jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Che‐Fan Huang | Jake Kline | Fernanda Negrão | Matthew T. Robey | Timothy K. Toby | Kenneth R. Durbin | Ryan T. Fellers | John J. Friedewald | Josh Levitsky | Michaël Abécassis | Rafael D. Melani | Neil L. Kelleher | Luca Fornelli
Source: ChemRxiv (preprint, 2023-06-27)
Field: Chemistry — Spectroscopy

Targeted Quantification of Proteoforms in Complex Samples by Proteoform Reaction Monitoring Existing mass spectrometric assays used for sensitive and specific measurements of target proteins across multiple samples, such as selected/multiple reaction monitoring (SRM/MRM) or parallel reaction monitoring (PRM), are peptide-based methods for bottom-up proteomics. Here, we describe an approach based on the principle of PRM for the measurement of intact proteoforms by targeted top-down proteomics termed Proteoform Reaction Monitoring (PfRM). We explore the ability of our method to circumvent traditional limitations of top-down proteomics such as sensitivity and reproducibility. We also introduce a new software, Proteoform Finder, specifically designed for easy analysis of PfRM data. PfRM was initially benchmarked by quantifying three standard proteins. Linearity of the assay was shown over almost three orders of magnitude in the femtomole range. We later applied our multiplexed PfRM assay to complex samples to quantify biomarker candidates in peripheral blood mononuclear cells (PBMCs) from liver transplanted patients, demonstrating its possible translational applications. These results demonstrate that PfRM has the potential to contribute to the accurate quantification of protein biomarkers for diagnostic purposes and to improve understanding of disease etiology at the proteoform level. Proteomics ; Selected reaction monitoring ; Computational biology ; Quantitative proteomics ; Biomarker ; Biomarker discovery ; Computer science ; Label-free quantification ; Chemistry ; Mass spectrometry ; Tandem mass spectrometry ; Chromatography ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Hui Peng | Limsoon Wong | Wilson Wen Bin Goh
Source: PLoS Computational Biology (article, 2023-03-17)
Field: Chemistry — Spectroscopy

ProInfer: An interpretable protein inference tool leveraging on biological networks In mass spectrometry (MS)-based proteomics, protein inference from identified peptides (protein fragments) is a critical step. We present ProInfer (Protein Inference), a novel protein assembly method that takes advantage of information in biological networks. ProInfer assists recovery of proteins supported only by ambiguous peptides (a peptide which maps to more than one candidate protein) and enhances the statistical confidence for proteins supported by both unique and ambiguous peptides. Consequently, ProInfer rescues weakly supported proteins thereby improving proteome coverage. Evaluated across THP1 cell line, lung cancer and RAW267.4 datasets, ProInfer always infers the most numbers of true positives, in comparison to mainstream protein inference tools Fido, EPIFANY and PIA. ProInfer is also adept at retrieving differentially expressed proteins, signifying its usefulness for functional analysis and phenotype profiling. Source codes of ProInfer are available at https://github.com/PennHui2016/ProInfer. Inference ; Computational biology ; Proteome ; Proteomics ; Computer science ; False positive paradox ; Bioinformatics ; Biology ; Artificial intelligence ; Biochemistry ; Gene Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Bioinformatics and Genomic Networks
Authors: Yanli Wang | Yi Ding
Source: physica status solidi (RRL) - Rapid Research Letters (article, 2023-10-31)
Field: Materials Science — Materials Chemistry

