Integrity static analysis of COTS/SOUP

This paper describes the integrity static analysis approach developed to support the justification of commercial off-the-shelf software (COTS) used in a safety-related system. The static analysis was part of an overall software qualification programme, which also included the work reported in our paper presented at Safecomp 2002. Integrity static analysis focuses on unsafe language constructs and “covert” flows, where one thread can affect the data or control flow of another thread. The analysis addressed two main aspects: the internal integrity of the code (especially for the more critical functions), and the intra-component integrity, checking for covert channels. The analysis process was supported by an aggregation of tools, combined and engineered to support the checks done and to scale as necessary. Integrity static analysis is feasible for industrial scale software, did not require unreasonable resources and we provide data that illustrates its contribution to the software qualification programme

Conceptual design study of a coal gasification combined-cycle powerplant for industrial cogeneration

A conceptual design study was conducted to assess technical feasibility, environmental characteristics, and economics of coal gasification. The feasibility of a coal gasification combined cycle cogeneration powerplant was examined in response to energy needs and to national policy aimed at decreasing dependence on oil and natural gas. The powerplant provides the steam heating and baseload electrical requirements while serving as a prototype for industrial cogeneration and a modular building block for utility applications. The following topics are discussed: (1) screening of candidate gasification, sulfur removal and power conversion components; (2) definition of a reference system; (3) quantification of plant emissions and waste streams; (4) estimates of capital and operating costs; and (5) a procurement and construction schedule. It is concluded that the proposed powerplant is technically feasible and environmentally superior

The Effects of Stacking on the Configurations and Elasticity of Single Stranded Nucleic Acids

Stacking interactions in single stranded nucleic acids give rise to configurations of an annealed rod-coil multiblock copolymer. Theoretical analysis identifies the resulting signatures for long homopolynucleotides: A non monotonous dependence of size on temperature, corresponding effects on cyclization and a plateau in the extension force law. Explicit numerical results for poly(dA) and poly(rU) are presented.Comment: 4 pages and 2 figures. Accepted in Phys. Rev. E Rapid Com

Towards Identifying and closing Gaps in Assurance of autonomous Road vehicleS - a collection of Technical Notes Part 1

This report provides an introduction and overview of the Technical Topic Notes (TTNs) produced in the Towards Identifying and closing Gaps in Assurance of autonomous Road vehicleS (Tigars) project. These notes aim to support the development and evaluation of autonomous vehicles. Part 1 addresses: Assurance-overview and issues, Resilience and Safety Requirements, Open Systems Perspective and Formal Verification and Static Analysis of ML Systems. Part 2: Simulation and Dynamic Testing, Defence in Depth and Diversity, Security-Informed Safety Analysis, Standards and Guidelines

Modelling background intensity in Affymetrix Genechips

DNA microarrays are devices that are able, in principle, to detect and quantify the presence of specific nucleic acid sequences in complex biological mixtures. The measurement consists in detecting fluorescence signals from several spots on the microarray surface onto which different probe sequences are grafted. One of the problems of the data analysis is that the signal contains a noisy background component due to non-specific binding. This paper presents a physical model for background estimation in Affymetrix Genechips. It combines two different approaches. The first is based on the sequence composition, specifically its sequence dependent hybridization affinity. The second is based on the strong correlation of intensities from locations which are the physical neighbors of a specific spot on the chip. Both effects are incorporated in a background functional which contains 24 free parameters, fixed by minimization on a training data set. In all data analyzed the sequence specific parameters, obtained by minimization, are found to strongly correlate with empirically determined stacking free energies for RNA/DNA hybridization in solution. Moreover, there is an overall agreement with experimental background data and we show that the physics-based model proposed in this paper performs on average better than purely statistical approaches for background calculations. The model thus provides an interesting alternative method for background subtraction schemes in Affymetrix Genechips.Comment: 8 pages, 4 figure

Towards Identifying and closing Gaps in Assurance of autonomous Road vehicleS - a collection of Technical Notes Part 2

This report provides an introduction and overview of the Technical Topic Notes (TTNs) produced in the Towards Identifying and closing Gaps in Assurance of autonomous Road vehicleS (Tigars) project. These notes aim to support the development and evaluation of autonomous vehicles. Part 1 addresses: Assurance-overview and issues, Resilience and Safety Requirements, Open Systems Perspective and Formal Verification and Static Analysis of ML Systems. This report is Part 2 and discusses: Simulation and Dynamic Testing, Defence in Depth and Diversity, Security-Informed Safety Analysis, Standards and Guidelines

Wigner crystal model of counterion induced bundle formation of rod-like polyelectrolytes

A simple electrostatic theory of condensation of rod-like polyelectrolytes under influence of polyvalent ions is proposed. It is based on the idea that Manning condensation of ions results in formation of the Wigner crystal on a background of a bundle of rods. It is shown that, depending on a single dimensionless parameter, this can be the densely packed three-dimensional Wigner crystal or the two-dimensional crystal on the rod surfaces. For DNA the location of charge on the spiral results in a model of the one-dimensional Wigner crystal. It is also argued that the Wigner crystal idea can be applied to self-assembly of other polyelectrolytes, for example, colloids and DNA-lipid complexes.Comment: 4 pages; typos corrected, references adde

Cosmology in a String-Dominated Universe

The string-dominated universe locally resembles an open universe, and fits dynamical measures of power spectra, cluster abundances, redshift distortions, lensing constraints, luminosity and angular diameter distance relations and microwave background observations. We show examples of networks which might give rise to recent string-domination without requiring any fine-tuned parameters. We discuss how future observations can distinguish this model from other cosmologies.Comment: 17 pages including 4 figures, of which one is in colo

Effective affinities in microarray data

In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. Although there is a general consensus about this approach, some discrepancies between different studies are evident. For instance, some authors have fitted the hybridization affinities from the microarray fluorescent intensities, while others used affinities obtained from melting experiments in solution. The former approach yields fitted affinities that at first sight are only partially consistent with solution values. In this paper we show that this discrepancy exists only superficially: a sufficiently complete model provides effective affinities which are fully consistent with those fitted to experimental data. This link provides new insight on the relevant processes underlying the functioning of DNA microarrays.Comment: 8 pages, 6 figure