<p>Lipopolysaccharide, the physical barrier that protects Gram-negative bacteria from various antibiotics and environmental stressors, is anchored to the outer membrane by the phosphorylated, acylated disaccharide of glucosamine known as lipid A. Besides being necessary for the viability of most Gram-negative bacteria, lipid A interacts directly with specific mammalian immune cell receptors, causing an inflammatory response that can result in septic shock. The lipid A biosynthetic pathway contains nine enzymatic steps, the sixth being the phosphorylation of the tetraacyldisaccharide-1-phosphate (DSMP) precursor to form lipid IV_A by the inner membrane-bound kinase LpxK, a divergent member of the P-loop containing nucleotide triphosphate hydrolase superfamily. LpxK is the only known P-loop kinase to act on a lipid at the membrane interface.</p><p> We report herein multiple crystal structures of <italic>Aquifex aeolicus</italic> LpxK in apo as well as ATP, ADP/Mg<super>2+</super>, AMP-PCP, and chloride-bound forms. LpxK consists of two &alpha;/&beta;/&alpha; sandwich domains connected by a two-stranded &beta;-sheet linker. The N-terminal domain, which has most structural homology to other P-loop kinase family members, is responsible for catalysis at the P-loop and positioning of the DSMP substrate for phosphoryl transfer on the inner membrane. The smaller C-terminal domain, a substructure unique to LpxK, helps bind the nucleotide substrate using a 25º hinge motion about its base which also assembles the necessary catalytic residues at the active site.</p><p> Using a thin-layer chromatography-based radioassay, we have performed extensive kinetic characterization of the enzyme and demonstrate that LpxK activity <italic>in vitro</italic> is dependent on the presence of detergent micelles, the use of divalent cations, and formation of a ternary LpxK-ATP/Mg<super>2+</super>-DSMP complex. Implementing steady-state kinetic analysis of multiple point mutants, we identify crucial active site residues. We propose that the interaction of D99 with H261 acts to increase the pK_a of the imidazole group, which in turn serves as the catalytic base to deprotonate the 4&rsquo;-hydroxyl of DSMP. An analogous mechanism has not yet been reported for any member of the P-loop kinase family.</p><p> The membrane/lipid binding characteristics of LpxK have also been also investigated through a crystal structure of the LpxK-lipid IV_A product complex along with point mutagenesis of residues in the DSMP binding pocket. Critical contacts with the bound lipid include interactions along the glucosamine backbone and the 1-position phosphate group, especially through R171. Furthermore, analysis of truncation mutants of the N-terminal helix of LpxK demonstrates that this substructure is a critical hydrophobic contact point with the membrane, and that both charge-charge and hydrophobic interactions contribute to the localization of LpxK at the lipid bilayer. </p><p> Overall, this work has contributed significantly to the limited knowledge surrounding membrane-bound enzymes that act upon lipid substrates. It has also provided insight into the process of enzyme evolution as LpxK, while containing a similar core domain as other P-loop kinases, has developed multiple subdomains required for both cellular localization and recognition of novel substrates. Finally, the presence of multiple crystal structures and detailed understanding of the LpxK catalytic mechanism will improve the chances of successfully targeting this essential step in lipid A biosynthesis in the pursuit of novel antimicrobials.</p> / Dissertation

