Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate equation models

Chemical reactions inside cells occur in compartment volumes in the range of atto- to femtolitres. Physiological concentrations realized in such small volumes imply low copy numbers of interacting molecules with the consequence of considerable fluctuations in the concentrations. In contrast, rate equation models are based on the implicit assumption of infinitely large numbers of interacting molecules, or equivalently, that reactions occur in infinite volumes at constant macroscopic concentrations. In this article we compute the finite-volume corrections (or equivalently the finite copy number corrections) to the solutions of the rate equations for chemical reaction networks composed of arbitrarily large numbers of enzyme-catalyzed reactions which are confined inside a small sub-cellular compartment. This is achieved by applying a mesoscopic version of the quasi-steady state assumption to the exact Fokker-Planck equation associated with the Poisson Representation of the chemical master equation. The procedure yields impressively simple and compact expressions for the finite-volume corrections. We prove that the predictions of the rate equations will always underestimate the actual steady-state substrate concentrations for an enzyme-reaction network confined in a small volume. In particular we show that the finite-volume corrections increase with decreasing sub-cellular volume, decreasing Michaelis-Menten constants and increasing enzyme saturation. The magnitude of the corrections depends sensitively on the topology of the network. The predictions of the theory are shown to be in excellent agreement with stochastic simulations for two types of networks typically associated with protein methylation and metabolism.Comment: 13 pages, 4 figures; published in The Journal of Chemical Physic

Search for Sterile Neutrinos with a Radioactive Source at Daya Bay

The far site detector complex of the Daya Bay reactor experiment is proposed as a location to search for sterile neutrinos with > eV mass. Antineutrinos from a 500 kCi 144Ce-144Pr beta-decay source (DeltaQ=2.996 MeV) would be detected by four identical 20-ton antineutrino targets. The site layout allows flexible source placement; several specific source locations are discussed. In one year, the 3+1 sterile neutrino hypothesis can be tested at essentially the full suggested range of the parameters Delta m^2_{new} and sin^22theta_{new} (90% C.L.). The backgrounds from six nuclear reactors at >1.6 km distance are shown to be manageable. Advantages of performing the experiment at the Daya Bay far site are described

Tevatron Beam Position Monitor Upgrade

This paper describes the development of a digital-based Beam Position System which was designed, developed, and adapted for the Tevatron during Collider Run II.Comment: 20 p

Gamma-Ray Emissions from Pulsars: Spectra of the TEV Fluxes from Outer-Gap Accelerators

We study the gamma-ray emissions from an outer-magnetospheric potential gap around a rotating neutron star. Migratory electrons and positrons are accelerated by the electric field in the gap to radiate copious gamma-rays via curvature process. Some of these gamma-rays materialize as pairs by colliding with the X-rays in the gap, leading to a pair production cascade. Imposing the closure condition that a single pair produces one pair in the gap on average, we explicitly solve the strength of the acceleration field and demonstrate how the peak energy and the luminosity of the curvature-radiated, GeV photons depend on the strength of the surface blackbody and the power-law emissions. Some predictions on the GeV emission from twelve rotation-powered pulsars are presented. We further demonstrate that the expected pulsed TeV fluxes are consistent with their observational upper limits. An implication of high-energy pulse phase width versus pulsar age, spin, and magnetic moment is discussed.Comment: Revised to compute absolute TeV spectra (22 pages, 9 figures

Slow light propagation in trapped atomic quantum gases

We study semi-classical slow light propagation in trapped two level atomic quantum gases. The temperature dependent behaviors of both group velocity and transmissions are compared for low temperature Bose, Fermi, and Boltzman gases within the local density approximation for their spatial density profile.Comment: 9 pages, 2 figure

Factors affecting ammonium uptake in streams - an inter-biome perspective

The Lotic Intersite Nitrogen experiment (LINX) was a coordinated study of the relationships between North American biomes and factors governing ammonium uptake in streams. Our objective was to relate inter-biome variability of ammonium uptake to physical, chemical and biological processes. 2. Data were collected from 11 streams ranging from arctic to tropical and from desert to rainforest. Measurements at each site included physical, hydraulic and chemical characteristics, biological parameters, whole-stream metabolism and ammonium uptake. Ammonium uptake was measured by injection of \u275~-ammonium and downstream measurements of 15N-ammonium concentration. 3. We found no general, statistically significant relationships that explained the variability in ammonium uptake among sites. However, this approach does not account for the multiple mechanisms of ammonium uptake in streams. When we estimated biological demand for inorganic nitrogen based on our measurements of in-stream metabolism, we found good correspondence between calculated nitrogen demand and measured assimilative nitrogen uptake. 4. Nitrogen uptake varied little among sites, reflecting metabolic compensation in streams in a variety of distinctly different biomes (autotrophic production is high where allochthonous inputs are relatively low and vice versa). 5. Both autotrophic and heterotrophic metabolism require nitrogen and these biotic processes dominate inorganic nitrogen retention in streams. Factors that affect the relative balance of autotrophic and heterotrophic metabolism indirectly control inorganic nitrogen uptake

Can uptake length in strams be determined by nutrient addition experiments? Results from an interbiome comparison study

Nutrient uptake length is an important parnmeter tor quantifying nutrient cycling in streams. Although nutrient tracer additions are the preierred method for measuring uptake length under ambient nutrient concentrations, short-term nutrient addition experiments have more irequently been used to estimate uptake length in streams. Theoretical analysis of the relationship between uptake length determined by nutrient addition experiments (Sw\u27) and uptake length determined by tracer additions (Sw)predicted that Sw\u27 should be consistently longer than 5, , and that the overestimate of uptake length by Sw( should be related to the level of nutrient addition above ambient concentrations and the degree of nutrient limitation. To test these predictions, we used data irom an interbiorne study of NH,- uptake length in which 15NH,- tracer and short-term NH,-a ddition experiments were performed in 10 streams using a uniform experimental approach. The experimental results largely contirmed the theoretical predictions: sw\u27 was consistently longer than Sw and Sw\u27:Sw ratios were directly related to the level of NH,- addition and to indicatvrs of N limitation. The experimentally derived Sw\u27:Sw, ratios were used with the theoretical results to infer the N limitation status of each stream. Together, the theoretical and experimental results showed the tracer experiments should be used whenever possible to determine nutrient uptake length in streams. Nutrient addition experiments may be useful for comparing uptake lengths between different streams or cliiferent times in the same stream. however, provided that nutrient additions are kept as low as possible and of similar miagnitude

Super-radiant light scattering from trapped Bose Einstein condensates

We propose a new formulation for atomic side mode dynamics from super-radiant light scattering of trapped atoms. A detailed analysis of the recently observed super-radiant light scattering from trapped bose gases [S. Inouye {\it et al.}, Science {\bf 285}, 571 (1999)] is presented. We find that scattered light intensity can exhibit both oscillatory and exponential growth behaviors depending on densities, pump pulse characteristics, temperatures, and geometric shapes of trapped gas samples. The total photon scattering rate as well as the accompanied matter wave amplification depends explicitly on atom number fluctuations in the condensate. Our formulation allows for natural and transparent interpretations of subtle features in the MIT data, and provides numerical simulations in good agreement with all aspects of the experimental observations.Comment: 24 pages,16 figures, submitted to Phys.Rev.