jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Bo Da | Yang Sun | Zhufeng Hou | Jiangwei Liu | Nguyen Thanh Cuong | Kazuhito Tsukagoshi | Hideki Yoshikawa | Shigeo Tanuma | Jin Hu | Zhaoshun Gao | Zejun Ding
Source: Physical Review Applied (article, 2020-04-21)
Field: Materials Science — Materials Chemistry

Measurement of the Low-Energy Electron Inelastic Mean Free Path in Monolayer Graphene Measuring the electron-transport properties of substrate-supported nanomaterials with the traditional two-point comparison method is difficult at electron energies below 50 eV, where core-level signals are too feeble to be detected against the strong secondary-electron background. Herein, a data-driven spectral analysis technique is used to study the low-energy electron-transport properties of substrate-supported target nanomaterials, while eliminating the influence of the substrate signal. Applying this technique, the electron-transport properties of the effective attenuation length and the inelastic mean free path (IMFP) can be determined with extremely high efficiency over the entire measured energy range of 6--600 eV. Further, these results show excellent agreement with other experimental and theoretical results. Significant differences are observed between monolayer graphene and the bulk graphite IMFP, which illustrates the importance of the nanometer effect in the electron-transport properties of the material. Furthermore, this technique is readily applicable to any ultrathin material that can be transferred onto a polycrystalline gold substrate. Inelastic mean free path ; Mean free path ; Graphene ; Materials science ; Substrate (aquarium) ; Monolayer ; Electron ; Electron transport chain ; Nanomaterials ; Molecular physics ; Nanotechnology ; Chemistry ; Physics ; Nuclear physics Graphene research and applications ; Electron and X-Ray Spectroscopy Techniques ; Surface and Thin Film Phenomena
Authors: Fantao Meng | Malik Muhammad Umair | Shufen Zhang | Yao Meng | Bingtao Tang
Source: Science China Materials (article, 2020-11-10)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Facile fabrication of encryption composite materials with trilayer quasi-amorphous heterostructure Materials science ; Encryption ; Explosive material ; Decoding methods ; Amorphous solid ; Optoelectronics ; Photonics ; Composite number ; Coding (social sciences) ; Heterojunction ; Computer science ; Fabrication ; Nanotechnology ; Composite material ; Computer network ; Telecommunications Gold and Silver Nanoparticles Synthesis and Applications ; Luminescence and Fluorescent Materials ; Photonic Crystals and Applications
Authors: Mary Alice Cusentino | Mitchell Wood | Aidan P. Thompson
Source: Nuclear Fusion (article, 2020-10-06)
Field: Materials Science — Materials Chemistry

Suppression of helium bubble nucleation in beryllium exposed tungsten surfaces One of the most severe obstacles to increasing the longevity of tungstenbased plasma facing components, such as divertor tiles, is the surface deterioration driven by sub-surface helium bubble formation and rupture.Supported by experimental observations at PISCES, this work uses molecular dynamics simulations to identify the microscopic mechanisms underlying suppression of helium bubble formation by the introduction of plasma-borne beryllium.Simulations of the initial surface material (crystalline W), early-time Be exposure (amorphous W-Be) and final WBe2 intermetallic surfaces were used to highlight the effect of Be.Significant differences in He retention, depth distribution, and cluster size were observed in the cases with beryllium present.Helium resided much closer to the surface in the Be cases with nearly 80% of the total helium inventory located within the first 2 nm.Moreover, coarsening of the He depth profile due to bubble formation is suppressed due to a one-hundred fold decrease in He mobility in WBe2, relative to crystalline W. This is further evidenced by the drastic reduction in He cluster sizes even when it was observed that both the amorphous W-Be and WBe2 intermetallic phases retain nearly twice as much He during cumulative implantation studies. Beryllium ; Helium ; Tungsten ; Bubble ; Materials science ; Nucleation ; Divertor ; Intermetallic ; Amorphous solid ; Plasma ; Atomic physics ; Composite material ; Nuclear physics ; Metallurgy ; Thermodynamics ; Crystallography ; Chemistry ; Physics ; Mechanics ; Alloy Fusion materials and technologies ; Nuclear Materials and Properties ; Advanced materials and composites
Authors: Soroor Hediyeh-zadeh | Andrew I. Webb | Melissa J. Davis
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-08-13)
Field: Chemistry — Spectroscopy

