jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Lenard Röder
Source: Research Square (preprint, 2023-04-20)
Field: Chemistry — Spectroscopy

Neural Network Architectures for Absorption Spectroscopy <title>Abstract</title> State-of-the-art neural network architectures in image classification and natural language processing were applied to absorption spectroscopy applications by interpreting the data structure accordingly. A model was designed for temporal interpolation of background spectra and a different model was created for gas concentration fitting. The networks were trained on experimental data provided by a wavelength modulation spectroscopy instrument and the best performing architectures were analyzed further to evaluate generalization performance, robustness and transferability. A BERT-styled fitter achieved the best performance on the validation set and reduced the mean squared error of fitted amplitude by 99.5 %. A U-Net styled convolutional neural network reduced the mean squared error of the interpolation by 93.2 %. Evaluation on a test set provided evidence that the combination of model interpolation and linear fitting was robust and the detection limit was improved by 52.4 %. Transferring the trained models to a different spectrometer setup was tested and showed no chaotic out-of-distribution effects. Additional fine-tuning further helped increasing the performance of the transferred model. Overall the proposed model architectures can be applied to spectroscopy tasks if the data structure is interpreted the right way and the pre-trained networks are robust and can be transferred to other spectrometer setups. Spectroscopy ; Absorption (acoustics) ; Absorption spectroscopy ; Artificial neural network ; Materials science ; Computer science ; Chemistry ; Artificial intelligence ; Physics ; Optics ; Astronomy ; Composite material Spectroscopy and Laser Applications ; Spectroscopy and Chemometric Analyses ; Spectroscopy and Quantum Chemical Studies
Authors: Nathalie Proos Vedin | Sílvia Escayola | Slavko Radenković | Miquel Solà | Henrik Ottosson
Source: ChemRxiv (preprint, 2023-12-11)
Field: Chemistry — Organic Chemistry

The n,π* States of Heteroaromatics: When are They the Lowest Excited States and in What Way Can They Be Aromatic or Antiaromatic? Heteroaromatic molecules are found in areas ranging from biochemistry to organic electronics. We analyze the n,π* excited states of 6π-electron heteroaromatic compounds with in-plane lone-pair orbitals (n(sigma), here labelled n), and use qualitative theory and quantum chemical computations, with a start at Mandado’s 2n+1 rule for aromaticity of separate spins. After excitation of an electron from n to π*, a (4n+2)π-electron species has 2n+2 π(alpha)-electrons and 2n+1 π(beta)-electrons (or vice versa), and becomes π(alpha)-antiaromatic and π(beta)-aromatic. Yet, the antiaromatic π(alpha)- and aromatic π(beta)-components often do not cancel, leading to either aromatic or antiaromatic residuals. We focus on vertically excited triplet n,π* states (3n,π*), which are most readily analyzed, but also explore singlet n,π* states (1n,π*), and explain which compounds have n,π* states with aromatic residuals as their lowest excited states (e.g., pyrazine and the phenyl anion). Our results show that if the π(beta)-electron population becomes more (less) uniformly distributed upon excitation, the system will have an (anti-)aromatic residual. Among isomeric heteroaromatics, the isomer which has the most aromatic residual in 3n,π* is often of lowest energy in this state. Five-membered ring heteroaromatics with one or two N, O and/or S atoms never have n,π* states as their first excited states (T1 and S1), while this is nearly always the case for six-membered ring heteroaromatics with electropositive heteroatoms and/or highly symmetric (D2h) diheteroaromatics. For the complete compound set, there is a visible yet modest correlation between the (anti)aromatic character of the n,π* state and the energy difference between the lowest n,π* and π,π* states (R2 = 0.42) while the correlation is significantly stronger for monosubstituted pyrazines (R2 = 0.84). Antiaromaticity ; Excited state ; Aromaticity ; Ring (chemistry) ; Chemistry ; Heteroatom ; Atomic orbital ; Singlet state ; Population ; Pi interaction ; Electron ; Computational chemistry ; Crystallography ; Atomic physics ; Molecule ; Physics ; Quantum mechanics ; Organic chemistry Synthesis and Properties of Aromatic Compounds ; Molecular Junctions and Nanostructures ; Fullerene Chemistry and Applications
Authors: Felix Kronenwett | Pia Klingenberg | Georg Maier | Thomas Längle | Elke Metzsch‐Zilligen | Jürgen Beyerer
Source:  (article, 2023-05-25)
Field: Chemistry — Analytical Chemistry

