http://www.rssboard.org/rss-specification 720 https://escholarship.org/uc/uclachemeng_oapdeposits/rss Recent eScholarship items from Open Access Policy Deposits Mon, 22 Jun 2026 12:36:26 +0000 https://escholarship.org/uc/item/02r1233p <h4>Background and objective</h4>Lung cancer is a leading cause of cancer-related mortality, due to delayed diagnosis and the complexity of selecting the optimal treatment method, given the genetic diversity and heterogeneity of the disease. Traditional invasive techniques, such as tissue biopsy, carry risks of severe complications and are often costly. Therefore, there is increasing interest in non-invasive alternatives, particularly liquid biopsy. This review aims to propose promising circulating metabolite biomarkers for lung cancer and their clinical applications.<h4>Methods</h4>A PubMed search [2014-2024] was conducted, focusing on fluid-based, non-invasive samples such as blood, urine, pleural effusion, and bronchoalveolar lavage fluid. Only English-language articles relevant to lung cancer metabolomics were included.<h4>Key content and findings</h4>Analysis of altered metabolites in lung cancer patients revealed significant metabolic pathway enrichments. Upregulated pathways... https://escholarship.org/uc/item/02r1233p Thu, 21 May 2026 00:00:00 +0000 Kim, Su Yoon, Jiyeon Zhang, Jing Lee, Seong Ku, Bon Park, Jun Chung, Chaeuk Heo, Jun Kang, Yea Kang, Da https://escholarship.org/uc/item/9xt3z631 Abstract Understanding the atomistic structure and fluxionality of Pt nanoparticles under reactive conditions is essential for rational design of effective catalysts, yet their structural complexity presents a great challenge. In this work, we combine grand canonical global optimization methods and machine learning potentials to explore the atomistic landscape of nanometer‐sized (1∼2&nbsp;nm) Pt nanoparticles under a pressure of hydrogen, resulting in a comprehensive library of Pt x H y nanoparticles with over one million low‐energy metastable structures. We found that hydrogen adsorption drives a size‐dependent transformation from an amorphous to a crystalline structure, leading to sharp phase transitions for smaller nanoparticles and smooth transformations for larger ones. This behavior is governed by a competition between distinct core configurations, as well as the formation of rigid and fluxional local domains, where stability is dictated by specific surface motifs at low... https://escholarship.org/uc/item/9xt3z631 Thu, 12 Feb 2026 00:00:00 +0000 Chen, Dongxiao Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/9bv697m9 Hydrogen sulfide (H₂S) is a toxic and corrosive impurity present in industrial gas streams. An effective method for H₂S removal is through reactive sorption with metal oxides. This work investigates the reaction of H₂S on CuO surfaces to produce water and CuS. Using density functional theory (DFT), the elementary steps involved in H₂S adsorption and dissociation on the CuO (111) and (1̄11) surfaces are modelled. The three-coordinated oxygen atoms (O₃c) on CuO surfaces are highly reactive and facilitate H₂S dissociation at room temperature, whereas four-coordinated oxygen atoms (O₄c) are less reactive, requiring higher temperatures for effective H₂S dissociation. Partial sulfidation of the surface, however, stabilizes the substitution of O₄c by sulfur, making the dissociation of H₂S thermodynamically favorable but kinetically demanding at room temperature. Proton transfer... https://escholarship.org/uc/item/9bv697m9 Thu, 12 Feb 2026 00:00:00 +0000 Jiang, David Chiang, Nicole López-Ausens, Tirso Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/8gk6z6wd Electrochemical CO₂ reduction (CO₂R) in acidic membrane electrode assemblies (MEAs) represents a promising pathway for sustainable chemical production, but achieving high selectivity, low cell voltage and long-term stability remains challenging. Current approaches using alkali cations can promote selectivity through cationic effects, but relying on H₂O as a weak proton donor results in high overpotential and severe precipitation, causing elevated cell voltage and poor operational stability. Here, we introduce NH₄ ⁺ as a proton-donating cation that simultaneously addresses these challenges in acidic MEAs. As a cation, it electromigrates to the catalyst surface, stabilizing *CO₂ intermediates and reducing localized H⁺ concentration for high selectivity. As a proton donor, it provides superior proton-donating ability compared to H₂O when H⁺ mass transport is limited, which decreases... https://escholarship.org/uc/item/8gk6z6wd Thu, 12 Feb 2026 00:00:00 +0000 Feng, Shijia Liu, Ziang Cheng, Dongfang Hu, Yunfeng Chen, Sizhe Zhang, Xinyuan Li, Jiabao Dong, Xiaorui Wang, Tianyu Wang, Ziwei Wu, Yulun Yin, Ya Zheng, Hongzhi Sautet, Philippe Wang, Xiaojun Zhu, Jia https://escholarship.org/uc/item/7wb7v0cc The development of noble metal catalysts with sustained high activity for methanol oxidation is essential for chemical production and for energy transformation with methanol fuel cells. Here, we report Pt oxide clusters supported on anatase TiO2, exhibiting enhanced methanol oxidation performance. Interfacial interactions between oxidized Pt clusters and TiO2 strongly influence electronic states and adsorption of intermediates, thereby shaping catalytic performance. Density functional theory (DFT) combined with Fourier-transform infrared spectroscopy (FTIR) revealed methanol adsorption and oxidation mechanisms. Using grand canonical basin hopping (GCBH), we identified stable and metastable model Pt6O x clusters on TiO2(101), with Pt6 partially oxidized to Pt6O10 under ambient conditions. Three methanol oxidation pathways were examined: partial oxidation to CO, formation of methyl formate (HCOOCH3) by C–O coupling, and complete oxidation to CO2, proceeding via the *OCH2O (dioxymethylene... https://escholarship.org/uc/item/7wb7v0cc Thu, 12 Feb 2026 00:00:00 +0000 Dutta, Supriti Anderson, Kristin K Yousuf, Raian Karim, Ayman M Morris, John R Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/63b0v97x Light alkenes are central building blocks in the chemical industry, yet their production from alkanes requires energy-intensive processes that generate substantial CO₂ emissions and suffer from catalyst deactivation and overoxidation. In this work, we demonstrate that alkane dehydrogenation can be accomplished at ambient temperature and pressure by modulating the voltage applied to an electrocatalyst surface. Voltage manipulation provides real-time control over the adsorption and dehydrogenation of alkanes, as well as the potential-driven desorption of dehydrogenated adsorbates. By using a newly developed sensitive gas chromatographic (GC) analysis method, we were able to quantify the formation of 1-butene from <i>n</i>-butane, as well as the formation of a distribution of shorter chain alkanes and alkenes. We show that the product distribution depends on the potential applied during adsorption and is sensitive to both catalyst identity and electrolyte composition.... https://escholarship.org/uc/item/63b0v97x Thu, 12 Feb 2026 00:00:00 +0000 Zhang, Gong Fuller, Lee Lucky, Christine Zielinski, Alexander J Cheng, Dongfang Mendoza, Enner Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Schreier, Marcel https://escholarship.org/uc/item/5qc1t0h9 Au supported on TiO2 is a promising photocatalyst due to its ability to catalyze reactions under illumination and store electrons for sustained reactivity in the dark. Using density functional theory (DFT), we investigate the structural evolution and reactivity of the Au/anatase-TiO2(001) interface under realistic conditions. Phase diagrams and charge analysis reveal that the Au nanoparticles supported on TiO₂ (Au/TiO2) interface can reversibly store electrons by transitioning between different charge states and structures via oxidation and reduction. This electron storage and the associated reducing potential, along with the atomic arrangement, promote key photoelectrochemical reactions, such as the oxygen reduction reaction (ORR) and the CO2 reduction reaction (CO2RR). Lattice titanium and oxygen vacancies act as active sites, with the two-electron (2e)-ORR pathway (H2O2 formation) kinetically favored due to a lower proton-coupled electron transfer barrier. The interface also... https://escholarship.org/uc/item/5qc1t0h9 Thu, 12 Feb 2026 00:00:00 +0000 Li, Yichen Cheng, Dongfang Son, Giyeong Shneidman, Anna V Lim, Kang Rui Garrick Aizenberg, Joanna Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/5q85g2q8 Lithium-ion batteries have become indispensable in modern energy storage, with applications ranging from portable electronics to electric vehicles. Enhancing their performance is a critical area of research. In this study, the impact of surface aluminum doping in silicon electrodes on the formation of the solid electrolyte interphase (SEI) during the early stages of battery cycling is investigated. The reduction mechanism of ethylene carbonate, a key SEI precursor, is studied using density functional theory calculations including the influence of potential and modeling the solvent as a continuum. Energy diagrams, both with and without hybrid solvation effects, indicate that the presence of aluminum promotes thermodynamically favorable SEI formation and adsorption on silicon surfaces. Moreover, the presence of aluminum maintains the favorable kinetic characteristics observed in the undoped system. These effects could have important consequences in reducing unstable SEI growth by... https://escholarship.org/uc/item/5q85g2q8 Thu, 12 Feb 2026 00:00:00 +0000 Bhimineni, Sree Harsha Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/4wv4339s The nanoscale structure of electrocatalyst surfaces governs the selectivity and kinetics of reactions including CO₍₂₎ electroreduction (CO₍₂₎R). Yet, their evolution under reaction conditions remains elusive, and the roles of surface hydroxyls (OH_ad) and the interfacial microenvironment in surface restructuring are poorly understood. Combining electrochemical atomic force microscopy, Raman spectroscopy, and grand canonical modeling, we reveal that OH_ad acts synergistically with CO_ad to restructure copper (Cu) electrocatalysts during COR. Mixed OH_ad/CO_ad coverage promotes lifting of surface atoms into metastable states, generating Cu adatoms and nanoclusters at mild cathodic potentials, which aggregate or dissolve at more negative potentials. This restructuring into low-coordinated Cu sites is accompanied by disordering of the interfacial water network. Nanocluster stability depends critically on CO partial... https://escholarship.org/uc/item/4wv4339s Thu, 12 Feb 2026 00:00:00 +0000 Wei, Jie Zhang, Zisheng Gee, Winston Wei, Yu Zhou, Ya-Wei Herran, Matias Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 Cuenya, Beatriz Roldan Kley, Christopher S https://escholarship.org/uc/item/30p1p198 The interfacial structure and electronic properties of gold (Au) nanoclusters supported on anatase TiO2 surfaces are key determinants of catalytic and photocatalytic activity for Au/TiO2 systems. Here, we present an atomistic study of realistic, ∼1.5 nm Au nanoclusters on reconstructed TiO2(001) and (101) facets under ambient air conditions, bridging the gap between small supported cluster models and experimental catalysts. We focus on the ability of Au/TiO2 to store photogenerated electrons that can be used later in dark conditions. Leveraging a high-dimensional Au–Ti–O neural-network potential coupled with stochastic surface walking and DFT refinement, we exhaustively sampled atomic configurations over 120,000 minima. Two distinct interfacial motifs emergeType (i), with oxygen adsorbed on Ti sites near the Au nanocluster, and Type (ii), with oxygen occupying Au3 hollow sites. While both motifs stabilize clusters on both facets, Type (ii) is notably more prevalent on (101),... https://escholarship.org/uc/item/30p1p198 Thu, 12 Feb 2026 00:00:00 +0000 Liu, Qian-Yu Li, Yichen Chen, Dongxiao Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/2gd3p4pm Understanding the atomistic structure and fluxionality of Pt nanoparticles under reactive conditions is essential for rational design of effective catalysts, yet their structural complexity presents a great challenge. In this work, we combine grand canonical global optimization methods and machine learning potentials to explore the atomistic landscape of nanometer-sized (1∼2&nbsp;nm) Pt nanoparticles under a pressure of hydrogen, resulting in a comprehensive library of Pt_xH_y nanoparticles with over one million low-energy metastable structures. We found that hydrogen adsorption drives a size-dependent transformation from an amorphous to a crystalline structure, leading to sharp phase transitions for smaller nanoparticles and smooth transformations for larger ones. This behavior is governed by a competition between distinct core configurations, as well as the formation of rigid and fluxional local domains, where stability is dictated by specific surface motifs... https://escholarship.org/uc/item/2gd3p4pm Thu, 12 Feb 2026 00:00:00 +0000 Chen, Dongxiao Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/24x8t4f2 As the energy demands of the world continue to grow, the electroreduction of captured CO₂ (c-CO₂RR) is an appealing alternative to the traditional CO₂ reduction reaction (CO₂RR) as it does not include the energetically unfavorable release of CO₂ from the capture agent. In this tutorial we cover the motivation behind the c-CO₂RR and CO₂RR, their respective mechanisms, and computational tools that have been used to model these reactions and to compare their reactivities. Emphasis is given to methods that have already been used to model the c-CO₂RR but a comparison to the methods used to explore the more understood CO₂RR is covered