jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Shusuke Kasamatsu
Source: The Brain & Neural Networks (article, 2021-03-05)
Field: Materials Science — Materials Chemistry

Monte Carlo Sampling of Configuration Disorder in Crystalline Materials 原子配置の不規則性は機能性結晶材料で発現する様々な機能の源泉である．これをシミュレーションによって解析するときに問題となるのが原子配置の場合の数の爆発である．ここでは，それに対応する方法として，第一原理計算を基盤とした原子配置のモンテカルロサンプリング手法について概観する．まず，種々の合金系で成功を収めているクラスター展開法について紹介する．その上で，クラスター展開法では難しい複雑な複合酸化物系の解析を可能にするための最近の我々の取組，すなわち，レプリカ交換モンテカルロ法の適用とニューラルネットワークモデルを使ったサンプリングの加速について紹介する． Monte Carlo method ; Sampling (signal processing) ; Statistical physics ; Computer science ; Statistics ; Physics ; Mathematics X-ray Diffraction in Crystallography ; Crystallization and Solubility Studies
Authors: Gloria Castellano | Adela León | Francisco Torrens
Source: Molecules (article, 2021-01-05)
Field: Chemistry — Organic Chemistry

Classification of Congeneric and QSAR of Homologous Antileukemic S–Alkylcysteine Ketones Based on a set of six vector properties, the partial correlation diagram is calculated for a set of 28 <i>S</i>-alkylcysteine diazomethyl- and chloromethyl-ketone derivatives. Those with the greatest antileukemic activity in the same class correspond to high partial correlations. A periodic classification is performed based on information entropy. The first four characteristics denote the group, and the last two indicate the period. Compounds in the same period and, especially, group present similar properties. The most active substances are situated at the bottom right. Nine classes are distinguished. The principal component analysis of the homologous compounds shows five subclasses included in the periodic classification. Linear fits of both antileukemic activities and stability are good. They are in agreement with the principal component analysis. The variables that appear in the models are those that show positive loading in the principal component analysis. The most important properties to explain the antileukemic activities (50% inhibitory concentration Molt-3 T-lineage acute lymphoblastic leukemia minus the logarithm of 50% inhibitory concentration Nalm-6 B-lineage acute lymphoblastic leukemia and stability <i>k</i>) are ACD log<i>D</i>, surface tension and number of violations of Lipinski's rule of five. After leave-<i>m</i>-out cross-validation, the most predictive model for cysteine diazomethyl- and chloromethyl-ketone derivatives is provided. Lipinski's rule of five ; Principal component analysis ; Lymphoblastic Leukemia ; Logarithm ; Chemistry ; Mathematics ; Combinatorics ; Stereochemistry ; Leukemia ; Biology ; Statistics ; Biochemistry ; Immunology Synthesis and biological activity ; Computational Drug Discovery Methods ; Click Chemistry and Applications
Authors: Uğur Güvenç | Burak Koçak | Yılmaz Koçak
Source: DergiPark (Istanbul University) (article, 2021-05-31)
Field: Materials Science — Polymers and Plastics

Portland Kompoze Çimentosunun Priz Süresine Metakaolin Etkisinin Bulanık Mantıkla Tahmini Metakaolin ; Mathematics ; Materials science ; Composite material Textile materials and evaluations ; Material Selection and Properties ; Recycling and Waste Management Techniques
Authors: Loukas Petrou | Kypros M. Kossifos | Marco A. Antoniades | Julius Georgiou
Source: Research Square (preprint, 2021-07-27)
Field: Materials Science — Electronic, Optical and Magnetic Materials

The first family of application-specific integrated circuits for programmable metasurfaces Integrated circuit ; Electronic circuit ; Computer science ; Computer architecture ; Electrical engineering ; Engineering Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Energy Harvesting in Wireless Networks
Authors: Alla P. Toropova | Andrey A. Toropov | Emilio Benfenati
Source: Research Square (preprint, 2021-03-22)
Field: Chemistry — Organic Chemistry

