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The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a low order Markov chain of order up to $r=6$. Although detailed balance seems to hold at the level of purine-pyrimidine notation it fails when all four basepairs are considered, suggesting spatial asymmetry and irreversibility. Furthermore, the block entropy does not increase linearly with the block size, reflecting the long range nature of the correlations in the human genomic sequences. To probe locally the spatial structure of the chain we study the exit distances from a specific symbol, the distribution of recurrence distances and the Hurst exponent, all of which show power law tails and long range characteristics. These results suggest that human DNA can be viewed as a non-equilibrium structure maintained in its state through interactions with a constantly changing environment. Based solely on the exit distance distribution accounting for the nonequilibrium statistics and using the Monte Carlo rejection sampling method we construct a model DNA sequence. This method allows to keep all long range and short range statistical characteristics of the original sequence. The model sequence presents the same characteristic exponents as the natural DNA but fails to capture point-to-point details.

The role of dimensionality (Euclidean versus fractal), spatial extent, boundary effects and system topology on the efficiency of diffusion-reaction processes involving two simultaneously-diffusing reactants is analyzed. We present numerically-exact values for the mean time to reaction, as gauged by the mean walklength before reactive encounter, obtained via application of the theory of finite Markov processes, and via Monte Carlo simulation. As a general rule, we conclude that for sufficiently large systems, the efficiency of diffusion-reaction processes involving two synchronously diffusing reactants (two-walker case) relative to processes in which one reactant of a pair is anchored at some point in the reaction space (one walker plus trap case) is higher, and is enhanced the lower the dimensionality of the system. This differential efficiency becomes larger with increasing system size and, for periodic systems, its asymptotic value may depend on the parity of the lattice. Imposing confining boundaries on the system enhances the differential efficiency relative to the periodic case, while decreasing the absolute efficiencies of both two-walker and one walker plus trap processes. Analytic arguments are presented to provide a rationale for the results obtained. The insights afforded by the analysis to the design of heterogeneous catalyst systems are also discussed., Comment: 15 pages, 8 figures, uses revtex4, accepted for publication in Physica A

An analytical method based on the classical ruin problem is developed to compute the mean reaction time between two walkers undergoing a generalized random walk on a 1d lattice. At each time step, either both walkers diffuse simultaneously with probability $p$ (synchronous event) or one of them diffuses while the other remains immobile with complementary probability (asynchronous event). Reaction takes place through same site occupation or position exchange. We study the influence of the degree of synchronicity $p$ of the walkers and the lattice size $N$ on the global reaction's efficiency. For odd $N$, the purely synchronous case ($p=1$) is always the most effective one, while for even $N$, the encounter time is minimized by a combination of synchronous and asynchronous events. This new parity effect is fully confirmed by Monte Carlo simulations on 1d lattices as well as for 2d and 3d lattices. In contrast, the 1d continuum approximation valid for sufficiently large lattices predicts a monotonic increase of the efficiency as a function of $p$. The relevance of the model for several research areas is briefly discussed., Comment: 21 pages (including 12 figures and 4 tables), uses revtex4.cls, accepted for publication in Physica A

We study the effect of fractal initial conditions in closed reactive systems in the cases of both mobile and immobile reactants. For the reaction $A+A\to A$, in the absence of diffusion, the mean number of particles $A$ is shown to decay exponentially to a steady state which depends on the details of the initial conditions. The nature of this dependence is demonstrated both analytically and numerically. In contrast, when diffusion is incorporated, it is shown that the mean number of particles $$ decays asymptotically as $t^{-d_f/2}$, the memory of the initial conditions being now carried by the dynamical power law exponent. The latter is fully determined by the fractal dimension $d_f$ of the initial conditions., Comment: 7 pages, 2 figures, uses epl.cls

