jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: R. L. Anderson | David S. D. Gunn | Tseden Taddese | Ennio Lavagnini | Patrick B. Warren | David J. Bray
Source: ChemRxiv (preprint, 2022-12-19)
Field: Chemistry — Organic Chemistry

Phase Behaviour of Alkyl Ethoxylate Surfactants in a Dissipative Particle Dynamics Model We present a dissipative particle dynamics (DPD) model capable of capturing the liquid state phase behaviour of non-ionic surfactants from the alkyl ethoxylate (CnEm) family. The model is based upon our recent work [Anderson et al., J. Chem. Phys. 2017, 147, 094503] but adopts tighter control of the molecular structure by setting the bond angles with guidance from molecular dynamics simulations. Changes to the geometry of the surfactants were shown to have little effect on the predicted micelle properties of sampled surfactants, or the water-octanol partition coefficients of small molecules, when compared to the original work. With these modifications the model is capable of reproducing the binary water-surfactant phase behaviour of nine surfactants (C8E4, C8E5, C8E6, C10E4, C10E6, C10E8, C12E6, C12E8 and C12E12) with a good degree of accuracy. Dissipative particle dynamics ; Pulmonary surfactant ; Alkyl ; Molecular dynamics ; Dissipative system ; Micelle ; Phase (matter) ; Particle (ecology) ; Work (physics) ; Chemical physics ; Octanol ; Thermodynamics ; Molecule ; Binary number ; Chemistry ; Materials science ; Partition coefficient ; Statistical physics ; Physics ; Computational chemistry ; Physical chemistry ; Organic chemistry ; Polymer ; Aqueous solution ; Mathematics Surfactants and Colloidal Systems ; Spectroscopy and Quantum Chemical Studies ; Electrostatics and Colloid Interactions
Authors: Stan Moore | Mitchell Wood | Kyle Cochrane | Aidan P. Thompson
Source:  (article, 2022-11-01)
Field: Materials Science — Materials Chemistry

Extreme-Scale Atomistic Simulations of Molten Metal Expansion. For some flyers and wire Scale (ratio) ; Materials science ; Physics Solidification and crystal growth phenomena ; Metallurgical Processes and Thermodynamics ; Aluminum Alloy Microstructure Properties
Authors: Oktay Göcenler | Cansu M. Yenici | Kerem Kahraman | Cengizhan Büyükdağ | Çağdaş Dağ
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-05-22)
Field: Materials Science — Materials Chemistry

Biomolecular solution X-ray scattering at n <sup>2</sup> STAR Beamline Abstract Small angle X-ray Scattering (SAXS) is a method for determining basic structural characteristics such as size, shape, and surface of particles. SAXS can generate low resolution models of biomolecules faster than any other conventional structural biology tools. SAXS data is mostly collected in synchrotron facilities to obtain the best scattering data possible however home source SAXS devices can also generate valuable data when optimized properly. Here, we examined sample data collection and optimization at home source SAXS beamline in terms of concentration, purity, and the duration of data acquisition. We validated that high concentration, monodisperse and ultra pure protein samples obtained by size exclusion chromatography are necessary for generating viable SAXS data using home source beamline. Longer data collection time does not always generate higher resolutions but at least one hour is required for generating a feasible model from SAXS data. Furthermore, with small optimizations both during data collection and later data analysis SAXS can determine properties such as oligomerization, molecular mass, and overall shape of particles in solution under physiological conditions. Small-angle X-ray scattering ; Beamline ; Scattering ; Synchrotron ; Materials science ; Resolution (logic) ; Small-angle scattering ; Dispersity ; Size-exclusion chromatography ; Crystallography ; Analytical Chemistry (journal) ; Optics ; Chemistry ; Physics ; Computer science ; Chromatography ; Artificial intelligence ; Beam (structure) ; Nuclear magnetic resonance ; Polymer chemistry Enzyme Structure and Function ; Protein Structure and Dynamics ; X-ray Spectroscopy and Fluorescence Analysis
Authors: Zan Hui Chen | Weicheng Chen | Zhenzhou Cheng | Guo-Wei Lu | Jiaqi Wang
Source: IEEE photonics journal (article, 2022-01-18)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Corrections to “Deep Learning-Assisted Enhanced Fano Resonances in Symmetry-Breaking SOI Metasurface” [Feb 22 Art. no. 5702107] In the above paper [1] there are errors which we correct here. Fano resonance ; Silicon on insulator ; Symmetry breaking ; Physics ; Symmetry (geometry) ; Fano plane ; Computer science ; Optoelectronics ; Condensed matter physics ; Quantum mechanics ; Plasmon ; Silicon ; Mathematics ; Geometry Metamaterials and Metasurfaces Applications ; Terahertz technology and applications ; Neural Networks and Reservoir Computing
Authors: B. Ostapovych | Ya. Kovalyshyn | N. Shcromyda
Source: Visnyk of the Lviv University Series Chemistry (article, 2022-01-01)
Field: Materials Science — General Materials Science

