A thermodynamic study of five homologous HPr proteins derived from organisms inhabiting diverse environments has been undertaken. The aim of this study was to further our understanding of protein stabilization in extremes of environment. Two of the proteins were derived from moderate thermophiles (Streptococcus thermophilus and Bacillus staerothermophilus) and two from haloalkaliphilic organisms (Bacillus halodurans and Oceanobacillus iheyensis); these proteins were compared with HPr from the mesophile Bacillus subtilus. Genes for three of these homologous HPr proteins were for the first time cloned from their respective organisms into expression vectors and they were over-expressed and purified in Escherichia coli. Stability measurements were performed on these proteins under a variety of solution conditions (varying pH, salinity and temperature) by thermal and solvent induced denaturation experiments. Stability curves were determined for every homologue and these reveal very similar conformational stability for these homologues at their habitat temperatures. The BstHPr homologue is the most thermostable and also has the highest G25; the stability of other homologues was ranked as Bst>Bh>St>Bs>OiHPr. Other key thermodynamic parameters, like Cp, have been estimated for all the homologues and it was found that these values are identical within errors of estimation. Also, it was found that the values of TS are very similar for these homologues. Together these observations allow us to propose a thermodynamic mechanism toward achieving higher Tm. The crystal structures of the BstHPr and a single tryptophan-containing variant (BstF29W) of this homologue are also reported here. Also reported is a domain-swapped dimeric structure for the BstF29W variant, together with a detailed investigation into the solution oligomeric nature of this protein. The crystal structure of BstHPr is analyzed to enumerate various stabilizating interactions like hydrogen bonds and salt-bridges and these were compared with those for the mesophilic homologue BsHPr. Finally, an analysis of sequence alignments together with structural information for these homologues has allowed design of numerous variants of both Bs and BstHPr. A detailed thermodynamic study of these variants is presented in an attempt to understand the origins of the differences in stability of the HPr homologues.

This dissertation studies three public transit operations control strategies with automatic vehicle location (AVL) data available. Specifically, holding control, stop-skipping control and vehicle dispatching with swapping are investigated. Moreover, AVL data from Tucson, Arizona are employed to investigate the methodologies for deriving vehicle operating parameters.The problem of holding vehicles at multiple holding stations can be modeled as a convex mathematical programming problem which can be solved to near optimality by a proposed heuristic. A simulation study on the holding problem suggests that holding control based on the proposed problem formulation can effectively reduce the total passenger cost. Also, multiple holding stations may offer more opportunities to regularize vehicle headways so that holding vehicles at multiple stations can further reduce the passenger cost compared to holding vehicles only at a single station.Stop-skipping is investigated to respond more rapidly to vehicle disruptions occurring in the middle of a route. Based on a preliminary analysis of the basic stop-skipping policy, a policy alternative is constructed. The stop-skipping strategy is formulated separately for both policies as a nonlinear integer programming problem. The problem solution relies on an exhaustive search method. Another simulation study is conducted to examine how the performance of the two policies change with the passenger distribution pattern, the vehicle disruption location and length, and the vehicle travel time variability. The simulation result suggests selective superiority of the two policies.The vehicle dispatching problem investigates the potential of integrating real-time swapping into the vehicle dispatching strategies at a transit transfer terminal. With a hypothetical study design, simulation is employed again to evaluate the significance of real-time swapping by comparing the performance of a swapping-holding combined strategy with the holding-only strategy. A sensitivity analysis is also employed to compare these two strategies among key transit operating factors.Finally, using three different understandings (assumptions) of vehicle operating behavior, regression methods are proposed for using AVL data to derive the vehicle running speeds and passenger boarding rates, which serve as inputs to the operations control models. The regression results show that the day-specific operating behavior may not be appropriate, and that operating behavior combining both trip-specific and day-specific effects seems to be slightly superior to the trip-specific behavior overall.