MSImpute: Imputation of label-free mass spectrometry peptides by low-rank approximation Abstract Recent developments in mass spectrometry (MS) instruments and data acquisition modes have aided multiplexed, fast, reproducible and quantitative analysis of proteome profiles, yet missing values remain a formidable challenge for proteomics data analysis. The stochastic nature of sampling in Data Dependent Acquisition (DDA), suboptimal preprocessing of Data Independent Acquisition (DIA) runs and dynamic range limitation of MS instruments impedes the reproducibility and accuracy of peptide quantification and can introduce systematic patterns of missingness that impact downstream analyses. Thus, imputation of missing values becomes an important element of data analysis. We introduce msIm pute , an imputation method based on low-rank approximation, and compare it to six alternative imputation methods using public DDA and DIA datasets. We evaluate the performance of methods by determining the error of imputed values and accuracy of detection of differential expression. We also measure the post-imputation preservation of structures in the data at different levels of granularity. We develop a visual diagnostic to determine the nature of missingness in datasets based on peptides with high biological dropout rate and introduce a method to identify such peptides. Our findings demonstrate that msImpute performs well when data are missing at random and highlights the importance of prior knowledge about nature of missing values in a dataset when selecting an imputation technique. Missing data ; Imputation (statistics) ; Computer science ; Data mining ; Preprocessor ; Data pre-processing ; Granularity ; Artificial intelligence ; Machine learning Advanced Proteomics Techniques and Applications ; Gene expression and cancer classification ; Metabolomics and Mass Spectrometry Studies
Authors: Shi Li | Balaji Sesha Sarath Pokuri | Sean M. Ryno | Asare Nkansah | Camron De’Vine | Baskar Ganapathysubramanian | Chad Risko
Source: Journal of Chemical Information and Modeling (article, 2020-01-14)
Field: Materials Science — Materials Chemistry

Determination of the Free Energies of Mixing of Organic Solutions through a Combined Molecular Dynamics and Bayesian Statistics Approach As new generations of thin-film semiconductors are moving toward solution-based processing, the development of printing formulations will require information pertaining to the free energies of mixing of complex mixtures. From the standpoint of in silico material design, this move necessitates the development of methods that can accurately and quickly evaluate these formulations in order to maximize processing speed and reproducibility. Here, we make use of molecular dynamics (MD) simulations, in combination with the two-phase thermodynamic (2PT) model, to explore the free energy of mixing surfaces for a series of halogenated solvents and high-boiling point solvent additives used in the development of thin-film organic semiconductors. Although the combined methods generally show good agreement with available experimental data, the computational cost to traverse the free-energy landscape is considerable. Hence, we demonstrate how a Bayesian optimization scheme, coupled with the MD and 2PT approaches, can drastically reduce the number of simulations required, in turn shrinking both the computational cost and time. Mixing (physics) ; Molecular dynamics ; Bayesian optimization ; Bayesian probability ; Thermodynamic integration ; Computer science ; Traverse ; Energy (signal processing) ; Statistical physics ; Point (geometry) ; Semiconductor ; Materials science ; Chemistry ; Physics ; Computational chemistry ; Mathematics ; Artificial intelligence ; Statistics Machine Learning in Materials Science ; Phase Equilibria and Thermodynamics ; Block Copolymer Self-Assembly
Authors: Maxim Ziatdinov
Source: arXiv (Cornell University) (article, 2020-03-19)
Field: Materials Science — Materials Chemistry

