Recent Submissions

  • Boosting electron transport in non-fullerene acceptors using non-chlorinated solvents

    Nugraha, Mohamad Insan; Ardhi, Ryanda Enggar Anugrah; Naphade, Dipti; Zhang, Weimin; Yuan, Youyou; Heeney, Martin; Anthopoulos, Thomas D. (Journal of Materials Chemistry C, Royal Society of Chemistry (RSC), 2023-09-08) [Article]
    Chlorinated solvents are commonly used to process organic semiconductor devices but have several negative environmental impacts. The choice of processing solvent significantly affects the layer microstructure and device performance, so replacing chlorinated solvents is non-trivial. Herein, we investigate the microstructural and electron-transporting properties of small-molecule non-fullerene acceptor (NFA) films and transistors processed from various non-chlorinated solvents. We show that the ensuing NFA transistors exhibit improved layer morphology, crystallinity, and electron mobility superior to those processed from chlorinated solvents. Our work highlights using non-chlorinated solvents to optimise charge transport in organic semiconductors and their devices while mitigating adverse environmental effects.
  • Multilayer Ferromagnetic Spintronic Devices for Neuromorphic Computing Applications

    Lone, Aijaz H.; zou, xuecui; Mishra, Kishan K.; Singaravelu, Venkatesh; Fariborzi, Hossein; Setti, Gianluca (arXiv, 2023-09-01) [Preprint]
    Spintronics has gone through substantial progress due to its applications in energy-efficient memory, logic and unconventional computing paradigms. Multilayer ferromagnetic thin films are extensively studied for understanding the domain wall and skyrmion dynamics. However, most of these studies are confined to the materials and domain wall/skyrmion physics. In this paper, we present the experimental and micromagnetic realization of a multilayer ferromagnetic spintronic device for neuromorphic computing applications. The device exhibits multilevel resistance states and the number of resistance states increases with lowering temperature. This is supported by the multilevel magnetization behavior observed in the micromagnetic simulations. Furthermore, the evolution of resistance states with spin-orbit torque is also explored in experiments and simulations. Using the multi-level resistance states of the device, we propose its applications as a synaptic device in hardware neural networks and study the linearity performance of the synaptic devices. The neural network based on these devices is trained and tested on the MNIST dataset using a supervised learning algorithm. The devices at the chip level achieve 90\% accuracy. Thus, proving its applications in neuromorphic computing. Furthermore, we lastly discuss the possible application of the device in cryogenic memory electronics for quantum computers.
  • Bacterioplankton dark CO2 fixation in oligotrophic waters

    Alothman, Afrah; López-Sandoval, Daffne C.; Duarte, Carlos M.; Agusti, Susana (Biogeosciences, Copernicus GmbH, 2023-08-31) [Article]
    Dark CO2 fixation by bacteria is believed to be particularly important in oligotrophic ecosystems. However, only a few studies have characterized the role of bacterial dissolved inorganic carbon (DIC) fixation in global carbon dynamics. Therefore, this study quantified the primary production (PP), total bacteria dark CO2 fixation (TBDIC fixation), and heterotrophic bacterial production (HBP) in the warm and oligotrophic Red Sea using stable-isotope labeling and cavity ring-down spectroscopy (13C–CRDS). Additionally, we assessed the contribution of bacterial DIC fixation (TBDIC %) relative to the total DIC fixation (totalDIC fixation). Our study demonstrated that TBDIC fixation increased the totalDIC fixation from 2.03 to 60.45 µg C L−1 d−1 within the photic zone, contributing 13.18 % to 71.68 % with an average value of 33.95 ± 0.02 % of the photic layer totalDIC fixation. The highest TBDIC fixation values were measured at the surface and deep (400 m) water with an average value of 5.23 ± 0.45 and 4.95 ± 1.33 µg C L−1 d−1, respectively. These findings suggest that the non-photosynthetic processes such as anaplerotic DIC reactions and chemoautotrophic CO2 fixation extended to the entire oxygenated water column. On the other hand, the percent of TBDIC contribution to totalDIC fixation increased as primary production decreased (R2=0.45, p<0.0001), suggesting the relevance of increased dark DIC fixation when photosynthetic production was low or absent, as observed in other systems. Therefore, when estimating the total carbon dioxide production in the ocean, dark DIC fixation must also be accounted for as a crucial component of the carbon dioxide flux in addition to photosynthesis.
  • Overcoming the kinetic and deactivation limitations of Ni catalyst by alloying it with Zn for the dry reforming of methane