Iki ekonominės krizės visuomenėje vyravo vartotojiškas požiūris, gauti kuo didesnes pajamas, noras turėti kuo daugiau, tačiau toks besaikis vartojimas pasaulį privedė prie finansinės krizės ir sukrėtė vyraujantį ekonominį modelį iki pat pamatų. Nepaisant technologinių pasiekimų, keičiantis gamybos ir vartojimo tempams kinta ir išteklių naudojimas bei aplinkos tarša. Nacionalinėje darnaus vystymosi strategijoje (toliau NDVS) (2009) iškeltas tikslas, kad Lietuva pagal ekonomikos lygį ir išteklių naudojimo efektyvumo rodiklius iki 2020 m. turi pasiekti 2003 m. ES–15 šalių vidurkį, o pagal aplinkos taršos rodiklius – neviršyti ES leistinų normatyvų, todėl labai svarbu žinoti, kaip siekiant šių tikslų gali keistis aplinkos būklė ir, ar pasiseks įgyvendinti darnaus vystymosi strategijoje numatytus aplinkosauginius tikslus. Darbo tikslas – išanalizuoti pagrindinius aplinkos sektoriaus darnaus vystymosi rodiklius ir nustatyti jų priklausomybę nuo ekonomikos pokyčių 2000–2020 m. Lietuvoje. Darbe buvo analizuojami pagrindiniai Lietuvos darnaus vystymosi ekonominiai, socialiniai ir aplinkosauginiai rodikliai 2000–2010 m., taip pat nustatyta aplinkos kintamųjų priklausomybė nuo ekonomikos (ne)augimo ir įvertintos galimos aplinkos kintamųjų tendencijos bei galimybės įgyvendinti iškeltus tikslus, pagal tris galimus ekonomikos vystymosi scenarijus 2010–2020 m. laikotarpiu. Sudarius tris galimus ekonomikos vystymosi scenarijus rezultatai parodė, kad jei šalies ūkis vystytųsi pagal pirmą (16... [toliau žr. visą tekstą] / Consumeristic approach to maximize income, the desire to have more has dominated in societies before the economic crisis, but that excessive consumption of the world has led to the financial crisis witch has shaken dominant economic model to the foundation. Despite technological achievements, changing production and consumption rates influence use of resources and environment pollution. The main aim of the National Sustainable Development Strategy (2009) is to achieve the average development level of EU15 in year 2003 according to the indicators of economic and social developments as well as to the efficiency in consumption of resources and to stay within the EU’s allowable limits by 2020. The aim of the study is to examine main sustainability indicators of environmental sphere and to assess their dependence from economic (GDP) changes over 2000–2020 periods in Lithuania. The main changes of indicators of sustainable development over 2000–2010 period were assessed in Lithuania. Also dependence of environment variables from economic (de)growth was examined and possible tendencies of environmental variables and opportunities to achieve foreseen targets, according to three possible scenarios for economic development over 2000–2020 periods were evaluated. Three possible scenarios for economic development has shown that if country’s economy develops according to the first (16 % GDP growth) or second (zero GDP growth) scenario, the aim set by NSDS (2009) to decouple the... [to full text]

The control and protection system of early nuclear power plants (Generation II) have been designed and built on the then reliable analog system. Technology has evolved in recent times and digital system has replaced most analog technology in most industries. Due to safety precautions and robust licensing requirements in the nuclear industry, the analog and digital system works concurrent to each other in most control and protection systems of nuclear power plants. Due to the ageing, regular maintenance and intermittent operation, the analog plant system often gives faulty signals. The objective of this thesis is to simulate a transient using a simulator to reduce the effects of system faults on the nuclear plant control and protection system, by detecting the faults early. The following steps will be performed: • validating the simulator measurements by simulating a normal operation, • detecting faults early on in the system These can be performed by resorting to a model that generates estimates of the correct sensors signal values based on actual readings and correlations among them. The next step can be performed by a fault detection module which determines early whether or not the plant systems are behaving normally and detects the fault. (Baraldi P. et al, 2010.) / Thesis (MSc (Engineering Sciences in Nuclear Engineering))--North-West University, Potchefstroom Campus, 2013.

The control and protection system of early nuclear power plants (Generation II) have been designed and built on the then reliable analog system. Technology has evolved in recent times and digital system has replaced most analog technology in most industries. Due to safety precautions and robust licensing requirements in the nuclear industry, the analog and digital system works concurrent to each other in most control and protection systems of nuclear power plants. Due to the ageing, regular maintenance and intermittent operation, the analog plant system often gives faulty signals. The objective of this thesis is to simulate a transient using a simulator to reduce the effects of system faults on the nuclear plant control and protection system, by detecting the faults early. The following steps will be performed: • validating the simulator measurements by simulating a normal operation, • detecting faults early on in the system These can be performed by resorting to a model that generates estimates of the correct sensors signal values based on actual readings and correlations among them. The next step can be performed by a fault detection module which determines early whether or not the plant systems are behaving normally and detects the fault. (Baraldi P. et al, 2010.) / Thesis (MSc (Engineering Sciences in Nuclear Engineering))--North-West University, Potchefstroom Campus, 2013.

