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At least 199 records · Page 11

MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition

Motivation: Untargeted mass spectrometry experiments enable the profiling of metabolites in complex biological samples. The collected fragmentation spectra are the metabolite’s fingerprints that are used for molecule identification and discovery. Two main mass spectrometry strategies exist for the collection of fragmentation spectra: data-dependent acquisition (DDA) and data-independent acquisition (DIA). In the DIA strategy, all the metabolites ions in predefined mass-to-charge ratio ranges are co-isolated and co-fragmented, resulting in multiplexed fragmentation spectra that are challenging to annotate. In contrast, in the DDA strategy, fragmentation spectra are dynamically and specifically collected for the most abundant ions observed, causing redundancy and sub-optimal fragmentation spectra collection. Yet, DDA results in less multiplexed fragmentation spectra that can be readily annotated. Results: We introduce the MS2Planner workflow, an Iterative Optimized Data Acquisition strategy that optimizes the number of high-quality fragmentation spectra over multiple experimental acquisitions using topological sorting. Our results showed that MS2Planner increases the annotation rate by 38.6% and is 62.5% more sensitive and 9.4% more specific compared to DDA. Availability and implementation MS2Planner code is available at https://github.com/mohimanilab/MS2Planner. The generation of the inclusion list from MS2Planner was performed with python scripts available at https://github.com/lfnothias/IODA_MS.

47 OTHER INSTRUMENTATION↗

Nanoconfined Grain Boundaries Increase the Conductivity of Polycrystalline Molecular Crystals

Soft-solid molecular crystals consist of crystalline grains and fluid grain boundaries (GBs) that enhance the grain binding and transport of Li + ions between the grains. The total ionic conductivity consists of ion migration in both the grains and GBs. To unravel these contributions in adiponitrile (Adpn):LiPF 6 molecular crystals, the GB volume fraction was varied by changing the size of the crystals and the Adpn:LiPF 6 molar ratio. Molecular dynamics (MD) simulations indicate that ion motion was subdiffusive in the grains and “well-diffusive” in the GBs, with GBs characterized as disordered nanoconfined regions of higher charge carrier concentration (∼1 M) than in saturated Adpn:LiPF 6 solutions (0.04 M), and Li + ions predominantly solvated by cyano groups with few contact ion pairs. The diffusivity in the GBs is at least an order of magnitude higher than that in the crystalline grains. The emergent picture is the grains as a reservoir of ions that migrate to faster-conducting GBs.

Crystals↗

Machine learning-assisted crystal engineering of a zeolite

Abstract It is shown that Machine Learning (ML) algorithms can usefully capture the effect of crystallization composition and conditions (inputs) on key microstructural characteristics (outputs) of faujasite type zeolites (structure types FAU, EMT, and their intergrowths), which are widely used zeolite catalysts and adsorbents. The utility of ML (in particular, Geometric Harmonics) toward learning input-output relationships of interest is demonstrated, and a comparison with Neural Networks and Gaussian Process Regression, as alternative approaches, is provided. Through ML, synthesis conditions were identified to enhance the Si/Al ratio of high purity FAU zeolite to the hitherto highest level (i.e., Si/Al = 3.5) achieved via direct (not seeded), and organic structure-directing-agent-free synthesis from sodium aluminosilicate sols. The analysis of the ML algorithms’ results offers the insight that reduced Na 2 O content is key to formulating FAU materials with high Si/Al ratio. An acid catalyst prepared by partial ion exchange of the high-Si/Al-ratio FAU (Si/Al = 3.5) exhibits improved proton reactivity (as well as specific activity, per unit mass of catalyst) in propane cracking and dehydrogenation compared to the catalyst prepared from the previously reported highest Si/Al ratio (Si/Al = 2.8).

