jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Xiaotong Liu | Xingchen Liu | Xiaodong Wen
Source: ChemRxiv (preprint, 2024-12-11)
Field: Materials Science — Materials Chemistry

AlchemBERT: Exploring Lightweight Language Models for Materials Informatics The advent of large language models (LLMs) has spurred numerous applications across various domains, including material design. However, we assert that without accurate prediction capabilities, effective material design is unattainable, as generating necessary structures becomes futile if their quality cannot be reliably evaluated. Matbench provides an excellent foundation for predictive tasks, yet prior efforts with LLMs have primarily focused on composition-related tasks using models such as GPT or LLaMA. In this study, we revisit BERT, a relatively small LLM with 110 million parameters, which is significantly smaller than GPT or LLaMA models containing billions of parameters. Remarkably, we demonstrate that BERT-base achieves comparable performance to these larger models in material property prediction tasks. Extending beyond composition tasks, we introduce BERT’s application in structure prediction using CIF (Crystallographic Information File) data and natural language descriptions of structures. Our results rival state-of-the-art composition models such as CrabNet and, in several tasks, even surpass traditional structure-based models like CGCNN, DeeperGATGNN, MegNet, DimeNet++, and knowledge-driven models such as MODNet. Notably, despite its parameter count, our approach excels on small datasets with minimal overfitting, indicating that fine-tuned LLMs can genuinely capture meaningful material insights. Our findings provide a new reference point for future LLM applications in material design, offering valuable insights for leveraging LLMs in this domain and introducing a paradigm shift for physicists and material scientists, emphasizing natural language descriptions over conventional model-centric design. We term this application of BERT in material design AlchemBERT, signifying its novel role in bridging natural language and structural representations. Overfitting ; Computer science ; Language model ; Bridging (networking) ; Materials informatics ; Data science ; Artificial intelligence ; Health informatics Machine Learning in Materials Science ; Material Selection and Properties
Authors: Mukhlif Mohsin Slaihim | Luay Ali Dhahi | Abeer Hussein Ali
Source: Journal of Angiotherapy (article, 2024-01-21)
Field: Chemistry — Organic Chemistry

