Ofer Biham

Self-organization and a dynamical transition in traffic-flow models.

A simple model that describes traffic flow in two dimensions is studied. A sharp jamming transition is found that separates between the low-density dynamical phase in which all cars move at maximal speed and the high-density jammed phase in which they are all stopped. Self-organization effects in both phases are studied and discussed.

Is the Geometry of Nature Fractal

The notion of the abundance of fractals is critically re-examined in light of surprising data regarding the scaling range in empirical reports on fractality.

Molecular hydrogen formation on astrophysically relevant surfaces

Recent experimental results about the formation of molecular hydrogen on astrophysically relevant surfaces under conditions close to those encountered in the interstellar medium are analyzed using rate equations. The parameters of the rate equation model are fitted to temperature-programmed desorption curves obtained in the laboratory. These parameters are the activation energy barriers for atomic hydrogen diffusion and desorption, the barrier for molecular hydrogen desorption, and the probability of spontaneous desorption of a hydrogen molecule upon recombination. The model is a generalization of the Polanyi-Wigner equation and provides a description of both first- and second-order kinetic processes within a single model. Using the values of the parameters that best fit the experimental results, the efficiency of hydrogen recombination on olivine and amorphous carbon surfaces is obtained for a range of hydrogen flux and surface temperature pertinent to a wide range of interstellar conditions.

Regulation of gene expression by small non-coding RNAs: a quantitative view

The importance of post‐transcriptional regulation by small non‐coding RNAs has recently been recognized in both pro‐ and eukaryotes. Small RNAs (sRNAs) regulate gene expression post‐transcriptionally by base pairing with the mRNA. Here we use dynamical simulations to characterize this regulation mode in comparison to transcriptional regulation mediated by protein–DNA interaction and to post‐translational regulation achieved by protein–protein interaction. We show quantitatively that regulation by sRNA is advantageous when fast responses to external signals are needed, consistent with experimental data about its involvement in stress responses. Our analysis indicates that the half‐life of the sRNA–mRNA complex and the ratio of their production rates determine the steady‐state level of the target protein, suggesting that regulation by sRNA may provide fine‐tuning of gene expression. We also describe the network of regulation by sRNA in Escherichia coli, and integrate it with the transcription regulation network, uncovering mixed regulatory circuits, such as mixed feed‐forward loops. The integration of sRNAs in feed‐forward loops provides tight repression, guaranteed by the combination of transcriptional and post‐transcriptional regulations.

Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence

In the face of antibiotics, bacterial populations avoid extinction by harboring a subpopulation of dormant cells that are largely drug insensitive. This phenomenon, termed “persistence,” is a major obstacle for the treatment of a number of infectious diseases. The mechanism that generates both actively growing as well as dormant cells within a genetically identical population is unknown. We present a detailed study of the toxin–antitoxin module implicated in antibiotic persistence of Escherichia coli. We find that bacterial cells become dormant if the toxin level is higher than a threshold, and that the amount by which the threshold is exceeded determines the duration of dormancy. Fluctuations in toxin levels above and below the threshold result in coexistence of dormant and growing cells. We conclude that toxin–antitoxin modules in general represent a mixed network motif that can serve to produce a subpopulation of dormant cells and to supply a mechanism for regulating the frequency and duration of growth arrest. Toxin–antitoxin modules thus provide a natural molecular design for implementing a bet-hedging strategy.

The Limited Scaling Range of Empirical Fractals

The notion of the abundance of fractals is critically re-examined in light of surprising data regarding the scaling range in empirical reports on fractality.

Master Equation for Hydrogen Recombination on Grain Surfaces

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.

Efficiency of Molecular Hydrogen Formation on Silicates

We report on laboratory measurements of molecular hydrogen formation and recombination on an olivine slab as a function of surface temperature under conditions relevant to those encountered in the interstellar medium. On the basis of our experimental evidence, we recognize that there are two main regimes of H coverage that are of astrophysical importance; for each of them we provide an expression giving the production rate of molecular hydrogen in interstellar clouds.

SCALING RANGE AND CUTOFFS IN EMPIRICAL FRACTALS

Fractal structures appear in a vast range of physical systems. A literature survey including all experimental papers on fractals which appeared in the six Physical Review journals (A\char21{}E and Letters) during the 1990s shows that experimental reports of fractal behavior are typically based on a scaling range

Genetic Toggle Switch without Cooperative Binding

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