Optimization and Parallelization of a force field for silicon using OpenMP

The force field by Lenosky and coworkers is the latest force field for silicon which is one of the most studied materials. It has turned out to be highly accurate in a large range of test cases. The optimization and parallelization of this force field using OpenMp and Fortan90 is described here. The optimized program allows us to handle a very large number of silicon atoms in large scale simulations. Since all the parallelization is hidden in a single subroutine that returns the total energies and forces, this subroutine can be called from within a serial program in an user friendly way.Comment: The program can be obtained upon request from the author ([email protected]

Abstract Hidden Markov Models: a monadic account of quantitative information flow

Hidden Markov Models, HMM's, are mathematical models of Markov processes with state that is hidden, but from which information can leak. They are typically represented as 3-way joint-probability distributions. We use HMM's as denotations of probabilistic hidden-state sequential programs: for that, we recast them as `abstract' HMM's, computations in the Giry monad $\mathbb{D}$, and we equip them with a partial order of increasing security. However to encode the monadic type with hiding over some state $\mathcal{X}$ we use $\mathbb{D}\mathcal{X}\to \mathbb{D}^2\mathcal{X}$ rather than the conventional $\mathcal{X}{\to}\mathbb{D}\mathcal{X}$ that suffices for Markov models whose state is not hidden. We illustrate the $\mathbb{D}\mathcal{X}\to \mathbb{D}^2\mathcal{X}$ construction with a small Haskell prototype. We then present uncertainty measures as a generalisation of the extant diversity of probabilistic entropies, with characteristic analytic properties for them, and show how the new entropies interact with the order of increasing security. Furthermore, we give a `backwards' uncertainty-transformer semantics for HMM's that is dual to the `forwards' abstract HMM's - it is an analogue of the duality between forwards, relational semantics and backwards, predicate-transformer semantics for imperative programs with demonic choice. Finally, we argue that, from this new denotational-semantic viewpoint, one can see that the Dalenius desideratum for statistical databases is actually an issue in compositionality. We propose a means for taking it into account

Parallel simulation of particle dynamics with application to micropolar peridynamic lattice modeling of reinforced concrete Structures

As the first goal of this thesis, we will explain a general purpose parallel particle dynamics code (pdQ2). We describe the re-architecting of pdQ (the MD/PD code that was developed in [Sakhavand 2011]) as pdQ2. pdQ2 is completely non-domain-specific in that user files are clearly separated from non-user files and no #ifdefs exist in the code. Thus, it operates as a particle simulation engine that is capable of executing any parallel particle dynamics model. As in the original pdQ, users can customize their own physical models without having to deal with complexities such as parallelization, but the ease of extensibility has been significantly improved. It is shown that pdQ2 is about four times as fast as pdQ using parallel supercomputers. In the second part of the thesis, we will model reinforced concrete structures based on peridynamic theory [Silling 1998]. We discard the continuum mechanics paradigm completely, and model reinforced concrete by introducing the micropolar peridynamic lattice model (MPLM)\u27. The MPLM models a structure as a close-packed particle lattice. In the MPLM, rather than viewing the structure as collection of truss or beam elements (as with traditional lattice models), the model is viewed as collection of particle masses (as with peridynamic models). The MPLM uses a finite number of equally-spaced interacting particles of finite mass. Thus, it does not need any ad hoc discretization and it is more straightforward to implement computationally. Also, the MPLM is conceptually simpler than both the lattice and peridynamic models [Gerstle et al. 2012]. After defining the MPLM, its application to reinforced concrete structures is investigated through several examples using pdQ2.\u2

Object-Oriented Implementation of the NAS Parallel Benchmarks using Charm++

This report describes experiences with implementing the NAS Computational Fluid Dynamics benchmarks using a parallel object-oriented language, Charm++. Our main objective in implementing the NAS CFD kernel benchmarks was to develop a code that could be used to easily experiment with different domain decomposition strategies and dynamic load balancing. We also wished to leverage the object-orientation provided by the Charm++ parallel object-oriented language, to develop reusable abstractions that would simplify the process of developing parallel applications. We first describe the Charm++ parallel programming model and the parallel object array abstraction, then go into detail about each of the Scalar Pentadiagonal (SP) and Lower/Upper Triangular (LU) benchmarks, along with performance results. Finally we conclude with an evaluation of the methodology used

Approaches to the determination of parallelism in computer programs

Approaches to the determination of parallelism in computer program

Cardiac cell modelling: Observations from the heart of the cardiac physiome project

In this manuscript we review the state of cardiac cell modelling in the context of international initiatives such as the IUPS Physiome and Virtual Physiological Human Projects, which aim to integrate computational models across scales and physics. In particular we focus on the relationship between experimental data and model parameterisation across a range of model types and cellular physiological systems. Finally, in the context of parameter identification and model reuse within the Cardiac Physiome, we suggest some future priority areas for this field

Refinement of Classical Proofs for Program Extraction

The A-Translation enables us to unravel the computational information in classical proofs, by first transforming them into constructive ones, however at the cost of introducing redundancies in the extracted code. This is due to the fact that all negations inserted during translation are replaced by the computationally relevant form of the goal. In this thesis we are concerned with eliminating such redundancies, in order to obtain better extracted programs. For this, we propose two methods: a controlled and minimal insertion of negations, such that a refinement of the A-Translation can be used and an algorithmic decoration of the proofs, in order to mark the computationally irrelevant components. By restricting the logic to be minimal, the Double Negation Translation is no longer necessary. On this fragment of minimal logic we apply the refined A-Translation, as proposed in (Berget et al., 2002). This method identifies further selected classes of formulas for which the negations do not need to be substituted by computationally relevant formulas. However, the refinement imposes restrictions which considerably narrow the applicability domain of the A-Translation. We address this issue by proposing a controlled insertion of double negations, with the benefit that some intuitionistically valid \Pi^0_2-formulas become provable in minimal logic and that certain formulas are transformed to match the requirements of the refined A-Translation. We present the outcome of applying the refined A-translation to a series of examples. Their purpose is two folded. On one hand, they serve as case studies for the role played by negations, by shedding a light on the restrictions imposed by the translation method. On the other hand, the extracted programs are characterized by a specific behaviour: they adhere to the continuation passing style and the recursion is in general in tail form. The second improvement concerns the detection of the computationally irrelevant subformulas, such that no terms are extracted from them. In order to achieve this, we assign decorations to the implication and universal quantifier. The algorithm that we propose is shown to be optimal, correct and terminating and is applied on the examples of factorial and list reversal.Die A-Übersetzung ermöglicht es, die rechnerische Information aus klassischen Beweisen einzuholen. Dennoch hat sie den Nachteil, dass die Programme, die man aus auf diese Weise transformierten Beweisen extrahiert, viele redundante Teile enthalten. Das liegt daran, dass die A-Übersetzung viele doppelte Negationen hinzufügt und alle diese Negationen durch die rechnerisch relevante Form der Ziel-Formel substituiert werden. In dieser Doktorarbeit werden Methoden dargestellt, um Teile der redundante Information in den extrahierten Programen zu entfernen. Einerseits wird das Einfügen der Negationen minimal gehalten und anderseits werden die nicht rechnerischen Teile als solche indentifiziert und ausgezeichnet. Wir bemerken zuerst, dass in der Minimallogik das Einfügen der doppelten Negationen nicht mehr nötig ist. Darüber hinaus, um das Ersetzen aller Negationen zu vermeiden, identifizieren (Berger et al., 2002) diejenigen, wo die Substitution nicht nötig ist. Diese verfeinerte A-Übersetzung hat aber den Nachteil, dass sie den Anwendungsbereich begrenzt. Um das zu beseitigen, wird in dieser Dissertation eine verfeinerte Doppel-Negation angewandt, die bestimmte Formeln so umsetzt, dass die verfeinerte A-Übersetzung darauf anwendbar ist. Als Zugabe kann diese Methode auch benutzt werden, um konstruktive Beweise mancher \Pi^0_2-Formeln in der Minimallogik durchzuführen. Dieses Verfahren wird durch Anwendung der verfeinerten A-Übersetzung auf eine Reihe von bedeutenden Fallstudien illustriert. Es werden das Lemma von Dickson, das unendliche Schubfachprinzip und das Erdös-Szekeres Theorem betrachtet. Dabei wird es festgestellt, dass ein Zusammenhang zu der Endrekursion und dem Rechnen mit Fortsezungen besteht. Ferner, um möglichst viel der überflüssigen Information zu entfernen, wird ein Dekorationsalgorithmus vorgelegt. Dadurch werden die rechnerisch irrelevanten Komponenten identifiziert und entsprechend annotiert, so dass sie während der Extraktion nicht berücksichtigt werden. Es wird gezeigt, dass das vorgeschlagene Dekorationsverfahren, das auf Beweisebene eingesetzt wird, optimal, korrekt und terminierend ist

Sulfur dioxide derivative prevents the prolongation of action potential during the isoproterenol-induced hypertrophy of rat cardiomyocytes

Exogenous SO2 is toxic especially to the pulmonary and cardiovascular system, similar to nitric-oxide, carbon-monoxide, and hydrogen-sulfide. Endogenous SO2 is produced in many cell types. The SO2 content of the rat heart has been observed to substantially decrease during isoproterenol-induced hypertrophy. This study sought to determine whether an SO2 derivative could inhibit the prolongation of action potentials during the isoproterenol-induced hypertrophy of rat cardiomyocytes and explore the ionic currents. Alongside electrocardiogram recordings, the voltage and current- clamped measurements were conducted in the enzymatically isolated left ventricular cardiomyocytes of Wistar rats. The consistency of the results was evaluated by the novel mathematical electrophysiology model. Our results show that SO2 significantly blocked the prolongation of QT-interval and action potential duration. Furthermore, SO2 did not substantially affect the Na+ currents and did not improve the decreased steady- state and transient outward K+ currents, but it reverted the reduced L-type Ca2+ currents (ICaL) to the physiological levels. Altered inactivation of ICaL was remarkably recovered by SO2. Interestingly, SO2 significantly increased the Ca2+ transients in hypertrophic rat hearts. Our mathematical model also confirmed the mechanism of the SO2 effect. Our findings suggest that the shortening mechanism of SO2 is related to the Ca2+ dependent inactivation kinetics of the Ca2+ current.This study was supported in part by Akdeniz University Scientific Research Coordination Unit (Project No: 2012.02.0122.009) and The Scientific and Technological Research Council of Turkey (TUBITAK, Project No: 117F020). These funding sources had no involvement in study design, writing of the report, decision to publish, or the collection, analysis, and interpretation of data