Reversible reaction-diffusion systems display anomalous dynamics characterized by a power-law relaxation toward stationarity. In this paper we study in the aging regime the nonequilibrium dynamical properties of some model systems with reversible reactions. Starting from the exact Langevin equations describing these models, we derive expressions for two-time correlation and autoresponse functions and obtain a simple aging behavior for these quantities. The autoresponse function is thereby found to depend on the specific nature of the chosen perturbation of the system.
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…
We study long-time properties of reversible reaction-diffusion systems of type A + B <-> C by means of perturbation expansion in powers of 1/t (inverse of time). For the case of equal diffusion coefficients we present exact formulas for the asymptotic forms of reactant concentrations and a complete, recursive expression for an arbitrary term of the expansions. Taking an appropriate limit we show that by studying reversible reactions one can obtain "singular" solutions typical of irreversible reactions.
We develop an effective numerical method of studying large-time properties of reversible reaction-diffusion systems of type A + B <-> C with initially separated reactants. Using it we find that there are three types of asymptotic reaction zones. In particular we show that the reaction rate can be locally negative and concentrations of species A and B can be nonmonotonic functions of the space coordinate x, locally significantly exceeding their initial values.
Brownian dynamics is a popular fine-grained method for simulating systems of interacting particles, such as chemical reactions. Though the method is simple to simulate, it is generally assumed that the dynamics is impossible to solve exactly and analytically, aside from some trivial systems. We here give the first exact analytical solution to a non-trivial Brownian dynamics system: the reaction $A+B\xrightleftharpoons[]{}C$ in equilibrium in one-dimensional periodic space. The solution is a function of the particles' diffusion coefficients, radii, length of space and unbinding distance.
Slowing down of the relaxation of the fluctuations around equilibrium is investigated both by stochastic simulations and by analysis of Master equation of reversible reaction networks consisting of resources and the corresponding products that work as catalysts. As the number of molecules $N$ is decreased, the relaxation time to equilibrium is prolonged due to the deficiency of catalysts, as demonstrated by the amplification compared to that by the continuum limit. This amplification ratio of the relaxation time is represented by a scaling function as $h = N \exp(-βV)$, and it becomes prominen…
The classical models for irreversible diffusion-influenced reactions can be derived by introducing absorbing boundary conditions to over-damped continuous Brownian motion (BM) theory. As there is a clear corresponding stochastic process, the mathematical description takes both Kolmogorov forward equation for the evolution of the probability distribution function and the stochastic sample trajectories. This dual description is a fundamental characteristic of stochastic processes and allows simple particle based simulations to accurately match the expected statistical behavior. However, in the t…
On example of diffusion-limited reversible $A+A \rightleftharpoons B$ reactions we re-examine two fundamental concepts of classical chemical kinetics - the notion of "Chemical Equilibrium" and the "Law of Mass Action". We consider a general model with distance-dependent reaction rates, such that any pair of $A$ particles, performing standard random walks on sites of a $d$-dimensional lattice and being at a distance $μ$ apart of each other at time moment $t$, may associate forming a $B$ particle at the rate $k_+(μ)$. In turn, any randomly moving $B$ particle may spontaneously dissociate at the …
The reversible reactions A+A<=>C and A+B<=>C are investigated. From the exact Langevin equations describing our model, we set up a systematic approximation scheme to compute the approach of the density of C particles to its equilibrium value. We show that for sufficiently long time t, this approach takes the form of a power law At^(-d/2), for any dimension d. The amplitude A is also computed exactly, but is expected to be model dependent. For uncorrelated initial conditions, the C density turns out to be a monotonic time function. The cases of correlated initial conditions and unequal diffusio…
We investigate reversible diffusion-influenced reactions of an isolated pair in two dimensions. To this end, we employ convolution relations that permit deriving the survival probability of the reversible reaction directly in terms of the survival probability of the irreversible reaction. Furthermore, we make use of the mean reaction time approximation to write the irreversible survival probability in restricted spaces as a single exponential. In this way, we obtain exact and approximative expressions in the time domain for the reversible survival probability for three different two dimensiona…
This paper concludes a three-Part series on the limits the laws of physics place on the sustained performance of reversible computers. Part I concerned aggregate performance in terms of computational operations per unit time, but neglected to consider interactions among computational sub-units or between computational sub-units and shared resources such as memory or chemical species. Part II extended the analysis to consider the former set of interactions. In this Part we extend the analysis to consider the latter set, with a particular focus on resource distribution in the first half. It is f…
We study diffusion of particles on the surface of a sphere toward a partially reactive circular target with partly reversible binding kinetics. We solve the coupled diffusion-reaction equations and obtain the exact expressions for the time-dependent concentration of particles and the total diffusive flux. Explicit asymptotic formulas are derived in the small target limit. This study reveals the strong effects of reversible binding kinetics onto diffusion-mediated reactions that may be relevant for many biochemical reactions on cell membranes.
The reversible A <-> B reaction-diffusion process, when species A and B are initially mixed and diffuse with different diffusion coefficients, is investigated using the boundary layer function method. It is assumed that the ratio of the characteristic time of the reaction to the characteristic time of diffusion is taken as a small parameter of the task. It was shown that diffusion-reaction process can be considered as a quasi-equilibrium process. Despite this fact the contribution of the reaction in changes of the species concentration is comparable with the diffusion contributions. Moreover t…
The validity of two fundamental concepts of classical chemical kinetics - the notion of "Chemical Equilibrium" and the "Law of Mass Action" - are re-examined for reversible \textit{diffusion-limited} reactions (DLR), as exemplified here by association/dissociation $A+A \rightleftharpoons B$ reactions. We consider a general model of long-ranged reactions, such that any pair of $A$ particles, separated by distance $μ$, may react with probability $ω_+(μ)$, and any $B$ may dissociate with probability $ω_-(λ)$ into a geminate pair of $A$s separated by distance $λ$. Within an exact analytical approa…
Many out of equilibrium phenomena, such as diffusion-limited reactions or target search processes, are controlled by first-passage events. So far the general determination of the mean first-passage time (FPT) to a target in confinement has left aside aging processes, involved in contexts as varied as glassy dynamics, tracer diffusion in biological membranes or transport of cold atoms in optical lattices. Here we consider general non-Markovian scale-invariant processes in arbitrary dimension, displaying aging, and demonstrate that all the moments of the FPT obey universal scalings with the conf…
For many real physico-chemical complex systems detailed mechanism includes both reversible and irreversible reactions. Such systems are typical in homogeneous combustion and heterogeneous catalytic oxidation. Most complex enzyme reactions include irreversible steps. The classical thermodynamics has no limit for irreversible reactions whereas the kinetic equations may have such a limit. We represent the systems with irreversible reactions as the limits of the fully reversible systems when some of the equilibrium concentrations tend to zero. The structure of the limit reaction system crucially d…
The principle of detailed balance states that in equilibrium each elementary process is equilibrated by its reverse process. For many real physico-chemical complex systems (e.g. homogeneous combustion, heterogeneous catalytic oxidation, most enzyme reactions etc), detailed mechanisms include both reversible and irreversible reactions. In this case, the principle of detailed balance cannot be applied directly. We represent irreversible reactions as limits of reversible steps and obtain the principle of detailed balance for complex mechanisms with some irreversible elementary processes. We prove…
We analyze from the renormalization group perspective a universality class of reaction-diffusion systems with absorbing states. It describes models where the vacuum state is not accessible, as the set of reactions $2 A \to A$ together with creation processes of the form $A \to n A$ with $n \geq 2$. This class includes the (exactly solvable in one-dimension) {\it reversible} model $2 A \leftrightarrow A$ as a particular example, as well as many other {\it non-reversible} reactions, proving that reversibility is not the main feature of this class as previously thought. By using field theoretical…
Chemical reaction systems operating in nonequilibrium open-system states arise in a great number of contexts, including the study of living organisms, in which chemical reactions, in general, are far from equilibrium. Here we introduce a theorem that relates forward and re-verse fluxes and free energy for any chemical process operating in a steady state. This rela-tionship, which is a generalization of equilibrium conditions to the case of a chemical process occurring in a nonequilibrium steady state, provides a novel equivalent definition for chemical reaction free energy. In addition, it is …
Certain biochemical reactions can only be triggered after binding of a sufficient number of particles to a specific target region such as an enzyme or a protein sensor. We investigate the distribution of the reaction time, i.e., the first instance when all independently diffusing particles are bound to the target. When each particle binds irreversibly, this is equivalent to the first-passage time of the slowest (last) particle. In turn, reversible binding to the target renders the problem much more challenging and drastically changes the distribution of the reaction time. We derive the exact s…
We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by systems lacking selective interactions. The scales at which the functional properties of these materials emerge are difficult to model, especially in the reversible regime where such properties result from many binding/unbinding events. This difficulty is related to large entropic barriers associated with the formation of intra-molecular loops. In this work …
Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but also allows fluctuation measurements which may reveal the structure and dynamics of the underlying biochemical network. Here, we study non-equilibrium reaction cycles, such as the mechanochemical cycle of molecular motors, the phosphorylation cycle of circadian clock proteins, or the transition state cycle of enzymes. Fluctuations in such cycles may be measured using either of two classical definitions of the randomness parameter, which we show to be equivalent in general mic…
The master equation for the reversible reaction A+A <--> 0 is considered in Poisson representation, where it is equivalent to a Langevin equation with imaginary noise for a complex stochastic variable ϕ. Such Langevin equations appear quite generally in field-theoretic treatments of reaction-diffusion problems. For this example we study the probability flow in the complex ϕplane both analytically and by simulation. We show that this flow has various curious features that must be expected to occur similarly in other Langevin equations associated with reaction-diffusion problems.
We study front propagation in the reversible reaction-diffusion system A + A <-> A on a 1-d lattice. Extending the idea of leading particle in studying the motion of the front we write a master equation in the stochastically moving frame attached to this particle. This approach provides a systematic way to improve on estimates of front speed obtained earlier. We also find that the leading particle performs a correlated random walk and this correlation needs to be taken into account to get correct value of the front diffusion coefficient.
Synaptic transmission between neurons is governed by a cascade of stochastic reaction-diffusion events that lead to calcium-induced vesicle release of neurotransmitter. Since experimental measurements of such systems are challenging due their nanometer and sub-millisecond scale, numerical simulations remain the principal tool for studying calcium dependent synaptic vesicle fusion, despite limitations of time-consuming calculations. In this paper we develop an analytical solution to rapidly explore dynamical stochastic reaction-diffusion problems, based on first-passage times. This is the first…
Following recent experiments on power law blinking behavior of single nano-crystals, we calculate two-time intensity correlation functions <I(t)I(t+t')> for these systems. We use a simple two state (on and off) stochastic model to describe the dynamics. We classify possible behaviors of the correlation function and show that aging, e.g., dependence of the correlation function on age of process t, is obtained for classes of the on time and off time distributions relevant to experimental situation. Analytical asymptotic scaling behaviors of the intensity correlation in the double time t and t' d…
Catalytically active macromolecules are envisioned as key building blocks in development of artificial nanomotors. However, theory and experiments report conflicting findings regarding their dynamics. The lack of consensus is mostly caused by a limited understanding of specifics of self-propulsion mechanisms at the nanoscale. Here, we study a generic model of a self-propelled nanoparticle that does not rely on a particular mechanism. Instead, its main assumption is the fundamental symmetry of microscopic dynamics of chemical reactions: the principle of microscopic reversibility. Significant co…
We rigorously analyze the low temperature non-equilibrium dynamics of the East model, a special example of a one dimensional oriented kinetically constrained particle model, when the initial distribution is different from the reversible one and for times much smaller than the global relaxation time. This setting has been intensively studied in the physics literature to analyze the slow dynamics which follows a sudden quench from the liquid to the glass phase. In the limit of zero temperature (i.e. a vanishing density of vacancies) and for initial distributions such that the vacancies form a re…
We examine numerically different zero-dimensional reaction-diffusion processes as candidate toy models for high-energy QCD evolution. Of the models examined -- Reggeon Field Theory, Directed Percolation and Reversible Processes -- only the latter shows the behaviour commonly expected, namely an increase of the scattering amplitude with increasing rapidity. Further, we find that increasing recombination terms, quantum loops and the heuristic inclusion of a running of the couplings, generically slow down the evolution.