Еfficiency of azorubin adsorption on polyaniline adsorbent Polymer adsorbents based on composites of conjugated polymers (polyaniline, polypyrrole) show very good adsorption capacity when used for extraction of noble metal ions from aqueous media, for removal of heavy metal cations and various anions, as well as for purification of water from synthetic organic dyes. good solubility in water and resistance to natural biological decomposition. We synthesized samples of powdered polyaniline during oxidative polycondensation of aniline under the action of ammonium peroxide disulfate and investigated the processes of adsorption of synthetic dye on the polymer surface from aqueous solutions on the example of azorubine, which is of practical importance for cleaning water resources. The intensity of peaks of the characteristic absorption bands of azorubine solutions under conditions of equilibrium adsorption of the dye on macromolecular polyaniline chains with a change in the mass of the adsorbent in the studied systems was measured by UV spectroscopy. The change in the concentration of azorubine during adsorption was evaluated by measuring the optical density of the solutions using a UV spectrophotometer Specord M40. It is shown that with an increase in the amount of adsorbent (PAN) in the initial solutions of azorubine, a decrease in the absorption intensity of the characteristic dye band in the UV region (λ≈515 nm) is observed, which is obviously due to an increase in the equilibrium adsorption of azorubine from its aqueous solution. on polyaniline powder. It is shown that the adsorption efficiency of the anionic dye increases up to 90 % with increasing mass of polyaniline in the adsorption mixture from 0.005 to 0.1 grams, which can be explained by the contribution of intermolecular interactions between the functional groups of the adsorbent and the substrate. Some decrease in the color intensity of azorubine solutions may also be due to the participation of redox groups of macromolecules of polyaniline and air oxygen in the oxidation of the adsorbed dye and the formation of colorless reaction products. Keywords : polyaniline, dye, adsorption, azorubine. Polyaniline ; Adsorption ; Aqueous solution ; Chemistry ; Aniline ; Absorption (acoustics) ; Polymer ; Inorganic chemistry ; Chemical engineering ; Materials science ; Organic chemistry ; Polymerization Material Properties and Applications ; Dye analysis and toxicity ; Water Quality Monitoring and Analysis
Authors: Amartya Bose
Source: The Journal of Chemical Physics (preprint, 2022-07-12)
Field: Chemistry — Spectroscopy

Zero-cost corrections to influence functional coefficients from bath response functions Recent work has shown that it is possible to circumvent the calculation of the spectral density and directly generate the coefficients of the discretized influence functionals using data from classical trajectory simulations. However, the accuracy of this procedure depends on the validity of the high temperature approximation. In this work, an alternative derivation based on the Kubo formalism is provided. This enables the calculation of additional correction terms that increases the range of applicability of the procedure to lower temperatures. Because it is based on the Kubo-transformed correlation function, this approach allows the direct use of correlation functions obtained from methods such as ring-polymer molecular dynamics and centroid molecular dynamics in determining the influence functional coefficients for subsequent system-solvent simulations. The accuracy of the original procedure and the corrected procedure is investigated across a range of parameters. It is interesting that the correction term comes at zero additional cost. Furthermore, it is possible to improve upon the correction using zero-cost physical intuition and heuristics making the method even more accurate. Discretization ; Statistical physics ; Formalism (music) ; Centroid ; Range (aeronautics) ; Heuristics ; Zero (linguistics) ; Intuition ; Applied mathematics ; Mathematics ; Physics ; Mathematical analysis ; Mathematical optimization ; Materials science Analytical Chemistry and Chromatography ; Spectroscopy and Quantum Chemical Studies ; Analytical Chemistry and Sensors
Authors: Hiroaki Okada | Satoshi Maeda
Source: ChemRxiv (preprint, 2022-10-31)
Field: Materials Science — Materials Chemistry

