jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Hafsa Jamshaid | Rajesh Mishra | Vijay Chandan | Shabnam Nazari | Muhammad Shoaib | Laurent Bizet | Tatiana Ivanova | Miroslav Müller | Petr Valášek
Source: Polymers (article, 2023-02-16)
Field: Materials Science — Polymers and Plastics

Mechanical and Thermo-Mechanical Performance of Natural Fiber-Based Single-Ply and 2-Ply Woven Prepregs This paper presents a study conducted on prepregs manufactured by a novel method for the impregnation of a thermoplastic matrix. Different composite prepregs based on polypropylene and reinforced with natural fibers (e.g., basalt and jute fibers) were developed. The mechanical and dynamic mechanical properties were investigated. DMA tests were conducted at 1 Hz frequency and properties such as storage modulus and damping (tan δ) were evaluated. The overall mechanical properties of the basalt fiber composites were found to be superior to that of the jute fiber-based samples. Thermo-gravimetric analysis (TG/DTG) of the composite samples showed that the thermal degradation temperatures of the basalt-based composites shifted to higher temperature regions compared to the PP or jute fiber composites. The addition of basalt fiber considerably improved the thermal stability of the composite samples. Microscopic images of the tensile fractured composite samples illustrated better fiber-matrix interfacial interaction due to the novel technology of prepregs. Single-ply and 2-ply prepregs showed significantly superior mechanical, thermal, and thermo-dynamical performance compared to the control sample (pure PP). 2-Ply composites demonstrated higher modulus, tensile strength, and storage modulus due to the higher fiber volume fraction. Basalt-based samples showed a minimum weight loss of about 57% up to 700 °C in contrast to 96.05% weight loss in the jute-based samples and 98.4% in the case of pure PP. The heat resistance index (T<sub>HRI</sub>) is more than twice for basalt compared to jute and PP. Furthermore, the superior thermal stability of basalt is reflected in its DSC curves, showing the highest endothermic peak. The technique of using the resin in the form of thermoplastic yarns offers cost effective and efficient alternatives for composite manufacturing. Composite material ; Materials science ; Basalt fiber ; Ultimate tensile strength ; Composite number ; Polypropylene ; Fiber ; Natural fiber ; Thermogravimetric analysis ; Thermal stability ; Dynamic mechanical analysis ; Biocomposite ; Volume fraction ; Polymer Natural Fiber Reinforced Composites ; Mechanical Behavior of Composites ; Additive Manufacturing and 3D Printing Technologies
Authors: Meng Zhang | Fenghua Zhao | Xue Zhang | Linda A. Brouwer | Janette K. Burgess | Martin C. Harmsen
Source: Materials Today Bio (article, 2023-10-24)
Field: Materials Science — Biomaterials

Fibroblasts alter the physical properties of dermal ECM-derived hydrogels to create a pro-angiogenic microenvironment This study aimed to investigate the impact of fibroblasts (MRC-5) on the extracellular matrix (ECM) microenvironment of endothelial cells (ECs) during the vascularization of skin-derived ECM hydrogel in vitro. Two types of ECs were studied: human dermal microvascular endothelial cells (HMEC) and human pulmonary microvascular endothelial cells (HPMEC). Results showed that the presence of MRC-5 fibroblasts increased the stiffness of the hydrogel and led to larger fiber diameters and increased porosity. Extensive collagen fiber remodeling occurred in the ECM hydrogel with MRC-5 fibroblasts. Additionally, higher levels of fibulin-1 and fibronectin were deposited in the hydrogel when co-cultured with MRC-5 fibroblasts. These findings suggest that MRC-5 fibroblasts play a role in modifying the ECM microenvironment, promoting vascularization through dynamic ECM remodeling. Extracellular matrix ; Fibronectin ; Fibulin ; Self-healing hydrogels ; Cell biology ; Chemistry ; Fibroblast ; Angiogenesis ; In vitro ; Cancer research ; Medicine ; Biology ; Biochemistry Electrospun Nanofibers in Biomedical Applications ; Wound Healing and Treatments ; Angiogenesis and VEGF in Cancer
Authors: Noah H. Somberg | João Medeiros‐Silva | Hyunil Jo | Jun Wang | William F. DeGrado | Mei Hong
Source: Protein Science (article, 2023-08-26)
Field: Chemistry — Spectroscopy

Hexamethylene amiloride binds the SARS‐CoV‐2 envelope protein at the protein–lipid interface The SARS-CoV-2 envelope (E) protein forms a five-helix bundle in lipid bilayers whose cation-conducting activity is associated with the inflammatory response and respiratory distress symptoms of COVID-19. E channel activity is inhibited by the drug 5-(N,N-hexamethylene) amiloride (HMA). However, the binding site of HMA in E has not been determined. Here we use solid-state NMR to measure distances between HMA and the E transmembrane domain (ETM) in lipid bilayers. <sup>13</sup> C, <sup>15</sup> N-labeled HMA is combined with fluorinated or <sup>13</sup> C-labeled ETM. Conversely, fluorinated HMA is combined with <sup>13</sup> C, <sup>15</sup> N-labeled ETM. These orthogonal isotopic labeling patterns allow us to conduct dipolar recoupling NMR experiments to determine the HMA binding stoichiometry to ETM as well as HMA-protein distances. We find that HMA binds ETM with a stoichiometry of one drug per pentamer. Unexpectedly, the bound HMA is not centrally located within the channel pore, but lies on the lipid-facing surface in the middle of the TM domain. This result suggests that HMA may inhibit the E channel activity by interfering with the gating function of an aromatic network. These distance data are obtained under much lower drug concentrations than in previous chemical shift perturbation data, which showed the largest perturbation for N-terminal residues. This difference suggests that HMA has higher affinity for the protein-lipid interface than the channel pore. These results give insight into the inhibition mechanism of HMA for SARS-CoV-2 E. Chemistry ; Lipid bilayer ; Transmembrane domain ; Crystallography ; Biophysics ; Biochemistry ; Membrane ; Biology Advanced NMR Techniques and Applications ; Electron Spin Resonance Studies ; Lipid Membrane Structure and Behavior
Authors: T. Mellor | A. Owens | Jonathan Tennyson | S. N. Yurchenko
Source: Monthly Notices of the Royal Astronomical Society (article, 2023-01-10)
Field: Chemistry — Spectroscopy

ExoMol line lists – XLVIII. High-temperature line list of thioformaldehyde (H2CS) ABSTRACT A comprehensive rotation–vibration (ro–vibrational) line list of thioformaldehyde (1H212C32S) that is applicable for elevated temperatures (${2000}{\, \mathrm{K}}$) is presented. The new MOTY line list covers the 0–8000 cm−1 range (wavelengths $\lambda \gt {1.3}{\, \mu \mathrm{m}})$ and contains around 43.5 billion transitions between 52.3 million states with rotational excitation up to J = 120. Line list calculations utilize a newly determined empirically refined potential energy surface (PES) – the most accurate H2CS PES to date – a previously published high-level ab initio dipole moment surface, and the use of an exact kinetic energy operator for solving the ro–vibrational Schrödinger equation. Post-processing of the MOTY line list is performed by replacing calculated energy levels with empirically derived values, vastly improving the accuracy of predicted line positions in certain spectral windows and making the line list suitable for high-resolution applications. The MOTY line list is available from the ExoMol data base at www.exomol.com and the CDS astronomical data base. Physics ; Line (geometry) ; Dipole ; Potential energy surface ; Ab initio ; Spectral line ; Potential energy ; Atomic physics ; Astrophysics ; Quantum mechanics ; Geometry Spectroscopy and Laser Applications ; Atmospheric Ozone and Climate ; Molecular Spectroscopy and Structure
Authors: Erin Garza | Vincent A. Bielinski | Josh L. Espinoza | Kona N. Orlandi | Josefa Rivera Alfaro | Tayah Bolt | Karen Beeri | Philip D. Weyman | Christopher L. Dupont
Source: ACS Synthetic Biology (article, 2023-10-19)
Field: Materials Science — Biomaterials

Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering While diatoms are promising synthetic biology platforms, there currently exists a limited number of validated genetic regulatory parts available for genetic engineering. The standard method for diatom transformation, nonspecific introduction of DNA into chromosomes via biolistic particle bombardment, is low throughput and suffers from clonal variability and epigenetic effects. Recent developments in diatom engineering have demonstrated that autonomously replicating episomal plasmids serve as stable expression platforms for diverse gene expression technologies. These plasmids are delivered via bacterial conjugation and, when combined with modular DNA assembly technologies, provide a flexibility and speed not possible with biolistic-mediated strain generation. In order to expand the current toolbox for plasmid-based engineering in the diatom <i>Phaeodactylum tricornutum</i>, a conjugation-based forward genetics screen for promoter discovery was developed, and application to a diatom genomic DNA library defined 252 <i>P. tricornutum</i> promoter elements. From this library, 40 promoter/terminator pairs were delivered via conjugation on episomal plasmids, characterized in vivo, and ranked across 4 orders of magnitude difference in reporter gene expression levels. Plasmid ; Phaeodactylum tricornutum ; Synthetic biology ; Biology ; Epigenetics ; Computational biology ; Transformation (genetics) ; Genome engineering ; Electroporation ; Genetics ; Gene ; Genome ; Diatom ; Genome editing ; Botany Diatoms and Algae Research ; Protist diversity and phylogeny ; Advanced biosensing and bioanalysis techniques
Authors: Pratik Jagtap | Michael R. Hoopmann | Benjamin A. Neely | Antony Harvey | Lukas Käll | Yasset Pérez‐Riverol | Milky Abajorga | Julie A. Thomas | Susan T. Weintraub | Magnus Palmblad
Source: Journal of Biomolecular Techniques JBT (article, 2023-08-07)
Field: Chemistry — Spectroscopy

The Association of Biomolecular Resource FacilitiesProteome Informatics Research Group Study on Metaproteomics(iPRG-2020) Metaproteomics research using mass spectrometry data has emerged as a powerful strategy to understand the mechanisms underlying microbiome dynamics and the interaction of microbiomes with their immediate environment. Recent advances in sample preparation, data acquisition, and bioinformatics workflows have greatly contributed to progress in this field. In 2020, the Association of Biomolecular Research Facilities Proteome Informatics Research Group launched a collaborative study to assess the bioinformatics options available for metaproteomics research. The study was conducted in 2 phases. In the first phase, participants were provided with mass spectrometry data files and were asked to identify the taxonomic composition and relative taxa abundances in the samples without supplying any protein sequence databases. The most challenging question asked of the participants was to postulate the nature of any biological phenomena that may have taken place in the samples, such as interactions among taxonomic species. In the second phase, participants were provided a protein sequence database composed of the species present in the sample and were asked to answer the same set of questions as for phase 1. In this report, we summarize the data processing methods and tools used by participants, including database searching and software tools used for taxonomic and functional analysis. This study provides insights into the status of metaproteomics bioinformatics in participating laboratories and core facilities. Metaproteomics ; Workflow ; Health informatics tools ; Computer science ; Data science ; Informatics ; Proteome ; Sequence database ; Bioinformatics ; Metagenomics ; Data mining ; Computational biology ; Biology ; Database ; Engineering Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Genomics and Phylogenetic Studies
Authors: Taehyun Park | Eunsong Kim | Jiwon Sun | Minseon Kim | Eunhwa Hong | Kyoungmin Min
Source: Materials Today Communications (article, 2023-10-05)
Field: Materials Science — Materials Chemistry

Rapid discovery of promising materials via active learning with multi-objective optimization Bayesian optimization ; Generality ; Computer science ; Multi-objective optimization ; Selection (genetic algorithm) ; Process (computing) ; Task (project management) ; Sampling (signal processing) ; Active learning (machine learning) ; Machine learning ; Mathematical optimization ; Materials science ; Mathematics Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Machine Learning and Algorithms
Authors: Sergei Manzhos | Manabu Ihara
Source: The Journal of Chemical Physics (article, 2023-01-05)
Field: Materials Science — Materials Chemistry

The loss of the property of locality of the kernel in high-dimensional Gaussian process regression on the example of the fitting of molecular potential energy surfaces Kernel-based methods, including Gaussian process regression (GPR) and generally kernel ridge regression, have been finding increasing use in computational chemistry, including the fitting of potential energy surfaces and density functionals in high-dimensional feature spaces. Kernels of the Matern family, such as Gaussian-like kernels (basis functions), are often used which allow imparting to them the meaning of covariance functions and formulating GPR as an estimator of the mean of a Gaussian distribution. The notion of locality of the kernel is critical for this interpretation. It is also critical to the formulation of multi-zeta type basis functions widely used in computational chemistry. We show, on the example of fitting of molecular potential energy surfaces of increasing dimensionality, the practical disappearance of the property of locality of a Gaussian-like kernel in high dimensionality. We also formulate a multi-zeta approach to the kernel and show that it significantly improves the quality of regression in low dimensionality but loses any advantage in high dimensionality, which is attributed to the loss of the property of locality. Gaussian process ; Kriging ; Kernel (algebra) ; Curse of dimensionality ; Locality ; Gaussian function ; Mathematics ; Statistical physics ; Gaussian ; Covariance ; Dimensionality reduction ; Kernel embedding of distributions ; Kernel method ; Applied mathematics ; Artificial intelligence ; Computer science ; Computational chemistry ; Support vector machine ; Statistics ; Physics ; Chemistry ; Combinatorics Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Mass Spectrometry Techniques and Applications
Authors: Saeed Eilbeigi | Mohammadreza Tavakkolizadeh | Amir R. Masoodi
Source: Materials (article, 2023-08-19)
Field: Materials Science — Materials Chemistry

Enhancing Mechanical Behavior and Energy Dissipation in Fiber-Reinforced Polymers through Shape Memory Alloy Integration: A Numerical Study on SMA-FRP Composites under Cyclic Tensile Loading Conventional fiber-reinforced polymers (FRPs) have a relatively linear stress-strain behavior up to the failure point. Therefore, they show brittle behavior until the failure point. Shape memory alloys, in addition to having high ductility and good energy dissipation capability, are highly resistant to corrosion and show good performance against fatigue. Therefore, using the SMA fibers in the production of FRPs can be a suitable solution to solve the problem of the brittle behavior of conventional FRPs. SMA fibers can be integrated with a polymeric matrix with or without conventional fibers and create a new material called SMA-FRP. This study investigates the effect of using different volume fractions of conventional fibers (carbon, glass, and aramid) and SMA fibers (NiTi) in the super-elastic phase and the effect of the initial strain of SMA fibers on the behavior of SMA-FRP composites under cyclic tensile loading. Specimens are designed to reach a target elastic modulus and are modeled using OpenSees (v. 3.5.0) finite element software. Analyzing the results shows that in the SMA-FRP composites that are designed to reach a target elastic modulus, with an increase in the volume fraction of SMA fibers, the maximum stress, residual strain, and strain hardening ratio are reduced, and the ability to energy dissipation capability and residual stress increases. It was also observed that increasing the percentage of the initial strain of SMA fibers increases the maximum stress and energy dissipation capability and reduces the residual strain and yield stress. In the investigation of the effect of the type of conventional fibers used in the construction of composites, it was found that the use of fibers that have a larger failure strain increases the maximum stress and energy dissipation capability of the composite and reduces the strain hardening ratio. In addition, increasing the elastic modulus of conventional fibers increases the residual strain and residual stress of the composites. Materials science ; Composite material ; Shape-memory alloy ; Brittleness ; Dissipation ; Fibre-reinforced plastic ; SMA* ; Ductility (Earth science) ; Aramid ; Strain hardening exponent ; Ultimate tensile strength ; Fiber ; Creep Shape Memory Alloy Transformations ; Structural Behavior of Reinforced Concrete ; Masonry and Concrete Structural Analysis
Authors: Nicolas Bergmann | Nicolas G. Hörmann | Karsten Reuter
Source: Journal of Chemical Theory and Computation (article, 2023-12-01)
Field: Chemistry — Electrochemistry