    Velisoju, Vijay Kumar; Virpurwala, Quaid Johar Samun; Attada, Yerrayya; Bai, Xueqin; Davaasuren, Bambar; Ben Hassine, Mohamed; Yao, Xueli; Lezcano, Gontzal; Kulkarni, Shekhar Rajabhau; Castaño, Pedro (Journal of CO2 Utilization, Elsevier BV, 2023-08-23) [Article]
    Stimulated by the capacity of Zn to improve the adoption of CO2 and CH4, we doped a Ni-supported ZrO2 catalyst with Zn to enhance its performance and stability in the dry reforming of methane. We prepared a set of catalysts with different Ni:Zn:Zr proportions and conducted extensive ex situ and in situ characterizations to prove that a Ni–Zn alloy was formed at 750 °C under reductive conditions. Combining a tailored morphology of the alloy nanoparticles, strong metal–support (ZnO–ZrO2) interactions, and additional oxygen vacancies created by Zn inclusion resulted in an enhanced catalyst with 15% higher initial activity and higher stability for over 100 h on stream than Zn-free catalyst. Our experimental and modeling results demonstrated that the catalyst with adjusted Ni:Zn:Zr proportion improves the adsorption and reaction rates of CH4 and CO2 while extending its lifetime through enhanced coke precursor gasification compared to its Zn-free counterpart.
  • A single-molecule study on polymer fluid dynamics in porous media.

    Sugar, Antonia; Serag, Maged F.; Buttner, Ulrich; Habuchi, Satoshi; Hoteit, Hussein (Lab on a chip, Royal Society of Chemistry (RSC), 2023-08-23) [Article]
    Understanding the dynamic behavior of polymeric fluids in porous media is essential for vast geoscience applications, particularly enhanced oil recovery and polymer-enhanced soil washing, to clean up soil contamination. During the past decades, the behavior of polymeric fluids in microscopic space has only been investigated using ensemble-averaged experimental methods in which a bulk phase behavior of the fluids characterizes flow mechanisms. Multiple flow mechanisms have been proposed based on ensemble-averaged data; however, microscale characterization of the interactions between polymers and solid surfaces and the mechanisms governing polymer retention and permeability reduction as well as the reversibility of polymer retention are lacking, resulting in a limited understanding of the flow mechanisms. Here we report direct visualization and multi-scale characterization of the dynamic behavior of polymer molecules in a representative porous medium by integrating microfluidics with single-molecule imaging. We demonstrate that the polymers' adsorption, entrapment and hydrodynamic retention contribute to their overall retention in porous media. Our study illustrates how microfluidics can help in understanding the dynamic behavior of polymers, their interactions with the solid/fluid interface and their effects on flow properties. Additionally, it demonstrates the role of microfluidic platforms in providing a more representative and accurate model for polymer retention and permeability reduction in porous media. The obtained insights encourage the development of improved models that better capture the behavior of complex fluids in confined environments and have significant implications for a wide range of applications in geoscience, materials science, and rheology.
  • Zeolite Synthesis in the Presence of Metallosiloxanes for the Quantitative Encapsulation of Metal Species for the Selective Catalytic Reduction (SCR) of NOx.