as well. https://escholarship.org/uc/item/24x8t4f2 Thu, 12 Feb 2026 00:00:00 +0000 Kowalski, Robert Michael Cheng, Dongfang Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/0kw0q9gh In this study, we determine the role of oxygen vacancies and preferred surface orientation on the charge storage properties of the lithium intercalation host, pseudohexagonal TT-Nb2O5. Two different morphologies were synthesized, namely nanosheets and nanowires. We employed a set of advanced characterization techniques including entropic potential measurements, high-resolution synchrotron X-ray diffraction and synchrotron X-ray absorption spectroscopy together with electrochemical measurements and density functional theory calculations. Our results indicate that the two morphologies exhibit different oxygen vacancy characteristics as nanosheets have oxygen vacancies limited to the surface while nanowires possess vacancies which tend to be located in the bulk solid. Oxygen vacancies in the bulk of TT-Nb2O5 lead to an appreciable increase in specific capacity compared to nanosheets where oxygen vacancies confined to specific crystallographic surfaces do not make a significant contribution... https://escholarship.org/uc/item/0kw0q9gh Thu, 12 Feb 2026 00:00:00 +0000 Zambotti, Andrea Nkala, Gugulethu Charmaine Dutta, Supriti Bhimineni, Sree Harsha Leport, Nicolas Laperruque, Aimeric Weker, Johanna Nelson Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Pilon, Laurent Dunn, Bruce https://escholarship.org/uc/item/05j894tc We investigated the mechanisms underlying strong metal-support interactions in CO oxidation using model systems where noble metal crystals support reducible, monolayer-thick CoO x films. The effect of the Co oxidation state, film thickness, and substrate identity were studied in varying reaction conditions using ambient pressure X-ray photoelectron spectroscopy. At low O2 pressures, the same oxide phase forms on both Pt(111) and Au(111) surfaces. But when heated at higher O2 pressures, the oxide phase depends on the substrate. We found that CoO x /Pt is more active for the CO oxidation reaction than CoO x /Au, even when both surfaces stabilize the same oxide phase. DFT calculations on these and related noble-metal-supported CoO x films reveal an SMSI-induced reactivity enhancement that strongly depends on the oxide film thickness and which is mediated by charge transfer between the metal and oxide. Charge transfer is also found to correlate with the reaction energy and activation... https://escholarship.org/uc/item/05j894tc Thu, 12 Feb 2026 00:00:00 +0000 Yan, George Chen, Hao https://orcid.org/0000-0003-3759-8352 Nguyen, Huy van Spronsen, Matthijs A Morales, Carlos Waluyo, Iradwikanari Hunt, Adrian Nemsak, Slavomir https://orcid.org/0000-0002-6103-2925 Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Salmeron, Miquel https://orcid.org/0000-0002-2887-8128 Kersell, Heath https://escholarship.org/uc/item/03f8q60d Aqueous zinc-ion batteries (AZIBs) have been regarded as promising candidates for large-scale energy storage. However, the poor reversibility of Zn electrodeposition at low current densities still remains a great challenge in developing practical AZIBs. In this work, a localized eutectic electrolyte (LEE) is proposed by introducing trioxane to a baseline eutectic electrolyte, 2.0 M Zn-(OTf)₂ in water/sulfolane (50:50 vol %), for reversible Zn anodes under challenging conditions (low N/P ratios and low current densities). Trioxane serves to disperse the aqueous eutectic domain and construct a solvation-sheath-repelled inner Helmholtz plane, thus regulating charge transfer kinetics to enable further suppression of electrolyte corrosion and improved Zn morphology. Zn||Zn_0.25V₂O₅·<i>n</i>H₂O full cells with a low N/P ratio (≤4) and a low current density of 100 mA cathode^-1 (corresponding to a 0.33 C rate) exhibit enhanced... https://escholarship.org/uc/item/03f8q60d Thu, 12 Feb 2026 00:00:00 +0000 Lyu, Huida Kim, Jung Tae Cheng, Dongfang Yuan, Xintong Anderson, Mackenzie Liang, Keyue Yu, Jiayi Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Kaner, Richard https://orcid.org/0000-0003-0345-4924 Li, Yuzhang https://escholarship.org/uc/item/9r31p6s2 Reactive capture of CO2 (RCC) offers an integrated approach that combines CO2 capture with its direct electrochemical conversion, eliminating the need for CO2 release from the capture agent. By avoiding the pH, pressure, and temperature swings required for the release step, RCC has the potential to reduce both energy consumption and capital costs compared to the conventional sequential process of CO2 capture, release, concentration, and conversion. Amines, widely used in industrial CO2 capture, face challenges in RCC systems due to their incompatibility with transition metal catalysts as well as their tendency to promote electrode corrosion and parasitic hydrogen evolution. Identifying suitable combinations of amines and catalysts is therefore critical to enabling integrated CO2 capture and conversion. This work systematically investigates the performance of four primary and four secondary amines for RCC on polycrystalline Cu catalysts. Among the eight tested amines, only dimethylamine... https://escholarship.org/uc/item/9r31p6s2 Fri, 21 Nov 2025 00:00:00 +0000 Choi, Jounghwan Banerjee, Avishek Ross, R Dominic Zhang, Zisheng Chiu, Shawn https://orcid.org/0009-0000-1927-0455 Sacci, Robert L Veith, Gabriel M Hahn, Christopher https://orcid.org/0000-0002-2772-6341 Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 Morales-Guio, Carlos G https://escholarship.org/uc/item/95h7v9g8 The dynamic restructuring of Cu surfaces under electrochemical CO₂ reduction conditions is crucial for determining their catalytic performance, particularly for multicarbon products such as ethylene and propanol. Temperature strongly influences this restructuring, yet its effect on surface states and CO₂RR selectivity remains unclear. Here, we explore the chemical space of Cu under CO and H coverage at different temperatures, including the change in adsorbate-induced surface roughening, by combining grand canonical DFT with global optimization methods to construct a potential-dependent grand canonical ensemble. By tuning the temperature, we modulate adsorbate chemical potentials, which alters the accessible surface states. Quasi-kinetic Monte Carlo simulations track the system's evolution during a simulated cathodic scan, revealing metastable structures at the CO₂RR onset potential (-1.1 V vs RHE). Our results show that increasing temperature tends... https://escholarship.org/uc/item/95h7v9g8 Fri, 21 Nov 2025 00:00:00 +0000 Wei, Yu Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 https://escholarship.org/uc/item/71r3g5gx The activity of aqueous-based carbon dioxide reduction (CO₂R) reactions is often limited by the solubility of CO₂. The addition of amines can increase the total dissolved carbon in water through the formation of bicarbonate and carbamate species, which has been used to a great effect to capture CO₂ from dilute streams. In this study, we explore the effect of 12 primary and secondary amines of varying Brønsted basicity, steric profile, and hydrogen-bonding capabilities on the aqueous CO₂R to CO activity of a molecular Ni(cyclam)Cl₂ catalyst with a Hg electrode. Addition of some of the amines results in greater activity and selectivity for CO production compared to equivalent aqueous solutions without added amines. Under optimal conditions (0.4 M 3-amino-propionitrile), there is an over sevenfold increase in partial current density and greater selectivity for CO compared to equivalent conditions with no amine. Interestingly,... https://escholarship.org/uc/item/71r3g5gx Fri, 21 Nov 2025 00:00:00 +0000 Mir, Qayoom Banerjee, Avishek Ihiri, Ferdawss Chiu, Shawn https://orcid.org/0009-0000-1927-0455 Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 Morales-Guio, Carlos Yang, Jenny Y https://orcid.org/0000-0002-9680-8260 https://escholarship.org/uc/item/0k4350sq Antibiotic resistance among Gram-negative organisms is a major challenge. Some molecules, including antimicrobial peptides such as polymyxin B (PMB), are antibacterial but toxic due to low specificity, causing poor clinical utility. Drug delivery to bacterial cells using a biocompatible nanomaterial is a possible approach to securing such drugs. We engineered a nonlytic phage to recognize the lipopolysaccharide of Gram-negative bacteria and cross-linked thousands of peptides per virion, making "PMB-M13^αLPS". PMB-M13^αLPS reduced the minimum inhibitory concentration <i>in vitro</i> by ∼2 orders of magnitude across multiple pathogen strains. Immunocompetent mice with multidrug-resistant <i>P. aeruginosa</i> pneumonia or corneal infection were effectively treated by PMB-M13^αLPS, which showed potency ∼2 orders of magnitude greater <i>in vivo</i> compared to that of PMB. PMB-M13^αLPS was well-tolerated, with no toxic effects. Conjugates of... https://escholarship.org/uc/item/0k4350sq Wed, 27 Aug 2025 00:00:00 +0000 Yang, Yanxi Vexler, Shelby Jordan, Maria C Abbondante, Serena Kang, Dayeon Peng, Huan Marshall, Michaela Naini, Bita V Jain, Saumya Lai, Yei-Chen Annabi, Nasim https://orcid.org/0000-0003-1879-1202 Roos, Kenneth P https://orcid.org/0000-0002-2823-5069 Pearlman, Eric https://orcid.org/0000-0003-0137-7582 Chen, Irene A https://orcid.org/0000-0001-6040-7927 https://escholarship.org/uc/item/03n6q3b3 From pages to patterns: Towards extracting catalytic knowledge from structure and text for transition-metal complexes and metal-organic frameworks https://escholarship.org/uc/item/03n6q3b3 Wed, 13 Aug 2025 00:00:00 +0000 Nandy, Aditya https://escholarship.org/uc/item/92q2w69m Propylene oxide, a key commodity of the chemical industry for a wide range of consumer products, is synthesized through sequential propane dehydrogenation and epoxidation reactions. However, the lack of a direct catalytic route from propane to propylene oxide reduces efficiency and represents a major challenge for catalysis science. Herein, we report the discovery of a highly active and selective catalyst, made of alumina-supported subnanometer copper clusters, which can directly convert propane to propylene oxide at temperatures as low as 150 °C. Moreover, at higher temperatures, on the same catalysts, the selectivity is switched to propylene. Accompanying theoretical calculations indicate that partially oxidized and/or hydroxylated clusters have low activation energies for both propane dehydrogenation and propylene epoxidation pathways, enabling direct conversion with very high selectivity for propylene oxide. The discovery of a low-temperature catalyst that can convert propane... https://escholarship.org/uc/item/92q2w69m Wed, 21 May 2025 00:00:00 +0000 Halder, Avik Warburton, Robert E Sun, Geng Cheng, Lei Assary, Rajeev S Seifert, Soenke Homer, Micaela Greeley, Jeffrey Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Curtiss, Larry A Vajda, Stefan https://escholarship.org/uc/item/6r32d8v4 Experiments and theory are combined to search for catalyst activity and stability descriptors for the direct reactive capture and conversion (RCC) of CO₂ in ammonia capture solutions using Cu, Ag, Au, Sn, and Ti electrodes. Two major phenomena emerge in RCC that are not predominant in the electrochemical CO₂ reduction (CO₂R) reaction, namely, the rapid corrosion and restructuring of the catalyst in the presence of the CO₂-ammonia adducts and the promotion of the competing hydrogen evolution reaction (HER). The prevalence of HER in RCC is correlated to the electrostatic attraction of the protonated amine to the electrode and the repulsion of the captured CO₂, using the potential of zero charge (PZC). The stability of catalysts under RCC conditions is a function of the applied potential and cannot be readily predicted using binding energy descriptors commonly used in the prediction of CO₂R activity. A direct correlation... https://escholarship.org/uc/item/6r32d8v4 Wed, 21 May 2025 00:00:00 +0000 Choi, Jounghwan Chiu, Shawn https://orcid.org/0009-0000-1927-0455 Banerjee, Avishek Sacci, Robert L Veith, Gabriel M Stieber, Chantal Hahn, Christopher https://orcid.org/0000-0002-2772-6341 Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 Morales-Guio, Carlos G https://escholarship.org/uc/item/6h42n4zv By hydrogenating carbon dioxide to value-added products such as methanol, heterogeneous catalysts can lower greenhouse gas emissions and generate alternative liquid fuels. The most common commercial catalyst for the reduction of CO₂ to methanol is Cu/ZnO/Al₂O₃, where ZnO improves conversion and selectivity toward methanol. The structure of this catalyst is thought to be Zn oxy(hydroxyl) overlayers on the nanometer scale on Cu. In the presence of CO₂ and H₂ under reaction conditions, the Cu substrate itself can be restructured and/or partially oxidized at its interface with ZnO, or the Zn might be reduced, possibly completely to a CuZn alloy, making the exact structure and stoichiometry of the active site a topic of active debate. In this study, we examine Zn₃ clusters on Cu(100) and Cu(111), as a subnano model of the catalyst. We use a grand canonical genetic algorithm to sample the system structure and stoichiometry... https://escholarship.org/uc/item/6h42n4zv Wed, 21 May 2025 00:00:00 +0000 Lavroff, Robert H Cummings, Edison Sawant, Kaustubh https://orcid.org/0000-0002-9599-3126 Zhang, Zisheng Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 https://escholarship.org/uc/item/5934197w The significant increase in CO₂ emissions from heavy fossil fuel utilization has raised serious concerns, highlighting the need for effective methods to convert CO₂ into value-added chemicals. Here, we report a computational investigation on the catalytic activity of ZrO₂-on-Cu inverse