Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction rates can be evaluated using rate equations. However, many physical systems are partitioned into microscopic domains, where the number of molecules in each domain is small and fluctuations are strong. Under these conditions, the simulation of reaction networks requires stochastic methods such as direct integration of the master equation. However, direct integration of the master equation is infeasible for complex networks, because the number of equations proliferates as the number of reactive species increases. Recently, the multiplane method, which provides a dramatic reduction in the number of equations, was introduced [A. Lipshtat and O. Biham, Phys. Rev. Lett. 93, 170601 (2004)]. The reduction is achieved by breaking the network into a set of maximal fully connected sub-networks (maximal cliques). Lower-dimensional master equations are constructed for the marginal probability distributions associated with the cliques, with suitable couplings between them. In this paper we test the multiplane method and examine its applicability. We show that the method is accurate in the limit of small domains, where fluctuations are strong. It thus provides an efficient framework for the stochastic simulation of complex reaction networks with strong fluctuations, for which rate equations fail and direct integration of the master equation is infeasible. The method also applies in the case of large domains, where it converges to the rate equation results.
A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated tempering were performed in order to study the intramolecular proton transfer reaction of malonaldehyde in aqueous solution. Conformational sampling in reaction coordinate space can be easily enhanced with this method, and the free energy along a reaction coordinate can be calculated accurately. Moreover, the simulated tempering umbrella sampling provides trajectory…
Reaction-diffusion systems with reversible reactions generically display power-law relaxation towards chemical equilibrium. In this work we investigate through numerical simulations aging processes that characterize the non-equilibrium relaxation. Studying a model which excludes multiple occupancy of a site, we find that the scaling behavior of the two-time correlation and response functions are similar to that discovered previously in an exactly solvable version with no restrictions on the occupation numbers. Especially, we find that the scaling of the response depends on whether the perturba…
These are lecture notes of a course that I gave to people doing research for their Ph.D. thesis in theoretical chemistry or spectroscopy. The course was given on December 9-13, 2002, in Han-sur-Lesse, Belgium. The lecture notes start with the lattice-gas model that is used to describe the reactions on a surface. I derive a Master Equation, which gives the evolution of this model. The Master Equation contains transition probabilities (or rate constants) for the reactions. I show how these transition probabilities can be obtained from quantum chemical calculations or from experiments. The Master…
Reactions at a strongly segregated interface of a symmetric binary polymer blend are investigated via Monte Carlo simulations. End functionalized homopolymers of different species interact at the interface instantaneously and irreversibly to form diblock copolymers. The simulations, in the framework of the bond fluctuation model, determine the time dependence of the copolymer production in the initial and intermediate time regime for small reactant concentration $ρ_0 R_g^3=0.163 ... 0.0406$. The results are compared to recent theories and simulation data of a simple reaction diffusion model. F…
An efficient Monte Carlo simulation method for bosonic reaction-diffusion systems which are mainly used in the renormalization group (RG) study is proposed. Using this method, one dimensional bosonic single species annihilation model is studied and, in turn, the results are compared with RG calculations. The numerical data are consistent with RG predictions. As a second application, a bosonic variant of the pair contact process with diffusion (PCPD) is simulated and shown to share the critical behavior with the PCPD. The invariance under the Galilean transformation of this boson model is also …
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 rea…
We study the reaction front for the process A+B -> C in which the reagents move subdiffusively. Our theoretical description is based on a fractional reaction-subdiffusion equation in which both the motion and the reaction terms are affected by the subdiffusive character of the process. We design numerical simulations to check our theoretical results, describing the simulations in some detail because the rules necessarily differ in important respects from those used in diffusive processes. Comparisons between theory and simulations are on the whole favorable, with the most difficult quantities …
We created an efficient algorithm suitable for graphics processing units (GPUs) to perform Monte Carlo simulations of a subset of reaction-diffusion models. The algorithm uses techniques that are specific to GPU programming, and combines these with the multispin technique known from CPU programming to create one of the fastest algorithms for reaction-diffusion models. As an example, the algorithm is applied to the pair contact process with diffusion (PCPD). Compared to a simple algorithm on the CPU, our GPU algorithm is approximately 4000 times faster. If we compare the performance of the GPU …
We analyze the two-species reaction-diffusion system including trapping reaction $A + B \to A$ as well as coagulation/annihilation reactions $A + A \to (A,0)$ where particles of both species are performing Lévy flights with control parameter $0 < σ< 2$, known to lead to superdiffusive behaviour. The density, as well as the correlation function for target particles $B$ in such systems, are known to scale with nontrivial universal exponents at space dimension $d \leq d_{c}$. Applying the renormalization group formalism we calculate these exponents in a case of superdiffusion below the critical d…
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 m…
Using the Monte Carlo simulation method for bosonic reaction-diffusion systems introduced recently [S.-C. Park, Phys. Rev. E {\bf 72}, 036111 (2005)], one dimensional bosonic models are studied and compared to the corresponding Langevin equations derived from the coherent state path integral formalism. For the single species annihilation model, the exact asymptotic form of the correlation functions is conjectured and the full equivalence of the (discrete variable) master equation and the (continuous variable) Langevin equation is confirmed numerically. We also investigate the cyclically couple…
We study a variation of the trapping reaction, A+B->A, in which both the traps (A) and the particles (B) undergo diffusion, and the traps upon meeting react according to A+A->0 or A. This two-species reaction-diffusion system is known to exhibit a non-trivial decay exponent for the B particles, and recently renormalization group methods have predicted an anomalous dimension in the BB correlation function. To test these predictions we develop a computer simulation method, motivated by the technique of Mehra and Grassberger, that determines the complete probability distribution of the B particle…
A highly efficient formulation of moment equations for stochastic reaction networks is introduced. It is based on a set of binomial moments that capture the combinatorics of the reaction processes. The resulting set of equations can be easily runcated to include moments up to any desired order. The number of equations is dramatically reduced compared to the master equation. This formulation enables the simulation of complex reaction networks, involving a large number of reactive species much beyond the feasibility limit of any existing method. It provides an equation-based paradigm to the anal…
In this paper, we address the modeling issues of cell movement and division with a special focus on the phenomenon of volume exclusion in a lattice-based, exact stochastic simulation framework. We propose a new exact method, called Reduced Rate Method -- RRM, that is substantially quicker than the previously used exclusion method, for large number of cells. In addition, we introduce three novel reaction types: the contact-inhibited, the contact-promoted, and the spontaneous reactions. To the best of our knowledge, these reaction types have not been taken into account in lattice-based stochasti…
Understanding kinetics including reaction pathways and associated transition rates is an important yet difficult problem in numerous chemical and biological systems especially in situations with multiple competing pathways. When these high-dimensional systems are projected on low-dimensional coordinates, which are often needed for enhanced sampling or for interpretation of simulations and experiments, one can end up losing the kinetic connectivity of the underlying high-dimensional landscape. Thus in the low-dimensional projection metastable states might appear closer or further than they actu…
In recent years, several particle-based stochastic simulation algorithms (PSSA) have been developed to study the spatially resolved dynamics of biochemical networks at a molecular scale. A challenge all these approaches have to address is to allow for simulations at cell-biologically relevant timescales without neither neglecting important spatial and biochemical properties of the simulated system nor introducing ad-hoc assumptions not based on physical principles. Here we describe a PSSA that permits large time steps while still retaining a high degree of accuracy. The approach addresses the …
Diffusion is often accompanied by a reaction or sorption which can induce temperature inhomogeneities. Monte Carlo simulations of Lennard-Jones atoms in zeolite NaCaA are reported with a hot zone presumed to be created by a reaction. Our simulations show that localised hot regions can alter both the kinetic and transport properties. Further, enhancement of the diffusion constant is greater for larger barrier height, a surprising result of considerable significance to many chemical and biological processes. We find an unanticipated coupling between reaction and diffusion due to the presence of …