36 MATERIALS SCIENCE↗

Pd‐Ru Alloy Nanocages with a Face‐Centered Cubic Structure and Their Enhanced Activity toward the Oxidation of Ethylene Glycol and Glycerol

Abstract This article reports a facile method for the synthesis of Pd‐Ru nanocages by activating the galvanic replacement reaction between Pd nanocrystals and a Ru(III) precursor with I ‐ ions. The as‐synthesized nanocages feature a hollow interior, ultrathin wall of ≈2.5 nm in thickness, and a cubic shape. Our quantitative study suggests that the reduction rate of the Ru(III) precursor can be substantially accelerated upon the introduction of I ‐ ions and then retarded as the ratio of I ‐ /Ru 3+ is increased. The Pd‐Ru nanocages take an alloy structure, with the Ru atoms in the nanocages crystallized in a face‐centered cubic structure instead of the hexagonal close‐packed phase taken by bulk Ru. Using Pd nanocubes with different edge lengths, the dimensions of the nanocages in the range of 6−18 nm can readily be tuned. When tested as catalysts toward the electro‐oxidation of ethylene glycol and glycerol, respectively, the Pd‐Ru cubic nanocages prepared from 18 nm Pd cubes exhibit 5.1‐ and 6.2‐fold enhancements in terms of mass activity relative to the commercial Pd/C. After 1000 cycles of accelerated durability test, the mass activities of the nanocages are still 3.3 and 3.7 times as high as that of the pristine commercial Pd/C catalyst, respectively.

Zhao, Ming↗

A Cartesian-diffusion Langevin method for hybrid kinetic-fluid Coulomb scattering in particle-in-cell plasma simulations

A novel, drag-diffusion Langevin method of hybrid, kinetic-fluid Coulomb scattering in plasmas is presented. Unlike previous methods, the frictional drag is always applied in the simulation frame of reference. The velocity-space diffusion is performed in the stationary-fluid frame of reference when anisotropic, and in the laboratory frame when isotropic. While the general method is mass-ratio independent, we focus on interactions of kinetic-ions and fluid-electrons to show first-order modifications to the electron velocity distribution function that are an important correction for the accurate calculation of electric resistivity. Inclusion of sub-cycling and a limit to the maximum collision frequency is shown to allow for arbitrarily large timesteps without numerical failure. Here the Langevin method is compared with a grid-based binary method and found to require a much less restrictive timestep in cases of ion–electron slowing and temperature equilibration; this finding differs from previous work and is dependent on the mass ratio.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Engineering Calcium-Bearing Mineral/Hydrogel Composites for Effective Phosphate Recovery

Effectively recovering phosphate from wastewater streams and reutilizing it as a nutrient will critically support sustainability. Here, to capture aqueous phosphate, we developed novel mineral-hydrogel composites composed of calcium alginate, calcium phosphate (CaP), and calcium silicate (CSH) (CaP + CSH/Ca-Alg). The CaP + CSH/Ca-Alg composites were synthesized by dripping a sodium alginate (Na-Alg) solution with ionic precursors into a calcium chloride bath. To change the mineral seed’s properties, we varied the calcium bath concentrations and the ionic precursor (sodium dibasic phosphate (NaH 2 PO 4 ) and/or sodium silicate (Na 2 SiO 3 )) amounts and their ratios. The added CSH in the mineral-hydrogel composites resulted in the release of calcium and silicate ions in phosphate-rich solutions, increasing the saturation ratio with respect to calcium phosphate within the mineral-hydrogel composites. The CSH addition to the mineral-hydrogel composites doubled the phosphate removal rate while requiring lesser initial amounts of Ca and P materials for synthesis. Furthermore, by incorporating both CSH and CaP mineral seeds in composites, we achieved a final concentration of 0.25 mg-P/L from an initial 6.20 mg-P/L. Moreover, the mineral-hydrogel composites can remove phosphate even under CaP undersaturated conditions. This suggests their potential to be a widely applicable and environmentally-sustainable treatment and recovery method for nutrient-rich wastewater.