Large‐Gap Quantum Spin Hall State in Double‐Transition‐Metal Homologous Compounds of WSi<sub>2</sub>N<sub>4</sub>: A First‐Principles Study Recently, the MoSi 2 N 4 (MoN) 4 n homologous compounds have been synthesized, extending the MA 2 Z 4 family materials to the superthick MA 2 Z 4 (MZ) n form. Herein, a first‐principles study on the double‐transition‐metal W 2 TiSi 2 N 6 and related group VI–IV M 2 M′Si 2 N 6 nanosheets is performed. Robust structural stability is affirmed in this W 2 TiSi 2 N 6 nanosheet from the energetic, mechanical, dynamical, and thermal perspectives. Unlike the WSi 2 N 4 and WSi 2 N 4 (WN) n systems, the W 2 TiSi 2 N 6 nanosheet exhibits a semimetal behavior with the top valence and bottom conduction bands touching each other at the Fermi level. With the inclusion of spin–orbit coupling, a nontrivial band gap is opened in the W 2 TiSi 2 N 6 nanosheet, which has a sizeable bulk gap of 0.11 eV. The Z 2 invariant is 1 and a pair of topologically protected edge states emerges in the gap region, confirming that W 2 TiSi 2 N 6 nanosheet is a quantum spin Hall (QSH) insulator. Through in‐plane strain engineering, the bulk gap can be further increased to 0.23 eV, which is sufficiently large for the room‐temperature QSH effect. Such a large‐gap QSH state is also present in other group VI–IV M 2 M′Si 2 N 6 systems with the combinations of MM′ = WZr, MoZr, and MoHf. This study demonstrates that the double‐metal M 2 M′Si 2 N 6 nanosheets are promising candidates to realize fascinating topological quantum states. Nanosheet ; Band gap ; Condensed matter physics ; Fermi level ; Valence (chemistry) ; Materials science ; Spin states ; Physics ; Nanotechnology ; Quantum mechanics MXene and MAX Phase Materials ; Boron and Carbon Nanomaterials Research ; 2D Materials and Applications
Authors: Jixue Zhou | Dongqing Zhao | Shouqiu Tang | Yu Liu | Suqing Zhang | Yunteng Liu | Jianhua Wu | Xiaocun Song | Hongtao Liu | Xinfang Zhang | Pengfei Yan | Xitao Wang
Source: Metals (article, 2023-07-26)
Field: Materials Science — Biomaterials

Microstructure and Mechanical Properties in a Gd-Modified Extruded Mg-4Al-3.5Ca Alloy In the present study, the microstructure and mechanical properties of a new Mg-4Al-3.5Ca-2Gd (AXE432) alloy are investigated. The microstructure of the as-cast AXE432 alloy consists of α-Mg, C14 (Mg2Ca), and C36((Mg, Al)2Ca) phases. After the heat treatment at 480 °C for 8 h, the C14 with fine lamellar structure changes from narrow stripes to micro-scale particles, and part of the C36 and the C14 dissolve into the α-Mg matrix, with many short needle-shaped C15 (Al2Ca) phase precipitating in the primary a-Mg grains. The AXE432 alloy extruded at a temperature as high as 420 °C exhibits a refined dynamically recrystallized (DRXed) microstructure with grain sizes less than 1.5 ± 0.5 μm and a strong {0001}&lt;101¯0&gt; basal texture with a maximum intensity of 5.62. A complex combination of the effects from grain size, texture, second-phase particles, and strain hardening results in balanced mechanical properties, with the tensile yield strength (TYS), ultimate tensile strength (UTS), elongation (El), compressive yield strength (CYS), and ultimate compressive strength (UCS) of 331.4 ± 2.1 MPa, 336.9 ± 3.8 MPa, 16.1 ± 2.3%, 270.4 ± 1.6 MPa and 574.5 ± 12.4 MPa, respectively. Materials science ; Microstructure ; Ultimate tensile strength ; Alloy ; Grain size ; Elongation ; Texture (cosmology) ; Compressive strength ; Lamellar structure ; Composite material ; Phase (matter) ; Metallurgy ; Chemistry Magnesium Alloys: Properties and Applications ; Aluminum Alloys Composites Properties ; Hydrogen Storage and Materials
Authors: Abdullah A. Alghamdi
Source: Molecular Frontiers Journal (article, 2023-10-26)
Field: Materials Science — Materials Chemistry

