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Register a new userEfficient Stochastic Simulations of Complex Reaction Networks on Surfaces
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Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are negligible and the reaction rates can be evaluated using rate equations, which are based on the mean-field approximation. However, in case that the surface is partitioned into a large number of disconnected microscopic domains, the number of reactants in each domain becomes small and it strongly fluctuates. This is, in fact, the situation in the interstellar medium, where some crucial reactions take place on the surfaces of microscopic dust grains. In this case rate equations fail and the simulation of surface reactions requires stochastic methods such as the master equation. However, in the case of complex reaction networks, the master equation becomes infeasible because the number of equations proliferates exponentially. To solve this problem, we introduce a stochastic method based on moment equations. In this method the number of equations is dramatically reduced to just one equation for each reactive species and one equation for each reaction. Moreover, the equations can be easily constructed using a diagrammatic approach. We demonstrate the method for a set of astrophysically relevant networks of increasing complexity. It is expected to be applicable in many other contexts in which problems that exhibit analogous structure appear, such as surface catalysis in nanoscale systems, aerosol chemistry in stratospheric clouds and genetic networks in cells.
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Homochirality, i.e. the dominance across all living matter of one enantiomer over the other among chiral molecules, is thought to be a key step in the emergence of life. Building on ideas put forward by Frank and many others, we proposed recently one such mechanism in G. Laurent et al., PNAS (2021) based on the properties of large out of equilibrium chemical networks. We showed that in such networks, a phase transition towards an homochiral state is likely to occur as the number of chiral species in the system becomes large or as the amount of free energy injected into the system increases. This paper aims at clarifying some important points in that scenario, not covered by our previous work. We first analyze the various conventions used to measure chirality, introduce the notion of chiral symmetry of a network, and study its implications regarding the relative chiral signs adopted by different groups of molecules. We then propose a generalization of Franks model for large chemical networks, which we characterize completely using methods of random matrices. This analysis can be extended to sparse networks, which shows that the emergence of homochirality is a robust transition.
We study the extreme events taking place on complex networks. The transport on networks is modelled using random walks and we compute the probability for the occurance and recurrence of extreme events on the network. We show that the nodes with smaller number of links are more prone to extreme events than the ones with larger number of links. We obtain analytical estimates and verify them with numerical simulations. They are shown to be robust even when random walkers follow shortest path on the network. The results suggest a revision of design principles and can be used as an input for designing the nodes of a network so as to smoothly handle an extreme event.
As a fundamental structural transition in complex networks, core percolation is related to a wide range of important problems. Yet, previous theoretical studies of core percolation have been focusing on the classical ErdH{o}s-Renyi random networks with Poisson degree distribution, which are quite unlike many real-world networks with scale-free or fat-tailed degree distributions. Here we show that core percolation can be analytically studied for complex networks with arbitrary degree distributions. We derive the condition for core percolation and find that purely scale-free networks have no core for any degree exponents. We show that for undirected networks if core percolation occurs then it is always continuous while for directed networks it becomes discontinuous when the in- and out-degree distributions are different. We also apply our theory to real-world directed networks and find, surprisingly, that they often have much larger core sizes as compared to random models. These findings would help us better understand the interesting interplay between the structural and dynamical properties of complex networks.
The position of a reaction front, propagating into a metastable state, fluctuates because of the shot noise of reactions and diffusion. A recent theory [B. Meerson, P.V. Sasorov, and Y. Kaplan, Phys. Rev. E 84, 011147 (2011)] gave a closed analytic expression for the front diffusion coefficient in the weak noise limit. Here we test this theory in stochastic simulations involving reacting and diffusing particles on a one-dimensional lattice. We also investigate a small noise-induced systematic shift of the front velocity compared to the prediction from the spatially continuous deterministic reaction-diffusion equation.
The probability distribution describing the state of a Stochastic Reaction Network evolves according to the Chemical Master Equation (CME). It is common to estimated its solution using Monte Carlo methods such as the Stochastic Simulation Algorithm (SSA). In many cases these simulations can take an impractical amount of computational time. Therefore many methods have been developed that approximate the Stochastic Process underlying the Chemical Master Equation. Prominent strategies are Hybrid Models that regard the firing of some reaction channels as being continuous and applying the quasi-stationary assumption to approximate the dynamics of fast subnetworks. However as the dynamics of a Stochastic Reaction Network changes with time these approximations might have to be adapted during the simulation. We develop a method that approximates the solution of a CME by automatically partitioning the reaction dynamics into discrete/continuous components and applying the quasi-stationary assumption on identifiable fast subnetworks. Our method does not require user intervention and it adapts to exploit the changing timescale separation between reactions and/or changing magnitudes of copy numbers of constituent species. We demonstrate the efficiency of the proposed method by considering examples from Systems Biology and showing that very good approximations to the exact probability distributions can be achieved in significantly less computational time.
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