jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yuta Saito | Alexander V. Kolobov | Paul Fons | Kirill V. Mitrofanov | Kotaro Makino | Junji Tominaga | John Robertson
Source: Applied Physics Letters (article, 2019-04-01)
Field: Materials Science — Materials Chemistry

Origin of resistivity contrast in interfacial phase-change memory: The crucial role of Ge/Sb intermixing Phase-change memories based on reversible amorphous-crystal transformations in pseudobinary GeTe-Sb2Te3 alloys are one of the most promising nonvolatile memory technologies. The recently proposed superlattice-based memory, or interfacial phase-change memory (iPCM), is characterized by significantly faster switching, lower energy consumption, and better endurance. The switching mechanism in iPCM, where both the SET and RESET states are crystalline, is still contentious. Here, using the ab initio density functional theory simulations, a conceptually new switching mechanism for iPCM is derived, which is based on the change in the potential landscape of the bandgap, associated with local deviations from the pseudobinary stoichiometry across the van der Waals gaps and the associated shift of the Fermi level. The crucial role in this process belongs to Ge/Sb intermixing on the cation planes of iPCM. These findings offer a comprehensive understanding of the switching mechanisms in iPCM and are an essential step forward to the insightful development of phase-change memory technology. Phase-change memory ; Materials science ; Superlattice ; Condensed matter physics ; Density functional theory ; Amorphous solid ; Non-volatile memory ; Ab initio quantum chemistry methods ; van der Waals force ; Phase (matter) ; Chemical physics ; Optoelectronics ; Nanotechnology ; Chemistry ; Computational chemistry ; Crystallography ; Physics ; Layer (electronics) Phase-change materials and chalcogenides ; Chalcogenide Semiconductor Thin Films ; Transition Metal Oxide Nanomaterials
Authors: Pierre‐Luc Latreille | Vahid Adibnia | Antone Nour | Jean‐Michel Rabanel | Augustine Lalloz | Jochen Arlt | Wilson C. K. Poon | Patrice Hildgen | Vincent A. Martinez | Xavier Banquy
Source: Nature Communications (article, 2019-09-20)
Field: Materials Science — Materials Chemistry

Spontaneous shrinking of soft nanoparticles boosts their diffusion in confined media Improving nanoparticles (NPs) transport across biological barriers is a significant challenge that could be addressed through understanding NPs diffusion in dense and confined media. Here, we report the ability of soft NPs to shrink in confined environments, therefore boosting their diffusion compared to hard, non-deformable particles. We demonstrate this behavior by embedding microgel NPs in agarose gels. The origin of the shrinking appears to be related to the overlap of the electrostatic double layers (EDL) surrounding the NPs and the agarose fibres. Indeed, it is shown that screening the EDL interactions, by increasing the ionic strength of the medium, prevents the soft particle shrinkage. The shrunken NPs diffuse up to 2 orders of magnitude faster in agarose gel than their hard NP counterparts. These findings provide valuable insights on the role of long range interactions on soft NPs dynamics in crowded environments, and help rationalize the design of more efficient NP-based transport systems. Nanoparticle ; Diffusion ; Nanotechnology ; Materials science ; Physics ; Thermodynamics Pickering emulsions and particle stabilization ; Advanced Cellulose Research Studies ; Surfactants and Colloidal Systems
Authors: Andrew L. Goodwin
Source: Nature Communications (article, 2019-10-01)
Field: Materials Science — Materials Chemistry

Opportunities and challenges in understanding complex functional materials Understanding complex functional materials suffers from needing to capture structural features on many length scales. By quantitatively combining complementary experimental measurements, realistic models can now be generated. Here, I discuss the strengths and limits of this approach, but also advocate focusing on the interactions that drive structural complexity instead. Computer science ; Data science ; Management science ; Engineering Machine Learning in Materials Science ; Electronic and Structural Properties of Oxides ; Catalysis and Oxidation Reactions
Authors: Leanne C. Nye | Jonathan P. Williams | Nyasha Munjoma | Marine P. M. Letertre | Muireann Coen | Robbin Bouwmeester | Lennart Martens | Jonathan R. Swann | Jeremy K. Nicholson | Robert S. Plumb | Michael McCullagh | Lee A. Gethings | Steven Lai | James Langridge | Johannes P.C. Vissers | Ian D. Wilson
Source: Journal of Chromatography A (article, 2019-06-27)
Field: Chemistry — Spectroscopy

