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Abstract The discovery of van der Waals intrinsic magnets has expanded the possibilities of realizing spintronics devices. We investigate the transmission, tunneling magnetoresistance ratio, and spin injection efficiency of bilayer LaI2 using a combination of first-principles calculations and the non-equilibrium Green’s function method. Multilayer graphene electrodes are employed to build a magnetic tunnel junction with bilayer LaI2 as ferromagnetic barrier. The magnetic tunnel junction turns out to be a perfect spin filter device with an outstanding tunneling magnetoresistance ratio of 653% under a bias of 0.1 V and a still excellent performance in a wide bias range. In combination with the obtained high spin injection efficiency this opens up great potential from the application point of view.

Magnesium (Mg) based materials hold immense potential for various applications due to their lightweight and high strength-to-weight ratio. However, to fully harness the potential of Mg alloys, structured analytics are essential to gain valuable insights from centuries of accumulated knowledge. Efficient information extraction from the vast corpus of scientific literature is crucial for this purpose. In this work, we introduce MagBERT, a BERT-based language model specifically trained for Mg-based materials. Utilizing a dataset of approximately 370,000 abstracts focused on Mg and its alloys, MagBERT is designed to understand the intricate details and specialized terminology of this domain. Through rigorous evaluation, we demonstrate the effectiveness of MagBERT for information extraction using a fine-tuned named entity recognition (NER) model, named MagNER. This NER model can extract mechanical, microstructural, and processing properties related to Mg alloys. For instance, we have created an Mg alloy dataset that includes properties such as ductility, yield strength, and ultimate tensile strength (UTS), along with standard alloy names. The introduction of MagBERT is a novel advancement in the development of Mg-specific language models, marking a significant milestone in the discovery of Mg alloys and textual information extraction. By making the pre-trained weights of MagBERT publicly accessible, we aim to accelerate research and innovation in the field of Mg-based materials through efficient information extraction and knowledge discovery.

Abstract Adaptation to hypothermia is important for skeletal muscle cells under physiological stress and is used for therapeutic hypothermia (mild hypothermia at 32 °C). We show that hypothermic preconditioning at 32 °C for 72 hours improves the differentiation of skeletal muscle myoblasts using both C2C12 and primary myoblasts isolated from 3 month and 18-month-old mice. We analyzed the cold-shock proteome of myoblasts exposed to hypothermia (32 °C for 6 and 48 h) and identified significant changes in pathways related to RNA processing and central carbon, fatty acid, and redox metabolism. The analysis revealed that levels of the cold-shock protein RBM3, an RNA-binding protein, increases with both acute and chronic exposure to hypothermic stress, and is necessary for the enhanced differentiation and maintenance of mitochondrial metabolism. We also show that overexpression of RBM3 at 37 °C is sufficient to promote mitochondrial metabolism, cellular proliferation, and differentiation of C2C12 and primary myoblasts. Proteomic analysis of C2C12 myoblasts overexpressing RBM3 show significant enrichment of pathways involved in fatty acid metabolism, RNA metabolism and the electron transport chain. Overall, we show that the cold-shock protein RBM3 is a critical factor that can be used for controlling the metabolic network of myoblasts.

Abstract This study introduces a plasmonic reduction catalyst, stable only in the presence of air, achieved by integrating Pt-doped Ru nanoparticles on black gold. This innovative black gold/RuPt catalyst showcases good efficiency in acetylene semi-hydrogenation, attaining over 90% selectivity with an ethene production rate of 320 mmol g−1 h−1. Its stability, evident in 100 h of operation with continuous air flow, is attributed to the synergy of co-existing metal oxide and metal phases. The catalyst’s stability is further enhanced by plasmon-mediated concurrent reduction and oxidation of the active sites. Finite-difference time-domain simulations reveal a five-fold electric field intensification near the RuPt nanoparticles, crucial for activating acetylene and hydrogen. Kinetic isotope effect analysis indicates the contribution from the plasmonic non-thermal effects along with the photothermal. Spectroscopic and in-situ Fourier transform infrared studies, combined with quantum chemical calculations, elucidate the molecular reaction mechanism, emphasizing the cooperative interaction between Ru and Pt in optimizing ethene production and selectivity.

