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The study of (anti-)deuteron production in pp collisions has proven to be a powerful tool to investigate the formation mechanism of loosely bound states in high energy hadronic collisions. In this paper the production of (anti-)deuterons is studied as a function of the charged particle multiplicity in inelastic pp collisions at s√=13 TeV using the ALICE experiment. Thanks to the large number of accumulated minimum bias events, it has been possible to measure (anti-)deuteron production in pp collisions up to the same charged particle multiplicity (dNch/dη∼26) as measured in p-Pb collisions at similar centre-of-mass energies. Within the uncertainties, the deuteron yield in pp collisions resembles the one in p-Pb interactions, suggesting a common formation mechanism behind the production of light nuclei in hadronic interactions. In this context the measurements are compared with the expectations of coalescence and Statistical Hadronisation Models (SHM).
The study of (anti-)deuteron production in pp collisions has proven to be a powerful tool to investigate the formation mechanism of loosely bound states in high energy hadronic collisions. In this paper the production of (anti-)deuterons is studied as a function of the charged particle multiplicity in inelastic pp collisions at s√=13 TeV using the ALICE experiment. Thanks to the large accumulated integrated luminosity, it has been possible to measure (anti-)deuteron production in pp collisions up to the same charged particle multiplicity (dNch/dη∼26) as measured in p-Pb collisions at similar centre-of-mass energies. Within the uncertainties, the deuteron yield in pp collisions resembles the one in p-Pb interactions, suggesting a common formation mechanism behind the production of light nuclei in hadronic interactions. In this context the measurements are compared with the expectations of coalescence and Statistical Hadronisation Models (SHM).
This volume contains the proceedings of the 12th International Workshop on Termination (WST 2012), to be held February 19–23, 2012 in Obergurgl, Austria. The goal of the Workshop on Termination is to be a venue for presentation and discussion of all topics in and around termination. In this way, the workshop tries to bridge the gaps between different communities interested and active in research in and around termination. The 12th International Workshop on Termination in Obergurgl continues the successful workshops held in St. Andrews (1993), La Bresse (1995), Ede (1997), Dagstuhl (1999), Utrecht (2001), Valencia (2003), Aachen (2004), Seattle (2006), Paris (2007), Leipzig (2009), and Edinburgh (2010). The 12th International Workshop on Termination did welcome contributions on all aspects of termination and complexity analysis. Contributions from the imperative, constraint, functional, and logic programming communities, and papers investigating applications of complexity or termination (for example in program transformation or theorem proving) were particularly welcome. We did receive 18 submissions which all were accepted. Each paper was assigned two reviewers. In addition to these 18 contributed talks, WST 2012, hosts three invited talks by Alexander Krauss, Martin Hofmann, and Fausto Spoto.
1D-3D hybrid modeling : from multi-compartment models to full resolution models in space and time
(2014)
Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator—which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved, highly detailed 3D-modeling approaches. We present the developed general framework for 1D/3D hybrid modeling and apply it to investigate electrically active neurons and their intracellular spatio-temporal calcium dynamics.
Contents:
Yuki Chiba, Santiago Escobar, Naoki Nishida, and David Sabel, and Manfred Schmidt-Schauß : Preface:
The Collection of all Abstracts of the Talks at WPTE 2015 xi
Brigitte Pientka : Mechanizing Meta-Theory in Beluga
Giulio Guerrieri : Head reduction and normalization in a call-by-value lambda-calculus
Adrián Palacios and Germán Vidal : Towards Modelling Actor-Based Concurrency in Term Rewriting
David Sabel and Manfred Schmidt-Schauß : Observing Success in the Pi-Calculus
Sjaak Smetsers, Ken Madlener, and Marko van Eekelen : Formalizing Bialgebraic Semantics in PVS 6.0
Klassische Bildmanipulation spielt sich meist im Zweidimensionalen, also in der reinen Bild-ebene ab. So werden beispielsweise Objekte aus Fotos entfernt, indem die dahinterliegende Struktur nachgezeichnet wird, oder es werden mehrere Teilbilder zu einem neuen, verfälschten Motiv zusammengesetzt. Bei der sogenannten Bildretuschierung werden unschöne Bereiche übermalt, um einen besseren Gesamteindruck zu erreichen. All diese Manipulationen haben im Grunde das gleiche Ziel: Das Erstellen einer möglichst realistischen Verfälschung der darge-stellten Szene indem die eigentlich dreidimensionalen Elemente in 2D imitiert werden.
