jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Minkai Xu | Wujie Wang | Shitong Luo | Chence Shi | Yoshua Bengio | Rafael Gómez‐Bombarelli | Jian Tang
Source: arXiv (Cornell University) (preprint, 2021-01-01)
Field: Chemistry — Inorganic Chemistry

An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming Predicting molecular conformations (or 3D structures) from molecular graphs is a fundamental problem in many applications. Most existing approaches are usually divided into two steps by first predicting the distances between atoms and then generating a 3D structure through optimizing a distance geometry problem. However, the distances predicted with such two-stage approaches may not be able to consistently preserve the geometry of local atomic neighborhoods, making the generated structures unsatisfying. In this paper, we propose an end-to-end solution for molecular conformation prediction called ConfVAE based on the conditional variational autoencoder framework. Specifically, the molecular graph is first encoded in a latent space, and then the 3D structures are generated by solving a principled bilevel optimization program. Extensive experiments on several benchmark data sets prove the effectiveness of our proposed approach over existing state-of-the-art approaches. Code is available at \url{https://github.com/MinkaiXu/ConfVAE-ICML21}. Benchmark (surveying) ; Computer science ; Bilevel optimization ; Autoencoder ; Code (set theory) ; Graph ; Space (punctuation) ; Theoretical computer science ; Algorithm ; Artificial intelligence ; Optimization problem ; Deep learning ; Programming language Metal-Organic Frameworks: Synthesis and Applications ; Computational Drug Discovery Methods ; Machine Learning in Materials Science
Authors: Meng Liu | Keqiang Yan | Bora Oztekin | Shuiwang Ji
Source: arXiv (Cornell University) (preprint, 2021-01-31)
Field: Materials Science — Materials Chemistry

GraphEBM: Molecular Graph Generation with Energy-Based Models We note that most existing approaches for molecular graph generation fail to guarantee the intrinsic property of permutation invariance, resulting in unexpected bias in generative models. In this work, we propose GraphEBM to generate molecular graphs using energy-based models. In particular, we parameterize the energy function in a permutation invariant manner, thus making GraphEBM permutation invariant. We apply Langevin dynamics to train the energy function by approximately maximizing likelihood and generate samples with low energies. Furthermore, to generate molecules with a desirable property, we propose a simple yet effective strategy, which pushes down energies with flexible degrees according to the properties of corresponding molecules. Finally, we explore the use of GraphEBM for generating molecules with multiple objectives in a compositional manner. Comprehensive experimental results on random, goal-directed, and compositional generation tasks demonstrate the effectiveness of our proposed method. Invariant (physics) ; Computer science ; Permutation (music) ; Theoretical computer science ; Generative grammar ; Function (biology) ; Graph ; Property (philosophy) ; Simple (philosophy) ; Energy (signal processing) ; Algorithm ; Statistical physics ; Artificial intelligence ; Physics ; Quantum mechanics Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Protein Structure and Dynamics
Authors: Kees Booij
Source: Environmental Toxicology and Chemistry (article, 2021-01-25)
Field: Chemistry — Analytical Chemistry

Passive Sampler Exchange Kinetics in Large and Small Water Volumes Under Mixed Rate Control by Sorbent and Water Boundary Layer Exchange kinetics of organic compounds between passive samplers and water can be partly or completely controlled by transport in the sorbent. In such cases diffusion models are needed. A model is discussed that is based on a series of cosines (space) and exponentials (time). The model applies to mixed rate control by sorbent and water boundary layer under conditions of fixed aqueous concentrations (open systems, infinite water volumes, in situ sampling) and fixed amounts (closed systems, finite water volumes, ex situ sampling). Details on the implementation of the model in computational software and spreadsheet programs are discussed, including numerical accuracy. Key parameters are Biot number (ratio of internal/external transfer resistance) and sorbent/water phase ratio. Small Biot numbers are always indicative of rate control by the water boundary layer, but for large Biot numbers this may still be the case over short time scales. Application to environmental monitoring of nonpolar compounds showed that diffusion models are rarely needed for sampling with commonly used single-phase polymers. For determining sorption coefficients in batch incubations, the model demonstrated a profound effect of sorbent/water phase ratio on time to equilibrium. Application of the model to sampling of polar organic compounds by extraction disks with or without a membrane showed that moderate to major sorbent-controlled kinetics is likely to occur. This implies that the use of sampling rate models for such samplers needs to be reconsidered. Environ Toxicol Chem 2021;40:1241-1254. © 2021 SETAC. Sorbent ; Sorption ; Biot number ; Diffusion ; Chemistry ; Sampling (signal processing) ; Boundary layer ; Phase boundary ; Kinetics ; Analytical Chemistry (journal) ; Phase (matter) ; Chromatography ; Thermodynamics ; Adsorption ; Organic chemistry ; Physics Analytical chemistry methods development ; Toxic Organic Pollutants Impact ; Pharmaceutical and Antibiotic Environmental Impacts
Authors: Eun-Bi Lim | Seungjoo Haam | Sang‐Wha Lee
Source: Colloids and Surfaces A Physicochemical and Engineering Aspects (article, 2021-03-12)
Field: Materials Science — Biomaterials