    Khairova, Rushana; Komaty, Sarah; Dikhtiarenko, Alla; Cerrillo, Jose L; Veeranmaril, Sudheesh Kumar; Telalovic, Selvedin; Tapia, Antonio Aguilar; Hazemann, Jean-Louis; Ruiz-Martinez, Javier; Gascon, Jorge (Angewandte Chemie (International ed. in English), Wiley, 2023-08-15) [Article]
    Metal encapsulation in zeolitic materials through one-pot hydrothermal synthesis (HTS) is an attractive technique to prepare zeolites with a high metal dispersion. Due to its simplicity and the excellent catalytic performance observed for several catalytic systems, this method has gained a great deal of attention over the last few years. While most studies apply synthetic methods involving different organic ligands to stabilize the metal under synthesis conditions, here we report the use of metallosiloxanes as an alternative metal precursor. Metallosiloxanes can be synthesized from simple and cost-affordable chemicals and, when used in combination with zeolite building blocks under standard synthesis conditions, lead to quantitative metal loading and high dispersion. Thanks to the structural analogy of siloxane with TEOS, the synthesis gel stabilizes by forming siloxane bridges that prevent metal precipitation and clustering. When focusing on Fe-encapsulation, we demonstrate that Fe-MFI zeolites obtained by this method exhibit high catalytic activity in the NH3-mediated selective catalytic reduction (SCR) of NOx along with a good H2O/SO2 tolerance. This synthetic approach opens a new synthetic route for the encapsulation of transition metals within zeolite structures.
  • Dual-Color Lasers in Interlayer-Free Solution Processed Polymeric Bilayer Devices

    Zhang, Zhiyuan; Zhang, Qi; Wei, Xuanxuan; Xiao, Zihan; Zhu, Shan; Fu, Shuai; Sun, Huizhi; Florica, Camelia Florina; Peng, Junbiao; Xia, Ruidong (ACS Applied Materials & Interfaces, American Chemical Society (ACS), 2023-08-10) [Article]
    Multiwavelength organic lasers have attracted considerable interest in recent years due to the cost efficiency, wide luminescence coverage, and simple processability of organics. In this work, by simply spin coating immiscible polymeric gain media in sequence, dual-wavelength (blue-green or blue-red) amplified spontaneous emission (ASE) was achieved in bilayer devices. The blue emission, water/alcohol-soluble conjugated polyelectrolyte, poly[(9,9-bis(3′-((N,N-dimethyl)-N-ethylammonium)-propyl)-2,7-fluorene)-alt-2,7-(9,9-dioctylfluorene)]dibromide (PFN-Br), was used as the bottom layer. The commercially available nonpolar solvent soluble polymer poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT) and its blend with poly(3-hexylthiophene) (P3HT) were used as the top active layers offering green and red emission, respectively. This novel compact configuration, without interlayers between the two active layers, offers potential for developing various applications. The carefully selected top and bottom layer polymers not only meet the conditions of immiscibility and different emission wavelength range but also have a common absorption band in UV, which allows simultaneous blue-green or blue-red dual-color ASE behaviors observed in the bilayer devices under the same 390 nm laser excitation. By introducing two-dimension (2D) square distributed feedback (DFB) gratings with different periods (300 nm for blue, 330 nm for green, and 390 nm for red) as cavities, single mode blue-green (Eth = 245 μJ cm-2) and blue-red (Eth = 189 μJ cm-2) lasers were achieved by focusing the excitation laser spot on different 2D DFB gratings area. Furthermore, we found it possible to gain sufficient light confinement for red emission along its diagonal direction (Λ ∼424 nm), whereas the 2D DFB gratings offer feedback for blue emission from the 300 nm period along the rectangle direction. Therefore, both blue and red lasers were eventually achieved in the same PFN-Br/F8BT:P3HT bilayer device on the single 2D DFB gratings with a period of 300 nm in this work.
  • Einkorn genomics sheds light on history of the oldest domesticated wheat

    Ahmed, Hanin; Heuberger, Matthias; Schoen, Adam; Koo, Dal-Hoe; Quiroz-Chávez, Jesús; Adhikari, Laxman; Raupp, John; Cauet, Stéphane; Rodde, Nathalie; Cravero, Charlotte; Callot, Caroline; Lazo, Gerard R.; Kathiresan, Nagarajan; Sharma, Parva K.; Moot, Ian; Yadav, Inderjit Singh; Singh, Lovepreet; Saripalli, Gautam; Rawat, Nidhi; Datla, Raju; Athiyannan, Naveenkumar; Ramirez-Gonzalez, Ricardo H.; Uauy, Cristobal; Wicker, Thomas; Tiwari, Vijay; Abrouk, Michael; Poland, Jesse; Krattinger, Simon G. (Springer Science and Business Media LLC, 2023-08-02) [Article]
    Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.
  • Design, Simulation, and Evaluation of Polymer-Based Microfluidic Devices via Computational Fluid Dynamics and Cell Culture “On-Chip”

