Master of Science / Department of Architectural Engineering and Construction Science / Kimberly W. Kramer / Soils conditions vary throughout the United States and effect the behavior of the foundation system for building structures. The structural engineer needs to design a foundation system for a superstructure that is compatible with the soil conditions present at the site. Foundation systems can be classified as shallow and deep, and behave differently with different soils. Shallow foundation systems are typically used on sites with stiff soils, such as compacted sands or firm silts. Deep foundation systems are typically used on sites with soft soils, such as loose sands and expansive clays. A parametric study is performed within this report analyzing tilt-up concrete structures in Dallas, Texas, Denver, Colorado, and Kansas City, Missouri to determine the most economical tilt-up wall panel and foundation support system. These three locations represent a broad region within the Midwest of low-seismic activity, enabling the use of Ordinary Precast Wall Panels for the lateral force resisting system. Tilt-up wall panels are slender load-bearing walls constructed of reinforced concrete, cast on site, and lifted into their final position. Both a 32 ft (9.75 m) and 40 ft (12 m) tilt-up wall panel height are designed on three foundation systems: spread footings, continuous footings, and drilled piers. These two wall heights are typical for single-story or two-story structures and industrial warehouse projects. Spread footings and continuous footings are shallow foundation systems and drilled piers are a deep foundation system. Dallas and Denver both have vast presence of expansive soils while Kansas City has more abundant stiff soils. The analysis procedure used for the design of the tilt-up wall panels is the Alternative Design of Slender Walls in the American Concrete Institute standard ACI 318-05 Building Code and Commentary Section 14.8. Tilt-up wall panel design is typically controlled by lateral instability as a result from lateral loads combining with the axial loads to produce secondary moments. The provisions in the Alternative Design of Slender Walls consider progressive collapse of the wall panel from the increased deflection resulting from the secondary moments. Each tilt-up wall panel type studied is designed in each of the three locations on each foundation system type and the most economical section is recommended.

Master of Science / Department of Architectural Engineering and Construction Science / Sutton F. Stephens / Cold‐formed steel has become a preferred building material for wall framing in many different types of structures. One of its main uses has been as non‐structural members in curtain wall assemblies of structural steel framed buildings. In an exterior wall application, the main purpose of the curtain wall is to transfer out of plane loads to the steel frame while not supporting any superimposed gravity loads. Therefore, when the curtain wall is in the plane of the structural steel frame, the vertical deflection of the spandrel beam directly above the wall must be known to provide the appropriate deflection gap between the beam and the curtain wall so that gravity loads are not transferred to the wall. Common practice is to size the gap for the deflection from 100% of the live load. In some cases, the deflection gap may be significant, and since this gap must also be provided in the exterior cladding of the wall, it creates a design issue for the architect. This report presents the results of an investigation into the feasibility of reducing the size of the deflection gap when the wall is located directly under the spandrel beam. In this study, analytical models were developed for common design situations of curtain walls constructed of cold‐formed steel studs in structural steel framed buildings. This study investigates two common stud heights combined with different floor live loads. Taking into account that wall studs have some available axial compressive strength, a procedure was developed to determine an appropriate reduction for the gap. Using an iterative process a relationship is made between the axial compressive strength of the stud and the amount of axial load the stud can support to establish a factor which gives the percentage the live load gap for 100% live load can be safely reduced by.

Master of Science / Department of Architectural Engineering and Construction Science / Sutton F. Stephens / Log construction is becoming increasingly popular throughout the U.S. Currently, seismic coefficients are not provided in model building codes for the design of the log shear walls as a lateral force resisting system for seismic forces. Current design practice is to use a response modification coefficient, R, of around 4.5. Several tests by other researchers on log shear walls showed strong energy dissipation and good lateral strength with stability after high displacements. This behavior of the log shear wall system is evidence that a higher R could possibly be used in design. The purpose of this study was to establish a response modification factor for single story log shear walls based on available shear wall tests using the definition of R provided in ATC-19. This research did not conduct testing according to the protocol and methodology of ATC-63. This work contains a history of the development of seismic design provisions in the U.S. and the evolution of the response modification coefficient. Common log construction practices are reviewed, with reference to ICC 400- Standard on Design and Construction of Log Structures. Using data provided by other researchers from physical testing and computer modeling of various types of log shear walls, an R of 6.0 is proposed based on the provisions of ATC-19. Finally, recommendations for further research to fully understand the behavior of the log shear wall system, including possible archetypes required by the methodology set forth in ATC-63, are provided.