We show that simple diffusive systems, such as the Lorentz gas and multibaker maps are perfectly compatible with the laws of irreversible thermodynamics, despite the fact that the moving particles, or their equivalents, in these models do not interact with each other, and that the dynamics takes place in low-dimensional phase spaces. The interaction of moving particles with scatterers provides the dynamical mechanism responsible for an approach to equilibrium, under appropriate conditions. This analysis provides a refutation of the criticisms expressed recently by Cohen and Rondoni [Physica A 306 (2002) 117-128]., Comment: 21 pages, 3 figures

We present a stochastic, time-discrete boolean model which mimics the mesoscopic dynamics of the desorption reactions $A+A\to A+S$ and $A+A\to S+S$ in a 1D lattice. In the continuous-time limit, we derive a hierarchy of dynamical equations for the subset of moments involving contiguous lattice sites. The solution of the hierarchy allows to compute the exact dynamics of the mean coverage for both microscopic and coarse-grained initial conditions, which turn out to be different from the mean field predictions. The evolution equations for the mean coverage and the second order moments are shown to be equivalent to those provided by a time-continuous Master equation. The important role of higher order fluctuations is brought out by the failure of a truncation scheme retaining only two-particle fluctuation correlations., Comment: 30 pages, 9 figures

We use a boolean cellular automaton model to describe the diffusion limited dynamics of the irreversible reaction A+A->A+S on a 1D lattice. We derive a set of equations for the dynamics of the empty interval probabilities from which explicit expressions for the particle concentration and the two-point correlation can be obtained. It is shown that the long time dynamics is in agreement with the off-lattice solution. The early time behavior, however, predicts a slower decay of the concentration., Comment: 10 pages. Accepted for publication in the June 2000 issue of the JSP (Volume 99, Issue 5/6)

We present a novel mechanism for thermalizing a system of particles in equilibrium and nonequilibrium situations, based on specifically modeling energy transfer at the boundaries via a microscopic collision process. We apply our method to the periodic Lorentz gas, where a point particle moves diffusively through an ensemble of hard disks arranged on a triangular lattice. First, collision rules are defined for this system in thermal equilibrium. They determine the velocity of the moving particle such that the system is deterministic, time reversible, and microcanonical. These collision rules can systematically be adapted to the case where one associates arbitrarily many degrees of freedom to the disk, which here acts as a boundary. Subsequently, the system is investigated in nonequilibrium situations by applying an external field. We show that in the limit where the disk is endowed by infinitely many degrees of freedom it acts as a thermal reservoir yielding a well-defined nonequilibrium steady state. The characteristic properties of this state, as obtained from computer simulations, are finally compared to the ones of the so-called Gaussian thermostated driven Lorentz gas., Comment: 13 pages (revtex) with 10 figures (encapsulated postscript)

We apply a recently proposed novel thermostating mechanism to an interacting many-particle system where the bulk particles are moving according to Hamiltonian dynamics. At the boundaries the system is thermalized by deterministic and time-reversible scattering. We show how this scattering mechanism can be related to stochastic boundary conditions. We subsequently simulate nonequilibrium steady states associated to thermal conduction and shear flow for a hard disk fluid. The bulk behavior of the model is studied by comparing the transport coefficients obtained from computer simulations to theoretical results. Furthermore, thermodynamic entropy production and exponential phase-space contraction rates in the stationary nonequilibrium states are calculated showing that in general these quantities do not agree., Comment: 16 pages (revtex) with 9 figures (postscript)

We present a mechanism for thermalizing a moving particle by microscopic deterministic scattering. As an example, we consider the periodic Lorentz gas. We modify the collision rules by including energy transfer between particle and scatterer such that the scatterer mimics a thermal reservoir with arbitrarily many degrees of freedom. The complete system is deterministic, time-reversible, and provides a microcanonical density in equilibrium. In the limit of the disk representing infinitely many degrees of freedom and by applying an electric field the system goes into a nonequilibrium steady state., Comment: 4 pages (revtex) with 4 figures (postscript)