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Mackie, Ewan Thomas Braid. "Rational term-structure models and geometric Levy martingales." Thesis, Imperial College London, 2011. http://hdl.handle.net/10044/1/9483.
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One of the most important problems in modern finance is to understand how best to model the occurrence of jumps in asset pricing models. With this issue in mind, the main topic of this thesis is the development of a set of asset pricing models, driven by Levy uncertainty, applicable across a wide range of asset classes. In particular, we model the term structure of interest rates in a Levy setting, by use of the so-called positive interest models of Flesaker and Hughston. We begin with a brief review of the term-structure literature. We then introduce elements of the theory of Levy processes and develop a rather general theory of geometric Levy models (GLMs) for dynamic asset pricing, paying attention in particular to issues concerning the relation between risk and return for the models under consideration. The special case of a GLM with constant parameters can be regarded as a natural generalisation of the standard geometric Brownian motion used in the Black-Scholes theory. General conditions are established under which assets show a positive risk premium in such a setting. The Flesaker-Hughston approach has the advantage that positive nominal interest rates are built in from the beginning. The resulting models are rational in the sense that the price of a discount bond is given by a ratio of integrals of families of positive martingales. We develop a class of models of this type, where the martingale families are modelled by parametric families of geometric Levy processes. Closed-form expressions are provided for the prices of discount bonds, the short rate of interest, and the prices of options on discount bonds, for various specific cases of Levy uncertainty. In the example of the geometric Brownian motion family we include a rather detailed discussion of the behaviour of the risk premium, and establish conditions under which it is positive. We put forward a proposal for a two-stage calibration of the rational Levy models to the market prices of options. Empirical studies are carried out on the calibration performance of (a) the rational Brownian model, and (b) the rational variance gamma model. We then develop a novel hedging strategy for a portfolio of options on discount bonds. The hedging strategy takes the form of a functional derivative of the option price with respect to the price of the underlying discount bond.
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Kalev, Petko S. "Rational expectations and the term structure of interest rates." Monash University, Dept. of Econometrics and Business Statistics, 2001. http://arrow.monash.edu.au/hdl/1959.1/8700.
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Lundh, Ann-Christin. "The rational design of catalytically active polypeptides with supersecondary structure." Göteborg : Department of Organic Chemistry, University of Göteborg, 1995. http://catalog.hathitrust.org/api/volumes/oclc/39066015.html.
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Schwellnus, Adrian. "Linear-Rational Term Structure Models With Flexible Level-Dependent Volatility." Master's thesis, University of Cape Town, 2018. http://hdl.handle.net/11427/29215.
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The Linear-Rational Framework for the modelling of interest rates is a framework which allows for the addition of spanned and unspanned factors, while maintaining a lower bound on rates and tractable valuation of interest rate derivatives, particularly swaptions. The advantages of having all these properties are significant. This dissertation presents the Linear-Rational Framework, and specializes the factor process to a class of diffusion models which allows for the degree of state dependence of volatility to be estimated. This dissertation then finds that the estimated state dependent volatility structure is significantly different to that of typical models, where it is set it a priori. The effect the added degree of freedom has on the model implied swaption skew is then analysed.
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Ramnarayan, Kalind. "Level Dependence in Volatility in Linear-Rational Term Structure Models." Master's thesis, Faculty of Commerce, 2019. http://hdl.handle.net/11427/31207.
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The degree of level dependence in interest rate volatility is analysed in the linearrational term structure model. The linear-rational square-root (LRSQ) model, where level dependence is set a priori, is compared to a specification where the factor process follows CEV-type dynamics which allows a more flexible degree of level dependence. Parameters are estimated using an unscented Kalman filter in conjunction with quasi-maximum likelihood. An extended specification for the state price density process is required to ensure reliable parameter estimates. The empirical analysis indicates that the LRSQ model generally overestimates level dependence. Although the CEV specification captures the degree of level dependence in volatility more accurately, it has a trade-off with analytical tractability. The optimal specification, therefore, depends on the type of model implementation and general economic conditions.
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Teter, David Michael. "Computational Alchemy: The Rational Design of New Superhard Materials." Diss., Virginia Tech, 1998. http://hdl.handle.net/10919/40510.
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First--principles electronic structure calculations have been
performed to help identify and direct the synthesis of new
superhard compounds. An improved figure of merit for hardness is
identified and used to show that carbon nitrides are not likely
to be harder than diamond.Ph. D.
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Mendes, Eduardo Mazoni Andrade Marcal. "Identification of nonlinear discrete systems with intelligent structure detection." Thesis, University of Sheffield, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.341141.
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Mata, David Garcia. "Understanding Protein Structure And Function Using Rational Design And Unnatural Amino Acids." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1338392020.
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Sinani, Klajdi. "Iterative Rational Krylov Algorithm for Unstable Dynamical Systems and Genaralized Coprime Factorizations." Thesis, Virginia Tech, 2016. http://hdl.handle.net/10919/64425.
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Generally, large-scale dynamical systems pose tremendous computational difficulties when applied in numerical simulations. In order to overcome these challenges we use several model reduction techniques. For stable linear models these techniques work very well and provide good approximations for the full model. However, large-scale unstable systems arise in many applications. Many of the known model reduction methods are not very robust, or in some cases, may not even work if we are dealing with unstable systems. When approximating an unstable sytem by a reduced order model, accuracy is not the only concern. We also need to consider the structure of the reduced order model. Often, it is important that the number of unstable poles in the reduced system is the same as the number of unstable poles in the original system. The Iterative Rational Krylov Algorithm (IRKA) is a robust model reduction technique which is used to locally reduce stable linear dynamical systems optimally in the $mathcal{H}_2$-norm. While we cannot guarantee that IRKA reduces an unstable model optimally, there are no numerical obstacles to the reduction of an unstable model via IRKA. In this thesis, we investigate IRKA's behavior when it is used to reduce unstable models. We also consider systems for which we cannot obtain a first order realization of the transfer function. We can use Realization-independent IRKA to obtain a reduced order model which does not preserve the structure of the original model. In this paper, we
implement a structure preserving algorithm for systems with nonlinear frequency dependency.Master of Science
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Armstrong, Kathryn Anne. "Computational structure-based modeling and analysis with application to rational and evolutionary molecular engineering." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/39844.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2007.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references (leaves 112-127).
The design and development of new proteins and small molecules has considerable practical application in medicine, industry, and basic science. Frequently, progress in this area is made by altering an existing small molecule or protein for new function. This thesis presents methods for the analysis and design of rationally and evolutionarily designed molecules and focuses on applying these methods to make protein and small molecule changes more strategically. First, electrostatic analysis of a series of small molecule neuraminidase inhibitors was used to demonstrate that charge optimization improves the electrostatic component of the binding free energy, despite changes in binding mode and discrete chemical constraints. Additionally, chemical changes suggested by charge optimization frequently corresponded to tighter-binding inhibitors, indicating that this technique would be useful for the design of future inhibitors. Second, computational sequence and structure analysis were used to study the PDZ3-CRIPT binding interaction and a method for sequence analysis was developed to locate residues important for binding specificity. Third, computational analysis of the horseradish peroxidase active site suggested five positions as candidates for mutation, and further studies of new mutant enzymes let to ideas for the improvement of computational enzyme design procedures. Finally, both computational protein design techniques and a model of the evolutionary process were used to study the efficiency of evolution as a tool for creating new proteins in the laboratory. We identified sequences that serve as better evolutionary starting points that others and provide a general framework for considering the impact of protein structure on the allowed sequence space and therefore on the challenges that each protein presents to evolutionary protein engineering procedures.
by Kathryn Anne Armstrong.
Ph.D.
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Hyland, Philip. "A rational emotive behaviour therapy perspective on the nature and structure of posttraumatic stress responses : the mediating and moderating effects of rational and irrational beliefs." Thesis, Ulster University, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.654102.
