jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Marta Hammerstad | Anne Kristine Rugtveit | Sondov Dahlen | Hilde Kristin Andersen | H.-P. Hersleth
Source: Antioxidants (article, 2023-06-06)
Field: Chemistry — Inorganic Chemistry

Functional Diversity of Homologous Oxidoreductases—Tuning of Substrate Specificity by a FAD-Stacking Residue for Iron Acquisition and Flavodoxin Reduction Although bacterial thioredoxin reductase-like ferredoxin/flavodoxin NAD(P)<sup>+</sup> oxidoreductases (FNRs) are similar in terms of primary sequences and structures, they participate in diverse biological processes by catalyzing a range of different redox reactions. Many of the reactions are critical for the growth, survival of, and infection by pathogens, and insight into the structural basis for substrate preference, specificity, and reaction kinetics is crucial for the detailed understanding of these redox pathways. <i>Bacillus cereus</i> (<i>Bc</i>) encodes three FNR paralogs, two of which have assigned distinct biological functions in bacillithiol disulfide reduction and flavodoxin (Fld) reduction. <i>Bc</i> FNR2, the endogenous reductase of the Fld-like protein NrdI, belongs to a distinct phylogenetic cluster of homologous oxidoreductases containing a conserved His residue stacking the FAD cofactor. In this study, we have assigned a function to FNR1, in which the His residue is replaced by a conserved Val, in the reduction of the heme-degrading monooxygenase IsdG, ultimately facilitating the release of iron in an important iron acquisition pathway. The <i>Bc</i> IsdG structure was solved, and IsdG-FNR1 interactions were proposed through protein-protein docking. Mutational studies and bioinformatics analyses confirmed the importance of the conserved FAD-stacking residues on the respective reaction rates, proposing a division of FNRs into four functionally unique sequence similarity clusters likely related to the nature of this residue. Ferredoxin ; Flavodoxin ; Cofactor ; Biochemistry ; Biology ; Reductase ; Sequence alignment ; Multiple sequence alignment ; NAD+ kinase ; Redox ; Structural similarity ; Peptide sequence ; Chemistry ; Enzyme ; Gene Metal-Catalyzed Oxygenation Mechanisms ; Redox biology and oxidative stress ; Heme Oxygenase-1 and Carbon Monoxide
Authors: Mika Hosokawa | Shiori Ito | Kaito Noda | Yusuke Kono | Ken‐ichi Ogawara
Source: Biological and Pharmaceutical Bulletin (article, 2023-09-30)
Field: Materials Science — Biomaterials

Preparation and Evaluation of Paclitaxel-Loaded PEGylated Niosomes Composed of Sorbitan Esters Niosomes are non-ionic surfactant (NIS)-based bilayer vesicles and, like liposomes, have great potential as drug-delivery systems. Our previous study revealed that polyethylene glycol (PEG) niosomes using different sorbitan ester (Span) surfactants (sorbitan monoester, Span 20, 40, 60, 80; sorbitan triester, Span 65) distributed within tumors similarly to PEG liposomes. The aim of this study was to encapsulate efficiently an anti-cancer drug, paclitaxel (PTX) into Span PEG niosomes, and evaluate PTX release profiles and anti-tumor efficacy of PTX-loaded Span PEG niosomes. Niosome sizes ranged between 100-150 nm, and the PTX encapsulation efficiency was more than 50%. All niosomes examined, in the presence of serum, yielded sustained PTX-release profiles. PTX release at 24 and 48 h from Span 80 PEG niosomes was significantly the highest among the other Span PEG niosomes examined. In C26 tumor-bearing mice, PTX-loaded Span 40 PEG niosomes (the lowest PTX release in vitro) suppressed tumor growth while PTX-loaded Span 80 PEG niosomes (the highest PTX release in vitro) did not. Thus, we succeeded in the control of PTX release from Span PEG niosomes by modifying the component of niosomes, and it influenced the effects of drugs loaded into niosomes. This demonstrates that the excellent NIS physicochemical properties of Spans make them an ideal candidate for anti-cancer drug-carrier niosomes. Niosome ; Sorbitan ; PEG ratio ; Polyethylene glycol ; Liposome ; Chemistry ; Chromatography ; Pharmacology ; Vesicle ; Membrane ; Biochemistry ; Medicine Nanoparticle-Based Drug Delivery ; Advancements in Transdermal Drug Delivery ; Erythrocyte Function and Pathophysiology
Authors: Marin Tharrault | Sabrine Ayari | Mehdi Arfaoui | Eva Desgué | Romaric Le Goff | Pascal Morfin | José M. Palomo | Michaël Rosticher | S. Jaziri | Bernard Plaçais | P. Legagneux | Francesca Carosella | Christophe Voisin | R. Ferreira | Emmanuel Baudin
Source: arXiv (Cornell University) (preprint, 2023-11-03)
Field: Materials Science — Materials Chemistry