On accelerating reaction optimization using computational Gibbs energy barriers: A numerical consideration utilizing a computational dataset Reaction optimization is a time- and resource-consuming step in organic synthesis. Recent advances in chemo- and materials-informatics provide systematic and efficient procedures utilizing tools like Bayesian optimization (BO). This study explores the possibility of reducing the required experiments further utilizing computational Gibbs energy barriers. To thoroughly validate the impact of using computational Gibbs energy barriers in BO-assisted reaction optimization, this study employs a computational Gibbs energy barrier dataset in the literature and performs an extensive numerical investigation virtually regarding the Gibbs energy barriers as experimental reactivity and those with systematic and random noises as computational reactivity. The present numerical investigation shows that even the computational reactivity affected by noises as much as 20 kJ/mol helps reduce the number of required experiments. Gibbs free energy ; Computer science ; Gibbs sampling ; Bayesian probability ; Reactivity (psychology) ; Bayesian optimization ; Mathematical optimization ; Artificial intelligence ; Mathematics ; Thermodynamics ; Physics Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Process Optimization and Integration
Authors: Alex Avdeef | Manfred Kansy
Source: Research Square (preprint, 2022-07-21)
Field: Chemistry — Spectroscopy

Trends in PhysChem Properties of Newly Approved Drugs over the Last Six Years; Predicting Solubility of Drugs Approved in 2021 Abstract For the ‘small-molecule’ NMEs (new molecular entities) approved in 2021 by the US FDA, quantitative solubility values were found for 28 drugs, nearly all from published New Drug Applications (NDAs). Comparisons of physicochemical properties over the last six years indicate that the NMEs are slowly continuing to increase in size and decrease in solubility. Since 2016, the intrinsic solubility values ( S 0 ) have decreased on the average by 0.50 log unit, the calculated octanol-water partition coefficients ( clogP ) have increased by 0.34 log unit, and the molecular weights ( MW ) have increased by 22 g·mol -1 (to 477, compared to 298 in older drugs). The average number of Hbond acceptors has remained constant, while the average number of H-bond donors and the Kier Φ molecular flexibility indices have decreased slightly. The reported solubility data for the 2021 small-molecule NMEs were processed using the program p DISOL-X to obtain S 0 values, normalized to 25 o C. The S 0 values ranged from 2 ng·mL -1 (avacopan) to 43 mg·mL -1 (viloxazine). In the new set, MW spanned from 233 g·mol -1 (dexmethylphenidate) to 1215 g·mol -1 (voclosporin). Values of clogP ranged from − 0.3 (serdexmethylphenidate, a quaternary ammonium molecule) to 8.1 (avacopan). Five different in-silico models were used to predict the aqueous intrinsic log solubility of the 28 novel NMEs: (i) Yalkowsky’s General Solubility Equation (GSE( classic )), (ii) Abraham’s Linear Solvation Equation (ABSOLV), (iii) Avdeef-Kansy ‘Flexible-Acceptor’ General Solubility Equation ((GSE( Φ,B )), (iv) Breiman’s Random Forest Regression (RFR), and (v) consensus model based on (ii) and (iii) above. The various models were retrained with an enlarged version of the Wiki- pS 0 database (currently at 7655 log S 0 entries of drug-relevant molecules). The consensus model (r 2 = 0.67, RMSE = 1.08) just slightly outperformed the other four models. The relatively-simple consensus prediction equation can be easily incorporated into spreadsheet calculations. As new drugs are approved, it will be important to continue monitoring the quality of measured solubility. Matching prediction to measurement is valuable when prediction methods are applied to virtual libraries, in order to seek opportunities to minimize pharmacokinetic risks of large, but otherwise promising, candidate molecules. Solubility ; Chemistry ; Molecule ; Solvation ; Aqueous solution ; Partition coefficient ; Chromatography ; Organic chemistry Analytical Chemistry and Chromatography ; Analytical Methods in Pharmaceuticals ; Computational Drug Discovery Methods
Authors: В. В. Усов | N. М. Shkatulyak | T. S. Sovkova | N.I. Rybak
Source: Physics and Chemistry of Solid State (article, 2022-09-29)
Field: Materials Science — Biomaterials

