jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Jordan Teeter | Na Yeon Kim | Topojit Debnath | Nicholas Sesing | Tekwam Geremew | Dylan Wright | Miaofang Chi | Adam Z. Stieg | Jianwei Miao | Roger K. Lake | Tina T. Salguero | Alexander A. Balandin
Source: Advanced Materials (article, 2024-10-14)
Field: Materials Science — Materials Chemistry

Achieving the 1D Atomic Chain Limit in Van der Waals Crystals Experiments with graphene have demonstrated that 2D van der Waals materials can be stable, robust, and efficiently manipulated at the level of individual atomic planes. However, the stability and manipulation of 1D van der Waals materials and individual atomic chains remains elusive. Here, the ability to exfoliate and process two representative van der Waals materials containing 1D motifs, namely MoI<sub>3</sub> and Ta<sub>2</sub>Se<sub>8</sub>I, at the scale of individual atomic chains is demonstrated. High-resolution transmission electron microscopy and atomic force microscopy studies confirm the presence of stable individual atomic chains of MoI<sub>3</sub> at room temperature. It is further shown that 1D van der Waals materials with low exfoliation energy, such as Ta<sub>2</sub>Se<sub>8</sub>I, can be processed with electron beams to achieve suspended individual atomic chains. Ab initio calculations corroborate the findings regarding the cleavage energies and the thermodynamic stability of individual atomic chains in these 1D van der Waals materials. These results demonstrate that the top-down approach in material processing can be extended to the scale of individual chains. van der Waals force ; Van der Waals radius ; Atomic units ; Exfoliation joint ; Materials science ; Van der Waals strain ; Van der Waals surface ; Chemical physics ; DLVO theory ; Hamaker constant ; Graphene ; Ab initio ; Nanotechnology ; Physical chemistry ; Chemistry ; Physics ; Colloid ; Molecule ; Quantum mechanics 2D Materials and Applications ; MXene and MAX Phase Materials ; Graphene research and applications
Authors: Chenchen Wu | Yu Duan | Lintao Yu | Yao Hu | Chenxi Zhao | C. Ji | Xiangdong Guo | Shu Zhang | Xiaokang Dai | Puyi Ma | Qian Wang | Shengjie Ling | Xiaoxia Yang | Qing Dai
Source: Nature Communications (article, 2024-05-31)
Field: Materials Science — Biomaterials

In-situ observation of silk nanofibril assembly via graphene plasmonic infrared sensor Silk nanofibrils (SNFs), the fundamental building blocks of silk fibers, endow them with exceptional properties. However, the intricate mechanism governing SNF assembly, a process involving both protein conformational transitions and protein molecule conjunctions, remains elusive. This lack of understanding has hindered the development of artificial silk spinning techniques. In this study, we address this challenge by employing a graphene plasmonic infrared sensor in conjunction with multi-scale molecular dynamics (MD). This unique approach allows us to probe the secondary structure of nanoscale assembly intermediates (0.8-6.2 nm) and their morphological evolution. It also provides insights into the dynamics of silk fibroin (SF) over extended molecular timeframes. Our novel findings reveal that amorphous SFs undergo a conformational transition towards β-sheet-rich oligomers on graphene. These oligomers then connect to evolve into SNFs. These insights provide a comprehensive picture of SNF assembly, paving the way for advancements in biomimetic silk spinning. SILK ; Fibroin ; Nanotechnology ; Materials science ; Graphene ; Nanoscopic scale ; Spider silk ; Molecular dynamics ; Infrared ; Plasmon ; Chemistry ; Optoelectronics ; Physics ; Composite material Silk-based biomaterials and applications ; Biochemical and Structural Characterization ; Neurobiology and Insect Physiology Research
Authors: Khaled Mahmud | Taki Yashir | Ahmed Zubair
Source: Nanoscale Advances (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