A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry: Application to the characterisation of metabolites in rat urine A comprehensive Collision Cross Section (CCS) library was obtained via Travelling Wave Ion Guide mobility measurements through direct infusion (DI). The library consists of CCS and Mass Spectral (MS) data in negative and positive ElectroSpray Ionisation (ESI) mode for 463 and 479 endogenous metabolites, respectively. For both ionisation modes combined, <sup>TW</sup>CCS<sub>N2</sub> data were obtained for 542 non-redundant metabolites. These data were acquired on two different ion mobility enabled orthogonal acceleration QToF MS systems in two different laboratories, with the majority of the resulting <sup>TW</sup>CCS<sub>N2</sub> values (from detected compounds) found to be within 1% of one another. Validation of these results against two independent, external <sup>TW</sup>CCS<sub>N2</sub> data sources and predicted <sup>TW</sup>CCS<sub>N2</sub> values indicated to be within 1-2% of these other values. The same metabolites were then analysed using a rapid reversed-phase ultra (high) performance liquid chromatographic (U(H)PLC) separation combined with IM and MS (IM-MS) thus providing retention time (t<sub>r</sub>), m/z and <sup>TW</sup>CCS<sub>N2</sub> values (with the latter compared with the DI-IM-MS data). Analytes for which <sup>TW</sup>CCS<sub>N2</sub> values were obtained by U(H)PLC-IM-MS showed good agreement with the results obtained from DI-IM-MS. The repeatability of the <sup>TW</sup>CCS<sub>N2</sub> values obtained for these metabolites on the different ion mobility QToF systems, using either DI or LC, encouraged the further evaluation of the U(H)PLC-IM-MS approach via the analysis of samples of rat urine, from control and methotrexate-treated animals, in order to assess the potential of the approach for metabolite identification and profiling in metabolic phenotyping studies. Based on the database derived from the standards 63 metabolites were identified in rat urine, using positive ESI, based on the combination of t<sub>r</sub>, <sup>TW</sup>CCS<sub>N2</sub> and MS data. Ion-mobility spectrometry ; Mass spectrometry ; Ion-mobility spectrometry–mass spectrometry ; Ion ; Chemistry ; Analytical Chemistry (journal) ; Chromatography ; Cross section (physics) ; Traveling wave ; Tandem mass spectrometry ; Selected reaction monitoring ; Physics ; Organic chemistry Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Analytical Chemistry and Chromatography
Authors: Vinay Bhardwaj | Ajeet Kaushik | Ziad Khatib | Madhavan Nair | Anthony J. McGoron
Source: Frontiers in Pharmacology (article, 2019-11-29)
Field: Materials Science — Biomaterials

Recalcitrant Issues and New Frontiers in Nano-Pharmacology Packaging of old pharma drugs into new packaging "nanoparticles" is called nano-pharmacology and the products are called nano-based drugs. The inception of nano-pharmacology research and development (R&D) is marked by the approval of the first nano-based drug Doxil<sup>®</sup> in 1995 by the Food and Drug Administration. However, even after more than two decades, today, there are only ∼20 nano-based drugs in the market to treat cancers and brain diseases. In this article we share the perspectives of nanotechnology scientists, engineers, and clinicians on the roadblocks in nano-pharmacology R&D. Also, we share our opinion on new frontiers in the field of nano-pharmacology R&D that may allow rapid and efficient transfer of nano-pharma technologies from R&D to market. Pharmacology ; Medicine Nanoparticle-Based Drug Delivery ; 3D Printing in Biomedical Research ; Nanoparticles: synthesis and applications
Authors: Hao Yang | Yanchang Li | Mingzhi Zhao | Feilin Wu | Xi Wang | Weidi Xiao | Yihao Wang | Junling Zhang | Fuqiang Wang | Feng Xu | Wenfeng Zeng | Christopher M. Overall | Si‐Min He | Hao Chi | Ping Xu
Source: Molecular & Cellular Proteomics (article, 2019-01-09)
Field: Chemistry — Spectroscopy

Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics <i>De novo</i> peptide sequencing for large-scale proteomics remains challenging because of the lack of full coverage of ion series in tandem mass spectra. We developed a mirror protease of trypsin, acetylated LysargiNase (Ac-LysargiNase), with superior activity and stability. The mirror spectrum pairs derived from the Ac-LysargiNase and trypsin treated samples can generate full <i>b</i> and <i>y</i> ion series, which provide mutual complementarity of each other, and allow us to develop a novel algorithm, pNovoM, for <i>de novo</i> sequencing. Using pNovoM to sequence peptides of purified proteins, the accuracy of the sequence was close to 100%. More importantly, from a large-scale yeast proteome sample digested with trypsin and Ac-LysargiNase individually, 48% of all tandem mass spectra formed mirror spectrum pairs, 97% of which contained full coverage of ion series, resulting in precision <i>de novo</i> sequencing of full-length peptides by pNovoM. This enabled pNovoM to successfully sequence 21,249 peptides from 3,753 proteins and interpreted 44-152% more spectra than pNovo+ and PEAKS at a 5% FDR at the spectrum level. Moreover, the mirror protease strategy had an obvious advantage in sequencing long peptides. We believe that the combination of mirror protease strategy and pNovoM will be an effective approach for precision <i>de novo</i> sequencing on both single proteins and proteome samples. Trypsin ; Proteome ; Protease ; Proteomics ; Proteases ; Computational biology ; Bottom-up proteomics ; Peptide ; Tandem mass spectrometry ; Chemistry ; Peptide sequence ; Biology ; Biochemistry ; Mass spectrometry ; Chromatography ; Enzyme ; Protein mass spectrometry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Genomics and Phylogenetic Studies
Authors: Marc Riera | Eric Yeh | Francesco Paesani
Source: ChemRxiv (preprint, 2019-12-06)
Field: Materials Science — Materials Chemistry

Data-Driven Many-Body Models for Molecular Fluids: CO2/H2O Mixtures as a Case Study &lt;div&gt; &lt;div&gt; &lt;div&gt; &lt;p&gt;In this study, we extend the scope of the many-body TTM-nrg and MB-nrg potential energy functions (PEFs), originally introduced for halide ion–water and alkali-metal ion–water interactions, to the modeling of carbon dioxide (CO&lt;sub&gt;2&lt;/sub&gt;) and water (H&lt;sub&gt;2&lt;/sub&gt;O) mixtures as prototypical examples of molecular fluids. Both TTM-nrg and MB-nrg PEFs are derived entirely from electronic structure data obtained at the coupled cluster level of theory and are, by construction, compatible with MB-pol, a many-body PEF that has been shown to accurately reproduce the properties of water. Although both TTM-nrg and MB-nrg PEFs adopt the same functional forms for describing permanent electrostatics, polarization, and dispersion, they differ in the representation of short-range contributions, with the TTM-nrg PEFs relying on conventional Born-Mayer expressions and the MB-nrg PEFs employing multidimensional permutationally invariant polynomials. By providing a physically correct description of many-body effects at both short and long ranges, the MB-nrg PEFs are shown to quantitatively represent the global potential energy surfaces of the CO&lt;sub&gt;2&lt;/sub&gt;–CO&lt;sub&gt;2&lt;/sub&gt; and CO&lt;sub&gt;2&lt;/sub&gt;–H&lt;sub&gt;2&lt;/sub&gt;O dimers and the energetics of small clusters as well as to correctly reproduce various properties in both gas and liquid phases. Building upon previous studies of aqueous systems, our analysis provides further evidence for the accuracy and efficiency of the MB-nrg framework in representing molecular interactions in fluid mixtures at different temperature and pressure conditions. &lt;/p&gt; &lt;/div&gt; &lt;/div&gt; &lt;/div&gt; Chemistry ; Physics Machine Learning in Materials Science ; Protein Structure and Dynamics ; Phase Equilibria and Thermodynamics
Authors: Kaito Kanahashi | Masatou Ishihara | Masataka Hasegawa | Hiromichi Ohta | Taishi Takenobu
Source: npj 2D Materials and Applications (article, 2019-11-08)
Field: Materials Science — Materials Chemistry

Giant power factors in p- and n-type large-area graphene films on a flexible plastic substrate Abstract This study reports on the thermoelectric properties of large-area graphene films grown by chemical vapor deposition (CVD) methods. Using the electric double layer gating technique, both the continuous doping of hole or electron carriers and modulation of the Fermi energy are achieved, leading to wide-range control of the Seebeck coefficient and electrical conductivity. Consequently, the maximum power factors of the CVD-grown large-area graphene films are 6.93 and 3.29 mW m –1 K –2 for p- and n-type carrier doping, respectively. These results are the best values among large-scale flexible materials, such as organic conducting polymers and carbon nanotubes, suggesting that CVD-grown large-area graphene films have potential for thermoelectric applications. Graphene ; Materials science ; Seebeck coefficient ; Chemical vapor deposition ; Thermoelectric effect ; Doping ; Optoelectronics ; Carbon nanotube ; Electron mobility ; Fermi level ; Nanotechnology ; Substrate (aquarium) ; Electrical resistivity and conductivity ; Electron ; Composite material ; Thermal conductivity ; Electrical engineering Advanced Thermoelectric Materials and Devices ; Graphene research and applications ; Thermal properties of materials
Authors: Wenxiang Wang | Lingbing Ge | Guodong Xue | Fang Miao | Pingan Chen | Hanjiao Chen | Yi-Wei Lin | Yong Ni | Jingyuan Xiong | Yuanyuan Hu | Jishan Wu | Yonghao Zheng
Source: Chemical Communications (article, 2019-12-24)
Field: Chemistry — Organic Chemistry

