Burroughs Large Systems

The Burroughs Large Systems Group produced a family of large 48-bit mainframes using stack machine instruction sets with dense syllables. The first machine in the family was the B5000 in 1961, which was optimized for compiling ALGOL 60 programs extremely well, using single-pass compilers. The B5000 evolved into the B5500 (disk rather than drum) and the B5700 (up to four systems running as a cluster). Subsequent major redesigns include the B6500/B6700 line and its successors, as well as the separate B8500 line. In the 1970s, the Burroughs Corporation was organized into three divisions with very different product line architectures for high-end, mid-range, and entry-level business computer systems. Each division's product line grew from a different concept for how to optimize a computer's instruction set for particular programming languages. "Burroughs Large Systems" referred to all of these large-system product lines together, in contrast to the COBOL-optimized Medium Systems (B2000,

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A Formal Specification for a Real-Time Train Controller

Simon Kramer

We give a formal specification for a real-time controller for trains that operate on the Italian railway network. The controller will control train movements and is part of a larger system destined to guarantee safety with respect to dangers originating from train traffic in the railway network. Based on an informal specification document from the Italian railway company, we construct a simple state-based model and formalise it in terms of the property-based specification language TRIO. The obtained specification being formal, we are able to perform certain verifications on it, such as checking its satisfiability and verifying correctness of refinement steps.

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Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks

Robin Alexander Denhardt-Eriksson

Modelling and analysis of biological systems is crucial in order to quantitatively explain and predict their behaviour. The importance of modelling in systems biology becomes even more evident when tackling complex, large systems. Approaches that rely on modelling can be used to tackle a range of problems, such as cellular signalling or using genetically modified bacteria to synthesize human proteins for medical purposes. These phenomena range across different spatiotemporal scales, whether it is predicting the decay of red blood cells for blood transfusion or finding engineering targets in order to increase the productivity of bioprocesses. Reconciling models with experimental data and quantifying how uncertainty propagates through these models is crucial to exploiting them to their full potential. Uncertainty impacts not only the calibration and validation of a model, but also the predictions extracted from it. Developing and implementing uncertainty quantification methods into these models is a key step in exploring their behaviour and accelerating the adoption of such methods in metabolic engineering. In this thesis I firstly propose to implement and explore uncertainty quantification methods on control coefficients obtained by Metabolic Control Analysis (MCA) of Genome Scale Metabolic Models (GEMs), with the goal of quantifying uncertainty propagation from model parameters to control coefficients. I additionally want to build Single Protein Models that describe the effects of Post Translational Modifications (PTMs). The nature of the experimental data available to calibrate these models makes uncertainty an inherent property, and therefore Global Sensitivty Analysis (GSA) techniques are well suited to describing the links between parameter uncertainty and model behaviour.

EPFL2021

Koopmans Meets Bethe-Salpeter: Excitonic Optical Spectra without GW

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The Bethe Salpeter equation (BSE) can be applied to compute from first-principles optical spectra that include the effects of screened electron hole interactions. As input, BSE calculations require single-particle states, quasiparticle energy levels, and the screened Coulomb interaction, which are typically obtained with many-body perturbation theory, whose cost limits the scope of possible applications. This work tries to address this practical limitation, instead deriving spectral energies from Koopmans-compliant functionals and introducing a new methodology for handling the screened Coulomb interaction. The explicit calculation of the W matrix is bypassed via a direct minimization scheme applied on top of a maximally localized Wannier function basis. We validate and benchmark this approach by computing the low-lying excited states of the molecules in Thiel's set and the optical absorption spectrum of a C-60 fullerene. The results show the same trends as quantum chemical methods and are in excellent agreement with previous simulations carried out at the time-dependent density functional theory or G(0)W(0)-BSE level. Conveniently, the new framework reduces the parameter space controlling the accuracy of the calculation, thereby simplifying the simulation of charge-neutral excitations, offering the potential to expand the applicability of first principles spectroscopies to larger systems of applied interest.

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