jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yajun Li | Jinman He | Xiuxia Zhang | Xiaodong Deng
Source: BMC Genomics (article, 2024-06-05)
Field: Materials Science — Biomaterials

The draft genome of Nitzschia closterium f. minutissima and transcriptome analysis reveals novel insights into diatom biosilicification Here, we described a draft genome of N. closterium f. minutissima and compared it with those of eight other diatoms, which provided new insight into its evolutionary features. Transcriptome analysis to identify DEGs in response to silicon will help to elucidate the underlying molecular mechanism of diatom biosilicification in N. closterium f. minutissima. Phaeodactylum tricornutum ; Biology ; Diatom ; Thalassiosira pseudonana ; Nitzschia ; Genome ; Phylogenetic tree ; Transcriptome ; Frustule ; Genome size ; Evolutionary biology ; Gene ; Thalassiosira weissflogii ; Haptophyte ; Genetics ; Botany ; Phytoplankton ; Ecology ; Gene expression Diatoms and Algae Research ; Genomics and Phylogenetic Studies ; Protist diversity and phylogeny
Authors: Andrew J. Arslanian | Vicki H. Wysocki
Source: Journal of the American Society for Mass Spectrometry (article, 2024-12-07)
Field: Chemistry — Spectroscopy

Roughhousing with Ions: Surface-Induced Dissociation and Electron Capture Dissociation as Diagnostics of Q-Cyclic IMS-TOF Instrument Tuning Gentleness Native mass spectrometry can characterize a range of biomolecular features pertinent to structural biology, including intact mass, stoichiometry, ligand-bound states, and topology. However, when an instrument's ionization source is tuned to maximize signal intensity or adduct removal, it is possible that the biomolecular complex's tertiary and quaternary structures can be rearranged in a way that no longer reflect its native-like conformation. This could affect downstream ion activation experiments, leading to erroneous conclusions about the native-like structure. One activation strategy is surface-induced dissociation (SID), which generally causes native-like protein complexes to dissociate along the weakest subunit interfaces, revealing critical information about the complex's native-like topology and subunit connectivity. If the quaternary structure has been disturbed, then the SID fingerprint will shift as well. Thus, SID was used to diagnose source-induced quaternary structure rearrangement and help tune an instrument's source and other upstream transmission regions to strike the balance between signal intensity, adduct removal, and conserving the native-like structure. Complementary to SID, electron-capture dissociation (ECD) can also diagnose rearranged quaternary structures and was used after in-source activation to confirm that the subunit interfaces were rearranged, opening the structure to electron capture and subsequent dissociation. These results provide a valuable guide for new practitioners of native mass spectrometry and highlight the importance of using standard protein complexes when tuning new instrument platforms for optimal native mass spectrometry performance. Chemistry ; Dissociation (chemistry) ; Mass spectrometry ; Protein quaternary structure ; Electron-capture dissociation ; Protein subunit ; Adduct ; Ion ; Tandem mass spectrometry ; Analytical Chemistry (journal) ; Crystallography ; Chemical physics ; Chromatography ; Physical chemistry ; Organic chemistry Mass Spectrometry Techniques and Applications ; Ion-surface interactions and analysis ; Analytical Chemistry and Chromatography
Authors: Lehlohonolo Mohale | Jibril Abdulsalam | Jean Mulopo
Source: Biomass Conversion and Biorefinery (article, 2024-08-20)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Nanoporous carbons from hydrothermally pre-treated avocado waste: experimental design, hydrogen storage behavior, and energy distribution analysis Abstract Avocado waste, which includes the peel and seed, is a promising biomass source for highly porous materials crucial to establishing an economical and efficient hydrogen economy. Hydrothermally pre-treated avocado waste was explored as a precursor for biocarbon optimized for hydrogen storage, employing the design of experiment to vary activation temperature and impregnation ratio. The resulting optimized biocarbon, synthesized at 800 °C with a 1:3 impregnation ratio, exhibited appreciable hydrogen uptake at 77 K and 1 bar, surpassing some reported literature values. Notably, the optimized biocarbon (AC 200 ), hydrothermally pretreated at 200 °C, demonstrated a remarkable 3.07 wt% hydrogen uptake, attributed to its narrower micropores facilitating extensive adsorption. The study employed a modified Langmuir model incorporating homotattic patch approximation for a universal isotherm model, providing insights into the surface characteristics of the optimized biocarbon in terms of adsorption site availability and energy distribution. The modeling offers insight into the heterogeneous surface characteristics, specifically regarding the availability of adsorption sites, elucidating the distinct behavior exhibited by each optimized biocarbon. Nanoporous ; Hydrogen storage ; Waste-to-energy ; Chemical engineering ; Waste management ; Hydrogen ; Materials science ; Chemistry ; Environmental science ; Organic chemistry ; Engineering ; Municipal solid waste Supercapacitor Materials and Fabrication ; Adsorption and biosorption for pollutant removal ; Catalysis for Biomass Conversion
Authors: R. S. Zhu | Yanting Wang
Source: Nature Communications (article, 2024-07-29)
Field: Materials Science — Materials Chemistry