The optical absorption in indirect semiconductor to semimetal PtSe2 arises from direct transitions $\rm{PtSe_2}$ is a van der Waals material transitioning from an indirect bandgap semiconductor to a semimetal with increasing thickness. Its absorption threshold has been conjectured to originate from interband indirect transitions. By quantitative comparison between broadband ($0.8 - 3.0\,\rm{eV}$) optical absorption of high-quality exfoliated crystals and DFT ab-initio simulations, we prove instead that the optical absorption arises only from direct transitions. This understanding allows us to shed light on the semiconductor to semimetal transition and to explore the effect of stacking and excitons on the optical absorption. Semimetal ; Semiconductor ; Absorption (acoustics) ; van der Waals force ; Stacking ; Exciton ; Condensed matter physics ; Ab initio ; Materials science ; Physics ; Optoelectronics ; Optics ; Band gap ; Quantum mechanics 2D Materials and Applications ; Semiconductor materials and interfaces ; Semiconductor Quantum Structures and Devices
Authors: Shuai A. Chen | K. T. Law
Source: arXiv (Cornell University) (preprint, 2023-03-27)
Field: Materials Science — Materials Chemistry

The Ginzburg-Landau theory of flat band superconductors with quantum metric Recent experimental study unveiled highly unconventional phenomena in the superconducting twisted bilayer graphene (TBG) with ultra flat bands, which cannot be described by the conventional BCS theory. For example, given the small Fermi velocity of the flat bands, the superconducting coherence length predicted by BCS theory is more than 20 times shorter than the measured values. A new theory is needed to understand many of the unconventional properties of flat band superconductors. In this work, we establish a Ginzburg-Landau (GL) theory from a microscopic flat band Hamiltonian. The GL theory shows how the properties of the physical quantities such as the critical temperature, the superconducting coherence length, the upper critical field and the superfluid density are governed by the quantum metric of the Bloch states. One key conclusion is that the superconducting coherence length is not determined by the Fermi velocity but by the size of the optimally localized Wannier functions which is limited by quantum metric. Applying the theory to TBG, we calculated the superconducting coherence length and the upper critical fields. The results match the experimental ones well without fine tuning of parameters. The established GL theory provides a new and general theoretical framework for understanding flat band superconductors with quantum metric. Physics ; Superconductivity ; Coherence length ; Condensed matter physics ; Superconducting coherence length ; Quantum mechanics ; Superfluidity ; Coherence (philosophical gambling strategy) ; Critical field ; Quantum ; BCS theory ; Hamiltonian (control theory) ; Fermi energy ; Pairing ; Mathematics Graphene research and applications ; Superconductivity in MgB2 and Alloys ; Physics of Superconductivity and Magnetism
Authors: Huanhuan Shi | Mengmeng Li | Shuai Fu | Christof Neumann | Xiaodong Li | Wenhui Niu | Yunji Lee | Mischa Bonn | Hai I. Wang | Andrey Turchanin | Ali Shaygan Nia | Sheng Yang | Xinliang Feng
Source: Angewandte Chemie (article, 2023-05-11)
Field: Materials Science — Materials Chemistry

High‐throughput Synthesis of Solution‐Processable van der Waals Heterostructures through Electrochemistry Abstract Two‐dimensional van der Waals heterostructures (2D vdWHs) have recently gained widespread attention because of their abundant and exotic properties, which open up many new possibilities for next‐generation nanoelectronics. However, practical applications remain challenging due to the lack of high‐throughput techniques for fabricating high‐quality vdWHs. Here, we demonstrate a general electrochemical strategy to prepare solution‐processable high‐quality vdWHs, in which electrostatic forces drive the stacking of electrochemically exfoliated individual assemblies with intact structures and clean interfaces into vdWHs with strong interlayer interactions. Thanks to the excellent combination of strong light absorption, interfacial charge transfer, and decent charge transport properties in individual layers, thin‐film photodetectors based on graphene/In 2 Se 3 vdWHs exhibit great promise for near‐infrared (NIR) photodetection, owing to a high responsivity (267 mA W −1 ), fast rise (72 ms) and decay (426 ms) times under NIR illumination. This approach enables various hybrid systems, including graphene/In 2 Se 3 , graphene/MoS 2 and graphene/MoSe 2 vdWHs, providing a broad avenue for exploring emerging electronic, photonic, and exotic quantum phenomena. Graphene ; Materials science ; Heterojunction ; Stacking ; Nanotechnology ; Optoelectronics ; Chemistry 2D Materials and Applications ; MXene and MAX Phase Materials ; Graphene research and applications
Authors: Jesse A. Jones | Michael P. Andreas | Tobias W. Giessen
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-09-18)
Field: Materials Science — Materials Chemistry

