jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Philippe Schwaller | Riccardo Petraglia | Valerio Zullo | Vishnu H Nair | Rico Andreas Haeuselmann | Riccardo Pisoni | Costas Bekas | Anna Iuliano | Teodoro Laino
Source: ChemRxiv (preprint, 2019-10-21)
Field: Materials Science — Materials Chemistry

Predicting Retrosynthetic Pathways Using a Combined Linguistic Model and Hyper-Graph Exploration Strategy &lt;div&gt;&lt;div&gt;&lt;div&gt;&lt;p&gt;We present an extension of our Molecular Transformer architecture combined with a hyper-graph exploration strategy for automatic retrosyn- thesis route planning without human intervention. The single-step ret- rosynthetic model sets a new state of the art for predicting reactants as well as reagents, solvents and catalysts for each retrosynthetic step. We introduce new metrics (coverage, class diversity, round-trip accuracy and Jensen-Shannon divergence) to evaluate the single-step retrosynthetic models, using the forward prediction and a reaction classification model always based on the transformer architecture. The hypergraph is con- structed on the fly, and the nodes are filtered and further expanded based on a Bayesian-like probability. We critically assessed the end-to-end framework with several retrosynthesis examples from literature and aca- demic exams. Overall, the frameworks has a very good performance with few weaknesses due to the bias induced during the training process. The use of the newly introduced metrics opens up the possibility to optimize entire retrosynthetic frameworks through focusing on the performance of the single-step model only.&lt;/p&gt;&lt;p&gt;&lt;br&gt;&lt;/p&gt;&lt;p&gt;Available on IBM RXN for Chemistry: https://rxn.res.ibm.com.&lt;br&gt;&lt;/p&gt;&lt;/div&gt;&lt;/div&gt;&lt;/div&gt; Retrosynthetic analysis ; Computer science ; Transformer ; Graph ; Artificial intelligence ; Theoretical computer science ; Engineering ; Chemistry ; Stereochemistry Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Chemical Synthesis and Analysis
Authors: Shahin Mohammad Nejad | Masoud Bozorg Bigdeli | Rajat Srivastava | Matteo Fasano
Source: Energies (article, 2019-02-27)
Field: Materials Science — Materials Chemistry

Heat Transfer at the Interface of Graphene Nanoribbons with Different Relative Orientations and Gaps Because of their high thermal conductivity, graphene nanoribbons (GNRs) can be employed as fillers to enhance the thermal transfer properties of composite materials, such as polymer-based ones. However, when the filler loading is higher than the geometric percolation threshold, the interfacial thermal resistance between adjacent GNRs may significantly limit the overall thermal transfer through a network of fillers. In this article, reverse non-equilibrium molecular dynamics is used to investigate the impact of the relative orientation (i.e., horizontal and vertical overlap, interplanar spacing and angular displacement) of couples of GNRs on their interfacial thermal resistance. Based on the simulation results, we propose an empirical correlation between the thermal resistance at the interface of adjacent GNRs and their main geometrical parameters, namely the normalized projected overlap and average interplanar spacing. The reported correlation can be beneficial for speeding up bottom-up approaches to the multiscale analysis of the thermal properties of composite materials, particularly when thermally conductive fillers create percolating pathways. Materials science ; Thermal conductivity ; Graphene ; Percolation (cognitive psychology) ; Heat transfer ; Thermal resistance ; Thermal ; Composite number ; Composite material ; Graphene nanoribbons ; Molecular dynamics ; Carbon nanotube ; Electrical conductor ; Thermal conduction ; Percolation threshold ; Interfacial thermal resistance ; Thermal transfer ; Displacement (psychology) ; Heat transfer enhancement ; Nanotechnology ; Mechanics ; Heat transfer coefficient ; Electrical resistivity and conductivity ; Thermodynamics ; Layer (electronics) ; Chemistry ; Physics Thermal properties of materials ; Graphene research and applications ; Composite Material Mechanics
Authors: Hitarth Buch | Indrajit N. Trivedi
Source: Decision Science Letters (article, 2019-09-17)
Field: Chemistry — Spectroscopy