A critical edge number revealed for phase stabilities of two-dimensional ball-stick polygons Phase behaviours of two-dimensional (2D) systems constitute a fundamental topic in condensed matter and statistical physics. Although hard polygons and interactive point-like particles are well studied, the phase behaviours of more realistic molecular systems considering intermolecular interaction and molecular shape remain elusive. Here we investigate by molecular dynamics simulation phase stabilities of 2D ball-stick polygons, serving as simplified models for molecular systems. Below the melting temperature T<sub>m</sub>, we identify a critical edge number <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub><mml:mrow><mml:mi>n</mml:mi></mml:mrow> <mml:mrow><mml:mi>c</mml:mi></mml:mrow> </mml:msub> <mml:mo>=</mml:mo> <mml:mn>4</mml:mn></mml:math> , at which a distorted square lattice emerges; when <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>n</mml:mi> <mml:mspace></mml:mspace> <mml:mo><</mml:mo> <mml:mspace></mml:mspace> <mml:msub><mml:mrow><mml:mi>n</mml:mi></mml:mrow> <mml:mrow><mml:mi>c</mml:mi></mml:mrow> </mml:msub> </mml:math> , the triangular system stabilizes at a spin-ice-like glassy state; when <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>n</mml:mi> <mml:mspace></mml:mspace> <mml:mo>></mml:mo> <mml:mspace></mml:mspace> <mml:msub><mml:mrow><mml:mi>n</mml:mi></mml:mrow> <mml:mrow><mml:mi>c</mml:mi></mml:mrow> </mml:msub> </mml:math> , the polygons stabilize at crystalline states. Moreover, in the crystalline state, T<sub>m</sub> is higher for polygons with more edges at higher pressures but exhibits a crossover for hexagon and octagon at low pressures. A theoretical framework taking into account the competition between entropy and enthalpy is proposed to provide a comprehensive understanding of our results, which is anticipated to facilitate the design of 2D materials. Statistical physics ; Molecular dynamics ; Phase transition ; Enthalpy ; Ball (mathematics) ; Intermolecular force ; Regular polygon ; Melting point ; Materials science ; Physics ; Chemical physics ; Condensed matter physics ; Thermodynamics ; Mathematics ; Geometry ; Molecule ; Quantum mechanics Graphene research and applications ; Theoretical and Computational Physics ; Material Dynamics and Properties
Authors: Jehwan Hwang | Yue Zhang | Bongjoong Kim | Jinheon Jeong | Jonghun Yi | Dong Rip Kim | Young L. Kim | Augustine Urbas | Gamini Ariyawansa | Baoxing Xu | Zahyun Ku | Chi Hwan Lee
Source: Advanced Science (article, 2024-09-03)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Wafer‐Scale Replication of Plasmonic Nanostructures via Microbubbles for Nanophotonics Quasi-3D plasmonic nanostructures are in high demand for their ability to manipulate and enhance light-matter interactions at subwavelength scales, making them promising building blocks for diverse nanophotonic devices. Despite their potential, the integration of these nanostructures with optical sensors and imaging systems on a large scale poses challenges. Here, a robust technique for the rapid, scalable, and seamless replication of quasi-3D plasmonic nanostructures is presented straight from their production wafers using a microbubble process. This approach not only simplifies the integration of quasi-3D plasmonic nanostructures into a wide range of standard and custom optical imaging devices and sensors but also significantly enhances their imaging and sensing performance beyond the limits of conventional methods. This study encompasses experimental, computational, and theoretical investigations, and it fully elucidates the operational mechanism. Additionally, it explores a versatile set of options for outfitting nanophotonic devices with custom-designed plasmonic nanostructures, thereby fulfilling specific operational criteria. Nanophotonics ; Plasmon ; Nanotechnology ; Scalability ; Replication (statistics) ; Nanostructure ; Materials science ; Wafer ; Computer science ; Optoelectronics Gold and Silver Nanoparticles Synthesis and Applications ; Plasmonic and Surface Plasmon Research ; ZnO doping and properties
Authors: Chia‐Feng Tsai | Chuan‐Chih Hsu | Yi‐Ting Wang | Hyeyoon Kim | Tao Liu
Source: Methods in molecular biology (article, 2024-01-01)
Field: Chemistry — Spectroscopy

