The natural history of bugs: using formal methods to analyse software related failures in space missions

Space missions force engineers to make complex trade-offs between many different constraints including cost, mass, power, functionality and reliability. These constraints create a continual need to innovate. Many advances rely upon software, for instance to control and monitor the next generation ‘electron cyclotron resonance’ ion-drives for deep space missions.Programmers face numerous challenges. It is extremely difficult to conduct valid ground-based tests for the code used in space missions. Abstract models and simulations of satellites can be misleading. These issues are compounded by the use of ‘band-aid’ software to fix design mistakes and compromises in other aspects of space systems engineering. Programmers must often re-code missions in flight. This introduces considerable risks. It should, therefore, not be a surprise that so many space missions fail to achieve their objectives. The costs of failure are considerable. Small launch vehicles, such as the U.S. Pegasus system, cost around $18 million. Payloads range from$4 million up to $1 billion for security related satellites. These costs do not include consequent business losses. In 2005, Intelsat wrote off$73 million from the failure of a single uninsured satellite. It is clearly important that we learn as much as possible from those failures that do occur. The following pages examine the roles that formal methods might play in the analysis of software failures in space missions

Fluorite Precipitation in a Calcareous Soil Irrigated with High Fluoride Water

Lysimeters filled with Freedom silt loam soil (fine-silty, mixed, mesic, Xerollic Calciorthids) were irrigated with geothermal well water from south central Idaho. The water contained 7 mg F/L. Alfalfa (Medicago sativa L.) was grown in the lysimeters and the water was applied at a rate to give either a 0.30 or 0.15 leaching fraction. After irrigating the 1.0 m deep soil samples for 600 d, over 98% of the added F remained in the soil. Soil extract and lysimeter leachate analysis showed that fluorite precipitation was occurring in the upper profile, but only after another fluoride adsorption mechanism was saturated and the fluoride and calcium ion activities exceeded the CaF? ion activity product. The F concentration in the upper profile extracts exceeded 20 mg F/L and with the additional high F water irrigation, the soluble F would be expected to leach deeper in the soil. Under field conditions the F would be expected to eventually move into the groundwater with continued irrigation with high F water

Partially quenched chiral perturbation theory without Φ0\Phi_0

This paper completes the argument that lattice simulations of partially quenched QCD can provide quantitative information about QCD itself, with the aid of partially quenched chiral perturbation theory. A barrier to doing this has been the inclusion of $\Phi_0$, the partially quenched generalization of the $\eta'$, in previous calculations in the partially quenched effective theory. This invalidates the low energy perturbative expansion, gives rise to many new unknown parameters, and makes it impossible to reliably calculate the relation between the partially quenched theory and low energy QCD. We show that it is straightforward and natural to formulate partially quenched chiral perturbation theory without $\Phi_0$, and that the resulting theory contains the effective theory for QCD without the $\eta'$. We also show that previous results, obtained including $\Phi_0$, can be reinterpreted as applying to the theory without $\Phi_0$. We contrast the situation with that in the quenched effective theory, where we explain why it is necessary to include $\Phi_0$. We also compare the derivation of chiral perturbation theory in partially quenched QCD with the standard derivation in unquenched QCD. We find that the former cannot be justified as rigorously as the latter, because of the absence of a physical Hilbert space. Finally, we present an encouraging result: unphysical double poles in certain correlation functions in partially quenched chiral perturbation theory can be shown to be a property of the underlying theory, given only the symmetries and some plausible assumptions.Comment: 45 pages, no figure

The 13-C(p,d) Reaction at 120 MeV

This research was sponsored by the National Science Foundation Grant NSF PHY 87-1440

Identifying cell-type-specific metabolic signatures using transcriptome and proteome analyses