42 ENGINEERING↗

Nonlinear kinetic simulation study of the ion–ion streaming instability in single- and multi-ion species plasmas

The nonlinear evolution of the ion–ion streaming instability (IISI) is studied using numerical techniques novel to this problem that afford direct insight into the evolution of the particle distributions of each species. Here, during the linear phase of the instability, we demonstrate quantitative agreement with linear kinetic theory. Subsequently, the electrostatic field generated by the IISI causes ring-like velocity distributions of ions to form that are both heated and slowed to varying degrees relative to their initial flows. Due to variation in the trapping conditions for ion species of differing charge-to-mass ratio, when flows of multiple species interact, the nonlinear evolution of each species can be starkly different: we show a case where a lighter ion species is completely stopped by a heavier ion species via the IISI alone (i.e., without collisions) and, for the first time, demonstrate how the IISI can introduce a relative flow between ion species that initially have the same flow velocities, thereby separating them.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Centrifugal-mirror confinement with strong azimuthal magnetic field

One practical challenge for the centrifugal-mirror confinement concept is the large radial voltage necessary to drive supersonic azimuthal rotation. In principle, the addition of a strong azimuthal field could reduce the required voltage, since the simple azimuthal E x B drift would be replaced by more rapid azimuthal trapped-particle precession. Also, if the mirror ratio is large enough, newly ionized ions are accelerated to the necessary parallel velocities in their first bounce orbit, both confining and significantly heating them. Unfortunately, MHD analysis shows that the centrifugal-force-confining plasma current is purely azimuthal. This implies that only the axial magnetic field contributes to the confining magnetic pressure, severely limiting the usefulness of the azimuthal magnetic field in a beta-limited plasma scenario.

Grad-Shafranov↗

Does Carrier Envelope Phase Affect the Ionization Site in a Neutral Diatomic Molecule?

A recent work shows how to extract the ionization site of a neutral diatomic molecule by comparing Quantum Trajectory Monte Carlo (QTMC) simulations with experimental measurements of the final electron momenta distribution. This method was applied to an experiment using a 40-femtosecond infrared pulse, finding that a downfield atom is roughly twice as likely to be ionized as an upfield atom in a neutral nitrogen molecule. However, an open question remains as to whether an assumption of the zero carrier envelope phase (CEP) used in the above work is still valid for short, few-cycle pulses where the CEP can play a large role. Given experimentalists’ limited control over the CEP and its dramatic effect on electron momenta after ionization, it is desirable to see what influence the CEP may have in determining the ionization site. In this paper, we employ QTMC techniques to simulate strong-field ionization and electron propagation from neutral N2 using an intense 6-cycle laser pulse with various CEP values. Comparing simulated electron momenta to experimental data indicates that the ratio of down-to-upfield ions remains roughly 2:1 regardless of the CEP. This confirms that the ionization site of a neutral molecule is determined predominantly by the laser frequency and intensity, as well as the ground-state molecular wavefunction, and is largely independent of the CEP.

Schimmoller, Alex↗

Data for Selected Ion Monitoring for Orbitrap-Based Metabolomics

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage.f

Mass Spectrometry↗

Structural evolution and magnetic hardness of (Sm,Zr)(Fe,Co,Ti) 12 alloy particles via reduction-diffusion

The quest for achieving high coercivity in Sm(Fe,Co,Ti) 12 alloys, despite their inherent strong magnetocrystalline anisotropy, has posed significant challenges. Recently, (Sm,Zr)(Fe,Co,Ti) 12 monocrystalline particles have exhibited coercivity μ 0 H c > 1.2 T, showcasing promising prospects and significant potential for both manufacturing and research endeavors. This study delves into the structural evolution of (Sm,Zr)(Fe,Co,Ti) 12 (1:12) alloy particles made via the calciothermic reduction-diffusion synthesis process as influenced by the molar ratios of Ca atoms to O 2- ions (Ca/O), annealing time and annealing temperature. Critical insight that informs conditions to optimize the magnetic response is gained via systematic experimentation and advanced electron microscopy. Complex structural features, including core-shell morphologies and intricate multiphase compositions within individual particles, are unveiled. An optimal Ca/O ratio of 1.30 produces particles with a coercivity up to μ 0 H c = 1.63 T, while higher Ca/O ratios induce the formation of a Sm-rich TbCu 7 -type (1: 7 ) phase, which only partially transforms into the desired 1:12 phase during annealing. Persistent remnants of the 1:7 phase locally impact atomic structure, particle morphology, and coercivity. Furthermore, these findings underscore the complex interplay between synthesis parameters, resulting structures, and magnetic properties, informing the design and optimization of high-performance permanent magnets comprised of the (1:12) compound.