Ab Initio-Based Modeling of Thermodynamic Cyclic Voltammograms: A Benchmark Study on Ag(100) in Bromide Solutions Experimental cyclic voltammograms (CVs) measured in the slow scan rate limit can be entirely described in terms of the thermodynamic equilibrium quantities of the electrified solid-liquid interface. They correspondingly serve as an important benchmark for the quality of first-principles calculations of interfacial thermodynamics. Here, we investigate the partially drastic approximations made presently in computationally efficient calculations for the well-defined showcase of an Ag(100) model electrode in Br-containing electrolytes, where the nontrivial part of the CV stems from the electrosorption of Br ions. We specifically study the entanglement of common approximations in the treatment of solvation and field effects, as well as in the way macroscopic averages of the two key quantities, namely, the potential-dependent adsorbate coverage and electrosorption valency, are derived from the first-principles energetics. We demonstrate that the combination of energetics obtained within an implicit solvation model and a perturbative second order account of capacitive double layer effects with a constant-potential grand-canonical Monte Carlo sampling of the adsorbate layer provides an accurate description of the experimental CV. However, our analysis also shows that error cancellation at lower levels of theory may equally lead to good descriptions even though key underlying physics such as the disorder-order transition of the Br adlayer at increasing coverages is inadequately treated. Solvation ; Thermodynamics ; Monte Carlo method ; Statistical physics ; Electrolyte ; Ab initio ; Ion ; Chemistry ; Benchmark (surveying) ; Grand canonical ensemble ; Limit (mathematics) ; Physics ; Materials science ; Computational chemistry ; Physical chemistry ; Electrode ; Quantum mechanics ; Mathematics Electrochemical Analysis and Applications ; Molecular Junctions and Nanostructures ; Electrocatalysts for Energy Conversion
Authors: Juan Ye | Hao Jin | Zhaoji Zu | Bing Yu | Hongping Xiang | Mingqiu Zhang
Source: Engineered Science (review, 2023-01-01)
Field: Materials Science — Polymers and Plastics

Dynamic crosslinked silicones and their composites: A review The introduction of diverse dynamic bonds into the polysiloxane crosslinked networks can form dynamic crosslinked silicones and their composites, which not only maintain the good physicochemical performance of polysiloxane but also exhibit novel healing ability and reprocessability.They have shown broad application prospects in smart coatings, sensors, and flexible devices.However, the trade-off between excellent dynamic behavior and high mechanical property is challenging their practical applications.To improve this situation, recent advances that highlight the molecular structure design, property modulation, and potential application of dynamic crosslinked silicones and their composites with self-healing and reprocessing abilities are reviewed herein.Firstly, self-healing silicones are discussed according to their dynamic crosslinked network that is transforming from a single dynamic bond to multiple dynamic bonds to optimize mechanical property and self-healing efficiency.Next, the recycling or reprocessing of dynamic crosslinked silicones is also reviewed in accordance with their reprocessing methods to meet special requirements from different fields.Then, dynamic crosslinked silicone composites are discussed in terms of kinds of nanofillers to further enhance properties and broaden functionalities.What is more, the promising prospects and facing challenges dynamic crosslinked silicones and their composites are also proposed to achieve an early realization of commercial applications. Materials science ; Silicone ; Self-healing ; Composite material ; Computer science Polymer composites and self-healing ; Advanced Sensor and Energy Harvesting Materials ; Silicone and Siloxane Chemistry
Authors: Simone Mathias | Marius Amerio-Cox | T. C. Jackson | David Douce | Ashley Sage | Peter Luke | Richard Sleeman | Carol Crean | Patrick Sears
Source: Journal of the American Society for Mass Spectrometry (article, 2023-12-12)
Field: Chemistry — Spectroscopy

Selectivity of Explosives Analysis with Ambient Ionization Single Quadrupole Mass Spectrometry: Implications for Trace Detection Ambient ionization (AI) is a rapidly growing field in mass spectrometry (MS). It allows for the direct analysis of samples without any sample preparation, making it a promising technique for the detection of explosives. Previous studies have shown that AI can be used to detect a variety of explosives, but the exact gas-phase reactions that occur during ionization are not fully understood. This is further complicated by differences in mass spectrometers and individual experimental set ups between researchers. This study investigated the gas-phase ion reactions of five different explosives using a variety of AI techniques coupled to a Waters QDa mass spectrometer to identify selective ions for explosive detection and identification based on the applied ambient ionization technique. The results showed that the choice of the ion source can have a significant impact on the number of ions observed. This can affect the sensitivity and selectivity of the data produced. The findings of this study provide new insights into the gas-phase ion reactions of explosives and could lead to the development of more sensitive and selective AI-based methods for their detection. Chemistry ; Mass spectrometry ; Explosive material ; DART ion source ; Chemical ionization ; Ambient ionization ; Ionization ; Ion-mobility spectrometry ; Analytical Chemistry (journal) ; Quadrupole mass analyzer ; Ion ; Ion source ; Chromatography ; Electron ionization ; Organic chemistry Mass Spectrometry Techniques and Applications ; Isotope Analysis in Ecology ; Advanced Chemical Sensor Technologies