jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Damien Bretagne | Arnaud Pâris | D.I. Matthews | Laëtitia Fougère | Nastassja Burrini | Gerd K. Wagner | Richard Daniellou | Pierre Lafite
Source: Journal of Biological Chemistry (article, 2024-02-13)
Field: Chemistry — Organic Chemistry

“Mix and match” auto-assembly of glycosyltransferase domains delivers biocatalysts with improved substrate promiscuity Glycosyltransferases (GT) catalyze the glycosylation of bioactive natural products, including peptides and proteins, flavonoids, and sterols, and have been extensively used as biocatalysts to generate glycosides. However, the often narrow substrate specificity of wild-type GTs requires engineering strategies to expand it. The GT-B structural family is constituted by GTs that share a highly conserved tertiary structure in which the sugar donor and acceptor substrates bind in dedicated domains. Here, we have used this selective binding feature to design an engineering process to generate chimeric glycosyltransferases that combine auto-assembled domains from two different GT-B enzymes. Our approach enabled the generation of a stable dimer with broader substrate promiscuity than the parent enzymes that were related to relaxed interactions between domains in the dimeric GT-B. Our findings provide a basis for the development of a novel class of heterodimeric GTs with improved substrate promiscuity for applications in biotechnology and natural product synthesis. Glycosyltransferase ; Protein engineering ; Glycosylation ; Substrate (aquarium) ; Directed evolution ; Biochemistry ; Chemistry ; Enzyme ; Substrate specificity ; Promiscuity ; Computational biology ; Stereochemistry ; Biology ; Gene ; Mutant Carbohydrate Chemistry and Synthesis ; Glycosylation and Glycoproteins Research ; Microbial Natural Products and Biosynthesis
Authors: Matthew Witman | Peter Schindler
Source: Digital Discovery (article, 2024-12-09)
Field: Materials Science — Materials Chemistry

MatFold: systematic insights into materials discovery models' performance through standardized cross-validation protocols A general-purpose, featurization-agnostic toolkit, MatFold, is provided to automate reproducible generation of cross-validation splits to assess out-of-distribution generalization and encourage further community use in materials model benchmarking. Computer science ; Systematic review ; Data science ; MEDLINE ; Chemistry Machine Learning in Materials Science ; X-ray Diffraction in Crystallography ; Computational Drug Discovery Methods
Authors: Darren C. Holland | Anthony R. Carroll
Source: Molecules (article, 2024-01-25)
Field: Chemistry — Spectroscopy

Structure Revision of Formyl Phloroglucinol Meroterpenoids: A Unified Approach Using NMR Fingerprinting and DFT NMR and ECD Analyses NMR fingerprints are valuable tools for analyzing complex natural product mixtures and identifying incorrectly assigned structures in the literature. Our diagnostic NMR fingerprints for formyl phloroglucinol meroterpenoids revealed discrepancies in the structures reported for eucalyprobusal C (<b>1a</b>) and eucalypcamal K (<b>2a</b>). NMR fingerprinting PCA analyses identified <b>1a</b> as an oxepine-diformyl phloroglucinol and <b>2a</b> as an oxepine 3-acyl-1-formyl phloroglucinol, contrary to their initial assignments as pyrano-diformyl and pyrano 3-acyl-1-formyl phloroglucinols, respectively. Extensive reinterpretation of their reported one- and two-dimensional NMR data, coupled with GIAO DFT-calculated <sup>1</sup>H and <sup>13</sup>C NMR chemical shift and DP4+ analyses, supported the unequivocal reassignment of eucalyprobusal C to <b>1b</b> and eucalypcamal K to <b>2b</b>. The absolute configurations of the revised oxepine-containing phloroglucinol meroterpenoids were confirmed via the reinterpretation of their reported ROESY and NOESY NMR data, along with comparative TDDFT-calculated and experimental ECD spectra. Phloroglucinol ; Chemistry ; Chemical shift ; Carbon-13 NMR ; Two-dimensional nuclear magnetic resonance spectroscopy ; Reinterpretation ; Proton NMR ; Stereochemistry ; Computational chemistry ; Structural isomer ; Organic chemistry ; Physical chemistry Molecular spectroscopy and chirality ; Natural Compound Pharmacology Studies ; Natural product bioactivities and synthesis
Authors: Eric Firestone | Richard J. Staples | Thomas W. Hamann
Source: Inorganic Chemistry (article, 2024-06-19)
Field: Materials Science — Materials Chemistry

