jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Philip Noell | Benjamin Pham | Ian Campbell | Brendan Donohoe | Demitri Maestas | Eric John Schindelholz | Michael Melia | Ryan Katona
Source: npj Materials Degradation (article, 2023-07-29)
Field: Materials Science — Materials Chemistry

Pit growth kinetics in aluminum: effects of salt loading and relative humidity Abstract The growth kinetics of localized corrosion, e.g. pits, in corrosive environments often controls the service life of metallic components. Yet, our understanding of these kinetics is largely based on coupon-level, e.g. mass-loss, studies which provide limited insights into the evolution of individual damage events. It is critical to relate observed cumulative loss trends, such as links between changing humidity and mass loss rates, to the growth kinetics of individual pits. Towards this goal, we leverage in-situ X-ray computed tomography to measure the growth rates of over sixty pits in aluminum in four different humid, chloride environments over ≈3 days of exposure. Pit growth rates and final volumes increased with increasing droplet volume, which was observed to increase with increasing humidity and salt loading. Two factors, droplet spreading and oxide jacking, dramatically increased pit growth rates and final volumes. Kinetics ; Relative humidity ; Materials science ; Corrosion ; Aluminium ; Humidity ; Oxide ; Metallurgy ; Growth rate ; Environmental science ; Composite material ; Meteorology ; Geography ; Mathematics ; Physics Corrosion Behavior and Inhibition ; Hydrogen embrittlement and corrosion behaviors in metals ; Concrete Corrosion and Durability
Authors: Coco M. Mao | Janani Sampath | Jim Pfaendtner
Source: ChemRxiv (preprint, 2023-08-29)
Field: Materials Science — Biomaterials

Molecular Driving Forces in the Self-Association of Silaffin Peptide R5 from MD Simulations The 19-residue silaffin-R5 peptide has been widely studied for its ability to precipitate uniform SiO2 particles through mild temperature and pH pathways, in the absence of any organic solvents. There is consensus that post-translational modification (PTM) of side chains has a large impact on the biomineralization process. Thus, it is imperative to understand the precise mechanisms that dictate the formation of SiO2 from R5 peptide, including the effects of PTM on peptide aggregation and peptide-surface adsorption. In this work, we use molecular dynamics (MD) simulations to study the aggregation of R5 dimer with multiple PTMs, with the presence of different ions in solution. Since this system has strong interactions with deep metastable states, we use parallel bias metadynamics with partitioned families to efficiently sample the different states of the system. We find that peptide aggregation is a prerequisite for biomineralization. We observe that the electrostatic interactions are essential in the R5 dimer aggregation; for wild type R5 that only has positively charged residues, phosphate ions HPO42- in the solution form a bridge between two peptides and are essential for peptide aggregation. Alternatively, the post translational modification phosphorylation, which renders neutral serine residues negative, enables R5 to aggregate without phosphate ion. The extent of phosphorylation and location of phosphorylated residues on R5 peptide results in different behavior and extent of aggregation - the aggregation trend of R5 peptide that we observe is in line with SiO2 precipitation observed in previous experimental studies, proving that peptide aggregation is a prerequisite for biomineralization. Peptide ; Biomineralization ; Dimer ; Chemistry ; Molecular dynamics ; Phosphorylation ; Biophysics ; Metadynamics ; Serine ; Computational chemistry ; Biochemistry ; Chemical engineering ; Organic chemistry ; Biology Calcium Carbonate Crystallization and Inhibition ; Bone and Dental Protein Studies ; Advanced Proteomics Techniques and Applications
Authors: Qihui Wang | Chongkang Zhao | Huahao Zheng | Qi Zhang | Xing Zhou | Ruozhou Wang | Zhitao Yan | Yi Sun | Xueming Li
Source: Coatings (article, 2023-06-22)
Field: Materials Science — Materials Chemistry