Innovative Piperidine-Catalyzation in Protecting Carbonyl Compounds with Implications for Angiogenesis and Inflammation Introduction: This study explores the application of piperidine-catalyzed protection, an innovative technique, for safeguarding various carbonyl compounds functioning as acetals in a generic reaction. Specifically, we investigate the catalysis of 2-amino-1,3-propanediol-2-methyl with various aromatic aldehydes, leading to the production of cis and trans-5-methyl-2-(mono or di-substitutions-phenyl)-1,3-dioxane-5-amine. Methods: Identification of all newly formed products is achieved through the utilization of spectroscopic techniques, including IR, 1H-NMR, and 13C-NMR spectroscopy. Molecular interactions and potential therapeutic applications of compounds E1 and E2 are demonstrated with cAMP-specific phosphodiesterase (1zkl) and oxidized purine nucleoside triphosphate hydrolase (5ws7). Detailed structural analyses highlight specific hydrogen bonds, pi-pi stacked interactions, and alkyl contacts formed by these compounds with target proteins. A comprehensive bioinformatics approach involves GO enrichment, STRING protein-protein association networks, KEGG pathway analysis, and Reactome pathways to elucidate biological processes, molecular functions, and cellular components associated with the compounds. Results: Compounds E1 and E2 exhibit diverse enrichment profiles, suggesting their involvement in various signaling cascades, neurotransmission, immune responses, and cancer pathways. Comparative analysis of five compound pairs (A1/A2, B1/B2, C1/C2, D1/D2, E1/E2) reveals subtle distinctions in enrichment patterns, implying unique pharmacological advantages for each pair. Conclusion: This study introduces a separate investigation on piperidine-catalyzed protection of carbonyl groups in aldehydes, presenting a practical approach. Emphasizing the significance of understanding distinct biological signatures, our findings guide therapeutic applications and compound optimization, particularly in the context of anti-cancer therapeutics. The compounds show potential in modulating neuronal function, neurotransmission, cancer mechanisms, and immune responses, suggesting promising avenues for future research and development. Chemistry ; Piperidine ; Context (archaeology) ; Nucleoside ; Alkyl ; Combinatorial chemistry ; Computational biology ; Stereochemistry ; Biology ; Organic chemistry Synthesis and Catalytic Reactions ; Click Chemistry and Applications ; Tuberculosis Research and Epidemiology
Authors: Anoop Kumar Pandey | D. D. Dubey | Satyendra Nath Tiwari | G. Mishra | Padmaker Pandey | Saba Ansari | V.N. MISHRA
Source: Romanian Journal of Biophysics (article, 2024-12-12)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Vibrational, electronic properties Pharmaceutical study of 4-Carboxy-3-Fluorophenylboronic acid and ability to form its dimer by using Density functional theory The motive of present article is to attract attention on conformational analysis and electronic features of 4-carboxy-3-fluorophenylboronic acid compound via computational method. To comply this, density functional theory (DFT) in combination with Becke 3-parameter Lee–Yang–Parr (B3LYP) functional was considered to identify possible conformers and hence the ground state conformation. The stability reaction of formation quantum theory of atoms in molecules (QTAIM), natural bond analysis (NBO) and thermodynamical stability of dimerization of 4-carboxy-3-fluorophenylboronic acid is computed by using DFT/6-31G(d, p) method. The Eigen value of highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), and related energy bandgap were computed at B3LYP. In addition to these, thermodynamic properties and nonlinear properties (NLO) are also computed. Study of NLO (nonlinear optical behavior) reveals the nonlinear properties of the title molecule. The UV-Vis spectra of title molecule were calculated by time dependent density functional theory (TDDFT/6-31G(d, p)) on optimized geometry by same level theory. The biological activity of title molecule is computed by PASS online server which predict 4000 types of biological activities, counting pharmacological effects, mechanisms of action, toxic and adverse effects, interaction with metabolic enzymes and transporters, influence on gene expression, etc. The title molecule showed good activity against antineoplastic (0.914), peptidyl transferase inhibitor (0.969), aminoacylase inhibitor (0.960), sugar-phosphatase inhibitor (0.913), ribulose-phosphate 3-epimerase inhibitor (0.896), antiviral (0.862), TP53 expression enhancer (0.860). To determine anti-inflammatory potential, we have performed docking of title molecule with drosophila, which is a muscleblind like splicing regulator 1 (MBNL1) protein, by using Swiss dock online server. Dimer ; Density functional theory ; Computational chemistry ; Chemistry ; Chemical physics ; Materials science ; Nanotechnology ; Organic chemistry Nonlinear Optical Materials Research ; Synthesis and Characterization of Heterocyclic Compounds ; Inorganic and Organometallic Chemistry
Authors: Linu Malakkal | Shuxiang Zhou | Himani Mishra | Jia Ke | Chao Jiang | Lingfeng He | Sudipta Biswas
Source: arXiv (Cornell University) (preprint, 2024-11-20)
Field: Materials Science — Materials Chemistry

Xenon-metal pair formation in UO2 investigated using DFT+U A recent experimental study on a spent uranium dioxide (UO2) fuel sample from Belgium Reactor 3 (BR3) identified a unique pair structure formed by the noble metal phase (NMP) and fission gas (xenon [Xe]) precipitate. However, the fundamental mechanism behind this structure remains unclear. The present study aims to provide an understanding of the interaction between five different metal precipitates (molybdenum [Mo], ruthenium [Ru], palladium [Pd], technetium [Tc], and rhodium [Rh]) and the Xe fission gas atoms in UO2, by using density functional theory (DFT) in combination with the Hubbard U correction to compute the formation energies involved. All DFT+U calculations were performed with occupation matrix control to ensure antiferromagnetic ordering of UO2. The calculated formation and binding energies of the Xe and solid fission products in the NMP reveal that these metal precipitates form stable pair structures with Xe. Notably, the formation energy of Xe-metal pairs is lower than that of the isolated single defects in all instances, with Pd and Mo showing the most favourable binding energy, likely accounting for the observed pair structure formation. Xenon ; Metal ; Materials science ; Crystallography ; Chemistry ; Atomic physics ; Physics ; Metallurgy Nuclear Materials and Properties ; Radioactive element chemistry and processing ; Nuclear reactor physics and engineering
Authors: Alasdair Keith | Elizabeth Sawyer | Desmond Choy | Yuhang Xie | George Biggs | James Klein | Paul Brear | David Wales | Paul Barker | Matej Kanduc | Emanuel Schneck | Roland Netz | Edward Smith | Panagiotis Theodorakis | Federico Caporaletti | Simone Napolitano | Aaron Wilson | Zi Foo | Ashini Jayasinghe | Caleb Stetson | Hyeonseok Lee | Harry Rollins | Akshay Deshmukh | John Lienhard | Attila Tortorella | Rosario Oliva | Concetta Giancola | Luigi Petraccone | Roland Winter | Pamela Svensson | Lucas Schwob | Oscar Grna | Isaak Unger | Olle Bjo | Nicusor Timneanu | Rebecka Lindblad | Anna-Lydia Vieli | Vicente Zamudio-Bayer | Martin Timm | Konstantin Hirsch | Carl Caleman | Marta Berholts | Aidar Gaisin | Elena Filatova | Peng-Yun Wang | Yu-Cheng Hsu | Pin-Hsun Chen | Guan-Yu Chen | Yi-Kai Liao | Po-Yuan Cheng | Da Yang | Francesco Ricci | Fredrik Nordstrom | Na Li | Bin Zhang | Yixuan Xue | Harold Park | Jin-Wu Jiang | R Ma rquez-Ru z | Guirado-Lo pez | Abhishek Kalpattu | Tristan Dilbeck | Kenneth Hanson | John Fourkas | S Sergey | Alexander Nikitin | Elizaveta Koryakov | Alexey Antipinskaya | Markov | V ; Ziyu Mikhail | Baozeng Liu | Xiaocha Zhou | Yuandong Xu | * Haoyang Feng | Chaoyang Dong | Yuqing Yang | Meng Zhou | Yajun Wei | * Hui Guo | Yaqing Wei | Jishan Su | Yingying Ben | Xia Zhang
Source: Physical Chemistry Chemical Physics (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Contents list Permissions Request permissions Contents list Phys. Chem. Chem. Phys., 2024, 26, 641 DOI: 10.1039/D4CP90007C This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given. Read more about how to correctly acknowledge RSC content. Acknowledgement ; Chromatin structure remodeling (RSC) complex ; Attribution ; Computer science ; Library science ; Physics ; Chemistry ; Psychology ; Computer security ; Social psychology Luminescence Properties of Advanced Materials ; Quantum Dots Synthesis And Properties ; Electronic and Structural Properties of Oxides
Authors: Mohammed Azzouzi | Steven P. Bennett | Víctor Posligua | Roberto Bondesan | Martijn A. Zwijnenburg | Kim E. Jelfs
Source: arXiv (Cornell University) (preprint, 2024-11-04)
Field: Materials Science — Materials Chemistry

Comparative Analysis of search Approaches to Discover Donor Molecules for Organic Solar Cells Identifying organic molecules with desirable properties from the extensive chemical space can be challenging, particularly when property evaluation methods are time-consuming and resource intensive. In this study, we illustrate this challenge by exploring the chemical space of large oligomers, constructed from monomeric building blocks, for potential use in organic photovoltaics (OPV). For this purpose, we developed a python package to search the chemical space using a building block approach: stk-search. We use stk-search to compare a variety of search algorithms, including those based upon Bayesian optimization and evolutionary approaches. Initially, we evaluated and compared the performance of different search algorithms within a precomputed search space. We then extended our investigation to the vast chemical space of molecules formed of 6 building blocks (6-mers), comprising over $10^{14}$ molecules. Notably, while some algorithms show only marginal improvements over a random search approach in a relatively small, precomputed, search space, their performance in the larger chemical space is orders of magnitude better. Specifically, Bayesian optimization identified a thousand times more promising molecules with the desired properties compared to random search, using the same computational resources. Organic solar cell ; Organic molecules ; Astrobiology ; Molecule ; Chemistry ; Nanotechnology ; Materials science ; Physics ; Organic chemistry Machine Learning in Materials Science ; Organic Electronics and Photovoltaics ; Molecular Junctions and Nanostructures
Authors: Lemessa Asefa Eressa | Zeleke Deressa Gerbi
Source: Advances in Condensed Matter Physics (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