Predictability as a probe of manifest and latent physics: The case of atomic scale structural, chemical, and polarization behaviors in multiferroic Sm-doped BiFeO3 The predictability of a certain effect or phenomenon is often equated with the knowledge of relevant physical laws, typically understood as a functional or numerically derived relationship between the observations and known states of the system. Correspondingly, observations inconsistent with prior knowledge can be used to derive new knowledge on the nature of the system or indicate the presence of yet unknown mechanisms. Here we explore the applicability of Gaussian Processes (GP) to establish predictability and uncertainty of local behaviors from multimodal observations, providing an alternative to this classical paradigm. Using atomic-resolution Scanning Transmission Electron Microscopy (STEM) of multiferroic Sm-doped BiFeO3 across a broad composition range, we directly visualize the atomic structure and structural, physical, and chemical order parameter fields for the material. GP regression is used to establish the predictability of the local polarization field from different groups of parameters, including the adjacent polarization values and several combinations of physical and chemical descriptors, including lattice parameters, column intensities, etc. We observe that certain elements of microstructure including charged and uncharged domain walls and interfaces with the substrate are best predicted with specific combinations of descriptors, and this predictability and their associated uncertainties are consistent across the composition series. The associated generative physical mechanisms are discussed. We argue that predictability and uncertainty in observational data offers a new pathway to probe the physics of condensed matter systems from multimodal local observations. Predictability ; Statistical physics ; Multiferroics ; Polarization (electrochemistry) ; Atomic units ; Condensed matter physics ; Materials science ; Chemical physics ; Chemistry ; Ferroelectricity ; Physics ; Dielectric ; Quantum mechanics Machine Learning in Materials Science ; Multiferroics and related materials ; Geochemistry and Geologic Mapping
Authors: Jiaying Xie | Yiliang Jin | Kelong Fan | Xiyun Yan
Source: Biophysics Reports (article, 2020-11-20)
Field: Materials Science — Materials Chemistry

The prototypes of nanozyme-based nanorobots Abstract Artificial nanorobot is a type of robots designed for executing complex tasks at nanoscale. The nanorobot system is typically consisted of four systems, including logic control, driving, sensing and functioning. Considering the subtle structure and complex functionality of nanorobot, the manufacture of nanorobots requires designable, controllable and multi-functional nanomaterials. Here, we propose that nanozyme is a promising candidate for fabricating nanorobots due to its unique properties, including flexible designs, controllable enzyme-like activities, and nano-sized physicochemical characters. Nanozymes may participate in one system or even combine several systems of nanorobots. In this review, we summarize the advances on nanozyme-based systems for fabricating nanorobots, and prospect the future directions of nanozyme for constructing nanorobots. We hope that the unique properties of nanozymes will provide novel ideas for designing and fabricating nanorobotics. Nanorobotics ; Computer science ; Nanotechnology ; Biomimetic materials ; Artificial intelligence ; Materials science Advanced Nanomaterials in Catalysis ; Nanocluster Synthesis and Applications ; Nanoplatforms for cancer theranostics
Authors: Thomas E. Miller | Beth Mortimer
Source: Frontiers in Ecology and Evolution (article, 2020-12-11)
Field: Materials Science — Biomaterials

Control vs. Constraint: Understanding the Mechanisms of Vibration Transmission During Material-Bound Information Transfer Material-bound vibrations are ubiquitous in the environment and are widely used as an information source by animals, whether they are generated by biotic or abiotic sources. The process of vibration information transfer is subject to a wide range of physical constraints, especially during the vibration transmission phase. This is because vibrations must travel through materials in the environment and body of the animal before reaching embedded mechanosensors. Morphology therefore plays a key and often overlooked role in shaping information flow. Web-building spiders are ideal organisms for studying vibration information transfer due to the level of control they have over morphological traits, both within the web (environment) and body, which can give insights for bioinspired design. Here we investigate the mechanisms governing vibration information transfer, including the relative roles of constraints and control mechanisms. We review the known and theoretical contributions of morphological and behavioral traits to vibration transmission in these spiders, and propose an interdisciplinary framework for considering the effects of these traits from a biomechanical perspective. Whereas morphological traits act as a series of springs, dampers and masses arranged in a specific geometry to influence vibration transmission, behavioral traits influence these morphologies often over small timescales in response to changing conditions. We then explore the relative roles of constraints and control mechanisms in shaping the variation of these traits at various taxonomic levels. This analysis reveals the importance of morphology modification to gain control over vibration transmission to mitigate constraints and essentially promote information transfer. In particular, we hypothesize that morphological computation is used by spiders during vibration information transfer to reduce the amount of processing required by the central nervous system (CNS); a hypothesis that can be tested experimentally in the future. We can take inspiration from how spiders control vibration transmission and apply these insights to bioinspired engineering. In particular, the role of morphological computation for vibration control could open up potential developments for soft robots, which could use multi-scale vibration sensory systems inspired by spiders to quickly and efficiently adapt to changing environments. Vibration ; Information transfer ; Transmission (telecommunications) ; Computer science ; Constraint (computer-aided design) ; Biological system ; Perspective (graphical) ; Information transmission ; Ecology ; Biology ; Engineering ; Physics ; Acoustics ; Artificial intelligence ; Mechanical engineering ; Telecommunications Silk-based biomaterials and applications ; Neurobiology and Insect Physiology Research ; Ichthyology and Marine Biology
Authors: Huayna Terraschke | Matthias Franzreb | Claudia Wickleder
Source: Chemistry - A European Journal (article, 2020-01-10)
Field: Materials Science — Materials Chemistry

