jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Xinyan Wang | Jichen Li | Lan Yang | Feiyang Chen | Yingze Wang | Junhan Chang | Junmin Chen | Linfeng Zhang | Kuang Yu
Source: ChemRxiv (preprint, 2022-11-23)
Field: Materials Science — Materials Chemistry

DMFF: An Open-Source AutomaticDifferentiable Platform for Molecular Force FieldDevelopment and Molecular DynamicsSimulation In the simulation of molecular systems, the underlying force field (FF) model plays an extremely important role, determining the reliability of the simulation. However, the quality of the state-of-the-art molecular force fields is still unsatisfactory in many cases, and the FF parameterization process largely relies on human experience, which is not scalable. To address this issue, we introduce DMFF, an open-source molecular FF development platform based on automatic differentiation technique. DMFF serves as a powerful tool for both top-down and bottom-up FF development. Using DMFF, both energies/forces and thermodynamic quantities such as ensemble averages and free energies can be evaluated in a differentiable way, realizing an automatic, yet highly flexible force field optimization workflow. DMFF also eases the evaluation of forces and virial tensors for complicated advance force fields, helping the fast validation of new models in molecular dynamics simulation. DMFF has been released as an opensource package under the LGPL-3.0 license and is available at https://github.com/deepmodeling/DMFF. Force field (fiction) ; Molecular dynamics ; Computer science ; Scalability ; Workflow ; Differentiable function ; Field (mathematics) ; Process (computing) ; Development (topology) ; Computational science ; Statistical physics ; Simulation ; Artificial intelligence ; Physics ; Chemistry ; Computational chemistry ; Mathematics ; Programming language Machine Learning in Materials Science ; Advanced Chemical Physics Studies ; Advanced Physical and Chemical Molecular Interactions
Authors: Svetoslav Nikolov | Julien Tranchida | Kushal Ramakrishna | Mani Lokamani | Attila Cangi | Mitchell Wood
Source: Journal of Materials Science (article, 2022-02-03)
Field: Materials Science — Materials Chemistry

Dissociating the phononic, magnetic and electronic contributions to thermal conductivity: a computational study in alpha-iron Abstract Computational tools to study thermodynamic properties of magnetic materials have, until recently, been limited to phenomenological modeling or to small domain sizes limiting our mechanistic understanding of thermal transport in ferromagnets. Herein, we study the interplay of phonon and magnetic spin contributions to the thermal conductivity in $$\alpha$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>α</mml:mi> </mml:math> -iron utilizing non-equilibrium molecular dynamics simulations. It was observed that the magnetic spin contribution to the total thermal conductivity exceeds lattice transport for temperatures up to two-thirds of the Curie temperature after which only strongly coupled magnon-phonon modes become active heat carriers. Characterizations of the phonon and magnon spectra give a detailed insight into the coupling between these heat carriers, and the temperature sensitivity of these coupled systems. Comparisons to both experiments and ab initio data support our inferred electronic thermal conductivity, supporting the coupled molecular dynamics/spin dynamics framework as a viable method to extend the predictive capability for magnetic material properties. Thermal conductivity ; Curie temperature ; Condensed matter physics ; Magnon ; Materials science ; Phonon ; Ferromagnetism ; Ab initio ; Thermodynamics ; Physics ; Quantum mechanics Thermal properties of materials ; Machine Learning in Materials Science ; Quantum and electron transport phenomena
Authors: Wei‐Hsin Chen | Wenting Wang | Qianqi Lin | David‐Benjamin Grys | Marika Niihori | Junyang Huang | Shu Hu | Bart de Nijs | Oren A. Scherman | Jeremy J. Baumberg
Source: ACS Nanoscience Au (article, 2022-12-24)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Plasmonic Sensing Assay for Long-Term Monitoring (PSALM) of Neurotransmitters in Urine A liquid-based surface-enhanced Raman spectroscopy assay termed PSALM is developed for the selective sensing of neurotransmitters (NTs) with a limit of detection below the physiological range of NT concentrations in urine. This assay is formed by quick and simple nanoparticle (NP) "mix-and-measure" protocols, in which Fe<sup>III</sup> bridges NTs and gold NPs inside the sensing hotspots. Detection limits of NTs from <i>PreNP</i> PSALM are significantly lower than those of <i>PostNP</i> PSALM, when urine is pretreated by affinity separation. Optimized PSALM enables the long-term monitoring of NT variation in urine in conventional settings for the first time, allowing the development of NTs as predictive or correlative biomarkers for clinical diagnosis. Detection limit ; Urine ; Colloidal gold ; Raman spectroscopy ; Surface-enhanced Raman spectroscopy ; Linear range ; Chromatography ; Chemistry ; Nanoparticle ; Nanotechnology ; Materials science ; Raman scattering ; Optics ; Physics ; Biochemistry Gold and Silver Nanoparticles Synthesis and Applications ; Spectroscopy Techniques in Biomedical and Chemical Research ; Advanced biosensing and bioanalysis techniques
Authors: Aurelia Li | Rocío Bueno-Pérez | David Fairen‐Jiménez
Source: Chemical Science (article, 2022-01-01)
Field: Chemistry — Spectroscopy