Regression-based Age Prediction of Plastic Waste using Hyperspectral Imaging In order to enable high quality recycling of polypropylene (PP) plastic, additional classification and separation into the degree of degradation is necessary. In this study, different PP plastic samples were produced and degraded by multiple extrusion and thermal treatment. Using near infrared spectroscopy, the samples were examined and regression models were trained to predict the degree of aging. The models of the multiple extruded samples showed high accuracy, despite only minor spectral changes. The accuracy of the models of the thermally aged samples varied with the design of the training set due to the non-linear aging process, but showed sufficient accuracy in prediction. Polypropylene ; Hyperspectral imaging ; Plastic waste ; Linear regression ; Regression analysis ; Regression ; Materials science ; Artificial intelligence ; Computer science ; Machine learning ; Mathematics ; Statistics ; Composite material ; Engineering ; Waste management Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Industrial Vision Systems and Defect Detection
Authors: Zhenghao Wu | Subhadeep Pal | Sinan Keten
Source: arXiv (Cornell University) (preprint, 2023-03-09)
Field: Materials Science — Polymers and Plastics

Implicit Chain Particle Model for Polymer Grafted Nanoparticles Matrix-free nanocomposites made from polymer grafted nanoparticles (PGN) represent a paradigm shift in materials science because they greatly improve nanoparticle dispersion and offer greater tunability over rheological and mechanical properties in comparison to neat polymers. Utilizing the full potential of PGNs requires a deeper understanding of how polymer graft length, density, and chemistry influence interfacial interactions between particles. There has been great progress in describing these effects with molecular dynamics (MD). However, the limitations of the length and time scales of MD make it prohibitively costly to study systems involving more than a few PGNs. Here, we address some of these challenges by proposing a new modeling paradigm for PGNs using a strain-energy mapping framework involving potential of mean force (PMF) calculations. In this approach, each nanoparticle is coarse-grained into a representative particle with chains treated implicitly, namely, the implicit chain particle model (ICPM). Using a chemistry-specific CG-MD model of PMMA as a testbed, we derive the effective interaction between particles arranged in a closed-packed lattice configuration by matching bulk dilation/compression strain energy densities. The strain-rate dependence of the mechanical work in ICPM is also discussed. Overall, the ICPM model increases the computational speed by approximately 5-6 orders of magnitude compared to the CG-MD models. This novel framework is foundational for particle-based simulations of PGNs and their blends and accelerates the understanding and predictions of emergent properties of PGN materials. Nanoparticle ; Molecular dynamics ; Materials science ; Polymer ; Particle (ecology) ; Nanotechnology ; Statistical physics ; Chemical physics ; Composite material ; Physics ; Chemistry ; Computational chemistry Polymer Nanocomposites and Properties ; Polymer Surface Interaction Studies ; Force Microscopy Techniques and Applications
Authors: A. Ayadim | Lucas Levrel | S Amokrane
Source: Modelling and Simulation in Materials Science and Engineering (article, 2023-05-31)
Field: Materials Science — Materials Chemistry

Structure and thermodynamics of liquid ruthenium and ruthenium-based alloys from <i>ab initio</i> and classical molecular dynamics with embedded atom model potentials Abstract The combination of classical and ab initio molecular dynamics simulations for computing structural and thermodynamic properties of metallic liquids is illustrated on the example of ruthenium and ruthenium-based alloys. The classical simulations used embedded atom model (EAM) potentials parametrized with the force matching method. The ab initio reference data were obtained using two electronic structure codes implementing the density functional theory plane wave/pseudopotential method. Several methodological aspects in the determination of structural and thermodynamic properties in the liquid phase are examined, first for pure ruthenium. The efficiency of this combined method is finally illustrated on the structure and the pressure of ternary alloys of platinum group metals of interest in the treatment of nuclear wastes. Pseudopotential ; Ruthenium ; Materials science ; Ab initio ; Thermodynamics ; Molecular dynamics ; SIESTA (computer program) ; Atom (system on chip) ; Density functional theory ; Ternary operation ; Electronic structure ; Ab initio quantum chemistry methods ; Computational chemistry ; Physical chemistry ; Chemical physics ; Molecule ; Chemistry ; Atomic physics ; Physics ; Catalysis ; Organic chemistry Machine Learning in Materials Science ; Spectroscopy and Quantum Chemical Studies ; Advanced Chemical Physics Studies
Authors: Олена О. Пилипенко | Олексій Воскобойнік | Liudmyla K. Sviatenko | С. І. Коваленко | Сергій І. Оковитий
Source: Journal of Chemistry and Technologies (article, 2023-07-25)
Field: Chemistry — Organic Chemistry