In this work, phase pure and highly crystalline O3-type layered oxide material (Na1Ni0.33Mn0.33Fe0.33O2-NNMF) was developed using; (i) a conventional solid-state synthesis route and (ii) a facile microwave-assisted sol–gel technique. A comparison of structural, thermal, and electrochemical properties is presented to elucidate the usefulness of the microwave-assisted sol–gel synthesis technique. A remarkable reduction in the sintering process time is noticed in the microwave-assisted sol–gel synthesis technique without compromising on the structural, thermal and electrochemical properties when compared to the conventional solid-state synthesis route confirming its decent cost-effectiveness. It is further noticed that NNMF developed through microwave-assisted sol–gel synthesis technique demonstrates superior thermal stability and comparable electrochemical performance as compared to the same material produced through the conventional sintering process. The decent electrochemical properties induced in NNMF during the microwave-assisted sol–gel synthesis technique can be attributed to the efficient diffusion of Na+ ions into/from the host structure during the intercalation/de-intercalation process as indicated by the high value of sodium diffusion coefficient (1 × 109-3.58 × 109m2s−1). The Potentiostatic Intermittent Titration Technique (PITT) analysis confirms single-phase Na+ intercalation/deintercalation in the host structure, regardless of the synthesis process. Finally, EIS analysis confirms the capacity fading of the developed materials during the cycling process is essentially due to an increase in the resistance with the increasing number of cycles due to the gradual thickening of formed SEI layer. The microwave-assisted sol–gel synthesis technique can be effectively employed for the production of many families of cathode materials at competitive cost facilitating their commercialization.

Abstract Herein, we have conducted a comprehensive study to uncover the thermal transport properties and hydrogen evolution reaction catalytic activity of recently synthesized holey graphyne. Our findings disclose that holey graphyne has a direct bandgap of 1.00 eV using the HSE06 exchange–correlation functional. The absence of imaginary phonon frequencies in the phonon dispersion ensures its dynamic stability. The formation energy of holey graphyne turns out to be − 8.46 eV/atom, comparable to graphene (− 9.22 eV/atom) and h-BN (− 8.80 eV/atom). At 300 K, the Seebeck coefficient is as high as 700 μV/K at a carrier concentration of 1 × 1010 cm-2. The predicted room temperature lattice thermal conductivity (κl) of 29.3 W/mK is substantially lower than graphene (3000 W/mK) and fourfold smaller than C3N (128 W/mK). At around 335 nm thickness, the room temperature κl suppresses by 25%. The calculated p-type figure of merit (ZT) reaches a maximum of 1.50 at 300 K, higher than that of holey graphene (ZT = 1.13), γ-graphyne (ZT = 0.48), and pristine graphene (ZT = 0.55 × 10–3). It further scales up to 3.36 at 600 K. Such colossal ZT values make holey graphyne an appealing p-type thermoelectric material. Besides that, holey graphyne is a potential HER catalyst with a low overpotential of 0.20 eV, which further reduces to 0.03 eV at 2% compressive strain.

The effect of precipitate coherency in an aged aluminum (Al) 2024 alloy is investigated using scanning transmission electron microscopy (STEM) and density functional theory (DFT) methods. The focus of the study is on understanding the effects of hydrogen (H2) entrapment in the alloy, which leads to the degradation of its corrosion resistance. We employed STEM to analyze the structure and strain properties of the alloy at high spatial resolution. This has been achieved by applying the geometrical phase analysis (GPA) to the acquired HRSTEM images. The determination of strain field around the precipitates was utilized to gauge the degree of coherency at the interface of the precipitates with Al matrix. We also applied density functional theory (DFT) simulations to investigate the interfacial energy at the interfaces of the precipitates with the Al matrix. The obtained results of the DFT simulations showed that the interfacial energy at the semi-coherent precipitates was determined to be 0.06 eV per atom, which was higher compared to the coherent precipitates. Our findings suggest that the semi-coherent precipitates have a less stable interface with the Al matrix. Furthermore, the study revealed that the H2 entrapped at the semi-coherent precipitate regions exhibits a binding energy which is 3.2 eV lower than that of the coherent precipitates. This implies that hydrogen binds more strongly at the semi-coherent precipitate cites, which enhances the process of the alloy embrittlement.

