jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Seamus R. Morrone | Michael R. Hoopmann | David Shteynberg | Ulrike Kusebauch | Robert L. Moritz
Source: ChemRxiv (preprint, 2023-02-09)
Field: Chemistry — Spectroscopy

Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-dependent Analysis Using Orbitrap Tribrid Mass Spectrometers The analysis of protein phosphorylation site identification by mass spectrometry-based methods continues to improve with increased efficiency at multiple points of the pipeline including affinity isolation, sample handling with automated protein digestion and phosphopeptide extraction routines, and more sensitive phosphopeptide detection capabilities. The role mass spectrometry parameters play in the quantity and quality of results is understudied, with some reports presenting improvements without sufficient details of how these parameters were derived, nor how they were fully optimized. Here, we systematically scrutinize and optimize parameters of two Orbitrap Tribrid mass spectrometers by varying instrument parameters at both the MS1 and MS2 levels using Titanium IMAC-enriched phosphopeptide samples to illustrate how the recovery of phosphopeptides, and the confidence of phosphosite localizations, vary accordingly. These optimized values are then used to compare different IMAC beads for phosphopeptide-enrichment, and optimal bead combinations used to further improve phosphopeptide detection. These results have implications for planning detailed phosphoprotein identification and quantitation experiments to provide confidence in detection, site localization and reproducibility. Phosphopeptide ; Mass spectrometry ; Orbitrap ; Chromatography ; Phosphoprotein ; Chemistry ; Computer science ; Phosphorylation ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Identification and Quantification in Food
Authors: Daniel Massatt | Stephen P. Shipman | Ilya Vekhter | Justin H. Wilson
Source: arXiv (Cornell University) (preprint, 2023-12-28)
Field: Materials Science — Materials Chemistry

Defect bound states in the continuum of bilayer electronic materials without symmetry protection We analyze a class of bound defect states in the continuum electronic spectrum of bilayer materials, which emerge independent of symmetry protection or additional degrees of freedom. Taking graphene as a prototypical example, our comparative analysis of AA- and AB-stacked bilayer graphene demonstrates that these states originate from the intrinsic algebraic structure of the tight-binding Hamiltonian when trigonal warping is neglected rather than any underlying symmetry. Inclusion of trigonal warping and higher-order hoppings broaden the bound states into long-lived resonances. This discovery provides a pathway to previously unexplored approaches in defect and band-structure engineering. We conclude with a proposed protocol for observing these states in scanning tunneling microscopy experiments. Bilayer graphene ; Scanning tunneling microscope ; Bilayer ; Bound state ; Hamiltonian (control theory) ; Symmetry (geometry) ; Physics ; Graphene ; Condensed matter physics ; Quantum tunnelling ; Quantum mechanics ; Theoretical physics ; Chemistry ; Membrane ; Mathematics ; Geometry Graphene research and applications ; Quantum and electron transport phenomena ; Surface and Thin Film Phenomena
Authors: Abhishek Sharma | Alex M. H. Wong
Source: arXiv (Cornell University) (preprint, 2023-02-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Bipartite Dielectric Huygens' Metasurface for Anomalous Refraction Huygens' metasurfaces - fundamentally based on Schelkunoff's equivalence principle, Huygens' metasurfaces consist of a two-dimensional array of Huygens' sources formed by co-located orthogonal electric and magnetic dipoles. Such metasurfaces provide electric and magnetic responses to an incoming electromagnetic (EM) wave, leading to unidirectional scattering and 2$π$ phase coverage. We herein report a near-reflectionless coarsely discretized dielectric Huygens' metasurface that performs anomalous refraction, offering a low-loss platform for wave manipulation at high frequencies as compared to their lossy metallic analogue. The coarse discretization dramatically simplifies the design, resulting in a metasurface that is highly efficient, cost-effective, and robust. In this paper, the proposed metasurface comprises two meta-atoms per period and is hence named the bipartite dielectric Huygens' metasurface. Through full-wave simulations at 28 GHz, we show that the proposed metasurface can reroute an incident EM wave from $θ_i=15^{\circ}$ to $θ_t=-44.5^{\circ}$ with very high efficiency: 87% of the scattered power is anomalously transmitted to $θ_t$. Based on our observations, a coarsely discretized dielectric Huygens' metasurface platform can be efficacious to design meta-devices with multifaceted functionalities in different frequency regimes. Physics ; Huygens–Fresnel principle ; Optics ; Dielectric ; Negative refraction ; Discretization ; Lossy compression ; Scattering ; Electromagnetic radiation ; Equivalence (formal languages) ; Refraction ; Dipole ; Metamaterial ; Computer science ; Mathematical analysis ; Mathematics ; Optoelectronics ; Quantum mechanics ; Pure mathematics Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Joanna Bons | Christie L. Hunter | Rita Chupalov | Jason Causon | Alexandra Antonoplis | Jacob Rose | Brendan MacLean | Birgit Schilling
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-04-29)
Field: Chemistry — Spectroscopy