Open-Cage Copper Complexes Modulate Coordination and Charge Transfer This study presents a novel copper-based redox shuttle that employs the PY5 pentadentate polypyridyl ligand in a dye-sensitized solar cell (DSSC). The [Cu(PY5)]<sup>2+</sup> complex exhibits a unique five-coordinate square pyramidal geometry, characterized by a strategically labile axial position, to facilitate efficient dye regeneration while minimizing electron recombination, thereby enhancing DSSC performance. Notably, the inclusion of 4-<i>tert</i>-butylpyridine (TBP) as an additive is shown to significantly modulate the electrochemical and photophysical properties of the copper complexes, attributed to its coordination to the vacant axial site. This interaction leads to an improved open-circuit voltage and overall device efficiency, with the complexes achieving promising efficiencies under standard solar irradiance. The findings underscore the potential of utilizing copper-based redox shuttles with designed ligand geometries to overcome the limitations of current DSSC materials, opening new avenues for the design and optimization of solar energy conversion devices. This work not only contributes to the fundamental understanding of the behavior of copper complexes in DSSCs but also paves the way for future research aimed at exploiting the full potential of such geometrical and electronic configurations for the development of more robust and efficient solar energy solutions. Chemistry ; Copper ; Dye-sensitized solar cell ; Cage ; Ligand (biochemistry) ; Redox ; Photochemistry ; Charge (physics) ; Inorganic chemistry ; Organic chemistry ; Physical chemistry ; Electrode ; Receptor Advanced Nanomaterials in Catalysis ; TiO2 Photocatalysis and Solar Cells ; Porphyrin and Phthalocyanine Chemistry
Authors: Andreea Mihaela Grămadă | Adelina-Gabriela Niculescu | Alexandra Cătălina Bîrcă | Alina Maria Holban | Alina Ciceu | Cornel Baltă | Hildegard Herman | Anca Hermenean | Alexandra Elena Stoica | Simona Ardelean | Adina Alberts | Alexandru Mihai Grumezescu | Monica Puticiu
Source: Polymers (article, 2024-12-30)
Field: Materials Science — Biomaterials

In Vitro and In Vivo Evaluation of rPET/Cu-Alg Nanofibers for Anti-Infective Therapy With the growing interest in nanofibers and the urgent need to address environmental concerns associated with plastic waste, there is an increasing focus on using recycled materials to develop advanced healthcare solutions. This study explores the potential of recycled poly(ethylene terephthalate) (PET) nanofibers, functionalized with copper-enhanced alginate, for applications in wound dressings. Nanofibers with desirable antimicrobial properties were developed using chemical recycling and electrospinning techniques, offering a sustainable and effective option for managing wound infections and promoting healing. SEM and FT-IR analyses confirmed that the obtained nanofibers possess optimal physicochemical properties, including well-organized morphology, appropriate dimensions, and structural integrity. Biological evaluations revealed significant antimicrobial activity, with the materials effectively inhibiting microbial adherence and biofilm formation while maintaining good biocompatibility in both in vitro and in vivo studies. These findings highlight the potential of recycled PET-based nanofibers as advanced wound dressing materials to reduce infection risks and support tissue regeneration in clinical applications. Nanofiber ; Electrospinning ; Biocompatibility ; Materials science ; Antimicrobial ; Wound dressing ; Regeneration (biology) ; In vivo ; Nanotechnology ; Biomedical engineering ; Polymer ; Composite material ; Medicine ; Biotechnology ; Microbiology ; Biology Electrospun Nanofibers in Biomedical Applications ; Advanced Sensor and Energy Harvesting Materials ; Microplastics and Plastic Pollution
Authors: Davide Cademartori | Maxime Hubert | Élise Bonnet | Jean‐Marc Bassat | Jérôme Laurencin
Source: International Journal of Hydrogen Energy (article, 2024-12-17)
Field: Materials Science — Materials Chemistry