catalysts for CO₂ hydrogenation to methanol, considering highly dispersed ZrO₂ trimers on Cu (111). Such clusters present a large ensemble of formate-containing configurations, Zr₃O_<i>n</i>(OH)_<i>m</i>(OCHO)_<i>l</i>, making the evaluation of the catalytic activity very challenging. We found that the sites on the various catalyst configurations exhibit markedly different activities for formate hydrogenation, despite their similar free energy and composition. To understand these differences in reactivity, we examined the structural and electronic nature of the low free-energy catalyst configurations... https://escholarship.org/uc/item/5934197w Wed, 21 May 2025 00:00:00 +0000 Yang, Zihan Kumari, Simran Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/30g079nh Cu is the most promising metal catalyst for CO2 electroreduction (CO2RR) to multi-carbon products, yet the structure sensitivity of the reaction and the stability versus restructuring of the catalyst surface under reaction conditions remain controversial. Here, atomic scale simulations of surface energies and reaction pathway kinetics supported by experimental evidence unveil that CO2RR does not take place on perfect planar Cu(111) and Cu(100) surfaces but rather on steps or kinks. These planar surfaces tend to restructure in reaction conditions to the active stepped surfaces, with the strong binding of CO on defective sites acting as a thermodynamic driving force. Notably, we identify that the square motifs adjacent to defects, not the defects themselves, as the active sites for CO2RR via synergistic effect. We evaluate these mechanisms against experiments of CO2RR on ultra-high vacuum-prepared ultraclean Cu surfaces, uncovering the crucial role of step-edge orientation in steering... https://escholarship.org/uc/item/30g079nh Wed, 21 May 2025 00:00:00 +0000 Cheng, Dongfang Nguyen, Khanh-Ly C Sumaria, Vaidish Wei, Ziyang Zhang, Zisheng Gee, Winston Li, Yichen Morales-Guio, Carlos G Heyde, Markus Roldan Cuenya, Beatriz Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/1k15663x Photon-driven catalytic reactions have long been explored as a way to reduce emissions by replacing fossil-fuel-derived process heat with solar energy. Light-harvesting plasmonic metal nanoparticles are promising photocatalysts because they can drive kinetically unfavorable reactions through combined non-thermal (hot charge carrier) and photothermal effects under illumination. Understanding the interplay between these effects is critical for optimizing these materials for sustainable photochemical production processes. Unfortunately, the simultaneous presence of these two mechanisms under relevant photocatalytic operating conditions has led to fierce debate in the plasmonic catalysis community about the relative contributions of each. This perspective examines frequently overlooked concepts when attempting to disentangle thermal and non-thermal effects in plasmon-driven, gas-phase heterogeneous photocatalysis. We focus on the rising use of hybrid plasmonic (antenna-reactor) materials,... https://escholarship.org/uc/item/1k15663x Wed, 21 May 2025 00:00:00 +0000 Chavez, Steven Acharya, Anubhab Dehghan, Zhila https://escholarship.org/uc/item/5bn5c9f0 Techno-economic analysis of distributed wellhead water treatment and desalination (DWTD) systems was carried out based on a three-year field study in three small, disadvantaged communities (DACs) to evaluate the reliability and affordability of upgrading their impaired well water. The local water supplies of the three study DACs, located in Salinas Valley, California, were contaminated with nitrate at levels (∼ 12-87 mg/L NO₃^--N) above the California maximum contaminant level (MCL) of 10 mg/L NO₃^--N, and had elevated water salinity (∼600-1,600 mg/L total dissolved solids(TDS)) above its secondary MCL (SMCL) of 500 mg/L TDS. Well water nitrate removal and salinity reduction were accomplished via reverse osmosis (RO) based DWTD systems that operated autonomously, supported by remote monitoring and supervisory cyberinfrastructure. Reliable DWTD operation provided treated water quality, with respect to nitrate and salinity, in the range... https://escholarship.org/uc/item/5bn5c9f0 Tue, 13 May 2025 00:00:00 +0000 Cohen, Yoram Soto, Maria Marki, Nora Jarma, Yakubu A Glickfeld, Madelyn Rogers, Mitchell Yip, Kenny Strauss, Phoebe Aguilar, Christian Khan, Bilal Rao, Prakash Hendrickson, Thomas https://orcid.org/0009-0003-8637-9612 https://escholarship.org/uc/item/8sr4w70n The nucleolus, once considered a mere 'ribosome factory', is now recognized as a dynamic hub influencing nearly every aspect of cellular life, from genome organization to stress response and ageing. Despite being a hallmark of eukaryotic cells, recent discoveries reveal that even prokaryotes exhibit nucleolus-like structures, hinting at ancient origins for nucleolar functions. This review explores the evolutionary journey of the nucleolus, tracing its roots back to early life and examining its structural and functional diversity across domains. We highlight key nucleolar proteins that play vital roles not only in ribosome production but also in regulating cell cycle, DNA repair and cellular stress, linking nucleolar activity directly to health and disease. Dysfunctions in nucleolar processes are implicated in cancer, ribosomopathies and neurodegenerative disorders, positioning the nucleolus as a critical target for innovative therapeutic strategies. As advanced imaging and molecular... https://escholarship.org/uc/item/8sr4w70n Thu, 3 Apr 2025 00:00:00 +0000 Muñoz-Velasco, Israel Herrera-Escamilla, Ana Karen Vázquez-Salazar, Alberto https://escholarship.org/uc/item/2hp8q383 Apart from conventional redox chemistries, exploring high-voltage anionic redox processes, such as pure oxygen or high-valent transition metal ion redox, poses challenges due to the instability of O nonbonding or O-dominant energy states. These states are associated with destructive behaviors in layered oxide cathodes, including local structural distortion, cationic disordering, and oxygen gas evolution. In this study, we suppress first-cycle voltage hysteresis and irreversible O2 evolution in Li-rich oxide cathodes through covalency competition induced by the substitution of electropositive groups. We found that the nonequivalent electron distribution within an asymmetric MA-O-MB backbone (metal-to-metal charge transfer via oxygen ligands) increases electron density on electronegative transition metal ions, preventing them from reaching unstable oxidation states within an operating voltage range. This phenomenon is observed across diverse transition metal combinations, providing... https://escholarship.org/uc/item/2hp8q383 Tue, 1 Apr 2025 00:00:00 +0000 Kim, Min-Ho Jang, Haeseong Lee, Eunryeol Seo, Jeongwoo Park, Jaehyun Choi, Ahreum Kim, Taewon Choi, Myeongjun Kim, Euna Jung, Yeong Kang, Seok Cho, Jaephil Li, Yuzhang Kim, Min Seo, Dong-Hwa Lee, Hyun-Wook https://escholarship.org/uc/item/9mc5k1wk On-purpose atomic scale design of catalytic sites, specifically active and selective at low temperature for a target reaction, is a key challenge. Here, we report teamed Pd₁ and Mo₁ single-atom sites that exhibit high activity and selectivity for anisole hydrodeoxygenation to benzene at low temperatures, 100-150 °C, where a Pd metal nanoparticle catalyst or a MoO₃ nanoparticle catalyst is individually inactive. The catalysts built from Pd₁ or Mo₁ single-atom sites alone are much less effective, although the catalyst with Pd₁ sites shows some activity but low selectivity. Similarly, less dispersed nanoparticle catalysts are much less effective. Computational studies show that the Pd₁ and Mo₁ single-atom sites activate H₂ and anisole, respectively, and their combination triggers the hydrodeoxygenation of anisole in this low-temperature range. The Co₃O₄ support... https://escholarship.org/uc/item/9mc5k1wk Thu, 27 Mar 2025 00:00:00 +0000 Tang, Yu Yan, George Zhang, Shiran Li, Yuting Nguyen, Luan Iwasawa, Yasuhiro Sakata, Tomohiro Andolina, Christopher Yang, Judith C Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Tao, Franklin Feng https://escholarship.org/uc/item/9jq993x6 The electrochemical hydrogenation (e-hydrogenation) of unsaturated compounds like imines or carbonyls presents a benign reduction method. It enables direct use of electrons as reducing agent, water as proton source, while bypassing the need for elevated temperatures or pressures. In this contribution, we discuss the active species in electrocatalytic reductive amination with the transformation of acetone and methylamine as model reaction. Surprisingly, lead impurities in the ppm-range proved to possess a significant effect in e-hydrogenation. Accordingly, the influence of applied potential and cathode material in presence of 1 ppm Pb was investigated. Finally, we transferred the insights to the reduction of acetone manifesting comparable observations as for imine reduction. The results suggest that previous studies on electrochemical reduction in the presence of lead electrodes should be re-evaluated. https://escholarship.org/uc/item/9jq993x6 Thu, 27 Mar 2025 00:00:00 +0000 Kümper, Justus Mürtz, Sonja D Guan, Yani Kumari, Simran Hausoul, Peter JC Kurig, Nils Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Palkovits, Regina https://escholarship.org/uc/item/8nv3k061 The protonation of CO is recognized as the rate-determining step in the generation of C1 products during the electrochemical CO₂ reduction reaction (CO₂RR) on Cu surfaces. However, the detailed mechanism and the precise proton source remain elusive. While density functional theory (DFT) calculations at the GGA level have been widely used, they struggle to accurately describe adsorbate-metal interactions and surface stability. Here, we employed the Random Phase Approximation (RPA), a method based on many-body perturbation theory, to overcome these limitations. We coupled the RPA framework with the linearized Poisson-Boltzmann equation to model solvation effects and a surface charging method to account for the influence of the electrochemical potential. Our study reveals that in neutral or alkaline electrolytes, adsorbed surface water acts as the proton source for *CO reduction to *COH over a broad potential range via the Grotthuss mechanism. At highly negative... https://escholarship.org/uc/item/8nv3k061 Thu, 27 Mar 2025 00:00:00 +0000 Cheng, Dongfang Wei, Ziyang Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/6r97b49v Engineering battery corrosion films by tuning electrical double layer composition https://escholarship.org/uc/item/6r97b49v Thu, 27 Mar 2025 00:00:00 +0000 Yuan, Xintong Cheng, Dongfang Liu, Bo Liang, Kaiyan Liang, Keyue Yu, Jiayi Mecklenburg, Matthew Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Li, Yuzhang https://escholarship.org/uc/item/6q29475k Facet-Dependence of Electron Storage in Gold-Decorated Titania Nanocrystals https://escholarship.org/uc/item/6q29475k Thu, 27 Mar 2025 00:00:00 +0000 Son, Giyeong Li, Yichen Shneidman, Anna V Han, Jae Hyo Aizenberg, Michael Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Aizenberg, Joanna https://escholarship.org/uc/item/5n97m88g Effect of water impurities on promoted and unpromoted cobalt-catalysts during the ammonia decomposition reaction https://escholarship.org/uc/item/5n97m88g Thu, 27 Mar 2025 00:00:00 +0000 Almisbaa, Zahra Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/4pq0p7xv Hydrogen Dissociation Controls 1‑Hexyne Selective Hydrogenation on Dilute Pd-in-Au Catalysts https://escholarship.org/uc/item/4pq0p7xv Thu, 27 Mar 2025 00:00:00 +0000 Ngan, Hio Tong Yan, George van der Hoeven, Jessi ES Madix, Robert J Friend, Cynthia M Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/4f9756jh Supported Pd-Au bimetallic nanoparticles make up a promising class of catalysts used for hydrogenation and oxidation reactions. Recently, the role of dynamic restructuring of Pd regions at and near the nanoparticle surface in response to modulating gas (H₂ and O₂) concentrations was highlighted for controlling the surface Pd oxide stoichiometry. Here, we investigate the mechanism of formation and decomposition of Pd hydride (PdH_<i>x</i>) at and near the bimetallic nanoparticle surfaces, a key species for controlling the activity, selectivity, and stability of Pd catalysts in many hydrogenation reactions. We employ modulation excitation X-ray absorption spectroscopy (ME-XAS) to directly observe the time scale of PdH_<i>x</i> formation and decomposition on the surface of Pd-Au nanoparticles. Density functional theory (DFT) calculations provide additional insights into the stability and energetics of PdH_<i>x</i> formation under... https://escholarship.org/uc/item/4f9756jh Thu, 27 Mar 2025 00:00:00 +0000 Routh, Prahlad K Liu, Xihan Redekop, Evgeniy Lim, Jin Soo Prodinger, Sebastian van der Hoeven, Jessi ES Aizenberg, Joanna Nachtegaal, Maarten Clark, Adam H Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Frenkel, Anatoly I https://escholarship.org/uc/item/32b3x1m5 Influence of Pd Concentration in Au–Pd Nanoparticles for the Hydrogenation of Alkynes https://escholarship.org/uc/item/32b3x1m5 Thu, 27 Mar 2025 00:00:00 +0000 Foucher, Alexandre C Ngan, Hio Tong Shirman, Tanya Filie, Amanda Duanmu, Kaining Aizenberg, Michael Madix, Robert J Friend, Cynthia M Aizenberg, Joanna Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Stach, Eric A https://escholarship.org/uc/item/1gr0f68z In traditional hydrogenation, where H₂ and substrates with unsaturated bonds are activated on the same catalyst (contact mode), competitive hydrogenation of multiple reducible groups often occurs. We employ an unbiased H-cell for selective hydrogenation of the nitro group when multiple reducible groups are present. The setup spatially separates H₂ and nitroarenes