ПОШУК НОВИХ ІНГІБІТОРІВ ТИРОЗИНКІНАЗИ СЕРЕД 2-(3-R-1H-1,2,4-ТРИАЗОЛ-5-ІЛ)АНІЛІНІВ ЯК ПОТЕНЦІЙНИХ ПРОТИПУХЛИННИХ АГЕНТІВ З ВИКОРИСТАННЯМ МОЛЕКУЛЯРНОГО ДОКІНГУ Дана робота присвячена in silico дослідженню 2-(3-R-1H-1,2,4-триазол-5-іл)анілінів як потенційних інгібіторів EGFR (pецептор епідермального фактора росту) та RET (перебудований під час трансфекції), які відіграють значну роль у регуляції фізіологічного циклу недрібноклітинного раку легень. Для дослідження було використано загальноприйняту програму для проведення молекулярного докінгу AutoDock Vina. Сім досліджуваних сполук та два стандартних препарати (вандетаніб та гефітиніб) були зістиковані з кристалографічними структурами білків EGFR та RET. Встановлено, що серед нових досліджуваних речовин найбільшу аффіність до EGFR та RET має 2-(3-(індоліл-2)-1H-1,2,4-триазол-5-іл)анілін (а5) з найвищою енергією зв'язування -9.7 та -8.7 ккал/моль, відповідно. Візуалізація молекулярного докінгу зазначеної сполуки з використанням програми Discovery Studio показала, що для неї характерне подібне до стандартних лігандів розміщення у активних центрах ензимів, стабільні водневі зв'язки та π-стекінгові взаємодії, які забезпечуються наявністю у молекулі індольного та анілінового фрагментів. Отже, нами виявлено новий ефективний ліганд, який можна використовувати як «базову» молекулу для подальшого фрагмент-орієнтованого дизайну з використанням методології молекулярної гібридизації (методи злиття, з’єднання або нарощування фрагментів) або структурної модифікації шляхом введення «фармакофорних» груп до молекули. Підсумовуючи наведені вище результати скринінгу, можна сказати, що 2-(3-R-1H-1,2,4-триазол-5-іл)аніліни потребують подальшого детального вивчення з точки зору ефективних інгібіторів тирозинкіназ для пошуку перспективних протипухлинних агентів для лікування недрібноклітинного раку легень. AutoDock ; In silico ; Studio ; Computer science ; Mathematics ; Chemistry ; Biochemistry Synthesis and Reactions of Organic Compounds
Authors: T Santhi | K. Arjunan | David Gnanasangeetha | Sarmina Duraisamy | T. Sasilatha | S. Rajendran
Source: Zastita materijala (article, 2023-09-08)
Field: Materials Science — Materials Chemistry

Influence of an emulsion coating on the corrosion resistance of hull plates made of mild steel in natural sea water The corrosion resistance of mild steel, used to make hull plates in ship technology, in sea water before paint coating [Nippon paint SUMO XTRA durable exterior emulsion coating (emulsion coating)] and after paint coating has been measured by electrochemical studies such as polarisation study and AC impedance spectra. It is observed that after paint coating, the corrosion resistance of mild steel hull plates increases. Polarization study reveals that after paint coating, the linear polarization resistance increases and corrosion current decrease. AC impedance spectra reveal that in the presence of paint coating charge transfer resistance value increases, impedance value increases, phase angle increases and double layer capacitance value decreases. The corrosion inhibition efficiency was greater than 99%. The hull plates made of mild steel may be coated with durable exterior emulsion coating (emulsion coating). This will control the corrosion of the hull plates in the sea water. There will be increase in the life time of the hull plates. Corrosion ; Coating ; Emulsion ; Materials science ; Hull ; Dielectric spectroscopy ; Composite material ; Polarization (electrochemistry) ; Carbon steel ; Metallurgy ; Electrochemistry ; Electrode ; Chemical engineering ; Chemistry Corrosion Behavior and Inhibition ; Concrete Corrosion and Durability ; Hydrogen embrittlement and corrosion behaviors in metals
Authors: Giulia Giubertoni | Liru Feng | K. Klein | Guido Giannetti | Yeji Choi | Anouk van der Net | Gerard Castro-Linares | Federico Caporaletti | Dimitra Micha | Johannes Hunger | Antoine Deblais | Daniel Bonn | Anđela Šarić | Ioana M. Ilie | Gijsje H. Koenderink | Sander Woutersen
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-08-02)
Field: Materials Science — Biomaterials

Elucidating the role of water in collagen self assembly by isotopically modulating collagen hydration Water is known to play an important role in collagen self assembly, but it is still largely unclear how water-collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H 2 O/D 2 O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self assembly. We dissolve collagen in H 2 O and D 2 O, and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D 2 O than in H 2 O, and collagen in D 2 O self assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus compared to H 2 O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D 2 O is less hydrated than in H 2 O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen-water interface, increasing the self assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions, which appear to be crucial in determining the acceleration of the initial nucleation rate. These results show that water acts as a mediator between collagen monomers, by moderating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self assembly. Nucleation ; Fibril ; Collagen fibril ; Hydrogen bond ; Kinetics ; Chemistry ; Monomer ; Self-assembly ; Crystallography ; Biophysics ; Molecular dynamics ; Chemical engineering ; Materials science ; Chemical physics ; Molecule ; Computational chemistry ; Organic chemistry ; Polymer ; Biochemistry Collagen: Extraction and Characterization ; Meat and Animal Product Quality ; Proteins in Food Systems
Authors: Jan G. Rittig | Kobi Felton | Alexei A. Lapkin | Alexander Mitsos
Source: arXiv (Cornell University) (preprint, 2023-05-31)
Field: Materials Science — Materials Chemistry

Gibbs-Duhem-Informed Neural Networks for Binary Activity Coefficient Prediction We propose Gibbs-Duhem-informed neural networks for the prediction of binary activity coefficients at varying compositions. That is, we include the Gibbs-Duhem equation explicitly in the loss function for training neural networks, which is straightforward in standard machine learning (ML) frameworks enabling automatic differentiation. In contrast to recent hybrid ML approaches, our approach does not rely on embedding a specific thermodynamic model inside the neural network and corresponding prediction limitations. Rather, Gibbs-Duhem consistency serves as regularization, with the flexibility of ML models being preserved. Our results show increased thermodynamic consistency and generalization capabilities for activity coefficient predictions by Gibbs-Duhem-informed graph neural networks and matrix completion methods. We also find that the model architecture, particularly the activation function, can have a strong influence on the prediction quality. The approach can be easily extended to account for other thermodynamic consistency conditions. Artificial neural network ; Computer science ; Generalization ; Consistency (knowledge bases) ; Binary number ; Backpropagation ; Gibbs free energy ; Applied mathematics ; Artificial intelligence ; Machine learning ; Statistical physics ; Mathematics ; Thermodynamics ; Physics ; Mathematical analysis Machine Learning in Materials Science ; Advanced Graph Neural Networks ; Advanced Memory and Neural Computing
Authors: Zhen Dong | Yi Zhu | Fangfei Zhang | Chunlong Wu | Ting Chen | Jiayi Chen | Wenhao Jiang | Qi Xiao | Shu Zheng | Kiryl D. Piatkevich | Tiannan Guo
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-11-29)
Field: Chemistry — Spectroscopy

Filter-aided expansion proteomics Abstract Integration of hydrogel-based tissue expansion and mass spectrometry-based proteomics enables high spatial resolution analysis of global protein expression in tissues. Here, we introduce a filter-aided tissue expansion proteomics (FAXP) method with optimized hydrogel preparation and treatment steps for spatial proteomics analysis of formalin-fixed paraffin-embedded (FFPE) specimens. Compared with our original ProteomEx method, FAXP, partially automated with robotics, exhibited 14.5-fold higher volumetric resolution, increased peptide yield leading to 250% more protein identifications, and 50% time consumption for sample preparation. We demonstrated its application in clinical colorectal tissue samples. We further integrated it with laser capture microdissection for proteomic analysis of subcellular organelles. Proteomics ; Laser capture microdissection ; Mass spectrometry ; Computational biology ; Chemistry ; Computer science ; Biomedical engineering ; Chromatography ; Biology ; Biochemistry ; Gene expression ; Medicine ; Gene Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Molecular Biology Techniques and Applications
Authors: Emily G. Meekel | P. G. Partridge | Robert A. I. Paraoan | Joshua J. B. Levinsky | Ben Slater | Claire L. Hobday | Andrew L. Goodwin
Source: arXiv (Cornell University) (preprint, 2023-12-21)
Field: Chemistry — Inorganic Chemistry

