Feedback and reversibility in substrate-enzyme reactions as discrete event models

A dierent approach in modeling reactions between substrate molecules and enzymes is presented in this report. The reactions are modeled using a discrete event model (DEM), mostly used in manufacturing or queueing systems. The DEM has been validated with the most used approach to modeling substrate-enzyme reactions, a set of ordinary dierential equations (ODEs). The substrate-enzyme model is extended with feedback of substrate and=or product molecules on the enzyme, resulting in inhibition or activation of the enzyme. A reversible reaction, where the enzyme can react with both the substrate and the product, is also modeled as a DEM and validated with an ODE model. The substrate-enzyme reaction models with feedback is extended to a steady-state system by adding a generator, convertor and exit. Stability of the steady-state system is analyzed and resulted in three distinct regions

Discrete event simulations for glycolysis pathway and energy balance

In this report, the biological network of the glycolysis pathway has been modeled using discrete event models (DEMs). The most important feature of this pathway is that energy is released. To create a stable steady-state system an energy molecule equilibrating enzyme and metabolic reactions have been added, resulting in the energy balance system. Stability and stochastic in uences on the results have been investigated and result in an unstable system, except for a small region of input parameters. To stabilize the energy balance system some feedback regulators are presented. It is shown that stochastic behavior has got a signicant in uence on a otherwise stable biological system

Particle design via spherical agglomeration: A critical review of controlling parameters, rate processes and modelling

Particle design via spherical agglomeration is a size enlargement technique used in various bulk and fine chemical industries, with recent interest extending into pharmaceuticals, in which an immiscible bridging liquid is added to agglomerate crystals prior to deliquoring. Spherical agglomeration has the potential to dramatically simplify downstream processing, and improves the handling of difficult, needle-shaped crystals. This review consolidates the understanding of the controlling process parameters, identifies the rate processes that control agglomerate attributes, and examines the modelling approaches taken in the literature to optimise the design of such systems. The most important controlling parameters are solvent system composition (requiring knowledge of the ternary phase diagram) and bridging liquid to solid ratio (BSR). Agglomerate size is a highly non-linear function of BSR with many literature systems showing qualitatively similar behaviour. However, there is no method to predict the optimum BSR. Other important process parameters are temperature, constituent particle properties, agitation rate and batch/residence time. Each parameter can have significant effects on the final agglomerate properties including agglomerate size, porosity, strength and dissolution profile. The rate processes in spherical agglomeration are analogous to those in wet granulation. A general classification of rate processes is proposed in this review including nucleation by distribution or immersion, consolidation, coalescence, layered growth and breakage. While many papers give proof of concept examples of spherical agglomeration for specific systems, only a few have focused explicitly on mechanistic understanding. There is significant scope for further work to quantify the effect of both process parameters and formulation properties on these rate processes. Recent developments in on-line monitoring using process analytical technologies (PAT) should enable these studies. Using the mechanistic understanding, population balance models can be developed to include kernels for each of the relevant rate processes. Such models should be powerful tools of process optimisation and model driven design with reduced experiments at all scales

An algebraic/numerical formalism for one-loop multi-leg amplitudes

We present a formalism for the calculation of multi-particle one-loop amplitudes, valid for an arbitrary number N of external legs, and for massive as well as massless particles. A new method for the tensor reduction is suggested which naturally isolates infrared divergences by construction. We prove that for N>4, higher dimensional integrals can be avoided. We derive many useful relations which allow for algebraic simplifications of one-loop amplitudes. We introduce a form factor representation of tensor integrals which contains no inverse Gram determinants by choosing a convenient set of basis integrals. For the evaluation of these basis integrals we propose two methods: An evaluation based on the analytical representation, which is fast and accurate away from exceptional kinematical configurations, and a robust numerical one, based on multi-dimensional contour deformation. The formalism can be implemented straightforwardly into a computer program to calculate next-to-leading order corrections to multi-particle processes in a largely automated way.Comment: 71 pages, 7 figures, formulas for rank 6 pentagons added in Appendix

Formulations of the 3+1 evolution equations in curvilinear coordinates

Following Brown, in this paper we give an overview of how to modify standard hyperbolic formulations of the 3+1 evolution equations of General Relativity in such a way that all auxiliary quantities are true tensors, thus allowing for these formulations to be used with curvilinear sets of coordinates such as spherical or cylindrical coordinates. After considering the general case for both the Nagy-Ortiz-Reula (NOR) and the Baumgarte-Shapiro-Shibata-Nakamura (BSSN) formulations, we specialize to the case of spherical symmetry and also discuss the issue of regularity at the origin. Finally, we show some numerical examples of the modified BSSN formulation at work in spherical symmetry.Comment: 19 pages, 12 figure

Strongly Hyperbolic Extensions of the ADM Hamiltonian

The ADM Hamiltonian formulation of general relativity with prescribed lapse and shift is a weakly hyperbolic system of partial differential equations. In general weakly hyperbolic systems are not mathematically well posed. For well posedness, the theory should be reformulated so that the complete system, evolution equations plus gauge conditions, is (at least) strongly hyperbolic. Traditionally, reformulation has been carried out at the level of equations of motion. This typically destroys the variational and Hamiltonian structures of the theory. Here I show that one can extend the ADM formalism to (i) incorporate the gauge conditions as dynamical equations and (ii) affect the hyperbolicity of the complete system, all while maintaining a Hamiltonian description. The extended ADM formulation is used to obtain a strongly hyperbolic Hamiltonian description of Einstein's theory that is generally covariant under spatial diffeomorphisms and time reparametrizations, and has physical characteristics. The extended Hamiltonian formulation with 1+log slicing and gamma--driver shift conditions is weakly hyperbolic.Comment: This version contains minor corrections and clarifications. The format has been changed to conform with IOP styl

Distant ionospheric photoelectron energy peak observations at Venus

The dayside of the Venus ionosphere at the top of the planet's thick atmosphere is sustained by photoionization. The consequent photoelectrons may be identified by specific peaks in the energy spectrum at 20–30 eV which are mainly due to atomic oxygen photoionization. The ASPERA-4 electron spectrometer has an energy resolution designed to identify the photoelectron production features. Photoelectrons are seen not only in their production region, the sunlit ionosphere, but also at more distant locations on the nightside of the Venus environment. Here, we present a summary of the work to date on observations of photoelectrons at Venus, and their comparison with similar processes at Titan and Mars. We expand further by presenting new examples of the distant photoelectrons measured at Venus in the dark tail and further away from Venus than seen before. The photoelectron and simultaneous ion data are then used to determine the ion escape rate from Venus for one of these intervals. We compare the observed escape rates with other rates measured at Venus, and at other planets, moons and comets. We find that the escape rates are grouped by object type when plotted against body radius

Measurement of three-jet differential cross sections d sigma-3jet / d M-3jet in p anti-p collisions at sqrt(s)=1.96 TeV

We present the first measurement of the inclusive three-jet differential cross section as a function of the invariant mass of the three jets with the largest transverse momenta in an event in p anti-p collisions at sqrt(s) = 1.96 TeV. The measurement is made in different rapidity regions and for different jet transverse momentum requirements and is based on a data set corresponding to an integrated luminosity of 0.7 fb^{-1} collected with the D0 detector at the Fermilab Tevatron Collider. The results are used to test the three-jet matrix elements in perturbative QCD calculations at next-to-leading order in the strong coupling constant. The data allow discrimination between parametrizations of the parton distribution functions of the proton.Comment: 10 pages, 4 figures, 2 tables, submitted to Phys. Lett. B, corrected chi2 values for NNPD

Measurement of W Polarisation at LEP

The three different helicity states of W bosons produced in the reaction e+ e- -> W+ W- -> l nu q q~ at LEP are studied using leptonic and hadronic W decays. Data at centre-of-mass energies \sqrt s = 183-209 GeV are used to measure the polarisation of W bosons, and its dependence on the W boson production angle. The fraction of longitudinally polarised W bosons is measured to be 0.218 \pm 0.027 \pm 0.016 where the first uncertainty is statistical and the second systematic, in agreement with the Standard Model expectation

Search for Anomalous Couplings in the Higgs Sector at LEP

Anomalous couplings of the Higgs boson are searched for through the processes e^+ e^- -> H gamma, e^+ e^- -> e^+ e^- H and e^+ e^- -> HZ. The mass range 70 GeV < m_H < 190 GeV is explored using 602 pb^-1 of integrated luminosity collected with the L3 detector at LEP at centre-of-mass energies sqrt(s)=189-209 GeV. The Higgs decay channels H -> ffbar, H -> gamma gamma, H -> Z\gamma and H -> WW^(*) are considered and no evidence is found for anomalous Higgs production or decay. Limits on the anomalous couplings d, db, Delta(g1z), Delta(kappa_gamma) and xi^2 are derived as well as limits on the H -> gamma gamma and H -> Z gamma decay rates