Studies in various tissues have revealed a central role of metabolic pathways in regulating adult stem cell function in tissue regeneration and tumor initiation. The unique metabolic dependences or preferences of adult stem cells, therefore, are emerging as a new category of therapeutic target. Recently, advanced methods including high-resolution metabolomics, proteomics, and transcriptomics have been developed to address the growing interest in stem cell metabolism. A practical framework integrating the omics analyses is needed to systematically perform metabolic characterization in a cell-type-specific manner. Here, we leverage recent advances in transcriptomics and proteomics research to identify cell-type-specific metabolic features by reconstructing cell identity using genes and the encoded enzymes involved in major metabolic pathways. We provide protocols for cell isolation, transcriptome and proteome analyses, and metabolite profiling and measurement. The workflow for mapping cell-type-specific metabolic signatures presented here, although initially developed for intestinal crypt cells, can be easily implemented for cell populations in other tissues, and is highly compatible with most public dataset

The nucleon's strange electromagnetic and scalar matrix elements

Quenched lattice QCD simulations and quenched chiral perturbation theory are used together for this study of strangeness in the nucleon. Dependences of the matrix elements on strange quark mass, valence quark mass and momentum transfer are discussed in both the lattice and chiral frameworks. The combined results of this study are in good agreement with existing experimental data and predictions are made for upcoming experiments. Possible future refinements of the theoretical method are suggested.Comment: 24 pages, 9 figure

Software design for the Tritium System Test Assembly

The control system for the Tritium Systems Test Assembly (TSTA) must execute complicated algorithms for the control of several sophisticated subsystems. It must implement this control with requirements for easy modifiability, for high availability, and provide stringent protection for personnel and the environment. Software techniques used to deal with these requirements are described, including modularization based on the structure of the physical systems, a two-level hierarchy of concurrency, a dynamically modifiable man-machine interface, and a specification and documentation language based on a computerized form of structured flowcharts

Gravitational fields as generalized string models

We show that Einstein's main equations for stationary axisymmetric fields in vacuum are equivalent to the motion equations for bosonic strings moving on a special nonflat background. This new representation is based on the analysis of generalized harmonic maps in which the metric of the target space explicitly depends on the parametrization of the base space. It is shown that this representation is valid for any gravitational field which possesses two commuting Killing vector fields. We introduce the concept of dimensional extension which allows us to consider this type of gravitational fields as strings embedded in D-dimensional nonflat backgrounds, even in the limiting case where the Killing vector fields are hypersurface orthogonal.Comment: latex, 25 page

Heavy-light mesons with staggered light quarks

We demonstrate the viability of improved staggered light quarks in studies of heavy-light systems. Our method for constructing heavy-light operators exploits the close relation between naive and staggered fermions. The new approach is tested on quenched configurations using several staggered actionsn combined with nonrelativistic heavy quarks. The B_s meson kinetic mass, the hyperfine and 1P-1S splittings in B_s, and the decay constant f_{B_s} are calculated and compared to previous quenched lattice studies. An important technical detail, Bayesian curve-fitting, is discussed at length.Comment: 38 pages, figures included. v2: Entry in Table IX corrected and other minor changes, version appearing in Phys. Rev.

The geometry of spontaneous spiking in neuronal networks

The mathematical theory of pattern formation in electrically coupled networks of excitable neurons forced by small noise is presented in this work. Using the Freidlin-Wentzell large deviation theory for randomly perturbed dynamical systems and the elements of the algebraic graph theory, we identify and analyze the main regimes in the network dynamics in terms of the key control parameters: excitability, coupling strength, and network topology. The analysis reveals the geometry of spontaneous dynamics in electrically coupled network. Specifically, we show that the location of the minima of a certain continuous function on the surface of the unit n-cube encodes the most likely activity patterns generated by the network. By studying how the minima of this function evolve under the variation of the coupling strength, we describe the principal transformations in the network dynamics. The minimization problem is also used for the quantitative description of the main dynamical regimes and transitions between them. In particular, for the weak and strong coupling regimes, we present asymptotic formulas for the network activity rate as a function of the coupling strength and the degree of the network. The variational analysis is complemented by the stability analysis of the synchronous state in the strong coupling regime. The stability estimates reveal the contribution of the network connectivity and the properties of the cycle subspace associated with the graph of the network to its synchronization properties. This work is motivated by the experimental and modeling studies of the ensemble of neurons in the Locus Coeruleus, a nucleus in the brainstem involved in the regulation of cognitive performance and behavior