Multi-model inference ranking and applications to physics at the Large Hadron Collider

In the measurement of the Higgs Boson decaying into two photons the parametrization of an appropriate background model is essential for fitting the Higgs signal mass peak over a continuous background. This diphoton background modeling is crucial in the statistical process of calculating exclusion limits and the significance of observations in comparison to a background-only hypothesis. It is therefore ideal to obtain knowledge of the physical shape for the background mass distribution as the use of an improper function can lead to biases in the observed limits. Using an Information-Theoretic (I-T) approach for valid inference we apply Akaike Information Criterion (AIC) as a measure of the separation for a fitting model from the data. We then implement a multi-model inference ranking method to build a fit-model that closest represents the Standard Model background in 2013 diphoton data recorded by the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC). Potential applications and extensions of this model-selection technique are discussed with reference to CMS detector performance measurements as well as in potential physics analyses at future detectors.

Symposium on Llangrose Lake: the ecology and conservation of a large nutrient-rich lake in South Wales

This paper summarises a meeting which discussed the ecology and conservation of Llangorse Lake in South Wales. The meeting was organised by the British Ecological Society (Aquatic Ecology Group), in association with the Countryside Council for Wales (CCW), Brecon Beacon National Park Authority (BBNPA) and Environment Agency Wales. It took place on 22 October 1998.

On the Role of Delays in Biological Systems : Analysis and Design

This work quantifies the nature of delays in genetic regulatory networks and their effect on system dynamics. It is known that a time lag can emerge from a sequence of biochemical reactions. Applying this modeling framework to the protein production processes, delay distributions are derived in a stochastic (probability density function) and deterministic setting (impulse function), whilst being shown to be equivalent under different assumptions. The dependence of the distribution properties on rate constants, gene length, and time-varying temperatures is investigated. Overall, the distribution of the delay in the context of protein production processes is shown to be highly dependent on the size of the genes and mRNA strands as well as the reaction rates. Results suggest longer genes have delay distributions with a smaller relative variance, and hence, less uncertainty in the completion times, however, they lead to larger delays. On the other hand large uncertainties may actually play a positive role, as broader distributions can lead to larger stability regions when this formalization of the protein production delays is incorporated into a feedback system.

Furthermore, evidence suggests that delays may play a role as an explicit design into existing controlling mechanisms. Accordingly, the reccurring dual-feedback motif is also investigated with delays incorporated into the feedback channels. The dual-delayed feedback is shown to have stabilizing effects through a control theoretic approach. Lastly, a distributed delay based controller design method is proposed as a potential design tool. In a preliminary study, the dual-delayed feedback system re-emerges as an effective controller design.

The isotopic composition of energetic particles emitted from a large solar flare

We report measurements of isotope abundance ratios for 5-50 MeV/nuc nuclei from a large solar flare that occurred on September 23, 1978. The measurements were made by the Heavy Isotope Spectrometer Telescope (HIST) on the ISEE-3 satellite orbiting the Sun near an Earth-Sun libration point approximately one million miles sunward of the Earth. We report finite values for the isotope abundance ratios ¹³C/¹²C, ¹⁵N/¹⁴N, ¹⁸O/¹⁶O, ²²Ne/ ²⁰Ne, ²⁵Mg/²⁴Mg, and ²⁶Mg/²⁴Mg, and upper limits for the isotope abundance ratios ³He/⁴He, ¹⁴C/¹²C, ¹⁷O/¹⁶O, and ²¹Ne/²⁰Ne.

We measured element abundances and spectra to compare the September 23, 1978 flare with other flares reported in the literature. The flare is a typical large flare with "low" Fe/O abundance (≤ 0.1).

For ¹³C/¹²C, ¹⁵N/¹⁴N, ¹⁸O/¹⁶O, ²⁵Mg/ ²⁴Mg, and ²⁶Mg/²⁴Mg, our measured isotope abundance ratios agree with the solar system abundance ratios of Cameron (1981). For neon we measure ²²Ne/²⁰Ne = 0.109 + 0.026 - 0.019, a value that is different with confidence 97.5% from the abundance measured in the solar wind by Geiss at al. (1972) of ²²Ne/²⁰Ne = 0.073 ± 0.001. Our measurement for ²²Ne/²⁰Ne agrees with the isotopic composition of the meteoritic component neon-A.

Separate arguments appear to rule out simple mass fractionation in the solar wind and in our solar energetic particle measurements as the cause of the discrepancy in the comparison of the apparent compositions of these two sources of solar material.

