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Estimation of real-time travel times on arterial streets has been a challenging task due to the intersection control delay as well as bottleneck delay from the downstream link. Therefore, few transportation professionals have conducted research at utilizing the dynamic flow methods to estimate travel times on arterial street networks. This thesis is to develop dynamic flow algorithms that estimates the real-time travel time on an arterial street network by utilizing the traffic information obtained from detectors. A modified method to the one adopted in HCM2000 in computing the intersection control delay is developed and utilized to estimate the real-time travel time for a short-time interval update under non-incident and incident situations. Simulation model is developed in CORSIM to validate developed algorithms under different traffic situations. / Master of Science

Made available in DSpace on 2014-12-17T14:03:39Z (GMT). No. of bitstreams: 1 DanielCL_DISSERT.pdf: 3446622 bytes, checksum: 86a8ec4f8ed7a90274cc61a7f0f71422 (MD5) Previous issue date: 2012-09-25 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / The Chromobacterium violaceum is a β-proteobacterium Gram-negative widely found in tropical and subtropical regions, whose genome was sequenced in 2003 showing great metabolic versatility and biotechnological and pharmaceutical potential. Given the large number of ORFs related to iron metabolism described in the genome of C. violaceum, the importance of this metal for various biological processes and due to lack of data about the consequences of excess of iron in free-living organisms, it is important to study the response mechanism of this bacterium in a culture filled with iron. Previous work showed that C. violaceum is resistant to high concentrations of this metal, but has not yet been described the mechanism which is used to this survival. Thus, to elucidate the response of C. violaceum cultured in high concentrations of iron and expecting to obtain candidate genes for use in bioremediation processes, this study used a shotgun proteomics approach and systems biology to assess the response of C. violaceum grown in the presence and absence of 9 mM of iron. The analysis identified 531 proteins, being 71 exclusively expressed by the bacteria grown in the presence of the metal and 100 just in the control condition. The increase in expression of proteins related to the TCA cycle possibly represents a metabolic reprogramming of the bacteria caused by high concentration of iron in the medium. Moreover, we observed an increase in the activity assay of superoxide dismutase and catalase as well as in Total Antioxidant Activity assay, suggesting that the metal is inducing oxidative stress in C. violaceum that increases the levels of violacein and antioxidant enzymes to better adapt to the emerging conditions. Are also part of the adaptive response changes in expression of proteins related to transport, including iron, as well as an increased expression of proteins related to chemotaxis response, which would lead the bacteria to change the direction of its movement away from the metal. Systems Biology results, also suggest a metabolic reprogramming with mechanisms coordinated by bottleneck proteins involved in transcription (GreA), energy metabolism (Rpe and TpiA) and methylation (AhcY) / A Chromobacterium violaceum ? uma β-proteobact?ria Gram-negativa encontrada amplamente em regi?es tropicais e subtropicais, cujo genoma foi sequenciado em 2003 mostrando grande versatilidade metab?lica e potencial biotecnol?gico e farmac?utico. Dada ? grande quantidade de ORFs relacionadas com o metabolismo de ferro descritas no genoma da C. violaceum, a import?ncia deste metal para diversos processos biol?gicos e devido ? car?ncia de dados a respeito das conseq??ncias do excesso do ferro em organismos de vida livre, ? importante estudar o mecanismo de resposta desta bact?ria em meio repleto com ferro. Trabalhos anteriores mostram que a C. violaceum apresenta resist?ncia a grandes concentra??es desse metal, embora ainda n?o tenha sido descrito qual mecanismo ? utilizado para esta sobreviv?ncia. Assim, visando elucidar a resposta da C. violaceum cultivada em alta concentra??o de ferro e esperando-se obter genes candidatos para serem utilizados em processos de biorremedia??o, o presente trabalho utilizou a abordagem de prote?mica em shotgun e Biologia de Sistemas para avaliar a resposta de C. violaceum cultivada na presen?a e aus?ncia de 9 mM de ferro. A an?lise identificou 531 prote?nas, sendo 71 expressas exclusivamente pela bact?ria cultivada na presen?a do metal e 100 apenas na condi??o controle. O aumento na express?o de prote?nas relacionadas com o ciclo do TCA possivelmente representa uma reprograma??o metab?lica na bact?ria causada pela grande concentra??o de ferro no meio. Al?m disso, foi observado um aumento no ensaio de atividade das enzimas Super?xido dismutase e Catalase, bem como no ensaio de Atividade Antioxidante Total, sugerindo que o metal est? induzindo um quadro de estresse oxidativo em C. violaceum, que passou a aumentar os n?veis de violace?na e enzimas antioxidantes para melhor se adaptar ? condi??o emergente. Tamb?m faz parte da resposta adaptativa a altera??o na express?o de prote?nas relacionados a transporte, inclusive de ferro, e com a resposta quimiot?xica, o que levaria a bact?ria a mudar a orienta??o de sua locomo??o afastando-se do metal. Os dados de Biologia de Sistemas tamb?m sugerem uma reprograma??o metab?lica com mecanismos coordenados por gargalos proteicos envolvidos com transcri??o (GreA), metabolismo energ?tico (Rpe e TpiA) e metila??o (AhcY)

Bus systems have a large passenger capacity when compared to personal vehicles and thus have the potential to improve urban mobility. However, buses that operate in mixed vehicle traffic can undermine the effectiveness of the road system as they travel at lower speeds, take longer to accelerate and stop frequently to board and alight passengers. In traffic flow theory, buses are known as slow-moving bottlenecks that have the potential to create queue-spillbacks and thus increase the probability of gridlock. Currently, traditional metropolitan transportation planning models do not account for these negative effects on roadway capacity. Also, research methods that study multimodal operations are often simulated or algorithmic which can only provide specific results for defined inputs. The objective of this research is to model and understand the effects of bus operations (e.g., headway, number of stops, number of routes) on system performance (e.g. urban corridor and network vehicular capacity) using a parsimonious analytical approach with a few parameters.The models are built using the Macroscopic Fundamental Diagram (MFD) of traffic which provides aggregate measures of vehicle density and flow. Existing MFD theory, which accounts for corridors with only one vehicle class are extended to include network roadway systems and bus operations. The results indicate that buses have two major effects on corridors: the moving bottleneck and the bus short-block effect. Also, these corridor effects are expanded to urban networks through a vehicle density-weighted average. The models have the potential to transform urban multimodal operations and management as they provide a simple tool to capture aggregate performance of transportation systems.

I investigated parasitic infection and immunocompetence in populations of introduced bird species in New Zealand (NZ) that had experienced a range of population bottlenecks (11-808 individuals), and compared these parameters to non-bottlenecked conspecifics in the United Kingdom (UK). My aims were two-fold; firstly to assess if population bottlenecks are linked to increased parasite loads and/or decreased immunocompetence, and secondly, to assess at what severity of bottleneck these effects become evident. I found that ectoparasite load (chewing lice, Order: Phthiraptera, Sub-Orders: Amblycera & Ischnocera) was significantly higher in the more severely bottlenecked species in NZ than in the UK, whilst this difference became non-significant at more moderate bottlenecks. The difference was mainly driven by the Sub-Order Amblycera. The prevalence of avian malaria (Plasmodium spp.) was significantly negatively correlated to bottleneck size within NZ, after controlling for body mass. Total leucocyte and differential lymphocyte counts were elevated in the less bottlenecked species that were infected with malaria, whilst the populations at the more severe end of the bottleneck spectrum did not exhibit such a response. Furthermore, heterophil/lymphocyte (HL) ratio (a parameter used as an indicator of environmental and/or immunological stress), was significantly raised in the more bottlenecked species when compared to their UK counterparts, and this difference was correlated with the size of the bottleneck. Immunocompetence was further assessed by the experimental challenge of six introduced birds species in NZ with the mitogen phytohaemagglutinin (PHA). Immune response to PHA was significantly correlated to bottleneck size, but in the opposite direction to that predicted; immune response was greater in the more bottlenecked species. However, this may be an indication of increased investment in immunity, due to increased parasite and pathogen pressure or differential investment in varying components of the immune system. Finally, the immune response to PHA was compared in nestlings of two species that had experienced very different bottlenecks (70 vs. 653). After controlling for ectoparasitic infestation, I found no difference between the two species; however, this finding may be confounded by interspecific competition. Overall, my findings suggest that more severe population bottlenecks may result in increased susceptibility to pathogens, and impact on the immune system. This has a number of implications for the development of conservation protocols, and future avenues of research are suggested.

The spin dynamics of electrons in inorganic and organic semiconducting nanostructures has become an area of interest in recent years. The controlled manipulation of an electron’s spin, and in particular its phase, is the primary requirement for applications in quantum information processing. The phase decoheres in a time known as the transverse relaxation time or T2 time. We have carried out a measurement of the ensemble-averaged transverse spin relaxation time (T2*) in bulk and few molecules of the organic semiconductor tris-(8-hydroxyquinolinolato aluminum) or Alq3. The Alq3 system exhibits two characteristic T2* times: the longer of which is temperature independent and the shorter is temperature dependent, indicating that the latter is most likely limited by spin-phonon interaction. Based on the measured data, we infer that the single-particle T2 time in Alq3 is probably long enough to meet Knill's criterion for fault-tolerant quantum computing even at room temperature. Alq3 is also an optically active organic, and we propose a simple optical scheme for spin qubit readout. Moreover, we found that the temperature-dependent T2* time is considerably shorter in bulk Alq3 powder than in few molecules confined in 1–2-nm-sized cavities. Because carriers in organic molecules are localized over individual molecules or atoms but the phonons are delocalized, we believe that this feature is caused by a phonon bottleneck effect. Organic fluorophore molecules, electrosprayed within nanometer sized pores of an anodic alumina film, exhibit unusually large molecule-specific red- or blue-shifts in the fluorescence peak. This molecular specificity allows us to resolve different constituents in a mixture optically, providing a unique new technology for bio- and chemical sensing. We have also observed that the fluorescence efficiency progressively increases with decreasing pore diameter. This trend cannot be explained by the usual photo carrier confinement model since the photo carriers are localized over individual molecules (or atoms) which are much smaller than the pore diameter. A more likely explanation is the metal enhanced fluorescence caused by the plasmon resonance of nanotextured aluminum lying at the bottom of the pores.

Changes to rivers that alter physical and thermal habitat may cause fish population abundance to decline, due to fewer individuals maturing and entering the adult population. The Weber River has become highly degraded with many dams and diversions altering fish habitat, river volume, velocity, and temperature, and limiting movement between reaches. Bluehead suckers (Catostomus discobolus) occupy only 47% of their historical range and the genetically-distinct Weber River (northern UT) population is declining and contains few young, juvenile fish. My objectives were to determine whether spawning and rearing habitat available in the Weber River may be limiting bluehead sucker reproductive success and population growth. I used reach-based surveys to locate and quantify spawning habitat in the Weber River and Ferron Creek (central Utah), a relatively unaltered river for comparison. I sampled slow-water backwaters near (< 1 km) spawning reaches for juvenile sucker and surveyed habitat characteristics. I conducted laboratory experiments to evaluate the effect different temperature and velocity treatments (12-19°C, 0.004-0.18 m/s) have on juvenile bluehead sucker growth. In the Weber River and Ferron Creek, reaches with gravel (4-64 mm diameter), cobble (64-256 mm diameter), and pools (6-26 pools/km) were used by spawning bluehead sucker. In Weber River backwaters, deeper backwaters contained significantly more juvenile sucker (18-378 sucker; range: 19-87 cm max depth). Laboratory results indicated that juvenile bluehead sucker growth was greatest in the cooler temperature and slower velocity treatments. Collectively these results suggest spawning habitat is limited by the availability of small, rocky substrate and pools and rearing habitat is limited by the availability of deep, slow backwaters at the optimal temperature. By evaluating factors that may limit bluehead sucker population growth, this study will provide a template for future restoration efforts directed at recovering this imperiled population.

The flow of goods to Russia has grown faster than the bottleneck can handle and the infrastructure on Finnish eastern borders has been stretched to the limit. The authors choose this topic according to their educational background and the direct and indirect future opportunities that can rise up for everybody by a possible solution. Purpose The main purpose of this thesis was to identify the main reasons for the inefficient border crossing process at the border station in Vaalimaa. The authors will analyse the current situation at the border crossing station in Vaalimaa from two different perspectives: Finnish Customs and Logistics Companies. The authors will propose a possible solution by improving the border crossing process Methodology Qualitative research method is used in order to get the most dependable information for the reasons of the problems. The aim was to get information about the current situation at the border crossing point in Vaalimaa rather than quantitative information. The qualitative research method will allow authors to go deeper inside the topic by interviewing the logistics companies, who are using the route via Finland to Russia and, as well as, Finnish customs and border guards, who are working in Vaalimaa. After the data collection, the authors will propose their own solution for the crossing border problems and they will conclude the research by measuring its validity and reliability. Conclusion The authors will present the main reasons for the inefficient border crossing process, which are bureaucracy, legislation issues, criminality level and poor IT-systems. In order to solve the problem and manage all the possible changes, Russia and EU should have a closely cooperation in any level. The authors after analysing the current situation in Vaalimaa, created the “One-stop” model as an improvement of the whole border crossing process.

The simulation as a stand alone optimization tool of a complex system such as a vertical integrated mining operation, significantly over simplifies the actual picture of the system processes involved resulting in an unaccountable effort and resources being spent on optimizing Non Value Added (NA) processes. This study purposed to develop a discrete stochastic simulation-optimization model to accurately capture the dynamics of the system and to provide a structured way to optimize the Value Added (VA) processes. The mine operation model to be simulated for this study is designed as a hybrid level throughput model to identify the VA processes in a mining operation. This study also allows a better understanding of the impact of variation on the likelihood of achieving any given overall result. The proposed discrete stochastic simulation- optimization model provides the ability for a process manager to gain realistic understanding of what a process can do if some factors constraining the process were to be optimized i.e. to conduct what-if analysis. Another benefit of this approached technique is to be able to estimate dependable and reasonable returns on a large optimization related expenditure. The inputs into the model are the capability of the processes which are entered using various variables depending on how much information is available; simple inputs for least amount of information to detailed inputs for well known process to combinational inputs for somewhere in between. The process bottlenecks are identified and measured using the outputs of the model which include production output, severity of constraints, capacity constraints and cumulative bottleneck plots. Once a base case has been identified and documented then the inputs can be modified to represent the business initiatives and the outputs can be compared to the base case to evaluate the true value of the initiative.