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Rational Emotive Behaviour Therapy (REBT: Ellis, 2001) represents the original cognitive behavioural therapy (eBT) model of psychopathology. Although there is much empirical support for the basic theory of REBT (see David, Lynn, & Ellis, 2010), the model has never been tested in the context of posttraumatic stress responses to adverse life events. The first empirical chapter of the thesis investigated the construct validity of the Attitudes and Belief Scale 2 (ABS-2: DiGiuseppe, Leaf, Exner, & Robin, 1988). This chapter employed traditional confirmatory factor analysis and confirmatory bifactor modelling to investigate the psychometric properties of the ABS-2. Results indicated that a bifactoral model conceptualisation was found to offer an adequate representation of the underlying factor structure of the scale. Based on these results, an abbreviated version of the ABS-2 with superior psychometric properties was thus constructed. In the second empirical chapter confirmatory bifactor modelling and composite reliability analysis were employed to investigate the psychometric properties of the Profile of Emotional Distress (PED: Opris & Macavei, 2007). The PED was designed to capture the qualitative distinction between dysfunctional emotions, as predicted by REBT theory. Results indicated that the PED does not capture the distinction between functional and dysfunctional negative emotions, however a bifactor model inclusive of a single general distress factor, and four method factors was found to be an acceptable fit of the data. The third empirical chapter utilised structural equation modelling to test the organisation of the irrational beliefs in the prediction of posttraumatic stress responses. A model consistent with the predictions of REBT theory was found to be a good fit of the data and explained a large percentage of variance in each symptom class of posttraumatic stress. The fourth empirical chapter provided the first piece of empirical evidence that generalised irrational beliefs impact upon posttraumatic stress symptoms via trauma-specific irrational beliefs; a frequently hypothesised relationship which had hitherto remained untested. Results of structural equation modelling offered support for this core hypothesis. Subsequently, the fifth empirical chapter investigated the impact of trauma-specific irrational beliefs in the prediction of reporting posttraumatic stress symptoms while controlling for a number of important sociodemographic factors. Binary logistic regression ~ .. ~ ... analysis was employed and found that three irrational belief process positively predicted belong to the strongly symptomatic group. Finally, the sixth empirical chapter employed sequential moderated multiple regression analysis to determine if rational beliefs could positively moderate the impact of irrational beliefs of posttraumatic stress symptoms. Rational beliefs were found to exert a negative, direct effect on posttraumatic stress symptoms, and to lessen the impact of irrational beliefs on posttraumatic stress responses.
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Eley, Clive William. "The rational design of photocatalytic semiconductor nanocrystals." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:ee29c922-857c-432a-8316-a7e04c822b1d.
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This thesis reports the successful rational design of three highly active photocatalytic semiconductor nanocrystal (SNC) systems by exploiting morphology effects and the electronic properties of type II semiconductor heterojunctions. Novel architectures of colloidal SNCs are produced with the aim of suppressing exciton recombination and improving charge extraction for the successful initiation of desirable redox chemistry. Rod-shaped niobium pentoxide Nb2O5 nanocrystals (NCs) are shown to exhibit significantly enhanced activity (10-fold increase in rate constant) relative to spherical-shaped NCs of the same material. The increase is attributed to Nb5+ Lewis acid site rich (001) surfaces, present in higher proportions in the rod morphology, which bind organic substrates from solution resulting in direct interaction with photogenerated charges on the surface of the NC. Building on the insights into morphology-activity dependence, type II semiconductor heterojunctions are exploited for their ability to increase exciton lifetimes and spatially separate charges. Two novel II-VI heterostructured semiconductor nanocrystals (HSNCs) systems are investigated: a series of CdX/ZnO (X = S, Se, Te) HSNCs and ZnS/ZnO HSNCs capped with two different surface ligands. In the first case, substantial photocatalytic activity improvement is observed for HSNCs (relative to pure ZnO analogues) according to the following trend: CdTe/ZnO > CdS/ZnO > CdSe/ZnO. The observed trend is explained in terms of heterojunction structure and fundamental chalcogenide chemistry. In the second case, both ZnS/ZnO HSNCs exhibit activity enhancement over analogous pure ZnO, but the degree of enhancement is found to be a function of surface ligand chemistry. Photocatalytic activity testing of all the materials investigated in this work is performed via the photodecomposition of methylene blue dye in aerated aqueous conditions under UVA (350 nm) irradiation. The synthetic techniques employed for the synthesis of colloidal SNCs investigated in this thesis range from chemical precipitation and solvothermal techniques to several different organometallic approaches. A wide variety of analytical techniques are employed for the chemical, structural and optical characterisation of SNC photocatalysts including: XRD, XPS, TEM, UV-vis absorption, PL spectroscopy and FTIR. Atom Probe Tomography (APT) is employed for the first time in the structural characterisation of II-VI heterojunctions in colloidal HSNCs. Overall, this thesis provides a useful contribution to the growing body of knowledge pertaining to the enhancement of photocatalytic SNCs for useful applications including: solar energy conversion to chemical fuels, the photodecomposition of pollutants and light-driven synthetic chemistry.
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Damry, Adam. "From Protein Sequence to Motion to Function: Towards the Rational Design of Functional Protein Dynamics." Thesis, Université d'Ottawa / University of Ottawa, 2019. http://hdl.handle.net/10393/39211.
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Protein dynamics are critical to the structure and function of proteins. However, due to the complexity they inherently bring to the protein design problem, dynamics historically have not been considered in computational protein design (CPD). Herein, we present meta-MSD, a new CPD methodology for the design of protein dynamics. We applied our methodology to the design of a novel mode of conformational exchange in Streptococcal protein G domain B1, producing dynamic variants we termed DANCERs. Predictions were validated by NMR characterization of selected DANCERs, confirming that our meta-MSD framework is suitable for the computational design of protein dynamics. We then performed a thorough NMR characterization of the sequence determinants of dynamics in one DANCER, isolating two mutations responsible for the novel dynamics this protein exhibits. The first, A34F, is responsible for destabilizing the highly stable native Gβ1 conformation, allowing the protein to sample other conformational states. The second, V39L mediates subtle interactions that stabilize the designed conformational trajectory in the context of the A34F mutation. Together, these results highlight the role of protein plasticity in the development of dynamics and the need for highly accurate computational tools to approach similar design problems. Finally, we present an NMR-based characterization of structural dynamics in a family of related red fluorescent proteins (RFPs) and pinpoint regions of the RFP structure where dynamics correlate to RFP brightness. This overview of the RFP dynamics-function relationship will be used in future projects to perform a computation design of functional dynamics in RFPs.
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Tzavalis, Elias. "Tests and applications of the rational expectations hypothesis of the term structure of interest rates." Thesis, London Business School (University of London), 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.361604.
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Kim, Dong Heon. "Essays on the term structure of interest rates, monetary policy, and business cycle /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2000. http://wwwlib.umi.com/cr/ucsd/fullcit?p9975875.
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Irving, Alexander John Dolman. "T.F. Torrance's natural theology understood in its intellectual context : the synthesis of rational structure and material content." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:6500d1b6-1d62-4d1a-aa67-176b091bdf4c.
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This thesis argues that the pertinent intellectual context for understanding Thomas F. Torrance's reconstruction of natural theology is the synthesis of the rational structure of knowledge and the material content of knowledge. The bridge between the synthesis of (i) rational structure and material content, and (ii) natural theology is the analogous relation Torrance set between the relation of natural theology and revealed theology and the relation of practical geometry and physics, which is constituted by the same formal relation of rational structure and material content. By examining Torrance's work on natural theology in this connection it is apparent that the germane methodological issue at stake is the manner of the relation between the rational structure of human understanding and the material content of God's self-revelation in theological cognition. Torrance's criticism of natural theology concerns its autonomous formulations in which theistic argumentation is established as an antecedent rational sub-structure, from which revealed theology is interpreted and cognized within an anthropocentric correlate system. Accordingly, Torrance's reconstruction of natural theology is the reconfiguration of the relation of rational structure and material content within theological rationality. Applied to the classical loci of natural theology, this takes the form of a reconceptualisation of the cosmological argument and ontological argument, such that the rational structure of theistic argumentation is determined through its connection to revelation at key points. The significance of this inversion of the relation of rational structure and material content extends outwards into Torrance's broader dogmatics, where natural theology is identified as the rational intra-structure of theology, which, in conjunction with revealed theology as material content, constitutes theological science. The result is a theological approach that sets itself as a development beyond Karl Barth's rejection of natural theology, which conceives of natural theology as the necessary but insufficient condition of theology, under the determination of God's self-revelation.
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Ruiz-Gómez, Gloria, John C. Hawkins, Jenny Philipp, Georg Künze, Robert Wodtke, Reik Löser, Karim Fahmy, and M. Teresa Pisabarro. "Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics." Public Library of Science, 2016. https://tud.qucosa.de/id/qucosa%3A30052.
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Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.
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Ruiz-Gómez, Gloria, John C. Hawkins, Jenny Philipp, Georg Künze, Robert Wodtke, Reik Löser, Karim Fahmy, and M. Teresa Pisabarro. "Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-215877.
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Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.
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Huang, Baohua. "Protein engineering: from structure-function relation studies of phospholipase A2 to rational design of a novel restriction endonuclease /." The Ohio State University, 1995. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487867541732847.
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Sysoiev, Volodymyr Viktorovych. "Determination of a rational structure of the security service integrated logistical support system based on regional logistics clusters." Thesis, Institute of Technology and Business in Ceske Budejovice, 2013. http://repository.kpi.kharkov.ua/handle/KhPI-Press/45905.