A new non-dominated sorting ions motion algorithm: Development and applications This paper aims a novel and a useful multi-objective optimization approach named Non-Dominated Sorting Ions Motion Algorithm (NSIMO) built on the search procedure of Ions Motion Algorithm (IMO). NSIMO uses selective crowding distance and non-dominated sorting method to obtain various non-domination levels and preserve diversity amongst the best set of solutions. The suggested technique is employed to various multi-objective benchmark functions having different characteristics like convex, concave, multimodal, and discontinuous Pareto fronts. The recommended method is analyzed on different engineering problems having distinct features. The results of the proposed approach are compared with other well-regarded and novel algorithms. Furthermore, we present that the projected method is easy to implement, capable of producing a nearly true Pareto front and algorithmically inexpensive. Sorting ; Algorithm ; Ion ; Computer science ; Motion (physics) ; Artificial intelligence ; Chemistry Mass Spectrometry Techniques and Applications
Authors: Moritz Heusel | Max Frank | Mario Köhler | Sabine Amon | Fabian Frommelt | George Rosenberger | Isabell Bludau | Simran Kaur Aulakh | Monika I. Linder | Yansheng Liu | Ben C. Collins | Matthias Gstaiger | Ulrike Kutay | Ruedi Aebersold
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2019-05-09)
Field: Chemistry — Spectroscopy

A global screen for assembly state changes of the mitotic proteome by SEC-SWATH-MS Summary Living systems integrate biochemical reactions that determine the functional state of each cell. Reactions are primarily mediated by proteins that have in systematic studies been treated as independent entities, disregarding their higher level organization into complexes which affects their activity and/or function and is thus of great interest for biological research. Here, we describe the implementation of an integrated technique to quantify cell state-specific changes in the physical arrangement of protein complexes, concurrently for thousands of proteins and hundreds of complexes. Applying this technique for comparison of human cells in interphase and mitosis, we provide a systematic overview of mitotic proteome reorganization. The results recall key hallmarks of mitotic complex remodeling and discover new events, such as a new model of nuclear pore complex disassembly, validated by orthogonal methods. To support the interpretation of quantitative SEC-SWATH-MS datasets, we extend the software CCprofiler and provide an interactive exploration tool, SECexplorer-cc . Highlights Quantification of proteome assembly state changes using SEC-SWATH-MS Systems-wide analysis of assembly state changes in the mitotic proteome Discovery and validation of a novel mitotic disassembly intermediate of the nuclear pore complex Higher sensitivity and information content compared to thermostability-based approaches for global measurement of proteome states SECexplorer , an online platform to browse results and investigate proteins newly implicated in cell division Proteome ; Mitosis ; Interphase ; Computational biology ; Proteomics ; Biology ; Cell division ; Cell biology ; Nuclear pore ; Function (biology) ; Computer science ; Cell ; Bioinformatics ; Biochemistry ; Nucleus Advanced Proteomics Techniques and Applications ; Bioinformatics and Genomic Networks ; Enzyme Structure and Function
Authors: Takuya Minami | Masaaki Kawata | Toshio Fujita | Katsumi Murofushi | Hiroshi Uchida | Kazuhiro Omori | Yoshishige Okuno
Source: MRS Advances (article, 2019-01-24)
Field: Materials Science — Materials Chemistry

Prediction of repeat unit of optimal polymer by Bayesian optimization Bayesian optimization ; Materials science ; Polymer ; Standard deviation ; Bayesian probability ; Range (aeronautics) ; Process (computing) ; Design of experiments ; Selection (genetic algorithm) ; Process optimization ; Biological system ; Computer science ; Artificial intelligence ; Statistics ; Mathematics ; Composite material ; Chemical engineering Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Fault Detection and Control Systems
Authors: Yasuhiro Kanno | Hiromasa Kaneko
Source: Chemometrics and Intelligent Laboratory Systems (article, 2019-06-26)
Field: Chemistry — Analytical Chemistry

Improvement of predictive accuracy in semi-supervised regression analysis by selecting unlabeled chemical structures Outlier ; Regression ; Linear regression ; Artificial intelligence ; Pattern recognition (psychology) ; Regression analysis ; Mathematics ; Bayesian probability ; Missing data ; Gaussian process ; Computer science ; Statistics ; Gaussian ; Machine learning ; Chemistry Spectroscopy and Chemometric Analyses ; Fault Detection and Control Systems ; Computational Drug Discovery Methods
Authors: Sha Liao | Meimei Zhao | Jing Luo | Kai Luo | Jingni Wu | Ruimin Liu | Shixiang Wang | Pu Jia | Yajun Bai | Xiaohui Zheng
Source: RSC Advances (article, 2019-01-01)
Field: Chemistry — Spectroscopy

