Rice University Research Repository
The Rice Research Repository (R-3) provides access to research produced at Rice University, including theses and dissertations, journal articles, research center publications, datasets, and academic journals. Managed by Fondren Library, R-3 is indexed by Google and Google Scholar, follows best practices for preservation, and provides DOIs to facilitate citation. Woodson Research Center collections, including Rice Images and Documents and the Task Force on Slavery, Segregation, and Racial Injustice, have moved here.
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Theoretical study of adsorption properties and CO oxidation reaction on surfaces of higher tungsten boride
(Springer Nature, 2024) Radina, Aleksandra D.; Baidyshev, Viktor S.; Chepkasov, Ilya V.; Matsokin, Nikita A.; Altalhi, Tariq; Yakobson, Boris I.; Kvashnin, Alexander G.
Most modern catalysts are based on precious metals and rear-earth elements, making some of organic synthesis reactions economically insolvent. Density functional theory calculations are used here to describe several differently oriented surfaces of the higher tungsten boride WB5-x, together with their catalytic activity for the CO oxidation reaction. Based on our findings, WB5-x appears to be an efficient alternative catalyst for CO oxidation. Calculated surface energies allow the use of the Wulff construction to determine the equilibrium shape of WB5-x particles. It is found that the (010) and (101) facets terminated by boron and tungsten, respectively, are the most exposed surfaces for which the adsorption of different gaseous agents (CO, CO2, H2, N2, O2, NO, NO2, H2O, NH3, SO2) is evaluated to reveal promising prospects for applications. CO oxidation on B-rich (010) and W-rich (101) surfaces is further investigated by analyzing the charge redistribution during the adsorption of CO and O2 molecules. It is found that CO oxidation has relatively low energy barriers. The implications of the present results, the effects of WB5-x on CO oxidation and potential application in the automotive, chemical, and mining industries are discussed.
StratoMod: predicting sequencing and variant calling errors with interpretable machine learning
(Springer Nature, 2024) Dwarshuis, Nathan; Tonner, Peter; Olson, Nathan D.; Sedlazeck, Fritz J.; Wagner, Justin; Zook, Justin M.
Despite the variety in sequencing platforms, mappers, and variant callers, no single pipeline is optimal across the entire human genome. Therefore, developers, clinicians, and researchers need to make tradeoffs when designing pipelines for their application. Currently, assessing such tradeoffs relies on intuition about how a certain pipeline will perform in a given genomic context. We present StratoMod, which addresses this problem using an interpretable machine-learning classifier to predict germline variant calling errors in a data-driven manner. We show StratoMod can precisely predict recall using Hifi or Illumina and leverage StratoMod’s interpretability to measure contributions from difficult-to-map and homopolymer regions for each respective outcome. Furthermore, we use Statomod to assess the effect of mismapping on predicted recall using linear vs. graph-based references, and identify the hard-to-map regions where graph-based methods excelled and by how much. For these we utilize our draft benchmark based on the Q100 HG002 assembly, which contains previously-inaccessible difficult regions. Furthermore, StratoMod presents a new method of predicting clinically relevant variants likely to be missed, which is an improvement over current pipelines which only filter variants likely to be false. We anticipate this being useful for performing precise risk-reward analyses when designing variant calling pipelines.
Three-dimensional printing of wood
(AAAS, 2024) Thakur, Md Shajedul Hoque; Shi, Chen; Kearney, Logan T.; Saadi, M. A. S. R.; Meyer, Matthew D.; Naskar, Amit K.; Ajayan, Pulickel M.; Rahman, Muhammad M.
Natural wood has served as a foundational material for buildings, furniture, and architectural structures for millennia, typically shaped through subtractive manufacturing techniques. However, this process often generates substantial wood waste, leading to material inefficiency and increased production costs. A potential opportunity arises if complex wood structures can be created through additive processes. Here, we demonstrate an additive-free, water-based ink made of lignin and cellulose, the primary building blocks of natural wood, that can be used to three-dimensional (3D) print architecturally designed wood structures via direct ink writing. The resulting printed structures, after heat treatment, closely resemble the visual, textural, olfactory, and macro-anisotropic properties, including mechanical properties, of natural wood. Our results pave the way for 3D-printed wooden construction with a sustainable pathway to upcycle/recycle natural wood.
Spontaneous reversal of spin chirality and competing phases in the topological magnet EuAl4
(Springer Nature, 2024) Vibhakar, Anuradha M.; Khalyavin, Dmitry D.; Orlandi, Fabio; Moya, Jamie M.; Lei, Shiming; Morosan, Emilia; Bombardi, Alessandro
Materials exhibiting a spontaneous reversal of spin chirality have the potential to drive the widespread adoption of chiral magnets in spintronic devices. Unlike the majority of chiral magnets that require the application of an external field to reverse the spin chirality, we observe the spin chirality to spontaneously reverse in the topological magnet EuAl4. Using resonant elastic x-ray scattering we demonstrate that all four magnetic phases in EuAl4 are single-k, where the first two magnetic phases are characterized by spin density wave order and the last two by helical spin order. A single spin chirality was stabilised across the 1mm2 sample, and the reversal of spin chirality occurred whilst maintaining a helical magnetic structure. At the onset of the helical magnetism, the crystal symmetry lowers to a chiral monoclinic space group, explaining the asymmetry in the chiral spin order, and establishing a mechanism by which the spin chirality could reverse via magnetostructural coupling.
The Okjökull Memorial and Geohuman Relations
(Berghahn Books, 2024) Howe, Cymene; Boyer, Dominic
Focusing on the life and death of Okjökull, the first of Iceland's major glaciers to disappear because of anthropogenic climate change, this article discusses the complex relationships between cryospheres and human communities in Iceland. It asks how distinctions between non-living entities and living beings can offer insights to anthropology, and transdisciplinarily, as a model for recognising mutual precarities between the living and non-living world in the face of anthropogenic climate change. Detailing the authors’ ethnographic encounters with Ok mountain and Okjökull (glacier), the authors argue that by attending to non-living forms, and by registering their ‘passing’ or loss, we are able to document and better comprehend threshold events in the larger life of the planet. Résumé En se concentrant sur la vie et la mort d'Okjökull, le premier des principaux glaciers islandais à disparaître en raison des changements climatiques anthropogéniques, cet article discute les relations complexes entre la cryosphère et les communautés humaines en Islande. Il questionne la manière dont les distinctions entre entités non vivantes et êtres vivants peuvent offrir des perspectives à l'anthropologie et la transdisciplinarité en tant que modèle pour reconnaitre des précarités mutuelles entre monde vivant et non vivant en face du changement climatique anthropogénique. En détaillant la rencontre ethnographique entre les auteurs, la montagne Ok et l'Okjökull (le glacier), les auteurs défendent l'idée qu'en prenant acte des formes non vivantes et en marquant leur « disparition » ou leur perte, nous sommes en mesure de documenter et de mieux comprendre les événements de bascule dans la vie de notre planète.