Littoral vegetation of Lake Tohopekaliga: community descriptions prior to a large-scale fisheries habitat-enhancement project

An extreme dry-down and muck-removal project was conducted at Lake Tohopekaliga, Florida, in 2003-2004, to remove dense vegetation from inshore areas and improve habitat degraded by stabilized water levels. Vegetation was monitored from June 2002 to December 2003, to describe the pre-existing communities in terms of composition and distribution along the environmental gradients. Three study areas (Treatment-Selection Sites) were designed to test the efficacy of different treatments in enhancing inshore habitat, and five other study areas (Whole-Lake Monitoring Sites) were designed to monitor the responses of the emergent littoral vegetation as a whole. Five general community types were identified within the study areas by recording aboveground biomasses and stem densities of each species. These communities were distributed along water and soils gradients, with water depth and bulk density explaining most of the variation. The shallowest depths were dominated by a combination of Eleocharis spp., Luziola fluitans, and Panicum repens; while the deeper areas had communities of Nymphaea odorata and Nuphar luteum; Typha spp.; or Paspalidium geminatum and Hydrilla verticillata. Mineralized soils were common in both the shallow and deep-water communities, while the intermediate depths had high percentages of organic material in the soil. These intermediate depths (occurring just above and just below low pool stage) were dominated by Pontederia cordata, the main species targeted by the habitat enhancement project. This emergent community occurred in nearly monocultural bands around the lake (from roughly 60–120 cm in depth at high pool stage) often having more diverse floating mats along the deep-water edge. The organic barrier these mats create is believed to impede access of sport fish to shallow-water spawning areas, while the overall low diversity of the community is evidence of its competitive nature in stabilized waters. With continued monitoring of these study areas long-term effects of the restoration project can be assessed and predictive models may be created to determine the efficacy and legitimacy of such projects in the future.

Structural and Biophysical Characterization of Variants of the Mechanosensitive Channel of Large Conductance (MSCL)

The ability to sense mechanical force is vital to all organisms to interact with and respond to stimuli in their environment. Mechanosensation is critical to many physiological functions such as the senses of hearing and touch in animals, gravitropism in plants and osmoregulation in bacteria. Of these processes, the best understood at the molecular level involve bacterial mechanosensitive channels. Under hypo-osmotic stress, bacteria are able to alleviate turgor pressure through mechanosensitive channels that gate directly in response to tension in the membrane lipid bilayer. A key participant in this response is the mechanosensitive channel of large conductance (MscL), a non-selective channel with a high conductance of ~3 nS that gates at tensions close to the membrane lytic tension.

It has been appreciated since the original discovery by C. Kung that the small subunit size (~130 to 160 residues) and the high conductance necessitate that MscL forms a homo-oligomeric channel. Over the past 20 years of study, the proposed oligomeric state of MscL has ranged from monomer to hexamer. Oligomeric state has been shown to vary between MscL homologues and is influenced by lipid/detergent environment. In this thesis, we report the creation of a chimera library to systematically survey the correlation between MscL sequence and oligomeric state to identify the sequence determinants of oligomeric state. Our results demonstrate that although there is no combination of sequences uniquely associated with a given oligomeric state (or mixture of oligomeric states), there are significant correlations. In the quest to characterize the oligomeric state of MscL, an exciting discovery was made about the dynamic nature of the MscL complex. We found that in detergent solution, under mild heating conditions (37 °C – 60 °C), subunits of MscL can exchange between complexes, and the dynamics of this process are sensitive to the protein sequence.

Extensive efforts were made to produce high diffraction quality crystals of MscL for the determination of a high resolution X-ray crystal structure of a full length channel. The surface entropy reduction strategy was applied to the design of S. aureus MscL variants and while the strategy appears to have improved the crystallizability of S. aureus MscL, unfortunately the diffraction qualities of these crystals were not significantly improved. MscL chimeras were also screened for crystallization in various solubilization detergents, but also failed to yield high quality crystals.

MscL is a fascinating protein and continues to serve as a model system for the study of the structural and functional properties of mechanosensitive channels. Further characterization of the MscL chimera library will offer more insight into the characteristics of the channel. Of particular interest are the functional characterization of the chimeras and the exploration of the physiological relevance of intercomplex subunit exchange.

Complexity of rupture propagation in large earthquakes in relation to tectonic environment

Complexity in the earthquake rupture process can result from many factors. This study investigates the origin of such complexity by examining several recent, large earthquakes in detail. In each case the local tectonic environment plays an important role in understanding the source of the complexity.

Several large shallow earthquakes (M_s > 7.0) along the Middle American Trench have similarities and differences between them that may lead to a better understanding of fracture and subduction processes. They are predominantly thrust events consistent with the known subduction of the Cocos plate beneath N. America. Two events occurring along this subduction zone close to triple junctions show considerable complexity. This may be attributable to a more heterogeneous stress environment in these regions and as such has implications for other subduction zone boundaries.

An event which looks complex but is actually rather simple is the 1978 Bermuda earthquake (M_s ~ 6). It is located predominantly in the mantle. Its mechanism is one of pure thrust faulting with a strike N 20°W and dip 42°NE. Its apparent complexity is caused by local crustal structure. This is an important event in terms of understanding and estimating seismic hazard on the eastern seaboard of N. America.

A study of several large strike-slip continental earthquakes identifies characteristics which are common to them and may be useful in determining what to expect from the next great earthquake on the San Andreas fault. The events are the 1976 Guatemala earthquake on the Motagua fault and two events on the Anatolian fault in Turkey (the 1967, Mudurnu Valley and 1976, E. Turkey events). An attempt to model the complex P-waveforms of these events results in good synthetic fits for the Guatemala and Mudurnu Valley events. However, the E. Turkey event proves to be too complex as it may have associated thrust or normal faulting. Several individual sources occurring at intervals of between 5 and 20 seconds characterize the Guatemala and Mudurnu Valley events. The maximum size of an individual source appears to be bounded at about 5 x 10²⁶ dyne-cm. A detailed source study including directivity is performed on the Guatemala event. The source time history of the Mudurnu Valley event illustrates its significance in modeling strong ground motion in the near field. The complex source time series of the 1967 event produces amplitudes greater by a factor of 2.5 than a uniform model scaled to the same size for a station 20 km from the fault.

Three large and important earthquakes demonstrate an important type of complexity --- multiple-fault complexity. The first, the 1976 Philippine earthquake, an oblique thrust event, represents the first seismological evidence for a northeast dipping subduction zone beneath the island of Mindanao. A large event, following the mainshock by 12 hours, occurred outside the aftershock area and apparently resulted from motion on a subsidiary fault since the event had a strike-slip mechanism.

An aftershock of the great 1960 Chilean earthquake on June 6, 1960, proved to be an interesting discovery. It appears to be a large strike-slip event at the main rupture's southern boundary. It most likely occurred on the landward extension of the Chile Rise transform fault, in the subducting plate. The results for this event suggest that a small event triggered a series of slow events; the duration of the whole sequence being longer than 1 hour. This is indeed a "slow earthquake".

Perhaps one of the most complex of events is the recent Tangshan, China event. It began as a large strike-slip event. Within several seconds of the mainshock it may have triggered thrust faulting to the south of the epicenter. There is no doubt, however, that it triggered a large oblique normal event to the northeast, 15 hours after the mainshock. This event certainly contributed to the great loss of life-sustained as a result of the Tangshan earthquake sequence.

What has been learned from these studies has been applied to predict what one might expect from the next great earthquake on the San Andreas. The expectation from this study is that such an event would be a large complex event, not unlike, but perhaps larger than, the Guatemala or Mudurnu Valley events. That is to say, it will most likely consist of a series of individual events in sequence. It is also quite possible that the event could trigger associated faulting on neighboring fault systems such as those occurring in the Transverse Ranges. This has important bearing on the earthquake hazard estimation for the region.

Biodiversity of macrozoobenthos in a large river, the Austrian Danube, including quantitative studies in a free-flowing stretch below Vienna: a short review

The Danube is ca. 2850 km in length and is the second largest river in Europe. The Austrian part of the Danube falls 156 metres in altitude over its 351 km length and, since the early 1950s, the river has been developed into a power-generating waterway, so that the continuity of the river is now interrupted by ten impounded areas. Only two stretches of the original free-flowing river are left, the Wachau region (above river-km 2005, west of Vienna) and the region downstream from the impoundment at Vienna (river-km 1921). Most of the recent theories and concepts related to invertebrates, in the context of the ecology of running waters, are based on studies on small streams, whereas investigations of large rivers have played a minor role for a long time, mainly due to methodological difficulties. The authors' recent detailed studies on macroinvertebrates in the free-flowing section of the Danube below Vienna, provide an excellent opportunity to survey or restate scientific hypotheses on the basis of a large river. In this review the main interest focuses on the investigation of biodiversity, i.e. the number of species and their relative proportions in the whole invertebrate community, as well as major governing environmental factors. The article summarises the species composition, the important environmental variables at the river cross-section and the effect of upstream impoundment on the riverbed and its fauna.

Development and Application of Embedding Methods for the Simulation of Large Chemical Systems

The high computational cost of correlated wavefunction theory (WFT) calculations has motivated the development of numerous methods to partition the description of large chemical systems into smaller subsystem calculations. For example, WFT-in-DFT embedding methods facilitate the partitioning of a system into two subsystems: a subsystem A that is treated using an accurate WFT method, and a subsystem B that is treated using a more efficient Kohn-Sham density functional theory (KS-DFT) method. Representation of the interactions between subsystems is non-trivial, and often requires the use of approximate kinetic energy functionals or computationally challenging optimized effective potential calculations; however, it has recently been shown that these challenges can be eliminated through the use of a projection operator. This dissertation describes the development and application of embedding methods that enable accurate and efficient calculation of the properties of large chemical systems.

Chapter 1 introduces a method for efficiently performing projection-based WFT-in-DFT embedding calculations on large systems. This is accomplished by using a truncated basis set representation of the subsystem A wavefunction. We show that naive truncation of the basis set associated with subsystem A can lead to large numerical artifacts, and present an approach for systematically controlling these artifacts.

Chapter 2 describes the application of the projection-based embedding method to investigate the oxidative stability of lithium-ion batteries. We study the oxidation potentials of mixtures of ethylene carbonate (EC) and dimethyl carbonate (DMC) by using the projection-based embedding method to calculate the vertical ionization energy (IE) of individual molecules at the CCSD(T) level of theory, while explicitly accounting for the solvent using DFT. Interestingly, we reveal that large contributions to the solvation properties of DMC originate from quadrupolar interactions, resulting in a much larger solvent reorganization energy than that predicted using simple dielectric continuum models. Demonstration that the solvation properties of EC and DMC are governed by fundamentally different intermolecular interactions provides insight into key aspects of lithium-ion batteries, with relevance to electrolyte decomposition processes, solid-electrolyte interphase formation, and the local solvation environment of lithium cations.

Do encontro ao sentido: o cuidado aos sujeitos adoecidos de câncer

Esta pesquisa objetivou compreender como se dão as práticas de cuidado dirigidas ao sujeito adoecido de câncer no cotidiano dos serviços de saúde. Para tanto, partimos do entendimento que o processo de adoecer traz repercussões nos modos de andar a vida dos sujeitos, especialmente no que diz respeito ao câncer, patologia que traz consigo metáforas ligadas à morte, sofrimento e dor. Ao dar início à busca pelos serviços de saúde, os sujeitos se deparam com uma série de entraves que podem não proporcionar alívio, não suprindo as necessidades que essa nova condição impõe. Encontramos, em muitos momentos, práticas que negam o caráter subjetivo da experiência da doença, não valorizando a narrativa dos sujeitos. Como trajetória metodológica, escolhemos desenvolver um estudo de natureza qualitativa, utilizando como instrumento privilegiado a entrevista semi aberta. Iniciamos as entrevistas com a consigna: conte como se deu o tratamento de sua doença desde a descoberta até o momento em que se encontra. Os dados coletados a partir do encontro com os sujeitos adoecidos foram complementados por informações contidas nos prontuários médicos, bem como por observações obtidas no momento da interação. O local de realização da pesquisa foi um hospital estadual de grande porte localizado na cidade de Fortaleza, estado do Ceará. As entrevistas foram realizadas no serviço de oncologia clínica do referido hospital. Ao todo foram entrevistados doze sujeitos que estavam em tratamento ambulatorial no serviço. Dos doze sujeitos, cinco eram mulheres e sete eram homens. As idades variaram de 29 a 65 anos. A análise dos dados se deu após imersão no material empírico, posteriormente materializado nas transcrições das entrevistas. Procuramos deixar que os sentidos aflorassem, confrontando com o material que já tínhamos disponível, surgindo daí as categorias empíricas. Dividimos as categorias em duas dimensões, a do sujeito e a da rede de serviços de saúde. Ao final da análise, constatamos alguns pontos que consideramos importantes no sentido de se tornarem dispositivos de mudança. Foi possível confirmar que os sujeitos sabem de si, e realizam um processo de construção do sentido sobre sua doença e das práticas terapêuticas. A doença produz mudanças no sujeito, e os força a ressignificarem sua rotina e hábitos de vida. Foi possível observar que o encontro com os serviços de saúde tem se dado de forma truncada. A luta pelo direito a saúde é árdua: pela demora na confirmação do diagnóstico, pela demora em conseguir marcar exames e receber seus resultados, pela falta de especialistas que saibam o que estão fazendo. Os sujeitos têm descoberto a doença quando esta se encontra avançada. A importância do diálogo, da escuta, da percepção do que o outro necessita é importante, por isso, valorizar os relatos dos sujeitos adoecidos de câncer se faz urgente.