The interaction mechanism between alkaloids and pepsin based on lum-AuNPs in the chemiluminescence analysis Herein, novel luminol functional gold nanoparticles (lum-AuNPs) were quickly prepared in an alkaline luminol solution with HAuCl<sub>4</sub>, which had the unique characteristics of uniform size and excellent luminescence properties. A self-made flow injection-chemiluminescence (FI-CL) system was established to study the interaction between pepsin (Pep) and five alkaloids (anisodamine, berberine, reserpine, jatrorrhizine and matrine) using lum-AuNPs as the CL probe. Based on the abovementioned home-made CL system, the possible interaction mechanisms of Pep with five alkaloids have been comprehensively discussed by molecular docking simulation, chemical thermodynamics and kinetic studies. The results indicated that there were obvious CL enhancement and inhibition effects on the lum-AuNPs CL system for the Pep and the complex of Pep/alkaloids, respectively. The possible mechanism for the interaction of Pep-five alkaloids was mainly mediated by the hydrophobic force. The binding constant <i>K</i> and binding site <i>n</i> for the Pep-alkaloid interaction are consistent with the list of Ber > Res > Ani, Jat > Mat, which is relative to the potential of groups of alkaloids interacting with the active site of Pep. Chemiluminescence ; Pepsin ; Chemistry ; Mechanism (biology) ; Chromatography ; Biochemistry ; Physics Molecular Sensors and Ion Detection ; Nanocluster Synthesis and Applications ; Gold and Silver Nanoparticles Synthesis and Applications
Authors: Albert Koulman | Samuel Furse | Mark Baumert | Gail Goldberg | Les Bluck
Source: Rapid Communications in Mass Spectrometry (article, 2019-04-22)
Field: Chemistry — Spectroscopy

Rapid profiling of triglycerides in human breast milk using liquid extraction surface analysis Fourier transform mass spectrometry reveals new very long chain fatty acids and differences within individuals We conclude that spotting on paper and the use of LESA-MS and CID on milk spots is not only a means for analysing milk in unprecedented detail for this preparation time, but is also amenable to conditions in which collecting and storing fresh milk samples for detailed profiling is prohibitively difficult. Chemistry ; Mass spectrometry ; Chromatography ; Fatty acid ; Triglyceride ; Breast milk ; Biochemistry ; Cholesterol Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Advanced Proteomics Techniques and Applications
Authors: Ayano Takai | Tomoya Tsubosaka | Yasuhiro Hirano | Naoki Hayakawa | Fumitaka Tani | Pekka Haapaniemi | Veronika Suni | Susumu Y. Imanishi
Source: PLoS ONE (article, 2019-12-02)
Field: Chemistry — Spectroscopy

Optimization of TripleTOF spectral simulation and library searching for confident localization of phosphorylation sites Tandem mass spectrometry (MS/MS) has been used in analysis of proteins and their post-translational modifications. A recently developed data analysis method, which simulates MS/MS spectra of phosphopeptides and performs spectral library searching using SpectraST, facilitates confident localization of phosphorylation sites. However, its performance has been evaluated only on MS/MS spectra acquired using Orbitrap HCD mass spectrometers so far. In this study, we have investigated whether this approach would be applicable to another type of mass spectrometers, and optimized the simulation and search conditions to achieve sensitive and confident site localization. Synthetic phosphopeptides and enriched K562 cell phosphopeptides were analyzed using a TripleTOF 6600 mass spectrometer before and after enzymatic dephosphorylation. Dephosphorylated peptides identified by X!Tandem database searching were subjected to spectral simulation of all possible single phosphorylations using SimPhospho software. Phosphopeptides were identified and localized by SpectraST searching against a library of the simulated spectra. Although no synthetic phosphopeptide was localized at 1% false localization rate under the previous conditions, optimization of the spectral simulation and search conditions for the TripleTOF datasets achieved the localization and improved the sensitivity. Furthermore, the optimized conditions enabled sensitive localization of K562 phosphopeptides at 1% false discovery and localization rates. These results suggest that accurate phosphopeptide simulation of TripleTOF MS/MS spectra is possible and the simulated spectral libraries can be used in SpectraST searching for confident localization of phosphorylation sites. Phosphopeptide ; Mass spectrometry ; Computer science ; Tandem mass spectrometry ; Orbitrap ; Chemistry ; Spectral line ; Phosphorylation ; Biological system ; Search engine ; Chromatography ; Physics ; Biochemistry ; Biology ; Information retrieval Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Ning Xu | Toshikazu Ono | Yoshio Hisaeda
Source: Chemistry - A European Journal (article, 2019-06-12)
Field: Materials Science — Materials Chemistry

