jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Mike Filius | Raman van Wee | Carlos de Lannoy | Ilja Westerlaken | Zeshi Li | Sung Hyun Kim | Cecilia de Agrela Pinto | Yunfei Wu | Geert‐Jan Boons | Martin Pabst | Dick de Ridder | Chirlmin Joo
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-09-28)
Field: Chemistry — Spectroscopy

Full-Length Single-Molecule Protein Fingerprinting Abstract Proteins are the primary functional actors of the cell. Hence, their identification is pivotal to advance our understanding of cell biology and disease. Current protein analysis methods are of limited use for distinguishing proteoforms. In particular, mass spectrometric methods often provide only ambiguous information on post-translational modification sites, and sequences of co-existing modifications may not be resolved. Here we demonstrate FRET-based single-molecule protein fingerprinting to map the location of individual amino acids and a post-translational modification within single full-length protein molecules. Using an approach that relies on transient binding of fluorescently labeled DNA strands to probe the amino acids on a protein one by one we show that we can fingerprint intrinsically disordered proteins as well as folded globular proteins with sub-nanometer resolution. We anticipate that this technology will be used for proteoform identification in biological and translational research with ultimate sensitivity. Computational biology ; Proteomics ; Chemistry ; Amino acid ; Identification (biology) ; Förster resonance energy transfer ; Posttranslational modification ; Small molecule ; Biophysics ; Resolution (logic) ; Biology ; Nanotechnology ; Biochemistry ; Computer science ; Physics ; Enzyme ; Materials science ; Artificial intelligence Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; RNA and protein synthesis mechanisms
Authors: Lindembergue Pereira Costa Júnior | Tatiara G. Almeida | Gabriella Amorim Muniz Falcão | Laura Hécker de Carvalho | Glória Maria Vinhas | Yêda Medeiros Bastos de Almeida
Source: Revista de Gestão e Secretariado (Management and Administrative Professional Review) (article, 2023-07-19)
Field: Materials Science — Biomaterials

Effect of organoclay and corn straw on the properties of poly (butylene adipate-co-terephthalate) (PBAT) hybrid composites The packaging industry requires permeable materials capable of offering freshness of the packaging content. The use of fillers can enhance these permeable properties to the polymeric material. This work investigates the effect of incorporating different fillers (organophilic clay and corn straw) on the rheological, mechanical, permeability, water absorption and biodegradability characteristics of poly (butylene adipate co-terephthalate) (PBAT) processed in an internal laboratory mixer. Extruded films and specimens injection molded were produced. The results of torque rheometry suggest polymer matrix degradation during processing slightly increase, also evidenced by MFR results. Composite films showed a drop in tensile strength, higher stiffness and lower elongation. Incorporation of the fillers in the PBAT matrix enhanced the permeability to oxygen gas of the produced films. The presence of fillers significantly increased the capacity of water absorption. The incorporation of C20A and, mainly, CS tends to accelerate the biodegradation of PBAT. Adding small amounts of organoclay C20A and CS to PBAT leads to a material that combines maintenance or improvement of biodegradation combined with higher permeability to oxygen, which indicates the potential use of these systems in packaging industry for maintenance of freshness of content. Materials science ; Ultimate tensile strength ; Composite material ; Biodegradation ; Absorption of water ; Adipate ; Polymer ; Rheology ; Organoclay ; Oxygen permeability ; Oxygen ; Chemistry ; Organic chemistry biodegradable polymer synthesis and properties ; Natural Fiber Reinforced Composites ; Polymer crystallization and properties
Authors: Badis Bakri | Hani Benguesmia | Aya Mira | Nassima M’ziou
Source: Diagnostyka (article, 2023-01-20)
Field: Materials Science — Materials Chemistry

Impact of heterogeneous cavities on the electrical constraints in the insulation of high-voltage cables In this paper, we use the comsol multiphysics software, which is based on the finite element method in AC/DC 2D electrostatic. Our study shows the effect of heterogeneous cavities on the functioning of electrical cables. Our mini-project contains the study of electric field distribution and potential of a model of high voltage cable; we took into account the absence and the presence of heterogeneous cavities. The study was conducted using numerical results with mathematical validation. The results are favorable and promising. Electrical engineering ; Electric field ; Power cable ; High voltage ; Electronics ; Electrical treeing ; Engineering ; Engineering physics ; Power electronics ; Voltage ; Mechanical engineering ; Materials science ; Physics ; Composite material ; Partial discharge High voltage insulation and dielectric phenomena ; Power Transformer Diagnostics and Insulation ; Thermal Analysis in Power Transmission
Authors: Jiahui Chen | Olaf J. Borkiewicz | Alexander Grishaev | Fan Zhang | Mrinal K. Bera | Uta Ruett | Igor Levin
Source: Chemistry - A European Journal (article, 2023-01-16)
Field: Materials Science — Materials Chemistry