Ziel dieser Arbeit ist es, von der reinen Zweidimensionalität eines Bildes Abstand zu nehmen und ein neues Verfahren zu entwickeln, Manipulationen im wirklichen 3D-Inhalt des Fotogra-fierten vorzunehmen. Dazu wird die klassische Bildmanipulation mit aktuellen Verfahren aus dem Bereich Multi View Stereo verknüpft. In einem ersten Schritt wird aus einer Fotoserie ein 3D-Modell mit passenden Texturen erstellt, welches anschließend nach Belieben manipuliert werden kann. Diese Veränderungen werden schließlich wieder in die Originalbilder übertragen, wodurch eine 3D-unterstützte Bildmanipulation realisiert wird.
Die praktische Umsetzung des vorgestellten Verfahrens basiert teilweise auf bereits vorhan-dener Software, die mit dem Ziel der Bildmanipulation neu kombiniert und durch eigene Um-setzungen ergänzt wird. So entsteht eine funktionierende Implementierung, die den kompletten Weg vom Original bis hin zum manipulierten Bild abdeckt.
The production of the hypertriton nuclei 3ΛH and 3Λ¯H¯¯¯¯ has been measured for the first time in Pb-Pb collisions at sNN−−−√ = 2.76 TeV with the ALICE experiment at LHC energies. The total yield, dN/dy ×B.R.(3ΛH→3He,π−)=(3.86±0.77(stat.)±0.68(syst.))×10−5 in the 0-10% most central collisions, is consistent with the predictions from a statistical thermal model using the same temperature as for the light hadrons. The coalescence parameter B3 shows a dependence on the transverse momentum, similar to the B2 of deuterons and the B3 of 3He nuclei. The ratio of yields S3 = 3ΛH/(3He ×Λ/p) was measured to be S3 = 0.60 ± 0.13 (stat.) ± 0.21 (syst.) in 0-10% centrality events; this value is compared to different theoretical models. The measured S3 is fully compatible with thermal model predictions. The measured 3ΛH lifetime, τ=181+54−39(stat.)±33(syst.) ps is compatible within 1σ with the world average value.
The production of the hypertriton nuclei 3ΛH and 3Λ¯H¯¯¯¯ has been measured for the first time in Pb-Pb collisions at sNN−−−√ = 2.76 TeV with the ALICE experiment at LHC energies. The total yield, dN/dy ×B.R.(3ΛH→3He,π−)=(3.86±0.77(stat.)±0.68(syst.))×10−5 in the 0-10% most central collisions, is consistent with the predictions from a statistical thermal model using the same temperature as for the light hadrons. The coalescence parameter B3 shows a dependence on the transverse momentum, similar to the B2 of deuterons and the B3 of 3He nuclei. The ratio of yields S3 = 3ΛH/(3He ×Λ/p) was measured to be S3 = 0.60 ± 0.13 (stat.) ± 0.21 (syst.) in 0-10% centrality events; this value is compared to different theoretical models. The measured S3 is fully compatible with thermal model predictions. The measured 3ΛH lifetime, τ=181+54−39(stat.)±33(syst.) ps is compatible within 1σ with the world average value.
The production of the hypertriton nuclei HΛ3 and H‾Λ¯3 has been measured for the first time in Pb–Pb collisions at sNN=2.76 TeV with the ALICE experiment at LHC. The pT-integrated HΛ3 yield in one unity of rapidity, dN/dy×B.R.(HΛ3→He3,π−)=(3.86±0.77(stat.)±0.68(syst.))×10−5 in the 0–10% most central collisions, is consistent with the predictions from a statistical thermal model using the same temperature as for the light hadrons. The coalescence parameter B3 shows a dependence on the transverse momentum, similar to the B2 of deuterons and the B3 of 3He nuclei. The ratio of yields S3=HΛ3/(He3×Λ/p) was measured to be S3=0.60±0.13(stat.)±0.21(syst.) in 0–10% centrality events; this value is compared to different theoretical models. The measured S3 is compatible with thermal model predictions. The measured HΛ3 lifetime, τ=181−39+54(stat.)±33(syst.)ps is in agreement within 1σ with the world average value.
An improved value for the lifetime of the (anti-)hypertriton has been obtained using the data sample of Pb-Pb collisions at sNN−−−√= 5.02 TeV collected by the ALICE experiment at the LHC. The (anti-)hypertriton has been reconstructed via its charged two-body mesonic decay channel and the lifetime has been determined from an exponential fit to the dN/d(ct) spectrum. The measured value, τ = 242+34−38 (stat.) ± 17 (syst.) ps, is compatible with all the available theoretical predictions, thus contributing to the solution of the longstanding hypertriton lifetime puzzle.
