jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Gloria Tabacchi | Ilaria Armenia | Giovanni Bernardini | Norberto Masciocchi | Antonietta Guagliardi | Ettore Fois
Source: ACS Applied Nano Materials (article, 2023-05-17)
Field: Materials Science — Biomaterials

Energy Transfer from Magnetic Iron Oxide Nanoparticles: Implications for Magnetic Hyperthermia Magnetic iron oxide nanoparticles (IONPs) have gained momentum in the field of biomedical applications. They can be remotely heated via alternating magnetic fields, and such heat can be transferred from the IONPs to the local environment. However, the microscopic mechanism of heat transfer is still debated. By X-ray total scattering experiments and first-principles simulations, we show how such heat transfer can occur. After establishing structural and microstructural properties of the maghemite phase of the IONPs, we built a maghemite model functionalized with aminoalkoxysilane, a molecule used to anchor (bio)molecules to oxide surfaces. By a linear response theory approach, we reveal that a resonance mechanism is responsible for the heat transfer from the IONPs to the surroundings. Heat transfer occurs not only via covalent linkages with the IONP but also through the solvent hydrogen-bond network. This result may pave the way to exploit the directional control of the heat flow from the IONPs to the anchored molecules-i.e., antibiotics, therapeutics, and enzymes-for their activation or release in a broader range of medical and industrial applications. Maghemite ; Iron oxide nanoparticles ; Heat transfer ; Magnetic nanoparticles ; Nanoparticle ; Materials science ; Iron oxide ; Chemical physics ; Nanotechnology ; Chemistry ; Thermodynamics ; Physics Nanoparticle-Based Drug Delivery ; Iron oxide chemistry and applications ; Characterization and Applications of Magnetic Nanoparticles
Authors: Aleksei Kabedev | Christel A. S. Bergström | Per Larsson
Source: Journal of Computer-Aided Molecular Design (article, 2023-12-16)
Field: Chemistry — Organic Chemistry

Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison Theoretical predictions of the solubilizing capacity of micelles and vesicles present in intestinal fluid are important for the development of new delivery techniques and bioavailability improvement. A balance between accuracy and computational cost is a key factor for an extensive study of numerous compounds in diverse environments. In this study, we aimed to determine an optimal molecular dynamics (MD) protocol to evaluate small-molecule interactions with micelles composed of bile salts and phospholipids. MD simulations were used to produce free energy profiles for three drug molecules (danazol, probucol, and prednisolone) and one surfactant molecule (sodium caprate) as a function of the distance from the colloid center of mass. To address the challenges associated with such tasks, we compared different simulation setups, including freely assembled colloids versus pre-organized spherical micelles, full free energy profiles versus only a few points of interest, and a coarse-grained model versus an all-atom model. Our findings demonstrate that combining these techniques is advantageous for achieving optimal performance and accuracy when evaluating the solubilization capacity of micelles. All-atom (AA) and coarse-grained (CG) umbrella sampling (US) simulations and point-wise free energy (FE) calculations were compared to their efficiency to computationally analyze the solubilization of active pharmaceutical ingredients in intestinal fluid colloids. Micelle ; Molecular dynamics ; Umbrella sampling ; Chemistry ; Dissipative particle dynamics ; Bioavailability ; Pulmonary surfactant ; Molecule ; Chemical physics ; Materials science ; Computational chemistry ; Organic chemistry ; Aqueous solution ; Polymer ; Bioinformatics Surfactants and Colloidal Systems ; Drug Solubulity and Delivery Systems ; Drug Transport and Resistance Mechanisms
Authors: Loredana Cristaldi | Parisa Esmaili | Giambattista Gruosso | Alessio La Bella | Massimo Mecella | Riccardo Scattolini | Ala Arman | Gian Antonio Susto | Letizia Tanca
Source:  (article, 2023-10-25)
Field: Chemistry — Analytical Chemistry