into two chambers connected by a proton-exchange membrane, thus adding barriers for a Langmuir-Hinshelwood-type mechanism that is common in thermocatalytic hydrogenation. Through a unique proton/electron transfer pathway that is specific to nitro functional group reduction to hydroxylamine, side reactions like C═C, C═O, and C≡C bond hydrogenation are fully avoided. Using Pd/C for H₂ activation, and CNT for selective proton/electron transfer to -NO₂ groups while being inert to C≡C, C═C, and C═O hydrogenation, the system effectively eliminates the competitive hydrogenation, achieving... https://escholarship.org/uc/item/1gr0f68z Thu, 27 Mar 2025 00:00:00 +0000 An, Hua Ding, Yani Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Sun, Geng Yan, Ning https://escholarship.org/uc/item/0t504452 Heterogeneous catalysis is key for chemical transformations. Understanding how catalysts' active sites dynamically evolve at the atomic scale under reaction conditions is a prerequisite for accurately determining catalytic mechanisms and predictably developing catalysts. We combine in situ time-dependent scanning tunneling microscopy observations and machine-learning-accelerated first-principles atomistic simulations to uncover the mechanism of restructuring of Pt catalysts under a pressure of carbon monoxide (CO). We show that a high CO coverage at a Pt step edge triggers the formation of atomic protrusions of low-coordination Pt atoms, which then detach from the step edge to create sub-nano-islands on the terraces, where under-coordinated sites are stabilized by the CO adsorbates. The fast and accurate machine-learning potential is key to enabling the exploration of tens of thousands of configurations for the CO-covered restructuring catalyst. These studies open an avenue to... https://escholarship.org/uc/item/0t504452 Thu, 27 Mar 2025 00:00:00 +0000 Sumaria, Vaidish Nguyen, Luan Tao, Franklin Feng Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/3cm310zb Glycolysis is a universal metabolic process that breaks down glucose to produce adenosine triphosphate (ATP) and biomass precursors. The Entner–Doudoroff (ED) pathway is a glycolytic pathway that parallels textbook glycolysis but yields half as much ATP. Accordingly, in organisms that possess both glycolytic pathways (for example, Escherichia coli), its raison dʼêtre remains a mystery. In this study, we found that the ED pathway provides a selective advantage during growth acceleration. Upon carbon and nitrogen upshifts, E. coli accelerates growth faster with than without the ED pathway. Concurrent isotope tracing reveals that the ED pathway flux increases faster than that of textbook glycolysis. We attribute the fast response time of the ED pathway to its strong thermodynamic driving force and streamlining of glucose import. Intermittent nutrient supply manifests the evolutionary advantage of the parallel glycolysis; thus, the dynamic nature of an ostensibly redundant pathway’s... https://escholarship.org/uc/item/3cm310zb Wed, 19 Mar 2025 00:00:00 +0000 Law, Richard C https://orcid.org/0000-0002-4944-9306 Nurwono, Glenn Park, Junyoung O https://orcid.org/0000-0001-9869-8993 https://escholarship.org/uc/item/206867bm Antimicrobial resistance remains a critical global health concern, necessitating the investigation of alternative therapeutic approaches. With the diminished efficacy of conventional small molecule drugs due to the emergence of highly resilient bacterial strains, there is growing interest in the potential for alternative therapeutic modalities. As naturally occurring viruses of bacteria, bacteriophage (or phage) are being re-envisioned as a platform to engineer properties that can be tailored to target specific bacterial strains and employ diverse antibacterial mechanisms. However, limited understanding of key pharmacological properties of phage is a major challenge to translating its use from preclinical to clinical settings. Here, we review modern advancements in phage-based antimicrobial therapy and discuss the in vivo pharmacokinetics and biodistribution of phage, addressing critical challenges in their application that must be overcome for successful clinical implementation. https://escholarship.org/uc/item/206867bm Wed, 19 Mar 2025 00:00:00 +0000 Kang, Dayeon Bagchi, Damayanti Chen, Irene A https://orcid.org/0000-0001-6040-7927 https://escholarship.org/uc/item/1zg4c2sz Metabolism is an indispensable part of T cell proliferation, activation and exhaustion, yet the metabolism of chimeric antigen receptor (CAR)-T cells remains incompletely understood. CARs are composed of extracellular domains—often single-chain variable fragments (scFvs)—that determine ligand specificity and intracellular domains that trigger signalling following antigen binding. Here, we show that CARs differing only in the scFv variously reprogramme T cell metabolism. Even without exposure to antigens, some CARs increase proliferation and nutrient uptake in T cells. Using stable isotope tracers and mass spectrometry, we observed basal metabolic fluxes through glycolysis doubling and amino acid uptake overtaking anaplerosis in CAR-T cells harbouring a rituximab scFv, unlike other similar anti-CD20 scFvs. Disparate rituximab and 14G2a-based anti-GD2 CAR-T cells are similarly hypermetabolic and channel excess nutrients to nitrogen overflow metabolism. Modest overflow metabolism... https://escholarship.org/uc/item/1zg4c2sz Sat, 1 Mar 2025 00:00:00 +0000 Lakhani, Aliya Chen, Ximin Chen, Laurence C Hong, Mihe Khericha, Mobina Chen, Yu Chen, Yvonne Y Park, Junyoung O https://orcid.org/0000-0001-9869-8993 https://escholarship.org/uc/item/88z9z2x1 One of the earliest living systems was likely based on RNA ("the RNA world"). Mineral surfaces have been postulated to be an important environment for the prebiotic chemistry of RNA. In addition to adsorbing RNA and thus potentially reducing the chance of parasitic takeover through limited diffusion, minerals have been shown to promote a range of processes related to the emergence of life, including RNA polymerization, peptide bond formation, and self-assembly of vesicles. In addition, self-cleaving ribozymes have been shown to retain activity when adsorbed to the clay mineral montmorillonite. However, simulation studies suggest that adsorption to minerals is likely to interfere with RNA folding and, thus, function. To further evaluate the plausibility of a mineral-adsorbed RNA world, here we studied the effect of the synthetic clay montmorillonite K10 on the malachite green RNA aptamer, including binding of the clay to malachite green and RNA, as well as on the formation of secondary... https://escholarship.org/uc/item/88z9z2x1 Thu, 27 Feb 2025 00:00:00 +0000 Saha, Ranajay Kao, Wei-Ling Malady, Brandon Heng, Xiao Chen, Irene A https://orcid.org/0000-0001-6040-7927 https://escholarship.org/uc/item/0p74029d Facing the global "superbug" crisis due to the emergence and selection for antibiotic resistance, phages are among the most promising solutions. Fighting multidrug-resistant bacteria requires precise diagnosis of bacterial pathogens and specific cell-killing. Phages have several potential advantages over conventional antibacterial agents such as host specificity, self-amplification, easy production, low toxicity as well as biofilm degradation. However, the narrow host range, uncharacterized properties, as well as potential risks from exponential replication and evolution of natural phages, currently limit their applications. Engineering phages can not only enhance the host bacteria range and improve phage efficacy, but also confer new functions. This review first summarizes major phage engineering techniques including both chemical modification and genetic engineering. Subsequent sections discuss the applications of engineered phages for bacterial pathogen detection and ablation... https://escholarship.org/uc/item/0p74029d Fri, 31 Jan 2025 00:00:00 +0000 Peng, Huan Chen, Irene A https://orcid.org/0000-0001-6040-7927 Qimron, Udi https://escholarship.org/uc/item/1nb063mr To elucidate interfacial dynamics during electrocatalytic reactions, it is crucial to understand the adsorption behavior of organic molecules on catalytic electrodes within the electric double layer (EDL). However, the EDL structure in aqueous environments remains intricate when it comes to the electrochemical amination of acetone, using methylamine as a nitrogen source. Specifically, the interactions of acetone and methylamine with the copper electrode in water remain unclear, posing challenges in the prediction and optimization of reaction outcomes. In this study, initial investigations employed impedance spectroscopy at the potential of zero charge to explore the surface preconfiguration. Here, the capacitance of the EDL was utilized as a primary descriptor to analyze the adsorption tendencies of both acetone and methylamine. Acetone shows an increase in the EDL capacitance, while methylamine shows a decrease. Experiments are interpreted using combined grand canonical density... https://escholarship.org/uc/item/1nb063mr Sun, 26 Jan 2025 00:00:00 +0000 Guan, Yani Kümper, Justus Kumari, Simran Heiming, Nick Mürtz, Sonja D Steinmann, Stephan N Palkovits, Stefan Palkovits, Regina Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/5v00z3sf Mounting evidence suggests metabolism instructs stem cell fate decisions. However, how fetal metabolism changes during development and how altered maternal metabolism shapes fetal metabolism remain unexplored. We present a descriptive atlas of in&nbsp;vivo fetal murine metabolism during mid-to-late gestation in normal and diabetic pregnancy. Using ¹³C-glucose and liquid chromatography-mass spectrometry (LC-MS), we profiled the metabolism of fetal brains, hearts, livers, and placentas harvested from pregnant dams between embryonic days (E)10.5 and 18.5. Our analysis revealed metabolic features specific to a hyperglycemic environment and signatures that may denote developmental transitions during euglycemic development. We observed sorbitol accumulation in fetal tissues and altered neurotransmitter levels in fetal brains isolated from hyperglycemic dams. Tracing ¹³C-glucose revealed disparate fetal nutrient sourcing depending on maternal glycemic states. Regardless... https://escholarship.org/uc/item/5v00z3sf Sat, 18 Jan 2025 00:00:00 +0000 Perez-Ramirez, Cesar A Nakano, Haruko Law, Richard C https://orcid.org/0000-0002-4944-9306 Matulionis, Nedas Thompson, Jennifer Pfeiffer, Andrew Park, Junyoung O https://orcid.org/0000-0001-9869-8993 Nakano, Atsushi Christofk, Heather R https://escholarship.org/uc/item/5zq5r66q We asked researchers from a range of disciplines across biology, engineering, and medicine to describe a current technological need. The goal is to provide a sample of the various technological gaps that exist and inspire future research projects. https://escholarship.org/uc/item/5zq5r66q Wed, 15 Jan 2025 00:00:00 +0000 Chen, Yvonne Y Evavold, Charles L Mann, Matthias Davenport, Emily R McFall-Ngai, Margaret Bienko, Magda Ueda, Hiroki R Tian, Lin Tjahjono, Nikki Anikeeva, Polina Liu, Jun-Jie Gogo Deans, Tara L Shen, Xiaohua https://escholarship.org/uc/item/5280v66f Urethral conditions affect children and adults, increasing the risk of urinary tract infections, voiding and sexual dysfunction, and renal failure. Current tissue replacements differ from healthy urethral tissues in structural and mechanical characteristics, causing high risk of postoperative complications. 3D bioprinting can overcome these limitations through the creation of complex, layered architectures using materials with location-specific biomechanical properties. This review highlights prior research and describes the potential for these emerging technologies to address ongoing challenges in urethral tissue engineering, including biomechanical and structural mismatch, lack of individualized repair solutions, and inadequate wound healing and vascularization. In the future, the integration of 3D bioprinting technology with advanced biomaterials, computational modeling, and 3D imaging could transform personalized urethral surgical procedures. https://escholarship.org/uc/item/5280v66f Mon, 30 Dec 2024 00:00:00 +0000 Booth, Daniel Afshari, Ronak https://orcid.org/0000-0003-4688-4406 Ghovvati, Mahsa Shariati, Kaavian Sturm, Renea https://orcid.org/0000-0001-8030-5637 Annabi, Nasim https://orcid.org/0000-0003-1879-1202 https://escholarship.org/uc/item/91v495bc Highly sensitive and selective choline microbiosensors were constructed by microcontact printing (μCP) of choline oxidase (ChOx) in a crosslinked, polyamine-functionalized zwitterionic polymer matrix on microelectrode arrays (MEAs). μCP has emerged as a potential means to create implantable, multiplexed sensor microprobes, which requires the targeted deposition of different sensor materials to specific microelectrode sites on a MEA. However, the less than sufficient enzyme loading and inadequate spatial resolution achieved with current μCP approaches has limited adoption of the method for electroenzymatic microsensors. A novel polymer, poly(2-methacryloyloxyethyl phosphorylcholine)-<i>g</i>-poly(allylamine hydrochloride) (PMPC-<i>g</i>-PAH), has been developed to address this challenge. PMPC-<i>g</i>-PAH contributes to a higher viscosity "ink" that enables thicker immobilized ChOx deposits of high spatial resolution while also providing a hydrophilic, biocompatible microenvironment... https://escholarship.org/uc/item/91v495bc Tue, 3 Dec 2024 00:00:00 +0000 Zhao, Ming Cao, Yan Huang, I-Wen Monbouquette, Harold G https://escholarship.org/uc/item/6k7881qs Successful&nbsp;nerve repair using bioadhesive hydrogels demands minimizing tissue-material interfacial mechanical mismatch to reduce immune responses and scar tissue formation. Furthermore, it