An improved value for the lifetime of the (anti-)hypertriton has been obtained using the data sample of Pb-Pb collisions at sNN−−−√= 5.02 TeV collected by the ALICE experiment at the LHC. The (anti-)hypertriton has been reconstructed via its charged two-body mesonic decay channel and the lifetime has been determined from an exponential fit to the dN/d(ct) spectrum. The measured value, τ = 242+34−38 (stat.) ± 17 (syst.) ps, is compatible with all the available theoretical predictions, thus contributing to the solution of the longstanding hypertriton lifetime puzzle.
50 years of amino acid hydrophobicity scales : revisiting the capacity for peptide classification
(2016)
Background: Physicochemical properties are frequently analyzed to characterize protein-sequences of known and unknown function. Especially the hydrophobicity of amino acids is often used for structural prediction or for the detection of membrane associated or embedded β-sheets and α-helices. For this purpose many scales classifying amino acids according to their physicochemical properties have been defined over the past decades. In parallel, several hydrophobicity parameters have been defined for calculation of peptide properties. We analyzed the performance of separating sequence pools using 98 hydrophobicity scales and five different hydrophobicity parameters, namely the overall hydrophobicity, the hydrophobic moment for detection of the α-helical and β-sheet membrane segments, the alternating hydrophobicity and the exact ß-strand score.
Results: Most of the scales are capable of discriminating between transmembrane α-helices and transmembrane β-sheets, but assignment of peptides to pools of soluble peptides of different secondary structures is not achieved at the same quality. The separation capacity as measure of the discrimination between different structural elements is best by using the five different hydrophobicity parameters, but addition of the alternating hydrophobicity does not provide a large benefit. An in silico evolutionary approach shows that scales have limitation in separation capacity with a maximal threshold of 0.6 in general. We observed that scales derived from the evolutionary approach performed best in separating the different peptide pools when values for arginine and tyrosine were largely distinct from the value of glutamate. Finally, the separation of secondary structure pools via hydrophobicity can be supported by specific detectable patterns of four amino acids.
Conclusion: It could be assumed that the quality of separation capacity of a certain scale depends on the spacing of the hydrophobicity value of certain amino acids. Irrespective of the wealth of hydrophobicity scales a scale separating all different kinds of secondary structures or between soluble and transmembrane peptides does not exist reflecting that properties other than hydrophobicity affect secondary structure formation as well. Nevertheless, application of hydrophobicity scales allows distinguishing between peptides with transmembrane α-helices and β-sheets. Furthermore, the overall separation capacity score of 0.6 using different hydrophobicity parameters could be assisted by pattern search on the protein sequence level for specific peptides with a length of four amino acids.
We present a higher-order call-by-need lambda calculus enriched with constructors, case-expressions, recursive letrec-expressions, a seq-operator for sequential evaluation and a non-deterministic operator amb that is locally bottom-avoiding. We use a small-step operational semantics in form of a single-step rewriting system that defines a (nondeterministic) normal order reduction. This strategy can be made fair by adding resources for bookkeeping. As equational theory we use contextual equivalence, i.e. terms are equal if plugged into any program context their termination behaviour is the same, where we use a combination of may- as well as must-convergence, which is appropriate for non-deterministic computations. We show that we can drop the fairness condition for equational reasoning, since the valid equations w.r.t. normal order reduction are the same as for fair normal order reduction. We evolve different proof tools for proving correctness of program transformations, in particular, a context lemma for may- as well as mustconvergence is proved, which restricts the number of contexts that need to be examined for proving contextual equivalence. In combination with so-called complete sets of commuting and forking diagrams we show that all the deterministic reduction rules and also some additional transformations preserve contextual equivalence.We also prove a standardisation theorem for fair normal order reduction. The structure of the ordering <=c a is also analysed: Ω is not a least element, and <=c already implies contextual equivalence w.r.t. may-convergence.
We present a higher-order call-by-need lambda calculus enriched with constructors, case-expressions, recursive letrec-expressions, a seq-operator for sequential evaluation and a non-deterministic operator amb that is locally bottom-avoiding. We use a small-step operational semantics in form of a single-step rewriting system that defines a (nondeterministic) normal order reduction. This strategy can be made fair by adding resources for bookkeeping. As equational theory we use contextual equivalence, i.e. terms are equal if plugged into any program context their termination behaviour is the same, where we use a combination of may- as well as must-convergence, which is appropriate for non-deterministic computations. We show that we can drop the fairness condition for equational reasoning, since the valid equations w.r.t. normal order reduction are the same as for fair normal order reduction. We evolve different proof tools for proving correctness of program transformations, in particular, a context lemma for may- as well as mustconvergence is proved, which restricts the number of contexts that need to be examined for proving contextual equivalence. In combination with so-called complete sets of commuting and forking diagrams we show that all the deterministic reduction rules and also some additional transformations preserve contextual equivalence.We also prove a standardisation theorem for fair normal order reduction. The structure of the ordering <=c a is also analysed: Ω is not a least element, and <=c already implies contextual equivalence w.r.t. may-convergence.
