Studies in clay chemistry

A study of clay chemistry has been approached with three aims: - to modify the conducting properties by intercalation of tetrathiafulvalene, - to study the electrochemistry of redox-active coordination compounds immobilised on clay coated electrodes, and - to study the role of clays as reagents in inorganic glass forming reactions using mainly solid-state magic-angle-spinning NMR. TTF was intercalated by smectites containing different interlayer and lattice cations. Evidence from ESR and 57Fe Mossbauer indicated charge-transfer from TTF to structural iron in natural montmorillonite, and to interlayer Cu2+ in Cu2+ exchanged laponite. No charge transfer was observed for laponite (Na+ form) itself. Ion exchange of TTF3(BF4)2 with laponite was found to proceed quantitatively. The intercalated species were believed to be (TTF)2+ dimers. Conductivity data showed an order of magnitude increase for the intercalated clays. The mechanism is thought to be ionic rather than CT as Na+ laponite showed a similar enhancement in conductivity. Mechanically robust colloidal clay films were prepared on platinum electrodes. After immersion in solutions containing redox active complexes [Co(bpy)3]3+ and [Cr(bpy)3]3+, the films became electroactive when a potential was applied. Cyclic voltammograms obtained for both complexes were found to be of the diffusion controlled type. For [Co(bpy)3]3+ immobilised on clay coated electrodes, a one-step oxidation and four-step reduction wave was observed corresponding to a one electron stepwise reversible reduction of Co(III), through Co(II), Co(I), Co(O) to Co(I) oxidation state. For [Cr(bpy)3]3+ the electrochemistry was complicated by the presence of additional waves corresponding to the dissociation of [Cr(bpy)3]3+ into the diaquo complex. ESR and diffuse reflectance data supported such a mechanism. 29Si, 27Al and 23Na MAS NMR spectroscopy, supported by powder XRD and FTIR, was used to probe the role of clays as reagents in glass forming reactions. 29Si MAS NMR was found to be a very sensitive technique for identifying the presence and relative abundance of crystalline and non-crystalline phases. In thermal reactions of laponite formation of new mineral phases such as forsterite, akermanite, sillimanite and diopside were detected. The relative abundance of each phase was dependent on thermal history, chemical nature and concentration of the modifier oxide present. In continuing work, the effect of selected oxides on the glass forming reactions of a model feldspar composition was investigated using solid state NMR alone. Addition of network modifying oxides generally produced less negative 29Si chemical shifts and larger linewidths corresponding to a wider distribution of Si-O-Si bond angles and lengths, and a dominant aluminosilicate phase with a less polymerised structure than the starting material. 29Si linewidths and 27Al chemical shifts were respectively correlated with cationic potential and Lewis acidity of the oxide cations. Anomalous Al(4) chemical shifts were thought to be due to precipitation of aluminate phases rather than a breakdown in Lowenstein's aluminium avoidance principle.

The human factors aspects of alarms in human supervisory control tasks.

This research thesis is concerned with the human factors aspects of industrial alarm systems within human supervisory control tasks. Typically such systems are located in central control rooms, and the information may be presented via visual display units. The thesis develops a human, rather than engineering, centred approach to the assessment, measurement and analysis of the situation. A human factors methodology was employed to investigate the human requirements through: interviews, questionnaires, observation and controlled experiments. Based on the analysis of current industrial alarm systems in a variety of domains (power generation, manufacturing and coronary care), it is suggested that often designers do not pay due considerations to the human requirements. It is suggested that most alarm systems have severe shortcomings in human factors terms. The interviews, questionnaire and observations led to the proposal of 'alarm initiated activities' as a framework for the research to proceed. The framework comprises of six main stages: observe, accept, analyse, investigate, correct and monitor. This framework served as a basis for laboratory research into alarm media. Under consideration were speech-based alarm displays and visual alarm displays. Non-speech auditory displays were the subject of a literature review. The findings suggest that care needs to be taken when selecting the alarm media. Ideally it should be chosen to support the task requirements of the operator, rather than being arbitrarily assigned. It was also indicated that there may be some interference between the alarm initiated activities and the alarm media, i.e. information that supports one particular stage of alarm handling may interfere with another.

