jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yin Fan | Y. Xiang | Hui‐Shen Shen
Source: Nanotechnology Reviews (article, 2019-12-18)
Field: Materials Science — Materials Chemistry

Temperature-dependent negative Poisson’s ratio of monolayer graphene: Prediction from molecular dynamics simulations Abstract A temperature-dependent intrinsic property of monolayer graphene, the negative Poisson’s ratio (NPR), is investigated in the present study. The classical molecular dynamics (MD) method is employed and the Erhart-Albe hybrid potential, i.e . the combination of the reactive empirical bond order (REBO) and the Tersoff potentials, is used for the graphene sheet in the numerical simulation. In the simulation process, the graphene sheet is assumed to be free standing with in-plane periodical boundary condition and under an ambient temperature up to 1000 K. Our study shows that the graphene NPR is decreased with the increase of temperature. Besides, we also perform the simulation of the graphene negative temperature expansion coefficient (NTEC) as an indirect validation of the present MD model. The characteristics of the nonlinear variations for both the NPR and the NTEC of a pristine graphene sheet are investigated. Our MD results at low temperature (0.1 K) further prove the intrinsic and anisotropic property of NPR for graphene. Graphene ; Molecular dynamics ; Materials science ; Monolayer ; Nonlinear system ; Chemical physics ; Nanotechnology ; Computational chemistry ; Chemistry ; Physics ; Quantum mechanics Graphene research and applications ; Thermal properties of materials ; Fullerene Chemistry and Applications
Authors: Mohsen Mirzaei | Jochem Verrelst | Safar Marofi | Mozhgan Abbasi | Hossein Azadi
Source: Remote Sensing (article, 2019-11-20)
Field: Chemistry — Analytical Chemistry

Eco-Friendly Estimation of Heavy Metal Contents in Grapevine Foliage Using In-Field Hyperspectral Data and Multivariate Analysis Heavy metal monitoring in food-producing ecosystems can play an important role in human health safety. Since they are able to interfere with plants' physiochemical characteristics, which influence the optical properties of leaves, they can be measured by in-field spectroscopy. In this study, the predictive power of spectroscopic data is examined. Five treatments of heavy metal stress (Cu, Zn, Pb, Cr, and Cd) were applied to grapevine seedlings and hyperspectral data (350-2500 nm), and heavy metal contents were collected based on in-field and laboratory experiments. The partial least squares (PLS) method was used as a feature selection technique, and multiple linear regressions (MLR) and support vector machine (SVM) regression methods were applied for modelling purposes. Based on the PLS results, the wavelengths in the vicinity of 2431, 809, 489, and 616 nm; 2032, 883, 665, 564, 688, and 437 nm; 1865, 728, 692, 683, and 356 nm; 863, 2044, 415, 652, 713, and 1036 nm; and 1373, 631, 744, and 438 nm were found most sensitive for the estimation of Cu, Zn, Pb, Cr, and Cd contents in the grapevine leaves, respectively. Therefore, visible and red-edge regions were found most suitable for estimating heavy metal contents in the present study. Heavy metals played a significant role in reforming the spectral pattern of stressed grapevine compared to healthy samples, meaning that in the best structures of the SVM regression models, the concentrations of Cu, Zn, Pb, Cr, and Cd were estimated with R<sup>2</sup> rates of 0.56, 0.85, 0.71, 0.80, and 0.86 in the testing set, respectively. The results confirm the efficiency of in-field spectroscopy in estimating heavy metals content in grapevine foliage. Hyperspectral imaging ; Partial least squares regression ; Multivariate statistics ; Environmental science ; Support vector machine ; Metal ; Linear regression ; Heavy metals ; Environmental chemistry ; Chemistry ; Mathematics ; Materials science ; Remote sensing ; Computer science ; Statistics ; Geology ; Metallurgy ; Artificial intelligence Spectroscopy and Chemometric Analyses ; Remote Sensing in Agriculture ; Leaf Properties and Growth Measurement
Authors: Rakesh Trivedi | Hampapathalu Adimurthy Nagarajaram
Source: Scientific Reports (article, 2019-11-08)
Field: Chemistry — Spectroscopy