Shell of Viviparid Snail as an Eco-Friendly Corrosion Inhibitor for Carbon Steel in 1 M HCl The shell of viviparid snail extract (SVSE) was prepared by a simple and environmentally friendly hydrolysis method and the corrosion inhibition of carbon steel (CS) by SVSE in 1 M HCl was investigated. HPLC and FTIR analysis showed that the main component of SVSE was a mixture of various amino acids. The results of electrochemical and surface analysis showed that SVSE is a hybrid corrosion inhibitor with a corrosion inhibition efficiency of 95.23%. In addition, the adsorption behavior of SVSE on CS surfaces was also investigated in depth by adsorption isotherms, quantum chemistry (QC) and molecular dynamics simulations (MDS). Corrosion ; Adsorption ; Environmentally friendly ; Carbon steel ; Corrosion inhibitor ; Electrochemistry ; Shell (structure) ; Fourier transform infrared spectroscopy ; Hydrolysis ; Chemistry ; Nuclear chemistry ; High-performance liquid chromatography ; Chemical engineering ; Materials science ; Inorganic chemistry ; Organic chemistry ; Electrode ; Composite material ; Physical chemistry Corrosion Behavior and Inhibition ; Concrete Corrosion and Durability ; Hydrogen embrittlement and corrosion behaviors in metals
Authors: Asen Dankov | Laurin Hensen | Mert Aydın | Namhyun Choi | Helene Giesler | Dennis Toker | Sebastian Schlücker | Roland Grzeschik
Source: ChemRxiv (preprint, 2023-09-06)
Field: Materials Science — Electronic, Optical and Magnetic Materials

BONAPARTE robot: improving the reproducibility and identifying critical parameters of the synthesis of gold nanoparticles In order to exploit the unique optical properties of gold nanoparticles, precise size and shape control is required. We have designed and constructed the highly customizable BONAPARTE (BOttom-up NAnoPARTiclE synthesis robot, which consists of components that are easy to obtain and cost-effective. Using the robot, critical reaction parameters such as pipetting speed, position and delays were examined. We found that the effect of both the pipetting speed and position have an influence on the final gold cluster size. The effect of the cluster size on the length of gold nanorods was investigated in a two-step seed-growth synthesis. Additionally, we showed time-critical steps in the synthesis of gold nanostars, can be performed with superior accuracy by the robot. Overall, the robot displayed improved reproducibility when compared to nanoparticle synthesis performed manually by persons of different experience. Reproducibility ; Colloidal gold ; Pipette ; Nanorod ; Nanoparticle ; Robot ; Computer science ; Nanotechnology ; Cluster (spacecraft) ; Materials science ; Position (finance) ; Gold cluster ; Exploit ; Artificial intelligence ; Chemistry ; Chromatography Gold and Silver Nanoparticles Synthesis and Applications ; Molecular Communication and Nanonetworks ; Micro and Nano Robotics
Authors: David Alsteens
Source: Frontiers in Biophysics (article, 2023-05-26)
Field: Chemistry — Spectroscopy

Grand challenges in biophysics FIELD GRAND CHALLENGE article Front. Biophys., 26 May 2023 Volume 1 - 2023 | https://doi.org/10.3389/frbis.2023.1215594 Cognitive science ; Biophysics ; Psychology ; Biology Advanced Proteomics Techniques and Applications ; RNA and protein synthesis mechanisms ; Advanced Fluorescence Microscopy Techniques
Authors: John C. Thomas | Wei Chen | Yihuang Xiong | Bradford A. Barker | Junze Zhou | Weiru Chen | Antonio Rossi | Nolan Kelly | Zhuohang Yu | Da Zhou | Shalini Kumari | Edward S. Barnard | Joshua A. Robinson | Mauricio Terrones | Adam Schwartzberg | D. Frank Ogletree | Eli Rotenberg | Marcus M. Noack | Sinéad M. Griffin | Archana Raja | David A. Strubbe | Gian‐Marco Rignanese | Alexander Weber‐Bargioni | Geoffroy Hautier
Source: Research Square (preprint, 2023-11-14)
Field: Materials Science — Materials Chemistry

A substitutional quantum defect in WS2 discovered by high-throughput computational screening and fabricated by site-selective STM manipulation <title>Abstract</title> Point defects in two-dimensional materials are of key interest for quantum information science. However, the space of possible defects is immense, making the identification of high-performance quantum defects extremely challenging. Here, we perform high-throughput (HT) first-principles computational screening to search for promising quantum defects within WS<sub>2</sub>, which present localized levels in the band gap that can lead to bright optical transitions in the visible or telecom regime. Our computed database spans more than 700 charged defects formed through substitution on the tungsten or sulfur site. We found that sulfur substitutions enable the most promising quantum defects. We computationally identify the neutral cobalt substitution to sulfur (Co$_{\rm S}^{0}$) as very promising and fabricate it with scanning tunneling microscopy (STM). The Co$_{\rm S}^{0}$ electronic structure measured by STM agrees with first principles and showcases an attractive new quantum defect. Our work shows how HT computational screening and novel defect synthesis routes can be combined to design new quantum defects. Quantum tunnelling ; Scanning tunneling microscope ; Quantum ; Electronic structure ; Nanotechnology ; Quantum computer ; Sulfur ; Throughput ; Band gap ; Materials science ; Optoelectronics ; Computer science ; Physics ; Condensed matter physics ; Quantum mechanics ; Telecommunications Machine Learning in Materials Science ; 2D Materials and Applications ; Electronic and Structural Properties of Oxides
Authors: Yuhan Chen | Nuwa Xi | Yanrui Du | Haochun Wang | Jianyu Chen | Sendong Zhao | Bing Qin
Source: arXiv (Cornell University) (preprint, 2023-09-11)
Field: Materials Science — Materials Chemistry

