jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Manuel Molano‐Mazón | João Barbosa | Jordi Pastor‐Ciurana | Marta Fradera | Ru‐Yuan Zhang | Jérémy Forest | Jorge del Pozo Lérida | Jian Li | Christopher J. Cueva | Jaime de la Rocha | Devika Narain | Guangyu Robert Yang
Source:  (preprint, 2022-02-07)
Field: Materials Science — Materials Chemistry

NeuroGym: An open resource for developing and sharing neuroscience tasks Artificial Neural Networks (ANNs) trained on specific cognitive tasks have re-emerged as a useful tool to study the brain. However, ANNs would better aid cognitive neuroscience if a given network could be easily trained on a wide range of tasks for which neural recordings are available. Moreover, unintentional divergent implementations of cognitive tasks can produce variable results, which limits their interpretability. Towards this goal, we present NeuroGym, an open-source Python package that provides a large collection of customizable neuroscience tasks to test and compare network models. Building upon the OpenAI Gym toolbox, NeuroGym tasks (1) are written in a high-level flexible Python framework; (2) possess a shared interface tailored to common needs of neuroscience tasks that facilitates their design and usage; (3) support the training of ANNs using both Reinforcement and Supervised Learning techniques. The toolbox allows easy assembly of new tasks by modifying existing ones in a hierarchical and modular fashion. These design features make it straightforward to take a network designed for one task and train it on many other tasks. NeuroGym is a community-driven effort that contributes to a rapidly evolving open ecosystem of neural network development, data analysis, and model-data comparison. Computer science ; Python (programming language) ; Toolbox ; Modular design ; Interpretability ; Computational neuroscience ; Artificial neural network ; Reinforcement learning ; Artificial intelligence ; Human–computer interaction ; Machine learning ; Cognition ; Neuroscience ; Programming language Machine Learning in Materials Science ; Ferroelectric and Negative Capacitance Devices ; Cell Image Analysis Techniques
Authors: Konstantinos Konstantinou | Stephen R. Elliott | Jaakko Akola
Source: Journal of Materials Chemistry C (article, 2022-01-01)
Field: Materials Science — Materials Chemistry

Inherent electron and hole trapping in amorphous phase-change memory materials: Ge<sub>2</sub>Sb<sub>2</sub>Te<sub>5</sub> Charge trapping is energetically favourable for electronic states in the band gap of glassy phase-change memory materials. Intrinsic near-linear triatomic environments in defective-octahedral configurations can capture extra electrons and holes. Materials science ; Trapping ; Electron ; Amorphous solid ; Phase (matter) ; Octahedron ; Condensed matter physics ; Charge (physics) ; Band gap ; Atomic physics ; Molecular physics ; Crystallography ; Crystal structure ; Optoelectronics ; Physics Phase-change materials and chalcogenides ; Nonlinear Optical Materials Studies ; Chalcogenide Semiconductor Thin Films
Authors: James Torres | Alexis Flores‐Betancourt | Raphaël P. Hermann
Source: The Journal of the Acoustical Society of America (article, 2022-05-01)
Field: Materials Science — Materials Chemistry

<i>RUScal</i>: Software for the analysis of resonant ultrasound spectroscopy measurements Resonant ultrasound spectroscopy is used to nondestructively measure the elastic resonances of small solids to elucidate the material's elastic properties or other qualities like size, shape, or composition. Here, we introduce the software RUScal for the purpose of determining elastic properties by analyzing the eigenfrequencies of solid specimens with common shapes, such as rectangular parallelepipeds, cylinders (solid and hollow tube), ellipsoids, and octahedrons, as well as irregularly shaped ellipsoids that can be described analytically. All symmetry classes are supported, from isotropic to triclinic, along with the option to add or remove up to three orthogonal mirror planes as well as the ability to reorient the crystal axes with respect the sample edges via Euler angles. Additional features include tools to help find initial sets of elastic constants, including grid exploration and Monte Carlo methods, a tool to analyze frequencies as a function of sample length or crystal orientation, an error analysis tool to assess fit quality, and formatting of the input and output files for batch fitting, e.g., as a function of temperature. This software was validated with published resonant ultrasound spectroscopy data for various materials, shapes, and symmetries with noted improvements in calculation time compared to finite element methods. Resonant ultrasound spectroscopy ; Isotropy ; Monte Carlo method ; Ellipsoid ; Anisotropy ; Software ; Orientation (vector space) ; Materials science ; Hyperelastic material ; Finite element method ; Geometry ; Physics ; Mathematics ; Optics ; Computer science ; Composite material ; Elastic modulus ; Statistics Machine Learning in Materials Science ; Ultrasonics and Acoustic Wave Propagation ; Thermography and Photoacoustic Techniques