Symmetry Reduction of Porphycenes with Finely Tuned Optical and Electronic Properties through Oxidative Cyclization of <i>E</i>/<i>Z</i>‐Mixed Dipyrroethenes The main obstacle to the widespread application of porphycenes lies in the lack of efficient and economical methods for their production. Discovery of new synthetic methodologies for porphycene derivatives are important for fine-tuning of their optical and electrochemical properties. Herein, the preparation of a set of AABB-, ABAB-, and ABBA-type meso-tetrasubstituted unsymmetric porphycenes is reported. Their synthesis involved the acid-catalyzed oxidative coupling of AA- and BB-dipyrroethenes, or AB-type dipyrroethenes, as precursors in yields of up to 19 %. The structures were unambiguously confirmed by X-ray crystallography. The type and position of substituents in the unsymmetric porphycenes enabled fine-tuning of the optical and electronic properties, which are discussed in terms of their UV/Vis absorption, fluorescence spectroscopies, cyclic voltammetry, and density functional theory calculations. Chemistry ; Cyclic voltammetry ; Fluorescence ; Electrochemistry ; Electronic structure ; Computational chemistry ; Crystallography ; Photochemistry ; Stereochemistry ; Physical chemistry ; Physics ; Electrode ; Optics Porphyrin and Phthalocyanine Chemistry ; Surface Chemistry and Catalysis ; Metal-Catalyzed Oxygenation Mechanisms
Authors: Wiktor Wolak | Anatoly B. Kolomeisky | Mirosław R. Dudek | Maciej Marć | Lidia Najder-Kozdrowska
Source: Journal of Physics D Applied Physics (article, 2019-08-09)
Field: Materials Science — Materials Chemistry

Enhancing silica surface deprotonation by using magnetic nanoparticles as heating agents Abstract In this work, we investigate the possibility of using magnetic nanoparticles embedded into the silica to locally heat up the silica-water interface where the increase in temperature of nanoparticles is induced by an external radio-frequency magnetic field. Through the use of the theoretical model, it is shown that such the process leads to an increase in the total negative charge of the silica surface due to the deprotonation of silanol groups. It is also shown that the efficiency of such an electric charging process depends on the size of nanoparticles. Moreover, the optimal size of nanoparticles allowing for a maximum charging efficiency is determined. This observation may prove to be very important from the point of view of potential applications as it may allow to fine-tune chemical reactions on the silica surface. Some aspects of this work related to the magnetically heated nanoparticles were verified by the experiment. Deprotonation ; Nanoparticle ; Magnetic nanoparticles ; Surface (topology) ; Chemical engineering ; Materials science ; Nanotechnology ; Chemistry ; Organic chemistry ; Engineering Mesoporous Materials and Catalysis ; Characterization and Applications of Magnetic Nanoparticles ; Minerals Flotation and Separation Techniques
Authors: Mark M. J. van Rijt | Adriano Ciaffoni | Alessandro Ianiro | Mohammad‐Amin Moradi | Aimee L. Boyle | Alexander Kros | Heiner Friedrich | Nico A. J. M. Sommerdijk | Joseph P. Patterson
Source: Chemical Science (article, 2019-01-01)
Field: Materials Science — Biomaterials

Designing stable, hierarchical peptide fibers from block co-polypeptide sequences Natural materials, such as collagen, can assemble with multiple levels of organization in solution. Achieving a similar degree of control over morphology, stability and hierarchical organization with equilibrium synthetic materials remains elusive. For the assembly of peptidic materials the process is controlled by a complex interplay between hydrophobic interactions, electrostatics and secondary structure formation. Consequently, fine tuning the thermodynamics and kinetics of assembly remains extremely challenging. Here, we synthesized a set of block co polypeptides with varying hydrophobicity and ability to form secondary structure. From this set we select a sequence with balanced interactions that results in the formation of high-aspect ratio thermodynamically favored nanotubes, stable between pH 2 and 12 and up to 80 °C. This stability permits their hierarchical assembly into bundled nanotube fibers by directing the pH and inducing complementary zwitterionic charge behavior. This block co-polypeptide design strategy, using defined sequences, provides a straightforward approach to creating complex hierarchical peptide-based assemblies with tunable interactions. Block (permutation group theory) ; Electrostatics ; Sequence (biology) ; Peptide ; Kinetics ; Nanotechnology ; Stability (learning theory) ; Well-defined ; Chemistry ; Self-assembly ; Materials science ; Chemical physics ; Computer science ; Physics ; Mathematics Supramolecular Self-Assembly in Materials ; Chemical Synthesis and Analysis ; Silk-based biomaterials and applications
Authors: Naseer Muhammad | Xiaopin Tang | Tao Fu | Qiang Liu | Zhengbiao Ouyang
Source: Materials Science and Engineering B (article, 2019-09-17)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Broadband polarization-insensitive absorption by metasurface with metallic pieces for energy harvesting application Materials science ; Metamaterial ; Absorption (acoustics) ; Optoelectronics ; Wavelength ; Polarization (electrochemistry) ; Broadband ; Optics ; Plasmon ; Metamaterial absorber ; Substrate (aquarium) ; Fabrication ; Chemistry ; Tunable metamaterials ; Physics Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Advanced Antenna and Metasurface Technologies
Authors: Emre Seyyal | Theresa Evans‐Nguyen
Source: Journal of the American Society for Mass Spectrometry (article, 2019-02-22)
Field: Chemistry — Analytical Chemistry

