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Title: Modeling of accelerator systems and experimental verification of Quarter-Wave Resonator steering
Creator: Benatti, Carla
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Increasingly complicated accelerator systems depend more and more on computing power and computer simulations for their operation as progress in the field has led to cutting-edge advances that require finer control and better understanding to achieve optimal performance. Greater ambitions coupled with the technical complexity of today's state-of-the-art accelerators necessitate corresponding advances in available accelerator modeling resources. Modeling is a critical component of any field of...
Show moreIncreasingly complicated accelerator systems depend more and more on computing power and computer simulations for their operation as progress in the field has led to cutting-edge advances that require finer control and better understanding to achieve optimal performance. Greater ambitions coupled with the technical complexity of today's state-of-the-art accelerators necessitate corresponding advances in available accelerator modeling resources. Modeling is a critical component of any field of physics, accelerator physics being no exception. It is extremely important to not only understand the basic underlying physics principles but to implement this understanding through the development of relevant modeling tools that provide the ability to investigate and study various complex effects. Moreover, these tools can lead to new insight and applications that facilitate control room operations and enable advances in the field that would not otherwise be possible. The ability to accurately model accelerator systems aids in the successful operation of machines designed specifically to deliver beams to experiments across a wide variety of fields, ranging from material science research to nuclear astrophysics. One such accelerator discussed throughout this work is the ReA facility at the National Superconducting Cyclotron Laboratory (NSCL) which re-accelerates rare isotope beams for nuclear astrophysics experiments. A major component of the ReA facility, as well as the future Facility for Rare Isotope Beams (FRIB) among other accelerators, is the Quarter-Wave Resonator (QWR), a coaxial accelerating cavity convenient for efficient acceleration of low-velocity particles. This device is very important to model accurately as it operates in the critical low-velocity region where the beam's acceleration gains are proportionally larger than they are through the later stages of acceleration. Compounding this matter, QWRs defocus the beam, and are also asymmetric with respect to the beam pipe, which has the potential to induce steering on the beam. These additional complications make this a significant device to study in order to optimize the accelerator's overall performance. The NSCL and ReA, along with FRIB, are first introduced to provide background and motivate the central modeling objectives presented throughout this work. In the next chapter, underlying beam physics principles are then discussed, as they form the basis from which modeling methods are derived. The modeling methods presented include multi-particle tracking and beam envelope matrix transport. The following chapter investigates modeling elements in more detail, including quadrupoles, solenoids, and coaxial accelerating cavities. Assemblies of accelerator elements, or lattices, have been modeled as well, and a method for modeling multiple charge state transport using linear matrix methods is also given.Finally, an experiment studying beam steering induced by QWR resonators is presented, the first systematic experimental investigation of this effect. As mentioned earlier, characterization of this steering on beam properties is important for accurate modeling of the beam transport through the linac. The measurement technique devised at ReA investigates the effect's dependence on the beam's vertical offset within the cavity, the cavity amplitude, and the beam energy upon entrance into the cavity. The results from this experiment agree well with the analytical predictions based on geometrical parameters calculated from on-axis field profiles. The incorporation of this effect into modeling codes has the potential to speed up complex accelerator operations and tuning procedures in systems using QWRs.
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Title: Computational chemistry : investigations of protein-protein interactions and post-translational modifications to peptides
Creator: Jones, Michael R. (Graduate of Michigan State University)
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Computational chemistry plays a vital role in understanding chemical and physical processes and has been useful in advancing the understanding of reactions in biology. Improper signaling of the nuclear factor-κB (NF-κB) pathway plays a critical role in many inflammatory disease states, including cancer, stroke, and viral infections. Aberrant regulation of this pathway happens upon the signal-induced degradation of the inhibitor of κB (IκB) proteins. The activation of IκB kinase (IKK) subunit...
Show moreComputational chemistry plays a vital role in understanding chemical and physical processes and has been useful in advancing the understanding of reactions in biology. Improper signaling of the nuclear factor-κB (NF-κB) pathway plays a critical role in many inflammatory disease states, including cancer, stroke, and viral infections. Aberrant regulation of this pathway happens upon the signal-induced degradation of the inhibitor of κB (IκB) proteins. The activation of IκB kinase (IKK) subunit β (IKKβ) or NF-κB Inducing Kinase (NIK), initiates this cascade of events. Understanding the structure-property relationships associated with IKKβ and NIK is essential for the development of prevention strategies. Although the signaling pathways are known, how the molecular mechanisms respond to changes in the intracellular microenvironment (i.e., pH, ionic strength, temperature) remains elusive. In this dissertation, computer simulation and modeling techniques were used investigate two protein kinases complexed with either small molecule activators or inhibitors in the active, inactive, and mutant states to correlate structure-property and structure-function relationships as a function of intracellular ionic strength. Additionally, radical-induced protein fragmentation pathways, as a result of reactions with reactive oxygen species, were investigated to yield insight into the thermodynamic preference of the fragmentation mechanisms. Analyses of the relationship between structure-activity and conformational-activity indicate that the protein-protein interactions and the binding of small molecules are sensitive to changes in the ionic strength and that there are several factors that influence the selectivity of peptide backbone cleavage. As there are many computational approaches for predicting physical and chemical properties, several methods were considered for the predictions of protein-protein dissociation, protein backbone fragmentation, and partition coefficients of drug-like molecules.
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Title: Toward a formalization of demographic transition theory
Creator: Lazer, S. Charles, 1946-
Date: 1969
Collection: Electronic Theses & Dissertations

Title: Logic simulation on massively parallel SIMD machines
Creator: Chung, Yunmo
Date: 1991
Collection: Electronic Theses & Dissertations

Title: Suicide, signals, and symbionts : evolving cooperation in agent-based systems
Creator: Vostinar, Anya E.
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Cooperation is ubiquitous in nature despite the constant pressure for organisms to cheat by receiving a benefit from cooperators, while not cooperating themselves. The continued evolution and persistence of countless forms of cooperation is a central topic in evolutionary theory. Extensive research has been done on the theoretical dynamics of cooperation through game theory and the natural examples of cooperation. However, it remains difficult to understand thoroughly the evolution of many...
Show moreCooperation is ubiquitous in nature despite the constant pressure for organisms to cheat by receiving a benefit from cooperators, while not cooperating themselves. The continued evolution and persistence of countless forms of cooperation is a central topic in evolutionary theory. Extensive research has been done on the theoretical dynamics of cooperation through game theory and the natural examples of cooperation. However, it remains difficult to understand thoroughly the evolution of many cooperative systems, due in part to the ancient origins of these systems and the long time scales required to see cooperation evolve in any natural populations. I have systematically analyzed the evolution of three broad types of cooperation: programmed cell death, quorum sensing, and mutualisms (cooperation across species). I have provided evidence that programmed cell death can originate due to kin selection. I have also created two new systems to enable the extensive exploration of factors that affect the evolution of public goods cooperation and mutualism. Using these systems, I determine the effects of environmental factors on the evolution of public goods cooperation and mutualism. By uniting the expansive theoretical work on these forms of cooperation with a fully-controlled experimental system, I contributed to our understanding of how these forms of cooperation can emerge and be maintained in industrial and medical applications that rely on bacterial cooperation.
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Title: Modeling and simulation of strongly coupled plasmas
Creator: Chowdhury, Rahnuma Rifat
Date: 2016
Collection: Electronic Theses & Dissertations
Description: The objective of this work is to develop new modeling and simulation tools for studying strongly coupled plasmas (SCP). Strongly coupled plasmas are different from traditional plasmas as potential energy is larger than the kinetic energy. The standard plasma model does not account for some major effects in SCP: 1) the change in the permittivity 2) the impact on relaxation of the charged particles undergoing Coulomb collisions in a system with weakly shielded long range interactions3) the...
Show moreThe objective of this work is to develop new modeling and simulation tools for studying strongly coupled plasmas (SCP). Strongly coupled plasmas are different from traditional plasmas as potential energy is larger than the kinetic energy. The standard plasma model does not account for some major effects in SCP: 1) the change in the permittivity 2) the impact on relaxation of the charged particles undergoing Coulomb collisions in a system with weakly shielded long range interactions3) the impact of statistical fluctuations in strongly coupled plasmas that leads to non-Markovian effects. Proper modeling of such systems through consideration of Lévy flight processes gives rise to fractional derivatives in time that result in an incorporation of time history in the model. A Lévy flight is a random walk in which the steps are defined in terms of the step-lengths, which have a certain probability distribution, with the directions of the steps being isotropic and random. Lévy processes in the plasma give rise to fluctuations in medium through which the electromagnetic waves are propagating. Averaging over the Lévy processes will allow us to relate to other important parameters in the plasma.