Authors: Shahrzad Zolfagharnassab | Abdul Rashid Mohamed Shariff | Reza Ehsani | Hawa Z. E. Jaafar | Ishak Aris
Source: Agriculture (article, 2022-10-26)
Field: Chemistry — Analytical Chemistry

Classification of Oil Palm Fresh Fruit Bunches Based on Their Maturity Using Thermal Imaging Technique The maturity of oil palm Fresh Fruit Bunches (FFB) is considered to be a significant factor that affects the profitability and salability of palm oil FFB. Typical methods of grading FFB consist of physical grading of fresh fruit, which is time-consuming and expensive, and the results are prone to human error. Therefore, this research attempts to formulate a thermal imaging method to indicate the precise maturity of oil palm fruits. A total of 297 oil palm FFBs were collected. The samples were divided into three groups: under-ripe, ripe, and over-ripe. Afterward, all the samples were scanned using a thermal imaging camera to calculate the real temperature of each sample. In order to normalize the measurement, the difference between the average temperature of the palm bunch and the ambient temperature (∆Temp) was considered as the main parameter. The results indicated that the mean ∆Temp of oil palm FFBs decreased consistently from under-ripe to over-ripe. The results of the ANOVA test demonstrated that the observed significance value was less than 0.05 in terms of ∆Temp, so there is a statistically significant difference in the means of all three maturity categories. It can be concluded that ∆Temp is a reliable index to classify the FFBs of oil palm. The classification analysis was conducted using the ∆Temp of the FFBs and its application as an index in Linear Discriminant Analysis (LDA), Mahalanobis Discriminant Analysis (MDA), Artificial Neural Network (ANN), and Kernel Nearest Neighbor (KNN). The highest degrees of overall accuracy (99.1% and 92.5%) were obtained through the ANN method. This study concludes that thermal images can be used as an index of oil palm maturity classification. Mathematics ; Linear discriminant analysis ; Palm oil ; Palm ; Horticulture ; Palm kernel ; Coefficient of determination ; Palm kernel oil ; Significant difference ; Food science ; Statistics ; Biology ; Physics Spectroscopy and Chemometric Analyses ; Coconut Research and Applications ; Oil Palm Production and Sustainability
Authors: Chia‐Ying Huang | Sylvain Aumonier | Sylvain Engilberge | Deniz Eriş | K.M. Smith | Filip Leonarski | J.A. Wojdyla | John H. Beale | Dominik Buntschu | A. Pauluhn | M.E. Sharpe | A. Metz | Vincent Oliéric | Meitian Wang
Source: Acta Crystallographica Section D Structural Biology (article, 2022-07-27)
Field: Materials Science — Materials Chemistry

Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography Continuous developments in cryogenic X-ray crystallography have provided most of our knowledge of 3D protein structures, which has recently been further augmented by revolutionary advances in cryoEM. However, a single structural conformation identified at cryogenic temperatures may introduce a fictitious structure as a result of cryogenic cooling artefacts, limiting the overview of inherent protein physiological dynamics, which play a critical role in the biological functions of proteins. Here, a room-temperature X-ray crystallographic method using temperature as a trigger to record movie-like structural snapshots has been developed. The method has been used to show how TL00150, a 175.15 Da fragment, undergoes binding-mode changes in endothiapepsin. A surprising fragment-binding discrepancy was observed between the cryo-cooled and physiological temperature structures, and multiple binding poses and their interplay with DMSO were captured. The observations here open up new promising prospects for structure determination and interpretation at physiological temperatures with implications for structure-based drug discovery. Limiting ; Crystallography ; Structural biology ; Biophysics ; Chemistry ; Protein structure ; Macromolecule ; Computational biology ; Nanotechnology ; Chemical physics ; Materials science ; Biology ; Biochemistry ; Engineering Enzyme Structure and Function ; Protein Structure and Dynamics ; ATP Synthase and ATPases Research