Identifying porous cage subsets in the Cambridge Structural Database using topological data analysis As rationally designable materials, the variety and number of synthesised metal-organic cages (MOCs) and organic cages (OCs) are expected to grow in the Cambridge Structural Database (CSD). In this regard, two of the most important questions are, which structures are already present in the CSD and how can they be identified? Here, we present a cage mining methodology based on topological data analysis and a combination of supervised and unsupervised learning that led to the derivation of - to the best of our knowledge - the first and only MOC dataset of 1839 structures and the largest experimental OC dataset of 7736 cages, as of March 2022. We illustrate the use of such datasets with a high-throughput screening of MOCs and OCs for xenon/krypton separation, important gases in multiple industries, including healthcare. Cage ; Porosity ; Topology (electrical circuits) ; Data mining ; Computer science ; Database ; Chemistry ; Mathematics ; Combinatorics ; Organic chemistry Molecular Sensors and Ion Detection ; Supramolecular Chemistry and Complexes ; Supramolecular Self-Assembly in Materials
Authors: Matthew R. Wilkinson | Uriel Martínez-Hernández | Laura Huggon | Chick C. Wilson | Bernardo Castro‐Dominguez
Source: CrystEngComm (article, 2022-01-01)
Field: Materials Science — Materials Chemistry

Predicting pharmaceutical crystal morphology using artificial intelligence We present the use of artificial intelligence to predict the morphology of crystallizing active pharmaceutical ingredients, first using publicly available data, and then using our own screening efforts to address the limitations we identified. Morphology (biology) ; Artificial intelligence ; Computer science ; Nanotechnology ; Materials science ; Geology Crystallization and Solubility Studies ; Computational Drug Discovery Methods ; Analytical Chemistry and Chromatography
Authors: Daniel López-Rodríguez | Bàrbara Micó‐Vicent | Jorge Jordán-Núñez | M. Moncho-Santonja | Eva Bou-Belda
Source: Dyes and Pigments (article, 2022-12-11)
Field: Materials Science — Materials Chemistry

Printing with hydrotalcite hybrid nanoclays and dispersed, reactive, direct dyes Hydrotalcite ; Thermogravimetric analysis ; Adsorption ; Textile ; Materials science ; Chemical engineering ; Screen printing ; Reactive dye ; Nanotechnology ; Chemistry ; Dyeing ; Composite material ; Organic chemistry ; Catalysis Layered Double Hydroxides Synthesis and Applications ; Phosphorus and nutrient management ; Mesoporous Materials and Catalysis
Authors: Xiaopeng Yang | Zhenyu Zhao | Chenhui Zhao | Yan Li | Attalla F. El‐kott | Mutasem Z. Bani‐Fwaz
Source: Journal of Oleo Science (article, 2022-01-01)
Field: Chemistry — Organic Chemistry

