arXiv subjects
Publications and source records attributed to Ofer Biham.
The standard analysis of reaction networks based on deterministic rate equations fails in confined geometries, commonly encountered in fields such as astrochemistry, thin film growth and cell biology. In these systems the small reactant population implies anomalous behavior of reaction rates, which can be accounted for only by following the full distribution of reactant numbers.
We discuss recent developments in the modeling of negative autoregulated genetic networks. In particular, we consider the temporal evolution of the population of mRNA and proteins in simple networks using rate equations. In the limit of low copy numbers, fluctuation effects become significant and more adequate modeling is then achieved using the master equation formalism. The analogy between regulatory gene networks and chemical reaction networks on dust grains in the interstellar medium is discussed. The analysis and simulation of complex reaction networks are also considered.
Molecular hydrogen has an important role in the early stages of star formation as well as in the production of many other molecules that have been detected in the interstellar medium. In this review we show that it is now possible to study the formation of molecular hydrogen in simulated astrophysical environments. Since the formation of molecular hydrogen is believed to take place on dust grains, we show that surface science techniques such as thermal desorption and time-of-flight can be used to measure the recombination efficiency, the kinetics of reaction and the dynamics of desorption. The analysis of the experimental results using rate equations gives useful insight on the mechanisms of reaction and yields values of parameters that are used in theoretical models of interstellar cloud chemistry.
The results of experiments on the formation of molecular hydrogen on low density and high density amorphous ice surfaces are analyzed using a rate equation model. The activation energy barriers for the relevant diffusion and desorption processes are obtained. The more porous morphology of the low density ice gives rise to a broader spectrum of energy barriers compared to the high density ice. Inserting these parameters into the rate equation model under steady state conditions we evaluate the production rate of molecular hydrogen on ice-coated interstellar dust grains.
Chemical reactions on dust grains are of crucial importance in interstellar chemistry because they produce molecular hydrogen and various organic molecules. Due to the submicron size of the grains and the low flux, the surface populations of reactive species are small and strongly fluctuate. Under these conditions rate equations fail and the master equation is needed for modeling these reactions. However, the number of equations in the master equation grows exponentially with the number of reactive species, severely limiting its feasibility. Here we present a method which dramatically reduces the number of equations, thus enabling the incorporation of the master equation in models of interstellar chemistry.
Motivated by recent observations of deuterated molecules in the interstellar medium, we examine the production of HD and D$_2$ molecules on dust grain surfaces. A mechanism for the enhanced production of these deuterated molecules is studied. This mechanism applies on grain surfaces on which D atoms stick more strongly than H atoms, under conditions of low flux and within a suitable range of temperatures. It is shown that under these conditions the production rates of HD and D$_2$ are greatly enhanced (vs. the H$_2$ production rate) compared with the expected rates based on the adsorption of gas-phase atomic abundances of D and H. The enhancement in the formation rate of HD is comparable with the enhancement due to gas-phase ion-molecule reactions in diffuse clouds.
The effect of unitary noise on the discrete one-dimensional quantum walk is studied using computer simulations. For the noiseless quantum walk, starting at the origin (n=0) at time t=0, the position distribution Pt(n) at time t is very different from the Gaussian distribution obtained for the classical random walk. Furthermore, its standard deviation, sigma(t) scales as sigma(t) ~ t, unlike the classical random walk for which sigma(t) ~ sqrt{t}. It is shown that when the quantum walk is exposed to unitary noise, it exhibits a crossover from quantum behavior for short times to classical-like behavior for long times. The crossover time is found to be T ~ alpha^(-2) where alpha is the standard deviation of the noise.
The Groverian entanglement measure, G(psi), is applied to characterize a variety of pure quantum states |psi> of multiple qubits. The Groverian measure is calculated analytically for certain states of high symmetry, while for arbitrary states it is evaluated using a numerical procedure. In particular, it is calculated for the class of Greenberger-Horne-Zeilinger states, the W states as well as for random pure states of n qubits. The entanglement generated by Grover's algorithm is evaluated by calculating G(psi) for the intermediate states that are obtained after t Grover iterations, for various initial states and for different sets of the marked states.
Abelian sandpile models, both deterministic, such as the Bak, Tang, Wiesenfeld (BTW) model [P. Bak, C. Tang and K. Wiesenfeld, Phys. Rev. Lett. {\bf 59}, 381 (1987)], and stochastic, such as the Manna model [S.S. Manna, J. Phys. A {\bf 24}, L363 (1991)], are studied on finite square lattices with open boundaries. The avalanche size distribution $P_L(n)$ is calculated for a range of system sizes, $L$. The first few moments of this distribution are evaluated numerically and their dependence on the system size is examined. The sandpile models are conservative in the sense that grains are conserved in the bulk and can leave the system only through the boundaries. It is shown that the conservation law provides an interesting connection between sandpile models and random walk models. Using this connection, it is shown that the average avalanche sizes, $ _L$, for the BTW and the Manna models are equal to each other, and both are equal to the average path-length of a random walker starting from a random initial site on the same lattice of size $L$. This is in spite of the fact that sandpile models with deterministic (BTW) and stochastic (Manna) toppling rules exhibit different critical exponents, indicating that they belong to different universality classes.
While most chemical reactions in the interstellar medium take place in the gas phase, those occurring on the surfaces of dust grains play an essential role. Chemical models based on rate equations including both gas phase and grain surface reactions have been used in order to simulate the formation of chemical complexity in interstellar clouds. For reactions in the gas phase and on large grains, rate equations, which are highly efficient to simulate, are an ideal tool. However, for small grains under low flux, the typical number of atoms or molecules of certain reactive species on a grain may go down to order one or less. In this case the discrete nature of the opulations of reactive species as well as the fluctuations become dominant, thus the mean-field approximation on which the rate equations are based does not apply. Recently, a master equation approach, that provides a good description of chemical reactions on interstellar dust grains, was proposed. Here we present a related approach based on moment equations that can be obtained from the master equation. These equations describe the time evolution of the moments of the distribution of the population of the various chemical species on the grain. An advantage of this approach is the fact that the production rates of molecular species are expressed directly in terms of these moments. Here we use the moment equations to calculate the rate of molecular hydrogen formation on small grains. It is shown that the moment equation approach is efficient in this case in which only a single reactive specie is involved. The set of equations for the case of two species is presented and the difficulties in implementing this approach for complex reaction networks involving multiple species are discussed.
The recombination of hydrogen in the interstellar medium, taking place on surfaces of microscopic dust grains, is an essential process in the evolution of chemical complexity in interstellar clouds. The H_2 formation process has been studied theoretically, and in recent years also by laboratory experiments. The experimental results were analyzed using a rate equation model. The parameters of the surface, that are relevant to H_2 formation, were obtained and used in order to calculate the recombination rate under interstellar conditions. However, it turned out that due to the microscopic size of the dust grains and the low density of H atoms, the rate equations may not always apply. A master equation approach that provides a good description of the H_2 formation process was proposed. It takes into account both the discrete nature of the H atoms and the fluctuations in the number of atoms on a grain. In this paper we present a comprehensive analysis of the H_2 formation process, under steady state conditions, using an exact solution of the master equation. This solution provides an exact result for the hydrogen recombination rate and its dependence on the flux, the surface temperature and the grain size. The results are compared with those obtained from the rate equations. The relevant length scales in the problem are identified and the parameter space is divided into two domains. One domain, characterized by first order kinetics, exhibits high efficiency of H_2 formation. In the other domain, characterized by second order kinetics, the efficiency of H_2 formation is low. In each of these domains we identify the range of parameters in which, the rate equations do not account correctly for the recombination rate. and the master equation is needed.
The dynamics of generalized Lotka-Volterra systems is studied by theoretical techniques and computer simulations. These systems describe the time evolution of the wealth distribution of individuals in a society, as well as of the market values of firms in the stock market. The individual wealths or market values are given by a set of time dependent variables $w_i$, $i=1,...N$. The equations include a stochastic autocatalytic term (representing investments), a drift term (representing social security payments) and a time dependent saturation term (due to the finite size of the economy). The $w_i$'s turn out to exhibit a power-law distribution of the form $P(w) \sim w^{-1-α}$. It is shown analytically that the exponent $α$ can be expressed as a function of one parameter, which is the ratio between the constant drift component (social security) and the fluctuating component (investments). This result provides a link between the lower and upper cutoffs of this distribution, namely between the resources available to the poorest and those available to the richest in a given society. The value of $α$ %as well as the position of the lower cutoff is found to be insensitive to variations in the saturation term, that represent the expansion or contraction of the economy. The results are of much relevance to empirical studies that show that the distribution of the individual wealth in different countries during different periods in the 20th century has followed a power-law distribution with $1 < α< 2$.
Financial time series typically exhibit strong fluctuations that cannot be described by a Gaussian distribution. In recent empirical studies of stock market indices it was examined whether the distribution P(r) of returns r(tau) after some time tau can be described by a (truncated) Levy-stable distribution L_{alpha}(r) with some index 0 < alpha <= 2. While the Levy distribution cannot be expressed in a closed form, one can identify its parameters by testing the dependence of the central peak height on tau as well as the power-law decay of the tails. In an earlier study [Mantegna and Stanley, Nature 376, 46 (1995)] it was found that the behavior of the central peak of P(r) for the Standard & Poor 500 index is consistent with the Levy distribution with alpha=1.4. In a more recent study [Gopikrishnan et al., Phys. Rev. E 60, 5305 (1999)] it was found that the tails of P(r) exhibit a power-law decay with an exponent alpha ~= 3, thus deviating from the Levy distribution. In this paper we study the distribution of returns in a generic model that describes the dynamics of stock market indices. For the distributions P(r) generated by this model, we observe that the scaling of the central peak is consistent with a Levy distribution while the tails exhibit a power-law distribution with an exponent alpha > 2, namely beyond the range of Levy-stable distributions. Our results are in agreement with both empirical studies and reconcile the apparent disagreement between their results.
This paper demonstrates that how well a state performs as an input to Grover's search algorithm depends critically upon the entanglement present in that state; the more entanglement, the less well the algorithm performs. More precisely, suppose we take a pure state input, and prior to running the algorithm apply local unitary operations to each qubit in order to maximize the probability P_max that the search algorithm succeeds. We prove that, for pure states, P_max is an entanglement monotone, in the sense that P_max can never be decreased by local operations and classical communication.
A quantitative comparison between experimental and Monte Carlo simulation results for the epitaxial growth of Cu/Cu(001) in the submonolayer regime is presented. The simulations take into account a complete set of hopping processes whose activation energies are derived from semi-empirical calculations using the embedded-atom method. The island separation is measured as a function of the incoming flux and the temperature. A good quantitative agreement between the experiment and simulation is found for the island separation, the activation energies for the dominant processes, and the exponents that characterize the growth. The simulation results are then analyzed at lower coverages, which are not accessible experimentally, providing good agreement with theoretical predictions as well.
Recent experimental results on the formation of molecular hydrogen on astrophysically relevant surfaces under conditions similar to those encountered in the interstellar medium provided useful quantitative information about these processes. Rate equation analysis of experiments on olivine and amorphous carbon surfaces provided the activation energy barriers for the diffusion and desorption processes relevant to hydrogen recombination on these surfaces. However, the suitability of rate equations for the simulation of hydrogen recombination on interstellar grains, where there might be very few atoms on a grain at any given time, has been questioned. To resolve this problem, we introduce a master equation that takes into account both the discrete nature of the H atoms and the fluctuations in the number of atoms on a grain. The hydrogen recombination rate on microscopic grains, as a function of grain size and temperature, is then calculated using the master equation. The results are compared to those obtained from the rate equations and the conditions under which the master equation is required are identified.
The recursion equation analysis of Grover's quantum search algorithm presented by Biham et al. [PRA 60, 2742 (1999)] is generalized. It is applied to the large class of Grover's type algorithms in which the Hadamard transform is replaced by any other unitary transformation and the phase inversion is replaced by a rotation by an arbitrary angle. The time evolution of the amplitudes of the marked and unmarked states, for any initial complex amplitude distribution is expressed using first order linear difference equations. These equations are solved exactly. The solution provides the number of iterations T after which the probability of finding a marked state upon measurement is the highest, as well as the value of this probability, P_max. Both T and P_max are found to depend on the averages and variances of the initial amplitude distributions of the marked and unmarked states, but not on higher moments.
A topological approach and understanding to the detection of unstable periodic orbits based on a recently proposed method (PRL 78, 4733 (1997)) is developed. This approach provides a classification of the set of transformations necessary for the finding of the orbits. Applications to the Ikeda and Henon map are performed, allowing a study of the distributions of Lyapunov exponents for high periods. Particularly the properties of the least unstable orbits up to period 36 are investigated and discussed.