Abstract Carbon nanotubes are explored as a means of coherently converting the orbital angular momentum of light to an excitonic form that is more amenable to quantum information processing. An analytical analysis, based on dynamical conductivity, is used to show that orbital angular momentum is conserved, modulo N, for a carbon nanotube illuminated by radially polarized, twisted light. This result is numerically demonstrated using real-time time-dependent density functional theory which captures the absorption of twisted light and the subsequent transfer of twisted excitons. The results suggest that carbon nanotubes are promising candidates for constructing optoelectronic circuits in which quantum information is more readily processed while manifested in excitonic form.

Abstract Trapping lithium polysulfides (LiPSs) on a material effectively suppresses the shuttle effect and enhances the cycling stability of Li–S batteries. For the first time, we advocate a recently synthesized two-dimensional material, biphenylene, as an anchoring material for the lithium-sulfur battery. The density functional theory calculations show that LiPSs bind with pristine biphenylene insubstantially with binding energy ranging from −0.21 eV to −1.22 eV. However, defect engineering through a single C atom vacancy significantly improves the binding strength (binding energy in the range −1.07 to −4.11 eV). The Bader analysis reveals that LiPSs and S8 clusters donate the charge (ranging from −0.05 e to −1.12 e) to the biphenylene sheet. The binding energy of LiPSs with electrolytes is smaller than those with the defective biphenylene sheet, which provides its potential as an anchoring material. Compared with other reported two-dimensional materials such as graphene, MXenes, and phosphorene, the biphenylene sheet exhibits higher binding energies with the polysulfides. Our study deepens the fundamental understanding and shows that the biphenylene sheet is an excellent anchoring material for lithium-sulfur batteries for suppressing the shuttle effect because of its superior conductivity, porosity, and strong anchoring ability.

Background: Hemoglobin (Hb) variants arise due to point mutations in globin chains and their pathological treatments rely heavily on the identification of the nature and location of the mutation in the globin chains. Traditional methods for diagnosis such as HPLC and electrophoresis have their own limitations. Therefore, the present study aims to develop and optimize a specific method of sample processing that could lead to improved sequence coverage and analysis of Hb variants by nano LC−MALDI MS/MS. Methods: In our study, we primarily standardized various sample processing methods such as conventional digestion with trypsin followed by 10% acetonitrile treatment, digestion with multiple proteases like trypsin, Glu−C, Lys−C, and trypsin digestion subsequent to 2,2,2 trifluoroethanol (TFE) treatment. Finally, the peptides were identified by LC−MALDI MS/MS. All of these sample processing steps were primarily tested with recombinant Hb samples. After initial optimization, we found that the TFE method was the most suitable one and the efficiency of this method was applied in Hb variant identification based on high sequence coverage. Results: We developed and optimized a method using an organic solvent TFE and heat denaturation prior to digestion, resulting in 100% sequence coverage in the β−chains and 95% sequence coverage in the α−chains, which further helped in the identification of Hb mutations. A Hb variant protein sequence database was created to specify the search and reduce the search time. Conclusion: All of the mutations were identified using a bottom−up non−target approach. Therefore, a sensitive, robust and reproducible method was developed to identify single substitution mutations in the Hb variants from the sequence of the entire globin chains. Biological Significance: Over 330,000 infants are born annually with hemoglobinopathies and it is the major cause of morbidity and mortality in early childhood. Hb variants generally arise due to point mutation in the globin chains. There is high sequence homology between normal Hb and Hb variant chains. Due to this high homology between the two forms, identification of variants by mass spectrometry is very difficult and requires the full sequence coverage of α− and β−chains. As such, there is a need for a suitable method that provides 100% sequence coverage of globin chains for variant analysis by mass spectrometry. Our study provides a simple, robust, and reproducible method that is suitable for LC−MALDI and provides nearly complete sequence coverage in the globin chains. This method may be used in the near future in routine diagnosis for Hb variant analysis.