Structural basis for peroxidase encapsulation in a protein nanocompartment Encapsulins are self-assembling protein nanocompartments capable of selectively encapsulating dedicated cargo proteins, including enzymes involved in iron storage, sulfur metabolism, and stress resistance. They represent a unique compartmentalization strategy used by many pathogens to facilitate specialized metabolic capabilities. Encapsulation is mediated by specific cargo protein motifs known as targeting peptides (TPs), though the structural basis for encapsulation of the largest encapsulin cargo class, dye-decolorizing peroxidases (DyPs), is currently unknown. Here, we characterize a DyP-containing encapsulin from the enterobacterial pathogen <i>Klebsiella pneumoniae</i>. By combining cryo-electron microscopy with TP mutagenesis, we elucidate the molecular basis for cargo encapsulation. TP binding is mediated by cooperative hydrophobic and ionic interactions as well as shape complementarity. Our results expand the molecular understanding of enzyme encapsulation inside protein nanocompartments and lay the foundation for rationally modulating encapsulin cargo loading for biomedical and biotechnological applications. Chemistry ; Encapsulation (networking) ; Nanoreactor ; Biochemistry ; Computational biology ; Nanotechnology ; Biophysics ; Biology ; Materials science ; Computer science Enzyme Structure and Function ; Bacterial Genetics and Biotechnology ; Bacteriophages and microbial interactions
Authors: Rui Zhang | Jianshun Zhang | Roger Schmidt | Jeremy L. Gilbert
Source: Building Simulation (article, 2023-12-27)
Field: Materials Science — Materials Chemistry

Mechanistic modeling of copper corrosions in data center environments Corrosion ; Relative humidity ; Economizer ; Environmental science ; Pollutant ; Reliability (semiconductor) ; Air pollution ; Environmental engineering ; Materials science ; Engineering ; Meteorology ; Metallurgy ; Mechanical engineering ; Chemistry Corrosion Behavior and Inhibition ; Recycling and Waste Management Techniques ; Building materials and conservation
Authors: Ghulam Abbas Khan | Yonghua Lü | Pei Wang
Source: 2D Materials (article, 2023-06-19)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Enhanced dual-band absorption of graphene mediated by an aluminum metastructure Abstract Graphene absorption from the visible to infrared spectrum has great potential and broad applications in miniature of modern optoelectronic biosensors and photodetectors. However, graphene has zero bandgap energy, which limits its absorption to 2.3% in the visible and infrared spectrums. Here, we propose a metastructure to optimize graphene absorption in the visible to near-infrared frequency regions. The metastructure, comprising an array of aluminum square blocks (Al-SBs) on a graphene layer, a silica spacer, and an Al reflector, is investigated for absorption enhancement. This work deciphers the effect of the periodicity of decorated Al-SBs on the evolution of dual-band absorption in single-layer graphene under normal incidence. The electromagnetic signatures of two excited modes indicate that surface plasmons and magnetic dipole plasmons are mediators of absorption. The investigation into the impact of geometrical parameters illustrates that the coexisting phenomena of a relative broad peak and a relative sharp peak have been achieved simultaneously with high efficiency. The dynamic manipulation of surface plasmons and magnetic dipole plasmons presents great potential for a diverse range of applications, such as sensing and imaging. By controlling the periodicity of Al-SBs, it is possible to achieve active control of surface plasmon resonance, and a detection range of 300 nm is observed. Dynamic control of the magnetic dipole plasmon is successfully achieved by modifying the electrical environment of the graphene layer, which is realized by altering the underlying spacer material. Collectively, the findings of this study demonstrate the significant potential of the suggested metastructure for its prospective applications in optoelectronic devices, including biosensors, photovoltaics, and photodetectors that rely on the dynamic control of surface and magnetic plasmon resonances. Graphene ; Materials science ; Plasmon ; Absorption (acoustics) ; Optoelectronics ; Surface plasmon ; Infrared ; Band gap ; Optics ; Surface plasmon resonance ; Nanotechnology ; Nanoparticle ; Composite material ; Physics Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Graphene research and applications
Authors: Mahmoud Payami
Source: arXiv (Cornell University) (preprint, 2023-02-26)
Field: Chemistry — Inorganic Chemistry