First-principles calculations on monolayer WX<sub>2</sub> (X = S, Se) as an effective drug delivery carrier for anti-tuberculosis drugs Tuberculosis (TB) remains a major global health concern, necessitating the exploration of novel drug delivery systems to combat the challenges posed by conventional approaches. We investigated the potential of monolayer transition metal dichalcogenides (TMDs) as an innovative platform for efficient and targeted delivery of antituberculosis drugs. Specifically, the electronic and optical properties of prominent TB drugs, isoniazid (INH) and pyrazinamide (PZA), adsorbed on tungsten diselenide (WSe<sub>2</sub>) and tungsten disulfide (WS<sub>2</sub>) monolayers were studied using first-principles calculations based on density functional theory (DFT). The investigation revealed that the band gaps of WSe<sub>2</sub> and WS<sub>2</sub> monolayers remain unaltered upon adsorption of PZA or INH, with negative adsorption energy indicating stable physisorption. We explored different vertical and horizontal configurations, and the horizontal ones were more stable. When INH and PZA drugs were horizontally adsorbed together on WSe<sub>2</sub>, the most stable configuration was found with an adsorption energy of -2.35 eV. Moreover, the adsorbed drugs could be readily released by light within the visible or near-infrared (NIR) wavelength range. This opened up possibilities for their potential application in photothermal therapy, harnessing the unique properties of these 2D materials. The comprehensive analysis of the band structures and density of states provides valuable insights into how the drug molecules contributed to the conduction and valence bands. The optical responses of anti-TB drugs adsorbed in 2D WSe<sub>2</sub> and WS<sub>2</sub> were similar to those of pristine 2D WSe<sub>2</sub> and WS<sub>2</sub>. We demonstrated the temperature-dependent release mechanism of our 2D WSe<sub>2</sub> and WS<sub>2</sub> drug complexes, confirming the feasibility of releasing the discussed anti-tuberculosis drugs by generating heat through photothermal therapy. These findings hold significant promise for developing innovative drug delivery systems that have enhanced efficacy for targeted and low-toxic TB treatment. Tungsten diselenide ; Pyrazinamide ; Drug delivery ; Nanotechnology ; Monolayer ; Tuberculosis ; Isoniazid ; Drug ; Materials science ; Medicine ; Pharmacology ; Chemistry ; Transition metal ; Organic chemistry MXene and MAX Phase Materials ; 2D Materials and Applications ; Advanced biosensing and bioanalysis techniques
Authors: Michael Bartolf‐Kopp | Tomasz Jüngst
Source: Advanced Healthcare Materials (article, 2024-04-12)
Field: Materials Science — Biomaterials

The Past, Present, and Future of Tubular Melt Electrowritten Constructs to Mimic Small Diameter Blood Vessels – A Stable Process? Melt Electrowriting (MEW) is a continuously growing manufacturing platform. Its advantage is the consistent production of micro- to nanometer fibers, that stack intricately, forming complex geometrical shapes. MEW allows tuning of the mechanical properties of constructs via the geometry of deposited fibers. Due to this, MEW can create complex mechanics only seen in multi-material compounds and serve as guiding structures for cellular alignment. The advantage of MEW is also shown in combination with other biotechnological manufacturing methods to create multilayered constructs that increase mechanical approximation to native tissues, biocompatibility, and cellular response. These features make MEW constructs a perfect candidate for small-diameter vascular graft structures. Recently, studies have presented fascinating results in this regard, but is this truly the direction that tubular MEW will follow or are there also other options on the horizon? This perspective will explore the origins and developments of tubular MEW and present its growing importance in the field of artificial small-diameter vascular grafts with mechanical modulation and improved biomimicry and the impact of it in convergence with other manufacturing methods and how future technologies like AI may influence its progress. Nanotechnology ; Process (computing) ; Biocompatibility ; Materials science ; Mechanical engineering ; Field (mathematics) ; Computer science ; Biomimetics ; Engineering ; Mathematics Electrospun Nanofibers in Biomedical Applications ; Advanced Sensor and Energy Harvesting Materials ; Tissue Engineering and Regenerative Medicine
Authors: Jens R. Coorssen | Matthew P. Padula
Source: Proteomes (article, 2024-04-19)
Field: Chemistry — Spectroscopy

Proteomics—The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience With growing recognition and acknowledgement of the genuine complexity of proteomes, we are finally entering the post-proteogenomic era. Routine assessment of proteomes as inferred correlates of gene sequences (i.e., canonical 'proteins') cannot provide the necessary critical analysis of systems-level biology that is needed to understand underlying molecular mechanisms and pathways or identify the most selective biomarkers and therapeutic targets. These critical requirements demand the analysis of proteomes at the level of proteoforms/protein species, the actual active molecular players. Currently, only highly refined integrated or integrative top-down proteomics (iTDP) enables the analytical depth necessary to provide routine, comprehensive, and quantitative proteome assessments across the widest range of proteoforms inherent to native systems. Here we provide a broad perspective of the field, taking in historical and current realities, to establish a more balanced understanding of where the field has come from (in particular during the ten years since Proteomes was launched), current issues, and how things likely need to proceed if necessary deep proteome analyses are to succeed. We base this in our firm belief that the best proteomic analyses reflect, as closely as possible, the native sample at the moment of sampling. We also seek to emphasise that this and future analytical approaches are likely best based on the broad recognition and exploitation of the complementarity of currently successful approaches. This also emphasises the need to continuously evaluate and further optimize established approaches, to avoid complacency in thinking and expectations but also to promote the critical and careful development and introduction of new approaches, most notably those that address proteoforms. Above all, we wish to emphasise that a rigorous focus on analytical quality must override current thinking that largely values analytical speed; the latter would certainly be nice, if only proteoforms could thus be effectively, routinely, and quantitatively assessed. Alas, proteomes are composed of proteoforms, not molecular species that can be amplified or that directly mirror genes (i.e., 'canonical'). The problem is hard, and we must accept and address it as such, but the payoff in playing this longer game of rigorous deep proteome analyses is the promise of far more selective biomarkers, drug targets, and truly personalised or even individualised medicine. Field (mathematics) ; State (computer science) ; Proteomics ; Data science ; Computer science ; Biology ; Mathematics Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Ubiquitin and proteasome pathways
Authors: Bo Wen | Jack Freestone | Michael Riffle | Michael J. MacCoss | William Stafford Noble | Uri Keich
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-06-03)
Field: Chemistry — Spectroscopy

Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment A pressing statistical challenge in the field of mass spectrometry proteomics is how to assess whether a given software tool provides accurate error control. Each software tool for searching such data uses its own internally implemented methodology for reporting and controlling the error. Many of these software tools are closed source, with incompletely documented methodology, and the strategies for validating the error are inconsistent across tools. In this work, we identify three different methods for validating false discovery rate (FDR) control in use in the field, one of which is invalid, one of which can only provide a lower bound rather than an upper bound, and one of which is valid but under-powered. The result is that the field has a very poor understanding of how well we are doing with respect to FDR control, particularly for the analysis of data-independent acquisition (DIA) data. We therefore propose a theoretical formulation of entrapment experiments that allows us to rigorously characterize the behavior of the various entrapment methods. We also propose a more powerful method for evaluating FDR control, and we employ that method, along with other existing techniques, to characterize a variety of popular search tools. We empirically validate our entrapment analysis in the fairly well-understood DDA setup before applying it in the DIA setup. We find that none of the DIA search tools consistently controls the FDR at the peptide level, and the tools struggle particularly with analysis of single cell datasets. False discovery rate ; Computer science ; Data mining ; Software ; Mascot ; Field (mathematics) ; Bounding overwatch ; Control (management) ; Artificial intelligence ; Mathematics ; Chemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Michael B. Prime | Saryu Fensin | David R. Jones | Joshua Dyer | Daniel T. Martinez
Source: Physical review. E (article, 2024-01-26)
Field: Materials Science — Materials Chemistry