Secretory proteins are important for microbial adaptation and survival in a particular environment. Till date, experimental secretomes have been reported for a few archaea. In this study, we have identified the experimental secretome of Picrophilous torridus and evaluated the efficacy of various signal peptide predictors (SPPs) in identifying signal peptides (SPs) in its experimental secretome. Liquid chromatography mass spectrometric (LC MS) analysis was performed for three independent P. torridus secretome samples and only those proteins which were common in the three experiments were selected for further analysis. Thus, 30 proteins were finally included in this study. Of these, 10 proteins were identified as hypothetical/uncharacterized proteins. Gene Ontology, KEGG and STRING analyses revealed that majority of the sercreted proteins and/or their interacting partners were involved in different metabolic pathways. Also, a few proteins like malate dehydrogenase (Q6L0C3) were multi-functional involved in different metabolic pathways like carbon metabolism, microbial metabolism in diverse environments, biosynthesis of antibiotics, etc. Multi-functionality of the secreted proteins reflects an important aspect of thermoacidophilic adaptation of P. torridus which has the smallest genome (1.5 Mbp) among nonparasitic aerobic microbes. SPPs like, PRED-SIGNAL, SignalP 5.0, PRED-TAT and LipoP 1.0 identified SPs in only a few secreted proteins. This suggests that either these SPPs were insufficient, or N-terminal SPs were absent in majority of the secreted proteins, or there might be alternative mechanisms of protein translocation in P. torridus.

Hydrodeoxygenation (HDO) reaction is a route with much to offer in the conversion and upgrading of bio-oils into fuels; the latter can potentially replace fossil fuels. The catalyst’s design and the feedstock play a critical role in the process metrics (activity, selectivity). Among the different classes of catalysts for the HDO reaction, the transition metal phosphides (TMP), e.g., binary (Ni2P, CoP, WP, MoP) and ternary Fe-Co-P, Fe-Ru-P, are chosen to be discussed in the present review article due to their chameleon type of structural and electronic features giving them superiority compared to the pure metals, apart from their cost advantage. Their active catalytic sites for the HDO reaction are discussed, while particular aspects of their structural, morphological, electronic, and bonding features are presented along with the corresponding characterization technique/tool. The HDO reaction is critically discussed for representative compounds on the TMP surfaces; model compounds from the lignin-derivatives, cellulose derivatives, and fatty acids, such as phenols and furans, are presented, and their reaction mechanisms are explained in terms of TMPs structure, stoichiometry, and reaction conditions. The deactivation of the TMP’s catalysts under HDO conditions is discussed. Insights of the HDO reaction from computational aspects over the TMPs are also presented. Future challenges and directions are proposed to understand the TMP-probe molecule interaction under HDO process conditions and advance the process to a mature level.

We have combined first-principles and semiclassical Boltzmann transport theory to demonstrate the potential superb electronic and thermal transport properties of bulk and monolayer bismuth oxyiodide (BiOI). The exfoliation energy required to produce monolayer BiOI (22.53 meV/Å2) is lower than that required to produce monolayer h-BN, implying possible manufacturing from bulk. The calculated phonon frequencies, complemented with an ab initio molecular dynamic simulation for 8 ps at elevated temperature (900 K), reveal the monolayer’s dynamic and structural stability. The calculated band gaps are indirect for both bulk and monolayer and amount to 2.04 eV and 2.07 eV, respectively. Our results indicate remarkably high Seebeck coefficients for BiOI in the bulk (227 µV/K at a hole concentration of 9.00 × 1020 cm−3) and in the monolayer form (200 µV/K at a hole concentration of 8.14 × 1013 cm−2) at 900 K. The lowest lattice thermal conductivities of 1.35 W/mK for the bulk and 1.44 W/mK for the monolayer are obtained at 900 K. Because of the high value of S2σ/τ for p-type doping, the figure of merit achieves peak values of 1.51 at a carrier concentration of 8.44 × 1020 cm−3 for bulk BiOI and 1.61 at a carrier concentration of 4.27 × 1013 cm−2 for monolayer BiOI.

Nascent polypeptide-associated complex (NAC) is a ribosome-associated molecular chaperone which is present only in archaea and eukaryotes. The primary function of NAC is to shield the newly synthesized polypeptide chains from inappropriate interactions with the cytosolic factors. Besides that, NAC has been implicated in diverse biological functions, which suggest that it might be a multifunctional protein. An elaborate study on NAC can provide useful information on protein folding in extreme conditions in which many archaea grow. Thus, in the present study, we have studied the biophysical and the biochemical characteristics of NAC of Picrophilus torridus, an extreme thermoacidophilic archaeon. The study of protein–protein interactions and binding partners of a protein provides useful insights into the new/unreported roles of a protein. Thus, in this study, we have identified the binding partners of NAC in P. torridus. The NAC protein of P. torridus was cloned, expressed, and purified, and its binding partners were isolated by a pull down assay followed by identification with liquid chromatography–mass spectrometry. To the best of our knowledge, this is the first report on the biophysical and the biochemical characterization of NAC from P. toridus and the identification of its interacting partners.