Engineering nanostructured electrodes for solid oxide cells (SOCs) via microstructural and electrochemical modelling Electrochemistry ; Electrode ; Materials science ; Oxide ; Nanotechnology ; Chemical engineering ; Metallurgy ; Chemistry ; Engineering ; Physical chemistry Advancements in Solid Oxide Fuel Cells ; Electronic and Structural Properties of Oxides ; Gas Sensing Nanomaterials and Sensors
Authors: Mads-Peter Verner Christiansen | Nikolaj Rønne | Bjørk Hammer
Source: Machine Learning Science and Technology (article, 2024-10-21)
Field: Materials Science — Materials Chemistry

Efficient ensemble uncertainty estimation in Gaussian processes regression Abstract Reliable uncertainty measures are required when using data-based machine learning interatomic potentials (MLIPs) for atomistic simulations. In this work, we propose for sparse Gaussian process regression (GPR) type MLIPs a stochastic uncertainty measure akin to the query-by-committee approach often used in conjunction with neural network based MLIPs. The uncertainty measure is coined ‘label noise’ ensemble uncertainty as it emerges from adding noise to the energy labels in the training data. We find that this method of calculating an ensemble uncertainty is as well calibrated as the one obtained from the closed-form expression for the posterior variance when the sparse GPR is treated as a projected process. Comparing the two methods, our proposed ensemble uncertainty is, however, faster to evaluate than the closed-form expression. Finally, we demonstrate that the proposed uncertainty measure acts better to support a Bayesian search for optimal structure of Au 20 clusters. Estimation ; Regression ; Statistics ; Kriging ; Econometrics ; Regression analysis ; Gaussian ; Gaussian process ; Computer science ; Mathematics ; Artificial intelligence ; Economics ; Physics Machine Learning in Materials Science ; Fault Detection and Control Systems ; Computational Drug Discovery Methods
Authors: Pierluigi Del Nostro | Jesper Friis | Emanuele Ghedini | Gerhard Goldbeck | Oskar Holtz | Otello Maria Roscioni | Francesco Antonio Zaccarini | Daniele Toti
Source:  (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Elementary Multiperspective Material Ontology: Leveraging Perspectives via a Showcase of EMMO-Based Domain and Application Ontologies The effectiveness of semantic technologies in ensuring interoperability is often hindered by the preference for internally developed knowledge bases and the presence of diverse conceptual frameworks and implementation choices. Foundational, upper-level ontologies based on FOL and OWL2-DL address interoperability and provide a robust foundation for domain and application ontologies. They emphasize logical rigor and expressiveness, aligning with the idea of shared ontologies for knowledge diffusion and reuse. In scientific and industrial contexts, a framework that accommodates scientific pluralism is essential. The Elementary Multiperspective Material Ontology (EMMO) meets this need, offering a rigorous yet pluralistic representation of knowledge through the mereocausal theory, focusing on parthood (mereology) and causation. EMMO’s adaptable architecture includes discipline-specific modules, enabling the representation of items from multiple perspectives, such as viewing an image as both an’Object’ and’Data’. This paper presents EMMO’s perspectives, including the Reductionistic, Holistic, Persistence, Contrast, Structural and Semiotics perspectives. It then proceeds to showcase four recently-developed ontologies based on EMMO, one at the domain level (CHAMEO) and three at the application level (BTO, HPO and MAEO), taking advantage of EMMO’s perspectives and therefore demonstrating its representational capabilities and versatility. Ontology ; Computer science ; Domain (mathematical analysis) ; World Wide Web ; Ontology components ; Open Biomedical Ontologies ; Upper ontology ; Information retrieval ; Semantic Web ; Suggested Upper Merged Ontology ; Epistemology Machine Learning in Materials Science ; Semantic Web and Ontologies
Authors: Hongqi Wang | Raveendran N. Shiju
Source: Reaction Chemistry & Engineering (review, 2024-10-24)
Field: Chemistry — Inorganic Chemistry

A mini review on aromatization of <i>n</i>-alkanes The catalytic aromatization of n -alkanes is an important process in the chemical industry, especially for the production of value-added aromatics from the abundant and unreactive small alkanes. Aromatization ; Catalysis ; Chemistry ; Organic chemistry Zeolite Catalysis and Synthesis ; Catalytic Processes in Materials Science ; Inorganic and Organometallic Chemistry
Authors: Chen Wang | Yue Chen
Source: Physical review. B./Physical review. B (article, 2024-12-09)
Field: Materials Science — Materials Chemistry