The effects of ionising radiation on polypropylene

The interaction of ionising radiation with polymers is described and the literature relating; to the effects on polypropylene is reviewed. Oxidative and free radical reactions are discussed with particular reference to post-irradiationeffects.Isotactic and atactic polypropylene were δ and electron irradiated to doses of up to 20 megarad. Irradiations weremainly made in air. A series of other polymers were also irradiated in a preliminary survey. Molar mass measurements are used to measure the radiationyield for chain scission G (s). Irradiation at room temperature causes significantly more chain scission than at 195K. Additional chain scission occurs on storage following irradiation at 195 K. Free radical concentrations are determined by electron spin resonance, and the decay rates measured. The radical formed in air is a peroxy radical and in vacuo is a hydrocarbon radical. At77K in vacuo the radical is -CH2 - C* (CH3) - CH2 - but additional radicals are produced on warning to room temperature. The effects of increasing tenparature on radicals formed in air are described. Electron spin resonance studies on atactic polypropylene,and isotactic polypropylene in hydrogen, sulphur dioxide and nitric oxide are reported.. The melting temperatures, spherulite growth rates, and isothermal crystallisation rates of irradiated polypropylene are compared to those of the non-irradiated polymer. Crystallisation is found to proceed with an Avrami integer n = 2. At a given crystallisation temperature, the overall crystallisation rate of irradiated polymer is less than the non-irradiated, but spherulite growth rates are identical. Thermogravimetric analysis is used to assess the thermal stability of irradiated polypropylene in nitrogen, air and oxygen. Hydroperoxide analysis is used to show that several molecules of oxygen are absorbed for each initial radical, and that hydroperoxides continue to be formed for a long period following irradiation. Possible solutions for minimising irradiation and post-irradiation degradation are suggested, together with some problems for further study.

The stability and formulation of topical analgesics

High-performance liquid chromatographic methods are developed for the simultaneous determination of various salicylates, their p-hydroxy isomers and nicotinic acid esters. The method is sensitive enough to detect trace amounts (~µM/L)of the product generated from cross reactivity between the drugs and the vehicle. The developed method also allows analysis of various topical products containing salicylate and nicotinate esters in their formulations. Applying this method, the degradation profiles of salicylates, nicotinates, p-hydroxy benzoate, o-methoxy benzoate and aspirin prodrugs in alkaline media are determined. The profile for alkyl salicylate degradation is found to be first order (A---? B) When the alcoholic radical is similar to that of the ester. In alcohol having a radical different from that of the ester function, the degradation is found to proceed through competitive transesterification and hydrolysis. The intermediates are identified following synthesis and isolation. The rate and extent of transesterification depends on the proportion of alcohol present in the system. Equations are presented to model the time profiles of reactant and product concentration. The reactions are base catalysed and the predominant pathway involves a concerted solvent attack upon the salicylate anion. Competitive hydrolysis of both ester components also follows this mechanism at moderate pH values but rates increase under strongly alkaline conditions as direct hydroxide attack becomes significant. In contrast, transesterification is independent of base concentration once full ionization is accomplished. The competitive hydrolysis is modelled using equations involving the dielectric constant of the medium. A range of other esters are also shown to undergo base-catalysed transesterification. In non-alcoholic solution phenyl salicylate undergoes a concentration-dependent oligomerisation which yields salsalate among the products. Competitive transesterification and hydrolysis also occur in products for topical use which have vehicles based upon alcohol, glycol or glycol polymers. Such reactions may compromise stability assessments, pharmaceutical integrity and delivery profiles.

Selective oxidation of cyclohexene through gold functionalized silica monolith microreactors

Two simple, reproducible methods of preparing evenly distributed Au nanoparticle containing mesoporous silica monoliths are investigated. These Au nanoparticle containing monoliths are subsequently investigated as flow reactors for the selective oxidation of cyclohexene. In the first strategy, the silica monolith was directly impregnated with Au nanoparticles during the formation of the monolith. The second approach was to pre-functionalize the monolith with thiol groups tethered within the silica mesostructure. These can act as evenly distributed anchors for the Au nanoparticles to be incorporated by flowing a Au nanoparticle solution through the thiol functionalized monolith. Both methods led to successfully achieving even distribution of Au nanoparticles along the length of the monolith as demonstrated by ICP-OES. However, the impregnation method led to strong agglomeration of the Au nanoparticles during subsequent heating steps while the thiol anchoring procedure maintained the nanoparticles in the range of 6.8 ± 1.4 nm. Both Au nanoparticle containing monoliths as well as samples with no Au incorporated were tested for the selective oxidation of cyclohexene under constant flow at 30 °C. The Au free materials were found to be catalytically inactive with Au being the minimum necessary requirement for the reaction to proceed. The impregnated Au-containing monolith was found to be less active than the thiol functionalized Au-containing material, attributable to the low metal surface area of the Au nanoparticles. The reaction on the thiol functionalized Au-containing monolith was found to depend strongly on the type of oxidant used: tert-butyl hydroperoxide (TBHP) was more active than H2O2, likely due to the thiol induced hydrophobicity in the monolith.

The effect of past earnings and dividend patterns on the information content of dividends when earnings are reduced

This study pursues two objectives: first, to provide evidence on the information content of dividend policy, conditional on past earnings and dividend patterns prior to an annual earnings decline; second, to examine the effect of the magnitude of low earnings realizations on dividend policy when firms have more-or-less established dividend payouts. The information content of dividend policy for firms that incur earnings reductions following long patterns of positive earnings and dividends has been examined (DeAngelo et al., 1992, 1996; Charitou, 2000). No research has examined the association between the informativeness of dividend policy changes in the event of an earnings drop, relative to varying patterns of past earnings and dividends. Our dataset consists of 4,873 U.S. firm-year observations over the period 1986-2005. Our evidence supports the hypotheses that, among earnings-reducing or loss firms, longer patterns of past earnings and dividends: (a) strengthen the information conveyed by dividends regarding future earnings, and (b) enhance the role of the magnitude of low earnings realizations in explaining dividend policy decisions, in that earnings hold more information content that explains the likelihood of dividend cuts the longer the past earnings and dividend patterns. Both results stem from the stylized facts that managers aim to maintain consistency with respect to historic payout policy, being reluctant to proceed with dividend reductions, and that this reluctance is higher the more established is the historic payout policy. © 2010 The Authors. Journal compilation © 2010 Accounting Foundation, The University of Sydney.

Formation of Polycyclic Aromatic Hydrocarbons and Nitrogen Containing Polycyclic Aromatic Compounds in Titan's Atmosphere, the Interstellar Medium and Combustion

Several different mechanisms leading to the formation of (substituted) naphthalene and azanaphthalenes were examined using theoretical quantum chemical calculations. As a result, a series of novel synthetic routes to Polycyclic Aromatic Hydrocarbons (PAHs) and Nitrogen Containing Polycyclic Aromatic Compounds (N-PACs) have been proposed. On Earth, these aromatic compounds originate from incomplete combustion and are released into our environment, where they are known to be major pollutants, often with carcinogenic properties. In the atmosphere of a Saturn's moon Titan, these PAH and N-PACs are believed to play a critical role in organic haze formation, as well as acting as chemical precursors to biologically relevant molecules. The theoretical calculations were performed by employing the ab initio G3(MP2,CC)/B3LYP/6-311G** method to effectively probe the Potential Energy Surfaces (PES) relevant to the PAH and N-PAC formation. Following the construction of the PES, Rice-Ramsperger-Kassel-Markus (RRKM) theory was used to evaluate all unimolecular rate constants as a function of collision energy under single-collision conditions. Branching ratios were then evaluated by solving phenomenological rate expressions for the various product concentrations. The most viable pathways to PAH and N-PAC formation were found to be those where the initial attack by the ethynyl (C2H) or cyano (CN) radical toward a unsaturated hydrocarbon molecule led to the formation of an intermediate which could not effectively lose a hydrogen atom. It is not until ring cyclization has occurred, that hydrogen elimination leads to a closed shell product. By quenching the possibility of the initial hydrogen atom elimination, one of the most competitive processes preventing the PAH or N-PAC formation was avoided, and the PAH or N-PAC formation was allowed to proceed. It is concluded that these considerations should be taken into account when attempting to explore any other potential routes towards aromatic compounds in cold environments, such as on Titan or in the interstellar medium.

Putting the Green in Bureaucracy: Practices of Quantification and Valuation in Environmental Regulation

While researchers have devoted considerable attention to exploring the ways that intentional environmental reregulation creates new avenues for capital accumulation (e.g. Smith, 2007; Castree, 2008), it remains somewhat unclear how the less grandiose day-to-day work of environmental regulators may also help create new sources of ecological value. Through an ethnographic study of environmental regulators tasked with enforcing key environmental laws, I shed light on the subtle ways that rule interpretation and scientific practice structure the frames, models, and methodologies regulators use to enact “best professional judgments” about ecological systems, and ultimately to assign particular values to nature. I also show the ways that non-human nature pushes back against such assessments, which in combination with the interpretive work of environmental regulation, opens spaces of conflict in at least two arenas: one focused on modes of quantification, where actors contend between economistic, ecological, statutory, and moral frames for making value assessments; and one focused on presentations of value, where actors contend between value assessments that best represent their self-defined interests. The ‘value settlements’ environmental regulators reach in these contested spaces allow processes of commensuration to proceed, and ultimately make nature legible for capitalization and exchange. Accounting for the ways that these basic regulatory practice help create ecological value is essential for creating a fuller picture of the ways capital and natural capital relate.

A tributação como instrumento de proteção ambiental no Brasil

The Federal Constitution of 1988 gave special treatment to the issue of the environment, raising this diffuse right to the status of a fundamental right. In order to preserve it, the constitutional order is provided with various means to this purpose, including the possibility of using taxation. Several principles both constitutional, as infraconstitucional, support the use of taxation as a legal instrument to protect the environment. There is an intense legal debate about the suitability, characteristics, purposes and principles which underlie and restrict the environmental taxation. Discussions and proposals for reform of the tax system in order to include the ecological aspect at its core have been developed. The use of taxation as a way to fund public expenditures related to environmental causes, promote the internalization of negative externalities and as a way to induce behavior to benefit the environment finds support in the Brazilian legal system. This paper seeks to demonstrate that the national tax system is fully able to act as a tool available to the state for the implementation of the fundamental right to an ecologically balanced environment, whether through the taxes fiscal role or due, mainly, through the phenomenon of extrafiscality. Also, it is intended, through doctrinal, jurisprudential analysis and concrete cases, to investigate whether the tax system can be effective in protecting the environment in the way it is currently constructed, or if there is need to proceed with changes in its structure in order to achieve this goal

Lacan, Gödel, a ciência e a verdade

Jaques Lacan, the thinker who proposes a return to the fundamentals of psychoanalysis in Freud states that the math would face as a privileged way of transmission of knowledge by the science. Although he was a follower of the mathematization of nature as the foundation of modern science, for him this principle does not imply eliminating the subject that produces it. That would be equivalent to saying that there can not be a language, whatever, even the math, that may "erases" the subject assumption in science. In the text The science and the truth we will try to introduce the idea, not so simple, by the way, the truth as the cause. Citing the framework of the causes in Aristotle, Lacan will speak of a homology between the truth as formal cause, in the case of science, and the truth as material cause, on the side of psychoanalysis. Among its aims with this text, he wants to establish that the unconscious of the subject would be none other than the subject of science. The famous incompleteness theorems of logical-mathematical Kurt Gödel enter here as a chapter of this issue. Recognized as true watershed, these theorems have to be remembered as revealing even outside the mathematical environment, and Lacan himself is not indifferent to this. He makes mention of Gödel's name and draws some observations apparently modest support for his own theory. Since some technical sophisticated knowledges awaits the reader who intends understand this supposed corroboration that Gödel provides to psychoanalysis, introduce the student of Lacan in the use he makes of the incompleteness theorems is the objective of this work. In The science and the truth, which fits us to locate the name of Gödel, one must question how seize such an idea without incurring the extrapolation and abuse of mathematical knowledge, almost trivial in this case. Thus, this paper aims to introduce the reader to the reasoning behind the theorems of Gödel, acquaint him about the Lacan’s mathematical claims, and indicate how to proceed using this implicit math in the text The science and the truth.

Estudo de viabilidade técnico-ambiental para implantação de parques eólicos: um estudo de caso em um fragmento do litoral setentrional do Rio Grande do Norte/Brasil

The use of energy from renewable sources is increasingly demanded by society, especially aeolian - whose raw material is wind. Investments in wind power have become significant in Brazil with emphasis on the Northeast and in particular the Rio Grande do Norte state. According to the Empresa de Pesquisa Energética (Energy Research Company) (2012 ) , investments in the state grew significantly since 2002 with a total accumulated power, by 2013, of approximately 3,400 MW . Even with the early experiences of exploitation of wind energy in 2002, it is still considered new and requires further study referring to the likely changes in the environment and society. In this case, it is of growing and urgent importance to deeply study the wind still in the survey phase of the project, ie , at the beginning of decision making on the most feasible to implement these parks site. Given the above, the question is: from a technical and environmental analysis, how to identify viable areas to install Aeolian parks, taking into account the factors of the environmental dynamics that are relevant to minimize the negative results to the environment and the society? Thus, this study conducted a study on technical and environmental feasibility, proposing a methodology of exploration of feasible wind farms in coastal areas. The study area was a fragment of the northern coast of Rio Grande do Norte and its natural landscape units were identified through the environmental characterization of the area, as well as it was elaborated the map of the land cover, restriction homes and urban areas and Permanent Preservation Areas - PPAs. The environmental fragility was subdivided in the fragility of the natural dynamic, mapped through relief, soils and geology of natural units, and the fragility of the ecosystem, originated by the land cover map. In addition to these maps, it was generated the wind resource for an area from a height of 50 and 100 meters. The intersection between the fragility maps, PPAs and Restriction of homes superimposed on maps of wind potential, provided the map of feasibility of Aeolian parks, resulting in the most favorable areas for its facilities in a technical and environmental point of view. From this study, the entrepreneur can evaluate whether or not to proceed with the studies in this area and especially decrease potential conflicts with society.

Avaliação de duas variedades de Passiflora edulis sobre as respostas comportamentais de camundongos e um possível mecanismo de ação

The medicinal plants constitute a rich source of biologically active compounds used for the treatment of many psychiatric disorders, such as anxiety disorders and depression. Generalized anxiety disorder has increased significantly, being the second most prevalent disorder in care facilities to public health. Depression is considered a chronic and common psychiatric disorder that affects 350 million people of all ages around the world. In this context, the pharmacological intervention conduits have been employed, effective, although leave to be desired when observed adverse effects. The genus Passiflora is commonly commercially known by its fruit, but is also widely used in traditional Brazilian medicine. Passiflora edulis displays considerable morphological variability. This plant produces two types of fruit: Purple (Passiflora edulis Sims fo. edulis) and yellow (Passiflora edulis fo. flavicarpa Degener). This study investigated the central effects of aqueous extract of the leaves of the two varieties of the species Passiflora edulis in tests used to assess behavior related to anxiety and depression, as well as investigating the potential effect of the antidepressant-like fractions of edulis fo. edulis and neuropharmacological mechanisms responsible for this action. To conduct this study used male Swiss mice (2 months old, weighing 30-35 g). The animals received the aqueous extract of the leaves of the two species of Passiflora: edulis fo. edulis (100, 300, 1000 mg / kg) and fractions ethyl acetate, butanol and aqueous waste (25, 50, 75, 100 mg / kg) and edulis fo. flavicarpa (30, 100, 300, 1000 mg / kg) or saline by gavage 60 minutes prior to the maze tests at high cross the open field test, test forced swim test and sedation induced by thiopental. To investigate the mechanism of action of the activity of antidepressant type of fractions the following drugs were used: PCPA (inhibitor of 5-HT synthesis) AMPT (inhibitor of catecholamine synthesis), DSP-4 (noradrenergic neurotoxin) and Sulpiride (antagonist selective dopamine D2 receptor). They were used as a standard positive control, fluoxetine and nortriptyline. The results of the phytochemical profile show very different characteristics to the aqueous extract of the varieties of Passiflora edulis "flavicarpa" and "edulis". The aqueous extracts of both varieties of Passiflora edulis share anxiolytic activity type (edulis fo. edulis 300 mg/kg; edulis fo. flavicarpa 300 and 1000 mg/kg) and antidepressant (edulis fo. edulis 300 mg/kg; edulis fo flavicarpa 1000 mg/kg), while the effect hipolocomotor/sedative was only seen for edulis fo. edulis (1000 mg/kg). Both fractions ethyl acetate, butanol aqueous extract edulis fo. edulis showed activity type antidepressant at a dose of 50 mg/kg in the forced swim test. The data suggest that the effect of antidepressant-like fractions edulis fo. edulis involves catecholaminergic and serotonergic neurotransmission, particularly dopaminergic, there is seen that pre-treatment DSP-4 is not affected antidepressant action of fractions as was dependent activation of dopamine D2 receptors.

Avaliação de duas variedades de Passiflora edulis sobre as respostas comportamentais de camundongos e um possível mecanismo de ação

The medicinal plants constitute a rich source of biologically active compounds used for the treatment of many psychiatric disorders, such as anxiety disorders and depression. Generalized anxiety disorder has increased significantly, being the second most prevalent disorder in care facilities to public health. Depression is considered a chronic and common psychiatric disorder that affects 350 million people of all ages around the world. In this context, the pharmacological intervention conduits have been employed, effective, although leave to be desired when observed adverse effects. The genus Passiflora is commonly commercially known by its fruit, but is also widely used in traditional Brazilian medicine. Passiflora edulis displays considerable morphological variability. This plant produces two types of fruit: Purple (Passiflora edulis Sims fo. edulis) and yellow (Passiflora edulis fo. flavicarpa Degener). This study investigated the central effects of aqueous extract of the leaves of the two varieties of the species Passiflora edulis in tests used to assess behavior related to anxiety and depression, as well as investigating the potential effect of the antidepressant-like fractions of edulis fo. edulis and neuropharmacological mechanisms responsible for this action. To conduct this study used male Swiss mice (2 months old, weighing 30-35 g). The animals received the aqueous extract of the leaves of the two species of Passiflora: edulis fo. edulis (100, 300, 1000 mg / kg) and fractions ethyl acetate, butanol and aqueous waste (25, 50, 75, 100 mg / kg) and edulis fo. flavicarpa (30, 100, 300, 1000 mg / kg) or saline by gavage 60 minutes prior to the maze tests at high cross the open field test, test forced swim test and sedation induced by thiopental. To investigate the mechanism of action of the activity of antidepressant type of fractions the following drugs were used: PCPA (inhibitor of 5-HT synthesis) AMPT (inhibitor of catecholamine synthesis), DSP-4 (noradrenergic neurotoxin) and Sulpiride (antagonist selective dopamine D2 receptor). They were used as a standard positive control, fluoxetine and nortriptyline. The results of the phytochemical profile show very different characteristics to the aqueous extract of the varieties of Passiflora edulis "flavicarpa" and "edulis". The aqueous extracts of both varieties of Passiflora edulis share anxiolytic activity type (edulis fo. edulis 300 mg/kg; edulis fo. flavicarpa 300 and 1000 mg/kg) and antidepressant (edulis fo. edulis 300 mg/kg; edulis fo flavicarpa 1000 mg/kg), while the effect hipolocomotor/sedative was only seen for edulis fo. edulis (1000 mg/kg). Both fractions ethyl acetate, butanol aqueous extract edulis fo. edulis showed activity type antidepressant at a dose of 50 mg/kg in the forced swim test. The data suggest that the effect of antidepressant-like fractions edulis fo. edulis involves catecholaminergic and serotonergic neurotransmission, particularly dopaminergic, there is seen that pre-treatment DSP-4 is not affected antidepressant action of fractions as was dependent activation of dopamine D2 receptors.

Programming Molecular Devices using Nucleic Acid Hairpins

Nucleic Acid hairpins have been a subject of study for the last four decades. They are composed of single strand that is

hybridized to itself, and the central section forming an unhybridized loop. In nature, they stabilize single stranded RNA, serve as nucleation

sites for RNA folding, protein recognition signals, mRNA localization and regulation of mRNA degradation. On the other hand,

DNA hairpins in biological contexts have been studied with respect to forming cruciform structures that can regulate gene expression.

The use of DNA hairpins as fuel for synthetic molecular devices, including locomotion, was proposed and experimental demonstrated in 2003. They

were interesting because they bring to the table an on-demand energy/information supply mechanism.

The energy/information is hidden (from hybridization) in the hairpin’s loop, until required.

The energy/information is harnessed by opening the stem region, and exposing the single stranded loop section.

The loop region is now free for possible hybridization and help move the system into a thermodynamically favourable state.

The hidden energy and information coupled with

programmability provides another functionality, of selectively choosing what reactions to hide and

what reactions to allow to proceed, that helps develop a topological sequence of events.

Hairpins have been utilized as a source of fuel for many different DNA devices. In this thesis, we program four different

molecular devices using DNA hairpins, and experimentally validate them in the

laboratory. 1) The first device: A

novel enzyme-free autocatalytic self-replicating system composed entirely of DNA that operates isothermally. 2) The second

device: Time-Responsive Circuits using DNA have two properties: a) asynchronous: the final output is always correct

regardless of differences in the arrival time of different inputs.

b) renewable circuits which can be used multiple times without major degradation of the gate motifs

(so if the inputs change over time, the DNA-based circuit can re-compute the output correctly based on the new inputs).

3) The third device: Activatable tiles are a theoretical extension to the Tile assembly model that enhances

its robustness by protecting the sticky sides of tiles until a tile is partially incorporated into a growing assembly.

4) The fourth device: Controlled Amplification of DNA catalytic system: a device such that the amplification

of the system does not run uncontrollably until the system runs out of fuel, but instead achieves a finite

amount of gain.

Nucleic acid circuits with the ability

to perform complex logic operations have many potential practical applications, for example the ability to achieve point of care diagnostics.

We discuss the designs of our DNA Hairpin molecular devices, the results we have obtained, and the challenges we have overcome

to make these truly functional.

Open-source virtual bronchoscopy for image guided navigation

This thesis describes the development of an open-source system for virtual bronchoscopy used in combination with electromagnetic instrument tracking. The end application is virtual navigation of the lung for biopsy of early stage cancer nodules. The open-source platform 3D Slicer was used for creating freely available algorithms for virtual bronchscopy. Firstly, the development of an open-source semi-automatic algorithm for prediction of solitary pulmonary nodule malignancy is presented. This approach may help the physician decide whether to proceed with biopsy of the nodule. The user-selected nodule is segmented in order to extract radiological characteristics (i.e., size, location, edge smoothness, calcification presence, cavity wall thickness) which are combined with patient information to calculate likelihood of malignancy. The overall accuracy of the algorithm is shown to be high compared to independent experts' assessment of malignancy. The algorithm is also compared with two different predictors, and our approach is shown to provide the best overall prediction accuracy. The development of an airway segmentation algorithm which extracts the airway tree from surrounding structures on chest Computed Tomography (CT) images is then described. This represents the first fundamental step toward the creation of a virtual bronchoscopy system. Clinical and ex-vivo images are used to evaluate performance of the algorithm. Different CT scan parameters are investigated and parameters for successful airway segmentation are optimized. Slice thickness is the most affecting parameter, while variation of reconstruction kernel and radiation dose is shown to be less critical. Airway segmentation is used to create a 3D rendered model of the airway tree for virtual navigation. Finally, the first open-source virtual bronchoscopy system was combined with electromagnetic tracking of the bronchoscope for the development of a GPS-like system for navigating within the lungs. Tools for pre-procedural planning and for helping with navigation are provided. Registration between the lungs of the patient and the virtually reconstructed airway tree is achieved using a landmark-based approach. In an attempt to reduce difficulties with registration errors, we also implemented a landmark-free registration method based on a balanced airway survey. In-vitro and in-vivo testing showed good accuracy for this registration approach. The centreline of the 3D airway model is extracted and used to compensate for possible registration errors. Tools are provided to select a target for biopsy on the patient CT image, and pathways from the trachea towards the selected targets are automatically created. The pathways guide the physician during navigation, while distance to target information is updated in real-time and presented to the user. During navigation, video from the bronchoscope is streamed and presented to the physician next to the 3D rendered image. The electromagnetic tracking is implemented with 5 DOF sensing that does not provide roll rotation information. An intensity-based image registration approach is implemented to rotate the virtual image according to the bronchoscope's rotations. The virtual bronchoscopy system is shown to be easy to use and accurate in replicating the clinical setting, as demonstrated in the pre-clinical environment of a breathing lung method. Animal studies were performed to evaluate the overall system performance.