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Development of an integrated logistical support system for all types of national security services requires the solution to a problem of definition its rational structure. The methodical approach proposes to consider this issue as a complex of two successive optimization tasks. In the first place, it assumes to determine regional logistics clusters amount and then to optimize their logistics infrastructure. The models and methods are developed to allow optimization of the integrated logistical support system structure according to a real transport network communications and a regional supply chain by a minimal total logistics costs criterion.
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Ahsan, Habib Polash. "Active learning efficiently converges on rational limits of toxicity prediction and identifies patterns for molecule design." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263553.
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付記する学位プログラム名: 充実した健康長寿社会を築く総合医療開発リーダー育成プログラム京都大学
新制・課程博士
博士(医学)
甲第23092号
医博第4719号
京都大学大学院医学研究科医学専攻
(主査)教授 黒田 知宏, 教授 上杉 志成, 教授 藤渕 航
学位規則第4条第1項該当
Doctor of Medical Science
Kyoto University
DFAM
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Roselle, Russell Paul. "Rational Corporate Risk Management Policy: An Extension of Traditional Risk Management Theory to Incorporate Observed Managerial Behavior." Thesis, Virginia Tech, 2006. http://hdl.handle.net/10919/31910.
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There is qualitative and anecdotal evidence that corporate management deviates from received risk management theory. These deviations include: an overall hesitancy to accept projects with greater levels of total risk, increased return requirements compensating for firm-specific risk, employment of hedging strategies, the insuring of diversifiable risks, corporate diversification outside of the industry constraint, and the utilization of portfolio and other variance reducing methods. The literature primarily contributes these behaviors to principal/agent conflicts.
Evidence from studies on these deviations support strong arguments based in resource scarcity, cost and availability of capital, employee/community stability, and the increases in bankruptcy costs that these risk management deviation are in the interest of shareholders. When considered in the context of the long-term impact on value, the observed deviations from received corporate risk management theory contribute substantively to the perpetuation of the firm as a long-term store of value.
This paper supports two hypotheses: (1) the deviation from received risk management theory by corporate managers is broadly practiced, and (2) these deviations are generally in the interest of shareholders.Master of Arts
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Henry, Olan Thomas John. "The rational expectations hypothesis of the term structure : an economic analysis of the U.S. treasury yield curve 1952-1991." Thesis, University of Reading, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.262456.
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Igun, Onotasamiderhi Tarric. "Employing the power of DNA-based microbial community structure analysis for the rational design of hydrocarbon contaminated soil remediation." Thesis, University of Newcastle upon Tyne, 2017. http://hdl.handle.net/10443/3796.
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The impact of activated carbon (AC) amendments on the biodegradation of crude oil in soil was studied in batch microcosms. AC amendment slowed down biodegradation and removal of hydrocarbon pollutants and was more evident when AC when added from the beginning compared to after 5 months. The microbial sequencing analysis revealed that the overall bacterial community shifted more due to crude oil addition compared to AC amendment at the start and after 5 months. AC amendments reduced and slightly reduced the abundance of hydrocarbon degraders belonging to Actinobacteria and classes Gammaproteobacteria and Alphaproteobacteria (Such as Rhodococcus, Marinobacter, and Parvibaculum) in crude oil batches with AC from start and AC after 5 months, respectively. The effect of biofuels on the natural attenuation of toluene was also investigated. 13C/12C-CO2 batch production showed that biofuel components were preferentially degraded in blended fuels. Ethanol had a more negative effect on toluene degradation compared to biodiesel, as it was preferentially degraded even with nutrient bio-stimulation. The microbial analysis revealed nutrient effect on the microbial communities with nitrifying bacteria Nitrospira seen to make significant gains in OTU ranking and relative abundance due to the nutrient amendment. The microbial community analysis also showed a distinction in microbial communities that degrade biodiesel, ethanol and toluene in the presence or absence of nutrients. For instance the results showed that Rhodococcus can degrade toluene in the presence of biodiesel when nutrients are surplus or scarce and can degrade toluene in the presence of ethanol only when nutrients are scarce. Indicating a lower effect of biodiesel on toluene degraders compared to ethanol. Pseudomonas was identified as a key ethanol degrader and thrives in presence of both ethanol and toluene when nutrient availability is high but has preference for ethanol as a carbon source. Nocardia is main biodiesel degrader when nutrient availability is high or low. This study has shown that the use of DNA microbial community analysis gives a broader insight into microbes involved in the physiological activities and how they are affected by certain treatments and the findings in this study would possibly aid the understanding of the impact of adsorbents on hydrocarbon pollutants and the effect of blended fuels have on the microbiology within soil. It is thereby recommended that during hydrocarbon soil remediation studies/interventions, DNA microbial community analysis should be carried out in conjunction with chemical analysis such as the one carried out in this study as this would inform the proper utilization of the remediation strategies. The work was carried out in batch studies and it is important to repeat it in column, mesocosms or field studies to see if there are any significant changes in the results.
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Alcón, Rovira Isaac. "Rational chemical design of Triarylmethyl-based devices and 2D materials." Doctoral thesis, Universitat de Barcelona, 2018. http://hdl.handle.net/10803/543567.
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In this PhD thesis I have studied through state-of-the-art quantum simulations (mainly within the density functional theory approach, DFT) triarylmethyl (TAM) based systems with potential for future nano-devices and designed a series of TAM-based 2D covalent organic frameworks (from now on TAM 2D-COFs). TAMs are organic radicals (i.e. open-shell molecules) which have been used for numerous applications during the last 20 years. In the first part of this PhD thesis I have studied a series of TAM-based systems in collaboration with the experimental groups led by Profs. Jaume Veciana and Concepció Rovira and Dr. Marta Mas-Torrent, respectively, both from the Institute of Materials Science of Barcelona (ICMAB). In such collaborative studies we have evaluated the potential of TAMs for different potential applications. In the first two works we assess the possibility of using closed-shell quinoidal TAMs which, upon being chemisorbed in metal substrates give rise to an open-shell (i.e. radical) monolayer. This is demonstrated by means of on-surface techniques such as X-ray photo-electron spectroscopy (XPS) and angle-resolved ultra-violet photo-electron spectroscopy (ARUPS) and our periodic density functional theory calculations. Complementing to this work I also present a second where a similar radical SAM is formed using, in this case, a TAM-based bi-radical compound. In a third collaborative study we study the E – Z isomerisation in a hydrogenated closed-shell TAM (the so-called H-PTM) bonded with an ethylene unit. An irreversible E to Z transformation is experimentally measured with no evident explanation. Based in DFT and ab initio molecular dynamics simulations (AIMD), I was able to provide a sensible hypothesis for such results based in a sterical blocking effect in the Z conformer. The last two chapters of this PhD thesis collect the computational works focused in making theoretical predictions of yet un-synthesized systems. In Chapter 4, I present a work were we studied how to control the unpaired electron in TAMs, finding out that in these molecules there exists a linear correlation between the aryl ring twist angles and the localization of their unpaired electron. Based on this study we then looked for TAM-based systems where the aryl rings’ twist angles could be externally manipulated. In such direction, I present TAM 2D-COFs (see above) as the only possible platform where aryl ring twist angles may be externally manipulated. As reported in the second publication of Chapter 4, uniaxially stretching the structure of our designed TAM 2D-COFs allows for a fine and reversible (i.e. elastic) twisting of all aryl rings within the 2D material. This allows controlling the localization of all unpaired electron in the network, as well as the band of the material and magnetic interactions. In the last work of this chapter we assess the possibility of having chemical persistence of TAM monomers and structural flexibility through a screening procedure based in force-field calculations. In the last chapter of this PhD thesis I present two studies where it is demonstrated that TAMs, upon being covalently bonded in para- one respect each other, present electrical conductive characteristics. In the first work, in collaboration with the experimental groups from ICMAB, this is demonstrated for a PTM dimer where one of the PTM units is reduced to the anion. The resulting negative charge is found to conduct between both PTM units at room temperature. Finally, in the last predictive work of this thesis, I present a work where we demonstrate based in hybrid DFT calculations that para-connected TAM 2D-COFs behave as semimetals with energetically close-lying semiconductor solutions.En esta tesis doctoral presentada por artículos he estudiado mediante cálculos DFT (density functional theory, del inglés) sistemas basados en moléculas triaril-metil (TAM) para potenciales aplicaciones futuras. Las moléculas TAM son compuestos orgánicos radicales (es decir, con un electrón desapareado) que se han utilizado para construir diversos materiales durante los últimos 20 años. En la primera parte de la tesis presento los estudios llevados a cabo en colaboración con grupos experimentales del Instituto de Ciencia de los Materiales de Barcelona (ICMAB) expertos en la síntesis de tales compuestos. En los primeros estudios de esta parte se ha llevado a cabo la formación de una mono-capa auto-ensamblada de TAMs en diferentes superficies metálicas. Mediante técnicas de superficie i cálculos DFT periódicos hemos demostrado que utilizando moléculas TAM de capa cerrada (es decir, diamagnéticas) se puede generar una mono-capa radical, o de capa abierta (es decir, paramagnética). En un tercer estudio en colaboración con los mismos grupos experimentales estudiamos la isomerización E – Z (o cis- trans-) irreversible en un sistema TAM-etileno (de capa cerrada). Los cálculos computacionales han sido claves en este estudio para entender el bloqueo cinético que se da en el isómero Z (cis-), lo cual impide su isomerización al isómero E (trans-), a pesar de ser éste último más estable termodinámicamente. En la segunda parte de esta tesis doctoral presento una serie de estudios en los cuales hemos diseñado materiales 2D basados en moléculas TAM, aún no preparados en el laboratorio. En estos estudios se demuestra el gran potencial de dichas redes basadas en moléculas TAM y su gran versatilidad electrónica a la nano-escala. Nuestros resultados demuestran que dichos materiales 2D se puede comportar tanto como aislantes eléctricos, como semiconductores o como semimetales (tales como el grafeno) según su diseño molecular. Además, en dicho materiales es posible controlar sus propiedades electrónicas mediante la manipulación del ángulo de giro de los anillos aril en cada unidad TAM.
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Chang, Eric P. "The Rational Design of Coiled-Coil Peptides towards Understanding Protein-Crystal Interactions and Amorphous-to-Crystalline Transitions." Bowling Green State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1363258701.
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Frouco, Gonçalo Daniel dos Santos. "Modulating chromatin structure and gene expression during African swine fever virus infection : new strategies for an efficient vaccine rational design." Doctoral thesis, Universidade de Lisboa, Faculdade de Medicina Veterinária, 2018. http://hdl.handle.net/10400.5/14927.
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Tese de Doutoramento em Ciências Veterinárias, na especialidade de Sanidade Animal.African swine fever virus (ASFV) is a nucleo-cytoplasmic large DNA virus which infects all members of the family Suidae, causing a fatal disease of domestic swine and wild boar. Since no effective vaccine or treatment is available, ASF is considered a global threat for pig husbandry. The ASFV genome encodes among others, enzymes required for virion assembly, genome transcription and replication, including a putative histone-like protein, pA104R. In bacteria, these proteins perform topological modification of the chromosome (twisting, bending and folding), playing important structural and regulatory functions. Since ASFV has a large genome, a viral histone-like protein may be important for packaging its genome within the virion particle and/or for viral replication and transcriptional events. In this study, the ASFV-pA104R activity was characterized and its DNA-binding activities were evaluated. pA104R binds both to ssDNA and dsDNA, although having higher affinity to ds-DNA, over a wide range of temperatures, pH values, and salt concentrations and in an ATP-independent manner, with an estimated binding site size of about 14 to 16 nucleotides. The arginine residue located in pA104R’s DNA-binding domain, at position 69, also revealed to be important for an efficient DNA-binding. Additionally, since pA104R together with the viral type II topoisomerase, pP1192R, displayed DNA-supercoiling activity, a synergistic effect between these viral is proposed. The expression of pA104R was observed in the late phase of infection in infected cells with the Vero-adapted ASFV isolate Ba71V, co-localizing with cell nucleus and viral factories. siRNA experiments showed that the knockdown of A104R induce a reduction of viral progeny, copy numbers of viral genomes and transcription of a late viral gene, revealing that pA104R plays a critical role in viral DNA replication and gene expression. Results obtained on these studies prompted us to pursue the objective to generate a defective infectious single cycle (DISC) ASFV lacking the A104R gene. Recombinant virus was successfully obtained, however the complementary cell line previously developed did not support its replication. The antiviral activity of four HDACi against ASFV was also evaluated in this study. The results showing the abrogation of viral replication by NaPB open new insights on its use as an antiviral strategy to control ASFV spreading. Overall our data strongly support that pA104R plays an important role on ASFV replication opening a new window for the design of ASF control measures through the development of efficient and safe vaccines and antivirals.
RESUMO - Modulação da estrutura cromatínica e da expressão génica durante a infeção do Vírus da Peste Suína Africana – novas estratégias para o desenvolvimento de uma vacina eficaz - O vírus da peste suína africana (VPSA) é um vírus de DNA nucleo-citoplasmático que infeta todos os membros da família Suidae, causando uma doença com elevada mortalidade em suínos domésticos e nos javalis. Atualmente não existe uma vacina ou tratamento eficaz, tornando a peste suína africana (PSA) uma ameaça para a suinicultura mundial. O genoma do VPSA codifica aproximadamente 150 proteínas, algumas delas bem caracterizadas, estando envolvidas na transcrição, replicação ou na montagem do virião. No entanto, e apesar de todos os esforços realizados nas últimas décadas, a função biológica de numerosas proteínas virais não é ainda conhecida. Esta lacuna aliada à necessidade de um melhor entendimento sobre a biologia do VPSA e as suas interações com o hospedeiro têm contribuído em grande parto para a dificuldade no desenvolvimento de uma vacina eficaz contra PSA. Por homologia de sequências proteicas, o genoma do VPSA codifica para uma proteína tipo histona (pA104R). Nas bactérias, estas proteínas são responsáveis por modular a topologia do DNA (torção, flexão e dobramento), desempenhando assim importantes funções estruturais e controlando a expressão de diferentes genes. O facto do genoma do VPSA codificar entre outras uma proteína viral semelhante a histonas bacterianas, reveste-se assim de enorme relevância pelo papel que que estas proteínas possam desempenhar na compactação do genoma na partícula viral e/ou para a sua replicação e transcrição. Neste contexto, este estudo pretendeu caracterizar o papel da VPSA-pA104R na replicação viral, tendo como objetivo contribuir para o conhecimento da biologia deste vírus e para averiguar se o gene A104R será um bom candidato para desenvolver uma vacina DISC (do inglês “defective infectious single cycle). Além disso, diferentes inibidores das histonas deacetilases (HDACs) foram testados como potenciais antivirais, eventualmente úteis no controlo da PSA Os principais objetivos deste trabalho foram assim os seguintes: (1) estudar VPSA-pA104R, através da clonagem, expressão, purificação e caracterização de sua atividade in vitro; (2) Compreender a relevância funcional de dois resíduos conservados de pA104R; (3) Avaliar os níveis de mRNA e proteína, bem como a localização intracelular de pA104R em células infetadas com VPSA, em diferentes tempos de infeção; (4) Desenvolver uma estratégia que permita a deleção da ORF A104R do genoma do VPSA e a obtenção de uma vacina DISC; (5) avaliar os níveis de acetilação das histonas das células infetadas para melhor compreensão do mecanismo de modulação dos mecanismos epigenéticos do hospedeiro pelo VPSA; (6) Avaliar o efeito dos inibidores das HDACs na infeção pelo VPSA. Neste estudo, a VPSA-pA104R foi expressa num sistema procariota baseado em Escherichia coli. Após a sua purificação, a sua atividade foi caracterizada através de ensaios EMSA (do inglês “electrophoretic mobility shift assay”) e concluiu-se que esta proteína viral se liga tanto a DNA de cadeia simples como dupla, embora tenha maior afinidade para o de cadeia dupla, e estimou-se que o local de ligação seja cerca de 14 a 16 nucleótidos. Esta ligação ao DNA continua presente em variadas condições de temperaturas, pH e concentrações de sal e é independente de ATP. A perda de atividade da proteína mutada pontualmente no resíduo de arginina localizado na posição 69, revelou que este resíduo é importante para uma ligação eficaz ao DNA. Além disto, foi possível concluir que a carga positiva deste aminoácido é determinante para a capacidade de ligação do pA104R ao DNA. Adicionalmente, uma vez que se observou atividade de superenrolamento de DNA quando a pA104R e uma topoisomerase tipo II viral, pP1192R, foram adicionados a DNA plasmídeo relaxado, este trabalho suporta que o VPSA codifica de facto para proteínas necessárias a compactação do seu genoma e ainda é proposto a existência de um efeito sinérgico entre as duas proteínas virais acima descritas. Como o objetivo de melhor compreender a importância da pA104R na infeção do VPSA, avaliou-se a dinâmica da sua expressão e a sua localização intracelular. A expressão de pA104R foi observada na fase tardia da infeção em células Vero infetadas com o isolado viral Ba71V, co-localizando com núcleo da célula e fábricas virais citoplasmáticas. Em relação à dinâmica de transcrição do gene A104R, apesar de ser típica de um gene tardio, foi possível detetar transcritos a partir das 2 horas pós-infeção (hpi). As experiências usando siRNA (do inglês “small interference RNA”) contra os transcritos do gene A104R, mostraram que a redução dos níveis de RNA deste gene induzem uma redução da progenia viral, do número de cópias de genomas virais e da transcrição de um gene viral tardio (B646L), revelando que o pA104R desempenha um papel crítico na replicação do DNA viral e na expressão de genes virais. Atualmente, as únicas medidas de controlo do VPSA são baseadas na deteção precoce da doença e na rápida aplicação de medidas biossanitárias como o abate de animais infetados, controlo do movimento de animais e a vigilância. As tentativas falhadas até agora em obter uma vacina inativada ou atenuada permitem que novas estratégias, como as vacinas DISC ganhem espaço na investigação do VPSA como uma revigorante estratégia para controlar o VPSA. Os resultados obtidos neste estudo, anteriormente descritos, suportam a ideia que um mutante de deleção no gene A104R replicará o seu genoma nas