Verification of a mixed high-order accurate DNS code for laminar turbulent transition by the method of manufactured solutions

This paper presents results on a verification test of a Direct Numerical Simulation code of mixed high-order of accuracy using the method of manufactured solutions (MMS). This test is based on the formulation of an analytical solution for the Navier-Stokes equations modified by the addition of a source term. The present numerical code was aimed at simulating the temporal evolution of instability waves in a plane Poiseuille flow. The governing equations were solved in a vorticity-velocity formulation for a two-dimensional incompressible flow. The code employed two different numerical schemes. One used mixed high-order compact and non-compact finite-differences from fourth-order to sixth-order of accuracy. The other scheme used spectral methods instead of finite-difference methods for the streamwise direction, which was periodic. In the present test, particular attention was paid to the boundary conditions of the physical problem of interest. Indeed, the verification procedure using MMS can be more demanding than the often used comparison with Linear Stability Theory. That is particularly because in the latter test no attention is paid to the nonlinear terms. For the present verification test, it was possible to manufacture an analytical solution that reproduced some aspects of an instability wave in a nonlinear stage. Although the results of the verification by MMS for this mixed-order numerical scheme had to be interpreted with care, the test was very useful as it gave confidence that the code was free of programming errors. Copyright (C) 2009 John Wiley & Sons, Ltd.

How do current term structure model behave beyond the last liquid point?: A comparison of the DNS and Smith-Wilson methods

A Work Project, presented as part of the requirements for the Award of a Master’s Double Degree in Finance from Maastricht University and NOVA – School of Business and Economics

File-based post-processing of DNS results for turbulent flames using MATLAB

Magdeburg, Univ., Fak. für Verfahrens- und Systemtechnik, Diss., 2015

Implantació del sistema Sauron per a la gestió del sistema DNS de la UdL

El sistema de noms de domini (DNS) proveeix d'un sistema distribuït per a la resolució de noms

A DNS Bases Approach To Electronic Persistance, or "If Your Pants Fit, Why Use Suspenders?"

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Eigenschaften heterotypisch interagierender Transmembranhelices ermittelt durch den Einsatz einer kombinatorischen DNS-Bibliothek

Membranproteine sind für Medizin und Forschung von großer Bedeutung. Allerdings gestaltet sich die Forschung an diesen Proteinen oft umständlich und schwierig. Da Membranproteine nur in geringem Maße wasserlöslich sind, können konventionelle biochemische Methoden zur Proteinanalyse nur begrenzt Anwendung finden. Im Rahmen dieser Dissertation wurde ein Reportersystem entwickelt, das zur Analyse von transmembranen Proteinen eingesetzt werden kann. Das System ermöglicht die Untersuchung von Interaktionstendenzen transmembraner, helicaler Proteinelemente in der biologischen Membran des Bakteriums Escherichia coli. Interaktionen transmembraner α-Helices sind bei der Signalweiterleitung über die zelluläre Membran von Bedeutung. So spielt beispielsweise bei vielen membranständigen Rezeptoren die Zusammenlagerung von einzelnen Einheiten zu Oligomeren für den Informationsfluss eine wichtige Rolle. Auch für die Faltung von Membranproteinen sind Interaktionen transmembraner α-Helices relevant. rnEine Validierung des Reportersystems wurde durch gezielte Untersuchungen an dem bakteriellen Aquaglyceroporin GlpF vorgenommen. Bereits vorliegende Strukturdaten für GlpF ließen eine Interaktion der Helices 1 und 2 sowie 1 und 4 des Kanals vermuten, was mit Hilfe des entwickelten Reportersystems bestätigt werden konnte. Eine moderate Interaktionstendenz konnte für beide Helix-Helix-Paarungen festgestellt werden. In der weiterführenden Anwendung des Systems wurden die Eigenschaften der Helix-Helix-Kontaktfläche von heterotypisch interagierenden Transmembranhelices in Bezug auf deren Aminosäurekomposition betrachtet. Dazu wurde zunächst eine auf Plasmiden basierende, kombinatorische DNS-Bibliothek angelegt, die für transmembrane Helices mit zufällig auftretenden Aminosäureresten codierte. Die Anordnung der variablen Seitenketten erfolgte so, dass in Verbindung mit dem Reportersystem eine Helix-Helix-Kontaktfläche randomisierter Aminosäurereste generiert wurde. Um Paare interagierender Helices zu erhalten, wurde ein Selektionsdruck auf E. coli-Zellen erzeugt, in denen die Expression der Transmembranhelices erfolgte. Nur in Zellen mit interagierenden Helices kam es zu einer Aktivierung von Stoffwechselgenen, die das Wachstum in einem Minimalmedium gestattete. Infolge konnten Aminosäurereste und Interaktionsmotive identifiziert werden, die für heterotypische Interaktionen von α-Helices in Membranen eine bedeutende Rolle spielen. Den höchsten Grad an Überrepräsentation an der Helix-Helix-Kontaktfläche zeigten Glycinseitenketten. Weiterhin überrepräsentiert waren Phenylalanin-, Cystein- und Alaninreste. Auch zeigte sich sowohl die Bedeutung des aus dem humanen Glycophorin A (GpA) bekannten Aminosäure-Sequenzmotivs GxxxG, als auch die des Interaktionsmotivs [klein]xxx[klein], in dem Glycin-, Alanin- oder Serinreste in Positionen getrennt durch drei unbestimmte Seitenketten enthalten sind. Weiterhin konnte gezeigt werden, dass bei der Ausbildung eines Helix-Helix-Dimers bestimmte Seitenketten häufiger als andere helixübergreifend in geringer Distanz zueinander auftraten. Hierbei hob sich in besonderem Maße die Paarung Glycin/Glycin hervor. Auch konnten die Paarungen Glycin/Cystein und Phenylalanin/Phenylalanin häufig vorgefunden werden. Darüber hinaus weist das häufige Auftreten von Glycinresten in geringer Distanz auf ein neuartiges Interaktionsmotiv hin. Anders als beim GxxxG-Motiv sind hierbei zwei Glycinreste nicht innerhalb einer Helix, sondern in zwei verschiedenen, interagierenden Transmembranhelices in geringem Abstand zueinander lokalisiert. Die Anwesenheit dieser kurzen Seitenketten in bestimmten Positionen könnte, ähnlich wie das GxxxG-Motiv, den Abstand zweier Helices zueinander verringern und so interhelicale Wechselwirkungen anderer Seitenketten begünstigen.

Warum Pentose- und nicht Hexose-Nucleinsäuren??. Teil V. (Purin-Purin)-Basenpaarung in der homo-DNS-Reihe: Guanin, Isoguanin, 2,6-Diaminopurin und Xanthin

Why Pentose- and Not Hexose-Nucleic Acids? Purine-Purine Pairing in homo-DNA: Guanine,Isoguanine, 2,6-Diaminopurine, and Xanthine This paper concludes the series of reports in this journal [1–4] on the chemistry of homo-DNA, the constitutionally simplifie dmodel system of hexopyranosyl-(6′ → 4′)-oligonucleotide systems stidued in our laboratory as potentially natural-nucleic-acid alternatives in the context of a chemical aetiology of nucleic-acid structure. The report describes the synthesis and pairing properties of homo-DNA oligonucleotides which contain as nucleobases exclusively purines, and gives, together with part III of the series [3], a survey of what we know today about purine-purine pairingin homo-DNA. In addition, the paper discusses those aspects of the chemistry of homo-DNA which, we think, influence the way how some of the structural features of DNA (and RNA) are to be interpreted on a qualitative level. Purine-purine pairing occurs in the homo-DNA domain in great variety. Most prominent is a novel tridentate Watson-Crick pair between guanine and isoguanine, as well as one between 2,6-diaminopurine and xanthinone, both giving rise to very stable duplexes containing the all-purine strands in antiparallel orientation. For the guanine-isoguanine pair, constitutional assignment is based on temperature-dependent UV and CD spectroscopy of various guanine- and isoguanine-containg duplexes in comparison with duplexes known to be paired in the reverse guanine is replaced by 7-carbauguanine. Isoguanine and 2,6-diaminopurine also have the capability of self-pariring in the reverse-Hoogsteen mode, as previously observed for adenine and guanine [3]. In this type of pairing, the interchangeably. Fig. 36 provides an overall survey of the relative strength of pairing in all possible purine-purine combinations. Watson-Crick pairing of isoguanine with guanine demands the former to participate in its 3H-tautomeric form; hitherto this specific tautomer had not been considered in the pairing chemistry of isoguanine. Whereas (cumulative) purine-purine pairing in DNA (reverse-Hoogsten or Hoogsteen) seems to occur in triplexes and tetrapalexes only, its occurrence in duplexes in a characteristic feature of homo-DNA chemistry. The occurrence of purine-purine Watson-Crick base pairs is probably a consequence of homo-DNA's quasi-linear ladder structure [1][4]. In a double helix, the distance between the two sugar C-atoms, on which a base pair is anchored, is expected to be constrained by the dimensions of the helix; in a linear duplex, however, there would be no restrictions with regard to base-pair length. Homo-DNA's ladder-like model also allows one to recognize one of the reasons why nucleic-acid duplexes prefer to pair in antiparallel, rather than parallel strand orientation: in homo-DNA duplexes, (averaged) backbone and base pair axes are strongly inclined toward one another [4]; the stronger this inclination, the higher the preference for antiparallel strand orientation is expected to be (Fig. 16). In retrospect, homo-DNA turns out to be one of the first artificial oligonucleotide systems (cf. Footnote 65) to demonstrate in a comprehensive way that informational base pairing involving purines and pyrimidines is not a capability unique to ribofuranosyl systems. Stability and helical shape of pairing complexes are not necessary conditions of one another; it is the potential for extensive conformational cooperativity of hte backbone structure with respect to the constellational demands of base pairing and base stacking that determines whether or nor a given type of base-carrying backbone structure is an informational pairing system. From the viewpoint of the chemical aetiology of nucleic-acid structure, which inspired our investigations on hexopyranosyl-(6′ → 4′)-oligonucleotide systems in the first place, the work on homo-DNA is only an extensive model study, because homo-DNA is not to be considered a potential natural-nucleic-acid altenratie. In retrospect, it seems fortunate that the model study was carried out, because without it we could hardly have comprehended the pairing behavior of the proper nucleic-acid alternatives which we have studied later and which will be discussed in Part VI of this series. The English footnotes to Fig. 1–49 provide an extension of this summary.

Detección de intrusiones basada en análisis de eventos del DNS

En este proyecto se hace un análisis en profundidad de las técnicas de ataque a las redes de ordenadores conocidas como APTs (Advanced Persistent Threats), viendo cuál es el impacto que pueden llegar a tener en los equipos de una empresa y el posible robo de información y pérdida monetaria que puede llevar asociada. Para hacer esta introspección veremos qué técnicas utilizan los atacantes para introducir el malware en la red y también cómo dicho malware escala privilegios, obtiene información privilegiada y se mantiene oculto. Además, y cómo parte experimental de este proyecto se ha desarrollado una plataforma para la detección de malware de una red en base a las webs, URLs e IPs que visitan los nodos que la componen. Obtendremos esta visión gracias a la extracción de los logs y registros de DNS de consulta de la compañía, sobre los que realizaremos un análisis exhaustivo. Para poder inferir correctamente qué equipos están infectados o no se ha utilizado un algoritmo de desarrollo propio inspirado en la técnica Belief Propagation (“Propagación basada en creencia”) que ya ha sido usada antes por desarrolladores cómo los de los Álamos en Nuevo México (Estados Unidos) para fines similares a los que aquí se muestran. Además, para mejorar la velocidad de inferencia y el rendimiento del sistema se propone un algoritmo adaptado a la plataforma Hadoop de Apache, por lo que se modifica el paradigma de programación habitual y se busca un nuevo paradigma conocido como MapReduce que consiste en la división de la información en conceptos clave-valor. Por una parte, los algoritmos que existen basados en Belief Propagation para el descubrimiento de malware son propietarios y no han sido publicados completamente hasta la fecha, por otra parte, estos algoritmos aún no han sido adaptados a Hadoop ni a ningún modelo de programación distribuida aspecto que se abordará en este proyecto. No es propósito de este proyecto desarrollar una plataforma comercial o funcionalmente completa, sino estudiar el problema de las APTs y una implementación que demuestre que la plataforma mencionada es factible de implementar. Este proyecto abre, a su vez, un horizonte nuevo de investigación en el campo de la adaptación al modelo MapReduce de algoritmos del tipo Belief Propagation basados en la detección del malware mediante registros DNS. ABSTRACT. This project makes an in-depth investigation about problems related to APT in computer networks nowadays, seeing how much damage could they inflict on the hosts of a Company and how much monetary and information loss may they cause. In our investigation we will find what techniques are generally applied by attackers to inject malware into networks and how this malware escalates its privileges, extracts privileged information and stays hidden. As the main part of this Project, this paper shows how to develop and configure a platform that could detect malware from URLs and IPs visited by the hosts of the network. This information can be extracted from the logs and DNS query records of the Company, on which we will make an analysis in depth. A self-developed algorithm inspired on Belief Propagation technique has been used to infer which hosts are infected and which are not. This technique has been used before by developers of Los Alamos Lab (New Mexico, USA) for similar purposes. Moreover, this project proposes an algorithm adapted to Apache Hadoop Platform in order to improve the inference speed and system performance. This platform replaces the traditional coding paradigm by a new paradigm called MapReduce which splits and shares information among hosts and uses key-value tokens. On the one hand, existing algorithms based on Belief Propagation are part of owner software and they have not been published yet because they have been patented due to the huge economic benefits they could give. On the other hand these algorithms have neither been adapted to Hadoop nor to other distributed coding paradigms. This situation turn the challenge into a complicated problem and could lead to a dramatic increase of its installation difficulty on a client corporation. The purpose of this Project is to develop a complete and 100% functional brand platform. Herein, show a short summary of the APT problem will be presented and make an effort will be made to demonstrate the viability of an APT discovering platform. At the same time, this project opens up new horizons of investigation about adapting Belief Propagation algorithms to the MapReduce model and about malware detection with DNS records.

DNS of a hot-wire anemometer in a turbulent channel flow

A body with a shape similar to a hot wire with its sheath, but no prongs, has been placed close to the wall of a turbulent channel at Re_tau = 600. The results of the channel flow, without the wire, agree with previous published ones, despite the modest resolution and domain size. A simplified, two-dimensional version of the wire at the same Reynolds number has been studied to compare the dynamic response of cold and hot wires, where a slightly bigger perturbation is seen in the hot case, but an almost identical dynamic response. The cold wire seems to be able to measure instantaneous velocity with total drag after proper calibration. Being a DNS, the complete description of the flow field around the wire is obtained.

Análisis de vulnerabilidades del DNS

El DNS (Domain Name System) es un sistema que permite localizar equipos y servicios de Internet a través de nombres descriptivos organizados de forma jerárquica gracias a un mecanismo de consulta/respuesta. Cuando un usuario escriba un nombre de dominio en una aplicación, los servidores DNS podrán traducirlo a otra información asociada con él mismo, como una dirección IP o un alias, por lo que el DNS puede entenderse como una base de datos globalmente jerarquizada que nació a causa de la necesidad de poder recordar fácilmente los nombres de todos los servidores conectados a Internet. La necesidad del uso del DNS y su carencia en sistemas de seguridad, han conformado un entorno propicio para multitud de ataques, entre los que se encuentran el MITM (Man In The Middle), caché poisoning, negación de servicios o fugas de información entre otros, generando situaciones comprometidas para multitud de usuarios. Para poder contrarrestarlos se han ido implementando un conjunto de modelos de seguridad, entre los que destacan algunos como el DNSSEC, con su uso de firmas criptográficas , el WSEC DNS con identificadores aleatorios o el DNS Curve que cifraba todo el contenido transmitido. Este proyecto consta de una breve introducción al DNS, donde se podrá conocer su estructura y entender su funcionamiento. Posteriormente se pasará a analizar conceptos de seguridad web, particularizándose en un examen exhaustivo de las vulnerabilidades en el DNS. Finalmente se estudiarán distintos modelos de seguridad que se han ido implementando a lo largo del tiempo para intentar solventar estos problemas junto con sus ventajas y desventajas.

Determinação a baixo custo de açúcares redutores totais em caldo-de-cana, empregando sistemas de análise por injeção em fluxo com o uso de DNS

Determinação a baixo custo de açúcares redutores totais em caldo-de-cana, empregando sistema de análise por injeção em fluxo com o uso de DNS Um sistema de análise por injeção em fluxo foi utilizado para a determinação de açúcares redutores totais em caldo-de-cana. O método é baseado na hidrólise da sacarose, seguido da oxidação dos açúcares redutores pelo ácido 3,5-dinitrosalicílico (DNS) em meio alcalino, e determinação espectrofotométrica em 510 nm. Visando obter melhor sensibilidade e seletividade, os parâmetros volume de amostra e comprimento dos reatores foram estudados para avaliar o comportamento das curvas analíticas. Foram utilizados mini-compressores de aquários no lugar de bomba peristálticas e cela espectrofotométrica em acrílico no lugar de cela de vidro importada, a fim de minimizar o consumo de reagentes e o custo do sistema FIA. O presente sistema foi comparado ao método Lane-Eynon recomendado pelo Ministério da Agricultura. Usando o teste-t, não foram constatadas diferenças significativas entre os resultados dos dois métodos, sendo que os desvios relativos foram ao redor de 1%. O método permite analisar cerca de 14 amostras h-1 com desvio padrão relativo inferior a 1,35%.