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Title: Modeling and simulations of evaporating spray, turbulent flow, and combustion in internal combustion engines
Creator: Srivastava, Shalabh
Date: 2015
Collection: Electronic Theses & Dissertations
Description: A multicomponent droplet evaporation model, which discretizes the one-dimensional mass and temperature profiles inside a droplet with a finite volume method and treats the liquid phase as thermodynamically real, has been developed and implemented into a large-eddy simulation (LES) code for evaporating and reacting spray simulations. Single drop evaporation results obtained by the variable property multicomponent model are shown to match with the constant property model in the limiting...
Show moreA multicomponent droplet evaporation model, which discretizes the one-dimensional mass and temperature profiles inside a droplet with a finite volume method and treats the liquid phase as thermodynamically real, has been developed and implemented into a large-eddy simulation (LES) code for evaporating and reacting spray simulations. Single drop evaporation results obtained by the variable property multicomponent model are shown to match with the constant property model in the limiting conditions. The LES code with the multicomponent model is used along with the Kelvin-Helmholtz - Rayleigh-Taylor (KH-RT) droplet breakup model to simulate realistic fuel sprays in a closed vessel and is found to reasonably well predict the experimentally observed non-linear behavior of spray penetration lengths with changing ambient conditions for n-hexadecane and 4 different multicomponent surrogate diesel fuels with 2-8 components. The effects of various modeling assumptions and gas and liquid parameters on the drop and spray evolution and evaporation are investigated in details.A previously studied single piston Rapid Compression Machine (RCM), extended to a twin-piston RCM, is simulated by LES for different stroke ratios of the two pistons, as a precursor to the study of opposed piston two-stroke engines. Opposed piston engines, which have recently generated interest due to their high power density and fuel economy, are mechanically simpler compared to conventional four-stroke engines but involve highly unsteady, turbulent and cycle-variant flows. LES of turbulent spray combustion in a generic single cylinder, opposed-piston, two-stroke engine configuration has been conducted with the two-phase filtered mass density function (FMDF) model, which is an Eulerian-Lagrangian-Lagrangian subgrid-scale probability density function (PDF) model for LES of two-phase turbulent reacting flows. The effects of various geometric parameters, operating conditions and spray parameters on the flow evolution, turbulence, spray and combustion in the engine are studied. The cycle-to-cycle variations in the flow variables like swirl and tumble are found to be significant while those in thermodynamic variables like temperature are negligible. The hybrid LES/FMDF methodology has been applied to simulate non-reacting turbulent spray for single-component and multi-component fuels and the consistency of the method has been established. The effects of spray parameters like nozzle hole diameter, injection pressure and injected fuel temperature on the spray penetration length are found to qualitatively follow experimental trends. Combustion simulations of n-dodecane fuel sprays are carried out for the opposed piston engine with a global kinetics mechanism and the consistency of the LES and FMDF components is demonstrated.
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Title: Investigating the impact of manmade reservoirs on large-scale hydrology and water resources using high-resolution modeling
Creator: Shin, Sanghoon
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Manmade reservoirs are important components of the terrestrial hydrologic system. Dam installments fragment river systems, and reservoir operations alter flow regimes. The total storage capacity of existing global reservoirs is large enough to hold one sixth of annual continental discharge to global oceans. Due to growing energy demands, hundreds of large dams are being built and planned around the world, especially in the developing countries. Therefore, there is an urgent need to develop a...