    Bakuova, Nurzhanna; Toktarkan, Sultanali; Dyussembinov, Darkhan; Azhibek, Dulat; Rakhymzhanov, Almas; Kostas, Konstantinos; Kulsharova, Gulsim (Biosensors, MDPI AG, 2023-07-22) [Article]
    Organ-on-a-chip (OoC) technology has experienced exponential growth driven by the need for a better understanding of in-organ processes and the development of novel approaches. This paper investigates and compares the flow behavior and filling characteristics of two microfluidic liver-on-a-chip devices using Computational Fluid Dynamics (CFD) analysis and experimental cell culture growth based on the Huh7 cell line. The conducted computational analyses for the two chips showed that the elliptical chamber chip proposed herein offers improved flow and filling characteristics in comparison with the previously presented circular chamber chip. Huh7 hepatoma cells were cultured in the microfluidic devices for 24 h under static fluidic conditions and for 24 h with a flow rate of 3 μL·min−1. Biocompatibility, continuous flow, and biomarker studies showed cell attachment in the chips, confirming the cell viability and their consistent cell growth. The study successfully analyzed the fluid flow behavior, filling characteristics, and biocompatibility of liver-on-a-chip prototype devices, providing valuable insights to improve design and performance and advance alternative methods of in vitro testing.
  • Impact of the SARS-CoV-2 nucleocapsid 203K/204R mutations on the inflammatory immune response in COVID-19 severity

    Shuaib, Muhammad; Adroub, Sabir; Mourier, Tobias; Mfarrej, Sara; Zhang, Huoming; Esau, Luke; Alsomali, Afrah; Alofi, Fadwa S; Ahmad, Adeel Nazir; Shamsan, Abbas; Khogeer, Asim; Hashem, Anwar M.; Almontashiri, Naif A. M.; Hala, Sharif; Pain, Arnab (Genome Medicine, Springer Science and Business Media LLC, 2023-07-21) [Article]
    Background: The excessive inflammatory responses provoked by SARS-CoV-2 infection are critical factors affecting the severity and mortality of COVID-19. Previous work found that two adjacent co-occurring mutations R203K and G204R (KR) on the nucleocapsid (N) protein correlate with increased disease severity in COVID-19 patients. However, links with the host immune response remain unclear. Methods: Here, we grouped nasopharyngeal swab samples of COVID-19 patients into two cohorts based on the presence and absence of SARS-CoV-2 nucleocapsid KR mutations. We performed nasopharyngeal transcriptome analysis of age, gender, and ethnicity-matched COVID-19 patients infected with either SARS-CoV-2 with KR mutations in the N protein (KR patients n = 39) or with the wild-type N protein (RG patients n = 39) and compared to healthy controls (n = 34). The impact of KR mutation on immune response was further characterized experimentally by transcriptomic and proteomic profiling of virus-like-particle (VLP) incubated cells. Results: We observed markedly elevated expression of proinflammatory cytokines, chemokines, and interferon-stimulated (ISGs) genes in the KR patients compared to RG patients. Using nasopharyngeal transcriptome data, we found significantly higher levels of neutrophils and neutrophil-to-lymphocyte (NLR) ratio in KR patients than in the RG patients. Furthermore, transcriptomic and proteomic profiling of VLP incubated cells confirmed a similar hyper-inflammatory response mediated by the KR variant. Conclusions: Our data demonstrate an unforeseen connection between nucleocapsid KR mutations and augmented inflammatory immune response in severe COVID-19 patients. These findings provide insights into how mutations in SARS-CoV-2 modulate host immune output and pathogenesis and may contribute to more efficient therapeutics and vaccine development.
  • Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study