Large Language Models, Computational Chemistry, and Digital Reticular Chemistry: A Perspective and Proposed Workflow In this article, I explore the synergy between Large Language Models (LLMs) and computational chemistry in the context of digital reticular chemistry and propose a workflow leveraging these technologies to advance research and discovery in the field. I argue that understanding the intricacies of new tools is imperative before integrating them into applications, and that the proposed workflow, though robust, merely offers a glimpse into the expansive potential and applications of this field. Workflow ; Expansive ; Computer science ; Context (archaeology) ; Field (mathematics) ; Perspective (graphical) ; Data science ; Chemistry ; Management science ; Engineering ; Artificial intelligence ; Physics ; Database ; Archaeology Machine Learning in Materials Science ; Expert finding and Q&A systems ; scientometrics and bibliometrics research
Authors: Eliza Ahmed | Basappa C. Yallur | Vinayak Adimule | Sheetal Batakurki
Source: Engineering chemistry (review, 2023-06-20)
Field: Chemistry — Inorganic Chemistry

Recent Advances on Copper Based Metal Organic Framework as Heterogenous Catalyst in Organic Coupling Reaction: A Review In synthetic organic chemistry, use of catalyst to accelerate the rate of reaction leading to high yield product is a common approach practiced by chemists. Numerous homogenous and heterogenous catalyst are widely used in chemical reactions, particularly metal based catalyst are widely used. The properties of metals and their oxides are fine-tuned by size reduction method bringing down to nano scale. Further hybrid materials are used for more specific applications among which metal organic frame works are listed in more number in last ten years. Herein this review focuses on use of metal organic framework in particular Copper metal based organic framework (Cu-MOF). Cu-MOF synthesis, properties and their applications are discussed. A detailed discussion on the use of Cu-MOF as a heterogeneous catalyst in various organic reactions. Catalysis ; Copper ; Metal-organic framework ; Organic synthesis ; Metal ; Materials science ; Yield (engineering) ; Organic reaction ; Nanotechnology ; Chemical engineering ; Chemistry ; Organic chemistry ; Metallurgy ; Engineering Metal-Organic Frameworks: Synthesis and Applications ; Chemical Synthesis and Reactions ; Nanomaterials for catalytic reactions
Authors: Yinran Wang | Lin Huang | Zhaomin Hou | Fang Guo
Source: Polymer Chemistry (article, 2023-01-01)
Field: Chemistry — Organic Chemistry

Polymerization of α-olefins and their copolymerization with ethylene by half-sandwich scandium catalysts with an N-heterocyclic carbene ligand By fine-tuning the ligand of half-sandwich scandium catalysts, the polymerization of α-olefins and their copolymerization with ethylene have been achieved, affording the corresponding polymers with high molecular weight and controllable composition. Copolymer ; Scandium ; Ethylene ; Polymerization ; Ligand (biochemistry) ; Carbene ; Polymer chemistry ; Catalysis ; Polymer ; Chemistry ; Materials science ; Organic chemistry Organometallic Complex Synthesis and Catalysis ; Catalytic Cross-Coupling Reactions ; Synthetic Organic Chemistry Methods
Authors: М. В. Новожилова | Julia Polozhentseva | М. П. Карушев
Source: Polymers (article, 2023-02-23)
Field: Materials Science — Polymers and Plastics

