The primary aim of the work presented in this thesis was to change the inducer specificity of the DntR protein in order to improve the response to DNT. The long-term goal is to use this protein in a biosensor for DNT, a signature compound for detection of the explosive TNT. Another aspect of this work was to understand the mechanisms of inducer binding and how the binding of an inducer molecule changes the DntR structure into a state that triggers transcriptional activation. In the papers included in this thesis the inducer specificity of wt DntR has been investigated under different conditions. The functional effects of specific mutations have also been investigated, in some cases in combination with structure determination using X-ray crystallography. In addition, structural data offering insights into the details of inducer binding and conformational changes upon inducer binding are presented and discussed in terms of mechanisms for transcriptional activation by DntR. Furthermore, a directed evolution strategy was employed in order to find variants of DntR with improved response to DNT. A variant with a large improvement in the DNT response was isolated and characterized. In optimized growth conditions, this DntR variant had a nearly 10-fold increase in fluorescence in response to DNT compared to wt DntR. Specific substitutions found in this DntR variant are suggested to be important for changing the inducer response. / Syftet med denna avhandling har varit att förbättra förmågan hos proteinet DntR att upptäcka DNT. Det långsiktiga målet har varit att använda DntR i en biosensor för att upptäcka sprängämnet TNT, som avger DNT som en ”signaturmolekyl”. En annan aspekt har varit att bättre förstå den detaljerade mekanismen för hur DntR fungerar. DntR är ett protein som binder till en viss DNA sekvens (promotor) och reglerar hur gener intill denna promotorsekvens läses av. När en inducerande molekyl som t.ex. DNT binder till DntR förändras proteinets struktur på ett sådant sätt att DntR kan aktivera transkription av de gener som finns intill promotor-sekvensen. För att mäta hur DntR reagerar på olika inducerande molekyler har DntR uttryckts i bakterien Escherichia coli, som också innehållit promotorn som DntR binder till. Intill promotorn sitter en gen som kodar för proteinet GFP. När en inducerande molekyl binder till DntR, slås avläses gfp-genen, och det fluorescerande proteinet GFP produceras. Ju mer GFP som produceras i cellerna, desto högre fluorescens kan uppmätas när cellerna analyseras.   I de artiklar som presenteras i avhandlingen har vi undersökt hur olika substitutioner i DntR proteinet påverkar specificiten och sensitiviteten och hur dessa egenskaper kan påverkas av olika experimentella faktorer. Effekten av substitutioner har relaterats till strukturdata, där bilder av hur proteinet ser ut på molekylär nivå har tagits fram. Dessutom presenteras även en bild av hur DntR förändras beroende på om inducerande molekyler är bundna eller inte. En sådan strukturbild ökar förståelsen för de mekanismer som gör att bindning av en inducerande molekyl orsakar en förändring av formen hos DntR på så sätt att avläsning av gener kan aktiveras. Vi har också använt en metod där evolutionära processer härmats för att få fram varianter av DntR med förbättrad respons till DNT. En variant med en drastisk ökning av DNT-responsen har isolerats, och dess egenskaper har karaktäriserats. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript

An effective electrochemical sensor for myoglobin (Myb) detection was developed using a simple procedure of denaturing the protein with guanidine hydrochloride and detecting the released heme group by cyclic voltammetry. The concentration of denaturant was optimized to obtain maximum current response for the analyte (Myb). To improve the sensitivity of the sensor, the working electrode, glassy carbon electrode was modified with a layer of Titania nanotubes (TNT). The direct electrochemical behavior of the modified electrode (TNT-GCE) was studied using cyclic voltammetry (CV). The performance of the sensor was investigated and optimized and the system was evaluated by monitoring the Myb concentration. Despite the reduced current response for the modified electrode compared to bare GCE, the sensitivity of the system was improved significantly by overcoming the large background current due to denaturant. The developed TNT modified electrode improved the detection limit of Myb and showed good stability, sensitivity and reproducibility. Under optimal conditions, the catalytic currents are linearly proportional to the concentrations of Myb in the wide range from 50 nM to 6 M. This approach provides improved sensitivity in the given range, and may provide a novel and efficient platform for the fabrication of sensors for other heme proteins.

No description available.

Topical inquiries for the Swedish Defence Research Agency (FOI) include analysis of explosive substances in different sample types. Research into explosives in complex matrixes can provide an analytical support function for forensic investigation i.e. tools for areas such as finding bomb factories, identification and risk analysis of home-made explosives (HME) and improvised explosive devices (IED) as well as preventive measures against maliciously intended use of explosives. Additionally, the research may lay the groundwork for indications of health- and environmental hazards. Utilizing state-of-the-art equipment and years of extensive expertise, FOI is able to carry out these types of research tasks to provide security and sustainability for society. The aim of this thesis project is to establish and validate developed methods for collecting, extracting, separating, and detecting trace amounts of explosives in various bodies of water using a solid-phase extraction (SPE) robot and a high-resolution (HR) mass spectrometer (MS) connected to an ultra-high-performance liquid chromatograph (UHPLC). Particular areas of interest include locations in the Stockholm archipelago where experimental detonations of explosives have taken place. Overall, UHPLC-HRMS analysis provides a powerful tool for analyzing explosives in complex matrixes with unambiguous and reliable measurement data. The compounds of investigation were hexogen (RDX), octogen (HMX), pentyl (PETN), and trotyl (TNT). To summarize, during the course of the thesis, trace amounts of some explosives were detected and quantified in various bodies of water. Furthermore, the applied method for the project was successful in qualitatively and quantitatively analyze the compounds of interest with limit of detection ranging between 0.33–11 μg/L (ppb) in various water sources.

Methods for rapid, safe and effective detection of unmapped buried ordnance are vital to the protection of humans and environmental quality throughout the world. This study aimed to investigate the use of phytosensing and to understand the physiological response of woody plants to 2,4,6-trinitrotoluene (TNT) contamination. Baccharis halimifolia were potted in soils containing various concentrations of TNT and physiological responses were observed over a 9-week experimental period. Measurements included the collection of remotely sensed data, such as hyperspectral reflectance and chlorophyll fluorescence, and traditional plant-level physiological data. In accordance with the hypothesis, low levels of TNT improved physiological response in plants due to the slight increase in nitrogen, while high levels of TNT induced stress. Key markers in stress responses were identified, specifically with reflectance indices and derivatives, which may separate TNT-contaminated plants from naturally stressed plants and would allow for accurate detection of buried ordnance at the landscape level.

Les travaux présentés dans ce mémoire de thèse s'inscrivent dans le cadre des études liées aux dégâts sur les structures et les blessures subies par les personnes à la suite d'explosions de charges explosives en milieu confiné et semi-confiné. Afin de mener cette étude, des expériences sont réalisées à petite échelle en laboratoire et sont complétées par des simulations numériques. Les ondes de choc sont obtenues grâce à la détonation d'une charge explosive gazeuse composée de propane-oxygène en proportion stoechiométrique. L'étude consiste donc à réaliser des expériences à petite échelle en laboratoire afin d'apprécier les champs de pression obtenus à la suite de la détonation d'une charge explosive au sein de deux configurations différentes. La première représente un atelier pyrotechnique et la seconde met en jeu un entrepôt de stockage de bouteilles de gaz. Les résultats expérimentaux sont ensuite confrontés à des résultats obtenus par simulations numériques réalisées grâce au logiciel AUTODYN. En complément de ces deux configuration principales, une étude est menée sur l'identification des pics de surpressions réfléchis grâce à une approche expérimentale appelée paroi par paroi. Une étude est également menée sur la détermination d'une équivalence massique entre le TNT et le mélange gazeux utilisé pour les expériences.

Les travaux de thèse présentés dans ce mémoire s'inscrivent dans le cadre du projet ANR BARPPRO. Ce programme de recherche vise à étudier l'influence d'une barrière de protection face à une explosion en régime de détonation. L'objectif est d'établir des méthodes de calcul rapides de classement des zones d'effets pour aider les industriels au dimensionnement des barrières de protection. L'une à partir d'abaques, valable pour des configurations en géométrie 2D, sur des plages spécifiées de paramètres importants retenus, avec une précision de +/- 5%. L'autre à partir d'une méthode d'estimation rapide basée notamment sur les chemins déployés, valable en géométrie 2D et en géométrie 3D, mais dont la précision estimée est de +/- 30%. Afin d'y parvenir, l'étude s'appuie sur trois volets : expérimental, simulation numérique et analytique. La partie expérimentale étudie plusieurs géométries de barrière de protection à petites échelles pour la détonation d'une charge gazeuse (propane-oxygène à la stoechiométrie). Les configurations expérimentées servent à la validation de l'outil de simulation numérique constitué du solveur HERA et de la plateforme de calcul TERA 100. Des abaques d'aide au dimensionnement ont pu être réalisés à partir de résultats fournis par l'outil de simulation (3125 configurations de barrière de protection, TNT). L'étude des différents phénomènes physiques présents a également permis de mettre en place une méthode d'estimation rapide basée sur des relations géométriques, analytiques et empiriques. L'analyse de ces résultats a permis d'établir quelques recommandations dans le dimensionnement d'une barrière de protection. Les abaques et le programme d'estimation rapide permettent à un ingénieur de dimensionner rapidement une barrière de protection en fonction de la configuration du terrain et de la position de la zone à protéger en aval du merlon.

Indiana University-Purdue University Indianapolis (IUPUI) / Canines are regularly utilized by law enforcement agencies to detect explosives. However, the mechanism by which canines respond to explosive vapors is not well understood, leading to difficulties in canine training and testing. It is known that the amount of vapor generated from explosive compounds is dependent upon several factors including sample amount, vapor pressure, and the degree of confinement. Underlying these factors is the basic process of evaporation of an unconfined explosive, which is rucial to understanding how explosive vapors behave in other, more confined, systems. In Stage One of this study, evaporation rates were determined for several explosive liquids using an analytical balance. These rates were compared to one another as well as to theoretical models for the evaporation of liquids. In general and as expected, mass decreased linearly with time and evaporation rates decreased logarithmically as boiling point increased. Several examples of solvent “pinning” on a metal surface were also observed. While an empirical model for the evaporation of unconfined explosive liquids was developed, a comprehensive model for the escape of explosive vapors from sealed containers (i.e., a suitcase, knapsack, or IED container itself) is needed. The second part of Stage One of this study was to determine that the flow rate of explosive vapors escaping from relatively large orifices does not conform to Fick’s Law of Diffusion. Fick’s model states that the flow rate is linearly dependent upon the cross sectional area of the orifice and the material’s diffusion coefficient. Instead, the flow rate was found to be linearly dependent upon the diameter of the orifice due to the tendency of the flow to diffuse outwards from its circular edge. A clear relationship between flow rate and diffusion coefficient was seen, however. Additional uncertainty arises concerning the complexity of the odor generated from explosive compounds. Because explosive vapors are often complex (they consist of multiple chemical compounds), confusion exists regarding the cause of canine alert; that is the “odor compound” that allows for canine detection of various explosives. Although 2, 4- dinitrotoluene (DNT) has been explored as a potential odor compound, the possibility of a nitrated explosive inherently producing nitrated gas upon decomposition has not. Stage Two of this study focused on evaluating nitrate as a potential cause of canine alerts. An LC/MS method for the detection of nitrate ions in Composition C-4 and flake trinitrotoluene (TNT) was developed and tested. Instrumental analysis was not successful in detecting nitrate ions in any of the explosives tested. The lack of nitrate was confirmed using a diphenylamine color test for nitrates, thus eliminating nitrate as an odor compound and cause of canine alert to nitroaromatic compounds. 2, 4-DNT has been introduced as a potential odor compound of TNT, however, the mechanisms behind its vapor emission have not been thoroughly explored. More specifically, due to the “sticky” nature of the 2, 4-DNT isomer, the effects of surface adhesion to container walls are of concern. In particular, whether the amount of material lost to surface adhesion is significant enough to effect canine detection of TNT. A second focus of Stage Two explored this concern. A GC/MS method for the detection and separation of TNT and DNT isomers in liquid extracts was developed and the amount of 2, 4-DNT residues adhering to container walls was quantified. These values, compared to the amount 2,4-DNT expected to saturate each container (determined by the Ideal Gas Law), showed a significant preference of 2,4-DNT in the solid phase as opposed to in the gas phase. The amount of residue adhering to the walls of a gallon can differed from expected values by nearly 70%. The amount of material extracted from a quart can exceeded expected values by 137%. The apparent sticky nature of 2, 4-DNT resulted in a significant loss of material needed to fully saturate a container and thus canine detection success may be affected. In the final stage of this study, theories regarding odor compounds and odor availability of nitromethane, TNT, and Composition C-4 were tested using certified explosives-detecting canines. These trials included thirty-three canine-handler teams from eight government agencies. The odor availability of nitromethane was tested by placing varying volumes of nitromethane in containers with differing degrees of confinement and studying the effects on canine detection success. The odor availability trial showed no significant effect of sample amount or degree of confinement on canine detection so long as the sample volume was sufficient to saturate its container. In this study that volume was determined to be < 1 mL. Detection of 2, 4-DNT, TNT-NESST (Non-Hazardous Explosives for Security Training and Testing), and flake TNT were also studied using certified canines. The purpose of this was to identify the odorant responsible for canine alert to the explosive TNT. These trials showed a significant response to 2, 4-DNT compared to TNT and its training aid; this suggests that 2, 4-DNT is the primary cause of canine alerts to TNT. Additionally, Composition C-4 and RDX-NESTT were tested along with potential odor compounds that included the manufacturing solvent, cyclohexanone, the energetic “taggant” 2, 3-dimethyl-2.3-dinitrobutane (DMNB), the plasticizer dioctyladipate (DOA) and its degradation product 2-ethyl-1-hexanol. While some response to DMNB and cyclohexanone was seen, the most significant response was to the actual Composition C-4. This suggests that the cause of canine alert to Composition C-4 is the explosive mixture as a whole and not a single chemical component of the mixture

With the increased frequency of accidental and deliberate explosions, the response of civil infrastructure systems to blast loading has become a research topic of great interest. However, with the high cost and complex safety and logistical issues associated with live explosives testing, North American blast resistant construction standards (e.g. ASCE 59-11 & CSA S850-12) recommend the use of shock tubes to simulate blast loads and evaluate relevant structural response. This study aims first at developing a 2D axisymmetric shock tube model, implemented in ANSYS Fluent, a computational fluid dynamics (CFD) software, and then validating the model using the classical Sod’s shock tube problem solution, as well as available shock tube experimental test results. Subsequently, the developed model is compared to a more complex 3D model in terms of the pressure, velocity and gas density. The analysis results show that there is negligible difference between the two models for axisymmetric shock tube performance simulation. However, the 3D model is necessary to simulate non-axisymmetric shock tubes. The design of a shock tube depends on the intended application. As such, extensive analyses are performed in this study, using the developed 2D axisymmetric model, to evaluate the relationships between the blast wave characteristics and the shock tube design parameters. More specifically, the blast wave characteristics (e.g. peak reflected pressure, positive phase duration and the reflected impulse), were compared to the shock tube design parameters (e.g. the driver section pressure and length, the driven v section length, and perforation diameter and their locations). The results show that the peak reflected pressure increases as the driver pressure increases, while a decrease of the driven length increases the peak reflected pressure. In addition, the positive phase duration increases as both the driver length and driven length are increased. Finally, although shock tubes generally generate long positive phase durations, perforations located along the expansion section showed promising results in this study to generate short positive durations. Finally, the developed 2D axisymmetric model is used to optimize the dimensions of a proposed large-scale conical shock tube system developed for civil infrastructure blast response evaluation applications. The capabilities of this proposed shock tube system are further investigated by correlating its design parameters to a range of explosion threats identified by different hemispherical TNT charge weight and distance scenarios. / Thesis / Master of Applied Science (MASc)

Ce travail de recherche doctoral en sciences de l'information et de la communication propose d'appréhender un média, la télévision, en France, au printemps 2005. Cette période correspond à un épisode de mutation qui voit l'ancienne télévision analogique migrer vers un environnement numérique et informatique. Notre propos cherche à explorer la notion de média en articulant trois dimensions : le contexte, le discours et le format. Il s'agit d'explorer des mécanismes qui configurent les pratiques médiatiques, au printemps 2005, à travers : la définition d'un contexte d'innovation technique, l'analyse de discours d'actualité qui affirment des lignes éditoriales et enfin, la valorisation de la programmation et la conception de formats de programmes qui intègrent la culture numérique. Les objets construits au cours de cette recherche sont des formes médiatiques, composées de codes identifiables et marquées par le contexte culturel de leur production. En tant que pratique médiatique, la programmation télévisuelle est transversale. Elle assure une continuité entre les trois dimensions : le contexte dans lequel elle est agencée, les discours qui la prennent pour objet, enfin, les codes et formats télévisuels qu'elle intègre. Notre projet consiste à étudier la programmation télévisuelle comme un objet médiatique complexe, configuré par les enjeux techniques, industriels et économiques liés à la diffusion d'une innovation. Ainsi, dans une première partie, les modalités de la médiatisation des choix de programmation seront appréhendées en observant les discours d'actualité produits et diffusés le 31 mars 2005, à l'occasion du lancement en France de la télévision numérique terrestre. La nature éditoriale du média télévision, et la programmation comme objet de discours d'autopromotion seront mises en évidence. Puis, dans une deuxième partie, les nouvelles formes de la médiation de la programmation seront examinées à travers un corpus web, composé des pages des sites des chaînes de télévision pré-numériques. / "Discurses on innovation and broadcast programming mediations. Television in the digital age". This doctoral research in information and communication sciences (Media Studies) offers to understand the functional behaviour of a media, the television, in France, during the spring 2005. This period corresponds to an episode of change that sees the old analog TV migrate to a digital environment. Our work seeks to explore the notion of media articulating three dimensions : context, discourse and format. This is to explore mechanisms that shape media practices in the spring of 2005, through : the definition of a technical innovation context, the analysis of the news discourse which affirms editorial strategies and finally, the development of broadcast programming and programs designs that incorporate the digital culture. The objects built in this research are media forms, composed of identifiable codes and marked by the cultural context of their production. As a media practice, television programming is transversal. It ensures continuity between the three dimensions: the context in which it is arranged, the speeches which are intended, finally, the television codes and formats that are integrated. Our project is to study broadcast programming as a complex media object, configured by the technical, industrial and economic issues related to the diffusion of an innovation. Thus, in a first part, the terms of the media coverage of the scheduling choices will be understood by observing the news discourses produced and distributed on March the 31st 2005, at the launching in France of the digital terrestrial television. The editorial nature of television, and the broadcast programming as an object of discourse of self-promotion will be highlighted. Then, in a second part, the new mediation forms of scheduling will be examined through a web corpus, consisting of pre-digital broadcasters web pages.