DFT+U study of UO$_2$: Correct lattice parameter and electronic band-gap Hubbard-corrected density functional theory, denoted by DFT+U method, was developed to enable correct prediction of insulating properties for strongly-correlated electron systems. UO$_2$ is an example having O-$2p$, U-$6d$, and U-$5f$ incomplete electronic shells. Usually, researchers apply the Hubbard correction only to the localized incomplete $5f$ electrons of U atoms and succeed to predict insulating property and good geometric properties by tweaking the Hubbard-U parameter. However, it turned out that in such a way it was impossible to obtain reasonable values for both geometry and electronic band-gap at the same time. In this work, we show that it is possible to produce good values for those properties just by applying and tuning the Hubbard corrections to all incomplete shells of O-$2p$, U-$6d$, and U-$5f$. Hubbard model ; Density functional theory ; Tweaking ; Electronic structure ; Electron ; Band gap ; Lattice (music) ; Condensed matter physics ; Physics ; Materials science ; Quantum mechanics ; Computer science ; Superconductivity Radioactive element chemistry and processing ; Nuclear Materials and Properties ; Nuclear reactor physics and engineering
Authors: Hsin‐Yu Chen | Jeremy W. Gordon | Nicholas Dwork | Brian Chung | Andrew Riselli | Sanjay Sivalokanathan | Robert Bok | James B. Slater | Daniel B. Vigneron | M. Roselle Abraham | Peder E. Z. Larson
Source: medRxiv (preprint, 2023-10-19)
Field: Chemistry — Spectroscopy

Probing Human Heart TCA Cycle Metabolism and Response to Glucose Load using Hyperpolarized [2- <sup>13</sup> C]Pyruvate MR Spectroscopy HP [2-<sup>13</sup>C]pyruvate imaging is safe and permits non-invasive assessment of TCA cycle intermediates and the acetyl buffer, acetylcarnitine, which is not possible using HP [1-<sup>13</sup>C]pyruvate. Cardiac metabolite measurement in the fasting/fed states provides information on cardiac metabolic flexibility and the acetylcarnitine pool. Acetylcarnitine ; Glycolysis ; Citric acid cycle ; Tricarboxylic acid ; Chemistry ; Internal medicine ; Metabolite ; Endocrinology ; Pyruvate dehydrogenase complex ; Metabolism ; Medicine ; Biochemistry Advanced NMR Techniques and Applications ; Advanced MRI Techniques and Applications ; Electron Spin Resonance Studies
Authors: Y. Shen | J. Sears | G. Fabbris | J. Li | J. Pelliciari | M. Mitrano | Weiwei He | Junjie Zhang | J. F. Mitchell | V. Bisogni | M. R. Norman | S. Johnston | M. P. M. Dean
Source: arXiv (Cornell University) (preprint, 2023-01-10)
Field: Materials Science — General Materials Science

Electronic character of charge order in square planar low valence nickelates Charge order is a central feature of the physics of cuprate superconductors and is known to arise from a modulation of holes with primarily oxygen character. Low-valence nickelate superconductors also host charge order, but the electronic character of this symmetry breaking is unsettled. Here, using resonant inelastic x-ray scattering at the Ni $L_2$-edge, we identify intertwined involvements of Ni $3d_{x^2-y^2}$, $3d_{3z^2-r^2}$, and O $2p_σ$ orbitals in the formation of diagonal charge order in an overdoped low-valence nickelate La$_{4}$Ni$_{3}$O$_{8}$. The Ni $3d_{x^2-y^2}$ orbitals, strongly hybridized with planar O $2p_σ$, largely shape the spatial charge distribution and lead to Ni site-centered charge order. The $3d_{3z^2-r^2}$ orbitals play a small, but non-negligible role in the charge order as they hybridize with the rare-earth $5d$ orbitals. Our results reveal that the low-energy physics and ground-state character of these nickelates are more complex than those in cuprates. Planar ; Character (mathematics) ; Valence (chemistry) ; Square (algebra) ; Charge (physics) ; Order (exchange) ; Physics ; Mathematics ; Computer science ; Quantum mechanics ; Geometry ; Business ; Computer graphics (images) Metallurgical and Alloy Processes ; Chemical and Physical Properties of Materials ; Magnetic Properties of Alloys
Authors: Wilson Phung | Corey E. Bakalarski | Trent Hinkle | Wendy Sandoval | Michael T. Marty
Source: ChemRxiv (preprint, 2023-05-09)
Field: Chemistry — Spectroscopy

