jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Mohammad G. Al‐Thiabat | Fadi G. Saqallah | Amirah Mohd Gazzali | Noratiqah Mohtar | Beow Keat Yap | Yee Siew Choong | Habibah A. Wahab
Source: Molecules (article, 2021-02-18)
Field: Chemistry — Organic Chemistry

Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight Folate receptor alpha (FRα) is known as a biological marker for many cancers due to its overexpression in cancerous epithelial tissue. The folic acid (FA) binding affinity to the FRα active site provides a basis for designing more specific targets for FRα. Heterocyclic rings have been shown to interact with many receptors and are important to the metabolism and biological processes within the body. Nineteen FA analogs with substitution with various heterocyclic rings were designed to have higher affinity toward FRα. Molecular docking was used to study the binding affinity of designed analogs compared to FA, methotrexate (MTX), and pemetrexed (PTX). Out of 19 FA analogs, analogs with a tetrazole ring (FOL03) and benzothiophene ring (FOL08) showed the most negative binding energy and were able to interact with ASP81 and SER174 through hydrogen bonds and hydrophobic interactions with amino acids of the active site. Hence, 100 ns molecular dynamics (MD) simulations were carried out for FOL03, FOL08 compared to FA, MTX, and PTX. The root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of FOL03 and FOL08 showed an apparent convergence similar to that of FA, and both of them entered the binding pocket (active site) from the pteridine part, while the glutamic part was stuck at the FRα pocket entrance during the MD simulations. Molecular mechanics Poisson-Boltzmann surface accessible (MM-PBSA) and H-bond analysis revealed that FOL03 and FOL08 created more negative free binding and electrostatic energy compared to FA and PTX, and both formed stronger H-bond interactions with ASP81 than FA with excellent H-bond profiles that led them to become bound tightly in the pocket. In addition, pocket volume calculations showed that the volumes of active site for FOL03 and FOL08 inside the FRα pocket were smaller than the FA-FRα system, indicating strong interactions between the protein active site residues with these new FA analogs compared to FA during the MD simulations. Chemistry ; Hydrogen bond ; Stereochemistry ; Docking (animal) ; Molecular dynamics ; Binding site ; Pyrimidine ; Molecular mechanics ; Lipinski's rule of five ; In silico ; Computational chemistry ; Biochemistry ; Molecule ; Organic chemistry Click Chemistry and Applications ; Nuclear Receptors and Signaling ; Computational Drug Discovery Methods
Authors: Tereza Paterova | Michal Prauzek | Jaromír Konecny | Štěpán Ožana | Petr Zmij | Martin Stankuš | Dieter Weise | Alexander Pierer
Source: Sensors (article, 2021-12-03)
Field: Materials Science — Materials Chemistry

Environment-Monitoring IoT Devices Powered by a TEG Which Converts Thermal Flux between Air and Near-Surface Soil into Electrical Energy Energy harvesting has an essential role in the development of reliable devices for environmental wireless sensor networks (EWSN) in the Internet of Things (IoT), without considering the need to replace discharged batteries. Thermoelectric energy is a renewable energy source that can be exploited in order to efficiently charge a battery. The paper presents a simulation of an environment monitoring device powered by a thermoelectric generator (TEG) that harvests energy from the temperature difference between air and soil. The simulation represents a mathematical description of an EWSN, which consists of a sensor model powered by a DC/DC boost converter via a TEG and a load, which simulates data transmission, a control algorithm and data collection. The results section provides a detailed description of the harvested energy parameters and properties and their possibilities for use. The harvested energy allows supplying the load with an average power of 129.04 μW and maximum power of 752.27 μW. The first part of the results section examines the process of temperature differences and the daily amount of harvested energy. The second part of the results section provides a comprehensive analysis of various settings for the EWSN device's operational period and sleep consumption. The study investigates the device's number of operational cycles, quantity of energy used, discharge time, failures and overheads. Energy harvesting ; Thermoelectric generator ; Renewable energy ; Battery (electricity) ; Automotive engineering ; Energy (signal processing) ; Computer science ; Thermal energy ; Electrical engineering ; Power (physics) ; Electric potential energy ; Process (computing) ; Thermoelectric effect ; Environmental science ; Simulation ; Engineering Advanced Thermoelectric Materials and Devices ; Innovative Energy Harvesting Technologies ; Energy Harvesting in Wireless Networks
Authors: Yuxiang Ni | Sébastian Volz
Source: Journal of Applied Physics (article, 2021-11-15)
Field: Materials Science — Materials Chemistry