Amino acid substitution scoring matrices specific to intrinsically disordered regions in proteins An amino acid substitution scoring matrix encapsulates the rates at which various amino acid residues in proteins are substituted by other amino acid residues, over time. Database search methods make use of substitution scoring matrices to identify sequences with homologous relationships. However, widely used substitution scoring matrices, such as BLOSUM series, have been developed using aligned blocks that are mostly devoid of disordered regions in proteins. Hence, these substitution-scoring matrices are mostly inappropriate for homology searches involving proteins enriched with disordered regions as the disordered regions have distinct amino acid compositional bias, and therefore expected to have undergone amino acid substitutions that are distinct from those in the ordered regions. We, therefore, developed a novel series of substitution scoring matrices referred to as EDSSMat by exclusively considering the substitution frequencies of amino acids in the disordered regions of the eukaryotic proteins. The newly developed matrices were tested for their ability to detect homologs of proteins enriched with disordered regions by means of SSEARCH tool. The results unequivocally demonstrate that EDSSMat matrices detect more number of homologs than the widely used BLOSUM, PAM and other standard matrices, indicating their utility value for homology searches of intrinsically disordered proteins. Substitution (logic) ; Amino acid ; Amino acid substitution ; Intrinsically disordered proteins ; Protein superfamily ; Homology (biology) ; Computational biology ; Homologous series ; Homologous chromosome ; Matrix (chemical analysis) ; Protein evolution ; Biology ; Chemistry ; Biochemistry ; Computer science ; Crystallography ; Gene ; Mutation Mass Spectrometry Techniques and Applications ; RNA and protein synthesis mechanisms ; Chemical Synthesis and Analysis
Authors: Weyde M. M. Lin | Nuri Yazdani | Olesya Yarema | Sebastian Volk | Maksym Yarema | Thomas Kirchartz | Vanessa Wood
Source: The Journal of Chemical Physics (article, 2019-12-27)
Field: Materials Science — Materials Chemistry

Simulating nanocrystal-based solar cells: A lead sulfide case study Nanocrystal-based solar cells are promising candidates for next generation photovoltaic applications; however, the most recent improvements to the device chemistry and architecture have been mostly trial-and-error based advancements. Due to complex interdependencies among parameters, determining factors that limit overall solar cell efficiency are not trivial. Furthermore, many of the underlying chemical and physical parameters of nanocrystal-based solar cells have only recently been understood and quantified. Here, we show that this new understanding of interfaces, transport, and origin of trap states in nanocrystal-based semiconductors can be integrated into simulation tools, based on 1D drift-diffusion models. Using input parameters measured in independent experiments, we find excellent agreement between experimentally measured and simulated PbS nanocrystal solar cell behavior without having to fit any parameters. We then use this simulation to understand the impact of interfaces, charge carrier mobility, and trap-assisted recombination on nanocrystal performance. We find that careful engineering of the interface between the nanocrystals and the current collector is crucial for an optimal open-circuit voltage. We also show that in the regime of trap-state densities found in PbS nanocrystal solar cells (∼10<sup>17</sup> cm<sup>-3</sup>), device performance exhibits strong dependence on the trap state density, explaining the sensitivity of power conversion efficiency to small changes in nanocrystal synthesis and nanocrystal thin-film deposition that has been reported in the literature. Based on these findings, we propose a systematic approach to nanocrystal solar cell optimization. Our method for incorporating parameters into simulations presented and validated here can be adopted to speed up the understanding and development of all types of nanocrystal-based solar cells. Nanocrystal ; Lead sulfide ; Solar cell ; Materials science ; Photovoltaic system ; Quantum dot solar cell ; Nanotechnology ; Trap (plumbing) ; Optoelectronics ; Quantum dot ; Polymer solar cell ; Physics ; Electrical engineering Quantum Dots Synthesis And Properties ; Chalcogenide Semiconductor Thin Films ; Perovskite Materials and Applications
Authors: Ani Iryani | Hadi Nur | Mardi Santoso | Djoko Hartanto
Source: Indonesian Journal of Chemistry (article, 2019-05-29)
Field: Chemistry — Spectroscopy