Show moreManmade reservoirs are important components of the terrestrial hydrologic system. Dam installments fragment river systems, and reservoir operations alter flow regimes. The total storage capacity of existing global reservoirs is large enough to hold one sixth of annual continental discharge to global oceans. Due to growing energy demands, hundreds of large dams are being built and planned around the world, especially in the developing countries. Therefore, there is an urgent need to develop a better understanding of the impact of the existing and new dams on hydrological, ecological, agricultural, and socio-economic systems. Owing to increasing computational power and needs to understand and simulate processes in small-scale, hydrological models are advancing towards hyper-resolution global hydrological models. One of benefits of the increased spatial resolution is that the dynamics of surface water inundation over natural river-floodplain systems and manmade reservoirs can be explicitly represented; however, existing global models are not capable of simulating the river-floodplain-reservoir inundation dynamics in an integrated manner. This dissertation addresses this important standing issue by developing a high-resolution, continental-scale model to simulate the spatial and temporal dynamics of reservoir storage and release, thus paving pathways toward hyper-resolution surface water modeling in continental- to global-scale hydrological and climate models. The newly developed model is applied to simulate reservoirs within the contiguous United States (CONUS) and the Mekong River Basin (MRB) in Southeast Asia. With respect to the model development, the following advances are made over the previous global reservoir modeling studies: (1) an existing algorithm for reservoir operation is improved by conducting analytical analysis and numerical experiments and by introducing new calibration features for reservoir operation; (2) the spatial extent and its seasonal dynamics of reservoirs are explicitly simulated and reservoirs are treated as an integral part of river-floodplain routing, thus reservoir storage is no longer isolated from river and floodplain storages; and (3) a novel approach for processing and integrating high-resolution digital elevation models (DEMs) in river-floodplain-reservoir routing is introduced. The newly developed reservoir scheme is integrated within the river-floodplain routing scheme of a continental hydrological model, LEAF-Hydro-Flood, which is set for the CONUS, where abundant data are available for model validation. Then, the reservoir scheme is integrated into a global hydrodynamics model, CaMa-Flood, to investigate the historical impact of manmade reservoirs in the MRB that is experiencing an unprecedented boom in hydropower dam construction. Using the new scheme, the role of flood dynamics in modulating the hydrology of the MRB and the potential impact of flow regulation by the dams on the inundation dynamics are investigated. The significance of hydrologic effect of increasing dams is compared with that of climate variability. The fully coupled river-reservoir-floodplain storage simulation approach presented in this dissertation provides an advancement in hydrological modeling in terms of the representation of surface water dynamics, which is indispensable for better attribution of the observed changes in the water cycle, prediction of changes in water resources, and the understanding of the continually changing environmental and ecological systems.
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Title: Advances in metal ion modeling
Creator: Li, Pengfei (Chemist)
Date: 2016
Collection: Electronic Theses & Dissertations
Description: Metal ions play fundamental roles in geochemistry, biochemistry and materials science.With the tremendous increasing power of the computational resources and largelyinventions of the computational tools, computational chemistry became a more and moreimportant tool to study various chemical processes. Force field modeling strategy, whichis built on physical background, offered a fast way to study chemical systems at atomiclevel. It could offer considerable accuracy when combined with the Monte...
Show moreMetal ions play fundamental roles in geochemistry, biochemistry and materials science.With the tremendous increasing power of the computational resources and largelyinventions of the computational tools, computational chemistry became a more and moreimportant tool to study various chemical processes. Force field modeling strategy, whichis built on physical background, offered a fast way to study chemical systems at atomiclevel. It could offer considerable accuracy when combined with the Monte Carlo orMolecular Dynamics simulation protocol. However, there are various metal ions and it isstill challenging to model them using available force field models. Generally there areseveral models available for modeling metal ions using the force field approach such asthe nonbonded model, the bonded model, the cationic dummy atom model, the combinedmodel, and the polarizable models. Our work concentrated on the nonbonded and bondedmodels, which are widely used nowadays. Firstly, we focused on filling in the blanks ofthis field. We proposed a noble gas curve, which was used to describe the relationshipbetween the van der Waals radius and well depth parameters in the 12-6 Lennard-Jonespotential. By using the noble gas curve and multiple target values (the hydration freeenergy, ion-oxygen distance, coordination number values), we have consistentlyparameterized the 12-6 Lennard-Jones nonbonded model for 63 different ions (including11 monovalent cations, 4 monovalent anions, 24 divalent cations, 18 trivalent cations,and 6 tetravalent cations) combined with three widely used water models (TIP3P, SPC/E, and TIP4PEW). Secondly, we found there is limited accuracy of the 12-6 model, whichmakes it hard to simulate different properties simultaneously for ions with formal chargeequal or larger than +2. By considering the physical origins of the 12-6 model, weproposed a new nonbonded model, named the 12-6-4 LJ-type nonbonded model. Wehave systematically parameterized the 12-6-4 model for 55 different ions (including 11monovalent cations, 4 monovalent anions, 16 divalent cations, 18 trivalent cations, and 6tetravalent cations) in the three water models. It was shown that the 12-6-4 model couldreproduce several properties at the same time, showing remarkable improvement over the12-6 model. Meanwhile, through the usage of a proposed combining rule, the 12-6-4model showed excellent transferability to mixed systems. Thirdly, we have developed theMCPB.py program to facilitate building of the bonded model for metal ion containingsystems, which can largely reduce human efforts. Finally, an application case of ametallochaperone - CusF was shown, and based on the simulations we hypothesized anion transfer mechanism.
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Title: Evolutionary dynamics of digitized organizational routines
Creator: Liu, Peng
Date: 2013
Collection: Electronic Theses & Dissertations
Description: This dissertation explores the effects of increased digitization on the evolutionary dynamics of organizational routines. Do routines become more flexible, or more rigid, as the mix of digital technologies and human actors changes? What are the mechanisms that govern the evolution of routines? The dissertation theorizes about the effects of increased digitization on path dependence and interdependence mechanisms, and therefore extends current theory on the evolutionary dynamics of...
Show moreThis dissertation explores the effects of increased digitization on the evolutionary dynamics of organizational routines. Do routines become more flexible, or more rigid, as the mix of digital technologies and human actors changes? What are the mechanisms that govern the evolution of routines? The dissertation theorizes about the effects of increased digitization on path dependence and interdependence mechanisms, and therefore extends current theory on the evolutionary dynamics of organizational routines by taking into account the effects of three basic phenomena: digitization, path dependence and interdependence.In this dissertation, I use computer-based simulation, grounded with data collected in field interviews, to model the evolution of routines. More specifically, this dissertation models routines as networks of action that are subject to an evolutionary process of random variation and selective retention. To assess the evolution of routine, I introduce the idea of evolutionary trajectory, which is defined as the product of the magnitude of change and the direction of change in the networks of action.The dissertation also addresses a foundational issue in the literature on organizational routines. Routines are generally believed to remain stable due to path dependence. An alternative explanation is that routines may be stable due to interdependence among actions, which tends to constrain the sequence in which actions can occur. I have developed a simulation that allows meto test the relative importance of these factors, a question that has never been addressed. By addressing this fundamental issue, I provide a deeper, theory driven explanation of the effects of digitization.
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Title: The evolution of digital communities under limited resources
Creator: Walker, Bess Linden
Date: 2012
Collection: Electronic Theses & Dissertations
Description: Schluter (1996) describes adaptive radiation as "the diversification of a lineage into species that exploit a variety of different resource types and that differ in the morphological or physiological traits used to exploit those resources". My research focuses on adaptive radiation in the context of limited resources, where frequency-dependence is an important driver of selection (Futuyma & Moreno, 1988; Dieckmann & Doebeli, 1999; Friesen et al., 2004). Adaptive radiation yields a community...
Show moreSchluter (1996) describes adaptive radiation as "the diversification of a lineage into species that exploit a variety of different resource types and that differ in the morphological or physiological traits used to exploit those resources". My research focuses on adaptive radiation in the context of limited resources, where frequency-dependence is an important driver of selection (Futuyma & Moreno, 1988; Dieckmann & Doebeli, 1999; Friesen et al., 2004). Adaptive radiation yields a community composed of distinct organism types adapted to specific niches.I study simple communities of digital organisms, the result of adaptive radiation in environments with limited resources. I ask (and address) the questions: How does diversity, driven by resource limitation, affect the frequency with which complex traits arise? What other aspects of the evolutionary pressures in this limited resource environment might account for the increase in frequency with which complex traits arise? Can we predict community stability when it encounters another community, and is our prediction different for communities resulting from adaptive radiation versus those that are artificially assembled?Community diversity is higher in environments with limited resources than in those with unlimited resources. The evolution of an example complex feature (in this case, Boolean EQU) is also more common in limited-resource environments, and shows a strong correlation with diversity over a range of resource inflow rates. I show that populations evolving in intermediate inflow rates explore areas of the fitness landscape in which EQU is common, and that those in unlimited resource environments do not. Another feature of the limited-resource environments is the reduced cost of trading off the execution of building block tasks for higher-complexity tasks. I find strong causal evidence that this reduced cost is a factor in the more common evolution of EQU in limited-resource environments.When two communities meet in competition, the fraction of each community's descendants making up the final post-competition community is strongly consistent across replicates. I find that three community-level factors, ecotypic diversity, community composition, and resource use efficiency can be used to predict this fractional community success, explaining up to 35% of the variation.In summary, I demonstrate the value of digital communities as a tractable experimental system for studying general community properties. They sit at the bridge between ecology and evolutionary biology and evolutionary computation, and offer comprehensible ways to translate ideas across these fields.
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