Asymmetric Monomer Design Enables Structural Control of M(Salen)-Type Polymers Conductive and electrochemically active polymers consisting of Salen-type metal complexes as building blocks are of interest for energy storage and conversion applications. Asymmetric monomer design is a powerful tool for fine-tuning the practical properties of conductive electrochemically active polymers but has never been employed for polymers of M(Salen)]. In this work, we synthesize a series of novel conducting polymers composed of a nonsymmetrical electropolymerizable copper Salen-type complex (Cu(3-MeOSal-Sal)en). We show that asymmetrical monomer design provides easy control of the coupling site via polymerization potential control. With in-situ electrochemical methods such as UV-vis-NIR (ultraviolet-visible-near infrared) spectroscopy, EQCM (electrochemical quartz crystal microbalance), and electrochemical conductivity measurements, we elucidate how the properties of these polymers are defined by chain length, order, and cross-linking. We found that the highest conductivity in the series has a polymer with the shortest chain length, which emphasizes the importance of intermolecular iterations in polymers of [M(Salen)]. Monomer ; Metal salen complexes ; Polymer ; Polymer chemistry ; Materials science ; Type (biology) ; Composite material ; Geology Conducting polymers and applications ; Organic Electronics and Photovoltaics ; Analytical Chemistry and Sensors
Authors: Xinbo Bai | Fucong Chen | Yuxin Wang | Juan Xu | Ruozhou Zhang | Mingyang Qin | Wenxin Cheng | Jinsong Zhang | Qiuyan Shi | Xu Wang | Beiyi Zhu | Jie Yuan | Qihong Chen | Jian Kang | Kun Jiang | Jiangping Hu | Yangmu Li | Kui Jin | Zhongxian Zhao
Source: Physical Review Materials (article, 2023-09-12)
Field: Materials Science — Materials Chemistry

Charge-carrier-type controlled superconducting dome in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>Zr</mml:mi><mml:msub><mml:mi mathvariant="normal">N</mml:mi><mml:mi>x</mml:mi></mml:msub><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mi>y</mml:mi></mml:msub></mml:mrow></mml:math> films Modifying the normal state charge carriers and the related Fermi surface can significantly affect a material's superconducting state. The recently discovered superconducting dome as a function of chemical concentration in transition metal nitrides provides a promising platform for achieving such control. However, this effort was hindered by synthesis techniques that cannot stabilize the material's structure in the presence of a significant number of nitrogen vacancies. In this study, we employed oxygen-assisting nitrogen gas flow with radio frequency magnetron sputtering to stabilize the crystal structure of nitrogen-deficient zirconium nitride thin films and explore the impact of normal state charge carrier types on the superconducting state. Our electrical and thermoelectrical transport measurements indicate a fine-tuning of the superconducting transition temperature, ${T}_{\mathrm{c}}$, through a shift from hole-type to electron-type charge carriers. Additionally, a concurrent strain release, reflected in the change of the film's crystal orientation, is observed in the process. Superconductivity ; Materials science ; Condensed matter physics ; Charge carrier ; Charge (physics) ; Nitride ; Crystal (programming language) ; Zirconium ; Sputter deposition ; Nitrogen ; Sputtering ; Thin film ; Nanotechnology ; Optoelectronics ; Layer (electronics) ; Physics ; Metallurgy ; Computer science Electronic and Structural Properties of Oxides ; Metal and Thin Film Mechanics ; Superconductivity in MgB2 and Alloys
Authors: Duraisamy Ramasamy | Prashantha Nagaraja | Aatika Nizam | Katharigatta N. Venugopala | H. Nagarajaiah | M. B. Madhusudana Reddy | D. Thirumalai
Source: ChemistrySelect (article, 2023-11-14)
Field: Chemistry — Organic Chemistry