Online Sol-gel Capillary Microextraction-Mass Spectrometry (CME-MS) Analysis of Illicit Drugs Providing rapid and sensitive sample cleanup, sol-gel capillary microextraction (CME) is a form of solid phase microextraction (SPME). The capillary format of CME couples easily with mass spectrometry (MS) by employing sol-gel sorbent coatings in inexpensive fused silica capillaries. By leveraging the syringe pump and six-port valve readily available on the commercial MS, we can obviate the need for chromatography for samples as complex as urine in quantitative assays. Two different sol-gel materials were studied as microextraction sorbents: one with a single ligand of octadecyl (C<sub>18</sub>) and the other with a dual-ligand combination of C<sub>18</sub> and phenyl (Phe) groups. The CME-MS method was optimized for flow rate and solvent desorption and studied for overall microextraction performance between the two sorbents studied. We extract illicit drugs including cocaine, heroin, amphetamine, methamphetamine, 3,4-methylenedioxymethamphetamine, and oxycodone, proving good run-to-run reproducibility (RSD% < 10%) and low detection limits (< 10 ng mL<sup>-1</sup>). The dual-ligand sorbent demonstrated superior performance due to typical hydrophobic properties of C<sub>18</sub> as well as potential π-π interactions of the Phe functionality and the aromatic moiety common to many drugs. This study demonstrates the advantage of fine-tuning sol-gel sorbents for application-specific CME-MS. We apply our method to the analysis of various drugs in synthetic and human urine samples and show low carryover effect (~ 5%) and low matrix effect in the presence of the urine matrix. Thus, the sol-gel CME-MS technique described herein stands to be an attractive alternative to other SPME-MS techniques. Chemistry ; Chromatography ; Solid-phase microextraction ; Mass spectrometry ; Sorbent ; Sample preparation ; Gas chromatography–mass spectrometry ; Adsorption ; Organic chemistry Analytical chemistry methods development ; Mass Spectrometry Techniques and Applications ; Forensic Toxicology and Drug Analysis
Authors: Li Han | Xixi Meng | Mengmeng Wang | Yu‐Xia Wang | Wei Shi | Peng Cheng
Source: Chinese Journal of Chemistry (article, 2019-02-26)
Field: Materials Science — Electronic, Optical and Magnetic Materials

A {Tb<sub>2</sub>Fe<sub>3</sub>} Pyramid Single‐Molecule Magnet with Ferromagnetic Tb‐Fe Interaction Summary of main observation and conclusion The influence of magnetic interactions to the magnetization dynamics was well experimentally studied in a 3d‐4f single‐molecule magnet (SMM) [Tb III 2 Fe III 3 ( μ 5 ‐O)L 2 (NO 3 ) 4 Cl] ( 1 , H 4 L = N , N , N ’, N ’‐tetrakis(2‐hydroxyethyl)ethylene diamine) and its diamagnetic‐ ion‐diluted samples. Significant ferromagnetic coupling between Tb III and Fe III ions and SMM behavior of 1 were observable, which proved clearly that the magnetic interaction between 3d‐4f spin carriers has also an excessive impact on fine‐tuning the magnetization dynamic behaviors of 3d‐4f complexes. Chemistry ; Diamagnetism ; Single-molecule magnet ; Ferromagnetism ; Magnetization ; Magnet ; Ion ; Inductive coupling ; Molecule ; Condensed matter physics ; Coupling (piping) ; Spin (aerodynamics) ; Terbium ; Crystallography ; Magnetic field ; Physics ; Materials science ; Metallurgy Magnetism in coordination complexes ; Lanthanide and Transition Metal Complexes ; Electron Spin Resonance Studies
Authors: H. Trabelsi
Source: Journal of Rare Earths (article, 2019-10-18)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Experimental evidence of magnetic training effect of electronic phase in Nd–Ca half-doped manganite Manganite ; Condensed matter physics ; Magnetic refrigeration ; Materials science ; Magnetization ; Magnetometer ; Electrical resistivity and conductivity ; Magnetic field ; Ferromagnetism ; Physics Magnetic and transport properties of perovskites and related materials ; Shape Memory Alloy Transformations ; Multiferroics and related materials