We study diffusion-reaction-advection models describing population dynamics of aquatic organisms subject to a constant drift, with reflecting upstream and outflow downstream boundary conditions. We consider three different models: single logistically growing species, two and three competing species. In the case of a single population, we determine conditions for existence, uniqueness and stability of non-trivial steady-state solutions. We analyze the dependence of such solutions on advection speed, growth rate and length of the habitat. Such analysis offers a possible explanation of the "drift paradox" in our context. We also introduce a spatially implicit ODE (nonspatial approximation) model which captures the essential behavior of the original PDE model. In the case of two competing species, we use a diffusion-advection version of the Lotka-Volterra competition model. Combining numerical and analytical techniques, in both the spatial and nonspatial approximation settings, we describe the effect of advection on competitive outcomes. Finally, in the case of three species, we use the nonspatial approximation approach to analyze and classify the possible scenarios as we change the flow speed in the habitat.

Traditionally, void ratio, e has been used as a state variable for predicting the liquefaction behaviour of soils under the Critical State (Steady State) framework. Recent publications show that void ratio, e may not be a good parameter for characterizing sand with fines as the steady state, SS data points move downward in e-log(p) space up to certain fines content termed as threshold fines content, TFC. Thus, it was difficult to apply SS concept on sand with fines as a small variation of fines content may lead to different SS line. Many researchers proposed to used equivalent granular void ratio, e* as an alternative state variable (i.e. in lieu of void ratio, e) in attempt to obtain a narrow trend line for SS data points irrespective of fc provided fc  TFC. The e* is obtained from e. For the conversion from e to e*, one need a parameter b which presents the active fraction of fines in overall force structure of sand. However, predicting the b is problematic. Most, if not all, of the b reported were determined by case-specific back-analysis, that is, the b-value was selected so that the test results for a given sand-fines type could be correlated with the equivalent granular void ratio, e* irrespective of fines content. This thesis examines the factors that affecting the b value by examining published work on binary packing. This leads to a simple semi-empirical equation for predicting the value of b based onparticle size ratio,  and fines content, fc. Published data and experimental results on Sydney sand appears to be in support of the proposed equation. The single relation of SS data points in e*-log(p) space for sand with fines is referred as Equivalent Granular Steady State Line, EG-SSL. The EG-SSL is then used to define the equivalent granular state parameter,*. A good correlation observed between * and q-p, q- q responses in undrained shearing. The e* and * are also used to modified a state dependent constitutive model. Seven model input parameters are needed in addition four to critical state input parameters. These parameters are obtained from drained test. The model is used to predict q-pand q- q responses for flow, non-flow and limited flow behaviour for 0% to 30% fines contents. The model predictions are in good agreement with experimental results. The effect of fines types (in terms of plasticity and angularity) on the prediction equation of b are also examined with four different types of fines. A negligible effect of fines type on the prediction equation of b is observed. The link between monotonic and cyclic loading behaviour for sand with fines are also examined with emphasis on cyclic instability and strain hardening behaviour after quasi steady state, QSS for a range of fines contents (provided that fc < TFC). It is found that a single set of rules could be used to correlate monotonic and cyclic behaviour for a range of fines contents at same *.

Στην παρούσα μεταπτυχιακή αυτή εργασία μελετήσαμε την συμπεριφορά για πρώτη φορά ενώσεων που είχαν σαν βάση την βενζοδισθιαζόλη. Συγκεκριμένα οι ενώσεις αυτές μελετήθηκαν με την χρήση των τεχνικών της φασματοσκοπίας διφωτονικής απορρόφησης της φασματοσκοπίας σταθερής κατάστασης και της φασματοσκοπίας φθορισμού χρονικής ανάλυσης. Αρχικά όσον αφορά την φασματοσκοπία διφωτονικής απορρόφησης, μπορέσαμε να οδηγηθούμε στα εξής συμπεράσματα: οι καλύτερες ενώσεις που παρουσιάζουν αρκετά μεγάλη διφωτονική απορρόφηση είναι τα γραμμικά μόρια (PK-439 και PK-452) σε σχέση με τα U-shaped μόρια με μέγιστη ενεργό διατομή ΔΦΑ ~2000GM. Επιπλέον παρατηρήσαμε ότι η χρήση της βενζοδισθιαζόλης σαν κεντρικός πυρήνας προκαλεί σημαντική αύξηση της διφωτονικής απορρόφησης, σε σχέση με την βενζοθιαζόλη. Τέλος, με την τεχνική της φασματοσκοπίας φθορισμού χρονικής ανάλυσης μπορέσαμε να οδηγηθούμε σε κάποιες διαπιστώσεις: συγκεκριμένα παρατηρήσαμε ότι όσο το μήκος κύματος καταγραφής μεγαλώνει, τόσο οι καμπύλες αποδιέγερσης γίνονται πιο αργές. Ακόμα διαπιστώσαμε ότι από την σύγκριση μορίων στο μήκος κύματος του μεγίστου, σε εκείνα τα μόρια που αποδιεγείρονται γρήγορα, ευνοούνται οι μη-ακτινοβολητικές διεργασίες και ταυτόχρονα παρουσιάζουν μικρή ενεργό διατομή ΔΦΑ. / --