We present a higher-order call-by-need lambda calculus enriched with constructors, case-expressions, recursive letrec-expressions, a seq-operator for sequential evaluation and a non-deterministic operator amb, which is locally bottom-avoiding. We use a small-step operational semantics in form of a normal order reduction. As equational theory we use contextual equivalence, i.e. terms are equal if plugged into an arbitrary program context their termination behaviour is the same. We use a combination of may- as well as must-convergence, which is appropriate for non-deterministic computations. We evolve different proof tools for proving correctness of program transformations. We provide a context lemma for may- as well as must- convergence which restricts the number of contexts that need to be examined for proving contextual equivalence. In combination with so-called complete sets of commuting and forking diagrams we show that all the deterministic reduction rules and also some additional transformations keep contextual equivalence. In contrast to other approaches our syntax as well as semantics does not make use of a heap for sharing expressions. Instead we represent these expressions explicitely via letrec-bindings.
We consider the isolated spelling error correction problem as a specific subproblem of the more general string-to-string translation problem. In this context, we investigate four general string-to-string transformation models that have been suggested in recent years and apply them within the spelling error correction paradigm. In particular, we investigate how a simple ‘k-best decoding plus dictionary lookup’ strategy performs in this context and find that such an approach can significantly outdo baselines such as edit distance, weighted edit distance, and the noisy channel Brill and Moore model to spelling error correction. We also consider elementary combination techniques for our models such as language model weighted majority voting and center string combination. Finally, we consider real-world OCR post-correction for a dataset sampled from medieval Latin texts.
This paper proves correctness of Nöcker's method of strictness analysis, implemented in the Clean compiler, which is an effective way for strictness analysis in lazy functional languages based on their operational semantics. We improve upon the work of Clark, Hankin and Hunt did on the correctness of the abstract reduction rules. Our method fully considers the cycle detection rules, which are the main strength of Nöcker's strictness analysis. Our algorithm SAL is a reformulation of Nöcker's strictness analysis algorithm in a higher-order call-by-need lambda-calculus with case, constructors, letrec, and seq, extended by set constants like Top or Inf, denoting sets of expressions. It is also possible to define new set constants by recursive equations with a greatest fixpoint semantics. The operational semantics is a small-step semantics. Equality of expressions is defined by a contextual semantics that observes termination of expressions. Basically, SAL is a non-termination checker. The proof of its correctness and hence of Nöcker's strictness analysis is based mainly on an exact analysis of the lengths of normal order reduction sequences. The main measure being the number of 'essential' reductions in a normal order reduction sequence. Our tools and results provide new insights into call-by-need lambda-calculi, the role of sharing in functional programming languages, and into strictness analysis in general. The correctness result provides a foundation for Nöcker's strictness analysis in Clean, and also for its use in Haskell.
In this paper we analyze the semantics of a higher-order functional language with concurrent threads, monadic IO and synchronizing variables as in Concurrent Haskell. To assure declarativeness of concurrent programming we extend the language by implicit, monadic, and concurrent futures. As semantic model we introduce and analyze the process calculus CHF, which represents a typed core language of Concurrent Haskell extended by concurrent futures. Evaluation in CHF is defined by a small-step reduction relation. Using contextual equivalence based on may- and should-convergence as program equivalence, we show that various transformations preserve program equivalence. We establish a context lemma easing those correctness proofs. An important result is that call-by-need and call-by-name evaluation are equivalent in CHF, since they induce the same program equivalence. Finally we show that the monad laws hold in CHF under mild restrictions on Haskell’s seq-operator, which for instance justifies the use of the do-notation.
Based on the quadratic residuosity assumption we present a non-interactive crypto-computing protocol for the greater-than function, i.e., a non-interactive procedure between two parties such that only the relation of the parties' inputs is revealed. In comparison to previous solutions our protocol reduces the number of modular multiplications significantly. We also discuss applications to conditional oblivious transfer, private bidding and the millionaires' problem.
Context unification is a variant of second-order unification and also a generalization of string unification. Currently it is not known whether context uni cation is decidable. An expressive fragment of context unification is stratified context unification. Recently, it turned out that stratified context unification and one-step rewrite constraints are equivalent. This paper contains a description of a decision algorithm SCU for stratified context unification together with a proof of its correctness, which shows decidability of stratified context unification as well as of satisfiability of one-step rewrite constraints.