Multiscale Richtmyer-Meshkov instability experiments to isolate the strain rate dependence of strength Theoretical analysis of Richtmyer-Meshkov instability (RMI) experiments for solid strength shows that the strain rate for a given shock should be inversely proportional to the length scale of the sine wave perturbations when η_{0}k, the nondimensional amplitude to wavelength ratio, is held fixed. To isolate the effect of strain rate on strength, free-surface RMI specimens of annealed copper were prepared with three perturbation regions with the same η_{0}k but different length scales, characterized by the wavelength λ varying by a factor of 4.9 from 65 to 130 to 320µm. Three such targets with different fixed η_{0}k^{'}s were impacted to a shock pressure of 25 GPa, and the instability evolution was measured with photon Doppler velocimetry. Strengths estimated by comparing hydrocode simulation to the data increased from 700 to 1200 MPa as λ decreased. The different η_{0}k targets exercised increasing amounts of plastic strain yet showed no evidence of strain hardening. Physical regime sensitivity analysis determined that for 320-65µm wavelength perturbations, the effective strain rates increased from 8.7×10^{6} to 3.3×10^{7}s^{-1}, a factor of 3.8. Thus, the predicted strain rate scaling was mostly achieved but slightly suppressed by increased strength at higher rates. The RMI strength estimates were plotted against constitutive testing data on copper from the literature to show striking evidence of the strength upturn at higher strain rates. Strain rate ; Work (physics) ; Richtmyer–Meshkov instability ; Strain (injury) ; Instability ; Sensitivity (control systems) ; Materials science ; Mechanics ; Thermodynamics ; Physics ; Composite material ; Engineering High-Velocity Impact and Material Behavior ; Laser-Plasma Interactions and Diagnostics ; Ion-surface interactions and analysis
Authors: Peterson Ricardo Fiorio | Carlos Augusto Alves Cardoso Silva | Rodnei Rizzo | José Alexandre Melo Demattê | Ana Cláudia dos Santos Luciano | Marcelo Andrade da Silva
Source: Heliyon (article, 2024-02-21)
Field: Chemistry — Analytical Chemistry

Prediction of leaf nitrogen in sugarcane (Saccharum spp.) by Vis-NIR-SWIR spectroradiometry Nitrogen is one of the essential nutrients for the production of agricultural crops, participating in a complex interaction among soil, plant and the atmosphere. Therefore, its monitoring is important both economically and environmentally. The aim of this work was to estimate the leaf nitrogen contents in sugarcane from hyperspectral reflectance data during different vegetative stages of the plant. The assessments were performed from an experiment designed in completely randomized blocks, with increasing nitrogen doses (0, 60, 120 and 180 kg ha<sup>-1</sup>). The acquisition of the spectral data occurred at different stages of crop development (67, 99, 144, 164, 200, 228, 255 and 313 days after cutting; DAC). In the laboratory, the hyperspectral responses of the leaves and the Leaf Nitrogen Contents (LNC) were obtained. The hyperspectral data and the LNC values were used to generate spectral models employing the technique of Partial Least Squares Regression (PLSR) Analysis, also with the calculation of the spectral bands of greatest relevance, by the Variable Importance in Projection (VIP). In general, the increase in LNC promoted a smaller reflectance in all wavelengths in the visible (400-680 nm). Acceptable models were obtained (R<sup>2</sup> > 0.70 and RMSE <1.41 g kg<sup>-1</sup>), the most robust of which were those generated from spectra in the visible (400-680 nm) and red-edge (680-750 nm), with values of R<sup>2</sup> > 0.81 and RMSE <1.24 g kg<sup>-1</sup>. An independent validation, leave-one-date-out cross validation (LOOCV), was performed using data from other collections, which confirmed the robustness and the possibility of LNC prediction in new data sets, derived, for instance, from samplings subsequent to the period of study. Saccharum ; Nitrogen ; Saccharum officinarum ; Agronomy ; Environmental science ; Biology ; Botany ; Horticulture ; Chemistry Spectroscopy and Chemometric Analyses ; Leaf Properties and Growth Measurement ; Water Quality Monitoring and Analysis
Authors: Zhiqiang Wang | Fengjun Li | Qian-Mei Deng | Zhou Wan | Xiangping Li | Zi‐Lan Deng
Source: Chinese Optics Letters (article, 2024-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Inverse-designed Jones matrix metasurfaces for high-performance meta-polarizers Polarizers have always been an important optical component for optical engineering and have played an indispensable part of polarization imaging systems. Metasurface polarizers provide an excellent platform to achieve miniaturization, high resolution, and low cost of polarization imaging systems. Here, we proposed freeform metasurface polarizers derived by adjoint-based inverse design of a full-Jones matrix with gradient-descent optimization. We designed multiple freeform polarizers with different filtered states of polarization (SOPs), including circular polarizers, elliptical polarizers, and linear polarizers that could cover the full Poincaré sphere. Note that near-unitary polarization dichroism and the ultrahigh polarization extinction ratio (ER) reaching 50 dB were achieved for optimized circular polarizers. The multiple freeform polarizers with filtered polarization state locating at four vertices of an inscribed regular tetrahedron of the Poincaré sphere are designed to form a full-Stokes parameters micropolarizer array. Our work provides a novel approach, we believe, for the design of meta-polarizers that may have potential applications in polarization imaging, polarization detection, and communication. Polarizer ; Optics ; Polarization (electrochemistry) ; Stokes parameters ; Extinction ratio ; Polarimetry ; Materials science ; Physics ; Birefringence ; Wavelength ; Scattering Metamaterials and Metasurfaces Applications ; Liquid Crystal Research Advancements ; Advanced Antenna and Metasurface Technologies
Authors: Shengkai Tang | Jun Wang | Xuexia Zhu | Dongdong Shen
Source: Toxics (article, 2024-01-08)
Field: Materials Science — Materials Chemistry