Sphingomyelin-based liposomes with different cholesterol contents and polydopamine coating as a controlled delivery system Sphingomyelin ; Liposome ; Coating ; Delivery system ; Chemistry ; Cholesterol ; Chromatography ; Biochemistry ; Organic chemistry ; Biomedical engineering ; Medicine Nanoparticle-Based Drug Delivery ; Lipid Membrane Structure and Behavior ; Advanced Drug Delivery Systems
Authors: Jun Zhao
Source: Frontiers in Materials (article, 2021-12-24)
Field: Chemistry — Inorganic Chemistry

Air-Flow Impacting: A New Mechanochemical Method for Continuous, Highly Efficient, Large-Scale Synthesis of Metal–Organic Frameworks and Mechanistic Research The novel air-flow impacting (AFI) synthesis technology for mechanochemical synthesis of MOFs (ZIF-67) was first reported. AFI was an improvement of the traditional mechanochemical synthesis method. The results indicated that ZIF-67 was successfully synthesized after 30 min at a rate of 60 kg h −1 . The as-prepared ZIF-67 was characterized by Fourier transform infrared spectroscopy (FT-IR), powder x-ray diffraction (P-XRD), thermogravimetric analysis (DTA/TG), scanning electron microscope (SEM), transmission electron microscope (TEM), and single-crystal x-ray diffraction. The kinetic analysis of the reaction mechanism was carried out by detecting the P-XRD patterns of the products with different reaction times. The synthesis belonged to the one-dimensional diffusion-controlled model. Thermogravimetric analysis ; Scanning electron microscope ; Fourier transform infrared spectroscopy ; Transmission electron microscopy ; Materials science ; Powder diffraction ; Diffraction ; Metal-organic framework ; Diffusion ; Single crystal ; Chemical engineering ; Analytical Chemistry (journal) ; Nanotechnology ; Chemistry ; Crystallography ; Physical chemistry ; Composite material ; Organic chemistry ; Optics Metal-Organic Frameworks: Synthesis and Applications ; Energetic Materials and Combustion ; Crystallography and molecular interactions
Authors: Raphael Lauenstein | Sophie L. Mader | Henrieta Derondeau | Oaikhena Zekeri Esezobor | Matthias Block | Armin J. Römer | Christian Jandl | Eberhard Riedle | Ville R. I. Kaila | Jürgen Hauer | Erling Thyrhaug | Corinna R. Hess
Source: Chemical Science (article, 2021-01-01)
Field: Chemistry — Organic Chemistry

The central role of the metal ion for photoactivity: Zn– <i>vs.</i> Ni–Mabiq Photoredox catalysts are integral components of artificial photosystems, and have recently emerged as powerful tools for catalysing numerous organic reactions. However, the development of inexpensive and efficient earth-abundant photoredox catalysts remains a challenge. We here present the photochemical and photophysical properties of a Ni-Mabiq catalyst ([Ni<sup>II</sup>(Mabiq)]OTf (<b>1</b>); Mabiq = 2-4:6-8-bis(3,3,4,4-tetramethyldihydropyrrolo)-10-15-(2,2-biquinazolino)-[15]-1,3,5,8,10,14-hexaene1,3,7,9,11,14-N<sub>6</sub>)-and of a Zn-containing analogue ([Zn<sup>II</sup>(Mabiq)OTf] (<b>2</b>))-using steady state and time resolved optical spectroscopy, time-dependent density functional theory (TDDFT) calculations, and reactivity studies. The Ni and Zn complexes exhibit similar absorption spectra, but markedly different photochemical properties. These differences arise because the excited states of <b>2</b> are ligand-localized, whereas metal-centered states account for the photoactivity of <b>1</b>. The distinct properties of the Ni and Zn complexes are manifest in their behavior in the photo-driven aza-Henry reaction and oxidative coupling of methoxybenzylamine. Reactivity (psychology) ; Metal ; Catalysis ; Photocatalysis ; Photochemistry ; Chemistry ; Ion ; Inorganic chemistry ; Metal ions in aqueous solution ; Organic chemistry Radical Photochemical Reactions ; Advanced Photocatalysis Techniques ; CO2 Reduction Techniques and Catalysts
Authors: Guangbing Liang | Yanhong Li | Chun‐Chuen Yang | Xun Hu | Qingyin Li | Wenbo Zhao
Source: RSC Advances (article, 2021-01-01)
Field: Chemistry — Inorganic Chemistry