Magnetism and Afterglow United: Synthesis of Novel Double Core–Shell Eu<sup>2+</sup>‐Doped Bifunctional Nanoparticles Afterglow-magnetic nanoparticles (NPs) offer enormous potential for bioimaging applications, as they can be manipulated by a magnetic field, as well as emitting light after irradiation with an excitation source, thus distinguishing themselves from fluorescent living cells. In this work, a novel double core-shell strategy is presented, uniting co-precipitation with combustion synthesis routes to combine an Fe<sub>3</sub> O<sub>4</sub> magnetic core (≈15 nm) with an afterglow SrAl<sub>2</sub> O<sub>4</sub> :Eu<sup>2+</sup> ,Dy<sup>3+</sup> outer coat (≈10 nm), and applying a SiO<sub>2</sub> protective middle layer (≈16 nm) to reduce the luminescence quenching caused by the Fe core ions. The resulting Fe<sub>3</sub> O<sub>4</sub> @SiO<sub>2</sub> @SrAl<sub>2</sub> O<sub>4</sub> :Eu<sup>2+</sup> ,Dy<sup>3+</sup> NPs emit green light attributed to the 4f<sup>6</sup> 5d<sup>1</sup> →4f<sup>7</sup> (<sup>8</sup> S<sub>7/2</sub> ) transition of Eu<sup>2+</sup> under UV radiation and for a few seconds afterwards. This bifunctional nanocomposite can potentially be applied for the detection and separation of cells or diagnostically relevant molecules. Afterglow ; Bifunctional ; Materials science ; Nanoparticle ; Luminescence ; Quenching (fluorescence) ; Magnetism ; Doping ; Nanotechnology ; Persistent luminescence ; Nanocomposite ; Fluorescence ; Photochemistry ; Analytical Chemistry (journal) ; Optoelectronics ; Chemistry ; Optics ; Physics ; Thermoluminescence ; Condensed matter physics Luminescence and Fluorescent Materials ; Nanocluster Synthesis and Applications ; Molecular Sensors and Ion Detection
Authors: Timothy R. Stachowski | M. Elizabeth Snell | Edward H. Snell
Source: PLoS ONE (article, 2020-11-17)
Field: Materials Science — Materials Chemistry

SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been successful in mitigating damage but not eliminating it altogether; however, cryo-cooling can be difficult in some cases and has also been shown to limit functionally relevant protein conformations. The doses used for X-ray crystallography are typically in the kilo-gray to mega-gray range. While disulfide bonds are among the most significantly affected species in proteins in the crystalline state at both cryogenic and higher temperatures, there is limited information on their response to low X-ray doses in solution, the details of which might inform biomedical applications of X-rays. In this work we engineered a protein that dimerizes through a susceptible disulfide bond to relate the radiation damage processes seen in cryo-cooled crystals to those closer to physiologic conditions. This approach enables a low-resolution technique, small angle X-ray scattering (SAXS), to detect and monitor a residue specific process. A dose dependent fragmentation of the engineered protein was seen that can be explained by a dimer to monomer transition through disulfide bond cleavage. This supports the crystallographically derived mechanism and demonstrates that results obtained crystallographically can be usefully extrapolated to physiologic conditions. Fragmentation was influenced by pH and the conformation of the dimer, providing information on mechanism and pointing to future routes for investigation and potential mitigation. The novel engineered protein approach to generate a large-scale change through a site-specific interaction represents a promising tool for advancing radiation damage studies under solution conditions. Small-angle X-ray scattering ; Dimer ; Radiation damage ; Crystallography ; Protein crystallization ; Materials science ; Chemistry ; Fragmentation (computing) ; Scattering ; Chemical physics ; Radiation ; Crystallization ; Organic chemistry ; Physics ; Optics ; Computer science Enzyme Structure and Function ; Biochemical and Molecular Research ; Heat shock proteins research
Authors: He Li | J. P. Conde | Ana Guerreiro | Gonçalo J. L. Bernardes
Source: Angewandte Chemie (article, 2020-06-18)
Field: Chemistry — Organic Chemistry