Extended <i>q</i>‐Range X‐Ray Scattering Reveals High‐Resolution Structural Details of Biomacromolecules in Aqueous Solutions We communicate a feasibility study for high-resolution structural characterization of biomacromolecules in aqueous solution from X-ray scattering experiments measured over a range of scattering vectors (q) that is approximately two orders of magnitude wider than used previously for such systems. Scattering data with such an extended q-range enables the recovery of the underlying real-space atomic pair distribution function, which facilitates structure determination. We demonstrate the potential of this method for biomacromolecules using several types of cyclodextrins (CD) as model systems. We successfully identified deviations of the tilting angles for the glycosidic units in CDs in aqueous solutions relative to their values in the crystalline forms of these molecules. Such level of structural detail is inaccessible from standard small angle scattering measurements. Our results call for further exploration of ultra-wide-angle X-ray scattering measurements for biomacromolecules. Scattering ; Small-angle X-ray scattering ; Aqueous solution ; Pair distribution function ; Anomalous scattering ; Range (aeronautics) ; Crystallography ; Resolution (logic) ; Chemistry ; Function (biology) ; Chemical physics ; Materials science ; Physics ; Optics ; Physical chemistry ; Computer science ; Quantum mechanics X-ray Diffraction in Crystallography ; Enzyme Structure and Function ; X-ray Spectroscopy and Fluorescence Analysis
Authors: YuZe TIAN | Jing JIN | HeLin YANG | LvRong FAN | JunJie HOU | Hai LIN
Source: Zhongguo kexue. Wulixue Lixue Tianwenxue (article, 2023-07-19)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Research progress on design and application of microwave electromagnetic metamaterial <p indent="0mm">Electromagnetic metamaterials have attracted extensive attention from academia and industry in the past two decades and have been widely utilized in military and civil applications. Electromagnetic metamaterials can overcome the limitations of traditional electromagnetic devices because of their extraordinary electromagnetic properties that natural media do not possess. Electromagnetic metamaterial have an excellent ability to manipulate electromagnetic waves in different spectra, which has resulted in the evolution of various electromagnetic functional devices. With the increasing demand for applications, the structures of electromagnetic metamaterials are becoming increasingly complex, and their functions are diversified. The fusion applications of new materials and new processes in metamaterial continue to emerge. The research on the design methodology of metamaterial driven by artificial intelligence and optimization theory is burgeoning. In this study, the development and application of electromagnetic metamaterial in the microwave field are briefly summarized based on the research findings and industry development in recent years. A total of 4949 electromagnetic metamaterial papers are included in the CNKI database as the corpus, and the LSTM model is introduced to statistically summarize the current development trend of electromagnetic metamaterial from the perspective of big data, providing valuable guidance for researchers engaged in this field. Metamaterial ; Microwave ; Microwave applications ; Metamaterial cloaking ; Engineering ; Physics ; Computer science ; Tunable metamaterials ; Telecommunications ; Optics ; Metamaterial absorber Metamaterials and Metasurfaces Applications ; Antenna Design and Analysis ; Advanced Antenna and Metasurface Technologies
Authors: Gábor Nagy | Nykola C. Jones | Søren Vrønning Hoffmann | Helmut Grubmueller
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-10-20)
Field: Chemistry — Spectroscopy

A Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models Circular Dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light, and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods. Globular protein ; Circular dichroism ; Intrinsically disordered proteins ; Protein secondary structure ; Macromolecule ; Chemistry ; Protein structure ; Reference data ; Absorbance ; Biological system ; Crystallography ; Biophysics ; Computer science ; Biology ; Biochemistry ; Data mining ; Chromatography Molecular spectroscopy and chirality ; Photosynthetic Processes and Mechanisms ; Spectroscopy and Quantum Chemical Studies
Authors: A. Gilad Kusne | Austin McDannald | Brian DeCost
Source: arXiv (Cornell University) (preprint, 2023-11-10)
Field: Materials Science — Materials Chemistry

Learning material synthesis-process-structure-property relationship by data fusion: Bayesian Coregionalization N-Dimensional Piecewise Function Learning Autonomous materials research labs require the ability to combine and learn from diverse data streams. This is especially true for learning material synthesis-process-structure-property relationships, key to accelerating materials optimization and discovery as well as accelerating mechanistic understanding. We present the Synthesis-process-structure-property relAtionship coreGionalized lEarner (SAGE) algorithm. A fully Bayesian algorithm that uses multimodal coregionalization to merge knowledge across data sources to learn synthesis-process-structure-property relationships. SAGE outputs a probabilistic posterior for the relationships including the most likely relationships given the data. Merge (version control) ; Property (philosophy) ; Computer science ; Process (computing) ; Probabilistic logic ; Key (lock) ; Machine learning ; Bayesian probability ; Artificial intelligence ; Bayesian network ; Function (biology) ; Data stream mining ; Data mining ; Information retrieval ; Biology Machine Learning in Materials Science
Authors: V. S. Dozhdikov | A. Yu. Basharin | P. R. Levashov
Source: Журнал технической физики (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