Synthesis of ZSM-5 zeolites from biomass power plant ash for removal of ionic dyes from aqueous solution: equilibrium isotherm, kinetic and thermodynamic analysis In this work, industrial biomass power plant ash was used to synthesize the ZSM-5 zeolites for the first time with the original intention to turn value-added material into wealth, and then committed to adsorption performance testing. Typical chemical structure and morphology of ZSM-5 zeolite were identified by comprehensive technologies. Uniquely, it was found that there was a low pressure hysteresis loop which was caused by crossed 10-membered rings in the N<sub>2</sub> adsorption-desorption isotherm. To investigate the adsorption performance for dyes, the zeolite samples were used to remove cationic (MB) and anionic (CR) dyes from aqueous. The results demonstrated that when it came to adsorbing MB, the isotherm was in line with the Redlich-Peterson model (<i>R</i> <sup>2</sup> > 0.99), whereas it was matched up with the Sips model (<i>R</i> <sup>2</sup> > 0.99) for adsorbing CR. Kinetic models were assigned to the pseudo-second order equation (<i>R</i> <sup>2</sup> ≥ 0.99) along with remarkable intraparticle diffusion. In the end, thermodynamic parameters were Δ<i>G</i> <sup>0</sup> < 0, and <i>E</i> <sub>a</sub> > 0. Especially, adsorbing MB was Δ<i>S</i> <sup>0</sup> > 0, and Δ<i>H</i> <sup>0</sup> > 0, whilst adsorbing CR was Δ<i>S</i> <sup>0</sup> < 0, and Δ<i>H</i> <sup>0</sup> < 0, which indicates that electrostatic interaction plays a significant role in the whole process. All in all, this work might encourage novel attempts to dispose of industrial biomass ash. Aqueous solution ; Chemistry ; Kinetic energy ; ZSM-5 ; Ionic strength ; Ionic bonding ; Zeolite ; Biomass (ecology) ; Thermodynamic equilibrium ; Inorganic chemistry ; Thermodynamics ; Chemical engineering ; Catalysis ; Physical chemistry ; Organic chemistry ; Ion Zeolite Catalysis and Synthesis ; Thermochemical Biomass Conversion Processes ; Catalysis and Hydrodesulfurization Studies
Authors: Alex Juckers | Petra Knerr | Frank Harms | Jochen Strube
Source: Processes (article, 2021-09-07)
Field: Materials Science — Materials Chemistry

Advanced Process Analytical Technology in Combination with Process Modeling for Endpoint and Model Parameter Determination in Lyophilization Process Design and Optimization Lyophilization is widely used in the preservation of thermolabile products. The main shortcoming is the long processing time. Lyophilization processes are mostly based on a recipe that is not changed, but, with the Quality by Design (QbD) approach and use of Process Analytical Technology (PAT), the process duration can be optimized for maximum productivity while ensuring product safety. In this work, an advanced PAT approach is used for the endpoint determination of primary drying. Manometric temperature measurement (MTM) and comparative pressure measurement are used to determine the endpoint of the batch while a modeling approach is outlined that is able to calculate the endpoint of every vial in the batch. This approach can be used for process development, control and optimization. Process engineering ; Process (computing) ; Computer science ; Quality by Design ; Process variable ; Batch processing ; Process optimization ; Process modeling ; Thermolabile ; Process simulation ; Process control ; Process analytical technology ; Work in process ; Engineering ; Chemistry ; Chemical engineering ; Operations management Crystallization and Solubility Studies ; Advanced Control Systems Optimization ; Process Optimization and Integration
Authors: Jacob Hirschhorn | Floyd Hilty | Michael Tonks | Jhonathan Rosales
Source: JOM (article, 2021-09-21)
Field: Materials Science — Materials Chemistry