Fine-tuning the diradical character of molecular systems <i>via</i> the heteroatom effect Heteroatoms were introduced as a novel modification strategy for fine-tuning the diradical character of molecular systems. Both the diradical character and the singlet-triplet energy gaps of diketopyrrolopyrrole based phenoxyl diradicaloids decreased as the size of the substituted heteroatoms (from O, S to Se atom) increased. Diradical ; Heteroatom ; Character (mathematics) ; Chemistry ; Computational chemistry ; Chemical physics ; Stereochemistry ; Organic chemistry ; Ring (chemistry) ; Physics ; Singlet state ; Quantum mechanics ; Mathematics Fullerene Chemistry and Applications ; Synthesis and Properties of Aromatic Compounds ; Porphyrin and Phthalocyanine Chemistry
Authors: Y. H. Wu | Melgious Jin Yan Ang | Mingzi Sun | Bolong Huang | Xiaogang Liu
Source: Journal of Physics D Applied Physics (article, 2019-06-13)
Field: Materials Science — Materials Chemistry

Expanding the toolbox for lanthanide-doped upconversion nanocrystals Abstract The ability to convert low-energy quanta into a quantum of higher energy is critical for a variety of applications, including photovoltaics, volumetric display, bioimaging, multiplexing sensing, super-resolution imaging, optogenetics, and potentially many others. Although the processes of second harmonic generation and multiphoton (or two-photon) absorption can be used to generate photon upconversion, lanthanide-doped upconversion nanocrystals have emerged as an attractive alternative for nonlinear upconversion of near-infrared light with pump intensities several orders of magnitude lower than required by conventional nonlinear crystals. Over the past five years, considerable efforts have been made to tune the photoluminescence of upconversion nanocrystals, and significant progress has been achieved. In this review, we focus on manipulation of the wavelength, emission intensity and lifetime of upconversion nanocrystals. Here, we outline the fundamental principle for the upconversion phenomenon, review the current experimental state-of-the-art for controlling photon upconversion in lanthanide-doped nanocrystals and highlight the prospects for multifunctional upconversion nanocrystals currently in development. Lanthanide ; Photon upconversion ; Toolbox ; Nanocrystal ; Doping ; Materials science ; Nanotechnology ; Optoelectronics ; Rare earth ; Computer science ; Chemistry ; Metallurgy ; Ion ; Programming language Luminescence Properties of Advanced Materials ; Radiation Detection and Scintillator Technologies ; Radioactive element chemistry and processing
Authors: Arturo Blanco‐Gómez | Ángel Fernández‐Blanco | Víctor Blanco | Jaime Rodrı́guez | Carlos Peinador | Marcos D. García
Source: Journal of the American Chemical Society (article, 2019-02-07)
Field: Chemistry — Organic Chemistry

Thinking Outside the “Blue Box”: Induced Fit within a Unique Self-Assembled Polycationic Cyclophane We present herein the development of a new polycationic molecular receptor, inspired by the ubiquitous cyclobis(paraquat- p-phenylene)cyclophane ("blue box"). Our analogue, the "white box", has been easily self-assembled on a preparative scale in water, using a template-assisted process by acyl hydrazone bonding of complementary bis(pyridinium)xylylene tweezers, followed by kinetic trapping of the empty receptor. The obtained macrocycle was found to display a marked pH responsiveness in water, because of an abnormal acidity of the amide protons within its structure. Consequently, and because of the concurrence of rotational isomerism under acidic conditions (fixed at higher pH values), the compound was found to display a dual behavior as a conformationally locked/flexible molecular host, being able to recognize appropriate aromatic substrates, in a lock and key or induced fit fashion, by a conjunction of π-π, C-H···π, and, crucially, the hydrophobic effect. Chemistry ; Cyclophane ; Crystallography ; Crystal structure Supramolecular Chemistry and Complexes ; Supramolecular Self-Assembly in Materials ; Molecular Sensors and Ion Detection
Authors: Md. Alim Iftekhar Rasel | Sanjleena Singh | Trung Dung Nguyen | Isaac O. Afara | Yuantong Gu
Source: Scientific Reports (article, 2019-04-10)
Field: Materials Science — Materials Chemistry