A Facile One‐Pot Solvent‐Free Synthesis, in Vitro and in Silico Studies of a Series of Tetrahydropyridine Derivatives as Breast Cancer Inhibitors Abstract Ammonium trifluoroacetate (ATA) catalysed synthesis of 1,2,5,6‐tetrahydropyridine (THP) derivatives, under eco‐friendly conditions via a facile one‐pot strategy. We have synthesized fifteen THP derivatives, and docked into the crystal structure of Phosphatase and Tensin Homolog deleted on Chromosome 10 (PTEN) tumour suppressor protein (PDB ID: 1D5R) based on drug‐likeness prediction and pharmacokinetic properties. Molecular docking simulation studies reveal that four of our synthesised compounds are potential hit candidates because they bound to the receptor through 5–7 conventional hydrogen bonds with −9.7 to −8.6 kcal/mol of binding energy. The compounds were evaluated using the in vitro inhibitory activity of MCF‐7 breast cancer cell lines. Identified hit compounds showed moderate inhibition at (160–320 μg/mL) and inhibitory concentration IC 50 values in the low micromolar range of 171.062, 189.803, 195.469 and 181.272 μg/mL respectively. The results obtained are very promising; therefore fine‐tuning the substituents of hit molecules with appropriate bioisosteres can lead to the development of potential leads. Tensin ; Chemistry ; In silico ; In vitro ; PTEN ; Protein Data Bank (RCSB PDB) ; Docking (animal) ; Hydrogen bond ; Molecule ; Stereochemistry ; Phosphatase ; Combinatorial chemistry ; Enzyme ; Biochemistry ; Signal transduction ; Organic chemistry ; PI3K/AKT/mTOR pathway Synthesis and biological activity ; Multicomponent Synthesis of Heterocycles ; Bioactive Compounds and Antitumor Agents
Authors: Donggang Jia | Alexandra Irger | Besancon, Lonni | Ondřej Strnad | Luo, Deng | Johanna Björklund | Anders Ynnerman | Ivan Viola
Source: arXiv (Cornell University) (preprint, 2023-04-08)
Field: Materials Science — Materials Chemistry

VOICE: Visual Oracle for Interaction, Conversation, and Explanation We present VOICE, a novel approach to science communication that connects large language models' (LLM) conversational capabilities with interactive exploratory visualization. VOICE introduces several innovative technical contributions that drive our conversational visualization framework. Our foundation is a pack-of-bots that can perform specific tasks, such as assigning tasks, extracting instructions, and generating coherent content. We employ fine-tuning and prompt engineering techniques to tailor bots' performance to their specific roles and accurately respond to user queries. Our interactive text-to-visualization method generates a flythrough sequence matching the content explanation. Besides, natural language interaction provides capabilities to navigate and manipulate the 3D models in real-time. The VOICE framework can receive arbitrary voice commands from the user and respond verbally, tightly coupled with corresponding visual representation with low latency and high accuracy. We demonstrate the effectiveness of our approach by applying it to the molecular visualization domain: analyzing three 3D molecular models with multi-scale and multi-instance attributes. We finally evaluate VOICE with the identified educational experts to show the potential of our approach. All supplemental materials are available at https://osf.io/g7fbr. Computer science ; Visualization ; Conversation ; Human–computer interaction ; Oracle ; Domain (mathematical analysis) ; Representation (politics) ; Matching (statistics) ; Artificial intelligence ; Programming language Machine Learning in Materials Science ; Topic Modeling ; Scientific Computing and Data Management
Authors: Mohammad Hossein Jandaghian | Abdolhannan Sepahi | Shahin Hosseini | Romina Esmaeilzade | Ehsan Nikzinat | Maryam Masoori | Kamal Afzali
Source: Journal of Applied Polymer Science (article, 2023-12-20)
Field: Materials Science — Polymers and Plastics

Splitting for strength: Manipulating polymerization reactor split ratios to control mechanical and rheological properties in bimodal polyethylene resins Abstract This study integrates advanced mathematical modeling and experimental methodologies to investigate the simultaneous impact of modifications in the split ratio and molecular weight (MW) of chains on the rheological and mechanical properties of bimodal polyethylene (BiPE) resins. The outcomes underscored the viability of fine‐tuning the molecular weight distribution (MWD) of a BiPE resin by augmenting the MW of high molecular weight (HMW) chains while simultaneously diminishing their proportion in the final alloy formulation. In addition, the experimental results illuminated the prospect of attaining a targeted melt flow index for the final polymers by elevating the MW of HMW chains alongside an increase in the proportion of low molecular weight chains. Significantly, these adjustments resulted in remarkable enhancements in the shear thinning index and strain hardening modulus of the fabricated resins. Rheology ; Materials science ; Molar mass distribution ; Polyethylene ; Polymer ; Melt flow index ; Strain hardening exponent ; Polymerization ; Composite material ; Modulus ; Ultra-high-molecular-weight polyethylene ; Polymer chemistry ; Chemical engineering ; Copolymer Polymer crystallization and properties ; Rheology and Fluid Dynamics Studies ; Mechanical Behavior of Composites
Authors: Iolanda Di Bernardo | Joan Ripoll-Sau | F. Calleja | Cosme G. Ayani | Rodolfo Miranda | Jose Ángel Silva-Guillén | Enric Cañadell | Manuela Garnica | Amadeo L. Vázquez de Parga
Source: arXiv (Cornell University) (preprint, 2023-01-16)
Field: Materials Science — Materials Chemistry