Review and Preliminary Investigation into Fuel Loss from Cermets Composed of Uranium Nitride and a Molybdenum-Tungsten Alloy for Nuclear Thermal Propulsion Using Mesoscale Simulations Cermet ; Materials science ; Tungsten ; Uranium ; Nitride ; Molybdenum ; Metallurgy ; Nuclear fuel ; Fissile material ; Alloy ; Mesoscale meteorology ; Nuclear engineering ; Ceramic ; Composite material ; Nuclear physics ; Neutron Nuclear Materials and Properties ; Nuclear reactor physics and engineering ; Fusion materials and technologies
Authors: Jarosław Widelski | Simon Vlad Luca | Adrianna Skiba | Monika Maciąg | Barbara Budzyńska | Laurence Marcourt | Jean‐Luc Wolfender | Krystyna Skalicka‐Woźniak
Source: International Journal of Molecular Sciences (article, 2021-02-12)
Field: Chemistry — Analytical Chemistry

Coumarins from Seseli devenyense Simonk.: Isolation by Liquid–Liquid Chromatography and Potential Anxiolytic Activity Using an In Vivo Zebrafish Larvae Model Different types of anxiety disorders have become the number one mental health issue in developed countries. The search for new, safer and effective drug-like molecules among naturally derived substances faces two difficulties: an efficient method of isolation compounds with a high-purity and high-throughput animal model for activity assay. Thus, the aim of the present study was to isolate by liquid-liquid chromatography high-purity rare coumarins from the fruits of <i>Seseli devenyense</i> Simonk. and evaluate their anxiolytic effect (defined as reversed thimotaxis) using a 5-days post-fertilization (dpf) <i>Danio rerio</i> larvae model. Liquid-liquid chromatography enabled the isolation of one simple hydroxycoumarin (devenyol) and four pyranocoumarins (cis-khellactone, d-laserpitin, isolaserpitin and octanoyllomatin). The anxiolytic effect was defined as a decrease in the time spent in the boundaries of the living space (also described as reversed thigmotaxis). Our results show that all isolated courmarins exerted a significant influence on the anxiety behavior (anxiolytic activity) in the zebrafish larvae model. According to our knowledge, this is the first report of anxiolytic activity of pyranocoumarins and devenyol. Anxiolytic ; Thigmotaxis ; Chromatography ; In vivo ; Chemistry ; Zebrafish ; Isolation (microbiology) ; Pharmacology ; Biology ; Biochemistry ; Microbiology ; Biotechnology Chromatography in Natural Products ; Plant chemical constituents analysis ; Bioactive Compounds and Antitumor Agents
Authors: Ahmed R. Gardouh | Ahmed S.G. Srag El-Din | Mohamed S. H. Salem | Yasser M. Moustafa | Shadeed Gad
Source: Drug Design Development and Therapy (article, 2021-07-01)
Field: Materials Science — Biomaterials

Starch Nanoparticles for Enhancement of Oral Bioavailability of a Newly Synthesized Thienopyrimidine Derivative with Anti-Proliferative Activity Against Pancreatic Cancer SNPs-TPD were superior in drug solubility and oral bioavailability than those obtained from TPD suspension. Bioavailability ; Differential scanning calorimetry ; ADME ; Chemistry ; Solubility ; Zeta potential ; Materials science ; Nanoparticle ; Biochemistry ; Organic chemistry ; Pharmacology ; In vitro ; Nanotechnology ; Medicine Nanoparticle-Based Drug Delivery ; Drug Solubulity and Delivery Systems ; Pancreatitis Pathology and Treatment
Authors: Katherine Lei | Howie Joress | Nils Persson | Jason Hattrick‐Simpers | Brian DeCost
Source: The Journal of Chemical Physics (article, 2021-08-03)
Field: Materials Science — Materials Chemistry

Aggressively optimizing validation statistics can degrade interpretability of data-driven materials models One of the key factors in enabling trust in artificial intelligence within the materials science community is the interpretability (or explainability) of the underlying models used. By understanding what features were used to generate predictions, scientists are then able to critically evaluate the credibility of the predictions and gain new insights. Here, we demonstrate that ignoring hyperparameters viewed as less impactful to the overall model performance can deprecate model explainability. Specifically, we demonstrate that random forest models trained using unconstrained maximum depths, in accordance with accepted best practices, often can report a randomly generated feature as being one of the most important features in generated predictions for classifying an alloy as being a high entropy alloy. We demonstrate that this is the case for impurity, permutation, and Shapley importance rankings, and the latter two showed no strong structure in terms of optimal hyperparameters. Furthermore, we demonstrate that, for the case of impurity importance rankings, only optimizing the validation accuracy, as is also considered standard in the random forest community, yields models that prefer the random feature in generating their predictions. We show that by adopting a Pareto optimization strategy to model performance that balances validation statistics with the differences between the training and validation statistics, one obtains models that reject random features and thus balance model predictive power and explainability. Interpretability ; Random forest ; Hyperparameter ; Computer science ; Machine learning ; Feature (linguistics) ; Artificial intelligence ; Credibility ; Data mining Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Hydrogen embrittlement and corrosion behaviors in metals
Authors: A. A. Gomes | Liudmyla Khvalbota | Andrea Machyňáková | Katarína Furdíková | Cláudia Alcaraz Zini | Ivan Špánik
Source: Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy (article, 2021-04-01)
Field: Chemistry — Analytical Chemistry