Thermal switching across the ultrafast amorphous to crystalline transition in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>Sc</mml:mi><mml:mrow><mml:mn>0.2</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi>Sb</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:msub><mml:mi>Te</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:mrow></mml:math> Tuning thermal energy transport via solid-state structure manipulation is a challenge and of vital technological importance in energy-related devices. Herein, we provide microscopic insights into the correlations among atomic motions, anharmonic lattice dynamics, and thermal switch across the ultrafast amorphous-to-crystalline transition in a promising subnanosecond phase-change material (PCM) ${\mathrm{Sc}}_{\text{0.2}}{\mathrm{Sb}}_{\text{2}}{\mathrm{Te}}_{\text{3}}$. We show a reversible octahedron-heptagon reconfiguration related to the Sc-centered atomic motifs with a slight distortion during the phase transition, which is responsible for the exceptional recrystallization kinetics. Our combined density fluctuations analysis with classical hydrodynamic theory demonstrates a jump of thermal conductivity $(\ensuremath{\kappa})$ with the highest predicted switch ratio of 2.4 accompanied by the order-disorder transition, corresponding to the octahedral alignment of Te atoms with an increased long-range translational symmetry. Our unified lattice dynamical approach rationalizes the $\ensuremath{\kappa}$ evolution by linking Te-dominated anharmonic lattice dynamics and thermal switching, which is further benchmarked by the heat-flux-independent, nonequilibrium simulations. These results provide physical insights into PCM's complex atomic dynamics and thermal switch mechanism. Anharmonicity ; Amorphous solid ; Phase transition ; Materials science ; Lattice (music) ; Crystal structure ; Metastability ; Molecular dynamics ; Physics ; Crystallography ; Condensed matter physics ; Thermodynamics ; Chemistry ; Quantum mechanics Phase-change materials and chalcogenides ; Advanced Thermoelectric Materials and Devices ; Thermal properties of materials
Authors: Panagiotis Mougkogiannis | Anna Nikolaidou | Andrew Adamatzky
Source: ACS Omega (article, 2024-11-05)
Field: Materials Science — Polymers and Plastics

Proteinoids–Polyaniline Interaction with Stimulated Neurons on Living and Plastic Surfaces The integration of proteinoid-polyaniline (PANI) nanofibers with neuromorphic architectures shows potential for developing computer systems that are adaptable, energy-efficient, and have the capacity of tolerating faults. This work examines the capacity of proteinoid-PANI nanofibers to imitate different spiking patterns in stimulated Izhikevich neurons. The proteinoid-PANI nanofibers exhibit diverse spiking behaviors on different substrates, showcasing a broad range of control and programmability, as confirmed by experimental characterization and computational modeling. K-means clustering technique measures the extent and selectivity of the proteinoid-PANI spiking behavior in response to various stimuli and spiking patterns. The presence of strong positive correlations between membrane potential and time suggests that the system is capable of producing reliable and consistent electrical activity patterns. Proteinoid-PANI samples demonstrate enhanced stability and consistency in numerous spiking modes when compared to simulated input neurons. The results emphasize the capability of proteinoid-PANI nanofibers as a bioinspired substance for neuromorphic computing and open up possibilities for their incorporation into neuromorphic structures and bioinspired computer models. Polyaniline ; Materials science ; Biophysics ; Composite material ; Biology ; Polymer Conducting polymers and applications ; Neuroscience and Neural Engineering ; Advanced Memory and Neural Computing
Authors: Mert O. Astam | Samuël A.M. Weima | Ting‐Hsuan Lee | Amy van Bezouw | Danqing Liu
Source: Matter (article, 2024-03-29)
Field: Materials Science — Materials Chemistry