Ecological Risks of Zinc Oxide Nanoparticles for Early Life Stages of Obscure Puffer (Takifugu obscurus) Nanoparticles of zinc oxide (ZnO NPs) are extensively used in various applications, and their widespread use leads to their environmental presence, particularly in wastewater treatment plant effluents, rivers, and soil. This study focuses on the obscure puffer, Takifugu obscurus, an economically important fish in China, aiming to assess the toxic effects of ZnO NPs on its early life stages, emphasizing the need for understanding the ecological implications of ZnO NP exposure in aquatic environments. Exposure during the hatching stage resulted in a significant decrease in hatching rates, with embryos displaying surface coating at higher ZnO NP concentrations. Newly hatched larvae experienced deformities, and post-hatching exposure led to pronounced reductions in survival rates, particularly with higher ZnO NP concentrations. Two-month-old juveniles exposed to increasing ZnO NP concentrations exhibited a consistent decline in survival rates, emphasizing concentration-dependent adverse effects. Biochemical analyses revealed elevated malondialdehyde (MDA) levels and decreased glutathione (GSH), superoxide dismutase (SOD), and catalase (CAT) activities in various tissues, indicating oxidative stress. This study underscores the ecological risks of ZnO NP contamination in aquatic environments, emphasizing the need for careful consideration of nanoparticle exposure in aquatic ecosystems. Hatching ; Catalase ; Aquatic ecosystem ; Superoxide dismutase ; Biology ; Malondialdehyde ; Zinc ; Environmental chemistry ; Oxidative stress ; Toxicology ; Aquatic animal ; Ecology ; Animal science ; Chemistry ; Fish <Actinopterygii> ; Fishery ; Biochemistry Nanoparticles: synthesis and applications
Authors: Faizan Faraz | Jie Tian | Taufeeq Ur Rehman Abbasi | Weiren Zhu
Source: Advanced Physics Research (article, 2024-08-11)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Recent Advances in Geometric Phase Metasurfaces: Principles and Applications Abstract The concept of geometric phase traversing numerous domains in physics and has been a continuous source of fascination and inspiration for researchers. Despite the extensive research surrounding geometric phase from decades, advances in technology continue to yield novel theories, innovative devices, and captivating applications, extending even to the realm of subwavelength scales. This review article provides a comprehensive exploration of geometric phase metasurfaces, delving into their design principles and categorizing them based on materials properties. In addition, multi‐fold and reconfigurable metasurfaces based on geometric principle are further explored with their unique capabilities and potential impact on a diverse range of applications, including beam steering, lensing, polarization conversion, and holographic imaging. By examining the state‐of‐the‐art in geometric phase metasurfaces, insights are aimed to offer into their current capabilities and limitations. Finally, the prospects and challenges are discussed that lie ahead for this promising field, paving the way for future advancements and innovations. Phase (matter) ; Computer science ; Geometric phase ; Physics Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis