jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Megan Y. Gee
Source: Scholar Commons (University of South Carolina) (article, 2019-01-01)
Field: Materials Science — Materials Chemistry

CDSE Quantum Dot Surface Chemistry Thermodynamics via Isothermal Titration Calorimetry: An Emphasis on the Fundamentals For several decades, the study and development of colloidal semiconductor nanocrystals, or quantum dots (QD), has become a rich field heralding improved integration into applications ranging from photovoltaics and photocatalysis to biomedical imaging and drug delivery. CdxSey is the most extensively studied QD system, however numerous compositional details still confound the nanocrystal field. Although CdSe QDs with native ligand coatings can show high fluorescence quantum yield and may be suitable for some applications, often times these original ligand layers are comprised of long aliphatic chains that preclude incorporation into biological matrices or severely impede charge transfer – depending on the end goal functionality. While the innermost core can be highly crystalline, due to the QD size regime a large fraction of the constituent atoms is found at the surface; the nature of which strongly influences optoelectronic properties. Indeed, the necessary ligand surfactant layer is anything but innocuous; dictating synthetic morphology, determining solubility, quenching or enhancing photoluminescence, or even modulating the nanocrystal’s band gap. A detailed, consistent and unambiguous profile for QD surface composition and thermodynamics would be extremely advantageous toward controlling and improving photophysical properties. This dissertation highlights several caveats for appropriately compiling a thermodynamic profile in situ for the dynamic nature of QD surfaces, and to describe approaches to address them. I have focused on developing commonly employed metrics for investigating CdSe QD surface chemistries. I begin by thoroughly considering how various purification techniques alter the most significant aspects of QD investigations and performance. Among these, I illustrate the gel permeation chromatography (GPC) approach that I helped to establish as a highly effective technique for nanoparticle purification. Finally, I delineate in several fundamental CdSe-based QD systems the capacity of isothermal titration calorimetry as a sensitive and precisely quantitative technique to directly probe reaction thermodynamics in organic phase. Even in cases where common spectroscopic techniques have been of limited use, ITC is employed to elucidate complex binding phenomena. Beginning with the highly reproducible GPC purification technique for a consistent QD starting material, this dissertation depicts my efforts to provide consistent equilibrium thermodynamic data for relevant QD surface chemistry interactions. Isothermal titration calorimetry ; Isothermal process ; Quantum dot ; Calorimetry ; Chemistry ; Thermodynamics ; Nanotechnology ; Physical chemistry ; Physics ; Materials science Quantum Dots Synthesis And Properties ; Molecular Junctions and Nanostructures ; Spectroscopy and Quantum Chemical Studies
Authors: Viktor Reshetnikov
Source: OPUS Repository (Kooperativer Bibliotheksverbund Berlin-Brandenburg) (article, 2019-01-01)
Field: Chemistry — Organic Chemistry

N-alkylaminoferrocenes for cancer-specific activation and/or organelle-targeting of known anticancer moieties Organelle ; Chemistry ; Cancer ; Cancer research ; Computational biology ; Biology ; Cell biology ; Nanotechnology ; Biochemistry ; Genetics ; Materials science Ferrocene Chemistry and Applications ; Metal complexes synthesis and properties ; Molecular Junctions and Nanostructures
Authors: V. Mendes | Marta Acebrón-García-de-Eulate | Nupur Verma | M. Błaszczyk | M.V.B. Dias | Tom L. Blundell
Source: Apollo (University of Cambridge) (article, 2019-11-26)
Field: Chemistry — Organic Chemistry