Structure studies of graded amorphous carbon obtained by liquid carbon quenching A new method for obtaining graded amorphous carbon using quenching of a graphite melt on a diamond substrate is proposed. Using molecular dynamics modeling of liquid carbon quenching on a cold diamond substrate, it is shown that the amorphous carbon obtained in the experiment is a material with a strongly gradient structure and properties along the depth of the sample. This is due to the quenching rate decrease with the distance from the substrate in the range of 10 14 -10 12 K/s. In this case, the density of amorphous carbon varies from 1.50 g/cm 3 to 1.93 g/cm 3 . The spatial change in the structural characteristics of the obtained amorphous carbon was studied: the distribution of carbon atoms according to the degree of chemical bond hybridization (sp 1 -, sp 2 -, sp 3 -), the radial distribution function, the angular distribution function, and a statistical analysis of carbon rings were carried out. It is shown that at a pressure in liquid of 1 GPa, the carbon structure within the quenched zone changes from a highly porous structure with a large number of sp 1 chains of carbon atoms near the substrate to an amorphous graphene structure at the periphery. Keywords: amorphous carbon, liquid carbon, quenching, molecular dynamics, radial distribution function. Quenching (fluorescence) ; Amorphous carbon ; Carbon fibers ; Materials science ; Graphite ; Diamond ; Graphene ; Radial distribution function ; Substrate (aquarium) ; Amorphous solid ; Molecular dynamics ; Diamond-like carbon ; Chemical physics ; Crystallography ; Chemistry ; Composite material ; Computational chemistry ; Nanotechnology ; Composite number ; Optics ; Fluorescence ; Physics Diamond and Carbon-based Materials Research ; Carbon Nanotubes in Composites ; Adsorption, diffusion, and thermodynamic properties of materials
Authors: Ibrahim Buba Garba | Tommaso Morresi | Charles Bouillaguet | Michele Casula | Lorenzo Paulatto
Source: Journal of Physics Condensed Matter (article, 2023-06-06)
Field: Materials Science — Materials Chemistry

Reciprocal space temperature-dependent phonons method from <i>ab-initio</i> dynamics We present a robust reciprocal-space implementation of the temperature-dependent effective potential method, our implementation can scale easily to large cell and long sampling time. It is interoperable with standard<i>ab-initio</i>molecular dynamics and with Langevin dynamics. We prove that both sampling methods can be efficient and accurate if a thermostat is used to control temperature and dynamics parameters are used to optimize the sampling efficiency. By way of example, we apply it to study anharmonic phonon renormalization in weakly and strongly anharmonic materials, reproducing the temperature effect on phonon frequencies, crossing of phase transition, and stabilization of high-temperature phases. Anharmonicity ; Phonon ; Thermostat ; Ab initio ; Statistical physics ; Renormalization ; Sampling (signal processing) ; Reciprocal lattice ; Dynamics (music) ; Physics ; Molecular dynamics ; Phase space ; Condensed matter physics ; Quantum mechanics ; Thermodynamics Thermal properties of materials ; Thermal Expansion and Ionic Conductivity ; High-pressure geophysics and materials
Authors: Yongjin Shin | Kenneth R. Poeppelmeier | James M. Rondinelli
Source: arXiv (Cornell University) (preprint, 2023-12-19)
Field: Materials Science — Materials Chemistry

Informatics-based learning of oxygen vacancy ordering principles in oxygen-deficient perovskites Ordered oxygen vacancies (OOVs) in perovskites can exhibit long-range order and may be used to direct materials properties through modifications in electronic structures and broken symmetries. Based on the various vacancy patterns observed in previously known compounds, we explore the ordering principles of OOVs in oxygen-deficient perovskite oxides with $AB\mathrm{O}_{2.5}$ stoichiometry to identify other OOV variants. We performed first-principles calculations to assess the OOV stability on a dataset of 50 OOV structures generated from our bespoke algorithm. The algorithm employs uniform planar vacancy patterns on (111) pseudocubic perovskite layers and the approach proves effective for generating stable OOV patterns with minimal computational loads. We find as expected that the major factors determining the stability of OOV structures include coordination preferences of transition metals and elastic penalties resulting from the assemblies of polyhedra. Cooperative rotational modes of polyhedra within OOV structures reduce elastic instabilities by optimizing the bond valence of $A$- and $B$-cations. This finding explains the observed formation of vacancy channels along low-index crystallographic directions in prototypical OOV phases. The identified ordering principles enable us to devise other stable vacancy patterns with longer periodicity for targeted property design in yet to be synthesized compounds. Vacancy defect ; Polyhedron ; Materials science ; Stoichiometry ; Valence (chemistry) ; Perovskite (structure) ; Oxygen ; Crystallography ; Planar ; Condensed matter physics ; Chemical physics ; Algorithm ; Computer science ; Chemistry ; Physics ; Mathematics ; Geometry ; Physical chemistry Advancements in Solid Oxide Fuel Cells ; Catalysis and Oxidation Reactions ; Magnetic and transport properties of perovskites and related materials
Authors: Brittany L. Bonnett | Dina Sheyfer | Pubudu N. Wimalasiri | Srikanth Nayak | Jyotsana Lal | Qingteng Zhang | Söenke Seifert | G. B. Stephenson | Michael J. Servis
Source: ChemRxiv (preprint, 2023-02-16)
Field: Materials Science — Materials Chemistry