Metastable polymorphic phases in monolayer TaTe2 Polymorphic phases and collective phenomena - such as charge density waves (CDWs) - in transition metal dichalcogenides (TMDs) dictate the physical and electronic properties of the material. Most TMDs naturally occur in a single given phase, but the fine-tuning of growth conditions via methods like molecular beam epitaxy (MBE) allows to unlock otherwise inaccessible polymorphic structures. Exploring and understanding the morphological and electronic properties of new phases of TMDs is an essential step to enable their exploitation in technological applications. Here, we use scanning tunneling microscopy to map MBE-grown monolayer TaTe2. We report the first observation of the 1H polymorphic phase, coexisting with the 1T, and demonstrate that their relative coverage can be controlled by adjusting synthesis parameters. Several super-periodic structures, compatible with CDWs, are observed to coexist on the 1T phase. Finally, we provide theoretical insight on the delicate balance between Te...Te and Ta-Ta interactions that dictates the stability of the different phases. Our findings demonstrate that TaTe2 is an ideal platform to investigate competing interactions, and indicate that accurate tuning of growth conditions is key to accessing metastable states in TMDs. Metastability ; Monolayer ; Molecular beam epitaxy ; Scanning tunneling microscope ; Chemical physics ; Charge density wave ; Materials science ; Phase transition ; Phase (matter) ; Nanotechnology ; Quantum tunnelling ; Transition metal ; Epitaxy ; Condensed matter physics ; Optoelectronics ; Chemistry ; Physics ; Layer (electronics) 2D Materials and Applications ; Quantum Dots Synthesis And Properties ; Molecular Junctions and Nanostructures
Authors: Mariusz Gackowski | Anne Selent | Ilari Ainasoja | Michal Mazur | Michael Hunger | Jerzy Dátka | Ville‐Veikko Telkki
Source: Microporous and Mesoporous Materials (article, 2023-04-29)
Field: Chemistry — Inorganic Chemistry

Cleansing effect during the TBAOH treatment of ultra-stable zeolite Y Zeolite ; Porosity ; Molecular sieve ; Amorphous solid ; Adsorption ; Leaching (pedology) ; Chemistry ; NMR spectra database ; Materials science ; Inorganic chemistry ; Spectral line ; Organic chemistry ; Catalysis Zeolite Catalysis and Synthesis ; Advanced NMR Techniques and Applications ; Chemical Synthesis and Characterization
Authors: V. Ramkumar | P. Kamachiyappan | A. Karuppusamy | A. Ashokkumar | D. Santhanaraj | Cadiam Mohan Babu | Seong‐Cheol Kim
Source: Journal of Molecular Liquids (article, 2023-07-25)
Field: Materials Science — Polymers and Plastics

Highly efficient color mixing system for the fine-tuning of white light–PLEDs using blue and red poly-chromophores Chromophore ; Materials science ; Polymer ; Fourier transform infrared spectroscopy ; Band gap ; Luminescence ; Photochemistry ; Fluorescence ; Analytical Chemistry (journal) ; Chemistry ; Chemical engineering ; Organic chemistry ; Optoelectronics ; Optics Conducting polymers and applications ; Luminescence and Fluorescent Materials ; Photochromic and Fluorescence Chemistry