Mycobacterial OtsA Structures Unveil Substrate Preference Mechanism and Allosteric Regulation by 2-Oxoglutarate and 2-Phosphoglycerate. Trehalose is an essential disaccharide for mycobacteria and a key constituent of several cell wall glycolipids with fundamental roles in pathogenesis. Mycobacteria possess two pathways for trehalose biosynthesis. However, only the OtsAB pathway was found to be essential in Mycobacterium tuberculosis, with marked growth and virulence defects of OtsA mutants and strict essentiality of OtsB2. Here, we report the first mycobacterial OtsA structures from Mycobacterium thermoresistibile in both apo and ligand-bound forms. Structural information reveals three key residues in the mechanism of substrate preference that were further confirmed by site-directed mutagenesis. Additionally, we identify 2-oxoglutarate and 2-phosphoglycerate as allosteric regulators of OtsA. The structural analysis in this work strongly contributed to define the mechanisms for feedback inhibition, show different conformational states of the enzyme, and map a new allosteric site.IMPORTANCE Mycobacterial infections are a significant source of mortality worldwide, causing millions of deaths annually. Trehalose is a multipurpose disaccharide that plays a fundamental structural role in these organisms as a component of mycolic acids, a molecular hallmark of the cell envelope of mycobacteria. Here, we describe the first mycobacterial OtsA structures. We show mechanisms of substrate preference and show that OtsA is regulated allosterically by 2-oxoglutarate and 2-phosphoglycerate at an interfacial site. These results identify a new allosteric site and provide insight on the regulation of trehalose synthesis through the OtsAB pathway in mycobacteria. Allosteric regulation ; Biology ; Trehalose ; Biochemistry ; Virulence ; Mycobacterium ; Microbiology ; Enzyme ; Bacteria ; Genetics ; Gene Carbohydrate Chemistry and Synthesis ; Biochemical and Molecular Research
Authors: Qiming Zou
Source: Insecta mundi (article, 2019-01-01)
Field: Materials Science — Materials Chemistry

Low-dimensional Materials with Protective Coatings for Applications under Extreme Conditions Traditional ceramic-based, conductive materials used under extreme conditions are severely limited due to their conditional electrical conductivity and poor stability under harsh circumstances. Advanced composite structures based on vertically aligned carbon nanotubes (VACNTs) and high-temperature ceramics are expected to address this grand challenge, in which ceramic serves as a shielding layer protecting the VACNTs from the oxidation and erosive environment, while the VACNTs work as a conductor. However, it is still a great challenge to fabricate VACNT/ceramic composite structures due to the limited infiltration of ceramics inside the VACNT arrays. Hence developing a feasible method to infiltrate ceramics into VACNT arrays is necessary. The following research topics are covered in this dissertation including 1) Thermal CVD growth of ultralong vertically aligned CNTs, 2) CVD growth of h-BN, silicon and gallium nitride thin films 3) Infiltration of Si, GaN and BN into dense VACNT arrays, 4) Defect free coating of 2D materials by sputtering and RTP, 5) Evaluation of thermal stability enhancement of the CNT-ceramic composites.Ultralong vertically aligned CNTs are fabricated using two different methods in this study. The mechanism and kinetics of which are discussed and compared. In addition, different level of infiltration was achieved via different CVD methods. As an example, in laser-assisted CVD, ceramics were quickly deposited at the VACNT subsurfaces/surfaces, resulting in noninfiltrated composite structures. Unlike laser-assisted CVD, thermal CVD activated the precursors inside and outside the VACNTs simultaneously, which realized uniform infiltrated VACNT/ceramic composite structures. Similar levels of infiltration were achieved in the case of boron nitride and silicon, and anisotropic conducting behavior exhibited by CNT-BN was discovered. The mechanism and kinetics of infiltration into VACNT/ceramic composites, which we attributed to the different temperature distributions and gas diffusion mechanism in VACNTs, were investigated. More importantly, the as-fabricated composite structures exhibited excellent multifunctional properties, such as excellent antioxidative ability (up to 1100 °C), high thermal stability (up to 1400 °C) and good high-velocity hot gas erosion resistance. As an extension to the CNT coating techniques, defect generation and removal of 2D materials via sputtering and RTP was studied as well. Materials science Silicone and Siloxane Chemistry ; Surface Modification and Superhydrophobicity
Authors: Huaizhi Mu | Yuting Gao | Fushan Cheng | Lin Lin | Gerong Wang | Fucai Xia
Source: Dendrobiology (article, 2019-06-25)
Field: Materials Science — Biomaterials

Transcriptomic analysis of different tissues in Korean arborvitae Korean arborvitae (Thuja koraiensis) is an evergreen shrub or small tree native to Korea and the extreme Changbai Mountain of China threatened by habitat loss. Due to the limited genomic sources of Korean arborvitae, it is important to explore transcriptome to understand this economically important plant. We used RNA-seq technology to characterize the transcriptome of root, stem and leaf in Korean arborvitae, respectively. Based on the bioinformatics analysis of assembled transcriptome data, transcriptional pathways and differentially expressed genes (DEGs) were identified. There were 152.26 million reads generated, and 446,568 unigenes with a mean size of 423.51 nt obtained via de novo assembly. Of these, 204,091 unigenes (45.70%) were further annotated by comparison to public protein databases. A total of 63,495 unigenes (14.22%) were associated into 130 pathways by searching against the KEGG database. DEGs analysis identified 11,890, 5,900 and 10,136 DEGs from the comparison of root vs. stem, root vs. leaf and stem vs. leaf, respectively. Besides, photosynthesis, plant hormone signal transduction and metabolism and biosynthesis of sugar and amino acids were changed in different tissues. We obtained 446,568 unigenes in Korean arborvitae and 11,890, 5,900 and 10,136 DEGs from the comparison of root vs. stem, root vs. leaf and stem vs. leaf, respectively. These results will aid in understanding and carrying out future studies on the molecular basis of Korean arborvitae and contribute to future artificial production and applications. Transcriptome ; Biology ; Botany ; Gene ; Gene expression ; Genetics Silk-based biomaterials and applications ; Neurobiology and Insect Physiology Research
Authors: Kevin A. Kovalchik
Source: cIRcle (University of British Columbia) (article, 2019-01-01)
Field: Chemistry — Spectroscopy

Parsing and analysis of mass spectrometry data of complex biological and environmental mixtures The chemical characterization of biological and environmental samples are areas of research which involve the analysis of highly complex chemical mixtures. While the samples from these two fields differ greatly in composition, they present similar challenges. Complex mixtures provide a challenge to the analytical chemist as compounds in the mixture can have matrix effects which interfere with the analysis. Indeed, these interfering compounds may even be analytes themselves. High resolution mass spectrometry, which separates and detects ions based on their mass-to-charge ratio, is a powerful tool in the analysis of such mixtures. The amount of data resulting from such analyses, however, can be intractable to manual analysis, necessitating the use of computational tools. Furthermore, for the data to be reliable it is important that the performance of the mass spectrometer is optimal and consistent, but the complexity of the data again makes manual interpretation of the quality difficult. Thus, there is a need for computational assistance in analysis as well as method optimization and quality control. In Chapter 2:, we present a review of considerations toward the design of a standard mass spectrometry-based method for the quantification of naphthenic acids. The study provides recommendations for how these considerations can be addressed. In Chapter 3:, we describe a computational method of resolving dicarboxylic acids in high resolution mass spectrometry data of mixtures of derivatized naphthenic acid fraction compounds. The study is a proof-of-concept and demonstrates that derivatization-based methods of analyzing these diacid components is feasible but requires further investigation. In Chapter 4: and Chapter 5:, we present two computational tools which assist in method optimization and quality control of Thermo Orbitrap mass spectrometer systems. Chapter 4: presents RawQuant, a software tool which extracts scan quantification and meta data from data-dependent analysis data files from Orbitrap mass spectrometer systems. The tool is designed to inform the user toward method optimization. Chapter 5: presents RawTools, which builds upon RawQuant by adding the ability to track important measures of mass spectrometer performance longitudinally across a multi-run experiment. The tool is demonstrated using a 140-file dataset and provides easy visual monitoring of instrument performance. Parsing ; Mass spectrometry ; Computer science ; Chemistry ; Natural language processing ; Chromatography Mass Spectrometry Techniques and Applications
Authors: Н. И. Москаленко | S. N. Parzhin | I. R. Dodov | M.S. Hamidullina | Azat Akhmetshin
Source: E3S Web of Conferences (article, 2019-01-01)
Field: Chemistry — Spectroscopy

Development of optical-electronic systems for the study of temporal trends in the atmosphere composition and temporal variations of the Earth’s climate Optical-electronic system for atmospheric composition registration is considered. It is intended to identify the influence of anthropogenic emissions into the atmosphere on its optical properties and the Earth’s climate on a planetary scale. Anthropogenic emissions into the atmosphere increase due to the growth of planet population and expansion of its economic activity. The increasing scale of influence of various ingredients of anthropogenic emissions on the atmosphere requires studying their optical properties and carrying out research on the atmospheric composition in order to identify temporal trends in the concentrations of small and trace components of the atmosphere and their influence on changes in the Earth’s climate. Atmosphere (unit) ; Environmental science ; Trace gas ; Atmospheric sciences ; Atmospheric composition ; Earth (classical element) ; Climate change ; Scale (ratio) ; Astrobiology ; Earth science ; Meteorology ; Geology ; Geography ; Physics Spectroscopy and Laser Applications ; Atmospheric Ozone and Climate ; Atmospheric and Environmental Gas Dynamics
Authors: Rostyslav Sohuyko | Khrystyna Pavliv | Oksana Masna-Chala | Ivan Diskovskyi | З. З. Масна
Source: Wiadomości Lekarskie (article, 2019-12-01)
Field: Materials Science — Polymers and Plastics

DENSITY AND MINERAL CONTENT DYNAMICS OF BONE TISSUE OF THE LOWER JAW OF THE RAT ON THE BACKGROUND OF OPIOID INFLUENCE AND AFTER ITS WITHDRAWAL Results and conclusions: The study showed that the density and mineral content of the bone tissue of the rat's mandible on the background of 6 weeks opioid action of nalbuphine and after its withdrawal have a pronounced dynamics, different and characteristic for each of the investigated parameters. The results of the atomic absorption spectral analysis of the bone tissue of the rat's mandible body allow the determination of the quantitative content of four macro-elements (Ca, P, Mg, Na) and four microelements (K, Fe, Sr, Zn) and investigate their dynamics during the experiment. On the background of the nalbuphine use absolute indices of calcium, phosphorus, magnesium, sodium, zinc and iron content increase, remaining above the norm after its withdrawal; the amount of potassium decreases and remains lower than norm and after the withdrawal of nalbuphine, and the amount of strontium is also reduced, but minimal, and after the withdrawal of nalbuphine has the same value as in intact animals. Nalbuphine ; Chemistry ; Potassium ; Population ; Zinc ; Magnesium ; Calcium ; Opioid ; Endocrinology ; Internal medicine ; Medicine ; Biochemistry ; Receptor Polymer Synthesis and Characterization ; Thallium and Germanium Studies
Authors: Carolina Machado Malheiro Rodrigues
Source: Open Repository of the University of Porto (University of Porto) (article, 2019-01-03)
Field: Materials Science — Biomaterials

Contribution of biochemical tools for the assessment of the ecological quality of fluvial ecosystems Ecosystem ; Quality (philosophy) ; Environmental resource management ; Fluvial ; Environmental science ; Ecology ; Geography ; Geology ; Biology Diatoms and Algae Research ; Water Quality and Pollution Assessment ; Environmental Science and Water Management
Authors: Grayson S. Doucette
Source:  (article, 2019-07-15)
Field: Materials Science — Materials Chemistry

COARSE TO FINE: TUNING MOLECULAR PACKING TO PINPOINT TRIPLET PAIR SEPARATION MECHANISMS AND THE ROLE OF MOLECULAR COUPLING Coupling (piping) ; Chemical physics ; Separation (statistics) ; Chemistry ; Materials science ; Computer science Silicone and Siloxane Chemistry
Authors: Luciano M. Santino
Source: Open Scholarship Institutional Repository (Washington University in St. Louis) (article, 2019-11-08)
Field: Materials Science — Polymers and Plastics

Self-Assembly of Conducting Polymer Nano- and Microstructures for Energy Storage Plastics are materials composed of many long chains of molecules with repeating subunits; strong interactions between neighboring molecules lead to the material used throughout the world. Plastics are commonly thought to be insulating, in stark contrast to the conductivity of metals. However, certain polymer structures were discovered to exhibit semiconducting properties, the subject of the Nobel Prize in Chemistry in 2000. Conducting polymers have a unique molecular structure with an electronically conjugated backbone, allowing electrons to freely travel both across the chain and in between chains. This work focuses on controlling the kinetics of the reaction between the vapors of an aromatic heterocycle pyrrole and aqueous iron(III) containing oxidants. With the methods introduced in this dissertation, the conducting polymer polypyrrole is formed with great control of molecular structure, allowing for the fine-tuning of properties like conductivity. Unique interactions during synthesis lead to the controlled deposition of polypyrrole nano- and microstructures, including fibers, tubes, webs, and thin films. These unique structures of polypyrrole are then analyzed for their performance as usable electronic materials, including transparent and flexible conductors as well as electrode materials for electrochemical energy storage devices. Nano- ; Materials science ; Microstructure ; Polymer ; Nanotechnology ; Composite material Conducting polymers and applications ; Advanced Sensor and Energy Harvesting Materials ; Supercapacitor Materials and Fabrication
Authors: Sensu Celasun | Dario Remmler | Timm Schwaar | Michael G. Weller | Filip Du Prez | Hans Boerner
Source:  (article, 2019-01-01)
Field: Chemistry — Spectroscopy

Digging into the sequential space of thiolactone precision polymers : a combinatorial strategy to identify functional domains Functional sequences of precision polymers based on thiolactone/Michael chemistry are identified from a large one-bead one-compound library. Single-bead readout by MALDI-TOF MS/MS identifies sequences that host m-THPC that is a second generation photo-sensitizer drug. The corresponding Tla/Michael-PEG conjugates make m-THPC available in solution and drug payload as well as drug release kinetics can be fine-tuned by the precision segment. Thiolactone ; Payload (computing) ; Polymer ; Combinatorial chemistry ; Nanotechnology ; Computer science ; Chemistry ; Materials science ; Stereochemistry ; Organic chemistry Analytical Chemistry and Chromatography ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Elisabetta Tobaldi
Source: Serveur des thèses de l'Université de Strasbourg (University of Strasbourg) (preprint, 2019-04-09)
Field: Materials Science — Biomaterials

Acid catalysed abiotic reactions in biological system : from design to in Vivo proof of concept This thesis object is acid-catalysed abiotic reactions in biological systems. They are defined as reaction systems composed by a xenobiotic substrate – a cyclic acetal in this work - stable in biological conditions and cleavable at low pH and a corresponding biocompatible heterogeneous acid catalyst. The challenge of this approach is to keep the catalyst active in a buffered biological media and still capable of hydrolysing the xenobiotic acetal substrate and to maintain the buffered pH of the living system in its original state. In the first part of this work we focus on the fine-tuning of cyclic acetals. We identify 4 acetal structures and we show that structural changes lead to a different reactivity in different pH ranges, each corresponding to possible applications in vivo, including stable linkers for antibody drug conjugates and linkers cleavable in physiological conditions for bioconjugation.The second part is focused on the biocompatible catalyst. Herein we identify two solid biocompatible catalysts, with different degree of hydrophobicity and adsorbance properties: Nafion NR-50 and PEG-AASA co-polymer. We demonstrate that, upon proper treatment, they can maintain an inner pH < 4, hydrolyse the substrate and do not affect the highly buffered biofluid used as solvent. Chemistry ; Humanities ; Art biodegradable polymer synthesis and properties ; Enzyme Catalysis and Immobilization
Authors: Marc S. Lavine
Source: Science (article, 2019-11-14)
Field: Chemistry — Physical and Theoretical Chemistry

Cross-linking a range of alkyl polymers Polymer Chemistry Some alkyl polymers, such as polyethylene, can be cross-linked by using peroxides or high-energy radiation or through the addition of a radical forming agent. Others, like polypropylene, are likely to undergo chain scission, and this process tends to be uncontrolled in the distribution of the cross-links. Lepage et al. developed a widely applicable approach using bis -diazirine molecules as cross-linking agents (see the Perspective by de Zwart et al. ). These molecules can be thermally or photochemically activated to form carbenes that readily insert into the polymer carbon-hydrogen bonds, thus leading to cross-linking. The bis -diazirine is nonexplosive, nonvolatile, and easily activated at relatively mild temperatures and thus could be used to fine-tune the properties of existing polymers through small chemical modifications. Science , this issue p. [875][1]; see also p. [800][2] [1]: /lookup/doi/10.1126/science.aay6230 [2]: /lookup/doi/10.1126/science.aaz7612 Alkyl ; Range (aeronautics) ; Polymer ; Materials science ; Chemistry ; Organic chemistry ; Composite material Chemical Reactions and Mechanisms ; Synthesis and properties of polymers ; Polymer Nanocomposite Synthesis and Irradiation