Large amounts of CH4 in the form of solid hydrates are stored on continental margins and in permafrost regions. If these CH4 hydrates could be converted into CO2 hydrates, they would serve double duty as CH4 sources and CO2 storage sites. Herein, we report the swapping phenomena between global warming gas and various structures of natural gas hydrate including sI, sII, and sH through 13C solid-state nuclear magnetic resonance, and FT-Raman spectrometer. The present outcome of 85% CH4 recovery rate in sI CH4 hydrate achieved by the direct use of binary N2 + CO2 guests is quite surprising when compared with the rate of 64 % for a pure CO2 guest attained in the previous approach. The direct use of a mixture of N2 + CO2 eliminates the requirement of a CO2 separation/purification process. In addition, the simultaneously-occurring dual mechanism of CO2 sequestration and CH4 recovery is expected to provide the physicochemical background required for developing a promising large-scale approach with economic feasibility. In the case of sII and sH CH4 hydrates, we observe a spontaneous structure transition to sI during the replacement and a cage-specific distribution of guest molecules. A significant change of the lattice dimension due to structure transformation induces a relative number of small cage sites to reduce, resulting in the considerable increase of CH4 recovery rate. The mutually interactive pattern of targeted guest-cage conjugates possesses important implications on the diverse hydratebased inclusion phenomena as clearly illustrated in the swapping process between CO2 stream and complex CH4 hydrate structure.

Rhomboids are unique membrane proteins that use a serine protease hydrolysis mechanism to cleave a transmembrane substrate within the lipid bilayer. This remarkable proteolytic activity is achieved by a core domain comprised of 6 transmembrane segments that form a hydrophilic cavity submerged in the membrane. In addition to this core domain, many rhomboids also possess aqueous domains of varying sizes at the N- and/or C-terminus, the sequences of which tend to be rhomboid-type specific. The functional role of these extramembranous domains is generally not well understood, although it is thought that they may be involved in regulation of rhomboid activity and specificity. While extramembranous domains may be important for rhomboid activity, they are absent in all x-ray crystal structures available. For this reason, we have focused on uncovering the structural and functional relationship between the rhomboid cytoplasmic domain and its catalytic transmembrane core. To investigate the structure and function of the bacterial rhomboid cytoplasmic domain, full-length rhomboids from Escherichia coli and Pseudomonas aeruginosa were studied using solution nuclear magnetic resonance (NMR) spectroscopy, mutation and activity assays. The P. aeruginosa rhomboid was purified in a range of membrane-mimetic media, evaluated for its functional status in vitro and investigated for its NMR spectroscopic properties. Results from this study suggested that an activity-modulating interaction might occur between the catalytic core transmembrane domain and the cytoplasmic domain. Further investigation of this hypothesis with the E. coli rhomboid revealed that protease activity relies on a short but critical sequence N-terminal to the first transmembrane segment. This sequence was found to have a direct impact on the rhomboid active site, and should be included in future structural studies of this catalytic domain. The structure of the cytoplasmic domain from the E. coli rhomboid was also determined by solution NMR. We found that it forms slowly-exchanging dimers through an exchange of secondary structure elements between subunits, commonly known as three-dimensional domain swapping. Beyond this rare example of domain swapping in a membrane protein extramembranous domain, we found that the rate of exchange between monomeric and dimeric states could be accelerated by transient interactions with large detergent micelles with a phosphocholine headgroup, but not by exposure to other weakly denaturing conditions. This novel example of micelle-catalyzed domain swapping interactions raises the possibility that domain swapping interactions might be induced by similar interactions in vivo. Overall, the results of this thesis have identified detergent conditions that preserve the highest level of activity for bacterial rhomboids, defined the minimal functional unit beyond what had been identified in available x-ray crystal structures, and characterized a novel micelle-catalyzed domain-swapping interaction by the cytoplasmic domain.