The MICS Project: A Data Science Pipeline for Industry 4.0 Applications The goal of the MICS (Made in Italy, Circular and Sustainable) project is to develop new models and techniques to support the entire pipeline for applying Data Science algorithms to data from industrial processes. Although many libraries and tools are already available to aid the analysis of data, we believe that each different application domain requires individual study to propose appropriate methods and tools that accommodate the specific peculiarities of its data. In this position paper, we discuss the following points by also outlining our case studies. Pipeline (software) ; Computer science ; Domain (mathematical analysis) ; Data science ; Data modeling ; Position (finance) ; Position paper ; Systems engineering ; Software engineering ; Data mining ; Engineering ; World Wide Web ; Programming language Spectroscopy and Chemometric Analyses ; Industrial Vision Systems and Defect Detection ; Digital Transformation in Industry
Authors: Krzysztof Dwiecki | Krzysztof Przybył | Dobrawa Dezor | Ewa Bąkowska | Sı́lvia M. Rocha
Source: Applied Sciences (article, 2023-08-18)
Field: Chemistry — Analytical Chemistry

Interactions of Oleanolic Acid, Apigenin, Rutin, Resveratrol and Ferulic Acid with Phosphatidylcholine Lipid Membranes—A Spectroscopic and Machine Learning Study Biologically active compounds present in the diet can interact with biological membranes (such as cell membranes), changing their properties. Their mutual interactions can influence their respective activities. In this study, we analyzed the interactions of oleanolic acid and phenolic compounds such as apigenin, rutin, resveratrol and ferulic acid with phosphatidylcholine membranes. Spectroscopic methods (fluorescence spectroscopy, dynamic light scattering) and machine learning were applied. The results of structural studies were compared with the antioxidant activity of the investigated substances in lipid membranes. In liposomes loaded with oleanolic acid, the pro-oxidant activity of resveratrol arises from changes in membrane structure, leading to an increased exposure of its hydrophilic region to external radicals. A similar mechanism may be involved in the pro-oxidant action of oleanolic acid. By contrast, apigenin, rutin and ferulic acid are present at the membrane surface. Their presence in this region protects the bilayer from radicals generated in the aqueous phase. Lower antioxidant activity observed in the case of ferulic aid is probably related to weaker interactions of this compound with the membrane, compared to the investigated flavonoids. Appropriate machine learning models for predicting oleanolic acid and phenolic compounds have been developed for the future application of intelligent predictive systems to optimizing manufacturing processes involving liposomes. The most effective regression model turned out to be the MLP 1:1-100-50-50-6:1, identifying resveratrol with a determination index of 0.83. Ferulic acid ; Oleanolic acid ; Chemistry ; Rutin ; Apigenin ; Membrane ; Resveratrol ; Liposome ; Antioxidant ; Biochemistry ; Flavonoid Spectroscopy and Chemometric Analyses ; Computational Drug Discovery Methods ; Essential Oils and Antimicrobial Activity
Authors: Ivan Timokhin | C. T. Chen | Wang, Ziwei | Qian Yang | Artem Mishchenko
Source: arXiv (Cornell University) (preprint, 2023-08-07)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Synthesis and characterisation of LK-99 Recently, two arXiv preprints (arXiv:2307.12008, arXiv:2307.12037) reported signatures of superconductivity above room temperature (SART) and at ambient pressure, striking worldwide experimental research efforts in replicating the results3-6, as well as theoretical attempts to explain the purported superconductivity7-11. The material of interest has chemical formula Pb$_{10-x}$Cu$_x$(PO$_4$)$_6$O, where $x \approx 1$, and was named by the authors as LK-99. It belongs to lead apatite family, and was synthesised from two precursors, lanarkite (PbSO$_4\cdot$PbO) and copper phosphide (Cu$_3$P). Here we performed a systematic study on LK-99, starting from solid-state synthesis, followed by characterisation and transport measurements. We did not observe any signatures of superconductivity in our samples of LK-99. Superconductivity ; Phosphide ; Solid-state ; Stoichiometry ; Physics ; Copper ; Mineralogy ; Materials science ; Analytical Chemistry (journal) ; Chemistry ; Condensed matter physics ; Physical chemistry ; Engineering physics ; Metallurgy ; Environmental chemistry ; Metal Crystal Structures and Properties ; Advanced Condensed Matter Physics ; Zeolite Catalysis and Synthesis
Authors: Shuai Yue | Xi Feng | You‐Sheng Cai | Salam A. Ibrahim | Ying Liu | Wen Huang
Source: Nutrients (article, 2023-10-13)
Field: Chemistry — Analytical Chemistry