The Self-organizing Vector of Atom-pairs Proportions: Use to Develop Models for Melting Points Atom (system on chip) ; Vector (molecular biology) ; Melting temperature ; Melting point ; Computer science ; Materials science ; Chemistry ; Parallel computing Chemical Thermodynamics and Molecular Structure ; Computational Drug Discovery Methods ; thermodynamics and calorimetric analyses
Authors: Selcan Karakuş | Işıl Sanrı Karapınar | Onur Pehlivan | Ayşe Elif Özsoy Özbay | Utku Yazgan
Source: Cement Wapno Beton (article, 2021-01-01)
Field: Materials Science — Materials Chemistry

Synthesis of novel chitosan/modified zeolite nanocomposites and their effect on the mechanical properties of cement mortars In this paper, a novel nanocomposite containing biodegradable chitosan [CS] and modified zeolite [mZeo] was introduced as a cement eco-nano additive and its effects on the mechanical properties of cement mortars were evaluated. The proposed nanocomposite was prepared by using a synergistic sonication-microwave method. The surface morphology and chemical compositions of mZeo and CS/ mZeo nanocomposites were determined using SEM, FTIR, XRF, and BET. Compressive and flexural strength of cement mortars containing mZeo and CS/mZeo in ratios of 0%, 0.2%, 0.5%, 1% and 2% by mass, were investigated. Experimental results showed a significant improvement in the mechanical properties of mortars containing the proposed nanocomposite. The use of nanoscale zeolite in cementitious composites was attempted for the first time within this study and the results so far have been very promising. Therefore, it is concluded that the proposed nanocomposite has great potential to be used as an alternative eco-nano additive, for cementitious composites. Nanocomposite ; Materials science ; Mortar ; Cement ; Cementitious ; Zeolite ; Composite material ; Flexural strength ; Compressive strength ; Chitosan ; Fourier transform infrared spectroscopy ; Sonication ; Chemical engineering ; Chemistry ; Organic chemistry Nanoparticles: synthesis and applications ; Concrete and Cement Materials Research ; Innovative concrete reinforcement materials
Authors: Çağdaş YILMAZ | Didem Demir | Nimet Bölgen | Ali Akdağlı
Source:  (article, 2021-08-15)
Field: Materials Science — Biomaterials

A novel formula derived by using ABC algorithm for calculation of the average fiber diameter of electrospun poly (Ԑ-caprolactone) scaffolds The characteristics of a scaffold that is the basic component of tissue engineering are considerably influenced by the fiber diameter of the fibrous scaffolds. Since the significant effect of the fiber diameter on the scaffold properties, many researchers have focused on estimating the fiber diameter based on the electrospinning parameters. With similar motivation, in this paper, a new and simple closed-form expression, which can help researchers in fabricating the electrospun poly (ԑ-caprolactone) (PCL) scaffold with desired fiber diameter, is presented. In order to construct the expression proposed, an experimental study has been performed to obtain the data set, in which 25 experimental data including average fiber diameter (AFD) values dependent on different combinations of parameters such as voltage, solution concentration, tip to collector (TTC) distance, and flow rate. Then, an expression has been constructed that is used to estimate the AFD of the electrospun PCL, and the coefficients of the expression were determined by using the artificial bee colony (ABC) algorithm. In order to validate the estimation ability of the expression, the metrics such as mean absolute error (MAE) and mean absolute percentage error (MAPE) have been used, and the optimization and test errors were respectively obtained as 3.30% and 1.27% in terms of MAPE. In addition, the results obtained were compared with those reported in the literature. Results show that our new expression can be successfully used to estimate the AFD of electrospun PCL prior to the electrospinning process. Thus, the number of test repetitions could be reduced by using the expression proposed, and time, cost, and labor could be saved in this way. This study contributes to the literature because there have been only a limited number of studies that focus on estimating the AFD of PCL nanofiber despite many studies about various polymers. Caprolactone ; Electrospinning ; Materials science ; Fiber ; Algorithm ; Composite material ; Computer science ; Polymer ; Copolymer Electrospun Nanofibers in Biomedical Applications ; Natural Fiber Reinforced Composites ; Conducting polymers and applications
Authors: Andrew Hoffman | Vipul Gupta | Michael Due Larsen | Soumya Nag | Ian Spinelli | D. M. Ruscitto | Raúl B. Rebak
Source: Microscopy and Microanalysis (article, 2021-07-30)
Field: Materials Science — Materials Chemistry

Advanced Characterization Techniques Enabling Commercial Development of Accident Tolerant Fuel Cladding An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button. Cladding (metalworking) ; Characterization (materials science) ; Nuclear engineering ; Materials science ; Engineering ; Nanotechnology ; Composite material Nuclear Materials and Properties ; Nuclear reactor physics and engineering ; Heat transfer and supercritical fluids
Authors: Paolo Di Sia
Source:  (preprint, 2021-12-25)
Field: Chemistry — Electrochemistry

Ways for improving the sensing of nano-bio-sensors The nano-bio-sensoristic sector is one of the mainstreams of nanotechnology and requires careful information for constant improvement of the nanodevice performance. The sensing/sensitivity plays a peculiar role, is a determinant characteristics, able to cause a great improvement of the device quality.The paper provides a detailed analysis on the casuistry for increasing the performanceof nano-systems through enhanced diffusion, studied with the use of a recent analytical transport model, able to accommodate previously not completely understood behaviours and to predict new interesting features at nanoscale. Nanodevice ; Nano- ; Nanotechnology ; Nanoscopic scale ; Materials science ; Computer science ; Engineering Electrochemical Analysis and Applications ; Surface and Thin Film Phenomena ; Gas Sensing Nanomaterials and Sensors
Authors: Ethan J. Walker | John Q. Bettinger | Kevin Welle | Jennifer R. Hryhorenko | Adrian M. Molina Vargas | Mitchell R. O’Connell | Sina Ghaemmaghami
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2021-12-20)
Field: Materials Science — Materials Chemistry

Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues Abstract The oxidation of protein-bound methionines to form methionine sulfoxides has a broad range of biological ramifications, making it important to delineate factors that influence methionine oxidation rates within a protein. This is especially important for biopharmaceuticals, where oxidation can lead to deactivation and degradation. Previously, neighboring residue effects and solvent accessibility (SA) have been shown to impact the susceptibility of methionine residues to oxidation. In this study, we provide proteome-wide evidence that oxidation rates of buried methionine residues are also strongly influenced by the thermodynamic folding stability of proteins. We surveyed the E. coli proteome using several proteomic methodologies and globally measured oxidation rates of methionines in the presence and absence of tertiary structure, as well as folding stabilities of methionine containing domains. The data indicate that buried methionines have a wide range of protection factors against oxidation which correlate strongly with folding stabilities. Concordantly, we show that in comparison to E. coli , the proteome of the thermophile T. thermophilus is significantly more stable and thus more resistant to methionine oxidation. These results indicate that oxidation rates of buried methionines from the native state of proteins can be used as a metric of folding stability. To demonstrate the utility of this correlation, we used native methionine oxidation rates to survey the folding stabilities of E. coli and T. thermophilus proteomes at various temperatures and suggest a model that relates the temperature dependence of the folding stabilities of these two species to their optimal growth temperatures. Methionine ; Proteome ; Protein folding ; Folding (DSP implementation) ; Thermophile ; Chemistry ; Residue (chemistry) ; Biochemistry ; Thermus thermophilus ; Biophysics ; Escherichia coli ; Amino acid ; Biology ; Enzyme Enzyme Structure and Function ; Redox biology and oxidative stress ; Mass Spectrometry Techniques and Applications
Authors: Nadiia Аrtyukhova | Ján Krmela | Аrtem Аrtyukhov | Vladimíra Krmelová | Mária Gavendová | Alžbeta Bakošová
Source: Bulletin of the Polish Academy of Sciences Technical Sciences (article, 2021-06-10)
Field: Materials Science — General Materials Science

Technology for porous ammonium nitrate production: modeling of drying machines’ operating modes The article deals with the technological principles regarding the final drying process of the porous ammonium nitrate (PAN) granules in multistage gravitational shelf dryers. The data on the dryer’s optimal technological operating modes are obtained. PAN samples are studied; the regularity of the porous structure change in the granule depending on the dryer’s hydrodynamic and thermodynamic conditions is established. Experimental data obtained during the research will be used to create a methodology for the engineering calculation of gravitational shelf dryers. Moreover, the data on the optimal operating conditions of the drying machines at the final drying stage will be used to improve the technology to form porous granules from agricultural ammonium nitrate. Ammonium nitrate ; Nitrate ; Production (economics) ; Porosity ; Process engineering ; Ammonium ; Environmental science ; Pulp and paper industry ; Materials science ; Chemistry ; Engineering ; Composite material ; Organic chemistry Material Properties and Applications ; Advanced Control Systems Optimization ; Advanced Theoretical and Applied Studies in Material Sciences and Geometry
Authors: Parth Desai
Source: Scholar Commons (University of South Carolina) (article, 2021-01-01)
Field: Materials Science — Materials Chemistry