células hospedeiras, mas não poderá compacta-lo dentro do virião, resultando num virião não-infecioso "vazio" que será incapaz de iniciar um segundo ciclo de infeção. Assim a infeção com este vírus mutante será capaz de estimular o sistema imunitário do hospedeiro, mas ao mesmo tempo será seguro, não produzindo progenia infeciosa. Assim outro objetivo deste trabalho foi então obter um vírus DISC deletado no gene A104R. Para isto, o vírus recombinante foi obtido por recombinação homóloga e uma linha Vero complementar, que expressa a pA104R, foi desenvolvida. Embora, o vírus recombinante tenha sido obtido com sucesso, a linha celular complementar desenvolvida não suporta a sua replicação e, como tal, a seleção e propagação do vírus recombinante não foi possível. Os baixos níveis de expressão de pA104R destas células quando comparados com os de células infetadas poderão explicar esta não complementação. Com base em estudos anteriores que mostram que VPSA regula o estado epigenético da célula hospedeira, o grau de acetilação das histonas de células infetadas foi avaliado e a atividade antiviral de quatro inibidores das HDACs (NaPB, VPA, TSA e SAHA) contra a infeção pelo VPSA também foi testada neste estudo. O VPSA induz uma hipoacetilação dos resíduos de lisina 9 e 14 da histona H3 (H3K9K14). Esta modificação epigenética corrobora outras reportadas noutros estudos e todas elas estão classicamente correlacionada com o silenciamento de genes em células eucarióticas e pode indicar que o VPSA subverte diferentes mecanismos celulares, controlando o acesso da maquinaria de transcrição aos genes hospedeiros. Adicionalmente, um dos inibidores das HDACs testados, o NaPB, reverte este estado de hipoacetilação da histona e inibe a replicação do VPSA, interferindo com a expressão de gene virais tardios. Os resultados obtidos neste estudo sugerem fortemente que a pA104R participa da modulação da topologia do DNA viral, estando envolvida na replicação, transcrição e/ ou compactação do DNA viral. Com o objetivo de desenvolver uma vacina DISC, o gene A104R poderá assim constituir um bom alvo a deletar. Esta nova estratégia poderá ser uma alternativa às tentativas até agora falhadas de obter uma vacina contra a PSA. Contudo, antes de uma vacina DISC ser realidade, um esforço científico no desenvolvimento de uma linha celular complementar será imperativo. Os resultados obtidos sugerem ainda que as HDACs celulares estão envolvidas no estabelecimento de infeção pelo VPSA e revelaram que o NaPB pode ser usado como uma estratégia antiviral adicional para controlar a propagação de vírus nas áreas de surto.
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Fernández, Sessarego Carlos. "How to legally protect humans if their existential structure is ignored?" IUS ET VERITAS, 2016. http://repositorio.pucp.edu.pe/index/handle/123456789/122494.
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The author makes a critical analysis of how over time it has tried to find the subject of study of Law and how it is distinguished from other beings that make up the universe. t hus the rational dimension of man has passed his ontological analysis as being in itself which makes it unique and spirit as the arrangement will be co-existential seeking protection for the same freedom he has. Finally, the author focuses on the own “freedom” of man and of which the other rights it has.El autor hace un análisis crítico de cómo a lo largo del tiempo se ha tratado de encontrar al sujeto de estudio del Derecho y cómo este se distingue de los demás seres que conforman el universo. e s así como de la dimensión racional del ser humano se ha pasado a su análisis ontólogico como ser en sí mismo cuyo espíritu lo hace único y en tanto que ser coexistencial le procura el ordenamiento una protección por la misma libertad que posee. Finalmente el autor se centra en esa “Libertad” propia del ser humano que genera los demás derechos que posee.
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Canzoneri, Joshua Craig. "Interaction of small molecules with nucleic acid targets: from RNA secondary structure to the riobosome." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/45769.
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Nucleic acids have proven to be viable targets for small molecule drugs. While many examples of such drugs are detailed in the literature, only a select few have found practical use in a clinical setting. These currently employed nucleic acid targeting therapies suffer from either debilitating off-target side effects or succumb to a resistance mechanism of the target. The need for new small molecules that target nucleic acids is evident. However, designing a novel drug to bind to DNA or RNA requires a detailed understanding of exactly what binding environments each nucleic acid presents. In an effort to broaden this knowledge, the work presented in this thesis details the binding location and affinity of known and novel nucleic acid binding small molecules with targets ranging from simple RNA secondary structure all the way to the complex structure of ribosomal RNA. Specifically, it is shown that the anthracycline class of antineoplastics prefer to bind at or near mismatch base pairs in both physiologically relevant iron responsive element RNA hairpin constructs as well as DNA hairpin constructs presenting mismatched base pairs. Also characterized in this thesis is a novel class of topoisomerase II / histone deacetylase inhibitor conjugates that display a unique affinity for DNA over RNA. Finally, the novel class of macrolide-peptide conjugates, known as peptolides, are shown to retain potent translation inhibition of the prokaryotic ribosome. The binding pocket of the peptolides, including a crevice previously unreachable by macrolides that extends away from the peptidyl transferase center toward the subunit interface, is confirmed in detail via chemical footprinting of the 70S ribosome. Overall, the identification of a novel binding site for the anthracycline class of drugs and the characterization of the two novel drug designs presented in this thesis will undoubtedly aid in the effort to design and discover new molecules that aim for nucleic acid targets. For example, the anthracycline derivative topoisomerase II / histone deacetylase inhibitor conjugates, with their differential mode of nucleic acid binding, may prove to have a unique side effect profile in a therapeutic application. The peptolide compounds also have the potential to be applied as novel antibiotics as they bind to an area of the prokaryotic ribosome unrelated to known macrolide resistance mutations. Furthermore, as a result of the observation of this thesis work that some peptolides also posses eukaryotic translation inhibition capabilities, they could prove to be useful in preventing the growth of rapidly proliferating eukaryotic cells such as plasmodium, leishmania, or tumor cells. Additionally, different head groups could be utilized in creating new peptolides; for example, an oxazolidinone antibiotic could be employed to sample a different binding area of the ribosome.
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Wineberg, Mark (Mark Lorne) Carleton University Dissertation Computer Science. "Program induction using an unmodified genetic algorithm; a rational reconstruction of genetic programming through the use of a static parse tree structure." Ottawa, 1993.
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Lundell, Katie A. "Electronic Transmutation: An Aid for the Rational Design of New Chemical Materials Using the Knowledge of Bonding and Structure of Neighboring Elements." DigitalCommons@USU, 2019. https://digitalcommons.usu.edu/etd/7525.
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Everything in the universe is made up of elements from the periodic table. Each element has its own role that it plays in the formation of things it makes up. For instance, pencil lead is graphite. A series of honeycomb-like structures made up of carbon stacked on top of one another. Carbon’s neighbor to the left, boron doesn’t like to form such stacked honeycomb-like structures. But, what if there was a way to make boron act like carbon so it did like to form such structures? That question is the basis of the electronic transmutation concept presented in this dissertation. Electronic transmutation states that an element, such as boron, can behave structurally like carbon (form stacked honeycomb structures) if you make them valence (outer most) isoelectronic (“iso”- same; “electronic”- electrons), so both would have the same number of outer most electrons. As a result, chemists would have a new tool to aid in the rational design of new materials.
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Landström, Joachim. "The theory of Homo comperiens, the firm's market price, and the implication for a firm's profitability /." Uppsala : Department of Business Studies, Uppsala universitet, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8268.
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Abraham, Punnoose Jibin. "Investigation on the Secondary Structures Formed in Full-length Telomere Overhang and Rational Design of Ligands for Targeting Telomere G-quadruplexes." Kent State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=kent1516742818621033.
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Garganas, Eugenie. "Testing the rational expectations hypothesis of the term structure for unstable emerging market interest rates with interbank data from Greece and the Czech Republic." Thesis, Imperial College London, 2002. http://hdl.handle.net/10044/1/11410.
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Salin, M. (Mikko). "Protein crystallographic studies of A-TIM—structure based development of new enzymes." Doctoral thesis, University of Oulu, 2010. http://urn.fi/urn:isbn:9789514261237.
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Abstract Enzymes are potentially superior as catalysts for many industrial chemical processes because of their high specificity, selectivity, minimum energy requirement and environmental friendliness. However, many challenges remain in order to exploit fully the potential of industrial enzymes. The qualities which are needed are catalytic proficiency, availability in high quantities, low price, low product inhibition, and high activity and stability under process conditions. Directed evolution and rational design are the most common strategies to produce enzymes with the desired properties. The TIM barrel is the most frequent and most versatile fold among naturally occurring enzymes. In all known TIM barrel enzymes, the catalytically active residues are located at one end of the barrel structure, while residues maintaining the stability of the fold are found on the opposite end of the barrel. This special architecture of the TIM barrel proteins makes it possible to change catalytic activity of the protein without compromising its stability, which is a perfect start for protein engineering studies. In this research project, a monomeric triosephosphate isomerase (TIM) variant with an engineered binding groove (A-TIM) was created by using a rational design approach. The major aims of this work were (i) to find novel binders and (ii) characterize the new, bigger binding groove using X-ray crystallographic methods. These studies have discovered that monomeric A-TIM can bind compounds completely different from the natural substrate. Studies on three different classes of binder molecules are reported: (i) true substrate analogues of wild type TIM, (ii) substrate analogues that have an extended hydrophobic tail, and (iii) more extended, phosphate containing substrate analogues. In addition to this, the A-TIM active site was shown to be competent. In general these studies illustrate the importance of protein crystallography for characterizing the binding properties of enzyme variants being studied in enzyme discovery projectsTiivistelmä Entsyymit voivat toimia ylivoimaisina katalyytteinä monissa kemianteollisuuden prosesseissa johtuen niiden hyvästä spesifisyydestä, valikoimiskyvystä, alhaisesta energiantarpeesta ja ympäristöystävällisyydestä. Näistä ominaisuuksista huolimatta entsyymien kaikkien mahdollisuuksien hyödyntämisen esteenä on monia haasteita. Tarvittavia ominaisuuksia ovat katalyyttinen tehokkuus, saatavuus suurina määrinä, alhainen hinta, alhainen tuoteinhibitio sekä korkea aktiivisuus ja stabiilisuus prosessiolosuhteissa. TIM-tynnyrirakenne on yleisin ja monipuolisin proteiinien laskostumisrakenne luonnossa esiintyvissä entsyymeissä. Tässä rakenteessa katalyyttisesti aktiiviset aminohappotähteet ovat sijoittuneet tynnyrirakenteen toiselle puolelle, kun taas stabiilisuuden kannalta tärkeät aminohappotähteet ovat sijoittuneet kokonaan toiselle puolelle. Tämä erityinen rakenne antaa mahdollisuuden muokata proteiinin katalyyttistä aktiivisuutta vaikuttamatta haitallisesti sen stabiilisuuteen. Tämä on täydellinen lähtökohta proteiininmuokkaukselle. Tässä tutkimusprojektissa käytettiin ns. järkiperäistä suunnittelua monomeerisen trioosifosfaatti-isomeraasivariantin (A-TIM) luomisessa. Tämän tutkimustyön pääasialliset tavoitteet olivat (i) uusien sitoutujien löytäminen ja (ii) uuden, suuremman sitoutumistaskun ominaisuuksien määrittäminen röntgenkristallografisilla menetelmillä. Tässä tutkimuksessa havaittiin, että A-TIM kykenee sitomaan yhdisteitä, jotka ovat täysin erilaisia luonnolliseen substraattiin verrattuna. Tässä tutkimuksessa kuvaillaan kolmenlaisia sitoutujia: (i) todelliset villityypin entsyymin substraattianalogit, (ii) substraattianalogit, joihin on liitetty hydrofobinen hiilivetyketju ja (iii) villityypin substraattia suuremmat sokerifosfaatit. Tämän lisäksi A-TIM:n aktiivisen keskuksen todistettiin olevan toimintakykyinen. Yleisellä tasolla tämä tutkimus osoittaa röntgenkristallografisten menetelmien tärkeyden entsyymienmuokkausprojekteissa, joissa entsyymivarianttien ominaisuuksien määritys on tärkeää
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Ye, Hongtu. "Study of the structure/function relationship in canine and human IgE as the basis for the development of rational therapeutic intervention strategies in allergic disease." Thesis, University of Sheffield, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.537989.
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Roberts, Sarah Elizabeth. "Synthesis of 2,4,5-Triaminocyclohexane Carboxylic Acid as a Novel 2-Deoxystreptamine Mimetic." Diss., CLICK HERE for online access, 2009. http://contentdm.lib.byu.edu/ETD/image/etd2890.pdf.
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Manzenrieder, Florian. "New approaches to discover protease inhibitors : by de novo rational structure based design (BACE1) and by development and use of 1̲hn31̲hn1P NMR as versatile tool to screen compound libraries /." München : Verl. Dr. Hut, 2009. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=017356959&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.
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Bowles, David P. Bowles. "Engineering the S7S8 Loop of Human Tumor Suppressor p53 and NMR Studies of E. coli Repressor of Primer and E. raikovi Er-23." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1531242395152643.
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Irazazabal, Luz Noemi. "Avaliação estrutural e funcional de novos peptídeos antimicrobianos obtidos a partir de desenho racional." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066418/document.
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Les peptides antimicrobiens sont considérés comme une nouvelle classe prometteuse d'agents anti-infectieux. Afin de développer de nouveaux agents efficaces et non toxiques, des stratégies de conception rationnelle peuvent être utilisées. Dans cette perspective, nous avons utilisé une approche computationnelle pour concevoir trois peptides synthétiques ([I5, R8] MP, EcDBS1R6 et PaDBS1R1). En déterminant la concentration minimale inhibitrice, nous avons montré que tous les peptides sont actifs contre les bactéries Gram-négatif et -positif. Seul [I5, R8] MP a montré une activité antifongique. La mesure de la concentration de peptide provoquant 50 % de mortalité cellulaire a permis de montrer que les peptides étaient faiblement ou non hémolytiques, sans toxicité vis-à-vis des cellules embryonnaires rénales humaines HEK-293. La cinétique bactéricide a révélé que PaDBS1R1 et [I5, R8] MP tuent rapidement E. coli en comparaison à S. aureus et que EcDBS1R6 élimine rapidement les deux souches. Des études de perméabilisation et de dépolarisation combinées à de la microscopie électronique à haute résolution (FEG-SEM) ont montré un mécanisme membranolytique des peptides. L'analyse de la structure des peptides par spectroscopie de dichroïsme circulaire et résonance magnétique nucléaire, ainsi que par modélisation moléculaire lors de leur interaction avec une membrane modèle, révèle une conformation en hélice alpha amphipatique. En conclusion, notre étude indique que l'évaluation structurale et fonctionnelle de peptides antimicrobiens synthétiques conçus de manière rationnelle représente une stratégie prometteuse pour le développement de nouveaux agents antimicrobiensAntimicrobial peptides (AMPs) have been considered as a potential novel class of antimicrobial compounds. In order to generate new potent and non-toxic antimicrobial agents, rational design strategies may be employed. In this view, we used a computational method to design three synthetic AMPs ([I5, R8] MP, EcDBS1R6 and PaDBS1R1). By determining the minimum inhibitory concentration, we found that all the peptides were active against Gram-negative and -positive bacteria. Only [I5, R8] MP was found to display antifungal activity. The determination of the peptide concentration producing 50% of cell lysis revealed low or no hemolytic activity, with no cytotoxicity towards human embryonic kidney cells HEK-293. During time-kill assays more rapid bactericidal effects were observed for PaDBS1R1 and [I5, R8] MP against E. coli compared to S. aureus. For the peptide EcDBS1R6, identical killing curves were obtained for both bacterial strains. Membrane permeabilization and depolarization studies combined with field emission gun scanning electron microscopy (SEM-FEG) revealed that a membranolytic mechanism occurs for these peptides. When analyzed by circular dichroism and nuclear magnetic resonance microscopy or by molecular dynamics simulations during interaction with a membrane model, peptides were shown to adopt an amphipathic alpha-helical conformation. In conclusion, our results indicate that the structural and functional evaluation of rationally designed synthetic AMPs represents a promising strategy for the development of potent novel antimicrobial agents
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Tonnelé, Claire. "Modélisation des propriétés photophysiques de capteurs chimiques pour des applications de détection de cations par fibre optique." Phd thesis, Université Sciences et Technologies - Bordeaux I, 2013. http://tel.archives-ouvertes.fr/tel-00918201.
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La présence croissante de diverses substances dans notre environnement, conséquencedes activités anthropiques de ces dernières décennies, a entraîné un besoingrandissant et urgent de nouveaux matériaux et dispositifs dans la quête de senseurschimiques efficaces et fiables. D'énormes progrès technologiques ont permis de mettreà disposition toute une gamme d'outils techniques pour leur développement, enprenant en compte les exigences à respecter en terme de sélectivité ou de rapidité deréponse, entre autres. Dans ce contexte, les méthodes de chimie quantique permettentune compréhension fondamentale des processus en jeu dans la détection des espèceschimiques, et par extension, l'élaboration de manière rationnelle de nouveauxmatériaux sensibles. Certaines molécules organiques pouvant être largementfonctionnalisées, elles constituent un point de départ idéal en raison des importantesmodulations possibles de leurs propriétés par des modifications structuralesappropriées.Cette étude vise à développer de manière rationnelle des chromoionophores pour lacomplexation de cations par une approche combinant méthodes de chimiecomputationnelles et caractérisation par spectroscopie optique. Deux pointsprincipaux ont été traités à l'aide de la Théorie de la Fonctionnelle de la Densité(DFT) et son extension dépendante du temps (TD-DFT): d'une part les relationsstructure moléculaire-propriétés optiques de chromophores, d'autre part le phénomènede complexation. En particulier, la détection de l'ion Zn2+, démontrée de manièrethéorique et expérimentale, est finalement réalisée après intégration du senseurmoléculaire dans un dispositif à fibre optique.
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Ali, Elda, and Tereza Kerpčarová. "Family buying behaviour : parents’ perspective of children influence on their buying behaviour." Thesis, Högskolan Kristianstad, Fakulteten för ekonomi, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:hkr:diva-19653.
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Even though power and influence of children on family buying behavior is growing little is known about their involvement. Previous studies of family and household consumption often neglect the role of children in decision-making, but nowadays, children are becoming one of the most powerful influencers in family buying behavior. They dominate family buying decision and can influence their parents in many product categories from cars till regular grocery shopping and therefore the question arises, what influences children when requesting products and what strategies they use to make their parents yield to their requests. Thus, this research paper tries to explain how are influence strategies that children use and family complexity related to parents buying behavior of groceries. The primary data have been collected through an electronic questionnaire, which resulted in sample of 164 parents respondents from around the globe. The data were analyzed by using various statistical tools and concluded that (1) aggressive, persuasion, rational and knowledge strategies are positively affecting parents buying behavior, (2) non-traditional family structure has positive impact on buying behavior, (3) older children have more influence power over parents buying behavior and (4) number of children has no significant influence on parents buying behavior.
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Guizzo, Homero Azevedo. "Testes da hipótese das expectativas racionais para o mercado de renda fixa brasileiro." reponame:Repositório Institucional do FGV, 2014. http://hdl.handle.net/10438/11535.
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Neste estudo foram realizados testes econométricos da validade da hipótese das expectativas racionais como explicação para a formação das taxas de juros no Brasil. O estudo compara os resultados destes testes para período de 1995 a 2002 com os resultados para o período de 2003 a 2013. Estes intervalos foram escolhidos por contarem com políticas econômicas e choques muito diversos. A comparação entre os dois períodos obtém alterações importantes, mas que não alteram a conclusão de que a hipótese das expectativas racionais não tem respaldo empírico como explicação para a formação da estrutura termo das taxas de juros no Brasil. Embora tenha caído significativamente, o prêmio de alongamento continuou estatisticamente significante.
The present study performs econometric tests of the validity of the rational expectations hypothesis to explain the Brazilian interest rates term structure. The study compares the results of these tests for the period 1995-2002 with the results for the period 2003-2013. These time frames were chosen due to their very different economic policies and shocks. The comparison between the two periods detects major changes, but that does not alter the conclusion that the hypothesis of rational expectations has no empirical support as an explanation for the behavior of the term structure of interest rates in Brazil. Although it has fallen significantly, long term rates premium remained statistically significant.
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Ramer, Heber M. "Emancipatory technology as liberal art education : a rationale and structure /." The Ohio State University, 1990. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487683401442298.
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Maerli, Andre. "Structural reliability analysis of FPSOs towards a rational design procedure." Thesis, University of Glasgow, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.284727.
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This report presents the structural reliability analysis of the hull girder ultimate strength for the ship shaped FPSO Triton. The ultimate strength of the hull girder was calculated using a component approach, where the behaviour of the hull is evaluated based on the behaviour of the single structural components. Three collapse conditions were investigated; failure initiated by plate compression, failure initiated by stiffener tension and failure initiated by stiffener compression. Only vertical bending moment has been considered and the hull girder loads are divided into stillwater and wave induced components. The two loading components have been considered independent and Ferry Borges - Castenheta load combination method has been applied to obtain load combination factors for the Full Load, Partial Load (50 % loaded) and Ballast condition. The distributions of the extreme values of the vertical wave bending moments (VWBM) were calculated, based on linear strip theory and a long-term formulation. The vertical mooring forces are small and they were considered to have an insignificant influence on the bending moment response. The reliability analysis was carried out using a SORM analysis. Annual reliability indices (ß) and probabilities of failures were calculated for hogging and sagging conditions. The calculated ß values were higher than the annual reliability indices proposed in DNV Classification Notes 30.6 for serious failures in redundant structures. This indicates that the design is safe and reliable for operation in this particular location.
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Miller, Raymond. "Galois module structure in wild extensions of the rationale function field." Thesis, University of Exeter, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390170.
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Sebens, Patricia Anne Shope. "Rationale and Structure for Adequate Public Education: A Value Critical Approach." Diss., Virginia Tech, 2006. http://hdl.handle.net/10919/26121.
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The purpose of this dissertation was to provide a functional definition of adequacy synthesized from the application of efficiency (E), equality/equity/dignity (EED), and excellence/quality (EQ) value clusters found in various state litigations pertaining to the financial systems used to distribute educational opportunity. Questions researched in this study were (a) In what manner might the tension of the paradoxical demands of community responsibility and individual rights housed within the principle of liberty be used creatively in the development of public policy? (b) How do the value clusters inherent in democracy allow for balance and affect the provision of adequate educational opportunity? (c) Using value critical analysis, how does funding litigation clarify the search for the meaning of adequate educational opportunity? (d) What themes appear throughout these cases that may be used to build consensus for the development of policy frameworks and the evaluation of present funding systems designed to provide adequate educational opportunity in a particular time and place?
As an examination of policy, legal research was used to analyze litigation in cases in which the provision of educational opportunity was challenged based on the terms of art under girding standards established for the delivery of public education. This study was implemented in five stages:
1. Values clusters to be examined were selected through the review of the history of educational opportunity in this nation and current literature addressing public values and education policy.
2. Through the examination of the paradox within the principle of liberty that guarantees individual rights and requires community responsibility, consideration was given to the creative tension, both principled and structural, that laid the foundation for and continues to drive the democratic process.
3. The role that policy development plays in establishing balance was outlined, noting the argumentation process used to transform knowledge through values, to create the framework necessary to take consistent action.
4. Value critical analysis examined the definition given to values clusters of efficiency (E), equality/equity/dignity (EED), and excellence/quality (EQ) as found in court cases adjudicated in the last fifty years affecting the provision of educational opportunities. Litigation was analyzed, considering the standards established for the delivery of public education in state constitutions, the value given to the terms of art underpinning those standards, and the definitions for those terms as established by the courts.
5. Using the information gleaned, a policy framework was developed to structure adequate educational opportunity for all children.Ph. D.
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Tan, Liansheng. "Structural and behavioural analyses to linear multivariable control systems." Thesis, Loughborough University, 1999. https://dspace.lboro.ac.uk/2134/10490.