Anti-breast Adenocarcinoma and Anti-urease Anti-tyrosinase Properties of 5-Pentylresorcinol as Natural Compound with Molecular Docking Studies 5-Pentylresorcinol is a type of the group of resorcinol compounds that is resorcinol in that has hydrogen atom at position 5 is replaced by a pentyl group. It has a role as a lichen metabolite. This compound showed excellent to good inhibitory activities against studied these enzymes with IC<sub>50</sub> values of 65.96 µM for urease and 34.81 µM for tyrosinase. Standard compounds for enzymes had IC<sub>50</sub> values of 1.94±0.24 µM against urease and 84.36±5.17 µM against tyrosinase. The IC<sub>50</sub> of 5-pentylresorcinol against MCF7 cell line was 165.72 µg/mL; against Hs 578Bst cell line was 102.14 µg/mL; against Hs 319.T cell line was 12.34 µg/mL; and against UACC-3133 cell line was 73.07 µg/mL, respectively. The chemical activities of 5-pentylresorcinol against urease and tyrosinase were evaluated using the molecular modeling study. The anti-cancer activity of 5-pentylresorcinol was also investigated by treating the compound on the BRCT repeat region from the breast cancer-associated protein (BRCA1), and their interactions were assessed utilizing the molecular docking calculations. The results revealed the probable interactions and their characteristics at an atomic level. The docking scores of 5-pentylresorcinol against urease, tyrosinase, and BRCA1 are -3.073, -5.262, and -3.238 (kcal/mol), respectively. Tyrosinase ; Urease ; Chemistry ; Docking (animal) ; Resorcinol ; Enzyme ; IC50 ; Stereochemistry ; Lead compound ; Biochemistry ; Organic chemistry ; In vitro Synthesis and biological activity ; melanin and skin pigmentation ; Computational Drug Discovery Methods
Authors: Parmeshwar Lal Meena | Jitendra Kumar Saini | Ajay Kumar Surela | Krishna Poswal
Source: The holistic approach to environment (article, 2022-09-19)
Field: Materials Science — Polymers and Plastics

Kineticand equilibrium study of trinitrophenol adsorption onto polyaniline tea wastenanocomposite from aqueous medium The current study is focused on the synthesis of polyaniline-tea waste nanocomposite (PANI-TWC) material as a competent adsorbent for the effective removal of trinitrophenol (TNP) from aqueous medium. Batch experiments were performed to examine the influence of the various adsorption parameters such as pH, dose of adsorbents, contact time and initial concentration of TNP on the adsorption process. The kinetic data were fitted with pseudo-first and pseudo-second-order models, and the kinetic studies were well explained by the pseudo-second-order kinetic model. Moreover, the adsorption isotherm study for TNP adsorption from aqueous solutions on the PANI-TWC was performed by Langmuir and Freundlich isotherm models. The adsorption equilibrium data were best fitted to the Langmuir isotherm, which indicated that the adsorption surfaces are homogeneous and the adsorption occurred in monolayers. Adsorption ; Freundlich equation ; Polyaniline ; Aqueous solution ; Monolayer ; Langmuir ; Langmuir adsorption model ; Nanocomposite ; Chemistry ; Chemical engineering ; Materials science ; Organic chemistry ; Composite material ; Nanotechnology ; Polymer Conducting polymers and applications ; Nanomaterials for catalytic reactions ; Adsorption and biosorption for pollutant removal
Authors: Golnoush Zamiri | Arman Amani Babadi | Vishal Chaudhary | Arshid Numan | Mohammad Khalid | Rashmi Walvekar | Ajit Khosla
Source: Journal of The Electrochemical Society (article, 2022-12-21)
Field: Materials Science — Materials Chemistry

