PubMed Health⌕ Search

Biomedical subjects

Azi Lipshtat

Publications and source records attributed to Azi Lipshtat.

9 recordsLinked to original sources

Topology of resultant networks shaped by evolutionary pressure.

Understanding the topology of complex systems abstracted to networks is important for unraveling their functional capabilities. Many such networks follow the small-world and scale-free regimes. Several models of artificially growing networks lead to this observed network topology. Most previously proposed models for growing networks, such as rich-get-richer and duplication-divergence, produce realistic network topologies but do not consider the effects of exogenous forces such as optimization for adaptation in shaping network topology. It is likely that such forces have shaped complex systems throughout their evolution. To develop further insights into possible mechanisms that shape networks, a model that uses several previously proposed network growth algorithms was developed to grow networks that adapt under exogenous stress. A decision tree problem was used to generate a complex Boolean function. Growing networks were required to adapt to correctly decode this function using an evolutionary selection process. Under this growth regimen all growing network models are similarly adaptable. The newly added nodes tend to cluster into pathways emanating from few inputs, regardless of the growth algorithm. Distribution of redundant pathways from inputs to the output follow a power-law function with a scaling exponent (approximately 1.3). Similar distribution of redundant pathways was observed from inputs in a cell signaling network and an air traffic control network. A flat distribution of redundant pathways from inputs was observed in growing networks that do not attempt to adapt. This analysis provides initial insights into distribution of pathways in naturally evolving complex systems that have defined input-output relationships.

Algorithms↗

Genetic toggle switch without cooperative binding.

Genetic switch systems with mutual repression of two transcription factors are studied using deterministic and stochastic methods. Numerous studies have concluded that cooperative binding is a necessary condition for the emergence of bistability in these systems. Here we show that, for a range of biologically relevant conditions, a suitable combination of network structure and stochastic effects gives rise to bistability even without cooperative binding.

Animals↗

Modeling of negative autoregulated genetic networks in single cells.

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.

Cell Physiological Phenomena↗

Reaction kinetics in a tight spot.

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.

Catalysis↗

Efficient simulations of gas-grain chemistry in interstellar clouds.

Chemical reactions on dust grains are of crucial importance in interstellar chemistry because they produce molecular hydrogen and various organic molecules. Because of 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 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.

Journal Article↗

Scaling anomalies in the coarsening dynamics of fractal viscous fingering patterns.

We analyze a recent experiment of Sharon et al. (2003) on the coarsening, due to surface tension, of fractal viscous fingering patterns (FVFPs) grown in a radial Hele-Shaw cell. We argue that an unforced Hele-Shaw model, a natural model for that experiment, belongs to the same universality class as model B of phase ordering. Two series of numerical simulations with model B are performed, with the FVFPs grown in the experiment and with diffusion limited aggregates as the initial conditions. We observed Lifshitz-Slyozov scaling t(1/3) at intermediate distances and slow convergence to this scaling at small distances. Dynamic scale invariance breaks down at large distances.

Journal Article↗

Exact results for hydrogen recombination on dust grain surfaces.

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. Molecular hydrogen plays an important role in absorbing the heat that emerges during gravitational collapse, thus enabling the formation of structure in the universe. The H2 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 H2 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 H2 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 H2 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 H2 formation. In the other domain, characterized by second order kinetics, the efficiency of H2 formation is low. In each of these domains we identify the range of parameters in which, due to the small size of the grains, the rate equations do not account correctly for the recombination rate and the master equation is needed.

Journal Article↗

Anomalous dynamic scaling in locally conserved coarsening of fractal clusters.

We report two-dimensional phase-field simulations of locally conserved coarsening dynamics of random fractal clusters with fractal dimension D=1.7 and 1.5. The correlation function, cluster perimeter, and solute mass are measured as functions of time. Analyzing the correlation function dynamics, we identify two different time-dependent length scales that exhibit power laws in time. The exponents of these power laws do not show any dependence on D; one of them is apparently the "classical" exponent 1/3. The solute mass versus time exhibits dynamic scaling with a D-dependent exponent, in agreement with a simple scaling theory.

Journal Article↗