Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

Geometric Universality of Currents

We discuss a non-equilibrium statistical system on a graph or network. Identical particles are injected, interact with each other, traverse, and leave the graph in a stochastic manner described in terms of Poisson rates, possibly dependent on time and instantaneous occupation numbers at the nodes of the graph. We show that under the assumption of constancy of the relative rates, the system demonstrates a profound statistical symmetry, resulting in geometric universality of the statistics of the particle currents. This phenomenon applies broadly to many man-made and natural open stochastic systems, such as queuing of packages over the internet, transport of electrons and quasi-particles in mesoscopic systems, and chains of reactions in bio-chemical networks. We illustrate the utility of our general approach using two enabling examples from the two latter disciplines.Comment: 15 pages, 5 figure

Ultracold Chemistry and its Reaction Kinetics

We study the reaction kinetics of chemical processes occurring in the ultracold regime and systematically investigate their dynamics. Quantum entanglement is found to play a key role in driving an ultracold reaction towards a dynamical equilibrium. In case of multiple concurrent reactions Hamiltonian chaos dominates the phase space dynamics in the mean field approximation.Comment: 15 pages, 5 figure

Kinetic Intersections as a Source of Information on Rate Coefficients

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Dissipation in noisy chemical networks: The role of deficiency

We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known to determine the possibility of complex behavior such as multistability and oscillations, is shown to also characterize the entropic balance. In particular, only when deficiency is zero does the average stochastic dissipation rate equal that of the corresponding deterministic model, where correlations are disregarded. In fact, dissipation can be reduced by the effect of noise, as occurs in a toy model of metabolism that we employ to illustrate our findings. This phenomenon highlights that there is a close interplay between deficiency and the activation of new dissipative pathways at low molecule numbers.Comment: 10 Pages, 6 figure

Symmetry and the thermodynamics of currents in open quantum systems

Symmetry is a powerful concept in physics, and its recent application to understand nonequilibrium behavior is providing deep insights and groundbreaking exact results. Here we show how to harness symmetry to control transport and statistics in open quantum systems. Such control is enabled by a first-order-type dynamic phase transition in current statistics and the associated coexistence of different transport channels (or nonequilibrium steady states) classified by symmetry. Microreversibility then ensues, via the Gallavotti-Cohen fluctuation theorem, a twin dynamic phase transition for rare current fluctuations. Interestingly, the symmetry present in the initial state is spontaneously broken at the fluctuating level, where the quantum system selects the symmetry sector that maximally facilitates a given fluctuation. We illustrate these results in a qubit network model motivated by the problem of coherent energy harvesting in photosynthetic complexes, and introduce the concept of a symmetry-controlled quantum thermal switch, suggesting symmetry-based design strategies for quantum devices with controllable transport properties.Comment: 12 pages, 6 figure