Single crystal characteristics of the Mg - 5% Li alloy, found from the polycrystalline experimental data and the Kearns texture parameters This work aimed to experimentally determine of the Kearns texture parameters, elastic moduli, mechanical properties (ultimate tensile strength and yield strength) of sheets of an alloy of Mg 5 wt. % Li after various types of processing: 1) extrusion at 350 ° C through a rectangular die; 2) rolling with a change in its direction by 90° and intermediate annealing at 350°C after each pass; 3) after the subsequent alternating bending (AB) by 0.5; one; 3 and 5 cycles and evaluation of the elastic and mechanical properties of the corresponding single crystal of the alloy under study using the indicated data. The moduli of elasticity and strength characteristics of the studied polycrystalline samples were determined in the rolling direction (RD) and transverse direction (TD). Using the found parameters of the Kearns texture and the elastic and mechanical properties of the sheets, the values of the elastic modules and the ultimate strength and yield strength of the single crystal of the above alloy were estimated. The found modules of elasticity of a single crystal of an alloy Mg-5 wt. % Li deviate from their values found in previous studies by no more than 7.5%. Elastic modules and strength characteristics of the studied samples of magnesium alloy Mg 5 wt. % Li calculated from the single crystal data deviate from the experimental data by no more than 10%. Materials science ; Ultimate tensile strength ; Crystallite ; Alloy ; Single crystal ; Elastic modulus ; Annealing (glass) ; Elasticity (physics) ; Composite material ; Crystallography ; Metallurgy ; Chemistry Magnesium Alloys: Properties and Applications ; Material Properties and Applications ; Surface Treatment and Coatings
Authors: Dmitry Veselov | N.A. Andriyanov
Source: Современные наукоемкие технологии (Modern High Technologies) (article, 2022-01-01)
Field: Chemistry — Spectroscopy

APPLICATION OF GENERATIVE MODELS FOR PREDICTION OF DRUG MOLECULAR COMPOUNDS . . , (Variational Auto Encoder, VAE). Python. , SMILES. . (Quantitative Estimate of Druglikeness, QED). QED . QED, . Generative grammar ; Drug ; Computer science ; Computational biology ; Artificial intelligence ; Pharmacology ; Medicine ; Biology Analytical Chemistry and Chromatography
Authors: A. Cagri Aydinkarahaliloglu | S. Jatar | Xiaojun Wang | Mary Fong | Vijay Gupta | Mariano Troccoli | Anthony J. Hoffman
Source: Research Square (preprint, 2022-03-02)
Field: Chemistry — Spectroscopy

Predicting Early Failure of Quantum Cascade Lasers During Accelerated Burn-in Testing Using Machine Learning Abstract Device life time is a significant consideration in the cost of ownership of quantum cascade lasers (QCLs). The life time of QCLs beyond an initial burn-in period has been studied previously; however, little attention has been given to predicting premature device failure where the device fails within several hundred hours of operation. Here, we demonstrate how standard electrical and optical device measurements obtained during an accelerated burn-in process can be used in a simple support vector machine to predict premature failure with high confidence. For every QCL that fails, at least one of the measurements is classified as belonging to a device that will fail prematurely—as much as 205 hours before the actual failure of the device. Furthermore, for devices that are operational at the end of the burn-in process, the algorithm correctly classifies all the measurements. This work will influence future device analysis and could lead to insights on the physical mechanisms of premature failure in QCLs. Cascade ; Burn-in ; Process (computing) ; Computer science ; Reliability engineering ; Quantum ; Laser ; Work (physics) ; Quantum cascade laser ; Mechanical engineering ; Physics ; Engineering ; Optics Spectroscopy and Laser Applications ; Atmospheric and Environmental Gas Dynamics ; Atmospheric Ozone and Climate
Authors: G. D. Yadav | C. R. Sinha | G. S. Kapur | B. P. Pal | Gourisankar Roymahapatra
Source: Zenodo (CERN European Organization for Nuclear Research) (article, 2022-08-31)
Field: Chemistry — Physical and Theoretical Chemistry

Preface of Education in Chemical Science and Technology Volume 2 Preface of Education in Chemical Science and Technology Volume 2 Volume (thermodynamics) ; Mathematics education ; Engineering ethics ; Engineering ; Psychology ; Physics ; Thermodynamics History and advancements in chemistry ; Chemistry and Chemical Engineering
Authors: Timothy Barnum | Mark A. Siebert | Kin Long Kelvin Lee | Ryan A. Loomis | P. Bryan Changala | Steven B. Charnley | Madelyn L. Sita | Ci Xue | Anthony J. Remijan | Andrew M. Burkhardt | Brett A. McGuire | Ilsa R. Cooke
Source: arXiv (Cornell University) (preprint, 2022-04-10)
Field: Chemistry — Spectroscopy