A Tip-Based Workflow for Sensitive IMAC-Based Low Nanogram Level Phosphoproteomics Phosphoproteomics ; Workflow ; Chemistry ; Computer science ; Biochemistry ; Database ; Phosphorylation Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Biosensors and Analytical Detection
Authors: Marissa Duckett | Megan Taylor | Claire Bowman | Nic M. Vega
Source: FEMS Microbiology Ecology (article, 2024-03-28)
Field: Materials Science — Materials Chemistry

Parallel evolution of alternate morphotypes of <i>Chryseobacterium gleum</i> during experimental evolution with <i>Caenorhabditis elegans</i> Microbial evolution within polymicrobial communities is a complex process. Here, we report within-species diversification within multispecies microbial communities during experimental evolution with the nematode Caenorhabditis elegans. We describe morphological diversity in the target species Chryseobacterium gleum, which developed a novel colony morphotype in a small number of replicate communities. Alternate morphotypes coexisted with original morphotypes in communities, as well as in single-species experiments using evolved isolates. We found that the original and alternate morphotypes differed in motility and in spatial expansion in the presence of C. elegans. This study provides insight into the emergence and maintenance of intraspecies diversity in the context of microbial communities. Biology ; Caenorhabditis elegans ; Caenorhabditis ; Experimental evolution ; Genetics ; Evolutionary biology ; Gene Nanoparticles: synthesis and applications ; Bacterial biofilms and quorum sensing ; Biocrusts and Microbial Ecology
Authors: C.J. Tang | A.J.S. Fernandes | M. Facão | Alexandre F. Carvalho | Weixia Chen | Haihong Hou | F.M. Costa
Source: Materials (article, 2024-06-18)
Field: Materials Science — Materials Chemistry

Fast, Efficient Tailoring Growth of Nanocrystalline Diamond Films by Fine-Tuning of Gas-Phase Composition Using Microwave Plasma Chemical Vapor Deposition Nanocrystalline diamond (NCD) films are attractive for many applications due to their smooth surfaces while holding the properties of diamond. However, their growth rate is generally low using common Ar/CH<sub>4</sub> with or without H<sub>2</sub> chemistry and strongly dependent on the overall growth conditions using microwave plasma chemical vapor deposition (MPCVD). In this work, incorporating a small amount of N<sub>2</sub> and O<sub>2</sub> additives into CH<sub>4</sub>/H<sub>2</sub> chemistry offered a much higher growth rate of NCD films, which is promising for some applications. Several novel series of experiments were designed and conducted to tailor the growth features of NCD films by fine-tuning of the gas-phase compositions with different amounts of nitrogen and oxygen addition into CH<sub>4</sub>/H<sub>2</sub> gas mixtures. The influence of growth parameters, such as the absolute amount and their relative ratios of O<sub>2</sub> and N<sub>2</sub> additives; substrate temperature, which was adjusted by two ways and inferred by simulation; and microwave power on NCD formation, was investigated. Short and long deposition runs were carried out to study surface structural evolution with time under identical growth conditions. The morphology, crystalline and optical quality, orientation, and texture of the NCD samples were characterized and analyzed. A variety of NCD films of high average growth rates ranging from 2.1 μm/h up to 6.7 μm/h were successfully achieved by slightly adjusting the O<sub>2</sub>/CH<sub>4</sub> amounts from 6.25% to 18.75%, while that of N<sub>2</sub> was kept constant. The results clearly show that the beneficial use of fine-tuning of gas-phase compositions offers a simple and effective way to tailor the growth characteristics and physical properties of NCD films for optimizing the growth conditions to envisage some specific applications. Diamond ; Chemical vapor deposition ; Materials science ; Nanocrystalline material ; Phase (matter) ; Chemical engineering ; Texture (cosmology) ; Microwave ; Growth rate ; Nitrogen ; Plasma-enhanced chemical vapor deposition ; Substrate (aquarium) ; Analytical Chemistry (journal) ; Deposition (geology) ; Nanotechnology ; Chemistry ; Composite material ; Organic chemistry Diamond and Carbon-based Materials Research ; Metal and Thin Film Mechanics ; Advanced materials and composites
Authors: Matheus G. B. Rodrigues | André L. Pesquero de Melo | Maurı́cio D. Coutinho-Neto | Camilo A. Angelucci
Source: ChemCatChem (article, 2024-12-09)
Field: Materials Science — Materials Chemistry