Authors: Hamed Almohammadi | Sayyed Ahmad Khadem | Massimo Bagnani | Alejandro D. Rey | Raffaele Mezzenga
Source: Nature Communications (article, 2022-05-19)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Shape and structural relaxation of colloidal tactoids Facile geometric-structural response of liquid crystalline colloids to external fields enables many technological advances. However, the relaxation mechanisms for liquid crystalline colloids under mobile boundaries remain still unexplored. Here, by combining experiments, numerical simulations and theory, we describe the shape and structural relaxation of colloidal liquid crystalline micro-droplets, called tactoids, where amyloid fibrils and cellulose nanocrystals are used as model systems. We show that tactoids shape relaxation bears a universal single exponential decay signature and derive an analytic expression to predict this out of equilibrium process, which is governed by liquid crystalline anisotropic and isotropic contributions. The tactoids structural relaxation shows fundamentally different paths, with first- and second-order exponential decays, depending on the existence of splay/bend/twist orientation structures in the ground state. Our findings offer a comprehensive understanding on dynamic confinement effects in liquid crystalline colloidal systems and may set unexplored directions in the development of novel responsive materials. Isotropy ; Relaxation (psychology) ; Chemical physics ; Materials science ; Colloid ; Anisotropy ; Liquid crystal ; Soft matter ; Physics ; Chemistry ; Optics ; Physical chemistry Liquid Crystal Research Advancements ; Pickering emulsions and particle stabilization ; Advanced Materials and Mechanics
Authors: Hangbo Zhou | Zhun‐Yong Ong | Gang Zhang | Yong‐Wei Zhang
Source: Nanoscale (review, 2022-01-01)
Field: Materials Science — Materials Chemistry

Computational predictions of quantum thermal transport across nanoscale interfaces Interfaces are essential elements in nanoscale devices and their properties can differ significantly from their bulk counterparts. Because interfaces often act as bottlenecks in heat dissipation, the prediction and control of the interfacial thermal conductance is critical to the design of nanoscale devices. In this review, we examine the recent advances in quantum interfacial thermal transport from a theoretical and computational perspective. We discuss in detail recent advances in the Atomistic Green's Function method which is an important tool for predicting interfacial thermal transport. We also discuss recent progress in the understanding of interfacial transport mechanisms, including the role of interfacial modes, the role of anharmonic phonon-phonon coupling, the role of electron-phonon interaction, and the ways to tune the interfacial thermal conductance. Finally, we give an overview of the challenges and opportunities in this research field. Nanoscopic scale ; Quantum ; Materials science ; Thermal ; Nanotechnology ; Engineering physics ; Physics ; Quantum mechanics ; Thermodynamics Thermal properties of materials ; Thermal Radiation and Cooling Technologies ; Thermography and Photoacoustic Techniques
Authors: Guoqiang Lan | Yu Wang | Jun‐Yu Ou
Source: Nanoscale Advances (article, 2022-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Optimization of metamaterials and metamaterial-microcavity based on deep neural networks Computational inverse-design and forward prediction approaches provide promising pathways for on-demand nanophotonics. Here, we use a deep-learning method to optimize the design of split-ring metamaterials and metamaterial-microcavities. Once the deep neural network is trained, it can predict the optical response of the split-ring metamaterial in a second which is much faster than conventional simulation methods. The pretrained neural network can also be used for the inverse design of split-ring metamaterials and metamaterial-microcavities. We use this method for the design of the metamaterial-microcavity with the absorptance peak at 1310 nm. Experimental results verified that the deep-learning method is a fast, robust, and accurate method for designing metamaterials with complex nanostructures. Metamaterial ; Absorptance ; Metamaterial antenna ; Optoelectronics ; Materials science ; Tunable metamaterials ; Split-ring resonator ; Computer science ; Optics ; Physics ; Reflectivity ; Omnidirectional antenna ; Telecommunications ; Antenna (radio) Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Sebastiano Cominelli | Davide Enrico Quadrelli | Carlo Sinigaglia | Francesco Braghin