Orientador: Angela Maria Sitta / Banca: Maria Aparecida Soares Ruas / Banca: Claudio Aguinaldo Buzzi / Resumo: Neste trabalho classificamos problemas de bifurcação Z2-equivariantes de corank 2 até co- dimensão 3 via técnicas da Teoria de Singularidades. A abordagem para classificar tais problemas é baseada no processo de redução à forma normal de Birkhoff para estudar a interação de modos Hopf-Pontos de Equilíbrio. O comportamento geométrico das soluções dos desdobramentos das formas normais obtidas é descrito pelos diagramas de bifurcação e estudamos a estabilidade assintótica desses ramos. / Abstract: In this work we classify the Z2-equivariant corank 2 bifurcation problems up to codimension 3 via Singularity Theory techniques. The approach to classify such problems is based on the Birkhoff normal form to study Hopf-Steady- State mode interaction. The geometrical behavior of the solutions of the unfolding of the normal forms is described by the bifurcation diagrams and we study the asymptotic stability of such branches. / Mestre

The calibration of modern internal combustion engines requires ever improving measurement data quality such that they comply with increasingly stringent emissions legislation. This study establishes methodology and a software tool to improve the quality of steady-state emissions measurements from engine dynamometer tests. Literature shows state of the art instrumentation are necessary to monitor the cycle-by-cycle variations that significantly alter emissions measurements. Test methodologies that consider emissions formation mechanisms invariably focus on thermal transients and preconditioning of internal surfaces. This work sought data quality improvements using three principle approaches. An adapted steady-state identifier to more reliably indicate when the test conditions reached steady-state; engine preconditioning to reduce the influence of the prior day’s operating conditions on the measurements; and test point ordering to reduce measurement deviation. Selection of an improved steady-state indicator was identified using correlations in test data. It was shown by repeating forty steady-state test points that a more robust steady-state indicator has the potential to reduce the measurement deviation of particulate number by 6%, unburned hydrocarbons by 24%, carbon monoxide by 10% and oxides of nitrogen by 29%. The variation of emissions measurements from those normally observed at a repeat baseline test point were significantly influenced by varying the preconditioning power. Preconditioning at the baseline operating condition converged emissions measurements with the mean of those typically observed. Changing the sequence of steady-state test points caused significant differences in the measured engine performance. Examining the causes of measurement deviation allowed an optimised test point sequencing method to be developed. A 30% reduction in measurement deviation of a targeted engine response (particulate number emissions) was obtained using the developed test methodology. This was achieved by selecting an appropriate steady-state indicator and sequencing test points. The benefits of preconditioning were deemed short-lived and impractical to apply in every-day engine testing although the principles were considered when developing the sequencing methodology.

This thesis is devoted to the theoretical study of slow thermodynamic processes in non-equilibrium stochastic systems. Its main result is a physically and mathematically consistent construction of relevant thermodynamic quantities in the quasistatic limit for a large class of non-equilibrium models. As an application of general methods a natural non-equilibrium generalization of heat capacity is introduced and its properties are analyzed in detail, including an anomalous far-from-equilibrium behavior. The developed methods are further applied to the related problem of time-scale separation where they enable to describe the effective dynamics of both slow and fast degrees of freedom in a more precise way. Powered by TCPDF (www.tcpdf.org)