From Artificially Real to Real: Leveraging Pseudo Data from Large Language Models for Low-Resource Molecule Discovery Molecule discovery serves as a cornerstone in numerous scientific domains, fueling the development of new materials and innovative drug designs. Recent developments of in-silico molecule discovery have highlighted the promising results of cross-modal techniques, which bridge molecular structures with their descriptive annotations. However, these cross-modal methods frequently encounter the issue of data scarcity, hampering their performance and application. In this paper, we address the low-resource challenge by utilizing artificially-real data generated by Large Language Models (LLMs). We first introduce a retrieval-based prompting strategy to construct high-quality pseudo data, then explore the optimal method to effectively leverage this pseudo data. Experiments show that using pseudo data for domain adaptation outperforms all existing methods, while also requiring a smaller model scale, reduced data size and lower training cost, highlighting its efficiency. Furthermore, our method shows a sustained improvement as the volume of pseudo data increases, revealing the great potential of pseudo data in advancing low-resource cross-modal molecule discovery. Our code and data are available at https://github.com/SCIR-HI/ArtificiallyR2R. Computer science ; Leverage (statistics) ; Data science ; Construct (python library) ; Data discovery ; Drug discovery ; Resource (disambiguation) ; Data mining ; Machine learning ; Bioinformatics ; World Wide Web Machine Learning in Materials Science ; Topic Modeling ; Machine Learning in Bioinformatics
Source: Malaysian Journal of Chemistry (article, 2023-03-09)
Field: Chemistry — Organic Chemistry

Enhanced Removal of Bemacid Blue Anthraquinone Dye by Magnetic Nanocomposite Bentonite-Fe3O4: Equilibrium, Kinetic and Thermodynamic Studies Magnetic nanocomposite materials have attracted increasing interest for their use in various scientific applications, including separation processes.The present study investigated the adsorption of the anthraquinone dye Bemacid Blue (BB-dye) on magnetic bentonite (M-Bt) intercalated with iron oxide (Fe3O4).The structural and morphological characteristics of the adsorbent were analysed by SEM, XRD, FTIR, BET, and pHPZC techniques.Batch kinetic and equilibrium experiments were conducted to assess the effect of the system variables, i.e., contact time, initial pH, adsorbent dosage, initial dye concentration and temperature.The results showed that the adsorption of the BB-dye was maximal in an acidic medium at pH 2.5.The adsorption was analysed using Langmuir, Freundlich and Dubinin-Radushkevich (D-R) isothermal models.Adsorption kinetics and isotherms were found to be in good agreement with pseudo 2 nd order kinetics and the Langmuir model.From the calculated thermodynamic parameters, the sorption was a spontaneous and exothermic process.Regeneration tests revealed that the magnetic sorbent could be recycled and reused for up to three successive cycles.These results indicate that the prepared nanocomposite M-Bt could be used for BB-dye removal in wastewater treatment considering its advantages such as cost, simplicity of preparation and environmental friendliness. Bentonite ; Nanocomposite ; Anthraquinone ; Kinetic energy ; Chemical engineering ; Materials science ; Thermodynamic equilibrium ; Chemistry ; Thermodynamics ; Nanotechnology ; Organic chemistry ; Physics Nanomaterials for catalytic reactions ; Water Quality Monitoring and Analysis
Authors: Fatih İslamoğlu | Naciye Erdoğan | Esra Hacifazlioğlu
Source: Analele Universităţii "Ovidius" Constanţa. Seria Chimie/"Ovidius" University Annals of Chemistry (article, 2023-01-01)
Field: Chemistry — Organic Chemistry