Evidence of phonon Anderson localization on the thermal properties of disordered atomic systems Localization is a well-known wave phenomenon that significantly impedes transport, as uncovered by a pioneering work of Anderson. The localization of thermal phonons based on the phonon wave nature is widely represented in disordered atomic systems. Compared with electron and photon localization, the observations of phonon localization are much rarer, owning to the broadband nature of phonon thermal transport. In this Perspective, we summarize the experimental and theoretical evidences of phonon Anderson localization in disordered atomic systems from the aspects of vibrational spectroscopy, thermal conductivity measurement, phonon transmission, phonon wave packet, phonon participation ratio, and energy distribution. Phonon ; Anderson localization ; Condensed matter physics ; Thermal conductivity ; Physics ; Materials science ; Quantum mechanics Thermal properties of materials ; Thermography and Photoacoustic Techniques ; Thermal Radiation and Cooling Technologies
Authors: Minh Anh Luong | N. Cherkashin | Béatrice Pécassou | C. Sabbione | Frédéric Mazen | A. Claverie
Source: Nanomaterials (article, 2021-06-30)
Field: Materials Science — Materials Chemistry

Effect of Nitrogen Doping on the Crystallization Kinetics of Ge2Sb2Te5 Among the phase change materials, Ge<sub>2</sub>Sb<sub>2</sub>Te<sub>5</sub> (GST-225) is the most studied and is already integrated into many devices. N doping is known to significantly improve some key characteristics such as the thermal stability of materials and the resistance drift of devices. However, the origin, at the atomic scale, of these alterations is rather elusive. The most important issue is to understand how N doping affects the crystallization characteristics, mechanisms and kinetics, of GST-225. Here, we report the results of a combination of in situ and ex situ transmission electron microscopy (TEM) investigations carried out on specifically designed samples to evidence the influence of N concentration on the crystallization kinetics and resulting morphology of the alloy. Beyond the known shift of the crystallization temperature and the observation of smaller grains, we show that N renders the crystallization process more "nucleation dominated" and ascribe this characteristic to the increased viscosity of the amorphous state. This increased viscosity is linked to the mechanical rigidity and the reduced diffusivity resulting from the formation of Ge-N bonds in the amorphous phase. During thermal annealing, N hampers the coalescence of the crystalline grains and the cubic to hexagonal transition. Making use of AbStrain, a recently invented TEM-based technique, we evidence that the nanocrystals formed from the crystallization of N-doped amorphous GST-225 are under tension, which suggests that N is inserted in the lattice and explains why it is not found at grain boundaries. Globally, all these results demonstrate that the origin of the effect of N on the crystallization of GST-225 is not attributed to the formation of a secondary phase such as a nitride, but to the ability of N to bind to Ge in the amorphous and crystalline phases and to unbind and rebind with Ge along the diffusion path of this atomic species during annealing. Crystallization ; Materials science ; Nucleation ; Amorphous solid ; Annealing (glass) ; Chemical engineering ; Doping ; Crystallography ; Nanocrystal ; Kinetics ; Chemical physics ; Transmission electron microscopy ; Nanotechnology ; Thermodynamics ; Chemistry ; Composite material ; Optoelectronics Phase-change materials and chalcogenides ; Nonlinear Optical Materials Studies ; Chalcogenide Semiconductor Thin Films
Authors: Pavlo Maruschak | Roman Vorobel | О. Z. Student | Iryna Ivasenko | H. V. Krechkovska | Olena Berehulyak | Teodor Mandziy | L. M. Svirs’ka | Olegas Prentkovskis
Source: Metals (article, 2021-11-04)
Field: Materials Science — Materials Chemistry

