Resolution Trees with Lemmas: Resolution Refinements that Characterize DLL Algorithms with Clause Learning

Resolution refinements called w-resolution trees with lemmas (WRTL) and with input lemmas (WRTI) are introduced. Dag-like resolution is equivalent to both WRTL and WRTI when there is no regularity condition. For regular proofs, an exponential separation between regular dag-like resolution and both regular WRTL and regular WRTI is given. It is proved that DLL proof search algorithms that use clause learning based on unit propagation can be polynomially simulated by regular WRTI. More generally, non-greedy DLL algorithms with learning by unit propagation are equivalent to regular WRTI. A general form of clause learning, called DLL-Learn, is defined that is equivalent to regular WRTL. A variable extension method is used to give simulations of resolution by regular WRTI, using a simplified form of proof trace extensions. DLL-Learn and non-greedy DLL algorithms with learning by unit propagation can use variable extensions to simulate general resolution without doing restarts. Finally, an exponential lower bound for WRTL where the lemmas are restricted to short clauses is shown

Types with potential: polynomial resource bounds via automatic amortized analysis

A primary feature of a computer program is its quantitative performance characteristics: the amount of resources such as time, memory, and power the program needs to perform its task. Concrete resource bounds for specific hardware have many important applications in software development but their manual determination is tedious and error-prone. This dissertation studies the problem of automatically determining concrete worst-case bounds on the quantitative resource consumption of functional programs. Traditionally, automatic resource analyses are based on recurrence relations. The difficulty of both extracting and solving recurrence relations has led to the development of type-based resource analyses that are compositional, modular, and formally verifiable. However, existing automatic analyses based on amortization or sized types can only compute bounds that are linear in the sizes of the arguments of a function. This work presents a novel type system that derives polynomial bounds from first-order functional programs. As pioneered by Hofmann and Jost for linear bounds, it relies on the potential method of amortized analysis. Types are annotated with multivariate resource polynomials, a rich class of functions that generalize non-negative linear combinations of binomial coefficients. The main theorem states that type derivations establish resource bounds that are sound with respect to the resource-consumption of programs which is formalized by a big-step operational semantics. Simple local type rules allow for an efficient inference algorithm for the type annotations which relies on linear constraint solving only. This gives rise to an analysis system that is fully automatic if a maximal degree of the bounding polynomials is given. The analysis is generic in the resource of interest and can derive bounds on time and space usage. The bounds are naturally closed under composition and eventually summarized in closed, easily understood formulas. The practicability of this automatic amortized analysis is verified with a publicly available implementation and a reproducible experimental evaluation. The experiments with a wide range of examples from functional programming show that the inference of the bounds only takes a couple of seconds in most cases. The derived heap-space and evaluation-step bounds are compared with the measured worst-case behavior of the programs. Most bounds are asymptotically tight, and the constant factors are close or even identical to the optimal ones. For the first time we are able to automatically and precisely analyze the resource consumption of involved programs such as quick sort for lists of lists, longest common subsequence via dynamic programming, and multiplication of a list of matrices with different, fitting dimensions

Types with potential: polynomial resource bounds via automatic amortized analysis

A primary feature of a computer program is its quantitative performance characteristics: the amount of resources such as time, memory, and power the program needs to perform its task. Concrete resource bounds for specific hardware have many important applications in software development but their manual determination is tedious and error-prone. This dissertation studies the problem of automatically determining concrete worst-case bounds on the quantitative resource consumption of functional programs. Traditionally, automatic resource analyses are based on recurrence relations. The difficulty of both extracting and solving recurrence relations has led to the development of type-based resource analyses that are compositional, modular, and formally verifiable. However, existing automatic analyses based on amortization or sized types can only compute bounds that are linear in the sizes of the arguments of a function. This work presents a novel type system that derives polynomial bounds from first-order functional programs. As pioneered by Hofmann and Jost for linear bounds, it relies on the potential method of amortized analysis. Types are annotated with multivariate resource polynomials, a rich class of functions that generalize non-negative linear combinations of binomial coefficients. The main theorem states that type derivations establish resource bounds that are sound with respect to the resource-consumption of programs which is formalized by a big-step operational semantics. Simple local type rules allow for an efficient inference algorithm for the type annotations which relies on linear constraint solving only. This gives rise to an analysis system that is fully automatic if a maximal degree of the bounding polynomials is given. The analysis is generic in the resource of interest and can derive bounds on time and space usage. The bounds are naturally closed under composition and eventually summarized in closed, easily understood formulas. The practicability of this automatic amortized analysis is verified with a publicly available implementation and a reproducible experimental evaluation. The experiments with a wide range of examples from functional programming show that the inference of the bounds only takes a couple of seconds in most cases. The derived heap-space and evaluation-step bounds are compared with the measured worst-case behavior of the programs. Most bounds are asymptotically tight, and the constant factors are close or even identical to the optimal ones. For the first time we are able to automatically and precisely analyze the resource consumption of involved programs such as quick sort for lists of lists, longest common subsequence via dynamic programming, and multiplication of a list of matrices with different, fitting dimensions

Massenspektrometrische Untersuchungen biomolekularer Makrokomplexe aus nativen Lösungen mit LILBID

The analysis of biomolecular macrocomplexes requires certain preconditions to be fulfilled. The preparation of biomolecular samples usually results in low yields. Due to this constraint of low availability any method should provide a sufficient sensitivity to cope with typical sample amounts. Biomolecules also often show a reduced stability, i.e. a propensity for fragmentation upon ionisation, which requires reasonable soft methods for the investigation. Furthermore macromolecular complexes usually are composed by means of non-covalent interactions presenting additional demands on the softness. This holds true for specific complexes like protein-ligand or DNA double strand binding. For the formation of non-covalent, specific complexes the biomolecules’ native structure and environment are a basic prerequisite and hence crucial. Therefore it is desirable during analysis to keep the biomolecules in a native environment to preserve their structure and weak interactions. One suitable method for analysing biomolecules is mass spectrometry. Mass spectrometry is capable of high throughput screening as well as determining masses with high accuracy and high sensitivity. Especially since the availability of MALDI-MS and ESI-MS mass spectrometry evolved to a versatile tool to investigate biomolecular complexes. Both, MALDI- and ESI-MS are sufficiently soft methods to observe fragile biomolecules. Yet both methods have their advantages and disadvantages. During the recent years an alternative mass spectrometric approach has been developed in our group, termed LILBID-MS (Laser Induced Liquid Bead Ionisation/Desorption). In LILBID microdroplets of aqueous solution containing buffer, salt and further additives among the analyte molecules are injected into vacuum and irradiated one-by-one by mid-IR laser pulses. The absorption of the energy by the water leads to a rapid ablation of the preformed analyte ions. LILBID is highly tolerant for the addition of salts and detergents allowing to study biomolecular complexes in a native environment. As LILBID-MS is soft enough to avoid fragmentation, specific non-covalent complexes can be analysed directly from their native environment by this method. In addition dissociation can be induced on demand by increasing the laser intensity which allows for the study of subunit compositions. A further prominent property of LILBID is the possibility to study hydrophobic membrane proteins due to the tolerated use of detergents. During the course of this work, several instrumental improvements mostly concerning ion focussing and beam steering were introduced. Together with refinements of different modes of measurement the result is a significantly improved signal-to-noise ratio as well as a further improvement in sensitivity. In addition the accessible m/z range for a given flight time has been vastly increased. The new possibilities that LILBID now offers for the study of biomolecular complexes were investigated. The ability to detect specific binding in LILBID-MS was investigated by means of nucleic acids and their interaction with proteins. It could be shown that the stability of a 16bp dsDNA corresponds to that in solution phase regarding the dependency on concentration and type of the salts used. In addition a competitive experiment with the well-known transcription factor p50 was used to demonstrate the detection of sequence-specific binding with LILBID. The improved sensitivity allowed to detect single stranded DNA at nanomolar concentrations and even the 2686bp plasmid pUC19 could be easily detected without fragmentation using a concentration of only 80nM. In case of the transcription factor p63 the mass spectrometric analysis could help to identify a new model of activation and inhibition. For the first time known quarternary structures of membrane proteins like the light-driven proton pump bacteriorhodopsin and the potassium channel KcsA could be detected with mass spectrometry. For the light-driven proton pump proteorhodopsin the type and the concentration of the used detergents significantly influenced the stability of this protein as well as the preferred quarternary structure.Massenspektrometrie ist eine wichtige Methode zur Charakterisierung von Biomolekülen, mit der unter anderem die Sequenz, quartäre Struktur, Konnektivität von Untereinheiten und Komplexierungen mit Liganden bestimmt werden können. Eine besondere Herausforderung dabei ist der schonende Transfer der Molekülionen von der flüssigen in die Gasphase. Als schonende Verfahren für massenspektrometrische Untersuchungen an Biomolekülen haben sich ESI und MALDI etabliert. Seit einigen Jahren wird in der Arbeitsgruppe von Prof. Brutschy ein alternatives Verfahren mit dem Namen LILBID (Laser Induced Liquid Bead Ionisation/Desorption) entwickelt. In LILBID werden die zu analysierenden Moleküle mittels eines IR-Lasers direkt aus wässrigen Lösungen desorbiert. LILBID stellt eine komplementäre massenspektrometrische Methode zu ESI und MALDI dar, da sie besonders für den Nachweis von sehr großen, nichtkovalenten Komplexen, insbesondere von Membranproteinen, geeignet ist. Am Beispiel von doppelsträngiger DNA wurde der Nachweis spezifischer, nichtkovalenter Komplexe mit LILBID charakterisiert. Es konnte gezeigt werden, dass die Stabilität eines 16-mer Doppelstranges in Abhängigkeit von der Art und der Konzentration des verwendeten Salzes derjenigen in Lösung entspricht. Anhand des Transkriptionsfaktors p50 wurde in einem kompetitiven Experiment der Nachweis der Bildung sequenzspezifischer Komplexe demonstriert. Instrumentelle Modifikationen am Massenspektrometer führten zu einer verbesserten Empfindlichkeit. So konnte ein DNA-Einzelstrang in einer Konzentration von 9 nM detektiert werden und für das 1,6 MDa Plasmid pUC19 wurde eine Konzentration von nur 80 nM benötigt. Darüber hinaus wurden spezifische Protein-RNA Komplexe untersucht. Im Fall von TAV 2B, einem Protein, dass RNA-Interferenz unterdrückt, konnte nachgewiesen werden, dass erst die Bindung an RNA eine Oligomerisierung des Proteins induziert. Am Beispiel der löslichen Proteine HvoLsm und p63 konnte gezeigt werden, dass die Wahl des Puffersystems entscheidend für die native Struktur ist. Im Fall des Transkriptionsfaktors p63 konnte erstmals ein Dimer nachgewiesen werden, der auf einen neuen Aktivierungsmechanismus beruht. Am Beispiel der lichtgetriebenen Protonenpumpe Bakteriorhodopsin und des Kaliumkanals KcsA wurden bekannte quartäre Strukturen von Membranproteinen erstmals massenspektrometrisch nachgewiesen. Für Proteorhodopsin wurde gezeigt, dass die Wahl des verwendeten Detergens maßgeblich die Struktur beeinflusst. Für den Ionenkanal Channelrhodopsin-2 wurde mit LILBID erstmals eine mögliche Stöchiometrie für den in Detergens gelösten Komplex gefunden. Schließlich wurde anhand einer F1Fo -ATP Synthase für Membranproteine gezeigt, wie die Wahl des Puffersystems die Komplexierung beeinflusst und dass diese Auswirkungen mit LILBID massenspektrometrisch nachgewiesen werden können

The Influence of the EU Environmental Management and Auditing Scheme on Environmental Innovations and Competitiveness in Germany: An Analysis on the Basis of Case Studies and a Large-Scale Survey

This paper investigates the effects of the EU Environmental Management and Auditing Scheme (EMAS) on environmental innovations and competitiveness in German facilities. It comprises twelve in-depth case studies and telephone interviews with 1277 EMAS-validated facilities. The surveys show a positive influence of EMAS on environmental organisational, process and product innovations. Moreover, the environmental report supports the diffusion of environmental innovations. The econometric analysis with binary probit models shows a significant positive impact of the maturity of environmental management systems on environmental innovations. Another determinant of environmental innovations is the strong participation of specific departments in further development of EMAS, especially of the R&D department. An effect of strategic importance of EMAS on market success could not be confirmed. Facilities with high learning processes by environmental management systems however have a significantly better performance concerning turnover and exports. --Environmental management systems,environmental innovation,technological progress,cleaner production