36 MATERIALS SCIENCE↗

Electric field reversals resulting from voltage waveform tailoring in Ar/O 2 capacitively coupled plasmas sustained in asymmetric systems

The etching of nanometer scale high-aspect-ratio (HAR) features into dielectric materials in low pressure radio frequency excited plasmas is often accompanied by charge accumulation inside the features which can slow etching rates and produce distortions such as twisting. The intra feature charging is at least partially produced by differences in electron and ion energy and angular distributions (EADs). Positive ions, accelerated to high energies having narrow angular spreads by the sheath electric field, can penetrate deeply into HAR features. Electrons typically arrive at the wafer with nearly thermal and isotropic distributions and do not penetrate deeply into HAR features. These disparities lead to differential charging of the inside of the feature, which can lead to reductions in etch rate and feature distortion due to ion deflection. With in-creasing aspect ratio of features, charging challenges are expected to continue for the foreseeable future. In this work, the use of tailored voltage waveforms in geometrically asymmetric capacitively coupled plasmas sustained in Ar/O 2 at 40 mTorr was computationally investigated with the goal of shaping the EAD of electrons incident onto the substrate to address differential charging. The tailored waveform consisted of a sinusoidal wave and its higher harmonics with a fundamental frequency of 1 MHz. Further, we found that electric field reversals in the sheath and presheath can occur during the anodic portion of the cycle. The electric field reversal increases the energy and decreases the angular spread of electrons incident onto the substrate. The magnitude of the electric field reversal can be controlled by the phase angle of the even harmonics and the gas composition. Due to its electronegative nature, increasing mole fractions of O 2 impedes electron transport to the surface which further increases the electric field reversal.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Mobility Selective Ion Soft-Landing and Characterization Enabled Using Structures for Lossless Ion Manipulation

In this study, while conventional ion-soft landing uses the mass-to-charge (m/z) ratio to achieve molecular selection for deposition, here we demonstrate the use of Structures for Lossless Ion Manipulation (SLIM) for mobility-based ion selection and deposition. The dynamic rerouting capabilities of SLIM were leveraged to enable the rerouting of a selected range of mobilities to a different SLIM path (rather than MS) that terminated at a deposition surface. A selected mobility range from a phosphazene ion mixture was rerouted and deposited with a current pulse (~150 pA) resembling its mobility peak. In addition, from a mixture of tetra-alkyl ammonium (TAA) ions containing chain lengths of C5–C8, selected chains (C6, C7) were collected on a surface, reconstituted into solution-phase, and subsequently analyzed with a SLIM-qToF to obtain an IMS/MS spectrum, confirming the identity of the selected species. Further, this method was used to characterize triply charged tungsten-polyoxometalate anions, PW 12 O 40 3– (WPOM). The arrival time distribution of the IMS/MS showed multiple peaks associated with the triply charged anion (PW 12 O 40 3– ), of which a selected ATD was deposited and imaged using TEM. Additionally, the identity of the deposited WPOM was ascertained using energy-dispersive (EDS) spectroscopy. Further, we present theory and computations that reveal ion landing energies, the ability to modulate the energies, and deposition spot sizes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deciphering yield modification of hadron-triggered semi-inclusive recoil jets in heavy-ion collisions

Jet quenching is recognized as critical evidence for the existence of the quark-gluon plasma (QGP) and serves as an essential probe to study its transport properties. Measurements of hadron-triggered semi-inclusive recoil jets have gained popularity due to its capability to probe jets over an extended phase space at low transverse momenta (p T ) and large radii. Recent ALICE measurements showed that the I AA , yield ratio of recoil jets between heavy-ion and p+p collisions, rises with jet p T and exceeds unity at high p T , contradicting conventional expectations that jet quenching should result in I AA values less than one. In this contribution, we re-examine the surface bias and study the effects of energy losses for both trigger hadrons and recoil jets on I AA , employing the Linear Boltzmann Transport (LBT) model to simulate jet-medium interactions. Our findings suggest that a large portion of hadrons used for the triggers undergoes substantial energy loss, despite surface bias. In particular, the energy loss of the trigger hadrons elevates the I AA baseline, corresponding to the case of no energy loss for recoil jets, to be greatly larger than unity. This enhancement of the baseline implies that the measured I AA values being larger than unity could still signal jet quenching.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Enhanced Reactivity of Accessible Protons in Sodalite Cages of Faujasite Zeolite