Photonic cognition of liquid crystal polymers for unlocking electrical locomotion The artificial replication of learning phenomena is an emerging domain with proven social impact. In this paper, we advance composite responsive material behavior toward learning by inducing memory-dependent functions through repeated exposure to a priming stimulus. For this, we integrate a photochromic spiropyran dopant into our liquid crystal network (LCN) to control its electrical actuation. UV light irradiation increases charge density by triggering the spiropyran-to-merocyanine zwitterion conversion, “gating” the permittivity of the LCN, and reducing the alternating electric field strength threshold required for actuation by up to 67.8% from its initial state. This UV-gating effect persists in the LCN as a memorized behavior. Resembling biological memory, the UV-gated memory is reversible and erased from the material over time. This is accelerated by up to 20% by irradiation with a green light “memory-wiping” agent. We envision that our work will contribute to the development of artificially intelligent materials for self-learning appliances and medical devices. Spiropyran ; Merocyanine ; Materials science ; Photochromism ; Gating ; Optoelectronics ; Nanotechnology ; Neuroscience ; Psychology Photochromic and Fluorescence Chemistry ; Photoreceptor and optogenetics research ; Advanced Materials and Mechanics
Authors: Beatriz Sequeira-Antunes | Hugo Alexandre Ferreira
Source: Chemosensors (review, 2024-11-27)
Field: Chemistry — Spectroscopy

µ-NMR Technology for Biomedical Applications: A Review Nuclear magnetic resonance (NMR) is a versatile method that non-invasively provides detailed insights into the atomic and molecular information of samples containing non-zero spin nuclei, facilitating observations of their structure, dynamics, and interactions. By miniaturizing NMR systems, micro-NMR (µ-NMR) devices overcome the limitations of traditional bulky NMR instruments, making them more portable, cost-effective, and suitable for a wide range of applications. As such, this review aims to provide a comprehensive overview of the recent advancements and potential applications of µ-NMR in the field of biomedicine. Beginning with an overview of the principles underlying NMR, this paper explains the fundamental concepts essential for understanding µ-NMR technology. It then delves into miniaturization techniques, detailing advancements in microcoils and probes and the development and integration with microfluidics, which have enhanced the sensitivity, portability, and versatility of µ-NMR devices. Ultimately, this review discusses the current biomedical applications of µ-NMR, including molecular imaging, metabolomics, biomarker detection, and point-of-care diagnosis, and highlights the potential of this technology to revolutionize precision medicine and healthcare. Despite the promising applications, challenges such as sensitivity, spectral resolution, and integration with other technologies are discussed, along with recent advances and innovations aimed at addressing these limitations. Engineering ethics ; Computer science ; Engineering Advanced NMR Techniques and Applications ; Advanced MRI Techniques and Applications ; NMR spectroscopy and applications
Authors: Ting Yang | Cuixia Yan | Shi Qiu | Yanghao Tang | Ao Du | Jinming Cai
Source: ACS Omega (article, 2024-07-18)
Field: Materials Science — Materials Chemistry

First-Principles Study of Penta-PtXY (X = Se, Te; Y = S, Te; X ≠ Y) Monolayer with Highly Anisotropic Electronic and Optical Properties Two-dimensional (2D) semiconducting materials with anisotropic physical properties have induced lively interest due to their application in the field of polarizing devices. Herein, we have designed a family of penta-PtXY (X = Se, Te; Y = S, Te; X ≠ Y) monolayers and predicted the electronic and optical properties based on the first-principles calculation. The results suggest that the penta-PtXY (X = Se, Te; Y = S, Te; X ≠ Y) monolayers are indirect-gap semiconductors with a medium bandgap of 2.29-2.66 eV. The penta-PtXY (X = Se, Te; Y = S, Te; X ≠ Y) monolayers own a remarkable mechanical anisotropy with a high Young's modulus anisotropic ratio (3.0). In addition, the penta-PtXY (X = Se, Te; Y = S, Te; X ≠ Y) monolayers exhibit a high anisotropy ratio of hole/electron mobility in the <i>x</i> and <i>y</i> directions (1.16-3.54). The results calculated by the G<sub>0</sub>W<sub>0</sub>+BSE method indicate that the single-layers also bear a salient optical anisotropy ratio (1.56-2.11). The integration of the anisotropic electronic, optical, and mechanical properties entitles penta-PtXY (X = Se, Te; Y = S, Te; X ≠ Y) monolayers as potential candidates in multifunctional polarized nanodevices. Monolayer ; Anisotropy ; Materials science ; Electronic structure ; Condensed matter physics ; Crystallography ; Chemistry ; Physics ; Optics ; Nanotechnology 2D Materials and Applications ; Chalcogenide Semiconductor Thin Films ; Perovskite Materials and Applications