Regulation of Tumor Apoptosis of Poriae cutis-Derived Lanostane Triterpenes by AKT/PI3K and MAPK Signaling Pathways In Vitro <i>Poria cocos</i> is traditionally used as both food and medicine. Triterpenoids in <i>Poria cocos</i> have a wide range of pharmacological activities, such as diuretic, sedative and tonic properties. In this study, the anti-tumor activities of poricoic acid A (PAA) and poricoic acid B (PAB), purified by high-speed counter-current chromatography, as well as their mechanisms and signaling pathways, were investigated using a HepG2 cell model. After treatment with PAA and PAB on HepG2 cells, the apoptosis was obviously increased (<i>p</i> < 0.05), and the cell cycle arrested in the G2/M phase. Studies showed that PAA and PAB can also inhibit the occurrence and development of tumor cells by stimulating the generation of ROS in tumor cells and inhibiting tumor migration and invasion. Combined Polymerase Chain Reaction and computer simulation of molecular docking were employed to explore the mechanism of tumor proliferation inhibition by PAA and PAB. By interfering with phosphatidylinositol-3-kinase/protein kinase B, Mitogen-activated protein kinases and p53 signaling pathways; and further affecting the expression of downstream caspases; matrix metalloproteinase family, cyclin-dependent kinase -cyclin, Intercellular adhesion molecules-1, Vascular Cell Adhesion Molecule-1 and Cyclooxygenase -2, may be responsible for their anti-tumor activity. Overall, the results suggested that PAA and PAB induced apoptosis, halted the cell cycle, and inhibited tumor migration and invasion through multi-pathway interactions, which may serve as a potential therapeutic agent against cancer. Protein kinase B ; Kinase ; PI3K/AKT/mTOR pathway ; Apoptosis ; Signal transduction ; Cell biology ; MAPK/ERK pathway ; Protein kinase A ; Biology ; Cell cycle ; Cell growth ; Chemistry ; Biochemistry ; Cancer research Chromatography in Natural Products ; Fungal Biology and Applications ; Phytochemical Studies and Bioactivities
Authors: Yuming Jiang | Rex Devasahayam Arokia Balaya | Dina Schuster | Benjamin A. Neely | Germán L. Rosano | Norbert Volkmar | Amanda Momenzadeh | Trenton M. Peters-Clarke | Susan Egbert | Simion Kreimer | Emma H. Doud | Oliver M. Crook | Amit Kumar Yadav | Muralidharan Vanuopadath | Martín L. Mayta | Anna G. Duboff | Nicholas M. Riley | Robert L. Moritz | Jesse G. Meyer
Source: PubMed (preprint, 2023-11-13)
Field: Chemistry — Spectroscopy

Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods to aid the novice and experienced researcher. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this work to serve as a basic resource for new practitioners in the field of shotgun or bottom-up proteomics. Proteomics ; Shotgun proteomics ; Proteome ; Bottom-up proteomics ; Identification (biology) ; Computational biology ; Mass spectrometry ; Quantitative proteomics ; Workflow ; Computer science ; Chemistry ; Bioinformatics ; Biology ; Tandem mass spectrometry ; Protein mass spectrometry ; Biochemistry ; Chromatography Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Andrey Ten | Claire A. West | Soojin Jeong | Elizabeth R. Hopper | Yi Wang | Baixu Zhu | Quentin M. Ramasse | Xingchen Ye | Emilie Ringe
Source: Nanoscale Advances (article, 2023-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Bimetallic copper palladium nanorods: plasmonic properties and palladium content effects Cu is an inexpensive alternative plasmonic metal with optical behaviour comparable to Au but with much poorer environmental stability. Alloying with a more stable metal can improve stability and add functionality, with potential effects on the plasmonic properties. Here we investigate the plasmonic behaviour of Cu nanorods and Cu-CuPd nanorods containing up to 46 mass percent Pd. Monochromated scanning transmission electron microscopy electron energy-loss spectroscopy first reveals the strong length dependence of multiple plasmonic modes in Cu nanorods, where the plasmon peaks redshift and narrow with increasing length. Next, we observe an increased damping (and increased linewidth) with increasing Pd content, accompanied by minimal frequency shift. These results are corroborated by and expanded upon with numerical simulations using the electron-driven discrete dipole approximation. This study indicates that adding Pd to nanostructures of Cu is a promising method to expand the scope of their plasmonic applications. Plasmon ; Nanorod ; Materials science ; Palladium ; Bimetallic strip ; Discrete dipole approximation ; Laser linewidth ; Nanotechnology ; Spectroscopy ; Electron energy loss spectroscopy ; Optoelectronics ; Transmission electron microscopy ; Chemical physics ; Metal ; Optics ; Dipole ; Chemistry ; Laser ; Physics ; Metallurgy Gold and Silver Nanoparticles Synthesis and Applications ; Nanomaterials for catalytic reactions ; Copper-based nanomaterials and applications
Authors: D. Steglich | Jacques Besson | Inken Reinke | Heike Helmholz | Monika Luczak | Vasil M. Garamus | Björn Wiese | Daniel Höche | Christian J. Cyron | Regine Willumeit‐Römer
Source: Journal of the mechanical behavior of biomedical materials/Journal of mechanical behavior of biomedical materials (article, 2023-06-01)
Field: Materials Science — Biomaterials

Strength and ductility loss of Magnesium-Gadolinium due to corrosion in physiological environment: Experiments and modeling We propose a computational framework to study the effect of corrosion on the mechanical strength of magnesium (Mg) samples. Our work is motivated by the need to predict the residual strength of biomedical Mg implants after a given period of degradation in a physiological environment. To model corrosion, a mass-diffusion type model is used that accounts for localised corrosion using Weibull statistics. The overall mass loss is prescribed (e.g., based on experimental data). The mechanical behaviour of the Mg samples is modeled by a state-of-the-art Cazacu-Plunkett-Barlat plasticity model with a coupled damage model. This allowed us to study how Mg degradation in immersed samples reduces the mechanical strength over time. We performed a large number of in vitro corrosion experiments and mechanical tests to validate our computational framework. Our framework could predict both the experimentally observed loss of mechanical strength and the ductility due to corrosion for both tension and compression tests. Corrosion ; Materials science ; Weibull distribution ; Ductility (Earth science) ; Magnesium ; Residual strength ; Metallurgy ; Diffusion ; Degradation (telecommunications) ; Composite material ; Computer science ; Creep ; Mathematics Magnesium Alloys: Properties and Applications ; Aluminum Alloys Composites Properties ; Corrosion Behavior and Inhibition
Authors: Bernadette Mohr | Diego van der Mast | Tristan Bereau
Source: Journal of Chemical Theory and Computation (article, 2023-07-03)
Field: Materials Science — Materials Chemistry

Condensed-Phase Molecular Representation to Link Structure and Thermodynamics in Molecular Dynamics Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an atomic representation originally developed for electronic properties: the Spectrum of London and Axilrod-Teller-Muto representation (SLATM). SLATM's expansion in one-, two-, and three-body interactions makes it amenable to probing structural ordering in molecular liquids. We show that such representation encodes enough critical information to permit the learning of thermodynamic properties via linear methods. We demonstrate our approach on the preferential insertion of small solute molecules toward cardiolipin membranes and monitor selectivity against a similar lipid. Our analysis reveals simple, interpretable relationships between two- and three-body interactions and selectivity, identifies key interactions to build optimal prototypical solutes, and charts a two-dimensional projection that displays clearly separated basins. The methodology is generally applicable to a variety of thermodynamic properties. Representation (politics) ; Molecular dynamics ; Statistical physics ; Computer science ; Chemical physics ; Biological system ; Chemistry ; Physics ; Computational chemistry ; Biology Machine Learning in Materials Science ; Protein Structure and Dynamics ; Spectroscopy and Quantum Chemical Studies
Authors: Mariko Takahashi | Harrison B. Chong | Siwen Zhang | Matthew J. Lazarov | Stefan Harry | Michelle Maynard | Ryan R. White | Heather E. Murrey | Brendan J. Hilbert | Jason R. Neil | Magdy Gohar | Maolin Ge | Junbing Zhang | Benedikt R. Dürr | Gregory V. Kryukov | Chih‐Chiang Tsou | Natasja Brooijmans | Aliyu Sidi Omar Alghali | Karla Rubio | Antonio Vilanueva | Drew Harrison | Ann-Sophie Koglin | Samuel Ojeda | Barbara Karakyriakou | Alexander Healy | Jonathan Assaad | Farah Makram | Inbal Rachman | Neha Khandelwal | Pei-Chieh Tien | George Popoola | Nicholas Chen | Kira Vordermark | Marianne Richter | Himani Patel | Tzu-yi Yang | Hanna Griesshaber | Tobias Hosp | Sanne van den Ouweland | Toshiro Hara | Lily Bussema | Rui Dong | Lei Shi | Martin Q. Rasmussen | Ana Carolina Martins Domingues | Aleigha Lawless | Jacy Fang | Satoshi Yoda | Linh Phuong Nguyen | Sarah Reeves | Farrah Nicole Wakefield | Adam Acker | Sarah E. Clark | Taronish D. Dubash | David E. Fisher | Shyamala Maheswaran | Daniel A. Haber | Genevieve M. Boland | Moshe Sade-Feldman | Russel Jenkins | Aaron N. Hata | Nabeel Bardeesy | Mario L. Suvà | Brent R. Martin | Brian B. Liau | Christopher J. Ott | Miguel N. Rivera | Michael S. Lawrence | Liron Bar‐Peled
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-10-23)
Field: Chemistry — Organic Chemistry

DrugMap: A quantitative pan-cancer analysis of cysteine ligandability Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors of a wide-range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed <i>DrugMap</i> , an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NFκB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NFκB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription factor activity. Cysteine ; Chemistry ; Biochemistry Click Chemistry and Applications ; Cancer, Lipids, and Metabolism ; Protein Degradation and Inhibitors
Authors: Lingyun Tang | Zhongquan Mao | Chutian Wang | Qi Fu | Chen Wang | Yichi Zhang | Jingyi Shen | Yuefeng Yin | Bin Shen | Dayong Tan | Qian Li | Yonggang Wang | Nikhil V. Medhekar | J. Wu | Huiqiu Yuan | Yanchun Li | Michael S. Fuhrer | Changxi Zheng
Source: Nature Communications (article, 2023-03-18)
Field: Materials Science — Materials Chemistry

Giant piezoresistivity in a van der Waals material induced by intralayer atomic motions The presence of the van der Waals gap in layered materials creates a wealth of intriguing phenomena different to their counterparts in conventional materials. For example, pressurization can generate a large anisotropic lattice shrinkage along the stacking orientation and/or a significant interlayer sliding, and many of the exotic pressure-dependent properties derive from these mechanisms. Here we report a giant piezoresistivity in pressurized β'-In<sub>2</sub>Se<sub>3</sub>. Upon compression, a six-orders-of-magnitude drop of electrical resistivity is obtained below 1.2 GPa in β'-In<sub>2</sub>Se<sub>3</sub> flakes, yielding a giant piezoresistive gauge π<sub>p</sub> of -5.33 GPa<sup>-1</sup>. Simultaneously, the sample undergoes a semiconductor-to-semimetal transition without a structural phase transition. Surprisingly, linear dichroism study and theoretical first principles modelling show that these phenomena arise not due to shrinkage or sliding at the van der Waals gap, but rather are dominated by the layer-dependent atomic motions inside the quintuple layer, mainly from the shifting of middle Se atoms to their high-symmetric location. The atomic motions link to both the band structure modulation and the in-plane ferroelectric dipoles. Our work not only provides a prominent piezoresistive material but also points out the importance of intralayer atomic motions beyond van der Waals gap. van der Waals force ; Condensed matter physics ; Materials science ; Stacking ; Piezoresistive effect ; Van der Waals radius ; Anisotropy ; Chemistry ; Physics ; Composite material ; Optics 2D Materials and Applications ; Advanced Thermoelectric Materials and Devices ; Acoustic Wave Resonator Technologies