Adsorption Study of Rhodamine B and Methylene Blue Dyes with ZSM-5 Directly Synthesized from Bangka Kaolin without Organic Template Rhodamine B (RB) and Methylene Blue (MB) dyes adsorption using adsorbent ZSM-5 synthesized from Bangka kaolin were investigated in this study. The effects of the initial concentration, contact time and temperature on the adsorption process were also analyzed. The effect of the initial concentration and contact time played an important role in the adsorption process; however, the effect differs significantly in both dyes. The temperature plays little role in the dye adsorption process. The results showed the adsorption process occurred in ZSM-5 adhere to Langmuir isothermal adsorption model showing that the adsorption process occurred to be monolayer. Based on the kinetics studies, the pseudo-first-order kinetic model represents the adsorption kinetics that occurs for both dyes onto the synthesized ZSM-5. Thermodynamic parameters namely Gibbs free energy (ΔG°), standard entropy changes (ΔS°) and standard enthalpy (ΔH°) reveal that the adsorption process onto ZSM-5 for both dyes was spontaneous and exothermic. Adsorption ; Chemistry ; Rhodamine B ; Gibbs free energy ; Methylene blue ; Enthalpy ; Langmuir adsorption model ; Monolayer ; Exothermic process ; Kinetics ; Isothermal process ; Exothermic reaction ; Langmuir ; Endothermic process ; Kinetic energy ; Chemical engineering ; Organic chemistry ; Catalysis ; Thermodynamics Adsorption, diffusion, and thermodynamic properties of materials ; Adsorption and biosorption for pollutant removal ; Clay minerals and soil interactions
Authors: Hrvoje Mikulčić | Qiming Jin | Hrvoje Stančin | Xuebin Wang | Li Shuaishuai | Houzhang Tan | Neven Duić
Source: Journal of Sustainable Development of Energy Water and Environment Systems (article, 2019-03-19)
Field: Materials Science — Materials Chemistry

Thermogravimetric Analysis Investigation of Polyurethane Plastic Thermal Properties Under Different Atmospheric Conditions Recycling and energy recovery of waste plastic are major categories of modern solid waste management systems. Since the lower heating values of plastics are around 30 MJ/kg, equivalent to traditional solid fuels, such as petroleum coke, coal and charcoal, waste plastics are considered as potential fossil fuels alternatives in various industrial sectors. Already nowadays, energy recovery of waste plastic is typically conducted by combustion in incinerators or cement kilns. However, due to various types of waste plastics, their thermochemical behaviour has been rarely investigated. Even more, the thermochemical behaviour of waste plastics under oxy-combustion conditions has even rarely been studied. In this study non-isothermal thermogravimetric analyser was used to study the thermochemical behaviour of polyurethane plastic waste under seven different atmospheric conditions. Polyurethane decomposition kinetic constants have been estimated by the simultaneous evaluations of seven weight loss curves measured for the heating rate of 20 K/min and a final temperature of 1,073 K. The obtained results showed that the combustion of polyurethane is mainly composed of two stages, and the higher oxygen concentration slightly influenced the first stage but highly accelerates the second Thermogravimetric analysis ; Polyurethane ; Materials science ; Thermal ; Composite material ; Environmental science ; Chemical engineering ; Meteorology ; Engineering ; Physics Thermal and Kinetic Analysis ; Polymer composites and self-healing ; Polymer crystallization and properties
Authors: Julija Zavadlav | Georgios Arampatzis | Petros Koumoutsakos
Source: Scientific Reports (article, 2019-01-08)
Field: Materials Science — Materials Chemistry

Bayesian selection for coarse-grained models of liquid water The necessity for accurate and computationally efficient representations of water in atomistic simulations that can span biologically relevant timescales has born the necessity of coarse-grained (CG) modeling. Despite numerous advances, CG water models rely mostly on a-priori specified assumptions. How these assumptions affect the model accuracy, efficiency, and in particular transferability, has not been systematically investigated. Here we propose a data driven comparison and selection for CG water models through a Hierarchical Bayesian framework. We examine CG water models that differ in their level of coarse-graining, structure, and number of interaction sites. We find that the importance of electrostatic interactions for the physical system under consideration is a dominant criterion for the model selection. Multi-site models are favored, unless the effects of water in electrostatic screening are not relevant, in which case the single site model is preferred due to its computational savings. The charge distribution is found to play an important role in the multi-site model's accuracy while the flexibility of the bonds/angles may only slightly improve the models. Furthermore, we find significant variations in the computational cost of these models. We present a data informed rationale for the selection of CG water models and provide guidance for future water model designs. Selection (genetic algorithm) ; Computer science ; Bayesian probability ; Model selection ; Artificial intelligence Material Dynamics and Properties ; Electrostatics and Colloid Interactions ; Nanopore and Nanochannel Transport Studies
Authors: Eline E. van Haaften | Renée Duijvelshoff | Bastiaan D. Ippel | Serge H. M. Söntjens | Michel H. C. J. van Houtem | Henk M. Janssen | Anthal I.P.M. Smits | Nicholas A. Kurniawan | Patricia Y. W. Dankers | Carlijn V. C. Bouten
Source: Acta Biomaterialia (article, 2019-05-17)
Field: Materials Science — Biomaterials

The degradation and performance of electrospun supramolecular vascular scaffolds examined upon in vitro enzymatic exposure Materials science ; Degradation (telecommunications) ; In vitro ; Electrospinning ; Supramolecular chemistry ; Biomedical engineering ; Enzyme ; Nanotechnology ; Composite material ; Biophysics ; Polymer ; Chemistry ; Biochemistry ; Medicine ; Computer science ; Organic chemistry ; Molecule ; Biology Electrospun Nanofibers in Biomedical Applications ; Bone Tissue Engineering Materials ; biodegradable polymer synthesis and properties
Authors: Eunbyul Hwang | Kicheol Kim | Chae Gyu Lee | Tae‐Hyuk Kwon | Sang‐Ho Lee | Seung Kyu Min | Byeong‐Su Kim
Source: Macromolecules (article, 2019-07-29)
Field: Chemistry — Organic Chemistry

Tailorable Degradation of pH-Responsive All-Polyether Micelles: Unveiling the Role of Monomer Structure and Hydrophilic–Hydrophobic Balance Polymeric micelles have been widely used as ideal drug-delivery vehicles with unique advantages. However, fine tuning of the degradation rates of micelles over a wide time frame remains challenging. Herein, we designed and synthesized a novel pH-responsive, hydrophobic epoxide monomer, tetrahydrofuranyl glycidyl ether (TFGE), carrying an acetal group as a cleavable linkage. The hydrolysis kinetics of TFGE was carefully evaluated with representative functional epoxide monomers, such as 1-ethoxyethyl glycidyl ether and tetrahydropyranyl glycidyl ether, via in situ 1H NMR spectroscopy and quantum mechanical calculations. Interestingly, the hydrolysis kinetics and the associated energy barrier were closely related not only to the cyclic/acyclic structure of the monomers but also to their hydrophobicity. Subsequently, a series of amphiphilic block copolymers (mPEG-b-PTFGE) were synthesized via anionic ring-opening polymerization and the self-assembled polymeric micelles were evaluated with respect to critical micelle concentration, encapsulation efficiency, drug release, and cell viability. Most notably, the release kinetics of the model compound from polymeric micelles exhibited a different trend, confirming the critical role of hydrophobicity in governing the pH-responsive hydrolysis of the polymeric micelles. This study provides new insights applicable to the design of functional monomers for tailoring the release profiles of polymeric micelles for smart drug delivery. Micelle ; Monomer ; Chemistry ; Copolymer ; Amphiphile ; Polymerization ; Polymer chemistry ; Kinetics ; Hydrolysis ; Glycidyl methacrylate ; Drug delivery ; Ring-opening polymerization ; Organic chemistry ; Chemical engineering ; Polymer ; Aqueous solution Advanced Polymer Synthesis and Characterization ; biodegradable polymer synthesis and properties ; Dendrimers and Hyperbranched Polymers
Authors: Xiufang Ma | Bingbing Chen | Yi‐Quan Zhang | Jinhui Yang | Quan Shi | Yulong Ma | Xiangyu Liu
Source: Dalton Transactions (article, 2019-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Enhancing single-molecule magnet behaviour through decorating terminal ligands in Dy<sub>2</sub> compounds The utilization of two isomorphic ligands with different substituents leads to two centrosymmetric Dy<sup>III</sup> dimers, namely, [Dy<sub>2</sub>(bfbpen)<sub>2</sub>(H<sub>2</sub>O)<sub>2</sub>]·2I<sup>-</sup> (1) and [Dy<sub>2</sub>(bcbpen)<sub>2</sub>(H<sub>2</sub>O)<sub>2</sub>]·2I<sup>-</sup>·0.5H<sub>2</sub>O (2) (H<sub>2</sub>bfbpen = N,N'-bis-(2-hydroxy-5-fluoro-benzyl)-N,N'-bis-(pyridin-2-ylmethyl)ethylenediamine and H<sub>2</sub>bcbpen = N,N'-bis-(2-hydroxy-5-chloro-benzyl)-N,N'-bis-(pyridin-2-ylmethyl)ethylenediamine). Although Dy ions in both compounds uniformly exhibit a square-antiprism geometry, the critical difference found in the terminal substituents of the two ligands fine-tunes the local crystal field around Dy centers and the dinuclear molecular structures of 1 and 2. Magnetic investigations unveil that both 1 and 2 display dynamic magnetic relaxation of single-molecule magnet (SMM) behaviour with different energy barriers of 20.9 K for 1 and 72.7 K for 2 under a zero direct-current (dc) field, as well as 26.9 K for 1 under a 1200 Oe dc field. Compared to 1, the stronger uniaxial anisotropy and magnetic exchange in 2 render it a better SMM as evidenced by the higher energy barrier. Ab initio calculations are also performed on both Dy<sub>2</sub> compounds to rationalize the observed discrepancy in their magnetic behaviours. The contribution illustrates that the SMM behaviour could be effectively enhanced by means of deliberate local structural manipulation. Terminal (telecommunication) ; Single-molecule magnet ; Magnet ; Molecule ; Crystallography ; Materials science ; Lanthanide ; Chemistry ; Nanotechnology ; Physics ; Computer science ; Magnetization ; Engineering ; Organic chemistry ; Electrical engineering ; Telecommunications ; Magnetic field Magnetism in coordination complexes ; Lanthanide and Transition Metal Complexes ; Organic and Molecular Conductors Research
Authors: Jie Zhang | Qi Wang | Jingkang Liu | Zhiqian Guo | Jinfeng Yang | Qiang Li | Shaoze Zhang | Chenxu Yan | Weihong Zhu
Source: ACS Applied Bio Materials (article, 2019-01-23)
Field: Materials Science — Materials Chemistry