First Principle Study of Structural, Electronic, Optical, and Thermodynamic Properties of Scandium‐Doped Zirconia (<i>Z</i><i>r</i><sub>1−<i>x</i></sub><i>S</i><i>c</i><sub><i>x</i></sub><i>O</i><sub>2</sub>, <i>x</i> = 0.125) The effect of scandium doping on the structural, electronic, optical, and thermodynamic properties of scandium‐doped zirconia (Zr 0.875 Sc 0.125 O 1.9375 ) was investigated by first‐principles calculations. The results of electronic property calculation show that the incorporation of scandium (Sc 3+ ) in ZrO 2 has reduced its bandgap due to the formation of scandium 3d states in the conduction band. The analysis of optical properties shows that scandium doping in ZrO 2 improves the real ( ε 1 ) and imaginary dielectric functions ( ε 2 ), extinction coefficient ( k ), refractive index ( n ), reflectivity ( R ), and absorption coefficient ( α ) properties thereby enhancing its photocatalytic and optical activities. The heat capacities of ZrO 2 and Sc‐ZrO 2 calculated at temperature of 800 K are 74.27 and 77.98 J/K/Nmol, respectively. The result of thermodynamic properties calculations show that doping scandium in zirconia enhances its entropy and specific heat capacity thereby allowing it to be thermodynamically stable for a wide range of electronic applications. Scandium ; Cubic zirconia ; Materials science ; Doping ; Thermodynamics ; Physics ; Optoelectronics ; Metallurgy ; Ceramic Electronic and Structural Properties of Oxides ; Advancements in Solid Oxide Fuel Cells ; Nuclear materials and radiation effects
Authors: Garbas A. dos Santos | Kélrie H. A. Mendes | Sarah G. G. de Oliveira | Gabriel J. P. Tonon | Neide Paloma Gonçalves Lopes | Thiago Henrique Rodrigues da Cunha | Mário Guimarães | Rodrigo L. Lavall | Paulo F.R. Ortega
Source: Preprints.org (preprint, 2024-09-27)
Field: Materials Science — Electronic, Optical and Magnetic Materials

High-Performance Dual-Redox-Mediator Supercapacitors Based on Buckypaper Electrodes and Hydrogel Polymer Electrolytes In recent years, the demand for solid, thin, and flexible energy storage devices has surged in modern consumer electronics, which require autonomy and long duration. In this context, hybrid supercapacitors have become strategic, leading to significant efforts to develop cells with an energy density close to that of batteries, while maintaining the power density of conventional supercapacitors. Motivated by these requirements, we report the development of a new high-performance dual-redox-mediator supercapacitor. In this study, cells were constructed using fully moldable buckypapers (BPs), composed of carbon nanotubes and cellulose nanofibers, as electrodes. We evaluated the compatibility of BPs with hydrogel polymer electrolytes, based on 1 mol L-1 H2SO4 and polyvinyl alcohol (PVA), supplemented with different redox species: methylene blue, indigo carmine, and hydroquinone. Solid cells were constructed containing two active redox species to maximize the specific capacity of each electrode. Considering the main results, the dual-redox-mediator supercapacitor exhibits a high energy density of 32.0 Wh kg-1 (at 0.8 kW kg-1) and is capable of delivering 25.9 Wh kg-1 at high power demands (4.0 kW kg-1). Stability studies conducted over 10,000 galvanostatic cycles revealed that the PVA polymer matrix benefits the system by inhibiting the crossover of redox species within the cell. Buckypaper ; Supercapacitor ; Electrolyte ; Dual (grammatical number) ; Electrode ; Materials science ; Redox ; Mediator ; Polymer ; Nanotechnology ; Chemical engineering ; Chemistry ; Capacitance ; Composite material ; Carbon nanotube ; Engineering ; Cell biology Supercapacitor Materials and Fabrication ; Advanced Theoretical and Applied Studies in Material Sciences and Geometry ; Catalytic Processes in Materials Science
Authors: Ahsan Khan | Muhammad Talha Shabbir | Navdeep Singh Grewal | Haijun Zhang | Jun Zhang | Ahsan Riaz | Khan Muhammad | Talha Shabbir | S Mahmud | M Rahman | M Kamruzzaman | H Khatun | M Ali | M Haque | S Sam | B Joseph | S Thomas | X Li | H Shi | K Pan | M Dai | W Wei | X Liu | Mahmud Ali | M Akter | M | C Lu | Y Ma | F Li | H Zhu | X Zeng | W Ding | N Grewal | G Sharma | K Kumar | U Batra | M Duan | L Luo | Y Liu | J Qian | H Qin | P Zeng | J Hou | X Mo | G Shen | X Tong | T Shen | X Zhou | J Zeng | J Tao | K Munir | E Xiang | M Gmez-Cerezo | Y Ali | S Ramachandra | N Yang | M Dargusch | L Wu | Y Li | Y Cheng | F Linghu | F Jiang | G Chen | N Singh | N Ahuja | A Mahapatro | J Espiritu | M Berangi | H Cwieka | K Iskhakova | A Kuehne | Florian Wieland | D | Y Zheng | H Yang | F Campos | A Bonhome-Espinosa | R Carmona | Jdg Durn | P Kuzhir | M Alaminos | A Khan | T Zhao | M Zheng | S Agarwal | J Curtin | B Duffy | S Jaiswal | P Bowen | R Guillory | E Shearier | J-M Seitz | J Drelich
Source: Biomedical Letters (article, 2024-02-14)
Field: Materials Science — Biomaterials

Recent progress in the application of biodegradable metal implants With the accumulation of data, magnesium-based degradable metal, iron-based degradable metal and zinc-based degradable metal implantable interventional devices have entered the clinic or carried out human experimental studies, and the future prospects are promising. In this paper, the definition, biodegradability and biocompatibility criteria and their classification are reviewed, and the research status and unsolved scientific problems of magnesium-based degradable metals, iron-based degradable metals and zinc-based degradable metals are introduced, and the future development opportunities and challenges of degradable metals are prospected. With a deeper understanding of scientific issues such as mechanical adaptation, degradation adaptation and tissue adaptation of degradable metal implants, more new materials, new technologies and new methods of degradable metals will be developed in the future, so as to effectively realize the precise adaptation of the two events of degradable metal material degradation and body tissue repair in time and geometric space. Biocompatibility ; Biodegradation ; Adaptation (eye) ; Zinc ; Materials science ; Metal ; Nanotechnology ; Degradation (telecommunications) ; Magnesium ; Biochemical engineering ; Metallurgy ; Computer science ; Chemistry ; Engineering ; Organic chemistry ; Biology Magnesium Alloys: Properties and Applications ; Bone Tissue Engineering Materials ; Orthopaedic implants and arthroplasty
Authors: Juan Bisquert | Nir Tessler
Source: arXiv (Cornell University) (preprint, 2024-08-18)
Field: Materials Science — Polymers and Plastics

Transient current responses of organic electrochemical transistors: Evaluating ion diffusion, chemical capacitance, and series elements For the successful implementation of organic electrochemical transistors in neuromorphic computing, bioelectronics, and real-time sensing applications it is essential to understand the factors that influence device switching times. Here we describe a physical-electrochemical model of the transient response to a step of the gate voltage. The model incorporates (1) ion diffusion inside the channel that governs the electronic conductivity, (2) horizontal electron transport, and (3) the external elements (capacitance, ionic resistance) of the ion dynamics in the electrolyte. We find a general expression of two different time constants that determine the vertical insertion process in terms of the kinetic parameters, in addition to the electronic transit time. We highlight the central role of the chemical capacitance in determining the modulation of the lateral conductivity. The different types of response of the drain current are classified, and we discuss the significance for synaptic operation in neuromorphic circuits. The model is confirmed by detailed simulations that enable to visualize the different ions distributions and dynamics. Electrolyte ; Transient (computer programming) ; Diffusion ; Current (fluid) ; Ionic bonding ; Electrochemistry ; Materials science ; Ionic liquid ; Chemistry ; Ion ; Electrical engineering ; Electrode ; Computer science ; Thermodynamics ; Engineering ; Physics ; Organic chemistry ; Catalysis ; Physical chemistry Conducting polymers and applications ; Analytical Chemistry and Sensors ; Electrochemical Analysis and Applications
Authors: Denis Mutebi | František Mikšík | Andrew M. Spring | Indri Yaningsih | Takahiko Miyazaki | Kyaw Thu
Source: Evergreen (article, 2024-12-01)
Field: Chemistry — Inorganic Chemistry

Zeolite Synthesis from Natural and Waste Materials and the Double Environmental Benefits Zeolites' synthesis from low-value precursors and their environmental benefits are reviewed.A case study approach is used where natural resource-based synthesis and a commercialchemical route are compared for environmental accountability, focusing on energy and material consumption and greenhouse gas emissions.Using natural or waste raw materials is recommended; it significantly reduces energy consumption by 0.02 kWh, lowers CO2 emissions by 0.3 kg, and decreases material costs by 6 USD/kg of zeolite produced, compared to chemical precursors.Wastematerials usage for zeolite fabrication is highlighted for its notable advantages, including land-space conservation, positive health impacts, and pollution mitigation.Key conditions for sustainable synthesis include proper aging, alkaline-fusion, aluminum-content adjustments, and waste-liquid recycling. Zeolite ; Natural (archaeology) ; Waste management ; Environmental science ; Chemistry ; Engineering ; Geology ; Organic chemistry ; Catalysis Zeolite Catalysis and Synthesis