The UniDec Processing Pipeline for Rapid Analysis of Biotherapeutic Mass Spectrometry Data Recent advances in native mass spectrometry (MS) and denatured intact protein MS have made these techniques essential for biotherapeutic characterization. As MS analysis has increased in throughput and scale, new data analysis workflows are needed to provide rapid quantitation from large datasets. Here, we describe the UniDec Processing Pipeline (UPP) for the analysis of batched biotherapeutic intact MS data. UPP is built into the UniDec software package, which provides fast processing, deconvolution, and peak detection. The user and programming interfaces for UPP read a spreadsheet that contains the data file names, deconvolution parameters, and quantitation settings. After iterating through the spreadsheet and analyzing each file, it returns a spreadsheet of results and HTML reports. We demonstrate the use of UPP to measure correct pairing percentage on a set of bispecific antibody data and to measure drug-to-antibody ratios from antibody-drug conjugates. Moreover, because the software is free and open-source, users can easily build on this platform to create customized workflows and calculations. Thus, UPP provides a flexible workflow that can be deployed in diverse settings and for a wide range of biotherapeutic applications. Pipeline (software) ; Workflow ; Computer science ; Deconvolution ; Software ; Measure (data warehouse) ; Throughput ; Set (abstract data type) ; Data mining ; Database ; Operating system ; Algorithm ; Programming language Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Mass Spectrometry Techniques and Applications
Authors: Sathya Perera | Lichang Wang
Source: ChemRxiv (preprint, 2023-06-12)
Field: Chemistry — Physical and Theoretical Chemistry

DFT Studies of Rotational Conformers of 4-Azido-N-Phenylmalemide DFT calculations were performed to study the rotational conformers of 4-Azido-N-Phenylmalemide using B3LYP with 7 basis sets, 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p), and 6-311++G(df,pd). DFT studies show that the two isomers of 4-Azido-N-Phenylmalemide have the same energetics. Furthermore, the rotational barrier between the isomers is 0.17 eV in N, N-dimethylacetamide (NNDMA) and 0.15 eV in tetrahydrofuran (THF). These indicate that the isomers are present in the solvents and can be easily converted between them. The azido asymmetric stretch differs by about 1 cm-1 between the isomers in NNDMA and less than 1 cm-1 in THF. The most significant effect of rotational conformers is in the coupling strength of fermi resonances with the most impact in THF environment. Therefore, the current DFT results show that isomers of 4-Azido-N-Phenylmalemide can be mostly detected in THF by 2D IR technique. Furthermore, the results from seven basis set provide consistent conclusion on the isomers, dependence of the basis sets may be useful information to the development of functionals in DFT method and may be served as a useful tool to understand coupling of vibrational modes of complex molecules and their isomers. Conformational isomerism ; Tetrahydrofuran ; Chemistry ; Basis set ; Molecule ; Density functional theory ; Computational chemistry ; Crystallography ; Organic chemistry Chemical Reactions and Mechanisms ; Molecular Spectroscopy and Structure ; Various Chemistry Research Topics
Authors: Hadrien Bense | Emmanuel Siéfert | Fabian Brau
Source: Physical Review Letters (article, 2023-11-03)
Field: Materials Science — Surfaces, Coatings and Films

Measurement of Capillary Forces Using Two Fibers Dynamically Withdrawn from a Liquid: Evidence for an Enhanced Cheerios Effect We study the capillary attraction force between two fibers dynamically withdrawn from a bath. We propose an experimental method to measure this force and show that its magnitude strongly increases with the retraction speed by up to a factor of 10 compared to the static case. We show that this remarkable increase stems from the shape of the dynamical meniscus between the two fibers. We first study the dynamical meniscus around one fiber and obtain experimental and numerical scaling of its size increase with the capillary number, which is not captured by the classical Landau-Levich-Derjaguin theory. We then show that the shape of the deformed air-liquid interface around two fibers can be inferred from the linear superposition of the interface around a single fiber. These results yield an analytical expression for the capillary force which compares well with the experimental data. Our study reveals the critical role of the retraction speed to create stronger capillary interactions, with potential applications in industry or biology. Capillary action ; Meniscus ; Fiber ; Superposition principle ; Surface tension ; Capillary number ; Mechanics ; Scaling ; Tension (geology) ; Physics ; Liquid liquid ; Materials science ; Composite material ; Optics ; Chemistry ; Thermodynamics ; Mathematics ; Geometry ; Compression (physics) ; Chromatography Surface Modification and Superhydrophobicity ; Experimental and Theoretical Physics Studies ; Microfluidic and Bio-sensing Technologies