Chemistry & Biochemistry Research Works
Permanent URI for this collectionhttp://hdl.handle.net/1903/15
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Item A Facile Synthesis of Bulk LiPON in Solution for Solid-State Electrolyte(2025) Gomez, Osma; Antar, Adam; Hall, Alex; Tapia-Aracayo, Leopoldo; Seo, Joshua; Kim, Nam; Sun, Zihan; Lim, Ryan; Chen, Fu; Li, Yue; Cumings, John; Rubloff, Gary; Lee, Sang Bok; Stewart, David; Wang, Yang; Lee, Sang Bok; Cumings, John; Rubloff, GaryItem Insoluble Acyclic Cucurbit[n]uril-Type Receptors Capture Iodine from the Vapor Phase(Wiley: Chemistry European Journal, 2024-09-27) Perera, Suvenika; Shaurya, Alok; Zeppuhar, Andrea; Chen, Fu; Zavalij, Peter Y.; Gaskell, Karen; Isaacs, Lyle; Isaacs, LyleNuclear energy makes large contributions toward meeting global energy needs, but societal concerns remain high given the impacts of the intended release of radioactive materials including 129I and 131I. In this paper we explore the use of a homologous series of acyclic CB[n] type hosts (H1–H4) as adsorbents of iodine from the vapor phase. We find that H2–H4, but not H1 – perform well in this application with uptake capacities of 2.2 g g−1, 1.5 g g−1, and 1.9 g g−1, respectively. The chemisorptive uptake process involves partial oxidation of catechol walled H2 to quinone walled host and capture of I3− and I5−. Solid H2 can be regenerated by treatment with Na2S2O4 and reused at least five times. The x-ray crystal structure of H2 is also reported.Item Acyclic Cucurbit[n]uril Bearing Alkyl Sulfate Ionic Groups - Electronic Supporting Data(Beilstein Journal of Organic Chemistry, 2025-01-09) Akakpo, Christian; Zavalij, Peter Y.; Isaacs, LyleThis dataset contains the electronic data files that support the publication.Item Quantifying modeling uncertainties in seismic analysis of dams: Insights from an international benchmark study(Wiley, 2023-12-19) Hariri-Ardebili, Mohammad AminAdvances in nonlinear dynamic analysis of dams have not completely resolved concerns over modeling confidence and analysis accuracy. Verification and validation offer accuracy assessment, but uncertainties persist during performance evaluation due to both epistemic (modeling) and aleatory (parametric) sources. Epistemic uncertainties arise from simplifications and modeling techniques. This paper addresses epistemic uncertainties in a gravity dam seismic analysis using data from the International Comnission on Large Dams (ICOLD) benchmark study. While the benchmark formulation included the finite element model of the dam, mechanical material properties, and dynamic loads, participants retained the flexibility to opt for best-practice modeling assumptions, simplifications, and other specifics. Notable response variability emerged, particularly in crack profiles and damage predictions. This study examines sources of variability, quantifying modeling uncertainty for the benchmark problem. More specifically, the modeling variability is quantified using the logarithmic standard deviation, also known as dispersion. This metric enables its incorporation into other seismic risk assessment and fragility studies. Under relatively low-intensity motion (peak ground acceleration [PGA] of 0.18 g in this case), modeling dispersion of 0.45, 0.30, 0.32, and 0.30 were calculated for the maximum dynamic crest displacement, maximum hydrodynamic pressure at the heel, heel and crest maximum acceleration, respectively. Additionally, the dispersion of the failure PGA was determined to be 0.7. Findings underscore the need for systematic seismic response modeling in dam engineering to enhance prediction accuracy. A better understanding of the sources and magnitudes of modeling uncertainties can help improve the reliability of dam seismic analysis and contribute to the development of more effective risk assessment and mitigation strategies.Item Comments regarding “Seismic damage analysis due to near-fault multipulse ground motion” by Guan Chen, Jiashu Yang, Ruohan Wang, Kaiqi Li, Yong Liu, Michael Beer; Earthquake Engineering & Structural Dynamics, 2023(Wiley, 2023-11-27) Hariri-Ardebili, Mohammad AminThis discussion is based