    Schweke, Hugo; Xu, Qifang; Tauriello, Gerardo; Pantolini, Lorenzo; Schwede, Torsten; Cazals, Frédéric; Lhéritier, Alix; Fernandez-Recio, Juan; Rodríguez-Lumbreras, Luis Angel; Schueler-Furman, Ora; Varga, Julia K.; Jiménez-García, Brian; Réau, Manon F.; Bonvin, Alexandre M. J. J.; Savojardo, Castrense; Martelli, Pier-Luigi; Casadio, Rita; Tubiana, Jérôme; Wolfson, Haim J.; Oliva, Romina; Barradas-Bautista, Didier; Ricciardelli, Tiziana; Cavallo, Luigi; Venclovas, Česlovas; Olechnovič, Kliment; Guerois, Raphael; Andreani, Jessica; Martin, Juliette; Wang, Xiao; Terashi, Genki; Sarkar, Daipayan; Christoffer, Charles; Aderinwale, Tunde; Verburgt, Jacob; Kihara, Daisuke; Marchand, Anthony; Correia, Bruno E.; Duan, Rui; Qiu, Liming; Xu, Xianjin; Zhang, Shuang; Zou, Xiaoqin; Dey, Sucharita; Dunbrack, Roland L.; Levy, Emmanuel D.; Wodak, Shoshana J (PROTEOMICS, Wiley, 2023-06-27) [Article]
    Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest resources on protein complexes and interfaces were exploited to derive a benchmark dataset consisting of 1677 homodimer protein crystal structures, including a balanced mix of physiological and non-physiological complexes. The non-physiological complexes in the benchmark were selected to bury a similar or larger interface area than their physiological counterparts, making it more difficult for scoring functions to differentiate between them. Next, 252 functions for scoring protein-protein interfaces previously developed by 13 groups were collected and evaluated for their ability to discriminate between physiological and non-physiological complexes. A simple consensus score generated using the best performing score of each of the 13 groups, and a cross-validated Random Forest (RF) classifier were created. Both approaches showed excellent performance, with an area under the Receiver Operating Characteristic (ROC) curve of 0.93 and 0.94, respectively, outperforming individual scores developed by different groups. Additionally, AlphaFold2 engines recalled the physiological dimers with significantly higher accuracy than the non-physiological set, lending support to the reliability of our benchmark dataset annotations. Optimizing the combined power of interface scoring functions and evaluating it on challenging benchmark datasets appears to be a promising strategy.
  • HPC-based genome variant calling workflow (HPC-GVCW)

    Zhou, Yong; Kathiresan, Nagarajan; Yu, Zhichao; Rivera, Luis; Thimma, Manjula; Manickam, Keerthana; Chebotarov, Dmytro; Mauleon, Ramil; Chougule, Kapeel; Wei, Xuehong; Gao, Tingting; Green, Carl Douglas; Zuccolo, Andrea; Ware, Doreen; Zhang, Jianwei; McNally, Kenneth; Wing, Rod Anthony (Cold Spring Harbor Laboratory, 2023-06-26) [Preprint]
    A high-performance computing genome variant calling workflow was designed to run GATK on HPC platforms. This workflow efficiently called an average of 27.3 M, 32.6 M, 168.9 M, and 16.2 M SNPs for rice, sorghum, maize, and soybean, respectively, on the most recently released high-quality reference sequences. Analysis of a rice pan-genome reference panel revealed 2.1 M novel SNPs that have yet to be publicly released.
  • Atomic-Scale Polarization and Strain at the Surface of Lead Halide Perovskite Nanocrystals.