Determination of the pKa value of some 1,2,4-triazol derivatives in forty seven different solvents using semi-empirical quantum methods (PM7, PM6, PM6-DH2, RM1, PM3, AM1, and MNDO) by MOPAC computer program Abstract In this study, we calculated the enthalpy (Δ H , kcal/mol), entropy (∆ S , cal/K·mol) and free energy (Δ G , kcal/mol) thermodynamic values of each molecule for forty-seven different solvent media according to semi-empirical quantum methods (PM7, PM6, PM6-DH2, RM1, PM3, AM1, and MNDO) using the MOPAC computer program. The theoretical pKa values were calculated by placing these values in the thermodynamic cycle. It was determined that the triazole derivative molecules examined in this study showed a very high acidity in trifluoroacetic acid and a very low acidity in cyclohexane. The fifth molecule of the triazole derivative molecules examined in this study showed a very high acidity (pKa :1.2457) in trifluoroacetic acid according to the RM1 semi-empirical quantum method. On the other hand, it was determined that the fourth molecule showed a very low acidity (pKa : 69.5668) in cyclohexane according to the RM1 semi-empirical quantum method. MNDO ; Chemistry ; Enthalpy ; Molecule ; Cyclohexane ; Trifluoroacetic acid ; Solvent ; Computational chemistry ; Physical chemistry ; Thermodynamics ; Organic chemistry ; Physics Free Radicals and Antioxidants ; Chemistry and Chemical Engineering ; Chemical and Physical Properties in Aqueous Solutions
Authors: Mhanna Mhanna | Mohamed Sy | Ali Elkhazraji | Aamir Farooq
Source: Research Square (preprint, 2023-02-24)
Field: Chemistry — Spectroscopy

A laser-based sensor for selective detection of benzene, acetylene, and carbon dioxide in the fingerprint region Abstract A mid-infrared laser-based sensor is designed and demonstrated for trace detection of benzene, acetylene, and carbon dioxide at ambient conditions. The sensor is based on a distributed feedback quantum cascade laser (DFB-QCL) emitting near 14.84 µm. Tunable diode laser absorption spectroscopy (TDLAS) and a multidimensional linear regression algorithm were employed to enable interference-free measurements of the target species. The laser wavelength was tuned over 673.8–675.1 cm-1 by a sine-wave injection current at 1 kHz repetition rate. Minimum detection limits of 0.22, 5.92, and 8.32 ppm were achieved for benzene, acetylene, and carbon dioxide, respectively. The developed sensor is insensitive to interference from overlapping absorbance spectra, and its performance was demonstrated by measuring the target species in known mixture samples. The sensor can be used to detect tiny leaks of the target species in petrochemical facilities and to monitor air quality in residential and industrial areas. Quantum cascade laser ; Tunable diode laser absorption spectroscopy ; Laser ; Materials science ; Interference (communication) ; Absorbance ; Benzene ; Acetylene ; Carbon dioxide sensor ; Analytical Chemistry (journal) ; Carbon dioxide ; Spectroscopy ; Absorption spectroscopy ; Wavelength ; Tunable laser ; Optoelectronics ; Optics ; Chemistry ; Environmental chemistry ; Chromatography Spectroscopy and Laser Applications ; Atmospheric and Environmental Gas Dynamics ; Atmospheric Ozone and Climate
Authors: Che Chen Tho | Xukun Feng | Zhuoling Jiang | Liemao Cao | Chit Siong Lau | San‐Dong Guo | Yee Sin Ang
Source: arXiv (Cornell University) (preprint, 2023-11-15)
Field: Materials Science — Materials Chemistry

Ultrathick MA$_2$N$_4$(M'N) Intercalated Monolayers with Sublayer-Protected Fermi Surface Conduction States: Interconnect and Metal Contact Applications Recent discovery of ultrathick $\mathrm{MoSi_2N_4(MoN)_n}$ monolayers open up an exciting platform to engineer 2D material properties via intercalation architecture. Here we computationally investigate a series of ultrathick MA$_2$N$_4$(M'N) monolayers (M, M' = Mo, W; A = Si, Ge) under both homolayer and heterolayer intercalation architectures in which the same and different species of transition metal nitride inner core layers are intercalated by outer passivating nitride sublayers, respectively. The MA$_2$N$_4$(M'N) monolayers are thermally, dynamically and mechanically stable with excellent mechanical strength and metallic properties. Intriguingly, the metallic states around Fermi level are localized within the inner core layers. Carrier conduction mediated by electronic states around the Fermi level is thus spatially insulated from the external environment by the native outer nitride sublayers, suggesting the potential of MA$_2$N$_4$(M'N) in back-end-of-line (BEOL) metal interconnect applications. Nitrogen vacancy defect at the outer sublayers creates `punch through' states around the Fermi level that bridges the carrier conduction in the inner core layers and the outer environment, forming a electrical contact akin to the `vias' structures of metal interconnects. We further show that MoSi$_2$N$_4$(MoN) can serve as a quasi-Ohmic contact to 2D WSe$_2$. These findings reveal the promising potential of ultrathick MA$_2$N$_4$(MN) monolayers as metal electrodes and BEOL interconnect applications. Materials science ; Monolayer ; Ohmic contact ; Fermi level ; Nitride ; Intercalation (chemistry) ; Metal ; Interconnection ; Nanotechnology ; Condensed matter physics ; Optoelectronics ; Layer (electronics) ; Chemistry ; Electron ; Metallurgy ; Inorganic chemistry ; Physics 2D Materials and Applications ; MXene and MAX Phase Materials ; Molecular Junctions and Nanostructures
Authors: Antti M. Salo | Pekka Rappu | M. Kristian Koski | Emma Karjalainen | Valerio Izzi | Kati Drushinin | Ilkka Miinalainen | Jarmo Käpylä | Jyrki Heino | Johanna Myllyharju
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-06-28)
Field: Materials Science — Biomaterials

