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A frequent source of pine tree mortality in recent years can be attributed to pine bark beetles and their vectored Ophiostomatoid fungi, an organism that has been observed to attract subterranean termites that preferentially recruit to this downed woody debris. This interaction may significantly modify biogeochemical fluxes in bark beetle mass mortality events, but studies are often limited to singular regions or single pine-dominated ecosystems. Two studies were designed to test the interactive effects of these associations on terrestrial biogeochemical cycles and decomposition processes, the first using replicated field trials in Mississippi, Arizona, and Honduras across two years and the second across five years in Mississippi. Both studies utilized Ophiostomatoid inoculation and invertebrate exclusion techniques to determine the individual and interactive contributions from biotic factors on biogeochemical cycling. Local drivers were found to have greater influence on biogeochemical cycling and decomposition before climate drivers overwhelmed their influence in later years.

Intercropping switchgrass (Panicum virgatum) between tree rows within young pine (Pinus spp.) plantations is a novel method to generate lignocellulosic biofuel feedstocks within intensively managed forests. Intensively managed pine supports diverse avian assemblages potentially affected by establishment and maintenance of a biomass feedstock. I sought to understand how establishing switchgrass on an operational scale affects bird communities within intercropped plantations as compared to typical intensively managed loblolly pine (Pinus taeda) plantations. I conducted breeding bird point counts, nest searching and monitoring, and coarse woody debris (CWD) surveys following establishment of intercropped switchgrass stands (6 replicates), traditionally-managed pine plantations, and switchgrass-only plots (0.1 km2 minimum) in Kemper Co., MS from 2011 to 2013. I found establishment of intercropping did not affect downed CWD, but reduced standing snags and green trees. I detected 59 breeding bird species from 11,195 detections and modeled nest survivorship for 17 species. Neotropical migrants and forest-edge associated species were less abundant in intercropped plots than controls for two years after establishment, and more abundant in year three. Short distance migrants and residents were scarce in intercropped and control plots initially, and did not differ between these treatments in any year. Species associated with pine-grass habitat structure were less abundant initially in intercropped plots, but converged with pine controls in subsequent years. Switchgrass monocultures provided minimal resources for birds. There was no evidence supporting an effect of intercropping on songbird nest survivorship. I found evidence for dominance of one species, yellow-breasted chat (Icteria virens), over another, indigo bunting (Passerina cyanea) in competition for nest sites, which illustrates how songbirds competing for nest sites can coexist in sympatry without the dominant species driving subordinate competitors to local extirpation. This dissertation, and related publications, are among the earliest research on wildlife response to intercropping. Forest managers implementing intercropping within pine plantations where vertebrate conservation is a management priority should be aware of potential changes to snag-utilizing species from reductions in green trees and snags. Songbird populations may lag behind traditional management for up to two years following establishment of switchgrass. Intercropping neither positively nor negatively affected songbird nest survival.

This thesis studies the large scale dimension theory of metric spaces. Background on dimension theory is provided, including topological and asymptotic dimension, and notions of nonpositive curvature in metric spaces are reviewed. The hyperbolic dimension of Buyalo and Schroeder is surveyed. Miscellaneous new results on hyperbolic dimension are proved, including a union theorem, an estimate for central group extensions, and the vanishing of hyperbolic dimension for countable abelian groups. A new quasi-isometry invariant called weak hyperbolic dimension (abbreviated $\wdim$) is introduced and developed. Weak hyperbolic dimension is computed for a variety of metric spaces, including the fundamental computation $\wdim \Hyp^n = n-1$. An estimate is proved for (not necessarily central) group extensions. Weak dimension is used to obtain the quasi-isometric nonembedding result $\Hyp^4 \not \rightarrow \Sol \times \Sol$ and possible directions for further nonembedding applications are explored. / Thesis / Doctor of Philosophy (PhD) / Shapes and spaces are studied from the "large scale" or "far away" point of view. Various notions of dimension for such spaces are studied.

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In a celebrated series of experimental observations, starling flocks have been shown to be characterized by scale-free, long-ranged spatial correlations in their velocity fluctuations. While this is expected for velocity orientation correlations on the basis of simple symmetry-breaking arguments, the same scaling-free behaviour for speed (i.e. the absolute value of birds’ velocity) correlations cannot be explained by the same symmetry-based argument. Possible explanations so far put forward required the implicit or explicit fine-tuning of a speed control parameter. In this work we explore a different possibility, investigating the effects of the experimental discrete temporal sampling of individual bird trajectories. We argue that observed velocity may well be a time coarse-grained observable, that is, the sum over many faster course corrections taken by the bird. A simple argument shows such a time coarse-grained speed to be linked with the squared fluctuations of (soft modes) transversal velocities, which may thus acquire a long-range correlation. Our idea is numerically tested by measuring spatial correlations between coarse-grained speeds in the on-lattice equilibrium XY model and the off-lattice out-of-equilibrium Vicsek model in two dimensions. Saturation of the speed correlation length is found in the equilibrium XY model, while in the non-equilibrium Vicsek model ordered symmetry-broken phase shows scale-free behaviour with a correlation length ξ is found to be proportional to system size L. We conclude that in non-equilibrium flocking models, the temporal coarse-graining procedure is able to reproduce scale-free behaviour at system sizes which are relevant to the experimental observations. We believe that this mechanism might find applications beyond the case of starling flocks and perhaps be relevant for other experimental observations of collective motion.

Recycled concrete aggregate (RCA) is often used as a replacement of virgin aggregate in road foundations (base course), embankments, hot-mix asphalt, and Portland cement concrete. However, the use of RCA in exfiltration drainage systems, such as French drains, is currently prohibited in many states of the U.S. The French drain system collects water runoff from the road pavement and transfers to slotted pipes underground and then filters through coarse aggregate and geotextile. The primary concerns with using RCA as a drainage media are the fines content and the precipitation of calcium carbonate to cause a reducing in filter fabric permittivity. Additional concerns include the potential for rehydration of RCA fines. The performance of RCA as drainage material has not been evaluated by many researchers and the limited information limits its use. A literature review has been conducted on the available information related to RCA as drainage material. A survey was issued to the Departments of Transportation across the nation in regards to using RCA particularly in French drains. Some state highway agencies have reported the use of RCA as base course; however, no state reports the use of RCA in exfiltration drainage systems. This thesis describes the investigations on the performance of RCA as backfill material in French drains. RCA was tested for its physical properties including, specific gravity, unit weight, percent voids, absorption, and abrasion resistance. RCA cleaning/washing methods were also applied to evaluate the fines removal processes. The potential for RCA rehydration was iv evaluated by means of heat of hydration, pH, compressive strength, and setting time. The permeability of RCA was tested using the No. 4 gradation. Long term permeability testing was conducted to evaluate the tendency for geotextile clogging from RCA fines. Calcium carbonate precipitation was also evaluated and a procedure to accelerate the precipitation process was developed. The results show that RCA has a high abrasion value, that is, it is very susceptible to break down from abrasion during aggregate handling such as transportation, stockpiling, or placing. The most effective cleaning method was found to be pressure washing with agitation. RCA has not demonstrated the tendency to rehydrate and harden when mixed with water. The permeability test results show that the No. 4 gradation does not restrict the flow of water; the flow rate is highly dependent on the hydraulic system itself, however excessive fines can cause large reductions in permeability over time. It has been determined that No. 4 gradation of RCA can provide a suitable drainage media providing the RCA is properly treated before its use.

Low-resolution, coarse-grained models are powerful computational tools to investigate the behavior of biological systems over time and length scales that are not accessible to all-atom Molecular Dynamics simulations. While several algorithms exist that aim at constructing accurate coarse-grained potentials, few works focus on the choice of the reduced representation, or mapping, to be employed to describe the high-resolution system with a lower number of degrees of freedom. This thesis proposes a series of approaches to investigate and characterise the representation problem in coarse-grained modelling of proteins. This is achieved by employing a collection of diverse methods, including statistical mechanics, machine learning algorithms and information-theoretical tools. The central mathematical object of this work is the mapping entropy, a Kullback-Leibler divergence that measures the intrinsic quality of a given reduced representation. When this quantity is minimised, we obtain the maximally informative coarse-grained mappings of a biomolecule, which cover the structure with an uneven level of detail. Tests conducted over a set of well-known proteins show that regions preserved with high probability are often related to important functional mechanisms of the molecule. Applications of the mapping entropy outside of the field of structural biology show promising results, leading to the identification of those combinations of features that retain the maximum amount of information about the high-resolution system. Additionally, a purely structural notion of scalar product and distance between coarse-grained mappings is introduced, which allow to analyse the metric and topological properties of the mapping space. The thorough exploration of such space leads to the discovery of qualitatively different reduced representations of the biomolecule of interest.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24656号 / 農博第2539号 / 新制||農||1097(附属図書館) / 学位論文||R5||N5437(農学部図書室) / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 北山 兼弘, 教授 田中 千尋, 教授 松浦 健二 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

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