Physical Sciences and Mathematics Commons^™

Introduction To Using Python In The Digital Humanities, Elisabeth Shook

Library Faculty Publications and Presentations

The materials here are from the Python for Digital Humanities Workshop taught on December 13, 2021 for the Boise State University Digital Humanities Group. This 3-hour workshop was created to provide both a very brief introduction to the various capabilities of Python and a small lesson in using Python to pull meaningful insight out of text files.

A Modular Strategy For Expanding Electron-Sink Capacity In Noncanonical Cluster Assemblies, Yume Mai, Alexandria K. Balzen, Rebecca K. Torren, Michael P. Callahan, Adam C. Colson

Chemistry and Biochemistry Faculty Publications and Presentations

A modular synthetic strategy is described whereby organometallic complexes exhibiting considerable electron-sink capacity may be assembled by using only a few simple molecular components. The Fe₂(PPh₂)₂(CO)₅ fragment was selected as a common electroactive component and was assembled around aromatic cores bearing one, two, or three isocyanide functional groups, with the resultant complexes possessing electron-sink capacities of two, four, and six electrons, respectively. The latter complex is noteworthy in that its electron-sink capacity was found to rival that of large multinuclear clusters (e.g., [Ni₃₂C₆(CO)₃₆]^6– and [Ni_{38 …}

Clmm: A Lsst-Desc Cluster Weak Lensing Mass Modeling Library For Cosmology, H. Wu

Physics Faculty Publications and Presentations

We present the v1.0 release of CLMM, an open source PYTHON library for the estimation of the weak lensing masses of clusters of galaxies. CLMM is designed as a stand-alone toolkit of building blocks to enable end-to-end analysis pipeline validation for upcoming cluster cosmology analyses such as the ones that will be performed by the Vera C. Rubin Legacy Survey of Space and Time-Dark Energy Science Collaboration (LSST-DESC). Its purpose is to serve as a flexible, easy-to-install, and easy-to-use interface for both weak lensing simulators and observers and can be applied to real and mock data to study the systematics …

Comparison Of Different Analytical Strategies For Classifying Invasive Wetland Vegetation In Imagery From Unpiloted Aerial Systems (Uas), Louis Will Jochems, Jodi Brandt, Andrew Monks, Megan Cattau, Nicholas Kolarik, Jason Tallant, Shane Lishawa

Human-Environment Systems Research Center Faculty Publications and Presentations

Detecting newly established invasive plants is key to prevent further spread. Traditional field surveys are challenging and often insufficient to identify the presence and extent of invasions. This is particularly true for wetland ecosystems because of difficult access, and because floating and submergent plants may go undetected in the understory of emergent plants. Unpiloted aerial systems (UAS) have the potential to revolutionize how we monitor invasive vegetation in wetlands, but key components of the data collection and analysis workflow have not been defined. In this study, we conducted a rigorous comparison of different methodologies for mapping invasive Emergent (Typha …

Exploring Hydrologic Responses To Different Wildfire Spatial Patterns Through The Lens Of Computational Modeling, Luke M. Telfer

Boise State University Theses and Dissertations

Severe wildfire disturbances are becoming increasingly common in high-elevation forests of the western United States. These fires alter watershed hydrologic processes, threatening critical downstream water resources and aquatic ecosystems. However, watershed-scale postfire hydrologic responses and water balance changes are highly uncertain. While postfire effects on individual processes such as runoff, infiltration, evapotranspiration, and snow dynamics are relatively well known, the role of wildfire spatial patterns in governing hydrologic connectivity and interactions between water balance components is poorly understood due to challenges associated with measuring and comparing fires at large scales. This thesis aims to examine pattern-related postfire interactions between various …

Bioactivity Assessment Of Veratrum Californicum Alkaloids, Madison Dirks

Boise State University Theses and Dissertations

The native Idaho plant Veratrum californicum is known to contain steroidal alkaloids that function as inhibitors of hedgehog signaling, a pathway utilized for the growth and differentiation of cells as well as proper tissue development. Veratrum californicum was originally noticed when pregnant ewes consumed the plant and later gave birth to lambs with craniofacial mutations such as a cyclopean eyes. These malformations were caused by the plant’s steroidal alkaloid cyclopamine blocking the hedgehog signaling pathway. This same pathway is used by more than 20 types of cancer for multiplication of cells. Additional alkaloids have been found in Veratrum californicum, …

Controls On The Frequency Content Of Near-Source Infrasound At An Open-Vent Volcano (Villarrica, Chile), Bryan Blake Rosenblatt

Boise State University Theses and Dissertations

The acoustic signals from open-vent volcanoes can contain specific information related to that volcano’s eruption dynamics and future activity. Thus, studying a specific volcano’s acoustics may provide critical warning mechanisms, signaling impending eruptions. Villarrica volcano, located in southern Chile, has an active lava lake that produces continuous infrasound with spectral peaks near 1 Hz and excursions of +/- ~0.2 Hz. The infrasound’s frequency content reveals key volcanic properties such as eruption style and crater shape. Leading up to Villarrica’s most recent paroxysm in 2015, infrasound spectral changes coincided with and indicated a rise in Villarrica’s lava lake level. As such, …

Dreams Of Molecular Beams: Indium Gallium Arsenide Tensile-Strained Quantum Dots And Advances Towards Dynamic Quantum Dots (Moleculare Radiorum Somnia: Indii Gallii Arsenicus Tensa Quanta Puncta Et Ad Dinamicae Quantae Puntae Progressus), Kevin Daniel Vallejo

Boise State University Theses and Dissertations

Through the operation of a molecular beam epitaxy (MBE) machine, I worked on developing the homoepitaxy of high quality InAs with a (111)A crystallographic orientation. By tuning substrate temperature, we obtained a transition from a 2D island growth mode to step- ow growth. Optimized MBE parameters (substrate temperature = 500 °C, growth rate = 0.12 ML/s and V/III ratio ⩾ 40) lead to growth of extremely smooth InAs(111)A films, free from hillocks and other 3D surface imperfections. We see a correlation between InAs surface smoothness and optical quality, as measured by photoluminescence spectroscopy. This work establishes InAs(111)A as a platform …

Fair And Efficient Consensus Protocols For Secure Blockchain Applications, Golam Dastoger Bashar

Boise State University Theses and Dissertations

In blockchain technology, consensus protocols serve as mechanisms to reach agreements among a distributed network of nodes. In this work, we propose three novel protocols for permissioned, healthcare, and supply chain blockchain.

(1) Proof of Queue (PoQ), for private blockchains, combines the lottery strategy of PoET with a specialized round-robin algorithm where each node has an equal chance to become a leader with equal access. PoQ is relatively scalable without any collision. Like PoET, PoQ uses Intel SGX, a Trusted Execution Environment, to generate a secure random waiting time to choose a leader and fairly distribute the leadership role to …

Fire Effects On Soil Properties: Amending Post-Fire Soils With Native Microbial Communities And Biochar To Improve Sagebrush Performance, Sabrina Marie Schuler

Boise State University Theses and Dissertations

Within the sagebrush steppe, fire has been shown to affect biogeochemical properties and the microbial community composition in soils. However, there is uncertainty about the magnitude and direction of these effects, since they vary by sites that differ in abiotic and biotic conditions. Moreover, differences in post-fire management strategies are likely to mediate the effect of fire on soil properties, thus further compounding this uncertainty. Any changes in soil biogeochemical properties following fire can prevent successful restoration of Artemisia tridentata sp. wyomingensis (sagebrush), leading to variable outcomes of restoration success in the sagebrush steppe. Previous research has shown that addition …

Training Wheels For Web Search: Multi-Perspective Learning To Rank To Support Children's Information Seeking In The Classroom, Garrett Allen

Boise State University Theses and Dissertations

Bicycle design has not changed for a long time, as they are well-crafted for those that possess the skills to ride, i.e., adults. Those learning to ride, however, often need additional support in the form of training wheels. Searching for information on the Web is much like riding a bicycle, where modern search engines (the bicycle) are optimized for general use and adult users, but lack the functionality to support non-traditional audiences and environments. In this thesis, we introduce a set of training wheels in the form of a learning to rank model as augmentation for standard search engines to …