on the paper by Chen et al. in 2023 (hereafter referred to as “the original paper/authors”). In their study, the original authors conducted a series of analyses using nonpulse, single-pulse, and multipulse ground motion records, evaluating their impact on a frame structure, a slope, and a gravity dam. Their key finding suggests that multipulse ground motion leads to more severe structural damage compared to nonpulse and single-pulse ground motions. However, it is important to note that the seismic damage analysis of the gravity dam in this paper does not adhere to state-of-the-practice recommendations. Consequently, drawing a definitive conclusion regarding the influence and importance of multipulse ground motion records on the seismic response of concrete dams requires further justification. This necessitates the incorporation of high-fidelity numerical models and probabilistic performance evaluation. We will discuss the significance of modeling assumptions, specifically addressing the dam–rock dynamic interaction in crack propagation and failure in dams.Item Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation(Springer Nature, 2023-11-08) Lemma, Betsegaw; Zhang, Di; Vamisetti, Ganga B.; Wentz, Bryan G.; Suga, Hiroaki; Brik, Ashraf; Lubkowski, Jacek; Fushman, DavidPost-translational modification of proteins with polyubiquitin chains is a critical cellular signaling mechanism in eukaryotes with implications in various cellular states and processes. Unregulated ubiquitin-mediated protein degradation can be detrimental to cellular homeostasis, causing numerous diseases including cancers. Recently, macrocyclic peptides were developed that selectively target long Lysine-48-linked polyubiquitin chains (tetra-ubiquitin) to inhibit ubiquitin-proteasome system, leading to attenuation of tumor growth in vivo. However, structural determinants of the chain length and linkage selectivity by these cyclic peptides remained unclear. Here, we uncover the mechanism underlying cyclic peptide's affinity and binding selectivity by combining X-ray crystallography, solution NMR, and biochemical studies. We found that the peptide engages three consecutive ubiquitins that form a ring around the peptide and determined requirements for preferential selection of a specific trimer moiety in longer polyubiquitin chains. The structural insights gained from this work will guide the development of next-generation cyclic peptides with enhanced anti-cancer activity.Item Structural modulation and spin glassiness upon oxidation in oxygen storage material LnFeMnO4+x for Ln = Y, Lu, and Yb(AIP, 2023-06-12) Li, Tianyu; Liou, Sz-Chian; Hong, Stephanie J.; Zhang, Qiang; Mandujano, H. Cein; Rodriguez, Efrain E.The mixed valence multiferroic LnFe2+Fe3+O4 (where Ln = Y, Lu, and Yb) can reversibly uptake oxygen into its lattice, which is evidenced by a crystallographic phase transition along with the appearance of structural modulations. In this study, we show that the Mn-substituted version of this multiferroic can also be readily oxidized to LnFe3+Mn3+O4.5 revealing similar oxygen storage behavior. Through neutron, electron, and synchrotron x-ray diffraction studies, we observe a structural modulation that we attribute to a displacement wave in the fully oxidized compound. This wave exhibits commensurability with a wavevector q = (−2/7, 1/7, 0). Bond valence summation analysis of plausible interstitial oxygen positions suggests that oxygen insertion likely occurs at the middle of the Fe/Mn–O bipyramid layers. The structural modulation of LnFeMnO4.5 is two-dimensional, propagates along the ab-plane, and is highly symmetric as 12 identical modulation vectors are observed in the diffraction patterns. The nature of the lanthanide, Ln3+, does not seem to influence such modulations since we observe identical satellite reflections for all three samples of Ln = Y, Lu, and Yb. Both LnFeMnO4 and LnFeMnO4.5 display spin glassy behavior with 2D short-range magnetic ordering being observed in LnFeMnO4. Analysis of the neutron diffraction data reveals a correlation length of ∼10 nm. Upon oxidation to LnFeMnO4.5, the short-range magnetic order is