Rhomboids are unique membrane proteins that use a serine protease hydrolysis mechanism to cleave a transmembrane substrate within the lipid bilayer. This remarkable proteolytic activity is achieved by a core domain comprised of 6 transmembrane segments that form a hydrophilic cavity submerged in the membrane. In addition to this core domain, many rhomboids also possess aqueous domains of varying sizes at the N- and/or C-terminus, the sequences of which tend to be rhomboid-type specific. The functional role of these extramembranous domains is generally not well understood, although it is thought that they may be involved in regulation of rhomboid activity and specificity. While extramembranous domains may be important for rhomboid activity, they are absent in all x-ray crystal structures available. For this reason, we have focused on uncovering the structural and functional relationship between the rhomboid cytoplasmic domain and its catalytic transmembrane core. To investigate the structure and function of the bacterial rhomboid cytoplasmic domain, full-length rhomboids from Escherichia coli and Pseudomonas aeruginosa were studied using solution nuclear magnetic resonance (NMR) spectroscopy, mutation and activity assays. The P. aeruginosa rhomboid was purified in a range of membrane-mimetic media, evaluated for its functional status in vitro and investigated for its NMR spectroscopic properties. Results from this study suggested that an activity-modulating interaction might occur between the catalytic core transmembrane domain and the cytoplasmic domain. Further investigation of this hypothesis with the E. coli rhomboid revealed that protease activity relies on a short but critical sequence N-terminal to the first transmembrane segment. This sequence was found to have a direct impact on the rhomboid active site, and should be included in future structural studies of this catalytic domain. The structure of the cytoplasmic domain from the E. coli rhomboid was also determined by solution NMR. We found that it forms slowly-exchanging dimers through an exchange of secondary structure elements between subunits, commonly known as three-dimensional domain swapping. Beyond this rare example of domain swapping in a membrane protein extramembranous domain, we found that the rate of exchange between monomeric and dimeric states could be accelerated by transient interactions with large detergent micelles with a phosphocholine headgroup, but not by exposure to other weakly denaturing conditions. This novel example of micelle-catalyzed domain swapping interactions raises the possibility that domain swapping interactions might be induced by similar interactions in vivo. Overall, the results of this thesis have identified detergent conditions that preserve the highest level of activity for bacterial rhomboids, defined the minimal functional unit beyond what had been identified in available x-ray crystal structures, and characterized a novel micelle-catalyzed domain-swapping interaction by the cytoplasmic domain.

In the representation of scattered data by smooth pp (:= piecewise polynomial) functions, perhaps the most important problem is to find an optimal triangulation of the given sample sites (called vertices). Of course, the notion of optimality depends on the desirable properties in the approximation or modeling problems. In this paper, we are concerned with optimal approximation order with respect to the given order r of smoothness and degree k of the polynomial pieces of the smooth pp functions. We will only consider C1 pp approximation with r = 1 and k = 4. The main result in this paper is an efficient method for triangulating any finitely many arbitrarily scattered sample sites, such that these sample sites are the only vertices of the triangulation, and that for any discrete data given at these sample sites, there is a C1 piecewise quartic polynomial on this triangulation that interpolates the given data with the fifth order of approximation.

Background: Different social, environmental and economical aspects indicate the current need for sustainability and build the imperative for a change in the fashion industry from the prevailing “take-make-dispose” consumption habit to more circular practices, which minimise the input of resources. According to research, the most direct way to capture value and design out waste and pollution in the textile system lays therewith in increasing the number of times a garment is worn. Therefore, the key challenge is to subvert the habit that garments are perceived as disposable and to increase their utilisation. Purpose: The purpose of this thesis is to investigate how sharing events influence the use phase of garments through the perspective of organisers and participants of such events. Method: The study implemented a qualitative research nature and followed thereby an exploratory research design and strategy. Through semi-structured interviews, event organisers of different organisations with a well-founded experience in sharing events - staged in a Circular Fashion environment - provided their insights on the influence sharing events obtain regarding the use phase of garments. The research strategy supplemented the theories and empirical data with the insights of participants of a sharing event through self-completion questionnaires. Conclusion: Besides their practical ability to pass on garments to various users, sharing events are indicated to prolong the garment usage by promoting a possible change in the consumer’s mindset. Doing so, different aspects connected to Event Management, -Strategy as well as additional offers and activities, besides swapping, are facilitating. As the research outcome hints, the sharing event model, as one of the simplest forms of collaborative garment consumption, is indicated to influence the usage by enabling a change from garment consumer to user.

"Uncertainty" is used broadly to refer to things that are unknown or incompletely understood. In operations management, basic sources of uncertainty may include decision uncertainty, model uncertainty, analytical uncertainty, data uncertainty, and so on. Although uncertainty is unavoidable in decision making, different mechanisms can be designed to mitigate the impact of uncertainty. One commonly used strategy is "decision postponement," wherein the decision maker purposefully delays some of the decisions to a time when uncertainty is reduced or resolved. This type of a recourse action provides the decision maker with increased ability to match supply with demand. In this dissertation, we study the value of decision postponement in the context of different settings, including capacity investment, revenue management, and supply chain coordination. These problems share one characteristic in common: decision postponement, and as such, are all modeled as two-stage stochastic programming problems. In the first stage, a set of decisions are made under uncertainty so as to maximize the expected profit or utility. Then in the second stage, all uncertainty is resolved and a deterministic optimization problem is solved to determine the postponed decisions, constrained by the first stage decisions. In capacity investment, we study the capacity, pricing, and production decisions of a monopolist producing substitutable products with flexible or dedicated resources. While the capacity decision needs to be made ex-ante, under demand uncertainty, pricing and production decisions can be postponed until after uncertainty is resolved. We show how key demand parameters (the nature of uncertainty, market size, market risk, and risk attitude) impact the optimal capacity decision under the linear demand function. In particular, we show that if the demand shock is multiplicative, then in terms of the "invest or not" decision, the firm will be immune to forecast errors in parameters of the underlying demand shock distribution. Furthermore, incorrectly modeling the demand shock as additive, when, in fact, it is multiplicative, may lead to overinvestment. On the other hand, while the concept of a growth in market size leads to similar conclusions under both additive and multiplicative demand shocks, how market risk affects the optimal capacity decision depends critically on the form of the demand shock. In addition, the decision-maker's attitude toward risk significantly affects the optimal capacity level, and its impact highly depends on the structure of the resource network. Our analysis provides insights and principles on the optimal capacity investment decision under various settings. In airline revenue management, a well-studied problem is the optimal allocation of seat inventory among different fare-classes, given a capacity for the flight and a demand distribution for each class. In practice, capacity on a flight does not have to be fixed; airlines can exercise some flexibility on the supply side by swapping aircraft of different capacities between flights as partial booking information is gathered. This provides the airline with the capability to more effectively match their supply and demand. In this dissertation, we study the seat inventory control problem considering the aircraft swapping option. Our analytical results demonstrate that booking limits considering the swapping option can be considerably different from those under fixed capacity. We also show that principles on the relationship between the optimal booking limits and demand characteristics (size and risk) developed for the fixed-capacity problem no longer hold when swapping is an option. We develop new principles and insights on how demand characteristics affect the optimal seat allocation under the swapping possibility. We also perform a numerical study, which indicates that the revenue impact of using the "true" optimal booking limits under the swapping possibility can be significant. In supply chain coordination, we consider the influenza vaccine supply chain, which, due to the biological complexity of the production process, has a unique characteristic in that production yield is highly uncertain. Given the market demand and price, a monopolist supplier must decide how much raw material to input into production in the first stage. However, since the yield is unknown and production is costly, it is not necessarily in the supplier's best interest to ensure that all market demand is met. The supplier's input quantity depends on the trade-off between the costs of overproduction and undersupply. This, in fact, is one of the reasons why the influenza vaccine manufacturers in the United States lack motivation to produce sufficient amounts of vaccine to meet all demand [Williams (2005), Chick et al. (2008)]. In operations management, it is a well-known result that decentralized supply chains, where each player is only interested in optimizing her own objective, often lead to poor overall performance for the supply chain. However, a higher efficiency is achievable through contracting on a set of transfer payments [Cachon (2004)]. A "coordinating" contract is referred to as one in which each player's objective is in accordance with the supply chain's objective. Given the fact that influenza vaccine plays an important role in health care industry, it is important to study how different contracts impact the influenza vaccine supply chain, where the uncertainty is on the supply side. We study a game in which the supplier and the retailer are engaged in certain type of contracts that specify how risk is shared between the players. We study both the pre-ordering and the post-ordering settings, which respectively refer to the cases where the retailer orders the vaccine before or after the vaccine production is completed. We show that pre-ordering wholesale price contracts dominate post-ordering wholesale price contracts in terms of the resulting supply chain efficiency, but neither of them are able to fully coordinate the supply chain. We also find that cost-sharing contracts are able to coordinate the supply chain, while payback and advance-ordering wholesale price contracts fail to do so. Finally, we prove that if the unsold vaccine can be salvaged with some positive value, then the supply chain can be easily coordinated with wholesale price contracts. In studying this type of stochastic programming problems, it is not only important to characterize the optimal solution, but also important to gain an understanding of how the optimal solution will be affected by environmental parameters. Since the most inaccurate part in stochastic programming often lies in the parameters of the distribution functions, it is both interesting and meaningful to investigate how the optimal solution varies with the intrinsic nature of the random variables. Consequently, we make use of stochastic order relationships to study the behavior of the optimal solutions when the underlying random variables become either "larger" or "more risky." / Ph. D.

Multi-robot task assignment (allocation) involves assigning robots to tasks in order to optimize the entire team’s performances. Until now, one of the most useful non-domain-specific ways to coordinate multi-robot systems is through task allocation mechanisms. This dissertation addresses the classic task assignment problems in which robots and tasks are eventually matched by forming a one-to-one mapping, and their overall performances (e.g., cost, utility, and risk) can be linearly summed. At a high level, this research emphasizes two facets of the multi-robot task assignment, including (1) novel extensions from classic assignment algorithms, and (2) completely newly designed task allocation methods with impressive new features. For the former, we first propose a strongly polynomial assignment sensitivity analysis algorithm as well as a means to measure the assignment uncertainties; after that we propose a novel method to address problems of multi-robot routing and formation morphing, the trajectories of which are obtained from projections of augmenting paths that reside in a new three-dimensional interpretation of embedded matching graphs. For the latter, we present two optimal assignment algorithms that are distributable and suitable for multi-robot task allocation problems: the first one is an anytime assignment algorithm that produces non-decreasing assignment solutions along a series of task-swapping operations, each of which updates the assignment configurations and thus can be interrupted at any moment; the second one is a new market-based algorithm with a novel pricing policy: in contrast to the buyers’ “selfish” bidding behaviors in conventional auction/market-based approaches, we employ a virtual merchant to strategically escalate market prices in order to reach a state of equilibrium that satisfies both the merchant and buyers. Both of these newly developed assignment algorithms have a strongly polynomial running time close to the benchmark algorithms but can be easily decentralized in terms of computation and communication.

The societal problem regarding the housing shortage has made the housing market inaccessible. With the reduced number of rental apartments and longer housing queues, people face more challenges finding a suitable home. Swapping intermediaries have emerged over the years to facilitate the search process to swap apartments. However, tenants are still struggling to find apartments to swap with. Limited research has been conducted about tenants' experiences and perspectives regarding the swapping process. Through an exploratory approach, this study examines what problems tenants encounter during the swapping process. The research findings indicate several opportunity areas for improving and streamlining the swapping process. The made recommendations were regarding the search process, listing information, and apartment viewings. Further, to create an efficient market, the platform needs to consider thickness, overcome congestion, and make participation safe and simple. / Det samhälleliga problemet gällande bostadsbristen har medfört en oåtkomlig bostadsmarknad. Med minskade antalet hyresrätter samt längre bostadsköer står människor inför större utmaningar att hitta ett passande boende. För att underlätta bytesprocessen av hyresrätter har antalet bytesplattformar ökat under åren. Dock kämpar fortfarande många hyresgäster med att hitta en lägenhet att byta med. Begränsat antal studier har genomförts på hyresgäster gällande deras upplevelser samt perspektiv på själva bytesprocessen. Genom användande av en undersökande metod, undersökte denna studie vilka problem hyresgästerna stöter på under bytesprocessen av hyresrätter. Forskningsresultatet indikerade att flera möjligheter finns för att förbättra och effektivisera bytesprocessen. De rekommendationer som gjordes inkluderade sökprocessen, annonssidan, samt lägenhetsvisningar. Vidare, för att skapa en effektiv bytesmarknad, måste plattformen beakta tjocklek, övervinna trängsel, samt göra användandet säkert och enkelt.