Anaerobic Catalyst Design for Alcohol Oxidation: Fine‐Tuning Copper/TEMPO with Bipyridine Proportions Abstract In this study, we investigate the indirect electro‐oxidation of benzyl alcohol (BA) using the copper/TEMPO catalytic system, which combines copper complexes with 2,2,6,6‐tetramethylpiperidin‐1‐oxyl (TEMPO) in an anaerobic medium. We reexamine the impact of bpy ligand proportions, exploring ratios of 1:1, 2:1, 3:1, and 4:1 on catalytic activity. Cyclic voltammetry and visible spectroscopy reveal distinct electrochemical characteristics and complex formations at different bpy ratios. Simulations uncover intricate energy equilibria involving ion coordination, varying with oxidation state, and bpy proportion. Theoretical and experimental spectra align, supporting the proposed structures. The Brønsted base, triethylamine (TEA), essential in this anaerobic system, shows different voltammetric profiles with each ligand ratio, revealing key interactions with bpy complexes. In the presence of BA, the 1:1 and 2:1 ratios exhibit indirect catalytic activity, with the 2:1 ratio yielding significantly higher current densities. This establishes a new optimal condition where formed in a 2:1 stoichiometry demonstrates superior activity with a lower redox potential, while maintaining labile coordination points for necessary interactions. Theoretical results also indicate weaker TEMPO coordination to . Catalysis ; Copper ; Anaerobic exercise ; Alcohol oxidation ; Alcohol ; Bipyridine ; Chemistry ; Organic chemistry ; Biology Catalytic Processes in Materials Science ; Oxidative Organic Chemistry Reactions ; Catalysis and Oxidation Reactions
Authors: Keisuke Ozawa | Teppei Suzuki | Shunsuke Tonogai | Tomoya Itakura
Source: Science and Technology of Advanced Materials Methods (article, 2024-09-23)
Field: Materials Science — Materials Chemistry

Graph-text contrastive learning of inorganic crystal structure toward a foundation model of inorganic materials Developing foundation models for materials science has attracted attention. However, there is a lack of studies on inorganic materials due to the difficulty in the comprehensive representation of geometric concepts composing crystals: local atomic environments, their connections, and the global symmetries. We present a contrastive learning of inorganic crystal structure (CLICS) for embedding the geometric concepts, which contrasts texts representing the contextual patterns of geometries with the crystal graphs. We demonstrate that the geometric concepts are integrally embedded on the CLICS feature space, through experiments of concept prediction from crystal graphs, similar structure search, and few-shot/imbalanced crystal structure classification. Foundation (evidence) ; Graph ; Linguistics ; Computer science ; Materials science ; Geography ; Theoretical computer science ; Archaeology ; Philosophy Machine Learning in Materials Science ; X-ray Diffraction in Crystallography
Authors: Wen Li | Borong Zhang | Zhaohui Shi | Lirong Zhang | Zhiyong Chang | Yunling Liu
Source: Separation and Purification Technology (article, 2024-05-07)
Field: Chemistry — Inorganic Chemistry