Infection Management of Virus-Diagnosing Biosensors Based on MXenes: An Overview The occurrence of sudden viral outbreaks, including (Covid-19, H1N1 flu, H5N1 flu) has globally challenged the existing medical facilities and raised critical concerns about saving affected lives, especially during pandemics. The detection of viral infections at an early stage using biosensors has been proven to be the most effective, economical, and rapid way to combat their outbreak and severity. However, state-of-the-art biosensors possess bottlenecks of long detection time, delayed stage detection, and sophisticated requirements increasing the cost and complexities of biosensing strategies. Recently, using two-dimensional MXenes as a sensing material for architecting biosensors has been touted as game-changing technology in diagnosing viral diseases. The unique surface chemistries with abundant functional terminals, excellent conductivity, tunable electric and optical attributes and high specific surface area have made MXenes an ideal material for architecting virus-diagnosing biosensors. There are numerous detecting modules in MXene-based virus-detecting biosensors based on the principle of detecting various biomolecules like viruses, enzymes, antibodies, proteins, and nucleic acid. This comprehensive review critically summarizes the state-of-the-art MXene-based virus-detecting biosensors, their limitations, potential solutions, and advanced intelligent prospects with the integration of internet-of-things, artificial intelligence, 5G communications, and cloud computing technologies. It will provide a fundamental structure for future research dedicated to intelligent and point-of-care virus detection biosensors. Biosensor ; MXenes ; Nanotechnology ; Computer science ; Point-of-care testing ; Biology ; Materials science MXene and MAX Phase Materials ; Advanced biosensing and bioanalysis techniques ; Energy Harvesting in Wireless Networks
Authors: Wenyu Fang | Yue Chen | Kuan Kuang | Mingkai Li
Source: Materials (article, 2022-09-27)
Field: Materials Science — Materials Chemistry

Excellent Thermoelectric Performance of 2D CuMN2 (M = Sb, Bi; N = S, Se) at Room Temperature 2D copper-based semiconductors generally possess low lattice thermal conductivity due to their strong anharmonic scattering and quantum confinement effect, making them promising candidate materials in the field of high-performance thermoelectric devices. In this work, we proposed four 2D copper-based materials, namely CuSbS<sub>2</sub>, CuSbSe<sub>2</sub>, CuBiS<sub>2</sub>, and CuBiSe<sub>2</sub>. Based on the framework of density functional theory and Boltzmann transport equation, we revealed that the monolayers possess high stability and narrow band gaps of 0.57~1.10 eV. Moreover, the high carrier mobilities (10<sup>2</sup>~10<sup>3</sup> cm<sup>2</sup>·V<sup>-1</sup>·s<sup>-1</sup>) of these monolayers lead to high conductivities (10<sup>6</sup>~10<sup>7</sup> Ω<sup>-1</sup>·m<sup>-1</sup>) and high-power factors (18.04~47.34 mW/mK<sup>2</sup>). Besides, as the strong phonon-phonon anharmonic scattering, the monolayers also show ultra-low lattice thermal conductivities of 0.23~3.30 W/mK at 300 K. As results show, all the monolayers for both p-type and n-type simultaneously show high thermoelectric figure of merit (<i>ZT</i>) of about 0.91~1.53 at room temperature. Materials science ; Thermoelectric effect ; Monolayer ; Condensed matter physics ; Phonon scattering ; Anharmonicity ; Thermoelectric materials ; Scattering ; Phonon ; Boltzmann equation ; Carrier scattering ; Semiconductor ; Copper ; Thermal conductivity ; Figure of merit ; Optoelectronics ; Nanotechnology ; Thermodynamics ; Physics ; Optics ; Metallurgy ; Composite material Advanced Thermoelectric Materials and Devices ; 2D Materials and Applications ; MXene and MAX Phase Materials
Authors: Segun D. Oladipo | Olayinka I. Akinpelu | Bernard Omondi
Source: Chemistry & Biodiversity (article, 2022-12-14)
Field: Chemistry — Organic Chemistry

Ligand‐Guided Investigation of a Series of Formamidine‐Based Thiuram Disulfides as Potential Dual‐Inhibitors of COX‐1and COX‐2 A series of thiuram disulfides 1-6 which had been previously synthesized and characterized,<sup>[1]</sup> were studied for their potential therapeutic properties. Target-fishing analyses through HitPick and SwissTarget prediction identified COX1 and COX2, which are essential biomolecules in cancer-related inflammations, as the possible targets for compounds 1 and 4 among all the compounds tested. These two proteins have enjoyed interest as targets for treating some neoplastic cancer types such as breast, colorectal, skin, pancreatic, haematological and head cancers. The inhibitory potency of 1 and 4 as lead anticancer drug candidates with dual-target ability against COX1 and COX2 was examined through molecular docking, molecular dynamics simulation and post-MD analyses such as binding energy calculation, RMSD, RMSF, and RoG. The two compounds had better docking scores and binding energies than the known inhibitors of COX1 and COX2. Insights from the RMSD, RMSF, and RoG suggested that both 1 and 4 showed observable influence on the structural stability of these targets throughout the simulation. The reported observations of the effects of 1 and 4 on the structures of COX1 and COX2 indicate their probable inhibitory properties against these target proteins and their potential as lead anticancer drug candidates. Chemistry ; Docking (animal) ; Molecular dynamics ; Stereochemistry ; Cancer research ; Ligand (biochemistry) ; Computational biology ; Pancreatic cancer ; Pharmacology ; Biochemistry ; Cancer ; Computational chemistry ; Receptor ; Internal medicine ; Medicine ; Biology Synthesis and biological activity ; Computational Drug Discovery Methods ; Synthesis and Biological Evaluation
Authors: Jovana Periša | Aleksandar Ćirić | Ivana Zeković | Vesna Đorđević | Milica Sekulić | Željka Antić | Miroslav D. Dramićanin
Source: Sensors (article, 2022-10-20)
Field: Materials Science — Materials Chemistry

Exploiting High-Energy Emissions of YAlO3:Dy3+ for Sensitivity Improvement of Ratiometric Luminescence Thermometry The sensitivity of luminescence thermometry is enhanced at high temperatures when using a three-level luminescence intensity ratio approach with Dy<sup>3+</sup>- activated yttrium aluminum perovskite. This material was synthesized via the Pechini method, and the structure was verified using X-ray diffraction analysis. The average crystallite size was calculated to be around 46 nm. The morphology was examined using scanning electron microscopy, which showed agglomerates composed of densely packed, elongated spherical particles, the majority of which were 80-100 nm in size. The temperature-dependent photoluminescence emission spectra (ex = 353 nm, 300-850 K) included Dy<sup>3+</sup> emissions in blue (458 nm), blue (483 nm), and violet (430 nm, T 600 K). Luminescence intensity ratio, the most utilized temperature readout method in luminescent thermometry, was used as the testing method: a) using the intensity ratio of Dy<sup>3+</sup> ions and <sup>4</sup>I<sub>15/2</sub>→<sup>6</sup>H<sub>15/2/</sub><sup>4</sup>F<sub>9/2</sub>→<sup>6</sup>H<sub>15/2</sub> transitions; and b) employing the third, higher energy <sup>4</sup>G<sub>11/2</sub> thermalized level, i.e., using the intensity ratio of <sup>4</sup>G<sub>11/2</sub>→<sup>6</sup>H<sub>15/2/</sub><sup>4</sup>F<sub>9/2</sub>→<sup>6</sup>H<sub>15/2</sub> transitions, thereby showing the relative sensitivities of 0.41% K<sup>-1</sup> and 0.86% K<sup>-1</sup> at 600 K, respectively. This more than doubles the increase in sensitivity and therefore demonstrates the method's usability at high temperatures, although the major limitation of the method is the chemical stability of the host material and the temperature at which the temperature quenching commences. Lastly, it must be noted that at 850 K, the emission intensities from the energetically higher levels were still increasing in YAP: Dy<sup>3+</sup>. Luminescence ; Analytical Chemistry (journal) ; Photoluminescence ; Materials science ; Yttrium ; Crystallite ; Scanning electron microscope ; Quenching (fluorescence) ; Optics ; Optoelectronics ; Fluorescence ; Chemistry ; Oxide ; Physics ; Composite material Luminescence Properties of Advanced Materials ; Glass properties and applications ; Optical properties and cooling technologies in crystalline materials
Authors: Yutian Zeng | Zhibin Xu | Jiaqing Guo | Xiantong Yu | Pengfei Zhao | Jun Song | Junle Qu | Yu Chen | Hao Li
Source: Molecules (article, 2022-08-12)
Field: Materials Science — Materials Chemistry