Tetrazine Carbon Nanotubes for Pretargeted In Vivo “Click‐to‐Release” Bioorthogonal Tumour Imaging Abstract The bioorthogonal inverse‐electron‐demand Diels–Alder (IEDDA) cleavage reaction between tetrazine and trans ‐cyclooctene (TCO) is a powerful way to control the release of bioactive agents and imaging probes. In this study, a pretargeted activation strategy using single‐walled carbon nanotubes (SWCNTs) that bear tetrazines (TZ@SWCNTs) and a TCO‐caged molecule was used to deliver active effector molecules. To optimize a turn‐on signal by using in vivo fluorescence imaging, we developed a new fluorogenic near‐infrared probe that can be activated by bioorthogonal chemistry and image tumours in mice by caging hemicyanine with TCO (tHCA). With our pretargeting strategy, we have shown selective doxorubicin prodrug activation and instantaneous fluorescence imaging in living cells. By combining a tHCA probe and a pretargeted bioorthogonal approach, real‐time, non‐invasive tumour visualization with a high target‐to‐background ratio was achieved in a xenograft mice tumour model. The combined advantages of enhanced stability, kinetics and biocompatibility, and the superior pharmacokinetics of tetrazine‐functionalised SWCNTs could allow application of targeted bioorthogonal decaging approaches with minimal off‐site activation of fluorophore/drug. Bioorthogonal chemistry ; Tetrazine ; Pretargeting ; Chemistry ; Click chemistry ; Fluorophore ; In vivo ; Nanoprobe ; Molecular imaging ; Fluorescence-lifetime imaging microscopy ; Combinatorial chemistry ; Fluorescence ; Biophysics ; Prodrug ; Preclinical imaging ; Nanotechnology ; Biochemistry ; Materials science ; Organic chemistry ; Nanoparticle Click Chemistry and Applications ; Advanced biosensing and bioanalysis techniques ; Nanoplatforms for cancer theranostics
Authors: Xinrui He | Jian Zhao | Zeqing Tan | Jiaxin Zhao | Xiao Cheng | Chuanjian Zhou
Source: CrystEngComm (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

Chalcone single crystals with red emission and photodimerization-triggered hopping behavior: the substituent effect and molecular packing effect Chalcone single crystals with distinctively different emission color and photoinduced mechanical response are designed and fabricated <italic>via</italic> fine-tuning the donor substituents. Chalcone ; Substituent ; Photochemistry ; Materials science ; Aggregation-induced emission ; Chemistry ; Crystallography ; Stereochemistry ; Fluorescence ; Optics Luminescence and Fluorescent Materials ; Crystallography and molecular interactions ; Photochromic and Fluorescence Chemistry
Authors: Sascha Keßler | Guillermo González‐Rubio | Elrike R. Reinalter | Michael Kovermann | Helmut Cölfen
Source: Chemical Communications (article, 2020-01-01)
Field: Chemistry — Organic Chemistry

Synthesis of nickel hexacyanoferrate nanocubes with tuneable dimensions <i>via</i> temperature-controlled Ni<sup>2+</sup>-citrate complexation The citrate-assisted growth of nickel hexacyanoferrate (NiHCF) nanocubes was investigated. Control over the complexation of Ni2+ ions with citrate at different temperatures enabled fine tuning of the nanocrystal (NC) dimensions and their self-assembly into mesocrystals. Our results introduce new concepts towards the synthesis of NiHCF NCs, potentially applicable to other members of the Prussian blue analogues family. Nickel ; Materials science ; Inorganic chemistry ; Chemical engineering ; Nuclear chemistry ; Chemistry ; Metallurgy Nanomaterials for catalytic reactions ; Covalent Organic Framework Applications ; Advanced Battery Materials and Technologies