    Chen, Shulin; Wang, Jiayi; Thomas, Simil; Mir, Wasim Jeelani; Shao, Bingyao; Lu, Jianxun; Wang, Qingxiao; Gao, Peng; Mohammed, Omar F.; Han, Yu; Bakr, Osman (Nano letters, 2023-06-21) [Article]
    Inorganic halide perovskite nanocrystals (NCs) are being widely explored as next-generation optoelectronic materials. Critical to understanding the optoelectronic properties and stability behavior of perovskite NCs is the material’s surface structure, where the local atomic configuration deviates from that of the bulk. Through low-dose aberration-corrected scanning transmission electron microscopy and quantitative imaging analysis techniques, we directly observed the atomic structure at the surface of the CsPbBr3 NCs. CsPbBr3 NCs are terminated by a Cs–Br plane, and the surface Cs–Cs bond length decreases significantly (∼5.6%) relative to the bulk, imposing compressive strain and inducing polarization, which we also observed in CsPbI3 NCs. Density functional theory calculations suggest such a reconstructed surface contributes to the separation of holes and electrons. These findings enhance our fundamental understanding of the atomic-scale structure, strain, and polarity at the surface of inorganic halide perovskites and provide valuable insights into designing stable and efficient optoelectronic devices.
  • Data sets for "HPC-based genome variant calling workflow (HPC-GVCW)"

    Zhou, Yong; Kathiresan, Nagarajan; Yu, Zhichao; Rivera, Luis; Thimma, Manjula; Manickam, Keerthana; Chebotarov, Dmytro; Mauleon, Ramil; Chougule, Kapeel; Wei, Xuehong; Gao, Tingting; Green, Carl Douglas; Zuccolo, Andrea; Zhang, Jianwei; Ware, Doreen; McNally, Kenneth; Wing, Rod Anthony (2023-06-14) [Dataset]
  • Detailed band alignment of high-B-composition BGaN with GaN and AlN

    AlQatari, Feras S.; Liao, Che-Hao; Aguileta Vazquez, Raul; Tang, Xiao; Lopatin, Sergei; Li, Xiaohang (Journal of Physics D: Applied Physics, IOP Publishing, 2023-06-06) [Article]
    The electronic structure of B0.097Ga0.903N was determined by examining its bandgap and valence band offset (VBO) in detail. The BGaN sample was grown using a horizontal reactor metalorganic chemical vapor deposition. For bandgap determination, three different techniques were utilized yielding similar results, which are: UV-Vis spectroscopy, Schottky photodiodes, and electron energy-loss spectroscopy. The bandgap was determined to be ~3.55 eV. For measuring the VBO, the valence edges and the core levels of Al 2s and Ga 2p were measured using x-ray photoelectron spectroscopy (XPS). The valence edges were then fitted and processed along with the core levels using the standard Kraut method for VBO determination with AlN. The BGaN/AlN alignment was found to be -1.1 ± 0.1 eV. Due to core level interference between GaN and BGaN, the Kraut method fails to provide precise VBO for this heterojunction. Therefore, a different technique is devised to analyze the measured XPS data which utilizes the alignment of the Fermi levels of the BGaN and GaN layers when in contact. Statistical analysis was used to determine the BGaN/GaN alignment with decent precision. The value was found to be -0.3 ± 0.1 eV.
  • Structural evolution and gas separation properties of thermally rearranged polybenzoxazole (TR-PBO), polymer-carbon transition (PCT) and early-stage carbon (ESC) membranes derived from a 6FDA-hydroxyl-functionalized Tröger's base polyimide

    Yerzhankyzy, Ainur; Wang, Yingge; Xu, Feng; Hu, Xiaofan; Ghanem, Bader; Ma, Xiaohua; Balcik, Marcel; Wehbe, Nimer; Han, Yu; Pinnau, Ingo (Journal of Membrane Science, Elsevier BV, 2023-05-29) [Article]
    The changes in physical, chemical, and gas permeation properties of a heat-treated hydroxyl-functionalized Tröger's base-derived intrinsically microporous polyimide, 6FDA-HTB, were systematically studied. Polyimide samples were heated-treated for 30 minutes at a fixed temperature to form (i) polybenzoxazole (PBO) by thermal rearrangement (TR) from ∼420 to ∼440 °C, (ii) polymer-carbon transition (PCT) from ∼460 to ∼500 °C, and (iii) early-stage carbon (ESC) membranes from >500 to 600 °C. As frequently observed in previous studies, TR-derived PBO membranes showed an increase in gas permeability with a concomitant decrease in gas-pair selectivity. The intermediate PCT region represents a transition state from a pure PBO to a partially carbonized polymer with superior properties by showing a simultaneous boost in gas permeability and gas-pair selectivity. The ESC membranes formed between 550 to 600 °C possessed further enhanced selectivity but reduced permeability due to tightening of the amorphous CMS structure. The mixed-gas separation properties of selected aged samples, pristine 6FDA-HTB, PBO (6FDA-HTB-420), intermediate PCT (6FDA-HTB-480), and early stage CMS analogs (6FDA-HTB-550 and 600), were investigated using a 1:1 CO2/CH4 feed up to 30 bar. In this series, early-stage CMS membranes displayed the best mixed-gas CO2/CH4 separation properties with performance significantly surpassing the 2018 polymer mixed-gas upper bound.
  • PfAP2-MRP DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages

    Subudhi, Amit Kumar; Subudhi, Amit; Satyam, Rohit; Lenz, Todd; Salunke, Rahul P; Shuaib, Muhammad; Isaioglou, Ioannis; Abel, Steven; Gupta, Mohit; Esau, Luke; Mourier, Tobias; Nugmanova, Raushan; Mfarrej, Sara; Sivapurkar, Rupali; Stead, Zenaida; Ben Rached, Fathia; Otswal, Yogesh; Sougrat, Rachid; Dada, Ashraf; Kadamany, Abdullah Fuaad; Fishle, Wolfgang; Merzaban, Jasmeen; Knuepfer, Ellen; Ferguson, David J.P.; Gupta, Ishaan; Le Roch, Karine G; Holder, Anthony A; Holder, Anthony A. (Cold Spring Harbor Laboratory, 2023-05-24) [Preprint]
    Malaria pathogenicity results from the parasites ability to invade, multiply within and then egress from the host red blood cell (RBC). Infected RBCs are remodeled, expressing antigenic variant proteins (such as PfEMP1, coded by the var gene family) for immune evasion and survival. These processes require the concerted actions of many proteins, but the molecular regulation is poorly understood. We have characterized an essential Plasmodium specific Apicomplexan AP2 (ApiAP2) transcription factor in Plasmodium falciparum (PfAP2-MRP; Master Regulator of Pathogenesis) during the intraerythrocytic developmental cycle (IDC). An inducible gene knockout approach showed that PfAP2-MRP is essential for development during the trophozoite stage, and critical for var gene regulation, merozoite development and parasite egress. ChIP-seq experiments performed at 16 hour post invasion (h.p.i.) and 40 h.p.i. matching the two peaks of PfAP2-MRP expression, demonstrate binding of PfAP2-MRP to the promoters of genes controlling trophozoite development and host cell remodeling at 16 h.p.i. and antigenic variation and pathogenicity at 40 h.p.i. Using single-cell RNA-seq and fluorescence-activated cell sorting, we show de-repression of most var genes in pfap2-mrp deleted parasites that express multiple PfEMP1 proteins on the surface of infected RBCs. In addition, the pfap2-mrp deleted parasites overexpress several early gametocyte marker genes at both 16 and 40 h.p.i., indicating a regulatory role in the sexual stage conversion. Using the Chromosomes Conformation Capture experiment (Hi-C), we demonstrate that deletion of PfAP2-MRP results in significant reduction of both intra-chromosomal and inter-chromosomal interactions in heterochromatin clusters. We conclude that PfAP2-MRP is a vital upstream transcriptional regulator controlling essential processes in two distinct developmental stages during the IDC that include parasite growth, chromatin structure and var gene expression.
  • Experimental and numerical investigation of polymer pore-clogging in micromodels.