Water Quality Responses To A Semi-Arid Beaver Meadow In Boise, Idaho, Luise Bayer Winslow

Boise State University Theses and Dissertations

Beavers have been instrumental in shaping the North American riverine landscape. However, land use change and beaver trapping have caused large decreases in beaver populations, resulting in fundamental changes to river morphology, hydrology, and biogeochemical function. Effective river restoration and remediation of arid western rivers relies on a comprehensive interpretation of how beaver activity influences water quantity and quality. In this study, I compared two stream reaches with and without beaver dams in a semi-arid watershed, to quantify the effects of beaver activity on hydrology and biogeochemistry. Within each reach, I combined dilution gauging and stream tracer experiments to determine …

Soil Structure And Soil Moisture Dynamics Inferred From Time-Lapse Electrical Resistivity Tomography, Travis Nielson, John Bradford, Jen Pierce, Mark Seyfried

Geosciences Faculty Publications and Presentations

The semi-arid sagebrush steppe in the western United States faces pressures from the agriculture industry, recreation use, invasive grasses, and a changing climate. A key to facilitating the healthy management of this ecosystem is understanding the distribution and behavior of soil moisture in the vadose zone in both natural and agricultural settings. Within unsaturated environments, soil moisture is spatially and temporally heterogeneous, and changes in porosity and permeability within arid soils complicate characterization of soil hydrologic properties. Importantly, accumulations of ‘caliche’ or pedogenic calcium carbonate in arid soils can greatly limit permeability; however, observing the role that caliche plays in …

An Efficient High-Order Meshless Method For Advection-Diffusion Equations On Time-Varying Irregular Domains, Varun Shankar, Grady B. Wright, Aaron L. Fogelson

Mathematics Faculty Publications and Presentations

We present a high-order radial basis function finite difference (RBF-FD) framework for the solution of advection-diffusion equations on time-varying domains. Our framework is based on a generalization of the recently developed Overlapped RBF-FD method that utilizes a novel automatic procedure for computing RBF-FD weights on stencils in variable-sized regions around stencil centers. This procedure eliminates the overlap parameter δ, thereby enabling tuning-free assembly of RBF-FD differentiation matrices on moving domains. In addition, our framework utilizes a simple and efficient procedure for updating differentiation matrices on moving domains tiled by node sets of time-varying cardinality. Finally, advection-diffusion in time-varying domains …

Volumetric Extrusive Rates Of Silicic Supereruptions From The Afro-Arabian Large Igneous Province, Jennifer E. Thines, Ingrid A. Ukstins, Corey Wall, Mark Schmitz

Geosciences Faculty Publications and Presentations

The main phase of silicic volcanism from the Afro-Arabian large igneous province preserves some of the largest volcanic eruptions on Earth, with six units totaling >8,600 km³ dense rock equivalent (DRE). The large volumes of rapidly emplaced individual eruptions present a case study for examining the tempo of voluminous silicic magma generation and emplacement. Here were report high-precision ²⁰⁶Pb/²³⁸U zircon ages and show that the largest sequentially dated eruptions occurred within 48 ± 34 kyr (29.755 ± 0.023 Ma to 29.707 ± 0.025 Ma), yielding the highest known long-term volumetric extrusive rate of silicic volcanism on …

Homflypt Skein Theory, String Topology And 2-Categories, Uwe Kaiser

Mathematics Faculty Publications and Presentations

We show that relations in Homflypt type skein theory of an oriented 3-manifold M are induced from a 2-groupoid defined from the fundamental 2-groupoid of a space of singular links M. The module relations are defined by homomorphisms related to string topology. They appear from a representation of the groupoid into free modules on a set of model objects. The construction on the fundamental 2-groupoid is defined by the singularity stratification and relates Vassiliev and skein theory. Several explicit properties are discussed, and some implications for skein modules are derived.

Spatiotemporal Variations In Liquid Water Content In A Seasonal Snowpack: Implications For Radar Remote Sensing, Randall Bonnell, Daniel Mcgrath, Keith Williams, Ryan Webb, Steven R. Fassnacht, Hans-Peter Marshall

Geosciences Faculty Publications and Presentations

Radar instruments have been widely used to measure snow water equivalent (SWE) and Interferometric Synthetic Aperture Radar is a promising approach for doing so from spaceborne platforms. Electromagnetic waves propagate through the snowpack at a velocity determined by its dielectric permittivity. Velocity estimates are a significant source of uncertainty in radar SWE retrievals, especially in wet snow. In dry snow, velocity can be calculated from relations between permittivity and snow density. However, wet snow velocity is a function of both snow density and liquid water content (LWC); the latter exhibits high spatiotemporal variability, there is no standard observation method, and …

The Ionic Selectivity Of Lysenin Channels In Open And Sub-Conducting States, Andrew Bogard, Pangaea W. Finn, Fulton Mckinney, Ilinca M. Flacau, Aviana R. Smith, Rosey Whiting, Daniel Fologea

Physics Faculty Publications and Presentations

The electrochemical gradients established across cell membranes are paramount for the execution of biological functions. Besides ion channels, other transporters, such as exogenous pore-forming toxins, may present ionic selectivity upon reconstitution in natural and artificial lipid membranes and contribute to the electrochemical gradients. In this context, we utilized electrophysiology approaches to assess the ionic selectivity of the pore-forming toxin lysenin reconstituted in planar bilayer lipid membranes. The membrane voltages were determined from the reversal potentials recorded upon channel exposure to asymmetrical ionic conditions, and the permeability ratios were calculated from the fit with the Goldman–Hodgkin–Katz equation. Our work shows that …

Effects Of Material Texture And Packing Density On The Interfacial Polarization Of Granular Soils, Hang Chen, Qifei Niu

Geosciences Faculty Publications and Presentations

Many electrical and electromagnetic (EM) methods operate at MHz frequencies, at which the interfacial polarization occurring at the solid-liquid interface in geologic materials may dominate the electrical signals. To correctly interpret electrical/EM measurements, it is therefore critical to understand how the interfacial polarization influences the effective electrical conductivity and permittivity spectra of geologic materials. We have used pore-scale simulation to study the role of material texture and packing in interfacial polarization in water-saturated granular soils. Synthetic samples with varying material textures and packing densities are prepared with the discrete element method. The effective electrical conductivity and permittivity spectra of these …

Seasonality Of Solute Flux And Water Source Chemistry In A Coastal Glacierized Watershed Undergoing Rapid Change: Wolverine Glacier Watershed, Alaska, Anna Bergstrom, Joshua C. Koch, Shad O'Neel, Emily Baker

Geosciences Faculty Publications and Presentations

As glaciers around the world rapidly lose mass, the tight coupling between glaciers and downstream ecosystems is resulting in widespread impacts on global hydrologic and biogeochemical cycling. However, a range of challenges make it difficult to conduct research in glacierized systems, and our knowledge of seasonally changing hydrologic processes and solute sources and signatures is limited. This in turn hampers our ability to make predictions on solute composition and flux. We conducted a broad water sampling campaign in order to understand the present-day partitioning of water sources and associated solutes in Alaska's Wolverine Glacier watershed. We established a relationship between …

Slope And Aspect Controls On Soil Climate: Field Documentation And Implications For Large-Scale Simulation Of Critical Zone Processes, Mark Seyfried, Gerald Flerchinger, Sage Bryden, Tim Link, Danny Marks, Jim Mcnamara

Geosciences Faculty Publications and Presentations

Soil climate, as quantified by soil temperature (T_S) and water content (θ), exerts important controls on critical zone processes. It may be sensitive to variations in local slope and aspect (SA), but this attribute remains poorly quantified at the local scale and unresolved in large-scale models. Estimation of SA effects on soil climate across multiple scales may facilitated using topographically modified, incoming clear-sky solar radiation (S_R,CS,T). We established six paired automated soil climate monitoring stations on opposing north-facing (NF) and south-facing (SF) slopes (4 yr) and collected spatial T_S and θ data within …

Cuts: Scaling Subgraph Isomorphism On Distributed Multi-Gpu Systems Using Trie Based Data Structure, Lizhi Xiang, Arif Khan, Edoardo Serra, Mahantesh Halappanavar, Aravind Sukumaran-Rajam

Computer Science Faculty Publications and Presentations

Subgraph isomorphism is a pattern-matching algorithm widely used in many domains such as chem-informatics, bioinformatics, databases, and social network analysis. It is computationally expensive and is a proven NP-hard problem. The massive parallelism in GPUs is well suited for solving subgraph isomorphism. However, current GPU implementations are far from the achievable performance. Moreover, the enormous memory requirement of current approaches limits the problem size that can be handled. This work analyzes the fundamental challenges associated with processing subgraph isomorphism on GPUs and develops an efficient GPU implementation. We also develop a GPU-friendly trie-based data structure to drastically reduce the intermediate …

Automated Detection Of Marine Glacier Calving Fronts Using The 2-D Wavelet Transform Modulus Maxima Segmentation Method, Julia Liu, Ellyn M. Enderlin, Hans-Peter Marshall, Andre Khalil

Geosciences Faculty Publications and Presentations

Changes in the calving front position of marine-terminating glaciers strongly influence the mass balance of glaciers, ice caps, and ice sheets. At present, quantification of frontal position change primarily relies on time-consuming and subjective manual mapping techniques, limiting our ability to understand changes to glacier calving fronts. Here we describe a newly developed automated method of mapping glacier calving fronts in satellite imagery using observations from a representative sample of Greenland’s peripheral marine-terminating glaciers. Our method is adapted from the 2-D wavelet transform modulus maxima (WTMM) segmentation method, which has been used previously for image segmentation in biomedical and other …

In Situ Determination Of Dry And Wet Snow Permittivity: Improving Equations For Low Frequency Radar Applications, Ryan Webb, Adrian Marziliano, Daniel Mcgrath, Randall Bonnell, Tate G. Meehan, Carrie Vuyovich, Hans-Peter Marshall

Geosciences Faculty Publications and Presentations

Extensive efforts have been made to observe the accumulation and melting of seasonal snow. However, making accurate observations of snow water equivalent (SWE) at global scales is challenging. Active radar systems show promise, provided the dielectric properties of the snowpack are accurately constrained. The dielectric constant (k) determines the velocity of a radar wave through snow, which is a critical component of time-of-flight radar techniques such as ground penetrating radar and interferometric synthetic aperture radar (InSAR). However, equations used to estimate k have been validated only for specific conditions with limited in situ validation for seasonal snow applications. …

Tracking Secondary Lahar Flow Paths And Characterizing Pulses And Surges Using Infrasound Array Networks At Volcán De Fuego, Guatemala, Ashley R. Bosa, Jeffrey B. Johnson, Silvio De Angelis, John J. Lyons, Amilcar Roca, Jacob F. Anderson, Amando Pineda

Geosciences Faculty Publications and Presentations

Lahars are one of the greatest hazards at many volcanoes, including Volcán de Fuego (Guatemala). On 1 December 2018 at 8:00 pm local Guatemala time (~2:06:00 UTC), an hour-long lahar event was detected at Volcán de Fuego by two permanent seismo-acoustic stations along the Las Lajas drainage on the southeast side. To establish the timing, duration, and speed of the lahar, infrasound array records were examined to identify both the source direction(s) and the correlated energy fluctuations at the two stations. Co-located seismic and acoustic signals were also examined, which indicated at least five distinct energy pulses within the lahar …

Inferring Vortex And Dust Devil Statistics From Insight, Brian Jackson, Justin Crevier, Michelle Szurgot, Ryan Battin, Clément Perrin, Sébastien Rodriguez

Physics Faculty Publications and Presentations

The InSight mission has operated on the surface of Mars for nearly two Earth years, returning detections of the first marsquakes. The lander also deployed a meteorological instrument package and cameras to monitor local surface activity. These instruments have detected boundary layer phenomena, including small-scale vortices. These vortices register as short-lived, negative pressure excursions and closely resemble those that could generate dust devils. Although our analysis shows that InSight encountered more than 900 vortices and collected more than 1000 images of the Martian surface, no active dust devils were imaged. In spite of the lack of dust devil detections, we …

Phosphine Generation Pathways On Rocky Planets, Arthur Omran, Christopher Oze, Brian Jackson, Chris Mehta, Laura M. Barge, Jeffrey Bada, Matthew A. Pasek

Physics Faculty Publications and Presentations

The possibility of life in the venusian clouds was proposed in the 1960s, and recently this hypothesis has been revived with the potential detection of phosphine (PH₃) in Venus' atmosphere. These observations may have detected ∼5–20 ppb phosphine on Venus (Greaves et al., 2020), which raises questions about venusian atmospheric/geochemical processes and suggests that this phosphine could possibly be generated by biological processes. In such a claim, it is essential to understand the abiotic phosphorus chemistry that may occur under Venus-relevant conditions, particularly those processes that may result in phosphine generation. Here, we discuss two related abiotic …

Review: Veratrum Californicum Alkaloids, Madison L. Dirks, Jared T. Seale, Joseph M. Collins, Owen M. Mcdougal

Chemistry and Biochemistry Faculty Publications and Presentations

Veratrum spp. grow throughout the world and are especially prevalent in high mountain meadows of North America. All parts of Veratrum plants have been used for the treatment of ailments including injuries, hypertension, and rheumatic pain since as far back as the 1600s. Of the 17–45 Veratrum spp., Veratrum californicum alkaloids have been proven to possess favorable medicinal properties associated with inhibition of hedgehog (Hh) pathway signaling. Aberrant Hh signaling leads to proliferation of over 20 cancers, including basal cell carcinoma, prostate and colon among others. Six of the most well-studied V. californicum alkaloids are cyclopamine (1), veratramine (2) …

The Hera Orebody: A Complex Distal (Au–Zn–Pb–Ag–Cu) Skarn In The Cobar Basin Of Central New South Wales, Australia, Corey Wall

Geosciences Faculty Publications and Presentations

The Hera Au–Pb–Zn–Ag deposit in the southeastern Cobar Basin of central New South Wales preserves calc-silicate veins and remnant sandstone/carbonate-hosted skarn within a reduced anchizonal Siluro-Devonian turbidite sequence. The skarn orebody distribution is controlled by a long-lived, basin margin fault system, that has intersected a sedimentary horizon dominated by siliciclastic turbidite, with lesser gritstone and thick sandstone intervals, and rare carbonate-bearing stratigraphy. Foliation (S1) envelopes the orebody and is crosscut by a series of late-stage east–west and north–south trending faults. Skarn at Hera displays mineralogical zonation along strike, from southern spessartine–grossular–biotite–actinolite-rich associations, to central diopside-rich–zoisite–actinolite/tremolite–grossular-bearing associations, through to the northern …

Synchronous Emplacement Of The Anorthosite Xenolith-Bearing Beaver River Diabase And One Of The Largest Lava Flows On Earth, Yiming Zhang, Nicholas L. Swanson-Hysell, Mark D. Schmitz, James D. Miller, Margaret S. Avery

Geosciences Faculty Publications and Presentations

New geochronologic and paleomagnetic data from the North American Midcontinent Rift (MCR) reveal the synchronous emplacement of the Beaver River diabase, the anorthosite xenoliths within it, and the Greenstone Flow—one of the largest lava flows on Earth. A U-Pb zircon date of 1091.83 ± 0.21 Ma (2σ) from one of the anorthosite xenoliths is consistent with the anorthosite cumulate forming as part of the MCR and provides a maximum age constraint for the Beaver River diabase. Paired with the minimum age constraint of a cross-cutting Silver Bay intrusion (1091.61 ± 0.14 Ma; 2σ), these data tightly …