Bifunctional Nitrogen and Fluorine Co-Doped Carbon Dots for Selective Detection of Copper and Sulfide Ions in Real Water Samples Copper ions (Cu<sup>2+</sup>) and sulfur ions (S<sup>2-</sup>) are important elements widely used in industry. However, these ions have the risk of polluting the water environment. Therefore, rapid and quantitative detection methods for Cu<sup>2+</sup> and S<sup>2-</sup> are urgently required. Using 2,4-difluorobenzoic acid and L-lysine as precursors, nitrogen and fluorine co-doped dots (N, F-CDs) were synthesized in this study via a hydrothermal method. The aqueous N, F-CDs showed excellent stability, exhibited satisfactory selectivity and excellent anti-interference ability for Cu<sup>2+</sup> detection. The N, F-CDs, based on the redox reactions for selective and quantitative detection of Cu<sup>2+</sup>, showed a wide linear range (0-200 μM) with a detection limit (215 nM). By forming the N, F-CDs@Cu<sup>2+</sup> sensing platform and based on the high affinity of S<sup>2-</sup> to Cu<sup>2+</sup>, the N, F-CDs@Cu<sup>2+</sup> can specifically detect S<sup>2-</sup> over a linear range of 0-200 μM with a detection limit of 347 nM. In addition, these fluorescent probes achieved good results when used for Cu<sup>2+</sup> and S<sup>2-</sup> detection in environmental water samples, implying the good potential for applications. Bifunctional ; Copper ; Sulfide ; Carbon fibers ; Fluorine ; Inorganic chemistry ; Ion ; Chemistry ; Nitrogen ; Materials science ; Organic chemistry ; Catalysis Carbon and Quantum Dots Applications ; Mercury impact and mitigation studies ; Molecular Sensors and Ion Detection
Authors: Yael Gutiérrez | Shirly Espinoza | Martin Zahradník | Krishna Khakurel | Josef Resl | Christoph Cobet | Kurt Hingerl | Matthias Duwe | Peter Thiesen | María Losurdo
Source: Thin Solid Films (article, 2022-11-05)
Field: Materials Science — Materials Chemistry

Characterizing optical phase-change materials with spectroscopic ellipsometry and polarimetry This paper discusses the fundamentals, applications, potential and limitations of polarized light reflection techniques for the characterization of phase-change materials (PCMs). These techniques include spectroscopic ellipsometry, time-resolved ellipsometry and imaging ellipsometry as well as polarimetry. We explore the capabilities of spectroscopic ellipsometry in the determination of the extinction coefficient of PCMs and the capabilities of imaging ellipsometry to characterize PCMs. We show that ellipsometry is capable of more than the determination of thickness and optical properties, and it can be exploited to gain information about crystallization/amorphization kinetics and mapping anisotropies. Ellipsometry ; Polarimetry ; Materials science ; Characterization (materials science) ; Optics ; Anisotropy ; Thin film ; Nanotechnology ; Physics ; Scattering Phase-change materials and chalcogenides ; Liquid Crystal Research Advancements ; Optical Polarization and Ellipsometry
Authors: Anna N. Morozovska | Sergei V. Kalinin | Mykola E. Yelisieiev | Jonghee Yang | Mahshid Ahmadi | Eugene А. Eliseev | Dean R. Evans
Source: Acta Materialia (article, 2022-07-03)
Field: Materials Science — Materials Chemistry

Dynamic control of ferroionic states in ferroelectric nanoparticles Ferroelectricity ; Materials science ; Nanoparticle ; Dielectric ; Dipole ; Ionic bonding ; Condensed matter physics ; Relaxation (psychology) ; Chemical physics ; Antiferroelectricity ; Polar ; Nanotechnology ; Polarization (electrochemistry) ; Optoelectronics ; Ion ; Physical chemistry ; Physics ; Chemistry Ferroelectric and Piezoelectric Materials ; Perovskite Materials and Applications ; Multiferroics and related materials