    Sugar, Antonia; Serag, Maged F.; Buttner, Ulrich; Fahs, Marwan; Habuchi, Satoshi; Hoteit, Hussein (Scientific reports, Springer Science and Business Media LLC, 2023-05-22) [Article]
    Polymers have been used effectively in the Oil & Gas Industry for a variety of field applications, such as enhanced oil recovery (EOR), well conformance, mobility control, and others. Polymer intermolecular interactions with the porous rock, in particular, formation clogging and the associated alterations to permeability, is a common problem in the industry. In this work, fluorescent polymers and single-molecule imaging are presented for the first time to assess the dynamic interaction and transport behavior of polymer molecules utilizing a microfluidic device. Pore-scale simulations are performed to replicate the experimental observations. The microfluidic chip, also known as a "Reservoir-on-a-Chip" functions as a 2D surrogate to evaluate the flow processes that take place at the pore-scale. The pore-throat sizes of an oil-bearing reservoir rock, which range from 2 to 10 nm, are taken into consideration while designing the microfluidic chip. Using soft lithography, we created the micromodel from polydimethylsiloxane (PDMS). The conventional use of tracers to monitor polymers has a restriction due to the tendency of polymer and tracer molecules to segregate. For the first time, we develop a novel microscopy method to observe the dynamic behavior of polymer pore-clogging and unclogging processes. We provide direct dynamic observations of polymer molecules during their transport within the aqueous phase and their clustering and accumulations. Pore-scale simulations were carried out to simulate the phenomena using a finite-element simulation tool. The simulations revealed a decline in flow conductivity over time within the flow channels that experienced polymer accumulation and retention, which is consistent with the experimental observation of polymer retention. The performed single-phase flow simulations allowed us to assess the flow behavior of the tagged polymer molecules within the aqueous phase. Additionally, both experimental observation and numerical simulations are used to evaluate the retention mechanisms that emerge during flow and how they affect apparent permeability. This work provides new insights to assessing the mechanisms of polymer retention in porous media.
  • The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions.

    Jiménez-García, Brian; Roel-Touris, Jorge; Barradas Bautista, Didier (Nucleic acids research, Oxford University Press (OUP), 2023-05-04) [Article]
    Computational docking is an instrumental method of the structural biology toolbox. Specifically, integrative modeling software, such as LightDock, arise as complementary and synergetic methods to experimental structural biology techniques. Ubiquitousness and accessibility are fundamental features to promote ease of use and to improve user experience. With this goal in mind, we have developed the LightDock Server, a web server for the integrative modeling of macromolecular interactions, along with several dedicated usage modes. The server builds upon the LightDock macromolecular docking framework, which has proved useful for modeling medium-to-high flexible complexes, antibody-antigen interactions, or membrane-associated protein assemblies.
  • Contrasting Capability of Single Atom Palladium for Thermocatalytic versus Electrocatalytic Nitrate Reduction Reaction

    Wu, Xuanhao; Nazemi, Mohammadreza; Gupta, Srishti; Chismar, Adam; Hong, Kiheon; Jacobs, Hunter; Zhang, Wenqing; Rigby, Kali; Hedtke, Tayler; Wang, Qingxiao; Stavitski, Eli; Wong, Michael S.; Muhich, Christopher; Kim, Jae-Hong (ACS Catalysis, American Chemical Society (ACS), 2023-05-03) [Article]
    The occurrence of high concentrations of nitrate in various water resources is a significant environmental and human health threat, demanding effective removal technologies. Single atom alloys (SAAs) have emerged as a promising bimetallic material architecture in various thermocatalytic and electrocatalytic schemes including nitrate reduction reaction (NRR). This study suggests that there exists a stark contrast between thermocatalytic (T-NRR) and electrocatalytic (E-NRR) pathways that resulted in dramatic differences in SAA performances. Among Pd/Cu nanoalloys with varying Pd–Cu ratios from 1:100 to 100:1, Pd/Cu(1:100) SAA exhibited the greatest activity (TOFPd = 2 min–1) and highest N2 selectivity (94%) for E-NRR, while the same SAA performed poorly for T-NRR as compared to other nanoalloy counterparts. DFT calculations demonstrate that the improved performance and N2 selectivity of Pd/Cu(1:100) in E-NRR compared to T-NRR originate from the higher stability of NO3* in electrocatalysis and a lower N2 formation barrier than NH due to localized pH effects and the ability to extract protons from water. This study establishes the performance and mechanistic differences of SAA and nanoalloys for T-NRR versus E-NRR.

View more