Localization and Quantification of Post-Translational Modifications of Proteins Using Electron Activated Dissociation Fragmentation on a Fast-Acquisition Time-of-Flight Mass Spectrometer ABSTRACT Protein post-translational modifications (PTMs) are crucial and dynamic players in a large variety of cellular processes and signaling, and proteomic technologies have emerged as the method of choice to profile PTMs. However, these analyses remain challenging due to potential low PTM stoichiometry, the presence of multiple PTMs per proteolytic peptide, PTM site localization of isobaric peptides, and labile PTM groups that lead to neutral losses. Collision-induced dissociation (CID) is commonly used for to characterize PTMs, but the application of collision energy can lead to neutral losses and incomplete peptide sequencing for labile PTM groups. In this study, we compared CID to an alternative fragmentation, electron activated dissociation (EAD), operated on a recently introduced fast-acquisition quadrupole-time-of-flight (QqTOF) mass spectrometer. We analyzed a series of synthetic modified peptides, featuring phosphorylated, succinylated, malonylated, and acetylated peptides. We performed targeted, quantitative parallel reaction monitoring (PRM or MRM HR ) assays to assess the performances of EAD to characterize, site-localize and quantify peptides with labile modifications. The tunable EAD kinetic energy allowed the preservation of labile modifications and provided better peptide sequence coverage with strong PTM-site localization fragment ions. Zeno trap activation provided significant MS/MS sensitivity gains by an average of 6–11-fold for EAD analyses, regardless of modification type. Evaluation of the quantitative EAD PRM workflows revealed high reproducibility with coefficients of variation of typically ∼2%, as well as very good linearity and quantification accuracy. This novel workflow, combining EAD and Zeno trap, offers confident, accurate, and robust characterization and quantification of PTMs. Chemistry ; Mass spectrometry ; Peptide ; Fragmentation (computing) ; Multiplex ; Dissociation (chemistry) ; Electron-transfer dissociation ; Ion trap ; Tandem mass spectrometry ; Biological system ; Analytical Chemistry (journal) ; Combinatorial chemistry ; Biophysics ; Chromatography ; Biochemistry ; Bioinformatics ; Computer science ; Physical chemistry Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Chemical Synthesis and Analysis
Authors: Thomas Häner | Damian S. Steiger | Helmut G. Katzgraber
Source: arXiv (Cornell University) (preprint, 2023-11-21)
Field: Materials Science — Materials Chemistry

Parallel Tempering for Logic Synthesis The task of logic synthesis is to map a technology-independent representation of an application to hardware-specific operations, taking into account various constraints and trading off different costs associated with the implementation. Constraints may include the target gate library and feasible connectivity, whereas the costs capture, for example, the required chip area and delay. Here we propose to use parallel tempering Monte Carlo to find low-level implementations of a given Boolean function. In contrast to previous work leveraging Markov chain Monte Carlo methods such as simulated annealing, we do not start with an initially correct (but suboptimal) implementation that is then further optimized. Instead, our approach starts with a random logic network that is subsequently modified in order to reduce the error to zero. We apply our method to the task of synthesizing Majority-$n$ in terms of Majority-$3$ gates with and without inverters, aiming for a low Majority-$3$ count. Our method is able to find solutions that are on par or better than previously known solutions. For example, for $n\in\{9,11,13\}$ our approach successfully finds inverter-free implementations using between 7% and 42% fewer Majority-$3$ gates. Computer science ; Simulated annealing ; Parallel tempering ; Logic gate ; Logic synthesis ; Markov chain ; Markov chain Monte Carlo ; Algorithm ; Monte Carlo method ; Task (project management) ; Computer engineering ; Parallel computing ; Mathematics ; Hybrid Monte Carlo ; Artificial intelligence ; Engineering ; Machine learning Machine Learning in Materials Science ; Parallel Computing and Optimization Techniques ; Software Engineering Research
Authors: Pradnya Badole | Mahesh V. Raut | Mr. Sanjivkumar Harinkhede
Source: International Journal for Research in Applied Science and Engineering Technology (article, 2023-01-31)
Field: Materials Science — Materials Chemistry

Review on Detection of Internal Defects in CFRP Strengthened Steel Structures Using Eddy Current Pulsed Thermography Abstract: This study investigates the effectiveness of the current pulse thermal technique (ESRT) in detecting internal defects in СFRР reinforced metal structures. This study covers various internal defects of FRР reinforced steel structures, including cracks, small tracks in СFRР, metal cracks / inter-steel cracks. We theoretically analyze the effect of these problems on the magnetic and thermal response of structures. To confirm the results of the theater, statistical and diagnostic tests were performed on steel plates reinforced with СFRР with various defects. Numerical and diagnostic results show that EСРТ can estimate observed deformations and show low temperature regions in EСРТ thermograms. In addition to the thermal characteristics of the thermograms, the appearance of the temperature profile and changes in temperature are also examined for reanalysis of the thermal analysis. In addition, based on the test results, the effectiveness of EСRT to restore the size and scope of errors was demonstrated. Overall, theoretical, numerical and experimental results show that EСRT is effective in diagnosing internal defects in CFRP-reinforced steel structures Thermography ; Materials science ; Thermal ; Eddy current ; Nondestructive testing ; Current (fluid) ; Structural engineering ; Composite material ; Optics ; Geology ; Infrared ; Engineering ; Meteorology Material Properties and Failure Mechanisms ; Thermography and Photoacoustic Techniques ; Engineering Diagnostics and Reliability
Authors: Rui Yao
Source: arXiv (Cornell University) (preprint, 2023-04-15)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Optical dielectric huygens metagrating performing near unity anomalous refraction at TM mode with extremely simple design We numerically demonstrate a highly efficient optica huygens metagrating with unprecedentedly simple structure (only one meta-atom per period) designed via aggressively discretized method which initially originated from discretized metasurface design, performing nearly lossless anomalous refraction under TM-polarized incident light. A 2D full-wave floquet simulation shows that the proposed metagrating anomalously transmits and incident light of 800 nm wavelength with up to 94% power efficiency, where the specular 2transmission is substantially suppressed. our findings can also help demarcate the boundary between metagrating and metasurface. Specular reflection ; Optics ; Physics ; Floquet theory ; Simple (philosophy) ; Refraction ; Wavelength ; Discretization ; Ray ; Mathematics ; Mathematical analysis ; Quantum mechanics Metamaterials and Metasurfaces Applications ; Orbital Angular Momentum in Optics ; Advanced Antenna and Metasurface Technologies
Authors: Munaf Rahimo
Source:  (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