We report Faujasite (FAU) zeolites (with Si/Al ratio of ca. 1.7) undergo mild dealumination at moderate ion exchange conditions (0.01 to 0.6 M of NH 4 NO 3 solutions) resulting in protons circumscribed by sodalite cages becoming accessible for reaction without conspicuous changes to bulk crystallinity. The ratio of protons in sodalite cages (H SOD ) to supercages (H SUP ) can be systematically manipulated from 0 to ca. 1 by adjusting ammonium concentrations used in ion exchange. The fraction of accessible protons in the sodalite cages is assessed by virtue of infrared spectra for H-D exchange of deuterated propane based on the band area ratio of OD 2620 /OD 2680 (OD SOD /OD SUP ). Protons in sodalite cages (H- SOD ) show higher rate constants of propane dehydrogenation (k D ) and cracking (k C ) than protons in supercages (H SUP ) plausibly due to confinement effects being more prominent in smaller voids. Rate constants of dehydrogenation and cracking including k D /k C ratios are also augmented as the fraction of accessible protons in the sodalite cages is enhanced. These effects of accessibility and reactivity of protons in sodalite cages hitherto inconspicuous are revealed herein via methods that systematically increase accessibility of cations located in sodalite cages.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experimental Investigation of the Effects of Magnetic Mirrors on Plasma Transport in the Prototype Material Plasma Exposure Experiment

The Prototype Material Plasma Exposure eXperiment (Proto-MPEX) at Oak Ridge National Laboratory is developing a helicon radio frequency (RF) source for plasma production along with microwave electron heating and RF ion heating. Proto-MPEX has several magnetic mirrors that affect plasma transport. The magnetic field near the helicon source is ~ 0.05 T, and the peak magnetic field in Proto-MPEX is ~ 1.8 T, which results in a large magnetic well for particles sourced at the helicon transporting toward the target region. Keeping the helicon source field and the target field constant, experiments have been conducted by methodically changing the magnetic field, at a local axial location, within the source and the target. Plasma flow measurements using Mach probes have shown a decrease in the flow as a function of the magnetic mirror ratio. Plasma flows were further investigated with ion cyclotron resonant heating (ICH). Results with the addition of ICH measured upstream of the antenna have shown a decrease in Mach number as a function of mirror ratio when compared to helicon discharges. Such flow behavior demonstrated slowing down of the plasma due to the increased reverse plasma flow toward the helicon plasma source. However, in high magnetic fields, when the resonant magnetic field moved away from the ICH antenna, no effects on the plasma flow due to ICH were observed.

Kafle, Nischal↗

Enhanced Reactivity of Accessible Protons in Sodalite Cages of Faujasite Zeolite

Abstract Faujasite (FAU) zeolites (with Si/Al ratio of ca. 1.7) undergo mild dealumination at moderate ion exchange conditions (0.01 to 0.6 M of NH 4 NO 3 solutions) resulting in protons circumscribed by sodalite cages becoming accessible for reaction without conspicuous changes to bulk crystallinity. The ratio of protons in sodalite cages (H SOD ) to supercages (H SUP ) can be systematically manipulated from 0 to ca. 1 by adjusting ammonium concentrations used in ion exchange. The fraction of accessible protons in the sodalite cages is assessed by virtue of infrared spectra for H‐D exchange of deuterated propane based on the band area ratio of OD 2620 /OD 2680 (OD SOD /OD SUP ). Protons in sodalite cages (H SOD ) show higher rate constants of propane dehydrogenation ( k D ) and cracking ( k C ) than protons in supercages (H SUP ) plausibly due to confinement effects being more prominent in smaller voids. Rate constants of dehydrogenation and cracking including k D / k C ratios are also augmented as the fraction of accessible protons in the sodalite cages is enhanced. These effects of accessibility and reactivity of protons in sodalite cages hitherto inconspicuous are revealed herein via methods that systematically increase accessibility of cations located in sodalite cages.

Li, Xinyu↗