Dengue virus is a pathogen of global concern and has a huge impact on public health system in low- and middle-income countries. The capsid protein of dengue virus is least conserved among related flavivirus and there is very limited information on the role of cytosolic proteins that interact with dengue virus capsid. We identified DEAD (Asp-Glu-Ala-Asp) Box Helicase 3, an X-Linked (DDX3X), cytosolic ATP-dependent RNA helicase as a dengue virus capsid-interacting protein. We show that the N-terminal region of capsid is important for interaction with DDX3X, while the N-terminal domain of DDX3X seems to be involved in interaction with dengue capsid. DDX3X was down-regulated in dengue virus infected cells at later stages of infection. Our results show that DDX3X is an antiviral protein as suppression of DDX3X expression by siRNA led to an increase in viral titers and overexpression of DDX3X led to inhibition of viral replication. Knock-down of DDX3X did not affect induction of type I interferon response upon infection suggesting that the effect of DDX3X knock-down is independent of the interferon-dependent pathways that DDX3X modulates under normal conditions. Thus, our study identifies DDX3X as a dengue virus capsid interacting protein and indicates a potential link between the antiviral functions of DDX3X and dengue capsid at later stages of dengue infection.

Cyclic di-AMP is a recently discovered signaling molecule which regulates various aspects of bacterial physiology and virulence. Here we report the characterization of c-di-AMP synthesizing and hydrolyzing proteins from Mycobacterium tuberculosis. Recombinant Rv3586 (MtbDisA) can synthesize c-di-AMP from ATP through the diadenylate cyclase activity. Detailed biochemical characterization of the protein revealed that the diadenylate cyclase (DAC) activity is allosterically regulated by ATP. We have identified the intermediates of the DAC reaction and propose a two-step synthesis of c-di-AMP from ATP/ADP. MtbDisA also possesses ATPase activity which is suppressed in the presence of the DAC activity. Investigations by liquid chromatography -electrospray ionization mass spectrometry have detected multimeric forms of c-di-AMP which have implications for the regulation of c-di-AMP cellular concentration and various pathways regulated by the dinucleotide. We have identified Rv2837c (MtbPDE) to have c-di-AMP specific phosphodiesterase activity. It hydrolyzes c-di-AMP to 5'-AMP in two steps. First, it linearizes c-di-AMP into pApA which is further hydrolyzed to 5'-AMP. MtbPDE is novel compared to c-di-AMP specific phosphodiesterase, YybT (or GdpP) in being a soluble protein and hydrolyzing c-di-AMP to 5'-AMP. Our results suggest that the cellular concentration of c-di-AMP can be regulated by ATP concentration as well as the hydrolysis by MtbPDE.

The glycosyl hydrolase 18 (GH18) family consists of active chitinases as well as chitinase like lectins/proteins (CLPs). The CLPs share significant sequence and structural similarities with active chitinases, however, do not display chitinase activity. Some of these proteins are reported to have specific functions and carbohydrate binding property. In the present study, we report a novel chitinase like lectin (TCLL) from Tamarindus indica. The crystal structures of native TCLL and its complex with N-acetyl glucosamine were determined. Similar to the other CLPs of the GH18 members, TCLL lacks chitinase activity due to mutations of key active site residues. Comparison of TCLL with chitinases and other chitin binding CLPs shows that TCLL has substitution of some chitin binding site residues and more open binding cleft due to major differences in the loop region. Interestingly, the biochemical studies suggest that TCLL is an N-acetyl glucosamine specific chi-lectin, which is further confirmed by the complex structure of TCLL with N-acetyl glucosamine complex. TCLL has two distinct N-acetyl glucosamine binding sites S1 and S2 that contain similar polar residues, although interaction pattern with N-acetyl glucosamine varies extensively among them. Moreover, TCLL structure depicts that how plants utilize existing structural scaffolds ingenuously to attain new functions. To date, this is the first structural investigation of a chi-lectin from plants that explore novel carbohydrate binding sites other than chitin binding groove observed in GH18 family members. Consequently, TCLL structure confers evidence for evolutionary link of lectins with chitinases.