Estimation of Fatigue Crack Growth Rate in Heat-Resistant Steel by Processing of Digital Images of Fracture Surfaces The micro- and macroscopic fatigue crack growth (FCG) rates of a wide class of structural materials were analyzed and it was concluded that both rates coincide either during high-temperature tests or at high stress intensity factor (SIF) values. Their coincidence requires a high level of cyclic deformation of the metal along the entire crack front as a necessary condition for the formation of fatigue striations (FS). Based on the analysis of digital fractographic images of the fatigue fracture surfaces, a method for the quantitative assessment of the spacing of FS has been developed. The method includes the detection of FS by binarization of the image based on the principle of local minima, rotation of the highlighted fragments of the image using the Hough transform, and the calculation of the distances between continuous lines. The method was tested on 34KhN3M steel in the initial state and after long-term operation (~3 × 105 h) in the rotor disk of a steam turbine at a thermal power plant (TPP). Good agreement was confirmed between FCG rates (both macro and microscopic, determined manually or using digital imaging techniques) at high SIF ranges and their noticeable discrepancy at low SIF ranges. Possible reasons for the discrepancy between the micro- and macroscopic FCG rates at low values of the SIF are analyzed. It has also been noted that FS is easier to detect on the fracture surface of degraded steel. Hydrogen embrittlement of steel during operation promotes secondary cracking along the FS, making them easier to detect and quantify. It is shown that the invariable value of the microscopic FCG rate at a low SIF range in the operated steel is lower than observable for the steel in the initial state. Secondary cracking of the operated steel may have contributed to the formation of a typical FS pattern along the entire crack front at a lower FCG rate than in unoperated steel. Materials science ; Fracture (geology) ; Paris' law ; Stress intensity factor ; Cracking ; Digital image ; Fractography ; Steam turbine ; Fracture mechanics ; Composite material ; Structural engineering ; Metallurgy ; Image processing ; Mechanical engineering ; Computer science ; Crack closure ; Engineering ; Image (mathematics) Material Properties and Failure Mechanisms ; Fatigue and fracture mechanics ; Non-Destructive Testing Techniques
Authors: Sergiana dos Passos Ramos | Michele Amendoeira Giaconia | Marcelo Assis | Paula C. Jimenez | Tatiana Martelli Mazzo | E. Longo | Veridiana Vera de Rosso | Anna Rafaela Cavalcante Braga
Source: Molecules (article, 2021-02-24)
Field: Materials Science — Biomaterials

Uniaxial and Coaxial Electrospinning for Tailoring Jussara Pulp Nanofibers Jussara pulp (<i>Euterpe edulis</i> Mart.) is rich in bioactive compounds known to be protective mediators against several diseases. In this context, nevertheless, anthocyanins, the most abundant natural pigment in jussara, are sensitive to temperature, pH, oxygen, and light conditions, leading to instability during food storage or digestion, and, thus jeopardizing the antioxidant proprieties retained by these flavonoids and limiting industrial application of the pulp. The production of nanostructures, from synthetic and natural polymers, containing natural matrices rich in bioactive compounds, has been widely studied, providing satisfactory results in the conservation and maintenance of the stability of these compounds. The current work aimed to compare uniaxial and coaxial electrospinning operation modes to produce core-shell jussara pulp nanofibers (NFs). Additionally, the parameters employed in the electrospinning processes were optimize using response surface methodology in an attempt to solve stability issues for the bioactive compounds. The best experimental conditions provided NFs with diameters ranging between 110.0 ± 47 and 121.1 ± 54 nm. Moreover, the coaxial setup improved jussara pulp NF formation, while further allowing greater integrity of NFs structures. Electrospinning ; Nanofiber ; Pulp (tooth) ; Materials science ; Coaxial ; Limiting ; Polymer ; Chemical engineering ; Pulp and paper industry ; Composite material ; Nanotechnology ; Computer science Electrospun Nanofibers in Biomedical Applications ; Nanocomposite Films for Food Packaging ; Advanced Cellulose Research Studies
Authors: Juami H. M. van Gils | Dea Gogishvili | Jan van Eck | Robbin Bouwmeester | Erik van Dijk | Sanne Abeln
Source: Centrum Wiskunde & Informatica (CWI), the national research institute for mathematics and computer science in the Netherlands (article, 2021-07-25)
Field: Chemistry — Spectroscopy

Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some 'sticky' hydrophobic residues to the solvent. These residues can play an important functional role, for example in protein-protein and membrane interactions. Here, we investigate how hydrophobic protein surfaces are by providing three measures for surface hydrophobicity: the total hydrophobic surface area, the relative hydrophobic surface area, and - using our MolPatch method - the largest hydrophobic patch. Secondly, we analyse how difficult it is to predict these measures from sequence: by adapting solvent accessibility predictions from NetSurfP2.0, we obtain well-performing prediction methods for the THSA and RHSA, while predicting LHP is more difficult. Finally, we analyse implications of exposed hydrophobic surfaces: we show that hydrophobic proteins typically have low expression, suggesting cells avoid an overabundance of sticky proteins. Hydrophobic effect ; Folding (DSP implementation) ; Proteome ; Lattice protein ; Chemistry ; Protein folding ; Biophysics ; Biochemistry ; Biology Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Protein Structure and Dynamics
Authors: B. Seychell | Tobias Beck
Source: Beilstein Journal of Organic Chemistry (review, 2021-01-04)
Field: Materials Science — Materials Chemistry

Molecular basis for protein–protein interactions This minireview provides an overview on the current knowledge of protein-protein interactions, common characterisation methods to characterise them, and their role in protein complex formation with some examples. A deep understanding of protein-protein interactions and their molecular interactions is important for a number of applications, including drug design. Protein-protein interactions and their discovery are thus an interesting avenue for understanding how protein complexes, which make up the majority of proteins, work. Chemistry ; Protein–protein interaction ; Computational biology ; Drug discovery ; Protein chemistry ; Biochemistry ; Biology Enzyme Structure and Function ; Photosynthetic Processes and Mechanisms ; Protein Structure and Dynamics
Authors: Karim Louca | Hamidreza Abdolvand | Charles Mareau | Marta Majkut | Jonathan P. Wright
Source: Communications Materials (article, 2021-01-13)
Field: Materials Science — Biomaterials

Formation and annihilation of stressed deformation twins in magnesium Abstract The mechanical response of polycrystalline materials to an externally applied load and their in-service performance depend on the local load partitioning among the constituent crystals. In hexagonal close-packed polycrystals such load partitioning is significantly affected by deformation twinning. Here we report in-situ compression-tension experiments conducted on magnesium specimens to measure the evolution of grain resolved tensorial stresses and formation and annihilation of twins. More than 13000 grains and 1300 twin-parent pairs are studied individually using three-dimensional synchrotron X-ray diffraction. It is shown that at the early stages of plasticity, the axial stress in twins is higher than that of parents, yet twins relax with further loading. While a sign reversal is observed for the resolved shear stress (RSS) acting on the twin habit plane in the parent, the sign of RSS within the majority of twins stays unchanged until twin annihilation during the load reversal. The variations of measured average stresses across parents and twins are also investigated. Crystal twinning ; Materials science ; Crystallite ; Annihilation ; Diffraction ; Deformation (meteorology) ; Plasticity ; Tension (geology) ; Condensed matter physics ; Composite material ; Crystallography ; Metallurgy ; Compression (physics) ; Physics ; Chemistry ; Optics ; Microstructure Magnesium Alloys: Properties and Applications ; Aluminum Alloys Composites Properties ; Microstructure and mechanical properties
Authors: Magdalena Jażdżewska | Dominika Beata Kwidzińska | Wiktor Seyda | Dariusz Fydrych | Andrzej Zieliński
Source: Materials (article, 2021-10-22)
Field: Materials Science — Materials Chemistry