Source: Proceedings of the Royal Society A Mathematical Physical and Engineering Sciences (article, 2022-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Design of arbitrarily shaped acoustic cloaks through partial differential equation-constrained optimization satisfying sonic-metamaterial design requirements We develop an optimization framework for the design of acoustic cloaks, with the aim of overcoming the limitations of usual transformation-based cloaks in terms of microstructure complexity and shape arbitrarity of the obstacle. This is achieved by recasting the acoustic cloaking design as a nonlinear optimal control problem constrained by a linear elliptic partial differential equation. In this setting, isotropic material properties’ distributions realizing the cloak take the form of control functions and a system of the first-order optimality conditions is derived accordingly. Such isotropic media can then be obtained in practice with simple hexagonal lattices of inclusions in water. For this reason, the optimization problem is directly formulated to consider suitable partitions of the control domain. Two types of inclusions are analysed, and long-wavelength homogenization is used to define the feasible set of material properties that is employed as a constraint in the optimization problem. In this manner, we link the stage of material properties optimization with that of microstructure design, aiming at finding the optimal implementable solution. The resulting cloak is numerically tested via coupled structural/acoustic simulations. As a further test benchmark, a concave target and the silhouette of a ship are considered other than the usual axisymmetric cloak. Homogenization (climate) ; Cloak ; Cloaking ; Metamaterial ; Isotropy ; Partial differential equation ; Optimization problem ; Mathematics ; Shape optimization ; Nonlinear system ; Topology optimization ; Mathematical optimization ; Computer science ; Mathematical analysis ; Finite element method ; Physics ; Optics Metamaterials and Metasurfaces Applications ; Acoustic Wave Phenomena Research ; Electromagnetic Scattering and Analysis
Authors: Teeradon Phlairaharn | Samuel Grégoire | Lukas R. Woltereck | Valdemaras Petrosius | Benjamin Furtwängler | Brian C. Searle | Erwin M. Schoof
Source: Journal of Proteome Research (article, 2022-10-26)
Field: Chemistry — Spectroscopy

High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps In recent years, the concept of cell heterogeneity in biology has gained increasing attention, concomitant with a push toward technologies capable of resolving such biological complexity at the molecular level. For single-cell proteomics using Mass Spectrometry (scMS) and low-input proteomics experiments, the sensitivity of an orbitrap mass analyzer can sometimes be limiting. Therefore, low-input proteomics and scMS could benefit from linear ion traps, which provide faster scanning speeds and higher sensitivity than an orbitrap mass analyzer, however at the cost of resolution. We optimized an acquisition method that combines the orbitrap and linear ion trap, as implemented on a tribrid instrument, while taking advantage of the high-field asymmetric waveform ion mobility spectrometry (FAIMS) pro interface, with a prime focus on low-input applications. First, we compared the performance of orbitrap- versus linear ion trap mass analyzers. Subsequently, we optimized critical method parameters for low-input measurement by data-independent acquisition on the linear ion trap mass analyzer. We conclude that linear ion traps mass analyzers combined with FAIMS and Whisper flow chromatography are well-tailored for low-input proteomics experiments, and can simultaneously increase the throughput and sensitivity of large-scale proteomics experiments where limited material is available, such as clinical samples and cellular subpopulations. Orbitrap ; Mass spectrometry ; Quadrupole ion trap ; Proteomics ; Ion trap ; Spectrum analyzer ; Chemistry ; Sensitivity (control systems) ; Computer science ; Analytical Chemistry (journal) ; Biological system ; Chromatography ; Electronic engineering Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Biosensors and Analytical Detection
Authors: João A. Rodrigues | Ana Martinho | Cátia Santa | Nuno Madeira | Manuel Coroa | Vítor Santos | Maria João Martins | Carlos N. Pato | A. Macedo | Bruno Manadas
Source: International Journal of Molecular Sciences (review, 2022-04-28)
Field: Chemistry — Spectroscopy

