Iyengar Laboratory

Azi Lipshtat, Ph.D.

Research Assistant Professor, Department of Pharmacology and Systems Therapeutics
E-mail: azi.lipshtat@mssm.edu

Mailing Address

One Gustave L. Levy Place,Box 1215 New York, NY 10029

Other Web Sites

MSSM Faculty Profile
Research ID

Training and Education

Ph.D. The Hebrew University of Jerusalem, Jerusalem, Israel

M.S. (2000) The Hebrew University of Jerusalem, Jerusalem, Israel

B.S. (1998) The Hebrew University of Jerusalem, Jerusalem, Israel

Research Interests

Coarsening dynamics

The dynamics of phase transition are considered to be "scale invariant". However, if the initial condition is a fractal cluster of one phase in the "sea" of the other phase, the scale invariance is broken. We have performed a comprehensive investigation of these dynamics, using numerical simulations of the Cahn-Hilliard equation. The simulation results closely resemble experimental results of Sharon et al. on the coarsening of fractal viscous fingering patterns in a radial Hele-Shaw cell. The scale invariance breaks down on large distances, whereas in small distances the "standard" Lifshitz-Slyozov scaling (t^1/3) holds.

Modeling of surface chemistry

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. We have established the method of master equation for interstellar surface reactions and identified the range of parameters in which this method is needed. In complex reaction networks, where many species are involved and reaction products act as reactants in other reactions, the number of equations in the master equation grows exponentially with the number of reactive species, severely limiting its feasibility. For these cases we have developed the multiplane method which dramatically reduces the number of equations, thus enabling the incorporation of the master equation in models of interstellar chemistry. This method is cased on decoupling of joint probabilities. We define a few sets of probabilities which holds the required correlations only, instead of taking care of all possible ones.

Modeling of genetic networks

Recent advances in molecular biology techniques have made possible the measurement of populations of proteins and mRNA's in simple genetic networks. Measurements of the average protein content of cells and their time dependence enabled to quantify the behavior of genetic networks. These measurements have been modeled using rate equations, mainly under quasi steady state conditions. However, real biological systems are likely be away from steady state. Furthermore, many components of cells appear in low copy numbers and are therefore subjected to large fluctuations. The modeling of these fluctuations requires the master equation formalism. We consider the modeling of simple genetic regulation networks using the master equation approach, and investigate the significance of noise and fluctuations in the dynamics of cell populations.

Publications

Ma'ayan A, Lipshtat A, Iyengar R, Sontag ED. Proximity of intracellular regulatory networks to monotone systems. IET Syst Biol. 2008 May;2(3):103.

Lipshtat A, Purushothaman SP, Iyengar R, Ma'ayan A. Functions of bifans in context of multiple regulatory motifs in signaling networks. Biophys J. 2008 Apr 1;94(7):2566-79.

Lipshtat A. "All possible steps" approach to the accelerated use of Gillespie's algorithm. J Chem Phys. 2007 May 14;126(18):184103.

Loinger A, Lipshtat A, Balaban NQ, Biham O. Stochastic simulations of genetic switch systems. Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Feb;75(2 Pt 1):021904.

Ma'ayan A, Lipshtat A, Iyengar R. Topology of resultant networks shaped by evolutionary pressure. Phys Rev E 2006;73;061912.

Lipshtat A, Loinger A, Balaban NQ, Biham O. Genetic Toggle Switch without Cooperative Binding. Phys Rev Lett. 2006 May 12;96(18):188101.

Biham O, Krug J, Lipshtat A and Michely T. Reaction kinetics in a tight spot. Small 2005; 502.

Lipshtat A, Perets HB, Balaban NQ, Biham O. Modeling of negative autoregulated genetic networks in single cells. Gene. 2005 Mar 14;347(2):265-71.

Lipshtat A, Meerson B, Conti M. Simulating coarsening dynamics of fractal clusters. Chaos. 2004 Dec;14(4):S13.

Lipshtat A, Biham O. Efficient simulations of gas-grain chemistry in interstellar clouds. Phys Rev Lett . 2004 Oct 22;93(17):170601.

Conti M, Lipshtat A, Meerson B. Scaling anomalies in the coarsening dynamics of fractal viscous fingering patterns. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Mar;69 (3 Pt 1):031406.

Lipshtat A, Biham O and Herbst E. Enhanced production of HD and D_2 molecules on small dust grains. Monthly Notices of the Royal Astronomical Society 2004; 348(3):1055-1064.

Biham O, Lipshtat A. Moment equations for chemical reactions on interstellar dust grains. Astronomy & Astrophysics. 2003; 400: 585-593.

Biham O, Lipshtat A. Exact results for hydrogen recombination on dust grain surfaces. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Nov;66 (5 Pt 2):056103.

Lipshtat A, Meerson B, Sasorov PV. Anomalous dynamic scaling in locally conserved coarsening of fractal clusters. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 May;65 (5 Pt 1):050501.

Presentations

Presentation, "Modeling of fluctuating reaction networks", at the 50th Annual Meeting of the Israel Physical Society, Haifa, Israel, December 2004.

Poster presentation at the Conference on Computational Physics 2004, Genoa, Italy, September 2004. (pdf of poster)

Presentation, "Chemical Reactions on Small Interstellar Dust Grains". Mini-symposium, "Molecules and Star Formation", at the International Symposium on Molecular Spectroscopy, Columbus, Ohio, June 2004.

Movie presented at the GNSP March Meeting, Montreal, Canada, March 2004. (view movie)

Poster presentation at the 46th Annual Meeting of the Israel Physical Society, Haifa, Israel, December 2000.

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