Understanding Power Semiconductor Technology Platforms for Building a Viable and Sustainable Product Roadmap Microstructured cell-arrayed thermoelectric power generators, which are able to convert (waste) heat into a few In this paper, key technical pillars for a power device technology and product development roadmap are discussed. First, the main performance requirements of power semiconductors are outlined to establish modern development trends that can lead to a viable power device development roadmap. The basic principles of power semiconductor “Technology Platforms” will be presented in relation to well- defined “Device Sections”. In addition, device classification and technology complexity aspects will be reviewed as important technical pillars in the roadmap building process. Understanding the above can help map out future development tasks targeting next generation products with improved performance over cost ratios.milliwatts or even watts of electrical energy, seem to be particularly attractive for the autonomous power supply of microelectronic circuitry and electronic or micromechatronic appliances without the use of batteries. However, the conversion efficiencies achieved so far are very small. A critical analysis shows that there is still a certain potential for improvements toward the theoretical limits, but that some expectations seem to be rather unrealistic and questionable in view of the physical and technological limitations. Microelectronics ; Technology roadmap ; Process (computing) ; Computer science ; Key (lock) ; Product (mathematics) ; Systems engineering ; Power (physics) ; New product development ; Manufacturing engineering ; Electrical engineering ; Engineering ; Business Advanced Thermoelectric Materials and Devices ; Machine Learning in Materials Science ; Hybrid Renewable Energy Systems
Authors: Luca Landi | Gino Zampieri | Eros Testi | Claudio Braccesi
Source:  (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

Full Guard Testing for Ejection in Machines, From Standard Requirements to Accurate Specification Machine Directive (2006/42/CE) states the requirements for designing machine safeguards.In addition, the standard ISO 14120 and the annexes deal with the design of guards for almost all types of machinery.Following the aim of the law and the mandatory statements, only a well-equipped laboratory can prove and validate the robustness, mechanical capability, stress, and strain state that can be reached during the ballistic impact.Those requirements claim the necessity of finding "the weakest point on guard," which is tough to fulfill in real testing devices.The paper presents the design of a new gas cannon device built for maximum flexibility during the test phase and able to shoot in any desired huge guards.Examples of weak points and design errors highlighted during tests will be discussed according to the most counterproductive point requirements.Opportunities to modify the state of the art of tests will be discussed at the end of the paper. Guard (computer science) ; Robustness (evolution) ; Flexibility (engineering) ; Computer science ; Reliability engineering ; Rigidity (electromagnetism) ; Directive ; Engineering ; Structural engineering High-Velocity Impact and Material Behavior ; Electromagnetic Launch and Propulsion Technology ; Energetic Materials and Combustion
Authors: Sungsool Wi | Conggang Li | Karen Pham | Woonghee Lee | Lucio Frydman
Source: Research Square (preprint, 2023-07-07)
Field: Chemistry — Spectroscopy

Short and long range 2D 15N-15N NMR correlations among peptide groups by novel solid state dipolar mixing schemes Abstract A recently developed homonuclear dipolar recoupling scheme, Adiabatic Linearly FREquency Swept reCOupling (AL FRESCO), was applied to record two-dimensional (2D) 15 N- 15 N correlations on uniformly 15 N-labeled GB1 powders. A major feature exploited in these 15 N- 15 N correlations was AL FRESCO’s remarkably low RF power demands, which enabled seconds-long mixing schemes when establishing direct correlations. These 15 N- 15 N mixing schemes proved efficient regardless of the magic-angle spinning (MAS) rate and, being nearly free from dipolar truncation effects, they enabled the detection of long-range, weak dipolar couplings, even in the presence of strong short-range dipolar couplings. This led to a connectivity information that was significantly better than that obtained with spontaneously proton-driven, 15 N spin-diffusion experiments. An indirect approach producing long-range 15 N- 15 N correlations was also tested, relying on short (ms-long) 1 H N - 1 H N mixings schemes while applying AL FRESCO chirped pulses along the 15 N channel. These indirect mixing schemes produced numerous long-distance N i -N i±n (n correlations, that might be useful for characterizing three-dimensional arrangements in proteins. Once again, these AL FRESCO mediated experiments proved more informative than variants based on spin-diffusion-based 1 H N - 1 H N counterparts. Homonuclear molecule ; Solid-state nuclear magnetic resonance ; Dipole ; Mixing (physics) ; Chemistry ; Molecular physics ; Spin diffusion ; Crystallography ; Physics ; Condensed matter physics ; Nuclear magnetic resonance ; Diffusion ; Molecule ; Quantum mechanics Advanced NMR Techniques and Applications ; NMR spectroscopy and applications ; Solid-state spectroscopy and crystallography
Authors: Zhihai Liu | Luyang Wang | Dao‐Xin Yao
Source: arXiv (Cornell University) (preprint, 2023-09-18)
Field: Materials Science — Materials Chemistry