Systematic Review and Meta-Analysis of Mass Spectrometry Proteomics Applied to Human Peripheral Fluids to Assess Potential Biomarkers of Schizophrenia Mass spectrometry (MS)-based techniques can be a powerful tool to identify neuropsychiatric disorder biomarkers, improving prediction and diagnosis ability. Here, we evaluate the efficacy of MS proteomics applied to human peripheral fluids of schizophrenia (SCZ) patients to identify disease biomarkers and relevant networks of biological pathways. Following PRISMA guidelines, a search was performed for studies that used MS proteomics approaches to identify proteomic differences between SCZ patients and healthy control groups (PROSPERO database: CRD42021274183). Nineteen articles fulfilled the inclusion criteria, allowing the identification of 217 differentially expressed proteins. Gene ontology analysis identified lipid metabolism, complement and coagulation cascades, and immune response as the main enriched biological pathways. Meta-analysis results suggest the upregulation of FCN3 and downregulation of APO1, APOA2, APOC1, and APOC3 in SCZ patients. Despite the proven ability of MS proteomics to characterize SCZ, several confounding factors contribute to the heterogeneity of the findings. In the future, we encourage the scientific community to perform studies with more extensive sampling and validation cohorts, integrating omics with bioinformatics tools to provide additional comprehension of differentially expressed proteins. The produced information could harbor potential proteomic biomarkers of SCZ, contributing to individualized prognosis and stratification strategies, besides aiding in the differential diagnosis. Proteomics ; Computational biology ; Metabolomics ; Bioinformatics ; Schizophrenia (object-oriented programming) ; Omics ; Biomarker discovery ; Medicine ; Confounding ; Biology ; Internal medicine ; Psychiatry ; Biochemistry ; Gene Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Tryptophan and brain disorders
Authors: Tayaallen Ramachandran | Mohammad Rashed Iqbal Faruque | Mohammad Tariqul Islam | Mayeen Uddin Khandaker | K.S. Almugren
Source: Scientific Reports (article, 2022-06-29)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Development of diverse coding metamaterial structure for radar cross section reduction applications Despite their widespread use for performing advanced electromagnetic properties, metamaterial suffers from several restrictions in this technological era. Generally, technology affects the way individuals communicate, learn, think and plays an important role in society today. For this reason, there has been a surge of interest in a coding metamaterial field that possesses the ability to manipulate electromagnetic waves and realize different functionalities. This research work investigates circular-shaped coding metamaterial for microwave frequency applications through several analyses. First, the 1-bit coding metamaterial that is made up of only "0" and "1" elements with 0 and π phase responses by adopting two types of unit cells such as square-shaped Rogers RT6002 substrate material with and without metamaterial structure were analysed in this work. The proposed element '1' successfully manifests several more than 180○ phase responses at several frequency ranges, for instance, 7.35 to 9.48 GHz, 12.87 to 14.25 GHz and 17.49 to 18 GHz (C, X, and Ku-bands), respectively. Besides that, three types of coding sequences were proposed and the radar cross-section (RCS) reduction values of the designs were numerically calculated by utilising Computer Simulation Technology (CST) software. Meanwhile, the single-layered coding metamaterial with 6 lattices was compared with double and triple-layered metamaterial structures. At 2 GHz, the triple-layered structure exhibit reduced RCS values with near to - 30 dBm<sup>2</sup> for all coding sequences. Therefore, the transmission coefficient results of the triple-layered coding metamaterial sequences were numerically calculated. Several advanced coding metamaterial designs were constructed and the properties were discussed in terms of RCS values and scattering patterns. Meanwhile, the scattering and effective medium parameters of the unit cell metamaterial structure were also analysed in this work. In a nutshell, the 1-bit coding metamaterial in a controlled sequence can control electromagnetic waves and realize different functionalities. Metamaterial ; Coding (social sciences) ; Microwave ; Computer science ; Radar cross-section ; Radar ; Physics ; Metamaterial antenna ; Telecommunications ; Electronic engineering ; Optoelectronics ; Mathematics ; Engineering Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis