Linear Spectroscopic Studies of Semiconductor Quantum Wells

Despite the short timescales on which electron dynamics occur in semiconductor nanostructures, much insight into these processes can be provided by studying them using linear, long timescale, spectroscopy. For instance, manufacturing processes unintentionally introduce fluctuations in the width of semiconductor quantum wells. These fluctuations subtly modulate the optical emission energies of electrons confined within the quantum well layers. It is therefore imperative to quantify these width fluctuations so their effect on electron confinement potentials can be accounted for in ultrafast spectroscopic studies of semiconductor quantum wells. The use of linear micro-photoluminescence spectroscopy makes quantifying this disorder possible. Additionally, coupling between electron states in asymmetric double quantum wells is of fundamental interest. Understanding incoherent, long-timescale electron coupling in this system allows us to provide insight into the dominant physical mechanisms that govern exciton coupling in general. For example, understanding the thermal mediation of coupling between wells could allow researchers to better model and predict electron behavior in useful semiconductor devices like solar cells and photodiodes. In this thesis, I present the development of micro-photoluminesence spectroscopy to study spatial disorder in semiconductor quantum wells. Additionally, I present the development of photoluminescence excitation spectroscopy to study the long-timescale, incoherent exciton coupling between adjacent wells in an asymmetric quantum well heterostructure

Calculating the virtual cohomological dimension of the automorphism group of a RAAG

We describe an algorithm to find the virtual cohomological dimension of the automorphism group of a right-angled Artin group. The algorithm works in the relative setting; in particular it also applies to untwisted automorphism groups and basis-conjugating automorphism groups. The main new tool is the construction of free abelian subgroups of certain Fouxe-Rabinovitch groups of rank equal to their virtual cohomological dimension, generalizing a result of Meucci in the setting of free groups.Comment: 15 pages, 2 figures. Revised background on RORGs, small changes elsewhere. Accepted to appear in Bulletin of the LM

Drivers and impacts of water level fluctuations in the Mississippi River delta: Implications for delta restoration

This review synthesizes the knowledge regarding the environmental forces affecting water level variability in the coastal waters of the Mississippi River delta and relates these fluctuations to planned river diversions. Water level fluctuations vary significantly across temporal and spatial scales, and are subject to influences from river flow, tides, vegetation, atmospheric forcing, climate change, and anthropogenic activities. Human impacts have strongly affected water level variability in the Mississippi River delta and other deltas worldwide. Collectively, the research reviewed in this article is important for enhancing environmental, economic, and social resilience and sustainability by assessing, mitigating, and adapting to geophysical changes that will cascade to societal systems in the coming decades in the economically and environmentally important Mississippi River delta. Specifically, this information provides a context within which to evaluate the impacts of diversions on the hydrology of the Mississippi delta and creates a benchmark for the evaluation of the impact of water level fluctuations on coastal restoration projects worldwide

Early Onset of Franciscan Subduction

The Franciscan subduction complex of California is considered a type example of a subduction-accretion system, yet the age of subduction initiation and relationship to the tectonic history of western North America remain controversial. Estimates for the timing of Franciscan subduction initiation are largely based either indirectly on regional tectonic arguments or from the ages of high-grade blocks within mélange. Many of the high-grade blocks record counterclockwise pressure-temperature paths with early amphibolite overprinted by later eclogite and blueschist; however, their origin and significance with respect to subduction initiation have been debated. In contrast, some high-grade blocks show evidence for clockwise pressure-temperature paths and an early eclogite assemblage overprinted by later amphibolite Zircon U-Pb ages from inclusions in garnet and Lu-Hf estimates of initial garnet growth ages from these samples record early eclogite metamorphism at ~176 Ma. Matrix zircon U-Pb ages and Lu-Hf estimates of final garnet growth ages record a barroisite-amphibolite assemblage overprint of eclogite at ~160 Ma. Combined with petrologic data and existing geochronology, the data suggest that (1) Franciscan subduction was underway by no later than 180 Ma, (2) continuous subduction metamorphism occurred for at least 100 Ma, and (3) Franciscan subduction initiation predated the formation of the overlying Coast Range Ophiolite, supporting models that form the ophiolite above an east dipping Franciscan subduction zone

Phosphorylation-dependent assembly of DNA damage response systems and the central roles of TOPBP1

The cellular response to DNA damage (DDR) that causes replication collapse and/or DNA double strand breaks, is characterised by a massive change in the post-translational modifications (PTM) of hundreds of proteins involved in the detection and repair of DNA damage, and the communication of the state of damage to the cellular systems that regulate replication and cell division. A substantial proportion of these PTMs involve targeted phosphorylation, which among other effects, promotes the formation of multiprotein complexes through the specific binding of phosphorylated motifs on one protein, by specialised domains on other proteins. Understanding the nature of these phosphorylation mediated interactions allows definition of the pathways and networks that coordinate the DDR, and helps identify new targets for therapeutic intervention that may be of benefit in the treatment of cancer, where DDR plays a key role. In this review we summarise the present understanding of how phosphorylated motifs are recognised by BRCT domains, which occur in many DDR proteins. We particularly focus on TOPBP1 – a multi-BRCT domain scaffold protein with essential roles in replication and the repair and signalling of DNA damage

Elementary amenable subgroups of R. Thompson's group F

The subgroup structure of Thompson's group F is not yet fully understood. The group F is a subgroup of the group PL(I) of orientation preserving, piecewise linear self homeomorphisms of the unit interval and this larger group thus also has a poorly understood subgroup structure. It is reasonable to guess that F is the "only" subgroup of PL(I) that is not elementary amenable. In this paper, we explore the complexity of the elementary amenable subgroups of F in an attempt to understand the boundary between the elementary amenable subgroups and the non-elementary amenable. We construct an example of an elementary amenable subgroup up to class (height) omega squared, where omega is the first infinite ordinal.Comment: 20 page

Frequency responses of age-structured populations: Pacific salmon as an example

Increasing evidence of the effects of changing climate on physical ocean conditions and long-term changes in fish populations adds to the need to understand the effects of stochastic forcing on marine populations. Cohort resonance is of particular interest because it involves selective sensitivity to specific time scales of environmental variability, including that of mean age of reproduction, and, more importantly, very low frequencies (i.e., trends). We present an age-structured model for two Pacific salmon species with environmental variability in survival rate and in individual growth rate, hence spawning age distribution. We use computed frequency response curves and analysis of the linearized dynamics to obtain two main results. First, the frequency response of the population is affected by the life history stage at which variability affects the population; varying growth rate tends to excite periodic resonance in age structure, while varying survival tends to excite low-frequency fluctuation with more effect on total population size. Second, decreasing adult survival strengthens the cohort resonance effect at all frequencies, a finding that addresses the question of how fishing and climate change will interact.Comment: much revised: the version accepted by Theoretical Population Biolog

Structural basis for recruitment of the CHK1 DNA damage kinase by the CLASPIN scaffold protein

CHK1 is a protein kinase that functions downstream of activated ATR to phosphorylate multiple targets as part of intra-S and G2/M DNA damage checkpoints. Its role in allowing cells to survive replicative stress has made it an important target for anti-cancer drug discovery. Activation of CHK1 by ATR depends on their mutual interaction with CLASPIN, a natively unstructured protein that interacts with CHK1 through a cluster of phosphorylation sites in its C-terminal half. We have now determined the crystal structure of the kinase domain of CHK1 bound to a high-affinity motif from CLASPIN. Our data show that CLASPIN engages a conserved site on CHK1 adjacent to the substrate-binding cleft, involved in phosphate sensing in other kinases. The CLASPIN motif is not phosphorylated by CHK1, nor does it affect phosphorylation of a CDC25 substrate peptide, suggesting that it functions purely as a scaffold for CHK1 activation by ATR