<p>Phospho-MurNAc-pentapeptide translocase (MraY) is a conserved membrane-spanning enzyme involved in the biosynthesis of bacterial cell walls. MraY generates lipid I by transferring the phospho-MurNAc-pentapeptide to the lipid carrier undecaprenyl-phosphate. MraY is a primary target for antibiotic development because it is essential in peptidoglycan synthesis and targeted by 5 classes of natural product antibiotics. The structure of this enzyme will provide insight into the catalytic mechanism and a platform for future antibiotic development. MraY genes from 19 bacteria were cloned, expressed, purified and assayed for biochemical stability. After initial crystallization screening, I found that MraY from Aquifex aeolicus (MraYAA) produced diffracting crystals. Recombinant MraYAA is functional and shows inhibition by the natural inhibitor capuramycin. After extensive optimization of crystallization conditions, we extended the resolution limit of the crystal to 3.3 Å. The crystal structure, the first structure of the polyprenyl-phosphate N-acetyl hexosamine 1-phosphate transferase (PNPT) superfamily, reveals the architecture of MraYAA and together with functional studies, allow us to identify the location of Mg2+ at the active site and the putative binding sites of both substrates. My crystallographic studies provide insights into the mechanism of how MraY attaches a building block of peptidoglycan to the carrier lipid.</p><p>Voltage-gated Na+ (NaV) channels initiate action potentials in neurons and cardiac myocytes. NaV channels are composed of a transmembrane domain responsible for voltage-dependent Na+ conduction and a cytosolic C-terminal domain (CTD) that regulates channel function through interactions with many auxiliary proteins including members of the fibroblast growth factor homologous factor (FHF) family and calmodulin (CaM). Through the collaboration between our lab and Geoffrey Pitt's lab, we report the first crystal structure of the ternary complex of the human NaV1.5 CTD, FGF13, and Ca2+-free CaM at 2.2 Å. Combined with functional experiments based on structural insights, we present a platform to understand roles of these auxiliary proteins in NaV channel regulation and the molecular basis of mutations that lead to neuronal and cardiac diseases. Furthermore, we identify a critical interaction that contributes to the specificity between individual NaV CTD isoforms and distinctive FHFs.</p> / Dissertation

The increasing concern about water quality and energy demand promotes the development of innovative and low-cost processes to improve the nutrient uptake and energy efficiency of existing wastewater treatments (WWT). In this context, the inclusion of a microalgae system (MAS) in the flowsheet of a WWT plant represents a sustainable alternative to conventional technologies, as it combines a low-cost nutrient uptake system with the production of biomass suitable for biofuel production. However, at present, the energy required to cultivate and process the algae cells is often too high to justify their use. The adoption of a low energy harvesting system and an efficient energy conversion process are the sine qua non requirements to guarantee the sustainability of the process. In this thesis, current and innovative harvesting technologies for large scale applications have been reviewed to identify the optimal working conditions of each system and their link to the main characteristics of the algae suspension. In particular, the performance of the Ballasted Dissolved Air Flotation (BDAF) system was investigated using different algae and compared to the conventional Dissolved Air Flotation (DAF). BDAF was demonstrably a very viable harvesting method where the use of floating microspheres as ballasting agents allowed significant coagulant savings, reduced the level of energy dissipation within the flotation chamber, and lowered the overall carbon emissions and the process costs. Cont/d.

Water management is a serious issue that affects the performance and durability of PEM fuel cells. It is known, from previous experimental investigations, that surface wettability has influence on water behaviour and fuel cell performance. This finding has lead researchers to develop numerical tools for further investigation of the liquid water behaviour in gas channels. The Volume-of-Fluid (VOF) method has been used in a wide range of studies for its advantage of showing the multi-phase interface in a Computational Fluid Dynamics (CFD) simulation to understand liquid water behaviour in gas channels. In this thesis, numerical study has been carried out to examine the behaviour of liquid water in gas channels. The dynamic movement of the liquid water in the channel and the associated pressure drop, water saturation and water coverage of the GDL have been investigated. Firstly, flow diffusion into the GDL was examined to determine its effect on liquid droplet behaviour in a small section of a gas channel. Furthermore, the effects of the percentage of flow diffusion, GDL wettability, pore size, and water inlet velocity were investigated. Fluid diffusion into GDL found to have insignificant impact on liquid water behaviour so further investigations has been carried with a solid GDL surface. Secondly, gas channel geometry effect on liquid water behaviour was studied. Square, semicircle, triangle, trapezoid with a long base and trapezoid with a short base were compared to find suitable cross section geometry to carry wall wettability investigations. Among the examined geometries, the square cross section showed reasonable results for both scenarios of geometry design, fixed Reynolds number and fixed GDL interface. The effect of wall wettability was assessed by comparing nine different wall/GDL wettability combinations for straight and bend channels. Wall wettability found to have an impact on liquid water behaviour but not as much as GDL wettability. It affects liquid water saturation in the channel by a great deal by accumulating water in the channel edges affecting water behaviour. This was also proven in the last test case of a long channel where water accumulation was investigated by running the calculation until the percentage of water saturation is stabilized. It is also concluded that changing wall wettability from hydrophobic to hydrophilic doubles the percentage of channel occupied by liquid water and increases the time to reach steady state.