A Search for Heterocycles in GOTHAM Observations of TMC-1 We have conducted an extensive search for nitrogen-, oxygen- and sulfur-bearing heterocycles toward Taurus Molecular Cloud 1 (TMC-1) using the deep, broadband centimeter-wavelength spectral line survey of the region from the GOTHAM large project on the Green Bank Telescope. Despite their ubiquity in terrestrial chemistry, and the confirmed presence of a number of cyclic and polycyclic hydrocarbon species in the source, we find no evidence for the presence of any heterocyclic species. Here, we report the derived upper limits on the column densities of these molecules obtained by Markov Chain Monte Carlo (MCMC) analysis and compare this approach to traditional single-line upper limit measurements. We further hypothesize why these molecules are absent in our data, how they might form in interstellar space, and the nature of observations that would be needed to secure their detection. Molecule ; Physics ; Chemistry ; Organic chemistry Spectroscopy and Laser Applications ; Atmospheric Ozone and Climate ; Atmospheric chemistry and aerosols
Authors: Hyung Joon Byun | Hyunwoo Nam | Jong-Seon Kim
Source: Research Square (preprint, 2022-12-09)
Field: Chemistry — Spectroscopy

Effect of the dual library on long-range (3 km) SF 6 (Hexafluoride Sulfur) detection efficiency by portable Stand-off FTIR (Fourier Transform Infrared) detector Abstract A critical limitation in developing portable Fourier transform-infrared (FTIR) stand-off chemical detectors is the detection library optimization, which reduces the number of false alarms and maintains the detection performance. Ideally, a detection library should be established through high-resolution (0.5 cm -1 ) FTIR spectroscopy in the laboratory. However, owing to the weight requirement of a portable FTIR stand-off detector, its optical system and mirror-moving range have limitations. Consequently, most portable FTIR stand-off detectors have been developed with a low resolution of approximately 4–16 cm -1 . In this study, we developed a portable FTIR stand-off detector with a dual library of SF 6 . Moreover, we investigated its detection efficiency effect depending on the single library condition through realistic long-range (3 km) SF 6 spectrum data in a field test. Fourier transform infrared spectroscopy ; Detector ; Fourier transform spectroscopy ; Fourier transform ; Infrared ; Resolution (logic) ; Materials science ; Range (aeronautics) ; Analytical Chemistry (journal) ; Spectroscopy ; Optics ; Computer science ; Chemistry ; Physics ; Artificial intelligence ; Chromatography Spectroscopy and Laser Applications ; Advanced Chemical Sensor Technologies ; Analytical Chemistry and Chromatography
Authors: Tianshu Hou | Peining Zhen | Ngai Wong | Quan Chen | Guoyong Shi | Shuqi Wang | Hai-Bao Chen
Source: arXiv (Cornell University) (preprint, 2022-05-17)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Multilayer Perceptron Based Stress Evolution Analysis under DC Current Stressing for Multi-segment Wires Electromigration (EM) is one of the major concerns in the reliability analysis of very large scale integration (VLSI) systems due to the continuous technology scaling. Accurately predicting the time-to-failure of integrated circuits (IC) becomes increasingly important for modern IC design. However, traditional methods are often not sufficiently accurate, leading to undesirable over-design especially in advanced technology nodes. In this paper, we propose an approach using multilayer perceptrons (MLP) to compute stress evolution in the interconnect trees during the void nucleation phase. The availability of a customized trial function for neural network training holds the promise of finding dynamic mesh-free stress evolution on complex interconnect trees under time-varying temperatures. Specifically, we formulate a new objective function considering the EM-induced coupled partial differential equations (PDEs), boundary conditions (BCs), and initial conditions to enforce the physics-based constraints in the spatial-temporal domain. The proposed model avoids meshing and reduces temporal iterations compared with conventional numerical approaches like FEM. Numerical results confirm its advantages on accuracy and computational performance. Electromigration ; Computer science ; Very-large-scale integration ; Interconnection ; Perceptron ; Finite element method ; Artificial neural network ; Scaling ; Integrated circuit ; Representation (politics) ; Reliability (semiconductor) ; Stress (linguistics) ; Algorithm ; Computational science ; Engineering ; Mathematics ; Artificial intelligence ; Structural engineering ; Physics ; Electrical engineering Copper Interconnects and Reliability ; Electronic Packaging and Soldering Technologies ; Magnetic Properties and Applications
Authors: Ji-Jen Hwang
Source: Biomedical Journal of Scientific & Technical Research (article, 2022-02-28)
Field: Materials Science — Materials Chemistry

"Impact of Deep Learning and Applications in Biomedicine" Regardless of the enormous benefits of deep learning, there are still problems with its application in the biomedical field. Biomedicine ; Medicine ; Biology ; Bioinformatics Machine Learning in Materials Science ; Computational Drug Discovery Methods ; SARS-CoV-2 detection and testing