is crucial to maintain the bioelectrical stimulation-mediated cell-signaling mechanism to overcome communication barriers within injured nerve tissues. Therefore, engineering bioadhesives for neural tissue regeneration necessitates the integration of electroconductive properties with tissue-like biomechanics. In this study, we propose a stretchable bioadhesive based on a custom-designed chemically modified elastin-like polypeptides (ELPs) and a choline-based bioionic liquid (Bio-IL), providing an electroconductive microenvironment to reconnect damaged nerve tissue. The stretchability akin to native neural tissue was achieved by incorporating hydrophobic ELP pockets, and a robust tissue adhesion was obtained due to multi-mode tissue-material interactions through covalent and noncovalent... https://escholarship.org/uc/item/6k7881qs Mon, 2 Dec 2024 00:00:00 +0000 Dhal, Jharana Ghovvati, Mahsa Baidya, Avijit Afshari, Ronak https://orcid.org/0000-0003-4688-4406 Cetrulo, Curtis L Abdi, Reza Annabi, Nasim https://orcid.org/0000-0003-1879-1202 https://escholarship.org/uc/item/6gp3x1sr Smart Manufacturing, or Industry 4.0, has gained significant attention in recent decades with the integration of Internet of Things (IoT) and Information Technologies (IT). As modern production methods continue to increase in complexity, there is a greater need to consider what variables can be physically measured. This advancement necessitates the use of physical sensors to comprehensively and directly gather measurable data on industrial processes; specifically, these sensors gather data that can be recontextualized into new process information. For example, artificial intelligence (AI) machine learning-based soft sensors can increase operational productivity and machine tool performance while still ensuring that critical product specifications are met. One industry that has a high volume of labor-intensive, time-consuming, and expensive processes is the semiconductor industry. AI machine learning methods can meet these challenges by taking in operational data and extracting... https://escholarship.org/uc/item/6gp3x1sr Wed, 20 Nov 2024 00:00:00 +0000 Ou, Feiyang Wang, Henrik Zhang, Chao Tom, Matthew Bom, Sthitie Davis, James F Christofides, Panagiotis D https://escholarship.org/uc/item/88k6x1c0 Modern life is essentially homochiral, containing D-sugars in nucleic acid backbones and L-amino acids in proteins. Since coded proteins are theorized to have developed from a prebiotic RNA World, the homochirality of L-amino acids observed in all known life presumably resulted from chiral transfer from a homochiral D-RNA World. This transfer would have been mediated by aminoacyl-RNAs defining the genetic code. Previous work on aminoacyl transfer using tRNA mimics has suggested that aminoacylation using D-RNA may be inherently biased toward reactivity with L-amino acids, implying a deterministic path from a D-RNA World to L-proteins. Using a model system of self-aminoacylating D-ribozymes and epimerizable activated amino acid analogs, we test the chiral selectivity of 15 ribozymes derived from an exhaustive search of sequence space. All of the ribozymes exhibit detectable selectivity, and a substantial fraction react preferentially to produce the D-enantiomer of the product. Furthermore,... https://escholarship.org/uc/item/88k6x1c0 Sat, 9 Nov 2024 00:00:00 +0000 Kenchel, Josh Vázquez-Salazar, Alberto Wells, Reno Brunton, Krishna Janzen, Evan Schultz, Kyle M Liu, Ziwei Li, Weiwei Parker, Eric T Dworkin, Jason P Chen, Irene A https://orcid.org/0000-0001-6040-7927 https://escholarship.org/uc/item/6503h02n Cytokine release syndrome (CRS) is a frequently observed side effect of chimeric antigen receptor (CAR)-T cell therapy. Here, we report self-regulating T cells that reduce CRS severity by secreting inhibitors of cytokines associated with CRS. With a humanized NSG-SGM3 mouse model, we show reduced CRS-related toxicity in mice treated with CAR-T cells secreting tocilizumab-derived single-chain variable fragment (Toci), yielding a safety profile superior to that of single-dose systemic tocilizumab administration. Unexpectedly, Toci-secreting CD19 CAR-T cells exhibit superior in vivo antitumor efficacy compared with conventional CD19 CAR-T cells. scRNA-seq analysis of immune cells recovered from tumor-bearing humanized mice revealed treatment with Toci-secreting CD19 CAR-T cells enriches for cytotoxic T cells while retaining memory T-cell phenotype, suggesting Toci secretion not only reduces toxicity but also significantly alters the overall T-cell composition. This approach of engineering... https://escholarship.org/uc/item/6503h02n Sat, 9 Nov 2024 00:00:00 +0000 Lin, Meng-Yin Nam, Eunwoo Shih, Ryan M Shafer, Amanda Bouren, Amber Ceja, Melanie Ayala Harris, Caitlin Khericha, Mobina Vo, Kenny H Kim, Minsoo Tseng, Chi-Hong Chen, Yvonne Y https://escholarship.org/uc/item/54k798sx The catalytic, regulatory and structural properties of RNA, combined with their extraordinary ubiquity in cellular processes, are consistent with the proposal that this molecule played a much more conspicuous role in heredity and metabolism during the early stages of biological evolution. This review explores the pivotal role of RNA in the earliest life forms and its relevance in modern biological systems. It examines current models that study the early evolution of life, providing insights into the primordial RNA world and its legacy in contemporary biology. https://escholarship.org/uc/item/54k798sx Fri, 8 Nov 2024 00:00:00 +0000 Muñoz-Velasco, Israel Cruz-González, Adrián Hernández-Morales, Ricardo Campillo-Balderas, José Alberto Cottom-Salas, Wolfgang Jácome, Rodrigo Vázquez-Salazar, Alberto https://escholarship.org/uc/item/44x3r7jv Timely and effective interventions after tracheal mucosal injury are lack in clinical practices, which elevate the risks of airway infection, tracheal cartilage deterioration, and even asphyxiated death. Herein, we proposed a biomaterial-based strategy for the repair of injured tracheal mucosal based on a copper hydrogen phosphate nanosheets (CuHP NSs) functionalized commercial hydrogel (polyethylene glycol disuccinimidyl succinate-human serum albumin, PH). Such CuHP/PH hydrogel achieved favorable injectability, stable gelation, and excellent adhesiveness within the tracheal lumen. Moreover, CuHP NSs within the CuHP/PH hydrogel effectively stimulate the proliferation and migration of endothelial/epithelial cells, enhancing angiogenesis and demonstrating excellent tissue regenerative potential. Additionally, it exhibited significant inhibitory effects on both bacteria and bacterial biofilms. More importantly, when injected injured site of tracheal mucosa under fiberoptic bronchoscopy... https://escholarship.org/uc/item/44x3r7jv Thu, 7 Nov 2024 00:00:00 +0000 Wang, Pengli Gao, Erji Wang, Tao Feng, Yanping Xu, Yong Su, Lefeng Gao, Wei Ci, Zheng Younis, Muhammad Rizwan Chang, Jiang Yang, Chen Duan, Liang https://escholarship.org/uc/item/17b7w6n2 The versatility of cellular metabolism in converting various substrates to products inspires sustainable alternatives to conventional chemical processes. Metabolism can be engineered to maximize the yield, rate, and titer of product generation. However, the numerous combinations of substrate, product, and organism make metabolic engineering projects difficult to navigate. A perfect trifecta of substrate, product, and organism is prerequisite for an environmentally and economically sustainable metabolic engineering endeavor. As a step toward this endeavor, we propose a reverse engineering strategy that starts with product selection, followed by substrate and organism pairing. While a large bioproduct space has been explored, the top-ten compounds have been synthesized mainly using glucose and model organisms. Unconventional feedstocks (e.g. hemicellulosic sugars and CO2) and non-model organisms are increasingly gaining traction for advanced bioproduct synthesis due to their specialized... https://escholarship.org/uc/item/17b7w6n2 Tue, 5 Nov 2024 00:00:00 +0000 Nurwono, Glenn OKeeffe, Samantha Liu, Nian Park, Jun https://escholarship.org/uc/item/5717s23g Bacterial nanocellulose (BNC) is a durable, flexible, and dynamic biomaterial capable of serving a wide variety of fields, sectors, and applications within biotechnology, healthcare, electronics, agriculture, fashion, and others. BNC is produced spontaneously in carbohydrate-rich bacterial culture media, forming a cellulosic pellicle via a nanonetwork of fibrils extruded from certain genera. Herein, we demonstrate engineering BNC-based scaffolds with tunable physical and mechanical properties through postprocessing. Human skeletal muscle myoblasts (HSMMs) were cultured on these scaffolds, and in vitro electrical stimulation was applied to promote cellular function for tissue engineering applications. We compared physiologic maturation markers of human skeletal muscle myoblast development using a 2.5-dimensional culture paradigm in fabricated BNC scaffolds, compared to two-dimensional (2D) controls. We demonstrate that the culture of human skeletal muscle myoblasts on BNC scaffolds... https://escholarship.org/uc/item/5717s23g Tue, 29 Oct 2024 00:00:00 +0000 Mastrodimos, Melina Jain, Saumya Badv, Maryam Shen, Jun Montazerian, Hossein Meyer, Claire E Annabi, Nasim https://orcid.org/0000-0003-1879-1202 Weiss, Paul S https://orcid.org/0000-0001-5527-6248 https://escholarship.org/uc/item/8xn649b1 Ba promoter effect on cobalt-catalyzed ammonia decomposition kinetics: A theoretical analysis https://escholarship.org/uc/item/8xn649b1 Thu, 26 Sep 2024 00:00:00 +0000 Almisbaa, Zahra Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/8gc050mj The dynamic restructuring of Cu has been observed under electrochemical conditions, and it has been hypothesized to underlie the unique reactivity of Cu toward CO₂ electroreduction. Roughening is one of the key surface phenomena for Cu activation, whereby numerous atomic vacancies and adatoms form. However, the atomic structure of such surface motifs in the presence of relevant adsorbates has remained elusive. Here, we explore the chemical space of Cu surface restructuring under coverage of CO and H in realistic electroreduction conditions, by combining grand canonical DFT and global optimization techniques, from which we construct a potential-dependent grand canonical ensemble representation. The regime of intermediate and mixed CO and H coverage─where structures exhibit some elevated surface Cu─is thermodynamically unfavorable yet kinetically inevitable. Therefore, we develop a quasi-kinetic Monte Carlo simulation to track the system's evolution during a simulated... https://escholarship.org/uc/item/8gc050mj Thu, 26 Sep 2024 00:00:00 +0000 Zhang, Zisheng https://orcid.org/0000-0002-4370-4038 Gee, Winston Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 https://escholarship.org/uc/item/8dz0t9nr Selective hydrogenation of α,β-unsaturated aldehydes to produce unsaturated alcohols remains a challenge in catalysis. Here, we explore, on the basis of first-principles simulations, single-atom alloy (SAA) catalysts on copper as a class of catalytic materials to enhance the selectivity for C═O bond hydrogenation in unsaturated aldehydes by controlling the binding strength of the C═C and C═O bonds. We show that on SAA of early transition metals such as Ti, Zr, and Hf, the C═O binding mode of acrolein is favored but the strong binding renders subsequent hydrogenation and desorption impossible. On SAA of late-transition metals, on the other hand, the C═C binding mode is favored and C═C bond hydrogenation follows, resulting in the production of undesired saturated aldehydes. Mid-transition metals (Cr and Mn) in Cu(111) appear as the optimal systems, since they favor acrolein adsorption via the C═O bond but with a moderate binding strength, compatible with catalysis. Additionally,... https://escholarship.org/uc/item/8dz0t9nr Thu, 26 Sep 2024 00:00:00 +0000 Ngan, Hio Tong Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/84d5m6cr Addressing sustainable energy storage remains crucial for transitioning to renewable sources. While Li-ion batteries have made significant contributions, enhancing their capacity through alternative materials remains a key challenge. Micro-crystalline silicon is a promising anode material due to its tenfold higher theoretical capacity compared to conventional graphite. However, its substantial volumetric expansion during cycling impedes practical application due to mechanical failure and rapid capacity fading. We propose a novel approach to mitigate this issue by incorporating trace amounts of aluminum into the micro-crystalline silicon electrode using ball milling. We employ density functional theory (DFT) to establish a theoretical framework elucidating how grain boundary sliding, a key mechanism involved in preventing mechanical failure, is facilitated by the presence of trace aluminum at grain boundaries. This, in turn, reduces stress accumulation within the material, reducing... https://escholarship.org/uc/item/84d5m6cr Thu, 26 Sep 2024 00:00:00 +0000 Bhimineni, Sree Harsha Ko, Shu-Ting Xia, Yantao Luo, Jian https://orcid.org/0000-0002-5424-0216 Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/7vr5k22n Unraveling the CO Oxidation Mechanism over Highly Dispersed Pt Single Atom on Anatase TiO2 (101) https://escholarship.org/uc/item/7vr5k22n Thu, 26 Sep 2024 00:00:00 +0000 Tesvara, Celine Yousuf, Raian Albrahim, Malik Troya, Diego Shrotri, Abhijit Stavitski, Eli Karim, Ayman M Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/7pv676tc The sulfur reduction reaction (SRR) plays a central role in high-capacity lithium sulfur (Li-S) batteries. The SRR involves an intricate, 16-electron conversion process featuring multiple