Enhanced elastic stability of a topologically disordered crystalline metal--organic framework By virtue of their open network structures and low densities, metal--organic frameworks (MOFs) are soft materials that exhibit elastic instabilities at low applied stresses. The conventional strategy for improving elastic stability is to increase the connectivity of the underlying MOF network, which necessarily increases material density and reduces porosity. Here we demonstrate an alternative paradigm, whereby elastic stability is enhanced in a MOF with an aperiodic network topology. We use a combination of variable-pressure single-crystal X-ray diffraction measurements and coarse-grained lattice-dynamical calculations to interrogate the high-pressure behaviour of the topologically aperiodic system TRUMOF-1, which we compare against that of its ordered congener MOF-5. We show that the topology of the former quenches the elastic instability responsible for pressure-induced framework collapse in the latter, much as irregularity in the shapes and sizes of stones acts to prevent cooperative mechanical failure in drystone walls. Our results establish aperiodicity as a counterintuitive design motif in engineering the mechanical properties of framework structures, relevant to MOFs and larger-scale architectures alike. Aperiodic graph ; Materials science ; Structural stability ; Elastic instability ; Lattice (music) ; Porosity ; Soft materials ; Crystallization ; Topology (electrical circuits) ; Diffraction ; Metal-organic framework ; Instability ; Nanotechnology ; Mechanics ; Composite material ; Structural engineering ; Physics ; Thermodynamics ; Chemistry ; Mathematics ; Engineering Metal-Organic Frameworks: Synthesis and Applications ; X-ray Diffraction in Crystallography ; Supramolecular Self-Assembly in Materials
Authors: Alina Marilena Pahontu | Daniela Simina Ștefan | Laura Chiriac | Ioan Călinescu | Annette Madelene Dăncilă | Mircea Ștefan
Source: Preprints.org (preprint, 2023-08-09)
Field: Materials Science — Materials Chemistry

Study of Bisphenol A Degradation Using Ultrasound and Aditional Chemical Compounds Bisphenol-A (BPA) represents an important co-monomer for obtaining polycarbonate, epoxy resins, flame retardants, in paint, and other chemicals products. Products containing BPA are widely used, and thus, we can find it in the environment: in the air, in the soil, in natural surface water and in sediments, underground water in landfills, and in wastewater. BPA disturbs human and animals’ health. This influences the enzymatic, androgenic, neurological, liver and reproductive systems at different stages of human life: like in fetal stage, children and adults’ stages. Taking these inconveniences into account, it is very important to remove BPA from water. Ultrasonic technology can be considered a verry sustainable and efficient method to remove BPA from water. The advantages of this method is easy to implement on existing water treatment and purification facilities, it does not produce residual compounds that produce sludge, the time required for degradation is of the order of 1-2 hours and the level of degradation is very high. In this work, we presented the studies on the efficiency of ultrasonics under air atmosphere on the degradation of BPA. The influence of the frequency and of some additional compounds such as carbon tetrachloride, FeSO4 7H2O (FS), and ethyl anthraquinone (EAC) was studied. Three different frequencies were used: 1146 KHz, 864 KHz, 580 KHz, at a power of 50 W. It was identified the efficiency of BPA degradation over a period of 60 minutes, with sampling every 15 minutes. Using the LC-MS/MS technique, the degradation compounds were identified that result from the application of ultrasound processes. Pathways of BPA degradation were also proposed. Degradation (telecommunications) ; Bisphenol A ; Environmental chemistry ; Monomer ; Chemistry ; Epoxy ; Pulp and paper industry ; Organic chemistry ; Polymer ; Computer science Ultrasound and Cavitation Phenomena