Impact of Nanoparticle Uptake on the Biophysical Properties of Cell for Biomedical Engineering Applications Nanomaterials are currently the state-of-the-art in the development of advanced biomedical devices and applications where classical approaches have failed. To date, majority of the literature on nanomaterial interaction with cells have largely focused on the biological responses of cells obtained via assays, with little interest on their biophysical responses. However, recent studies have shown that the biophysical responses of cells, such as stiffness and adhesive properties, play a significant role in their physiological function. In this paper, we investigate cell biophysical responses after uptake of nanoparticles. Atomic force microscopy was used to study changes in cell stiffness and adhesion upon boron nitride (BN) and hydroxyapatite (HAP) nanoparticle uptake. Results show increase in cell stiffness with varying nanoparticle (BN and HAP) concentration, while a decrease in cell adhesion trigger by uptake of HAP. In addition, changes in the biochemical response of the cell membrane were observed via Raman spectroscopy of nanoparticle treated cells. These findings have significant implications in biomedical applications of nanoparticles, e.g. in drug delivery, advanced prosthesis and surgical implants. Nanoparticle ; Nanotechnology ; Nanomaterials ; Materials science ; Adhesion ; Cell adhesion ; Cell ; Biophysics ; Cell function ; Drug delivery ; Chemistry ; Biology ; Biochemistry Nanoparticles: synthesis and applications ; Cellular Mechanics and Interactions ; Bone Tissue Engineering Materials
Authors: Jaime Gómez-Bolívar | Iryna P. Mikheenko | Lynne E. Macaskie | Mohamed L. Merroun
Source: Nanomaterials (article, 2019-06-05)
Field: Materials Science — Materials Chemistry

Characterization of Palladium Nanoparticles Produced by Healthy and Microwave-Injured Cells of Desulfovibrio desulfuricans and Escherichia coli Numerous studies have focused on the bacterial synthesis of palladium nanoparticles (bio-Pd NPs), via uptake of Pd (II) ions and their enzymatically-mediated reduction to Pd (0). Cells of <i>Desulfovibrio desulfuricans</i> (obligate anaerobe) and <i>Escherichia coli</i> (facultative anaerobe, grown anaerobically) were exposed to low-dose radiofrequency (RF) radiation(microwave (MW) energy) and the biosynthesized Pd NPs were compared. Resting cells were exposed to microwave energy before Pd (II)-challenge. MW-injured Pd (II)-treated cells (and non MW-treated controls) were contacted with H<sub>2</sub> to promote Pd(II) reduction. By using scanning transmission electron microscopy (STEM) associated with a high-angle annular dark field (HAADF) detector and energy dispersive X-ray (EDX) spectrometry, the respective Pd NPs were compared with respect to their mean sizes, size distribution, location, composition, and structure. Differences were observed following MWinjury prior to Pd(II) exposure versus uninjured controls. With <i>D. desulfuricans</i> the bio-Pd NPs formed post-injury showed two NP populations with different sizes and morphologies. The first, mainly periplasmically-located, showed polycrystalline Pd nano-branches with different crystal orientations and sizes ranging between 20 and 30 nm. The second NPpopulation, mainly located intracellularly, comprised single crystals with sizes between 1 and 5 nm. Bio-Pd NPs were produced mainly intracellularly by injured cells of <i>E. coli</i> and comprised single crystals with a size distribution between 1 and 3 nm. The polydispersity index was reduced in the bio-Pd made by injured cells of <i>E. coli</i> and <i>D. desulfuricans</i> to 32% and 39%, respectively, of the values of uninjured controls, indicating an increase in NP homogeneity of 30-40% as a result of the prior MWinjury. The observations are discussed with respect to the different locations of Pd(II)-reducing hydrogenases in the two organisms and with respect to potential implications for the catalytic activity of the produced NPs following injury-associated altered NP patterning. Palladium ; Escherichia coli ; Nuclear chemistry ; Dispersity ; Nanoparticle ; Transmission electron microscopy ; Materials science ; Chemistry ; Nanotechnology ; Catalysis ; Biochemistry Nanoparticles: synthesis and applications ; Environmental remediation with nanomaterials ; Bone Tissue Engineering Materials