lithium polysulfide intermediates and reaction branches1–3. Establishing the complex reaction network is essential for rational tailoring of the SRR for improved Li-S batteries, but represents a daunting challenge4–6. Herein we systematically investigate the electrocatalytic SRR to decipher its network using the nitrogen, sulfur, dual-doped holey graphene framework as a model electrode to understand the role of electrocatalysts in acceleration of conversion kinetics. Combining cyclic voltammetry, in situ Raman spectroscopy and density functional theory calculations, we identify and directly profile the key intermediates (S8, Li2S8, Li2S6, Li2S4 and Li2S) at varying potentials and elucidate their conversion pathways. Li2S4 and Li2S6 were predominantly observed, in which Li2S4 represents the key... https://escholarship.org/uc/item/7pv676tc Thu, 26 Sep 2024 00:00:00 +0000 Liu, Rongli Wei, Ziyang Peng, Lele Zhang, Leyuan Zohar, Arava Schoeppner, Rachel Wang, Peiqi Wan, Chengzhang Zhu, Dan Liu, Haotian https://orcid.org/0000-0002-8941-5207 Wang, Zhaozong Tolbert, Sarah H Dunn, Bruce Huang, Yu https://orcid.org/0000-0003-1793-0741 Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Duan, Xiangfeng https://escholarship.org/uc/item/6fc983fg Ba promoter effect on cobalt-catalyzed ammonia decomposition kinetics: A theoretical analysis https://escholarship.org/uc/item/6fc983fg Thu, 26 Sep 2024 00:00:00 +0000 Almisbaa, Zahra Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/631288vk Hydrazine assisted water electrolysis provides an attractive pathway for low-voltage hydrogen production while at the same time mitigating the hazardous hydrazine environmental pollutants. Herein we report the design and synthesis of Ru decorated Ag nanoparticles (NPs) where the Ag-Ru interfaces act as highly effective bifunctional electrocatalysts for the hydrazine oxidation reaction (HzOR) and the hydrogen evolution reaction (HER). The electrocatalysts with Ag-Ru interfaces demonstrate improved HzOR performance with lower overpotential, enhanced mass activity (MA) and highly selective oxidation of hydrazine into N2. Density functional theory (DFT) computations reveal the Ag-Ru interfaces feature higher barrier for N-N bond cleavage and easier N2 desorption, contributing to the electrocatalytic activity and selectivity. At the same time, improved HER performance is also observed due to the more favourable hydrogen desorption. Together, by employing the Ru decorated Ag NPs as... https://escholarship.org/uc/item/631288vk Thu, 26 Sep 2024 00:00:00 +0000 Fu, Xiaoyang Cheng, Dongfang Zhang, Ao Zhou, Jingxuan Wang, Sibo Zhao, Xun Chen, Jun https://orcid.org/0000-0002-3439-0495 Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Huang, Yu https://orcid.org/0000-0003-1793-0741 Duan, Xiangfeng https://escholarship.org/uc/item/4ms1883b The decomposition of dimethyl methyl phosphonate (DMMP), a simulant for the nerve agent sarin, was investigated on Cu₄/TiO₂(110) and K/Cu₄/TiO₂(110) surfaces using a combination of near-ambient-pressure X-ray photoelectron spectroscopy (NAP-XPS) and density functional theory calculations (DFT). Mass-selected Cu₄ clusters and potassium (K) atoms were deposited onto TiO₂(110) as a metal catalyst and alkali promoter to improve the reactivity and recyclability of the TiO₂ surface after exposure to DMMP. Surface reaction products resulting from decomposition of DMMP were probed by NAP-XPS measurements of phosphorus (P) 2p and carbon 1s core-level spectra. The Cu₄/TiO₂(110) surface is found to be very active for DMMP decomposition with highly reduced P-species observed even at room temperature (RT). The codeposition of K atoms and Cu₄ clusters further improves the reactivity... https://escholarship.org/uc/item/4ms1883b Thu, 26 Sep 2024 00:00:00 +0000 Bonney, Matthew J Tesvara, Celine Sautet, Philippe https://orcid.org/0000-0002-8444-3348 White, Michael G https://escholarship.org/uc/item/3pz7n0fs Identifying the Optimal Pd Ensemble Size in Dilute PdAu Alloy Nanomaterials for Benzaldehyde Hydrogenation https://escholarship.org/uc/item/3pz7n0fs Thu, 26 Sep 2024 00:00:00 +0000 Kaiser, Selina K van der Hoeven, Jessi ES Yan, George Lim, Kang Rui Garrick Ngan, Hio Tong Garg, Sadhya Karatok, Mustafa Aizenberg, Michael Aizenberg, Joanna Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Friend, Cynthia M Madix, Robert J https://escholarship.org/uc/item/2075v1pf In the context of carbon reutilization, the direct electroreduction of captured CO₂ (c-CO₂RR) appears as an appealing approach since it avoids the energetically costly separation of CO₂ from the capture agent. In this process, CO₂ is directly reduced from its captured form. Here, we investigate the influence of the capture agent and proton source on that reaction from a combination of theory and experiment. Specifically, we consider methoxide-captured CO₂, NH₃-captured CO₂, and bicarbonate on silver electrocatalysts. We show that the proton source plays a key role in the interplay of the chemistries for the electroreduction of protons, free CO₂, and captured CO₂. Our density functional theory calculations, including the influence of the potential, demonstrate that a proton source with smaller p<i>K</i>_a improves the reactivity for c-CO₂RR, but also increases... https://escholarship.org/uc/item/2075v1pf Thu, 26 Sep 2024 00:00:00 +0000 Kowalski, Robert Michael Banerjee, Avishek Yue, Chudi Gracia, Sara G Cheng, Dongfang Morales-Guio, Carlos G Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/1c85345z Hierarchical design enables sufficient activated CO2 for efficient electrolysis of bicarbonate to CO https://escholarship.org/uc/item/1c85345z Thu, 26 Sep 2024 00:00:00 +0000 Shen, Mengxin Ji, Liyao Cheng, Dongfang Wang, Ziwei Xue, Qinwen Feng, Shijia Luo, Yao Chen, Shuying Wang, Jiahao Zheng, Hongzhi Wang, Xiaojun Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Zhu, Jia https://escholarship.org/uc/item/11x151wt CO₂ electroreduction (CO₂ R) operating in acidic media circumvents the problems of carbonate formation and CO₂ crossover in neutral/alkaline electrolyzers. Alkali cations have been universally recognized as indispensable components for acidic CO₂ R, while they cause the inevitable issue of salt precipitation. It is therefore desirable to realize alkali-cation-free CO₂ R in pure acid. However, without alkali cations, stabilizing *CO₂ intermediates by catalyst itself at the acidic interface poses as a challenge. Herein, we first demonstrate that a carbon nanotube-supported molecularly dispersed cobalt phthalocyanine (CoPc@CNT) catalyst provides the Co single-atom active site with energetically localized d states to strengthen the adsorbate-surface interactions, which stabilizes *CO₂ intermediates at the acidic interface (pH=1). As a result, we realize CO₂ conversion to CO in pure acid with a... https://escholarship.org/uc/item/11x151wt Thu, 26 Sep 2024 00:00:00 +0000 Feng, Shijia Wang, Xiaojun Cheng, Dongfang Luo, Yao Shen, Mengxin Wang, Jingyang Zhao, Wei Fang, Susu Zheng, Hongzhi Ji, Liyao Zhang, Xing Xu, Weigao Liang, Yongye Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Zhu, Jia https://escholarship.org/uc/item/1w65n1zr Cu dissolution has been identified as the dominant process that causes cathode degradation and losses even under cathodic conditions involving methylamine. Despite extensive experimental research, our fundamental and theoretical understanding of the atomic-scale mechanism for Cu dissolution under electrochemical conditions, eventually coupled with surface restructuring processes, is limited. Here, driven by the observation that the working Cu electrode is corroded using mixtures of acetone and methylamine even under reductive potential conditions (-0.75 V <i>vs.</i> RHE), we employed Grand Canonical density functional theory to understand this dynamic process under potential from a microscopic perspective. We show that amine ligands in solution directly chemisorb on the electrode, coordinate with the metal center, and drive the rearrangement of the copper surface by extracting Cu as adatoms in low coordination positions, where other amine ligands can coordinate and stabilize a... https://escholarship.org/uc/item/1w65n1zr Mon, 23 Sep 2024 00:00:00 +0000 Guan, Yani Kümper, Justus Mürtz, Sonja D Kumari, Simran Hausoul, Peter JC Palkovits, Regina Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/05t8r1j1 Heterogeneous nanocatalysts play a crucial role in both the chemical and energy industries. Despite substantial advancements in theoretical, computational and experimental studies, identifying their active sites remains a major challenge. Here we utilize atomic electron tomography to determine the three-dimensional atomic structure of PtNi and Mo-doped PtNi nanocatalysts for the electrochemical oxygen reduction reaction. We then employ the experimental atomic structures as input to first-principles-trained machine learning to identify the active sites of the nanocatalysts. Through the analysis of the structure–activity relationships, we formulate an equation termed the local environment descriptor, which balances the strain and ligand effects to provide physical and chemical insights into active sites in the oxygen reduction reaction. The ability to determine the three-dimensional atomic structure and chemical composition of realistic nanoparticles, combined with machine learning,... https://escholarship.org/uc/item/05t8r1j1 Tue, 10 Sep 2024 00:00:00 +0000 Yang, Yao Zhou, Jihan Zhao, Zipeng Sun, Geng Moniri, Saman Ophus, Colin https://orcid.org/0000-0003-2348-8558 Yang, Yongsoo Wei, Ziyang Yuan, Yakun Zhu, Cheng Liu, Yang Sun, Qiang Jia, Qingying Heinz, Hendrik Ciston, Jim https://orcid.org/0000-0002-8774-5747 Ercius, Peter https://orcid.org/0000-0002-6762-9976 Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Huang, Yu https://orcid.org/0000-0003-1793-0741 Miao, Jianwei https://escholarship.org/uc/item/6d22q26w Creating a living system from nonliving matter is a great challenge in chemistry and biophysics. The early history of life can provide inspiration from the idea of the prebiotic "RNA World" established by ribozymes, in which all genetic and catalytic activities were executed by RNA. Such a system could be much simpler than the interdependent central dogma characterizing life today. At the same time, cooperative systems require a mechanism such as cellular compartmentalization in order to survive and evolve. Minimal cells might therefore consist of simple vesicles enclosing a prebiotic RNA metabolism. The internal volume of a vesicle is a distinctive environment due to its closed boundary, which alters diffusion and available volume for macromolecules and changes effective molecular concentrations, among other considerations. These physical effects are mechanistically distinct from chemical interactions, such as electrostatic repulsion, that might also occur between the membrane... https://escholarship.org/uc/item/6d22q26w Mon, 19 Aug 2024 00:00:00 +0000 Saha, Ranajay https://orcid.org/0000-0001-6001-7363 Choi, Jongseok A Chen, Irene A https://orcid.org/0000-0001-6040-7927 https://escholarship.org/uc/item/0z44q22f The relationship between genotype and phenotype, or the fitness landscape, is the foundation of genetic engineering and evolution. However, mapping fitness landscapes poses a major technical challenge due to the amount of quantifiable data that is required. Catalytic RNA is a special topic in the study of fitness landscapes due to its relatively small sequence space combined with its importance in synthetic biology. The combination of in vitro selection and high-throughput sequencing has recently provided empirical maps of both complete and local RNA fitness landscapes, but the astronomical size of sequence space limits purely experimental investigations. Next steps are likely to involve data-driven interpolation and extrapolation over sequence space using various machine learning techniques. We discuss recent progress in understanding RNA fitness landscapes, particularly with respect to protocells and machine representations of RNA. The confluence of technical advances may significantly... https://escholarship.org/uc/item/0z44q22f Wed, 31 Jul 2024 00:00:00 +0000 Saha, Ranajay Vázquez-Salazar, Alberto Nandy, Aditya Chen, Irene A https://orcid.org/0000-0001-6040-7927 https://escholarship.org/uc/item/1xt4p1pb Topical instillation of eye drops remains the most common and easiest route of ocular drug administration, representing the treatment of choice for many ocular diseases. Nevertheless, low ocular bioavailability of topically applied drug molecules can considerably limit their efficacy. Over the last several decades, numerous drug delivery systems (DDS) have been developed in order to improve drug bioavailability on the ocular surfaces. This review systematically covers the most recent advances of DDS applicable by topical instillation, that have shown better performance in in vivo models compared to standard eye drop formulations. These delivery systems are based on in situ forming gels, nanoparticles and combinations of both. Most of the DDS have been developed using natural or synthetic polymers. Polymers offer many advantageous properties for designing advanced DDS including biocompatibility, gelation properties and/or mucoadhesiveness. However, despite the high number of studies... https://escholarship.org/uc/item/1xt4p1pb Sun, 21 Jul 2024 00:00:00 +0000 Jumelle, Clotilde Gholizadeh, Shima Annabi, Nasim https://orcid.org/0000-0003-1879-1202 Dana, Reza https://escholarship.org/uc/item/2dw661m5 Abstract: Addressing sustainable energy storage remains crucial for transitioning to renewable sources. While Li‐ion batteries have made significant contributions, enhancing their capacity through alternative materials remains a key challenge. Micro‐sized