The parallel TASEP, fixed particle number and weighted Motzkin paths

In this paper the totally asymmetric exclusion process (TASEP) with parallel update on an open lattice of size $L$ is considered in the maximum-current region. A formal expression for the generating function for the weight of configurations with $N$ particles is given. Further an interpretation in terms of $(u,l,d)$-colored weighted Motzkin paths is presented. Using previous results (Woelki and Schreckenberg 2009 {\it J. Stat. Mech} P05014, Woelki 2010 {\it Cellular Automata}, pp 637-645) the generating function is compared with the one for a possible 2nd-class particle dynamics for the parallel TASEP. It is shown that both become physically equivalent in the thermodynamic limit.Comment: 11 pages, 3 figure

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

MS FT-2-2 7 Orthogonal polynomials and quadrature: Theory, computation, and applications

Quadrature rules find many applications in science and engineering. Their analysis is a classical area of applied mathematics and continues to attract considerable attention. This seminar brings together speakers with expertise in a large variety of quadrature rules. It is the aim of the seminar to provide an overview of recent developments in the analysis of quadrature rules. The computation of error estimates and novel applications also are described

Generalized averaged Gaussian quadrature and applications

A simple numerical method for constructing the optimal generalized averaged Gaussian quadrature formulas will be presented. These formulas exist in many cases in which real positive GaussKronrod formulas do not exist, and can be used as an adequate alternative in order to estimate the error of a Gaussian rule. We also investigate the conditions under which the optimal averaged Gaussian quadrature formulas and their truncated variants are internal

Self-assembly of Artificial DNA Nano and Microscale Motifs

Nanotechnology attempts to control matter at the nanometer scale so that new types of materials, components and devices for a wide variety of applications can be developed. There are two approaches possible. The first stems from semiconductor technology in which improvements in processing small structures have led to a drastic reduction in the size of electronic components. The inverse approach - which is used in this work - orientates itself around structures based on biological systems, in which highly dynamic nanometer size components assemble themselves. In this thesis it is shown how defined structures with sizes ranging from nanometers to micrometres and made up of DNA molecules can self assemble. Self-assembly has four defining features: structured particles, a suitable environment, a driving force and reversible binding. DNA molecules are relatively stable and can be synthesised with arbitrary sequences of four units, diffuse freely in an aqueous buffer under Brownian motion, and can bind and unbind (using hydrogen bonding) with one another in the practical temperature range between 0 and 100°C. They are thus useful building blocks for self-assembly. A review is provided of some physical properties of DNA, and of self-assembled DNA ‘motifs’ and devices developed to date, along with examples that have been demonstrated here in the laboratory. Such examples include DNA nanotubes, lattices, and ‘origami’ structures. The idea of assembling structures - not by creating and breaking hydrogen bonds using temperature changes - but rather by changing the concentration of small molecules known as denaturants is introduced. The denaturants also form hydrogen bonds and can occupy the binding sites of the DNA molecules. Decreasing the concentration of denaturants frees the binding sites and allows the self-assembly of structures. This is demonstrated with successful motifs, and provides an isothermal assembly technique that allows the use of many temperature-sensitive components in DNA self-assembly. It is shown that self-assembled motifs are useful as templates for nanoscale objects such as fluorescent molecules, which can be set out in defined geometries. Moreover, using newly developed optical super-resolution techniques, such geometries are resolved below the optical diffraction limit, providing the possibility for nanoscale optical calibration standards. And finally the intrinsic stability of three-dimensional structures as compared to two-dimensional structures is investigated, in that the assembly and ‘melting’ of DNA nanotubes is shown to be fundamentally different to that of DNA lattices, with the closed form of the tubes providing a natural and significantly higher stability. This will be useful for designing and building stronger structures in DNA nanotechnology

Fire performance of residential shipping containers designed with a shaft wall system

seven story building made of shipping containers is planned to be built in Barcelona, Spain. This study mainly aimed to evaluate the fire performance of one of these residential shipping containers whose walls and ceiling will have a shaft wall system installed. The default assembly consisted of three fire resistant gypsum boards for vertical panels and a mineral wool layer within the framing system. This work aimed to assess if system variants (e.g. less gypsum boards, no mineral wool layer) could still be adequate considering fire resistance purposes. To determine if steel temperatures would attain a predetermined temperature of 300-350ºC (a temperature value above which mechanical properties of steel start to change significantly) the temperature evolution within the shaft wall system and the corrugated steel profile of the container was analysed under different fire conditions. Diamonds simulator (v. 2020; Buildsoft) was used to perform the heat transfer analysis from the inside surface of the container (where the fire source was present) and within the shaft wall and the corrugated profile. To do so gas temperatures near the walls and the ceiling were required, so these temperatures were obtained from two sources: (1) The standard fire curve ISO834; (2) CFD simulations performed using the Fire Dynamics Simulator (FDS). Post-flashover fire scenarios were modelled in FDS taking into account the type of fuel present in residential buildings according to international standards. The results obtained indicate that temperatures lower than 350ºC were attained on the ribbed steel sheet under all the tested heat exposure conditions. When changing the assembly by removing the mineral wool layer, fire resistance was found to still be adequate. Therefore, under the tested conditions, the structural response of the containers would comply with fire protection standards, even in the case where insulation was reduced.Postprint (published version

Going viral : an integrated view on virological data analysis from basic research to clinical applications

Viruses are of considerable interest for several fields of life science research. The genomic richness of these entities, their environmen- tal abundance, as well as their high adaptability and, potentially, pathogenicity make treatment of viral diseases challenging. This thesis proposes three novel contributions to antiviral research that each concern analysis procedures of high-throughput experimen- tal genomics data. First, a sensitive approach for detecting viral genomes and transcripts in sequencing data of human cancers is presented that improves upon prior approaches by allowing de- tection of viral nucleotide sequences that consist of human-viral homologs or are diverged from known reference sequences. Sec- ond, a computational method for inferring physical protein contacts from experimental protein complex purification assays is put for- ward that allows statistically meaningful integration of multiple data sets and is able to infer protein contacts of transiently binding protein classes such as kinases and molecular chaperones. Third, an investigation of minute changes in viral genomic populations upon treatment of patients with the mutagen ribavirin is presented that first characterizes the mutagenic effect of this drug on the hepatitis C virus based on deep sequencing data.Viren sind von beträchtlichem Interesse für die biowissenschaftliche Forschung. Der genetische Reichtum, die hohe Vielfalt, wie auch die Anpassungsfähigkeit und mögliche Pathogenität dieser Organismen erschwert die Behandlung von viralen Erkrankungen. Diese Promotionsschrift enthält drei neuartige Beiträge zur antiviralen Forschung welche die Analyse von experimentellen Hochdurchsatzdaten der Genomik betreffen: erstens, ein sensitiver Ansatz zur Entdeckung viraler Genome und Transkripte in Sequenzdaten humaner Karzinome, der die Identifikation von viralen Nukleotidsequenzen ermöglicht, die von Referenzgenomen ab- weichen oder homolog zu humanen Faktoren sind. Zweitens, eine computergestützte Methode um physische Proteinkontakte von experimentellen Proteinkomplex-Purifikationsdaten abzuleiten welche die statistische Integration von mehreren Datensätzen erlaubt um insbesondere Proteinkontakte von flüchtig interagierenden Proteinklassen wie etwa Kinasen und Chaperonen aus den Daten ableiten zu können. Drittens, eine Untersuchung von kleinsten Änderungen viraler Genompopulationen während der Behandlung von Patienten mit dem Mutagen ribavirin die zum ersten Mal die mutagene Wirkung dieses Medikaments auf das Hepatitis C Virus mittels Tiefensequenzdaten nachweist

Non-covalent interactions in organotin(IV) derivatives of 5,7-ditertbutyl- and 5,7-diphenyl-1,2,4-triazolo[1,5-a]pyrimidine as recognition motifs in crystalline self- assembly and their in vitro antistaphylococcal activity

Non-covalent interactions are known to play a key role in biological compounds due to their stabilization of the tertiary and quaternary structure of proteins [1]. Ligands similar to purine rings, such as triazolo pyrimidine ones, are very versatile in their interactions with metals and can act as model systems for natural bio-inorganic compounds [2]. A considerable series (twelve novel compounds are reported) of 5,7-ditertbutyl-1,2,4-triazolo[1,5-a]pyrimidine (dbtp) and 5,7-diphenyl- 1,2,4-triazolo[1,5-a]pyrimidine (dptp) were synthesized and investigated by FT-IR and 119Sn M\uf6ssbauer in the solid state and by 1H and 13C NMR spectroscopy, in solution [3]. The X-ray crystal and molecular structures of Et2SnCl2(dbtp)2 and Ph2SnCl2(EtOH)2(dptp)2 were described, in this latter pyrimidine molecules are not directly bound to the metal center but strictly H-bonded, through N(3), to the -OH group of the ethanol moieties. The network of hydrogen bonding and aromatic interactions involving pyrimidine and phenyl rings in both complexes drives their self-assembly. Noncovalent interactions involving aromatic rings are key processes in both chemical and biological recognition, contributing to overall complex stability and forming recognition motifs. It is noteworthy that in Ph2SnCl2(EtOH)2(dptp)2 \u3c0\u2013\u3c0 stacking interactions between pairs of antiparallel triazolopyrimidine rings mimick basepair interactions physiologically occurring in DNA (Fig.1). M\uf6ssbauer spectra suggest for Et2SnCl2(dbtp)2 a distorted octahedral structure, with C-Sn-C bond angles lower than 180\ub0. The estimated angle for Et2SnCl2(dbtp)2 is virtually identical to that determined by X-ray diffraction. Ph2SnCl2(EtOH)2(dptp)2 is characterized by an essentially linear C-Sn-C fragment according to the X-ray all-trans structure. The compounds were screened for their in vitro antibacterial activity on a group of reference staphylococcal strains susceptible or resistant to methicillin and against two reference Gramnegative pathogens [4] . We tested the biological activity of all the specimen against a group of staphylococcal reference strains (S. aureus ATCC 25923, S. aureus ATCC 29213, methicillin resistant S. aureus 43866 and S. epidermidis RP62A) along with Gram-negative pathogens (P. aeruginosa ATCC9027 and E. coli ATCC25922). Ph2SnCl2(EtOH)2(dptp)2 showed good antibacterial activity with a MIC value of 5 \u3bcg mL-1 against S. aureus ATCC29213 and also resulted active against methicillin resistant S. epidermidis RP62A

Microscopy Conference 2017 (MC 2017) - Proceedings

Das Dokument enthält die Kurzfassungen der Beiträge aller Teilnehmer an der Mikroskopiekonferenz "MC 2017", die vom 21. bis 25.08.2017, in Lausanne stattfand