Unconventional transport properties in systems with triply degenerate quadratic band crossings A quadratic band crossing (QBC) is a crossing of two bands with quadratic dispersion, which has been intensively investigated due to its appearance in Bernal-stacked bilayer graphene. Here, we study an extension of QBCs, the triply degenerate quadratic band crossing (TQBC), which is a three-band crossing node containing two quadratic dispersing bands and a flat band. We focus on two types of TQBCs. The first type contains a symmetry-protected QBC and a free-electron band, the prototype of which is the AA-stacked bilayer squareoctagon lattice. In a magnetic field, such a TQBC exhibits an anomalous Landau level structure, leading to a distinctive quantum Hall effect which displays an infinite ladder of Hall plateaus when the chemical potential approaches zero. The other type of TQBC can be viewed as a pseudospin-1 extension of the bilayer-graphene QBC. Under perturbations, this type of TQBCs may split into linear pseudospin-1 Dirac-Weyl fermions. When tunneling through a potential barrier, the transmission probability of the first type decays exponentially with the barrier width for any incident angle, similar to the free-electron case, while the second type hosts an all-angle perfect reflection when the energy of the incident particles is equal to half the barrier height. Physics ; Condensed matter physics ; Degenerate energy levels ; Bilayer graphene ; Landau quantization ; Quantum tunnelling ; Electronic band structure ; Lattice (music) ; Electron ; Quadratic equation ; Fermion ; Quantum mechanics ; Graphene ; Geometry ; Mathematics Graphene research and applications ; Quantum and electron transport phenomena ; Topological Materials and Phenomena
Authors: Stefan Ernst | Patrick Scheidegger | S. Diesch | Leandro Lorenzelli | Christian L. Degen
Source: PubMed (preprint, 2023-01-12)
Field: Materials Science — Materials Chemistry

Temperature Dependence of Photoluminescence Intensity and Spin Contrast in Nitrogen-Vacancy Centers We report on measurements of the photoluminescence properties of single nitrogen-vacancy centers in diamond at temperatures between 4 K and 300 K. We observe a strong reduction of the PL intensity and spin contrast between ca. 10 K and 100 K that recovers to high levels below and above. Further, we find a rich dependence on magnetic bias field and crystal strain. We develop a comprehensive model based on spin mixing and orbital hopping in the electronic excited state that quantitatively explains the observations. Beyond a more complete understanding of the excited-state dynamics, our work provides a novel approach for probing electron-phonon interactions and a predictive tool for optimizing experimental conditions for quantum applications. Photoluminescence ; Excited state ; Vacancy defect ; Condensed matter physics ; Spin (aerodynamics) ; Diamond ; Nitrogen-vacancy center ; Materials science ; Phonon ; Intensity (physics) ; Atomic physics ; Molecular physics ; Physics ; Optoelectronics ; Optics Diamond and Carbon-based Materials Research ; Electronic and Structural Properties of Oxides ; High-pressure geophysics and materials