silicon is a promising anode material due to its tenfold higher theoretical capacity compared to conventional graphite. However, its substantial volumetric expansion during cycling impedes practical application due to mechanical failure and rapid capacity fading. A novel approach is proposed to mitigate this issue by incorporating trace amounts of aluminum into the micro‐sized silicon electrode using ball milling. Density functional theory (DFT) is employed to establish a theoretical framework elucidating how grain boundary sliding, a key mechanism involved in preventing mechanical failure is facilitated by the presence of trace aluminum at grain boundaries. This, in turn, reduces stress accumulation within the material, reducing... https://escholarship.org/uc/item/2dw661m5 Thu, 18 Jul 2024 00:00:00 +0000 Bhimineni, Sree Harsha Ko, Shu‐Ting Cornwell, Casey Xia, Yantao Tolbert, Sarah H Luo, Jian https://orcid.org/0000-0002-5424-0216 Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/0cs3k50q Developments in the field of microfluidics have triggered technological revolutions in many disciplines, including chemical synthesis, electronics, diagnostics, single-cell analysis, micro- and nanofabrication, and pharmaceutics. In many of these areas, rapid growth is driven by the increasing synergy between fundamental materials development and new microfluidic capabilities. In this Review, we critically evaluate both how recent advances in materials fabrication have expanded the frontiers of microfluidic platforms and how the improved microfluidic capabilities are, in turn, furthering materials design. We discuss how various inorganic and organic materials enable the fabrication of systems with advanced mechanical, optical, chemical, electrical and biointerfacial properties — in particular, when these materials are combined into new hybrids and modular configurations. The increasing sophistication of microfluidic techniques has also expanded the range of resources available... https://escholarship.org/uc/item/0cs3k50q Tue, 16 Jul 2024 00:00:00 +0000 Hou, Xu Zhang, Yu Shrike Santiago, Grissel Trujillo-de Alvarez, Mario Moisés Ribas, João Jonas, Steven J https://orcid.org/0000-0002-8111-0249 Weiss, Paul S https://orcid.org/0000-0001-5527-6248 Andrews, Anne M https://orcid.org/0000-0002-1961-4833 Aizenberg, Joanna Khademhosseini, Ali https://escholarship.org/uc/item/21425629 Ocular inflammation is commonly associated with eye disease or injury. Effective and sustained ocular delivery of therapeutics remains a challenge due to the eye physiology and structural barriers. Herein, we engineered a photocrosslinkable adhesive patch (GelPatch) incorporated with micelles (MCs) loaded with Loteprednol etabonate (LE) for delivery and sustained release of drug. The engineered drug loaded adhesive hydrogel, with controlled physical properties, provided a matrix with high adhesion to the ocular surfaces. The incorporation of MCs within the GelPatch enabled solubilization of LE and its sustained release within 15 days. <i>In vitro</i> studies showed that MC loaded GelPatch supported cell viability and growth. In addition, subcutaneous implantation of the MC loaded GelPatch in rats confirmed its <i>in vivo</i> biocompatibility and stability within 28 days. This non-invasive, adhesive, and biocompatible drug eluting patch can be used as a matrix for the delivery... https://escholarship.org/uc/item/21425629 Tue, 4 Jun 2024 00:00:00 +0000 Chen, Xi Gholizadeh, Shima Ghovvati, Mahsa Wang, Ziqing Jellen, Marcus J Mostafavi, Azadeh Dana, Reza Annabi, Nasim https://orcid.org/0000-0003-1879-1202 https://escholarship.org/uc/item/4tg967h2 The SUVmax is a measure of FDG uptake and is related with tumor aggressiveness in thyroid cancer, however, its association with molecular pathways is unclear. Here, we investigated the relationship between SUVmax and gene expression profiles in 80 papillary thyroid cancer (PTC) patients. We conducted an analysis of DEGs and enriched pathways in relation to SUVmax and tumor size. SUVmax showed a positive correlation with tumor size and correlated with glucose metabolic process. The genes that indicate thyroid differentiation, such as SLC5A5 and TPO, were negatively correlated with SUVmax. Unsupervised analysis revealed that SUVmax positively correlated with DNA replication(r = 0.29, p = 0.009), pyrimidine metabolism(r = 0.50, p &lt; 0.0001) and purine metabolism (r = 0.42, p = 0.0001). Based on subgroups analysis, we identified that PSG5, TFF3, SOX2, SL5A5, SLC5A7, HOXD10, FER1L6, and IFNA1 genes were found to be significantly associated with tumor aggressiveness. Both high SUVmax... https://escholarship.org/uc/item/4tg967h2 Fri, 31 May 2024 00:00:00 +0000 Ju, Sang-Hyeon Lee, Seong Eun Yi, Shinae Choi, Na Rae Kim, Kun Ho Kim, Seong Min Koh, June-Young Kim, Seon-Kyu Kim, Seon-Young Heo, Jun Young Park, Junyoung O https://orcid.org/0000-0001-9869-8993 Park, Seongyeol Koo, Bon Seok Kang, Yea Eun https://escholarship.org/uc/item/0kv843gq Abnormal human trabecular meshwork (HTM) cell function and extracellular matrix (ECM) remodeling contribute to HTM stiffening in primary open-angle glaucoma (POAG). Most current cellular HTM model systems do not sufficiently replicate the complex native three dimensional (3D) cell-ECM interface, limiting their use for investigating POAG pathology. Tissue-engineered hydrogels are ideally positioned to overcome shortcomings of current models. Here, we report a novel biomimetic HTM hydrogel and test its utility as a POAG disease model. HTM hydrogels were engineered by mixing normal donor-derived HTM cells with collagen type I, elastin-like polypeptide and hyaluronic acid, each containing photoactive functional groups, followed by UV crosslinking. Glaucomatous conditions were induced with dexamethasone (DEX), and effects of the Rho-associated kinase (ROCK) inhibitor Y27632 on cytoskeletal organization and tissue-level function, contingent on HTM cell-ECM interactions, were assessed.... https://escholarship.org/uc/item/0kv843gq Wed, 29 May 2024 00:00:00 +0000 Li, Haiyan Bagué, Tyler Kirschner, Alexander Strat, Ana N Roberts, Haven Weisenthal, Robert W Patteson, Alison E Annabi, Nasim https://orcid.org/0000-0003-1879-1202 Stamer, W Daniel Ganapathy, Preethi S Herberg, Samuel https://escholarship.org/uc/item/6c99k6rh Neutrophil heterogeneity is involved in autoimmune diseases, sepsis, and several cancers. However, the link between neutrophil heterogeneity and T-cell immunity in thyroid cancer is incompletely understood. We investigated the circulating neutrophil heterogeneity in 3 undifferentiated thyroid cancer (UTC), 14 differentiated thyroid cancer (DTC) (4 Stage IV, 10 Stage I–II), and healthy controls (n = 10) by transcriptomic data and cytometry. Participants with UTC had a significantly higher proportion of immature high-density neutrophils (HDN) and lower proportion of mature HDN in peripheral blood compared to DTC. The proportion of circulating PD-L1+ immature neutrophils were significantly increased in advanced cancer patients. Unsupervised analysis of transcriptomics data from circulating HDN revealed downregulation of innate immune response and T-cell receptor signaling pathway in cancer patients. Moreover, UTC patients revealed the upregulation of glycolytic process and glutamate... https://escholarship.org/uc/item/6c99k6rh Wed, 15 May 2024 00:00:00 +0000 Lee, Seong Eun Koo, Bon Seok Sun, Pureum Yi, Shinae Choi, Na Rae Yoon, Jiyeon Kim, Seon-Young Kim, Seon-Kyu Park, Seongyeol Lakhani, Aliya O’Keeffe, Samantha Park, Junyoung O https://orcid.org/0000-0001-9869-8993 Kang, Da Hyun Kang, Yea Eun https://escholarship.org/uc/item/9nb9w6p6 We uncovered and reconstituted a concise biosynthetic pathway of the strained dipeptide (+)-azonazine A from marine-derived Aspergillus insulicola. Formation of the hexacyclic benzofuranoindoline ring system from cyclo-(l-Trp-N-methyl-l-Tyr) is catalyzed by a P450 enzyme through an oxidative cyclization. Supplementing the producing strain with various indole-substituted tryptophan derivatives resulted in the generation of a series of azonazine A analogs. https://escholarship.org/uc/item/9nb9w6p6 Wed, 17 Apr 2024 00:00:00 +0000 Liu, Mengting Ohashi, Masao Zhou, Qingyang Sanders, Jacob N McCauley, Erin P Crews, Phillip Houk, KN Tang, Yi https://escholarship.org/uc/item/9jh9b2wd A hybrid approach combining water-splitting electrochemistry and H₂-oxidizing, CO₂-fixing microorganisms offers a viable solution for producing value-added chemicals from sunlight, water, and air. The classic wisdom without thorough examination to date assumes that the electrochemistry in such a H₂-mediated process is innocent of altering microbial behavior. Here, we report unexpected metabolic rewiring induced by water-splitting electrochemistry in H₂-oxidizing acetogenic bacterium <i>Sporomusa ovata</i> that challenges such a classic view. We found that the planktonic <i>S. ovata</i> is more efficient in utilizing reducing equivalent for ATP generation in the materials-biology hybrids than cells grown with H₂ supply, supported by our metabolomic and proteomic studies. The efficiency of utilizing reducing equivalents and fixing CO₂ into acetate has increased from less than 80% of chemoautotrophy to more than 95%... https://escholarship.org/uc/item/9jh9b2wd Wed, 17 Apr 2024 00:00:00 +0000 Xie, Yongchao Erşan, Sevcan Guan, Xun Wang, Jingyu Sha, Jihui Xu, Shuangning Wohlschlegel, James A https://orcid.org/0000-0001-8289-2222 Park, Junyoung O https://orcid.org/0000-0001-9869-8993 Liu, Chong https://escholarship.org/uc/item/4qr9t31n Many statistical methods have been developed for the analysis of microbial community profiles, but due to the complexity of typical microbiome measurements, inference of interactions between microbial features remains challenging. We develop a Bayesian zero-inflated rounded log-normal kernel method to model interaction between microbial features in a community using multivariate count data in the presence of covariates and excess zeros. The model carefully constructs the interaction structure by imposing joint sparsity on the covariance matrix of the kernel and obtains a reliable estimate of the structure with a small sample size. The model also includes zero inflation to account for excess zeros observed in data and infers differential abundance of microbial features associated with covariates through log-linear regression. We provide simulation studies and real data analysis examples to demonstrate the developed model. Comparison of the model to a simpler model and popular alternatives... https://escholarship.org/uc/item/4qr9t31n Thu, 11 Apr 2024 00:00:00 +0000 Zhang, Shuangjie Shen, Yuning Chen, Irene A https://orcid.org/0000-0001-6040-7927 Lee, Juhee https://escholarship.org/uc/item/4zp7z72c Chimeric antigen receptor (CAR)-T cell therapy has shown remarkable clinical efficacy against B-cell malignancies, yet marked vulnerability to antigen escape and tumor relapse exists. Here we report the rational design and optimization of bispecific CAR-T cells with robust activity against heterogeneous multiple myeloma (MM) that is resistant to conventional CAR-T cell therapy targeting B-cell maturation antigen (BCMA). We demonstrate that BCMA/CS1 bispecific CAR-T cells exhibit superior CAR expression and function compared to T cells that co-express individual BCMA and CS1 CARs. Combination therapy with anti–PD-1 antibody further accelerates the rate of initial tumor clearance in vivo, while CAR-T cell treatment alone achieves durable tumor-free survival even upon tumor re-challenge. Taken together, the BCMA/CS1 bispecific CAR presents a promising treatment approach to prevent antigen escape in CAR-T cell therapy against MM, and the vertically integrated optimization process... https://escholarship.org/uc/item/4zp7z72c Mon, 8 Apr 2024 00:00:00 +0000 Zah, Eugenia Nam, Eunwoo Bhuvan, Vinya Tran, Uyen Ji, Brenda Y Gosliner, Stanley B Wang, Xiuli Brown, Christine E Chen, Yvonne Y https://escholarship.org/uc/item/0906p9dm The expression of synthetic receptors in primary T cells enables the programming of user-defined responses when designing T-cell therapies. Chimeric antigen receptors (CARs) are synthetic receptors that have demonstrated efficacy in cancer therapy by targeting immobilized antigens on the surface of malignant cells. Recently, we showed they can also rewire T-cell responses to soluble ligands. In contrast to other synthetic receptors, CARs are not only readily engineered by rational design, but also clinically translatable, with robust function in primary human T cells. This protocol discusses design principles for CARs responsive to soluble ligands and delineates steps for producing T cells expressing synthetic receptors. Functional assays for quantifying the ability of CAR T cells to sense and respond to soluble ligands are also presented. This protocol provides a framework for proficient immune-cell researchers to test novel T-cell therapies targeting soluble ligands in &lt;2 weeks. https://escholarship.org/uc/item/0906p9dm Sun, 7 Apr 2024 00:00:00 +0000 Chang, ZeNan L Hou, Andrew J Chen, Yvonne Y https://escholarship.org/uc/item/8nq9h8hz Thermodynamic Equilibrium versus Kinetic Trapping: Thermalization of Cluster Catalyst Ensembles Can Extend Beyond Reaction Time Scales https://escholarship.org/uc/item/8nq9h8hz Mon, 1 Apr 2024 00:00:00 +0000 Poths, Patricia https://orcid.org/0000-0003-4193-526X Vargas, Santiago Sautet, Philippe https://orcid.org/0000-0002-8444-3348 Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 https://escholarship.org/uc/item/8543t9bq The growing concern over the escalating levels of anthropogenic CO₂ emissions necessitates effective strategies for its conversion to valuable chemicals and fuels. In this research, we embark on a