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This thesis is devoted to a number of structural and behavioural problems in linear multivariable control system theory. The first problem addresses the subject of determination of the finite and infinite frequency structure of a rational matrix. A novel method is proposed that determines the finite and infinite frequency structure of any rational matrix. Some neat and numerically stable algorithms are developed to implement this method. The second problem concerns the resol vent decompositions of a regular polynomial matrix and solutions of regular polynomial matrix descriptions (PMDs). Regarding these fundamental is'sues, three contributions are made therein. Firstly, based on a general resolvent decomposition a complete solution of regular PMDs is presented that takes into account both the non-zero initial conditions of the pseudo state and the non-zero initial conditions of the input. Secondly, two special resolvent decompositions are proposed, both of which are applied to formulate the solution of the regular PMDs. The first one is formulated in terms of the finite, infinite, and the generalised infinite Jordan pairs, which is a refinement of the results given by Gohberg et al. [74] and Vardulakis [25]. The second resolvent decomposition is proposed on the Weierstrass canonical form of the generalised companion matrix of the polynomial matrix. Thirdly, a new characterization of the impulsive free initial conditions of regular PMDs is given and the relationship between the finite and infinite frequency structure of a regular polynomial matrix and its generalised companion matrix is determined. In the third problem a generalization of the chain-scattering representation for general plants is presented. Through the notion of input-output consistency, the conditions under which the generalised chain-scattering representation and the dual generalised chain-scattering representation exist are proposed. Some algebraic system properties of the GCSRs and DGCSRs are studied. The fourth problem is devoted to a new notion of realization of behaviour. We introduce a notion realization of behavior which is shown to be a generalization of the classical concept of a realization of transfer function. By using this approach, the input-output structures of the generalized chain-scattering representations and the dual generalized chain-scattering representations are investigated in a behavioral theory context. The last problem is devoted to the subjects of system wellposedness and internal stability. We present certain generalisations to the classical concepts of wellposedness and internal stability. The input consistency and output uniqueness of the closed-loop system in the standard control feedback configurations are discussed. Based on this, a number of notions are introduced such as fully internal wellposedness, externally internal wellposedness, and externally internal stability, which characterize the rich input-output and stability features of the general control systems in a general setting. On the basis of these notions the extended JL control problem is defined in a general setting.
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Zhang, Yunxin, and 张云鑫. "On the admissible pairs of rational homogeneous manifolds of Picard number 1 and geometric structures defined by their varieties of minimal rational tangents." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/206439.
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In a series of works, Jun-Muk Hwang and Ngaiming Mok have developed a geometric theory of uniruled projective manifolds, especially those of Picard Number 1, relying on the study of Varieties of Minimal Rational Tangents (VMRT) from both the algebro-geometric and the G-structure perspectives. Based on this theory, Ngaiming Mok and Jaehyun Hong studied the standard embedding between two Rational Homogeneous Spaces (RHS) associated to long simple roots which are of different dimensions. In this thesis, I consider admissible pairs of RHS (X0, X) of Picard number 1 and locally closed complex submanifolds S ⊂ X inheriting VMRT sub-structures modeled on X0 = G0/P0 ⊂ X = G/P de_ned by taking intersections of VMRT of X with tangent space of S. Moreover, if any such S modeled on (X0, X) is necessarily the image of a standard embedding i : X0 → X, (X0, X) is said to be rigid. In this thesis, it is proved that an admissible pair (X0, X) is rigid whenever X is associated to a long simple root and X0 is non-linear and de_ned by a marked Dynkin sub-diagram. In the case of the pair (S0, S) of compact Hermitian Symmetric Spaces (cHSS), all the admissible pairs (S0, S) are completely classified. Based on this classification, a sufficient condition for the pair (S0, S) to be non-rigid is established through explicitly constructing a submanifold S ⊂ S such that S can never be obtained from the image of any standard embedding i : S0 → S. Besides, the term special pair is coined for those (S0; S) sorted out through classification, and the algebraicity of submanifolds modeled on special pairs is confirmed by checking a modified form of the non-degeneracy condition defined by Hong and Mok is satisfied. However, the question as to whether these special pairs are rigid, as pointed out in this thesis, remains to be investigated. Finally, pairs of hyperquadrics (Q^n, Q^m) are studied separately. Since non-rigidity is trivial, in these cases it is interesting to establish a characterization of the standard embedding i : Q^n→Q^m under some stronger condition. In this thesis, the latter problem is solved in terms of the partial vanishing of second fundamental forms.published_or_final_version
Mathematics
Doctoral
Doctor of Philosophy
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Sun, Zhen Kun. "Rational design of mesoporous materials with Core/shell structures with applications for sustainability." Doctoral thesis, Université Laval, 2015. http://hdl.handle.net/20.500.11794/26106.
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Les matériaux mésoporeux sont devenus des nanomatériaux d’une grande importance, et le contrôle des structures des matériaux mésoporeux est essentiel pour une variété d'applications pratiques. Les matériaux «cœur/coquille» structurés sont un type de matériaux hybrides qui non seulement possèdent les propriétés des composants individuels, mais présentent également de effets synergiques entre le «cœur» et la «coquille». La conception de matériaux mésoporeux et «cœur/coquille» structurés pour les appliquer avec succès dans la pratique devrait être une force de progrès importante pour le développement continu. Cette thèse se concentre principalement sur deux aspects: (1) une conception de matériaux mésoporeux «cœur/coquille» structurés en vue de résoudre les problèmes de synthèse, qui entravent leurs nouvelles applications et (2) l'application de matériaux mésoporeux dans la capture du CO2 cyclique pour améliorer la durabilité des sorbants de CO2 en prenant avantage du concept de «cœur/coquille». Visant le cyclage de l’hydroxyde de calcium, une technologie attrayante pour la capture du CO2 à grande échelle, nous avons établi un nouveau mésoporeux «cœur/coquille» structuré à base de CaO qui présentait une grande stabilité et d'excellentes performances de résistance à l’attrition, attribuées aux avantages des matériaux mésoporeux et à la configuration de «cœur/coquille». Notre procédé de fabrication peut être facilement réalisé à grande échelle et répond aux exigences de la circulation entre des réacteurs en lit fluidisé. Les nanoparticules métalliques ont normalement tendance à se coaguler ensemble dans des réactions catalytiques, et sont difficiles à séparer. Par conséquent, nous avons démontré une synthèse de microsphères Fe3O4@C-Pd@mSiO2 à composants multiples et polyvalentes avec une structure «cœur/coquille» bien définie et des nanoparticules catalytiques de Pd confinées, et ayant des canaux mésoporeux ordonnés et facilement accessibles. Récemment, des méthodes diverses ont été proposées pour fabriquer un revêtement de matériaux mésoporeux sur un cœur par un processus de «soft-templating». Cependant, les diamètres des mésopores générés sont généralement très faibles (< 3 nm), ce qui peut limiter leurs nouvelles applications. Ici, nous avons réalisé la synthèse de microsphères «cœur/coquille» structurées superparamagnétiques possédant une coquille externe de silice mésoporeuse ordonnée à larges pores (4,5 nm), en adoptant un copolymère tribloc comme agent tensioactif directeur de structure.Mesoporous materials, especially ordered ones have become ones of great importance nanomaterials, which possess regular, uniform and interpenetrating mesopores in nanoscale. Morphology and texture controls towards mesoporous materials are critical for a variety of practical applications, the ultimate goal of which are the realization of their functional design. Core/shell composite materials are a type of functional hybrid materials which not only possess the properties of the individual components, but also exhibit some new or synergistic effects between the core and the shell. The design of mesoporous materials with unique core/shell configuration and multifunctions to make them successfully applied in practice, should be an important driving force for the continuous development of current material science. This thesis mainly focuses on two aspects: (1) careful design of core/shell structured mesoporous materials in order to solve the problem and difficulty in synthesis, which hinders their further applications and (2) application of mesoporous materials in cyclic CO2 capture to enhance the durability of CO2 sorbents by taking advantage of the core/shell concept. Aiming at the calcium looping cycle, an attractive technology for large-scale CO2 capture, we have prepared novel mesoporous core/shell structured CaO-based sorbents which exhibit highly stable cyclability and excellent attrition-resistance performances, attributed to advantages of both mesoporous materials and unique core/shell configuration. Our fabrication method could easily be realized in large-scale and meet the requirements of circulating fluidized bed reactors. Owing to their high surface energies, metallic nanoparticles normally tend to aggregate together during catalytic reactions, and their separation from a complex heterogeneous system is another obstacle. In this regards, we have demonstrated a facile and versatile synthesis of multicomponent and multifunctional microspheres Fe3O4@C-Pd@mSiO2 with well-defined core/shell structures, confined catalytic Pd nanoparticles and accessible ordered mesopore channels. Recently, various methods have been proposed for coating mesoporous shells on cores by soft-templating process. However, the generated mesopores are usually very small (< 3 nm), which may limit their further applications. In this work, we have accomplished the synthesis of superparamagnetic core/shell structured microspheres possessing an outer shell of ordered mesoporous silica with large pores (4.5 nm) by adopting triblock-copolymer Pluronic P123 as soft-template.