Saponin-Based Near-Infrared Nanoparticles with Aggregation-Induced Emission Behavior: Enhancing Cell Compatibility and Permeability Fluorescence imaging is critical for physiological activities and cell biology but limited by the poor solubility, cell compatibility, and permeability. Herein, we develop a novel engineering methodology to prepare biocompatible and penetrable aggregation-induced emission (AIE) nanoparticles with the assistance of flash nanoprecipitation (FNP) technology. On the basis of the donor-π-acceptor (D-π-A) system, the AIE building block of tricyano-methylene-pyridine (<b>TCM</b>) is fine-tuned to long emission wavelength by modulating the π-conjugation bridge and electron-donating group, thereby achieving high solid fluorescent quantum yield, near-infrared (NIR) characteristic, large Stokes shift, and excellent photostability. On the basis of the FNP technology, the amphiphilic saponin solution and <b>TCMN-5</b> in organic solvent are quickly mixed in the multi-inlet vortex mixer (MIVM), followed by saponin-encapsulation of the hydrophobic AIE nucleation with inhibiting further growth of nanoparticles. The biocompatible amphiphilic saponin such as α-hederin can encapsulate and micellize the AIE <b>TCM</b> fluorophore for efficient cell imaging. The kinetic FNP technology can not only modulate the uniform diameter size, but also distinctly increase the micelle stability when compared to the conventional thermodynamic self-aggregation method, which provides an alternative opportunity for scale-up preparation of drugs and probes in delivery vehicles. Amphiphile ; Fluorophore ; Chemistry ; Nanoparticle ; Fluorescence ; Micelle ; Nanotechnology ; Chemical engineering ; Materials science ; Organic chemistry ; Aqueous solution ; Polymer ; Copolymer Luminescence and Fluorescent Materials ; Nanoplatforms for cancer theranostics ; Molecular Sensors and Ion Detection
Authors: Eduardo Anaya‐Plaza | Ana Aljarilla | Grégory Beaune | Nonappa Nonappa | Jaakko V. I. Timonen | Andrés de la Escosura | Tomás Torres⊗ | Mauri A. Kostiainen
Source: Advanced Materials (article, 2019-08-08)
Field: Materials Science — Materials Chemistry

Phthalocyanine–Virus Nanofibers as Heterogeneous Catalysts for Continuous‐Flow Photo‐Oxidation Processes The generation of highly reactive oxygen species (ROS) at room temperature for application in organic synthesis and wastewater treatment represents a great challenge of the current chemical industry. In fact, the development of biodegradable scaffolds to support ROS-generating active sites is an important prerequisite for the production of environmentally benign catalysts. Herein, the electrostatic cocrystallization of a cationic phthalocyanine (Pc) and negatively charged tobacco mosaic virus (TMV) is described, together with the capacity of the resulting crystals to photogenerate ROS. To this end, a novel peripherally crowded zinc Pc (1) is synthesized. With 16 positive charges, this photosensitizer shows no aqueous aggregation, and is able to act as a molecular glue in the unidimensional assembly of TMV. A step-wise decrease of ionic strength in mixtures of both components results in exceptionally long fibers, constituted by hexagonally bundled viruses thoroughly characterized by electron and confocal microscopy. The fibers are able to produce ROS in a proof-of-concept microfluidic device, where they are immobilized and irradiated in several cycles, showing a resilient performance. The bottom-up approach also enables the light-triggered disassembly of fibers after use. This work represents an important example of a biohybrid material with projected application in light-mediated heterogeneous catalysis. Singlet oxygen ; Materials science ; Phthalocyanine ; Catalysis ; Photosensitizer ; Cationic polymerization ; Chemical engineering ; Nanotechnology ; Aqueous solution ; Ionic bonding ; Nanofiber ; Tobacco mosaic virus ; Photochemistry ; Oxygen ; Organic chemistry ; Chemistry ; Polymer chemistry ; Virus Porphyrin and Phthalocyanine Chemistry ; Covalent Organic Framework Applications ; Advanced Photocatalysis Techniques