Crossover from rate-equation to diffusion-controlled kinetics in two-particle coagulation

Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis

We develop a theoretical approach that uses physiochemical kinetics modelling to describe cell population dynamics upon progression of viral infection in cell culture, which results in cell apoptosis (programmed cell death) and necrosis (direct cell death). Several model parameters necessary for computer simulation were determined by reviewing and analyzing available published experimental data. By comparing experimental data to computer modelling results, we identify the parameters that are the most sensitive to the measured system properties and allow for the best data fitting. Our model allows extraction of parameters from experimental data and also has predictive power. Using the model we describe interesting time-dependent quantities that were not directly measured in the experiment and identify correlations among the fitted parameter values. Numerical simulation of viral infection progression is done by a rate-equation approach resulting in a system of "stiff" equations, which are solved by using a novel variant of the stochastic ensemble modelling approach. The latter was originally developed for coupled chemical reactions.

Quantum Annealing via Environment-Mediated Quantum Diffusion

We show that quantum diffusion near a quantum critical point can provide an efficient mechanism of quantum annealing. It is based on the diffusion-mediated recombination of excitations in open systems far from thermal equilibrium. We find that, for an Ising spin chain coupled to a bosonic bath and driven by a monotonically decreasing transverse field, excitation diffusion sharply slows down below the quantum critical region. This leads to spatial correlations and effective freezing of the excitation density. Still, obtaining an approximate solution of an optimization problem via the diffusion-mediated quantum annealing can be faster than via closed-system quantum annealing or Glauber dynamics.

Analytic solutions for some reaction-diffusion scenarios

Motivated currently by the problem of coalescence of receptor clusters in mast cells in the general subject of immune reactions, and formerly by the investigation of exciton trapping and sensitized luminescence in molecular systems and aggregates, we present analytic expressions for survival probabilities of moving entities undergoing diffusion and reaction on encounter. Results we provide cover several novel situations in simple 1-d systems as well as higher-dimensional counterparts along with a useful compendium of such expressions in chemical physics and allied fields. We also emphasize the importance of the relationship of discrete sink term analysis to continuum boundary condition studies.

Measurement of a reaction-diffusion crossover in exciton-exciton recombination inside carbon nanotubes using femtosecond optical absorption

Exciton-exciton recombination in isolated semiconducting single-walled carbon nanotubes was studied using femtosecond transient absorption. Under sufficient excitation to saturate the optical absorption, we observed an abrupt transition between reaction- and diffusion-limited kinetics, arising from reactions between incoherent localized excitons with a finite probability of ~0.2 per encounter. This represents the first experimental observation of a crossover between classical and critical kinetics in a 1D coalescing random walk, which is a paradigm for the study of nonequilibrium systems.

Phase transition of triplet reaction-diffusion models

The phase transitions classes of reaction-diffusion systems with multiparticle reactions are an open challenging problem. Large scale simulations are applied for the 3A --> 4A, 3A --> 2A and the 3A --> 4A, 3A --> [formula : see text] triplet reaction models with site occupation restriction in one dimension. Static and dynamic mean-field scaling are observed with signs of logarithmic corrections suggesting d(c) = 1 upper critical dimension for this family of models.

Spatial fluctuations and anomalous reaction order in a reactive scheme involving a cooperative full desorption

Anomalous reaction rates have been found in the hydrogen desorption of H-terminated surfaces in semiconductor epitaxy, with a reaction order shifting from two to one, or even taking fractional values. We analyze the issue in terms of a cooperative full desorption (CFD) reaction A+A--k3-->S+S , coupled to an adsorption reaction S--k1-->A and an alternative desorption route A--k2-->S . Steady state properties of the three-step reactive scheme are analyzed in a one-dimensional lattice in the absence of diffusion. Microscopic Monte Carlo simulations show anomalous spatial distributions of reactants in the stationary state: depending on the reaction rate constants of the overall scheme, either a local "aggregation" or a local "dispersion" of A -particles is observed. The CFD reaction itself is well described by a fractional order kinetics that takes into account these anomalies and that depends on the kinetic rate constants of the overall adsorption-desorption reaction mechanism. The problem is addressed with an analytical approach for the active neighborhood of a reactant, which provides a closed expression of the reaction order as a function of the kinetic parameters. This approach is in excellent agreement with numerical simulations. Spatial correlations, as well as fluctuation correlations, are also formalized in terms of the kinetic constants. We discuss the results in the context of the hydrogen evolution reaction on silicon surfaces.

Reaction-controlled diffusion

The dynamics of a coupled two-component nonequilibrium system is examined by means of continuum field theory representing the corresponding master equation. Particles of species A may perform hopping processes only when particles of different type B are present in their environment. Species B is subject to diffusion-limited reactions. If the density of B particles attains a finite asymptotic value (active state), the A species displays normal diffusion. On the other hand, if the B density decays algebraically approximately t(-alpha) at long times (inactive state), the effective attractive A-B interaction is weakened. The combination of B decay and activated A hopping processes gives rise to anomalous diffusion, with mean-square displacement <x-->(A)(t)(2)> approximately t(1-alpha) for alpha<1. Such algebraic subdiffusive behavior ensues for nth-order B annihilation reactions (nB-->) with n>/=3, and n=2 for d<2. The mean-square displacement of the A particles grows only logarithmically with time in the case of B pair annihilation (n=2) and d>/=2 dimensions. For radioactive B decay (n=1), the A particles remain localized. If the A particles may hop spontaneously as well, or if additional random forces are present, the A-B coupling becomes irrelevant, and conventional diffusion is recovered in the long-time limit.

Single species diffusion-influenced reaction A+A-->alphaA: validity of the smoluchowski approach

We investigate the single species diffusion-influenced reaction, A+A-->alphaA with a finite reactivity in all dimensions. The reaction model includes a pure coagulation (alpha=1) or a pure annihilation (alpha=0) model. We apply the hierarchical Smoluchowski approach to study the dimensional aspects of the fluctuation, reactivity, particle size, and alpha(0</=alpha</=1). The theoretical results are compared with those of the Monte Carlo simulations in one, two, and three regular dimensions. The simulation results reveal that the classical Smoluchowski approach is exact in the short time limit in all dimensions and in the long time limit in three dimensions. The hierarchical Smoluchowski approach is found to be numerically exact at all times in two and three dimensions. A numerical method to obtain the exact result of the annihilation for a finite reactivity in one dimension is presented. We also propose a quite accurate analytic solution for an arbitrary alpha for the infinite reactivity in one dimension.

Early stages of homopolymer collapse

Interest in the protein folding problem has motivated a wide range of theoretical and experimental studies of the kinetics of the collapse of flexible homopolymers. In this paper, a phenomenological model is proposed for the kinetics of the early stages of homopolymer collapse following a quench from temperatures above to below the straight theta temperature. In the first stage, nascent droplets of the dense phase are formed, with little effect on the configurations of the bridges that join them. The droplets then grow by accreting monomers from the bridges, thus causing the bridges to stretch. During these two stages, the overall dimensions of the chain decrease only weakly. Further growth of the droplets is accomplished by the shortening of the bridges, which causes the shrinking of the overall dimensions of the chain. The characteristic times of the three stages scale as N0, N(1/5), and N(6/5), respectively, where N is the degree of polymerization of the chain.