Collagen prolyl 4-hydroxylases have sequence specificity towards different X-Pro-Gly triplets ABSTRACT Formation of 4-hydroxyproline (4Hyp) in -X-Pro-Gly- collagen sequences is essential for the thermal stability of collagen molecules. 4Hyp formation is catalyzed by collagen prolyl 4-hydroxylases (C- P4H). Here we identify specific roles for the two main C-P4H isoenzymes by 4Hyp analysis of type I and IV collagens. Loss of C-P4H-I mainly affected prolines preceded by an X-position amino acid with a positively charged or a polar uncharged side chain. In contrast, loss of C-P4H-II affected triplets with a negatively charged glutamate or aspartate in the X-position, and their hydroxylation was found to be important as loss of C-P4H-II alone resulted in reduced collagen melting temperature and altered assembly of collagen fibrils and basement membrane. The C-P4H isoenzyme differences in substrate specificity were explained by selective substrate binding to the active site resulting in differences in Km and Vmax values. In conclusion, this study provides a molecular level explanation for the need of multiple C-P4H isoenzymes to generate collagen molecules capable to assemble into intact extracellular matrix structures. Hydroxyproline ; Proline ; Hydroxylation ; Chemistry ; Isozyme ; Extracellular matrix ; Stereochemistry ; Elastin ; Substrate (aquarium) ; Amino acid ; Side chain ; Biochemistry ; Hydroxylysine ; Molecule ; Collagen helix ; Crystallography ; Triple helix ; Enzyme ; Lysine ; Biology ; Polymer ; Genetics ; Organic chemistry Collagen: Extraction and Characterization ; Bone and Dental Protein Studies ; Cancer-related gene regulation
Authors: Barış Demirbay
Source: Polymer Engineering and Science (article, 2023-10-21)
Field: Materials Science — Polymers and Plastics

Film formation kinetics of polystyrene latex‐based nanocomposites with a broad particle size distribution Abstract The present study article aims to clarify the effect of colloidal polystyrene (PS) latexes with a broad particle size distribution on film formation kinetics of multi‐walled carbon nanotube (MWCNT)‐added polymer nanocomposites by considering theoretical film formation models. Experimentally, light transmitted from nanocomposite films, each having different weight fractions of MWCNT, was recorded at different annealing temperatures via UV–Visible spectrophotometry. Optical data set was then theoretically elaborated by taking into account void closure and Prager‐Tirrell models. Activation energies of viscous flow (Δ H ) and backbone motion for reptating PS chains (Δ E B ), minimum film formation ( T 0 ) and healing ( T h ) temperatures were then computed from optical data. Experimental results revealed that Δ H required for void closure phenomenon remained unaffected by both nanofiller and size distribution of latexes. On the other hand, it was found that Δ E B for backbone motion promoted upon the addition of nano‐fillers into latex particles. Our experimental findings suggested that film formation from MWCNT‐added latex films with a broad particle size distribution mainly originates from void closure mechanism since Δ H for viscous flow suppresses Δ E B acquired for backbone motion of repeating PS chains to a great extent. Highlights A broad size distribution effect of PS on film formation was investigated. Voids closure and Prager‐Tirrell models were applied to spectroscopic data. Activation energy of viscous flow is unaffected by size distribution of PS. Latex film formation with varying size distribution stems from void closure. Materials science ; Polystyrene ; Nanocomposite ; Void (composites) ; Kinetics ; Particle size ; Composite material ; Particle-size distribution ; Polymer ; Carbon nanotube ; Colloid ; Annealing (glass) ; Chemical engineering Polymer crystallization and properties ; Polymer Nanocomposites and Properties ; Surfactants and Colloidal Systems