Fine-tuning porosity of In-MOFs with ncb topology based on reticular chemistry for one-step purification C2H4 from ternary C2H6/C2H4/C2H2 mixtures Isonicotinic acid ; Ternary operation ; Terephthalic acid ; Chemistry ; Adsorption ; Ligand (biochemistry) ; Ternary numeral system ; Porosity ; Inorganic chemistry ; Chemical engineering ; Nuclear chemistry ; Organic chemistry ; Hydrazide Metal-Organic Frameworks: Synthesis and Applications ; Gas Sensing Nanomaterials and Sensors ; Advanced Photocatalysis Techniques
Authors: Miriam C. Rodríguez González | Iván M. Ibarburu | Clara Rebanal | Manuel Vázquez Sulleiro | S. Rahul | Alicia Naranjo | Cosme G. Ayani | Manuela Garnica | F. Calleja | Emilio M. Pérez | Amadeo L. Vázquez de Parga | Steven De Feyter
Source: Nanoscale (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Clicking beyond suspensions: understanding thiol–ene chemistry on solid-supported MoS<sub>2</sub> Molecular functionalization of MoS<sub>2</sub> has attracted a lot of attention due to its potential to afford fine-tuned hybrid materials that benefit from the power of synthetic chemistry and molecular design. Here, we report on the on-surface reaction of maleimides on bulk and molecular beam epitaxy grown single-layer MoS<sub>2</sub>, both in ambient conditions as well as ultrahigh vacuum using scanning probe microscopy. Molecular beam epitaxy ; Solid surface ; Thiol ; Nanotechnology ; Materials science ; Layer (electronics) ; Chemical engineering ; Ene reaction ; Chemistry ; Epitaxy ; Chemical physics ; Stereochemistry ; Organic chemistry ; Engineering 2D Materials and Applications ; MXene and MAX Phase Materials ; Chalcogenide Semiconductor Thin Films
Authors: Taeho Kim | Jin Kuen Park | Jae‐Min Oh
Source: Bulletin of the Korean Chemical Society (article, 2024-09-01)
Field: Materials Science — Materials Chemistry

Supramolecular chemistry for the incorporation of multi‐guest molecules into two‐dimensional metal hydroxide hosts Abstract The incorporation of functional molecules into the interlayer space of layered double hydroxide (LDH) has been extensively studied for its role in immobilization, stabilization, manipulation of the molecular configuration, and the release from the host. To create dramatically enhanced properties and achieve unexpectedly high performances, it is necessary to incorporate multi‐guests as well as control the guest‐guest interaction. In the present review, we have summarized the multi‐guest incorporation into LDH based on the supramolecular chemistry, which provides insights into non‐covalent molecular interaction through host‐guest chemistry. Four well‐known intercalation methods in LDH, that is, coprecipitation, ion exchange, reconstruction, and exfoliation‐reassembly, are generally applied to multi‐guest intercalation. Combinative methods, in which two different intercalation approaches are combined, are also summarized. The multi‐guest incorporation, despite the difficulty involved in its synthesis design, could provide fine‐tuned and enhanced properties that are useful for a variety of applications. Intercalation (chemistry) ; Supramolecular chemistry ; Hydroxide ; Exfoliation joint ; Molecule ; Coprecipitation ; Chemistry ; Host–guest chemistry ; Nanotechnology ; Metal hydroxide ; Covalent bond ; Combinatorial chemistry ; Materials science ; Inorganic chemistry ; Organic chemistry ; Graphene Layered Double Hydroxides Synthesis and Applications ; Polyoxometalates: Synthesis and Applications ; Inorganic Chemistry and Materials
Authors: Kenichi Endo | Stefano Canossa | Fabian Heck | Davide Μ. Proserpio | M. Satukbugra Istek | Friedrich Stemmler | Joris van Slageren | Bettina V. Lotsch
Source: ChemRxiv (preprint, 2024-07-19)
Field: Chemistry — Inorganic Chemistry

MOCOFs: Crystalline porous frameworks based on double extension of metal–organic and covalent organic linkages Reticular chemistry is a powerful strategy to design solid materials with fine-tuned chemical functionality and porosity, such as metal–organic frameworks (MOFs) and covalent organic frameworks (COFs). While MOFs typically show high crystallinity due to their highly reversible coordinative bonds, the organic backbone of COFs provides high chemical stability. Here, we combine the best of both worlds by introducing metal–organic–covalent–organic frameworks (MOCOFs), a new class of reticular materials through the double extension of metal–organic and covalent organic linkages. Several MOCOFs are obtained by the reactions between a cobalt aminoporphyrin and dialdehydes, which are interconnected by cobalt–amine coordination and imine condensation to form 3D networks. The MOCOFs show an unprecedented chiral topological net, large surface area, high crystallinity, and chemical stability owing to the two types of extended linkages. Thus, MOCOFs present a new reticular design strategy that further diversifies the chemical and structural space of porous solids. Covalent bond ; Crystallinity ; Cobalt ; Imine ; Metal-organic framework ; Chemical stability ; Covalent organic framework ; Materials science ; Porosity ; Chemical engineering ; Chemistry ; Polymer chemistry ; Nanotechnology ; Organic chemistry ; Adsorption ; Catalysis Metal-Organic Frameworks: Synthesis and Applications ; Covalent Organic Framework Applications ; Supramolecular Chemistry and Complexes