Critical Fluctuations in Liquid-Liquid Extraction Organic Phases Controlled by Extractant and Diluent Molecular Structure Extractant aggregation in liquid-liquid extraction organic phases impacts extraction energetics and is related to the deleterious efficiency-limiting liquid-liquid phase transition known as third phase formation. Using small angle x-ray scattering, we find that structural heterogeneities across a wide range of compositions in binary mixtures of malonamide extractants and alkane diluents are well described by Ornstein-Zernike scattering. This suggests that structure in these simplified organic phases originates from the critical point associated with the liquid-liquid phase transition. To confirm this, we measure the temperature dependence of the organic phase structure, finding critical exponents consistent with the 3D Ising model. Molecular dynamics simulations were also consistent with this mechanism for extractant aggregation. Due to the absence of water or any other polar solutes required to form reverse-micellar-like nanostructures, these fluctuations are inherent to the binary extractant/diluent mixture. Our previous work found pseudobinary critical fluctuations near the critical point for more complex organic phases with extracted polar solutes, including water, acid and metal ions. Taken together, these results suggest this mechanism for explaining organic phase aggregation may dominate over a wide range of conditions encountered in practical liquid-liquid extraction organic phases. We also show how the molecular structure of the extractant and diluent modulate these critical concentration fluctuations by shifting the critical temperature: critical fluctuations are suppressed by increasing extractant alkyl tail lengths or decreasing diluent alkyl chain lengths. This is consistent with how extractant and diluent molecular structure are known to impact metal and acid loading capacity in many-component LLE organic phases, suggesting phase behavior of practical systems may be effectively studied in simplified organic phases. Overall, the explicit connection between molecular structure, aggregation and phase behavior demonstrated here will enable the design of more efficient separations processes. Diluent ; Chemistry ; Extraction (chemistry) ; Critical point (mathematics) ; Phase (matter) ; Molecular dynamics ; Alkyl ; Liquid–liquid extraction ; Chemical physics ; Liquid liquid ; Phase transition ; Thermodynamics ; Chromatography ; Organic chemistry ; Computational chemistry Crystallization and Solubility Studies ; Phase Equilibria and Thermodynamics ; Extraction and Separation Processes
Authors: Alistair J. Sterling | Russell C. Smith | Edward A. Anderson | Fernanda Duarte
Source: ChemRxiv (preprint, 2023-10-12)
Field: Chemistry — Organic Chemistry

Beyond strain release: Delocalization-enabled organic reactivity The release of strain energy is a fundamental driving force for organic reactions. However, absolute strain energy alone is an insufficient predictor of reactivity, as evidenced by the similar ring strain but disparate reactivity of cyclopropanes and cyclobutanes. In this work, we demonstrate that electronic delocalization is a key factor that operates alongside strain release to boost, or even dominate, reactivity. This delocalization principle extends across a wide range of molecules containing three-membered rings such as epoxides, aziridines and propellanes, and also applies to strain-driven cycloaddition reactions. Our findings lead to a ‘rule of thumb’ for the accurate prediction of activation barriers in such systems, which can be easily applied to reactions involving many of the strained building blocks commonly encountered in organic synthesis, medicinal chemistry, polymer science and bioconjugation. Given the significance of electronic delocalization in organic chemistry, for example in aromatic 𝜋-systems and hyperconjugation, we anticipate that this concept will serve as a versatile tool to understand and predict strain-based organic reactivity. Reactivity (psychology) ; Delocalized electron ; Ring strain ; Cyclobutanes ; Cycloaddition ; Strain (injury) ; Chemistry ; Computational chemistry ; Chemical physics ; Molecule ; Organic chemistry ; Catalysis ; Biology Cyclopropane Reaction Mechanisms ; Molecular Junctions and Nanostructures ; Synthesis and Properties of Aromatic Compounds