Mechanical Properties and Residual Stress Measurements of Grade IV Titanium and Ti-6Al-4V and Ti-13Nb-13Zr Titanium Alloys after Laser Treatment Nowadays, surface engineering focuses on research into materials for medical applications. Titanium and its alloys are prominent, especially Ti-6Al-4V and Ti-13Nb-13Zr. Samples made of pure grade IV titanium and the titanium alloys Ti-6Al-4V and Ti-13Nb-13Zr were modified via laser treatment with laser beam frequency f = 25 Hz and laser beam power P = 1000 W during a laser pulse with duration t = 1 ms. Subsequently, to analyze the properties of the obtained surface layers, the following tests were performed: scanning electron microscopy, chemical and phase composition analysis, wetting angle tests and roughness tests. The assessment of the impact of the laser modification on the internal stresses of the investigated materials was carried out by comparing the values of the stresses of the laser-modified samples to those of the reference samples. The obtained results showed increased values of tensile stresses after laser modification: the highest value was found for the Ti-6Al-4V alloy at 6.7434 GPa and the lowest for pure grade IV titanium at 3.742 GPa. After laser and heat treatment, a reduction in the stress was observed, together with a significant increase in the hardness of the tested materials, with the highest value for Ti-6Al-4V alloy at 27.723 GPa. This can provide better abrasion resistance and lower long-term toxicity, both of which are desirable when using Ti-6Al-4V and Ti-13Nb-13Zr alloys for implant materials. Materials science ; Titanium ; Titanium alloy ; Laser ; Residual stress ; Ultimate tensile strength ; Alloy ; Scanning electron microscope ; Composite material ; Surface finish ; Microstructure ; Laser power scaling ; Wetting ; Metallurgy ; Optics Titanium Alloys Microstructure and Properties ; Additive Manufacturing Materials and Processes ; High Entropy Alloys Studies
Authors: Thomas E. Gartner | Salvatore Torquato | Roberto Car | Pablo G. Debenedetti
Source: Nature Communications (article, 2021-06-07)
Field: Materials Science — Materials Chemistry

Manifestations of metastable criticality in the long-range structure of model water glasses Much attention has been devoted to water's metastable phase behavior, including polyamorphism (multiple amorphous solid phases), and the hypothesized liquid-liquid transition and associated critical point. However, the possible relationship between these phenomena remains incompletely understood. Using molecular dynamics simulations of the realistic TIP4P/2005 model, we found a striking signature of the liquid-liquid critical point in the structure of water glasses, manifested as a pronounced increase in long-range density fluctuations at pressures proximate to the critical pressure. By contrast, these signatures were absent in glasses of two model systems that lack a critical point. We also characterized the departure from equilibrium upon vitrification via the non-equilibrium index; water-like systems exhibited a strong pressure dependence in this metric, whereas simple liquids did not. These results reflect a surprising relationship between the metastable equilibrium phenomenon of liquid-liquid criticality and the non-equilibrium structure of glassy water, with implications for our understanding of water phase behavior and glass physics. Our calculations suggest a possible experimental route to probing the existence of the liquid-liquid transition in water and other fluids. Metastability ; Polyamorphism ; Criticality ; Critical point (mathematics) ; Phase transition ; Amorphous solid ; Phase (matter) ; Molecular dynamics Material Dynamics and Properties ; Advanced Physical and Chemical Molecular Interactions ; Pickering emulsions and particle stabilization
Authors: Mousalreza Faramarzi Palangar | Uzma Amin | Hanieh Bakhshayesh | Ghulam Ahmad | Ahmed Abu‐Siada | Mohammad Mirzaie
Source: IEEE Transactions on Instrumentation and Measurement (article, 2021-01-01)
Field: Materials Science — Materials Chemistry

Identification of Composite Insulator Criticality Based on a New Leakage Current Diagnostic Index In this article, a new method is proposed to identify the health condition of composite insulators through investigating the leakage current (LC) along with the electric potential (EP) and electric field stress (EFS) profiles. In this regard, variations of the LC harmonics and the distribution profiles of the EP and EFS are investigated through a series of experimental and simulation analyses conducted on composite insulators under various environmental and pollution conditions. Fast Fourier transform (FFT) and a COMSOL-multiphysics environment are utilized to analyze this variation. The results reveal a strong correlation between the LC harmonics and the insulator health condition. A new diagnostic criticality index based on the third to the fifth harmonic ratios of the insulator LC is proposed to quantify the composite insulator criticality and predict the likelihood of flashover occurrence. The EP and EFS analyses can be used to provide a complementary diagnosis of the insulator's health state under severe pollution and humidity conditions. The proposed analysis enables the transmission line network operator to get an insight into the insulators' functional status, thus improving the network reliability through avoiding insulator failure and adopting a proper condition-based maintenance scheme. Insulator (electricity) ; Harmonics ; Transmission line ; Criticality ; Harmonic analysis ; Materials science ; Electronic engineering ; Fast Fourier transform ; Arc flash ; Acoustics ; Computer science ; Engineering ; Electrical engineering ; Optoelectronics ; Physics ; Voltage High voltage insulation and dielectric phenomena ; Electrical Fault Detection and Protection ; Power Transformer Diagnostics and Insulation