Cardiovascular disease, mostly atherosclerosis, is responsible for one third of all deaths globally, rising to more than 50% in the Western World. Risk factors include smoking, diet, and familial history. Doppler ultrasound can provide estimates of blood velocity and wall shear rate. Clinically, maximum velocity is used to categorise patients for surgery, although Doppler velocity measurement is prone to errors and in need of validation. Wall shear stress—which can be derived from wall shear rate—plays a role in disease initiation and progression, although its clinical utility is unclear due to difficulties associated with its measurement. This thesis investigates the use of Doppler ultrasound as a tool to estimate blood velocity and wall shear rate. A simplified method for estimation of wall shear rate in healthy arteries is developed that uses spectral Doppler ultrasound. This method is based upon the theory of oscillatory flow in rigid pipes, requiring two measurements that are readily available with clinical ultrasound machines. This method is compared to a similar method based on colour flow imaging. The spectral Doppler method underestimated the theoretic value of wall shear rate by between 7 and 22%, with results varying between phantoms. Errors for the colour method were on average 35% greater. Test measurements from one healthy volunteer demonstrated that this method can be applied in-vivo. In more advanced stages of disease, peak velocity distal to a stenosis is of clinical interest and the simplified method for wall shear rate estimation is invalid. Steady flow in a series of simplified stenosis geometries was studied using a dual-beam Doppler system to obtain velocity vectors. These measurements were compared with data from an equivalent system that used particle image velocimetry (PIV) and was considered the gold standard. For Reynolds numbers at the stenosis throat of less than 800, flow remained laminar over the region studied, although distal flow separation did occur. For higher throat Reynolds numbers—corresponding to more severe stenoses or increased flow rates—asymmetric recirculation regions developed; the transition to turbulence occurred more proximally, with a corresponding reduction in stenotic jet and recirculation length. Qualitative agreement was observed in the velocity profile shapes measured using ultrasound and PIV at throat Reynolds numbers less than 800. Above this threshold the qualitative agreement between the velocity profiles became poorer as both downstream distance and the degree of stenosis increased. Peak axial velocity distal to the stenosis was underestimated, on average, by 15% in the ultrasound system. Estimation of shear rate remained difficult with both experimental techniques. Under a Newtonian approximation, the normalised wall shear stresses agree qualitatively. Under pulsatile flow conditions using an idealised flow waveform, superior qualitative agreement was observed in the velocity profiles at diastole than at systole. Similar to the steady flow behaviour, this agreement deteriorated with stenosis severity. The current generation of clinical ultrasound machines are capable of estimating the wall shear rate in healthy arteries. In the presence of significant arterial disease, errors in the peak velocity may result in mis-selection of patients for surgery, while estimation of the wall shear stress remains extremely problematic; particularly with identifying the wall location and measuring velocities close to the wall.

The wooden multi-storey building industry is facing persistent sound transmission problems at low frequencies. Inserting elastomers within wall-floor junctions is common usage nevertheless no accurate studies have elucidated the real behavior of those nonlinear combined materials yet. Deeper knowledge is needed to create a relevant FE model which will help industry to use those materials efficiently.The nonlinear dynamic behavior of the elastomers inserted in wooden junctions is analyzed while the static load acting on them is varying. The specific situation where those elastomers were tested is a scaled room made of two walls and one floor.An experimental study was conducted on this prototype wooden construction and a numerical analysis was performed on the Finite Element model of it. The frequency response functions of several positions were measured on the physical setup.The study showed that loaded structures (up to 2 times the load of the floor) had a lower damping ratio. Having the structure standing on really stiff or elastic material does not differ when comparing experimental and analytical modal parameters.Those results depict the behavior of elastomers for different load cases and are definitely a step forward for the conception of a reliable FE model.

Cylindrical shells are widely used in civil engineering. Examples include cooling towers, pipelines, nuclear containment vessels, steel silos and tanks for storage of bulk solids and liquids, and pressure vessels. The loading condition for these shells is quite varied depending on the function of the shell. Axial compression, global bending, external or internal pressure and wind loading are some of the most common loading forms for realistic structures. The failure of these cylindrical shell structures is often controlled by elastic or elastic-plastic buckling failure. Yield failure may occur in thick cylinders in some situations. A cylindrical shell under different loading conditions may display quite different buckling behaviour. The objective of this thesis is to investigate the characteristics of different buckling behaviours of cylindrical shell structures under axial compression, global bending, uniform external pressure and wind pressure. Some challenging practical problems in the design of these shell structures are explored. This thesis is expected to have some far-reaching impacts in defining how to design cylindrical shell structures to give them adequate strength to resist extreme events. Many aspects will be based on the latest Eurocode (EN 1993-1-6, 2007) and Recommendations (ECCS EDR5, 2008). The results show both some strength and some weaknesses in the Eurocode in design of shell structures. New methods are proposed for some practical problems. Some new conclusions and suggestions are derived and are expected to provide some useful knowledge for the improvement of the Eurocode in cylindrical shell design in general.

Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Maceration enzymes for the wine industry are preparations containing mainly pectinases, cellulases and hemicellulases, used during wine making to degrade the berry cell walls and release polyphenolic and aroma molecules to increase wine quality. These types of enzymes are also used for the harvesting of revenue-generating molecules from pomace (skins, pulp and seeds from grape processing waste), or as processing aids when used in the production of bioethanol. Grape berry cell walls are recalcitrant towards degradation, therefore knowledge about their structures and compositions, as well as how the application of enzymes modify these structures is essential in order to optimise these processes. The aim of this study was to extend current knowledge by using a mixture of existing and novel methodologies to study grape berry cell walls by focusing on the profiles of polymers present in the walls. Cell wall profiling techniques used in this study include the Comprehensive Microarray Polymer Profiling (CoMPP) method that employs monoclonal antibodies and Carbohydrate Binding Modules (CBM) which specifically recognise the polymers in the plant cell wall. With this method we measured the abundance of specific polymers and traced the fluctuation in their levels of abundance as influenced by external factors such as enzyme hydrolysis. The CoMPP method was coupled with monosaccharide profile analysis by GC-MS to determine the building blocks of the cell wall polymers, as well as with Infrared Spectroscopy to monitor the changes in the bulk chemistry profile. Data sets generated by the cell wall profiling methods were analysed with uni- and multivariate statistical methods to detect the major patterns in the data. This study highlighted the cell wall differences on the polymer level, in the berry skin cells of Pinotage grapes at different ripeness levels and how it changes during a standard wine fermentation, leading to the release of homogalacturonans and the exposing of arabinogalactan proteins. When maceration enzymes were added, further depectination was evident and the enzymes unravelled the cell wall of the ripe grapes. In overripe grapes no additional degradation could be observed due to maceration enzyme actions, presumably indicating that the endogenous grape enzymes already caused extensive degradation. When purified enzymes were incubated under buffered conditions with isolated skin cell walls from Pinotage grapes or with Chardonnay grape pomace, different levels of enzymatic hydrolysis were observed and defined. The sequence in which cell wall polymers were extracted, and the influence of specific enzymes in facilitating the extraction process, provided important information on the accessibility of specific cell wall polymers. Synergistic action between, for example an endo-polygalacturonase (EPG) and an endo-glucanase (EG) was demonstrated with CoMPP. This EPG and EG synergism was also demonstrated with a yeast strain (a Saccharomyces paradoxus x S. cerevisiae hybrid) fermented in a buffered pomace suspension. This yeast strain has a native EPG and was engineered to also express a recombinant EG from a genome integrated cassette. The cell walls isolated from the pomace after fermentation were unravelled and depectination took place, as evident from CoMPP data. The cell wall profiling techniques used in this study were proven to be fast and sensitive. It provided insights into the structure of grape cell walls and was used to evaluate the changes due to ripening, fermentation, enzymatic hydrolysis and a heat pre-processing treatment. In addition to the knowledge gained, we also demonstrated that these techniques can be used to evaluate different enzymes and enzyme combinations as well as the potential of microorganisms to degrade grape tissue. / AFRIKAANSE OPSOMMING: Maserasie ensieme vir die wynindustrie is ensiem mengsels wat hoofsaaklik pektinases, sellulases en hemisellulases bevat en word tydens wynbereiding gebruik om die druifkorrel se selwand af te breek, die polifenole en aroma molekules vry te stel en sodoende die wyn kwaliteit te verbeter. Hierdie soort ensieme word ook gebruik om inkomste-genererende molekules vanuit druiweprosesserings afval (doppe, pulp en pitte) te isoleer, en ook as prosesserings hulpmiddels in die produksie van bioetanol. Druifkorrel selwande is weerstandig teen ensiem afbraak en daarom is kennis oor die struktuur en samestelling van die selwand, asook hoe die selwand strukture deur die toediening van ensieme verander word noodsaaklik om sodoende hierdie prosesse te optimaliseer. Die doel van hierdie studie was om die huidige kennis uit te brei deur bestaande asook nuwe metodes te gebruik om die druifkorrel selwand te bestudeer met die fokus op die polimeerprofiel van die selwande. Selwand karakteriserings tegnieke wat in hierdie studie gebruik is sluit in die Comprehensive Microarray Polymer Profiling (CoMPP) metode wat monoklonale teenliggaampies en koolhidraat bindende modules (Carbohydrate binding modules, CBMs) wat spesifiek die selwandpolimere van die plant selwand herken, gebruik. Met hierdie metode het ons die vlakke van spesifieke polimere gemeet asook die skommeling in hulle vlakke soos dit beïnvloed is deur eksterne faktore soos ensiem hidroliese. Die CoMPP metode is tesame met monosakkaried profiel analise, met behulp van GC-MS, wat die boublokke van die selwand polimere bepaal, asook infrarooi spektroskopie om die veranderinge in die oorhoofse chemiese profiel te bepaal, gebruik. Datastelle wat met die selwand karakteriserings tegnieke gegenereer is, is ontleed met een- en multiveranderlike statistiese metodes om die hoof tendense in die data op te spoor. Hierdie studie het die selwand verskille, op die polimeervlak, van Pinotage druiwe uitgelig. Verskillende rypheidsgrade asook hoe dit verander tydens ‘n standaard wynfermentasie is gevolg. Laasgenoemde het die vrystelling van homogalakturonaan en die ontbloting van arabinogalaktoproteïene tot gevolg gehad. Met die byvoeging van maserasie ensieme was dit duidelik dat addisionele pektienverwydering plaasgevind het en dat die ensieme die selwand van die ryp druiwe ontrafel het. In oorryp druiwe was daar geen addisionele selwand afbreking sigbaar as gevolg van die aksie van maserasie ensieme nie, wat moontlik aandui dat die inherente druif ensieme reeds uitgebreide selwand afbraak versoorsaak het. Wanneer gesuiwerde ensieme met geïsoleerde selwande van Pinotage druiwedoppe en met Chardonnay druiweprosesserings afval geïnkubeer is onder gebufferde kondisies, is verskillende vlakke van ensiematiese hidroliese waargeneem en geklassifiseer. Die volgorde waarin die selwand polimere geëkstraheer is, asook die invloed van spesifieke ensieme in die bevordering van die ekstraksie proses, het belangrike inligting verskaf oor die toeganglikheid van spesifieke selwand polimere. Sinergistiese aksie tussen, byvoorbeeld ‘n endo-poligalakturonase (EPG) en ‘n endo-glukanase (EG) is geidentifiseer met behulp van die CoMPP data. Hierdie EPG en EG sinergisme is ook geïllustreer met ‘n gisras (‘n Saccharomyces paradoxus x S. cerevisiae hibried) wat in ‘n gebufferde druifprosesserings afval suspensie gefermenteer het. Hierdie gisras het ‘n endogene EPG en is ontwerp om ook ‘n rekombinante EG uit te druk vanaf ‘n genoom geïntegreerde kasset. Die selwande van die druiweprosesserings afval wat na die fermentasie geïsoleer is, was ontrafel en pektienverwydering het plaasgevind, soos bevestig met CoMPP data. In hierdie studie is bewys dat die selwand karakteriserings tegnieke vinnig en sensitief is. Dit het insigte verskaf oor die struktuur van die druifselwand en is gebruik om die veranderinge as gevolg van rypheidsverskille, wynfermentasie, ensiem hidroliese en hitte prosessering te evalueer. Buiten die bydraes tot kennis oor hierdie onderwerpe, is die bruikbaarheid van hierdie tegnieke ook aangetoon, veral in die evaluasie van verskillende ensieme en ensiemkombinasies, asook mikroörganismes vir die afbraak van druifweefsel.