significantly suppressed.Item Cryptococcus neoformans Infection in the Central Nervous System: The Battle between Host and Pathogen(MDPI, 2022-10-12) Chen, Yanli; Shi, Zoe W.; Strickland, Ashley B.; Shi, MeiqingCryptococcus neoformans (C. neoformans) is a pathogenic fungus with a global distribution. Humans become infected by inhaling the fungus from the environment, and the fungus initially colonizes the lungs. If the immune system fails to contain C. neoformans in the lungs, the fungus can disseminate to the blood and invade the central nervous system, resulting in fatal meningoencephalitis particularly in immunocompromised individuals including HIV/AIDS patients. Following brain invasion, C. neoformans will encounter host defenses involving resident as well as recruited immune cells in the brain. To overcome host defenses, C. neoformans possesses multiple virulence factors capable of modulating immune responses. The outcome of the interactions between the host and C. neoformans will determine the disease progression. In this review, we describe the current understanding of how C. neoformans migrates to the brain across the blood–brain barrier, and how the host immune system responds to the invading organism in the brain. We will also discuss the virulence factors that C. neoformans uses to modulate host immune responses.Item Cryptococcal Immune Reconstitution Inflammatory Syndrome: From Clinical Studies to Animal Experiments(MDPI, 2022-12-07) Shi, Zoe W.; Chen, Yanli; Ogoke, Krystal M.; Strickland, Ashley B.; Shi, MeiqingCryptococcus neoformans is an encapsulated pathogenic fungus that initially infects the lung but can migrate to the central nervous system (CNS), resulting in meningoencephalitis. The organism causes the CNS infection primarily in immunocompromised individuals including HIV/AIDS patients, but also, rarely, in immunocompetent individuals. In HIV/AIDS patients, limited inflammation in the CNS, due to impaired cellular immunity, cannot efficiently clear a C. neoformans infection. Antiretroviral therapy (ART) can rapidly restore cellular immunity in HIV/AIDS patients. Paradoxically, ART induces an exaggerated inflammatory response, termed immune reconstitution inflammatory syndrome (IRIS), in some HIV/AIDS patients co-infected with C. neoformans. A similar excessive inflammation, referred to as post-infectious inflammatory response syndrome (PIIRS), is also frequently seen in previously healthy individuals suffering from cryptococcal meningoencephalitis. Cryptococcal IRIS and PIIRS are life-threatening complications that kill up to one-third of affected people. In this review, we summarize the inflammatory responses in the CNS during HIV-associated cryptococcal meningoencephalitis. We overview the current understanding of cryptococcal IRIS developed in HIV/AIDS patients and cryptococcal PIIRS occurring in HIV-uninfected individuals. We also describe currently available animal models that closely mimic aspects of cryptococcal IRIS observed in HIV/AIDS patients.Item Localized Photoactuation of Polymer Pens for Nanolithography(MDPI, 2023-01-25) Huang, Zhongjie; Li, Shaopeng; Zhang, Jiaqi; Pang, Huan; Ivankin, Andrey; Wang, YuhuangLocalized actuation is an important goal of nanotechnology broadly impacting applications such as programmable materials, soft robotics, and nanolithography. Despite significant recent advances, actuation with high temporal and spatial resolution remains challenging to achieve. Herein, we demonstrate strongly localized photoactuation of polymer pens made of polydimethylsiloxane (PDMS) and surface-functionalized short carbon nanotubes based on a fundamental understanding of the nanocomposite chemistry and device innovations in directing intense light with digital micromirrors to microscale domains. We show that local illumination can drive a small group of pens (3 × 3 over 170 µm × 170 µm) within a massively two-dimensional array to attain an out-of-plane motion by more than 7 µm for active molecular printing. The observed effect marks a striking three-order-of-magnitude improvement over the state of the art and suggests new opportunities for active actuation.