What can a Worm Learn? Nonlinear Categorization by Caenorhabditis elegans using a Hydrochloric Acid Gradient Spring Valley High Caenorhabditis elegans ; Hydrochloric acid ; Nonlinear system ; Biology ; Computer science ; Chemistry ; Physics ; Genetics Crystallization and Solubility Studies
Authors: Navjeet Kaur | Jyotsna Kaushal | Pooja Mahajan
Source: Research Square (preprint, 2021-08-19)
Field: Chemistry — Analytical Chemistry

Evaluation of Kinetic and Equilibrium studies for Phytoremediation of Methylene Blue Dye (Triarylmethane) and Congo Red (Diazo) using Trachyspermum Ammi L. Abstract Phytoremediation developed as a green-clean, solar-driven and innovative technique for the eradication of contaminants from the environment from last two decades. In the present research work, phytoremediation potential of an ornamental plant Trachyspermum ammi L. ( T. ammi ) was examined for the removal of a triarylmethane-Methylene blue (MB) and di-azo-Congo red (CR) dye. The various parameters such as initial dye concentration, contact time, and pH were focused to explore the dye removal capability of T. ammi. The increase in initial dye concentration affects the decolorization potential of the T. ammi . The decolorization potential of T. ammi found to be reduced with enhancing the initial dye concentration of both the dyes. The plant achieved condition of equilibrium after the 40 h of contact time with both MB and CR dye. The favorable pH for T. ammi for the MB dye was observed as 5 while for CR dye was 6. The kinetics of phytoremediation reaction with both MB and CR dyes were studied with help of pseudo-first order, pseudo-second order, and Elovich models and the results were well appropriated to pseudo-first order with the correlation value R 2 ≥ 0.95 for MB and R 2 ≥ 0.97 for CR. The Langmuir and Freundlich isotherms studies of phytoremediation reaction found in favor of Freundlich equilibrium isotherm with correlation R 2 ≥ 0.99 for both MB and CR dyes. The mechanism of T. ammi for removal of dyes was supported with the help of analytical techniques such as Fourier Transform-Infrared Spectroscopy (FTIR) and Scanning Electron Microscope (SEM). Diazo ; Methylene blue ; Phytoremediation ; Chemistry ; Congo red ; Kinetic energy ; Medicinal chemistry ; Environmental chemistry ; Organic chemistry ; Photocatalysis ; Heavy metals ; Physics ; Adsorption Dye analysis and toxicity ; Potato Plant Research ; Enzyme-mediated dye degradation
Authors: Nicholas W. M. Ritchie | Dale E. Newbury
Source: Microscopy and Microanalysis (article, 2021-07-30)
Field: Materials Science — Surfaces, Coatings and Films

NeXL: A Platform for Innovation in Microanalysis NeXL is a series of loosely coupled software packages in the Julia language (https://julialang.org/) implementing X-ray microanalysis routines. NeXLCore (https: Microanalysis ; Action (physics) ; Electron probe microanalysis ; Computer science ; Chemistry ; Materials science ; Metallurgy ; Physics Electron and X-Ray Spectroscopy Techniques ; Advanced Materials Characterization Techniques ; Advanced X-ray and CT Imaging
Authors: Zongxiu Nie | Yuze Li | Lixia Jiang | Zhenpeng Wang | Xiaohua Cao | Lingwei Meng | Jinghan Fan | Guanghui Wang | Caiqiao Xiong
Source: Research Square (preprint, 2021-02-12)
Field: Chemistry — Spectroscopy

Rapid Mass Spectrometric Diagnosis of Bladder Cancer via Urine Carbonyl Metabolic Fingerprints Abstract The diagnosis of bladder cancer (BC) is currently based on cystoscopy, which is invasive and expensive. Here, we described a non-invasive, low-cost BC diagnosis method based on a desorption, separation, and ionization mass spectrometry platform (DSI-MS) that adopts N, N- Dimethylethylenediamine (DMED) as a differential labeling reagent. The DSI-MS platform avoids the interferences from intra- and/or inter-samples, while the DMED increases detection sensitivity and distinguishes carboxyl, aldehyde, and ketone groups from untreated samples. Carbonyl metabolic fingerprints of urine from 28 BC patients and 38 controls were portrayed and significant differences of some potential biomarkers were observed. The mechanisms of the changes have been discussed. Logistic regression (LR) was applied to discriminate BC from controls and an accuracy of 87% was achieved. We believe this patient-friendly method provides a hopeful approach for BC rapid point-of-care diagnostic. Urine ; Reagent ; Bladder cancer ; Chromatography ; Chemistry ; Cystoscopy ; Mass spectrometry ; Differential diagnosis ; Ketone ; Aldehyde ; Cancer ; Medicine ; Internal medicine ; Pathology ; Urinary system ; Biochemistry ; Organic chemistry Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Isotope Analysis in Ecology
Authors: Kelle Hart | Chelsea R. Thompson | Clay Burger | Dylan Hardwick | Amanda Michaud | Abdul H.M. Al Bulushi | Cole Pridemore | Carson Ward | Jixin Chen
Source:  (preprint, 2021-08-27)
Field: Chemistry — Physical and Theoretical Chemistry

Remote Learning of COVID-19 Kinetic Analysis in a Physical Chemistry Laboratory Class The COVID-19 pandemic has affected many in-person laboratory courses across the world. The viral spreading model is complicated but parameters, such as its reproduction number, Rt, can be estimated with the susceptible, infectious, or recovered (SIR) model. COVID-19 data for many states and countries are widely available online. This provides an opportunity for the students to analyze its spreading kinetics remotely. Here, we reported a lab carried out online during the third week of the spring semester of 2021 to minimize social contacts. Due to the wide interest in developing online physical chemistry and analytical labs during the pandemic, we’d like to share this lab design. The method, technique, procedure, and grading are described in this report. The student participants were able to apply the kinetic techniques learned in physical chemistry to successfully analyze an ongoing real-world problem through a remote learning environment and prepare this report. Coronavirus disease 2019 (COVID-19) ; Grading (engineering) ; Pandemic ; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ; Computer science ; 2019-20 coronavirus outbreak ; Multimedia ; Chemistry ; Virology ; Infectious disease (medical specialty) ; Biology ; Medicine ; Ecology Various Chemistry Research Topics ; SARS-CoV-2 detection and testing ; Molecular Communication and Nanonetworks
Authors: Andrew J. Miles | Robert W. Janes | B.A. Wallace
Source: BIROn (Birkbeck, University of London) (article, 2021-06-15)
Field: Chemistry — Spectroscopy

Tools and methods for Circular Dichroism Spectroscopy of proteins Circular dichroism (CD) spectroscopy is a widely-used method in biochemistry, structural biology and pharmaceutical chemistry. More than 24 000 papers published in the past decade have included CD characterisations of proteins; many of those studies have also included other complementary chemical, biophysical, and computational chemistry methods. This tutorial review describes the background to the technique of CD spectroscopy and good practice methods for high quality data collection. It specifically focuses on both established and new methods and tools available for experimental design and interpretation, data processing, visualisation, analysis, validation, archiving, and accession, including tools developed to enhance the complementarity of this method with other structural and chemical biology studies. Circular dichroism ; Complementarity (molecular biology) ; Structural biology ; Chemistry ; Spectroscopy ; Computer science ; Nanotechnology ; Computational biology ; Materials science ; Crystallography ; Biochemistry ; Physics ; Biology ; Genetics Molecular spectroscopy and chirality ; Analytical Chemistry and Chromatography ; Spectroscopy and Quantum Chemical Studies
Authors: Phillip J. Barry
Source:  (preprint, 2021-11-22)
Field: Materials Science — Materials Chemistry

$ZrO_{2}$ electronic properties The improvement of electronic and optical properties of the Zirconium dioxide $ZrO_{2}$ is very significance for the industrial applications. Here, we apply the first-principles calculations to study the influence of noble metals on the electronic and optical properties of the monoclinic $ZrO_{2}$ Monoclinic crystal system ; Zirconium dioxide ; Zirconium ; Materials science ; Electronic structure ; Nanotechnology ; Crystallography ; Metallurgy ; Computational chemistry ; Chemistry ; Crystal structure Machine Learning in Materials Science