Slovak Tokaj wines classification with respect to geographical origin by means of one class approaches Mathematics ; Wine ; Counterfeit ; Slovak ; Statistics ; Artificial intelligence ; Pattern recognition (psychology) ; Food science ; Chemistry ; Computer science ; Geography Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Fermentation and Sensory Analysis
Authors: Asif Ali | Fakhera Ikram | Farasat Iqbal | Hira Fatima | Azra Mehmood | Maruf Yinka Kolawole | Aqif Anwar Chaudhry | Saadat Anwar Siddiqi | Ihtesham Ur Rehman
Source: Frontiers in Materials (article, 2021-10-13)
Field: Materials Science — Biomaterials

Improving the in vitro Degradation, Mechanical and Biological Properties of AZ91-3Ca Mg Alloy via Hydrothermal Calcium Phosphate Coatings For many years, calcium phosphate coatings to tailor the degradation behavior of magnesium and magnesium-based alloys for orthopaedic applications have received lots of research attention. However, prolong degradation behavior, its effect on biological and mechanical properties as well as osteoblastic response to single-step hydrothermally deposited calcium phosphate coatings remain poorly documented. In this study, Alamar blue assay, cell attachment, live/dead assay, and qRT-PCR were done to study the biological response of the coatings. Furthermore, immersion testing in SBF for 28 days and compression testing of the degraded samples were carried out to examine the degradation behavior and its effect on mechanical properties. The results indicated that coatings have a significant influence on both the substrate performance and structural integrity of coated AZ91-3Ca alloy. Immersion test revealed that coating deposited at pH 7, 100°C (CP7100) improves the hydrogen evolution rate by 65% and the degradation rate by 60%. As the degradation performance of coated samples improves so does the mechanical strength. CP7100 samples successfully retained 90% of their compressive strength after 14 days of immersion while bare AZ91-3Ca alloy lost its mechanical integrity. Furthermore, biological studies show that cells are happily proliferating, differentiating, and adhering to the coating surfaces, which indicates, improved osteointegration and osteogenesis with no sign of alkaline poisoning. qRT-PCR results showed that calcium phosphate coatings enhanced the mRNA levels for RUNX2 , Col1A , and ALP that may exhibit a speedy bone recovery. Thus, calcium phosphate coatings produced via a single-step hydrothermal method improve the degradation behavior, mechanical integrity and stimulate the differentiation of osteoblast lining. This leads toward faster bone regeneration, which shows a great potential of these coatings to be used on degradable implants as a bioactive protective layer. Materials science ; Calcium ; Coating ; Phosphate ; Degradation (telecommunications) ; Magnesium ; Compressive strength ; Alloy ; Magnesium alloy ; Nuclear chemistry ; Composite material ; Chemistry ; Metallurgy ; Biochemistry Magnesium Alloys: Properties and Applications ; Aluminum Alloys Composites Properties ; Corrosion Behavior and Inhibition
Authors: Elias Bareinboim | Judea Pearl
Source: Proceedings of the AAAI Conference on Artificial Intelligence (article, 2021-09-20)
Field: Chemistry — Electrochemistry

Transportability of Causal Effects: Completeness Results The study of transportability aims to identify conditions under which causal information learned from experiments can be reused in a different environment where only passive observations can be collected. The theory introduced in [Pearl and Bareinboim, 2011] (henceforth [PB, 2011]) defines formal conditions for such transfer but falls short of providing an effective procedure for deciding, given assumptions about differences between the source and target domains, whether transportability is feasible. This paper provides such procedure. It establishes a necessary and sufficient condition for deciding when causal effects in the target domain are estimable from both the statistical information available and the causal information transferred from the experiments. The paper further provides a complete algorithm for computing the transport formula, that is, a way of fusing experimental and observational information to synthesize an estimate of the desired causal relation. Completeness (order theory) ; Computer science ; Pearl ; Domain (mathematical analysis) ; Observational study ; Relation (database) ; Data mining ; Theoretical computer science ; Machine learning ; Artificial intelligence ; Mathematics ; Statistics Electrochemical Analysis and Applications