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

Post-Archean granitic rocks: contrasting petrogenetic processes and tectonic environments

Granitic rocks represent a ubiquitous component of upper continental crust but their origin remains highly controversial. This controversy stems from the fact that the granites may result from fractionation of mantle-derived basaltic magmas or partial melting of different crustal protoliths at contrasting pressure\u2013temperature conditions, either water-fluxed or fluid-absent. Consequently, many different mechanisms have been proposed to explain the compositional variability of granites ranging from whole igneous suites down to mineral scale. This Special Publication presents an overview of the state of the art and envisages future avenues towards a better understanding of granite petrogenesis

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

Coaxial Wire Measurements In NLC Accelerating Structures

The coaxial wire method provides an experimental way of measuring wake fields without the need for a particle beam. A special setup has been designed and is in the process of being fabricated at SLAC to measure the loss factors and synchronous frequencies of dipole modes in both traveling and standing wave structures for the Next Linear Collider (NLC). The method is described and predictions based on electromagnetic field simulations are discussedComment: Paper presented at the 2002 8th European Particle Accelerator Conference (EPAC 2002) Paris, France, June 3rd -June 7th, 200

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