the probability distributions of the possible state of a system, and therefore the information encoded in it. Nevertheless, important information may be codified also in the temporal dynamics, an aspect which is not usually taken into account. The idea of calculating entropy based on permutation patterns (that is, permutations defined by the order relations among values of a time series) has received a lot of attention in the last years, especially for the understanding of complex and chaotic systems. Permutation entropy directly accounts for the temporal information contained in the time series; furthermore, it has the quality of simplicity, robustness and very low computational cost. To celebrate the tenth anniversary of the original work, here we analyze the theoretical foundations of the permutation entropy, as well as the main recent applications to the analysis of economical markets and to the understanding of biomedical systems.Facultad de Ingenierí

The Augmented Jump Chain -- a sparse representation of time-dependent Markov jump processes

Modern methods of simulating molecular systems are based on the mathematical theory of Markov operators with a focus on autonomous equilibrated systems. However, non-autonomous physical systems or non-autonomous simulation processes are becoming more and more important. We present a representation of non-autonomous Markov jump processes as autonomous Markov chains on space-time. Augmenting the spatial information of the embedded Markov chain by the temporal information of the associated jump times, we derive the so-called augmented jump chain. The augmented jump chain inherits the sparseness of the infinitesimal generator of the original process and therefore provides a useful tool for studying time-dependent dynamics even in high dimensions. We furthermore discuss possible generalizations and applications to the computation of committor functions and coherent sets in the non-autonomous setting. After deriving the theoretical foundations we illustrate the concepts with a proof-of-concept Galerkin discretization of the transfer operator of the augmented jump chain applied to simple examples.Comment: 22 pages, 8 figure

The Augmented Jump Chain

Modern methods of simulating molecular systems are based on the mathematical theory of Markov operators with a focus on autonomous equilibrated systems. However, non‐autonomous physical systems or non‐autonomous simulation processes are becoming more and more important. A representation of non‐autonomous Markov jump processes is presented as autonomous Markov chains on space‐time. Augmenting the spatial information of the embedded Markov chain by the temporal information of the associated jump times, the so‐called augmented jump chain is derived. The augmented jump chain inherits the sparseness of the infinitesimal generator of the original process and therefore provides a useful tool for studying time‐dependent dynamics even in high dimensions. Furthermore, possible generalizations and applications to the computation of committor functions and coherent sets in the non‐autonomous setting are discussed. After deriving the theoretical foundations, the concepts with a proof‐of‐concept Galerkin discretization of the transfer operator of the augmented jump chain applied to simple examples are illustrated