comprehensive investigation of the nature of zirconia on a copper inverse catalyst under the conditions of CO₂ hydrogenation to methanol. We employ density functional theory calculations in combination with the Grand Canonical Basin Hopping method, enabling an exploration of the free energy surface including a variable amount of adsorbates within the relevant reaction conditions. Our focus centers on a model three-atom Zr cluster on a Cu(111) surface decorated with various OH, O, and formate ligands, noted Zr₃O_<i>x</i> (OH)_<i>y</i> (HCOO)_<i>z</i>/Cu(111), revealing major changes in the active site induced by various reaction parameters such as the gas pressure, temperature, conversion levels, and CO₂/H₂... https://escholarship.org/uc/item/8543t9bq Mon, 1 Apr 2024 00:00:00 +0000 Kumari, Simran Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/3hf0t6z7 In acidic conditions, the electroreduction of CO or CO₂ (noted CO₍₂₎RR) on metal surfaces is conventionally hindered by intense competition with the hydrogen evolution reaction (HER). In this study, we present first-principles calculations of a mechanism wherein the formation of H-induced Cu adatoms on Cu(111) serves as a pivotal trigger for CORR in acidic environments. Through an analysis of the grand canonical surface state population, we elucidate that these newly formed adatoms create an array of active sites essential for both CO adsorption and subsequent reduction. Our ensemble-based kinetic models unveil the role of adatoms, enhancing the HER while simultaneously initiating CORR. Notably, the cumulative activity of the HER and CORR is contingent upon the combination of various surface states, with their individual contributions varying based on the electrode potential and pH. The interplay between surface state dynamics and electrochemical activity... https://escholarship.org/uc/item/3hf0t6z7 Mon, 1 Apr 2024 00:00:00 +0000 Cheng, Dongfang Alexandrova, Anastassia N https://orcid.org/0000-0002-3003-1911 Sautet, Philippe https://orcid.org/0000-0002-8444-3348 https://escholarship.org/uc/item/2p47v3bb One of the most significant and surprising recent developments in nanocrystal studies was the observation of superfluorescence from a system of self-assembled, colloidal perovskite nanocrystals [G. Rainò, M. A. Becker, M. I. Bodnarchuk, R. F. Mahrt, M. V. Kovalenko, and T. Stöferle, "Superfluorescence from lead halide perovskite quantum dot superlattices," <i>Nature</i>, vol. 563, no. 7733, pp. 671-675, 2018]. Superfluorescence is a quantum-light property in which many dipoles spontaneously synchronize in phase to create a collective, synergistic photon emission with a much faster lifetime. Thus, it is surprising to observe this in more inhomogenous systems as solution-processed and colloidal structures typically suffer from high optical decoherence and non-homogeneous size distributions. Here we outline recent developments in the demonstration of superfluorescence in colloidal and solution-processed systems and explore the chemical and materials science opportunities allowed... https://escholarship.org/uc/item/2p47v3bb Wed, 27 Mar 2024 00:00:00 +0000 Russ, Brendan Eisler, Carissa N https://orcid.org/0000-0002-5755-5280 https://escholarship.org/uc/item/5f1563rc We demonstrate the utility of block polyelectrolyte (bPE) additives to enhance viscosity and resolve challenges with the three-dimensional (3D) printability of extrusion-based biopolymer inks. The addition of oppositely charged bPEs to solutions of photocurable gelatin methacryloyl (GelMA) results in complexation-driven self-assembly of the bPEs, leading to GelMA/bPE inks that are printable at physiological temperatures, representing stark improvements over GelMA inks that suffer from low viscosity at 37 °C, leading to low printability and poor structural stability. The hierarchical microstructure of the self-assemblies (either jammed micelles or 3D networks) formed by the oppositely charged bPEs, confirmed by small-angle X-ray scattering, is attributed to the enhancements in the shear strength and printability of the GelMA/bPE inks. Varying bPE concentration in the inks is shown to enable tunability of the rheological properties to meet the criteria of pre- and postextrusion... https://escholarship.org/uc/item/5f1563rc Tue, 26 Mar 2024 00:00:00 +0000 Göckler, Tobias Albreiki, Fahed Li, Defu Grimm, Alisa Mecklenburg, Felix Urueña, Juan Manuel Schepers, Ute Srivastava, Samanvaya https://orcid.org/0000-0002-3519-7224 https://escholarship.org/uc/item/3572w0vw High-throughput sequencing technology has enabled researchers to profile microbial communities from a variety of environments, but analysis of multivariate taxon count data remains challenging. We develop a Bayesian nonparametric (BNP) regression model with zero inflation to analyse multivariate count data from microbiome studies. A BNP approach flexibly models microbial associations with covariates, such as environmental factors and clinical characteristics. The model produces estimates for probability distributions which relate microbial diversity and differential abundance to covariates, and facilitates community comparisons beyond those provided by simple statistical tests. We compare the model to simpler models and popular alternatives in simulation studies, showing, in addition to these additional community-level insights, it yields superior parameter estimates and model fit in various settings. The model's utility is demonstrated by applying it to a chronic wound microbiome... https://escholarship.org/uc/item/3572w0vw Wed, 20 Mar 2024 00:00:00 +0000 Shuler, Kurtis Verbanic, Samuel Chen, Irene A https://orcid.org/0000-0001-6040-7927 Lee, Juhee https://escholarship.org/uc/item/2v86060x Advances in sequencing technology have allowed researchers to sequence DNA with greater ease and at decreasing costs. Main developments have focused on either sequencing many short sequences or fewer large sequences. Methods for sequencing mid-sized sequences of 600–5,000&nbsp;bp are currently less efficient. For example, the PacBio Sequel I system yields ~ 100,000–300,000 reads with an accuracy per base pair of 90–99%. We sought to sequence several DNA populations of ~ 870&nbsp;bp in length with a sequencing accuracy of 99% and to the greatest depth possible. We optimised a simple, robust method to concatenate genes of ~ 870&nbsp;bp five times and then sequenced the resulting DNA of ~ 5,000&nbsp;bp by PacBioSMRT long-read sequencing. Our method improved upon previously published concatenation attempts, leading to a greater sequencing depth, high-quality reads and limited sample preparation at little expense. We applied this efficient concatenation protocol to sequence nine DNA... https://escholarship.org/uc/item/2v86060x Wed, 20 Mar 2024 00:00:00 +0000 Kanwar, Nisha Blanco, Celia Chen, Irene A https://orcid.org/0000-0001-6040-7927 Seelig, Burckhard https://escholarship.org/uc/item/0j25292c Sparse identification modeling and predictive control of wafer temperature in an atomic layer etching reactor https://escholarship.org/uc/item/0j25292c Wed, 20 Mar 2024 00:00:00 +0000 Ou, Feiyang Abdullah, Fahim Wang, Henrik Tom, Matthew Orkoulas, Gerassimos Christofides, Panagiotis D https://escholarship.org/uc/item/8131w567 A major limitation to developing chimeric antigen receptor (CAR)-T cell therapies for solid tumors is identifying surface proteins highly expressed in tumors but not in normal tissues. Here, we identify Tyrosinase Related Protein 1 (TYRP1) as a CAR-T cell therapy target to treat patients with cutaneous and rare melanoma subtypes unresponsive to immune checkpoint blockade. TYRP1 is primarily located intracellularly in the melanosomes, with a small fraction being trafficked to the cell surface via vesicular transport. We develop a highly sensitive CAR-T cell therapy that detects surface TYRP1 in tumor cells with high TYRP1 overexpression and presents antitumor activity in vitro and in vivo in murine and patient-derived cutaneous, acral and uveal melanoma models. Furthermore, no systemic or off-tumor severe toxicities are observed in an immunocompetent murine model. The efficacy and safety profile of the TYRP1 CAR-T cell therapy supports the ongoing preparation of a phase I clinical... https://escholarship.org/uc/item/8131w567 Tue, 27 Feb 2024 00:00:00 +0000 Jilani, Sameeha Saco, Justin D Mugarza, Edurne Pujol-Morcillo, Aleida Chokry, Jeffrey Ng, Clement Abril-Rodriguez, Gabriel Berger-Manerio, David Pant, Ami https://orcid.org/0009-0003-7391-7207 Hu, Jane Gupta, Rubi Vega-Crespo, Agustin Baselga-Carretero, Ignacio Chen, Jia M Shin, Daniel Sanghoon Scumpia, Philip Radu, Roxana A https://orcid.org/0000-0002-5064-6403 Chen, Yvonne Ribas, Antoni https://orcid.org/0000-0003-3669-8458 Puig-Saus, Cristina https://escholarship.org/uc/item/5b86q7g4 We report biosynthetic pathways that can synthesize and transform conjugated octaenes and nonaenes to complex natural products. The biosynthesis of (-)-PF1018 involves an enzyme PfB that can control the regio-, stereo-, and periselectivity of multiple reactions starting from a conjugated octaene. Using PfB as a lead, we discovered a homologous enzyme, BruB, that facilitates diene isomerization, tandem 8π-6π-electrocyclization, and a 1,2-divinylcyclobutane Cope rearrangement to generate a new-to-nature compound. https://escholarship.org/uc/item/5b86q7g4 Tue, 27 Feb 2024 00:00:00 +0000 Niwa, Kanji Ohashi, Masao Xie, Kaili Chiang, Chen-Yu Jamieson, Cooper S Sato, Michio Watanabe, Kenji Liu, Fang Houk, KN Tang, Yi https://escholarship.org/uc/item/3k43s4p4 We demonstrate facile fabrication of highly filled, lightweight organic-inorganic composites comprising polyurethanes covalently linked with naturally occurring clinoptilolite microparticles. These polyurethane/clinoptilolite (PUC) composites are shown to mitigate particle aggregation usually observed in composites with high particle loadings and possess enhanced thermal insulation and acoustic attenuation compared with conventionally employed materials (e.g., drywall and gypsum). In addition to these functional properties, the PUC composites also possess flexural strengths and strain capacities comparable to and higher than ordinary Portland cement (OPC), respectively, while being ∼1.5× lighter than OPC. The porosity, density, and mechanical and functional properties of these composites are tuned by systematically varying their composition (diisocyanate, polyurethane, and inorganic contents) and the nature of the organic (reactivity and source of polyol) components. The fabrication... https://escholarship.org/uc/item/3k43s4p4 Mon, 26 Feb 2024 00:00:00 +0000 Iyer, Divya Galadari, Mohammad Wirawan, Fernaldy Huaco, Vanessa Martinez, Ricardo Gallagher, Michael T Pilon, Laurent https://orcid.org/0000-0001-9459-8207 Ono, Kanji Simonetti, Dante A Sant, Gaurav N Srivastava, Samanvaya https://orcid.org/0000-0002-3519-7224 https://escholarship.org/uc/item/47b842k8 Orthopedic surgical procedures based on the use of conventional biological graft tissues are often associated with serious post-operative complications such as immune rejection, bacterial infection, and poor osseointegration. Bioresorbable bone graft substitutes have emerged as attractive alternatives to conventional strategies because they can mimic the composition and mechanical properties of the native bone. Among these, bioactive glasses (BGs) hold great potential to be used as biomaterials for bone tissue engineering owing to their biomimetic composition and high biocompatibility and osteoinductivity. Here, we report the development of a novel composite biomaterial for bone tissue engineering based on the incorporation of a modified strontium- and lithium-doped 58S BG (i.e., BG-5/5) into gelatin methacryloyl (GelMA) hydrogels. We characterized the physicochemical properties of the BG formulation via different analytical techniques. Composite hydrogels were then prepared by... https://escholarship.org/uc/item/47b842k8 Sun, 25 Feb 2024 00:00:00 +0000 Moghanian, Amirhossein Portillo‐Lara, Roberto Sani, Ehsan Shirzaei Konisky, Hailey Bassir, Seyed Hossein Annabi, Nasim https://orcid.org/0000-0003-1879-1202 https://escholarship.org/uc/item/2rq4c9cm The role of the serine/glycine metabolic pathway (SGP) has recently been demonstrated in tumors; however, the pathological relevance of the SGP in thyroid cancer remains unexplored. Here, we perform metabolomic profiling of 17 tumor-normal pairs; bulk transcriptomics of 263 normal thyroid, 348 papillary, and 21 undifferentiated thyroid cancer samples; and single-cell transcriptomes from 15 cases, showing the impact of mitochondrial one-carbon metabolism in thyroid tumors. High expression of serine hydroxymethyltransferase-2 (SHMT2) and methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) is associated with low thyroid differentiation scores and poor clinical features. A subpopulation of tumor cells with high mitochondrial one-carbon pathway activity is observed in the single-cell dataset. SHMT2 inhibition significantly compromises mitochondrial respiration and decreases cell proliferation and tumor size in vitro and in vivo. Collectively, our results highlight the importance of... https://escholarship.org/uc/item/2rq4c9cm Tue, 13 Feb 2024 00:00:00 +0000 Lee, Seong Eun Park, Seongyeol Yi, Shinae Choi, Na Rae Lim, Mi Ae Chang, Jae Won Won, Ho-Ryun Kim, Je Ryong Ko, Hye Mi Chung, Eun-Jae Park, Young Joo Cho, Sun Wook Yu, Hyeong Won Choi, June Young Yeo, Min-Kyung Yi, Boram Yi, Kijong Lim, Joonoh Koh, Jun-Young Lee, Min Jeong Heo, Jun Young Yoon, Sang Jun Kwon, Sung Won Park, Jong-Lyul Chu, In Sun Kim, Jin Man Kim, Seon-Young Shan, Yujuan Liu, Lihua Hong, Sung-A Choi, Dong Wook Park, Junyoung O https://orcid.org/0000-0001-9869-8993 Ju, Young Seok Shong, Minho Kim, Seon-Kyu Koo, Bon Seok Kang, Yea Eun