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Supporting Data and Code for "From Qutrit Toric Code to Parafermion Defects in Trapped Ions"
<ul> <li>Code for Quantum Circuit Construction, Submission, and Data Analysis.</li> <li>Raw Experimental Data from Quantinuum H2</li> </ul> <p>To use the codebase, navigate to the z3/ directory and then run <code>pip install -r requirements.txt</code><br>To generate all the plots/data run main.ipynb</p>
Native qudit entanglement in a trapped ion quantum processor
<p>Source data underlying the graphical representations used in the figures.</p>
Cold CAS Ion Trap - 22 pole trap with ring electrodes for astrochemistry
<p>Raw experimental data and post-processing scripts for: "Cold CAS Ion Trap – 22 pole trap with ring electrodes for<br> astrochemistry".</p> <p>DOI: 10.1080/00268976.2023.2217744</p>
Fig. 4 in Distribution of 5,6-dihydro-α-pyrones by electrospray ionization ion trap mass spectrometry in different aerial parts of Hyptis monticola
Fig. 4. UHPLC base peak ion chromatogram of CH2Cl2-soluble extract from leaves of Hyptis monticola. UHPLC-ESI-MS instrumental conditions: column C-18 (2.1 × 150 mm, 2 μm); mobile phase, gradient CH3CN:H2O; flow rate, 0.25 mL/min. Peaks assignments: tR 36.7 min =monticolide A (1); tR 27.6 min = monticolide B (2), tR 23.6 min = monticolide C (3); tR 29.6 min = monticolide D (4); tR 31.1 min = monticolide E (5); tR 19.1 min = monticolide F (6).
Fig. 6 in Distribution of 5,6-dihydro-α-pyrones by electrospray ionization ion trap mass spectrometry in different aerial parts of Hyptis monticola
Fig. 6. Average for the relative quantification of monticolides A-F (1–6) in different plant organs (n = 15, mean with SD).
Fig. 3 in Distribution of 5,6-dihydro-α-pyrones by electrospray ionization ion trap mass spectrometry in different aerial parts of Hyptis monticola
Fig. 3. Comparison of leaves extracts base peak chromatograms obtained with different solvents by UHPLC-ESI(+)-IT-MS. Analytical conditions: gradient mobile phase of CH3CN and 0.1% (v/v) aqueous formic acid; flow rate 0.25 mL/min; column C-18, 2.1 × 150 mm, 2 μm; sample concentration 0.5 mg/mL; mass spectrometry detection with ESI ionization in positive mode in the range of m/z 200 to 500. Peaks assignments: monticolides A-F, compounds 1–6.
Fig. 2 in Distribution of 5,6-dihydro-α-pyrones by electrospray ionization ion trap mass spectrometry in different aerial parts of Hyptis monticola
Fig. 2. Recycling HPLC chromatogram for the separation of diacetylated monticolides B (2) and C (3) from the CCC fractions 8–12 (see, Fig. S1). Chromatographic conditions: mobile phase CH3CN; flow rate, 4.7 mL/min; NH2 column, 19 × 150 mm, 10 μm, DAD detector (290 nm); sample concentration, 30 mg/mL.
Fig. 5 in Distribution of 5,6-dihydro-α-pyrones by electrospray ionization ion trap mass spectrometry in different aerial parts of Hyptis monticola
Fig. 5. PCA score plot of different extracts based on the relative abundances of total diagnostic ions for the distribution of monticolides A-F (1–6), which were registered by UHPLC-ESI(+)-IT-MS. Extracts prepared from flowers (HFL), leaves (HFO) and branches (HG). Codes were assigned according to the corresponding season and altitude as follows: HFL1, HFO1 and HG1-Spring collected at a low-altitude (1229 m) in 2013; HFL2, HFGO2 and HG2-winter collected at a low-altitude (1245 m) in 2017; HFL3, HFO3 and HG3-winter collected at a high-altitude (1310 m) in 2017; HFL4, HFO4 and HG4-summer collected at a low-altitude (1245 m) in 2018; and HFL5, HFO5 and HG5-summer collected at a high-altitude (1310 m) in 2018.
Fig. 7 in Glucosinolate profiles and phylogeny in Barbarea compared to other tribe Cardamineae (Brassicaceae) and Reseda (Resedaceae), based on a library of ion trap HPLC-MS/MS data of reference desulfoglucosinolates
Fig. 7. Levels of major glucosinolates in leaves of first year rosette plants of the Gtype (A) and P-type (B) of Barbarea vulgaris in plants subjected to various challenges or no challenge as control. The contrasting general profile of the types is evident from dominance of BAR in the G-type and EBAR in the P-type. Treatment codes are: Control, un-challenged plants harvested after 7 days; Pieris 3d and Pieris 7d, herbivory by Pieris brassicae larvae until harvest at either day 3 or day 7; Plutella, herbivory by Plutella xylostella for 4 days; CuCl2, spraying of leaves with 10 mM CuCl2 (aq.) followed by recovery for 4 days. Bars represent means, whiskers indicate standard deviation (N = 3 for each group).
Fig. 6 in Glucosinolate profiles and phylogeny in Barbarea compared to other tribe Cardamineae (Brassicaceae) and Reseda (Resedaceae), based on a library of ion trap HPLC-MS/MS data of reference desulfoglucosinolates
Fig. 6. Lack of the aliphatic glucosinolate (GSL) Pren (107) in B. vulgaris and spiking of pure (intact) Pren for establishing the limit of detection. A. Total ion chromatogram for the three dominating peaks in G-type B. vulgaris (dGSL preparation). B. Extracted ion trace for desulfo Pren in the same extract as A, showing lack of detection. C, D, E. Results of serial spiking of the crude extract with serial 10-fold dilutions of Pren before the desulfation procedure, showing linearity also at low levels and ability to detect trace levels.
Fig. 9 in Glucosinolate profiles and phylogeny in Barbarea compared to other tribe Cardamineae (Brassicaceae) and Reseda (Resedaceae), based on a library of ion trap HPLC-MS/MS data of reference desulfoglucosinolates
Fig. 9. Extracted ion HPLC-MS chromatograms of desulfoglucosinolates prepared from glucosinolates (GSLs) in seeds (A–F) or leaves (G) of Reseda luteola and seeds of Reseda odorata (H). The three major peaks (A, B, C) represent PE, IM and BAR, much like many Barbarea spp. Focus on minor peaks (D) allowed conclusive identification of EBAR, confirmed by tR and the characteristic MS2 spectrum. A range of putative derivatives were not detected (E, F), but an unidentified hydroxybutylGSL was present (G), as was a known glycoside in R. odorata.
Fig. 5 in Glucosinolate profiles and phylogeny in Barbarea compared to other tribe Cardamineae (Brassicaceae) and Reseda (Resedaceae), based on a library of ion trap HPLC-MS/MS data of reference desulfoglucosinolates
Fig. 5. MS2 spectra of desulfated glucosinolates (GSLs) confirming the identity of two 2-3homoMet-derived GSLs in C. hirsuta. While the spectrum of desulfo Buen contains only the usual fragments for this type of dGSL (a, [anhydroGlc+Na]+; b, [thioGlc+Na]+), the spectrum of desulfo Peen contains an additional usual fragment (c, [M-anhydroGlc Na]+) and two unusual + fragment ions suggesting a structure-specific cyclization and exchange of O during fragmentation: 201, [gluconolactone Na]+ and 152, [C H NS Na]+. + 6 11 + The unusual fragments can be rationalized as fragment a plus O and fragment c minus O, respectively.
Fig. 3 in Glucosinolate profiles and phylogeny in Barbarea compared to other tribe Cardamineae (Brassicaceae) and Reseda (Resedaceae), based on a library of ion trap HPLC-MS/MS data of reference desulfoglucosinolates
Fig. 3. HPLC-MS chromatograms of desulfoglucosinolates (dGSLs) prepared from glucosinolates (GSLs) in Planodes virginica (A) and Nasturtium officinale (B–C) seeds, showing qualitative similarities and quantitative contrasts. Major peaks (B) from N. officinale revealed many of the same GSLs as in A, but levels of EBAR (40R) were much lower while levels were much higher for the biosynthetic precursor PE (105). A focus on trace peaks from N. officinale (C) revealed sharp peaks representing a range of minor constituents. Due to the closely eluting peaks, the latter chromatograms (B–C) were made by combining extracted ion chromatograms corresponding to [M+Na]+ of the indicated dGSLs. In C, the m/z 366 signal of d105 was omitted to allow visualization of minor coeluting peaks. An asterisk after a peak number indicates tentative identification. HPLC-MS conditions as in Olsen et al. (2016). TIC, total ion chromatogram, EIC, extracted ion chromatogram.
Fig. 4 in Glucosinolate profiles and phylogeny in Barbarea compared to other tribe Cardamineae (Brassicaceae) and Reseda (Resedaceae), based on a library of ion trap HPLC-MS/MS data of reference desulfoglucosinolates
Fig. 4. HPLC-MS chromatogram of desulfoglucosinolates (dGSLs) prepared from glucosinolates (GSLs) from leaves (A) and petioles (B) of horseradish (Armoracia rusticana), focusing on trace level GSLs. The chromatograms were made by combining extracted ion chromatograms corresponding to [M+Na]+ of the indicated dGSLs, from analyses that were much overloaded with respect to the dominating dGSL d107 from Pren. In panel A, an insert shows magnification of the chromatogram from 5.2 to 5.8 min. Neither suggested BAR nor EBAR were detectable. In panel B, only extracted ion chromatograms of m/z 382 (BAR/EBAR), 352 (BZ), 366 (PE), 380 (3PP), 394 (4PB), 408 (5PP at high tR and 6mSOh at 5.4 min), 422 (7mSOh) and 436 (8mSOo) are included. Unlabeled trace peaks did not exhibit a combination of tR and m/z suitable for any of the mentioned candidates. HPLC conditions as in Olsen et al. (2016). Panel A depicts analysis of the Copenhagen garden accession; panel B from the naturalized population at Lake Fures¨o. An asterisk after a peak number indicates tentative identification.
Fig. 2 in Glucosinolate profiles and phylogeny in Barbarea compared to other tribe Cardamineae (Brassicaceae) and Reseda (Resedaceae), based on a library of ion trap HPLC-MS/MS data of reference desulfoglucosinolates
Fig. 2. Detection of thioglucose-acylated glucosinolates (GSLs) by HPLC-MS of desulfated derivatives prepared from the indicated species. (A–C) Analysis of seeds of Arabidopsis thaliana Col-0 used as reference material for characteristic GSLs. Shown are the total ion chromatogram (A) and extracted ion chromatograms for sodium adducts of desulfo 6′Bz 4BzOb (d125) (B) and desulfo 6′Bz 4mSb (d127) (C). (D–F) Analysis of seeds of Barbarea grayi for dominating GSLs. Shown are total ion chromatograms (D), and extracted ion chromatograms for sodium adducts of desulfo 6'iF BAR (d131S) (E) and desulfo 6'iF PE (d129) (F).
Fig. 1 in Glucosinolate profiles and phylogeny in Barbarea compared to other tribe Cardamineae (Brassicaceae) and Reseda (Resedaceae), based on a library of ion trap HPLC-MS/MS data of reference desulfoglucosinolates
Fig. 1. MS2 spectra of pairs of desulfoglucosinolates with and without a side chain double bond. Four short chain desulfoglucosinolates were investigated, including Na+ adducts of all (A–D) and in addition H+ adducts of the methylthio substituted (E–F), as indicated in each spectrum. The desulfo derivative of the putative 9mSn ([89]), poorly characterized in the literature, was also investigated (G).
Probing surface charge densities on optical fibers with a trapped ion
<p>We describe a novel method to measure the surface charge densities on optical fibers placed in the vicinity of a trapped ion, where the ion itself acts as the probe. Surface charges distort the trapping potential, and when the fibers are displaced, the ion’s equilibrium position and secular motional frequencies are altered. We measure the latter quantities for different positions of the fibers and compare these measurements to simulations in which unknown charge densities on the fibers are adjustable parameters. Values ranging from −10 to +50 e/µm2 were determined. Our results will benefit the design and simulation of miniaturized experimental systems combining ion traps and integrated optics, for example, in the fields of quantum computation, communication and metrology. Furthermore, our method can be applied to any setup in which a dielectric element can be displaced relative to a trapped charge-sensitive particle.</p>
Fig. 1. 6 in Distribution of 5,6-dihydro-α-pyrones by electrospray ionization ion trap mass spectrometry in different aerial parts of Hyptis monticola
Fig. 1. 6-Heptyl-5,6-dihydro-2H-pyran-2-ones, monticolides A-F (1–6), isolated from H. monticola.
High Energy Laboratory Astrophysics using an X-Ray Microcalorimeter with an Electron Beam Ion Trap Project
"Since the summer of 2000 we have successfully deployed a high resolution x-ray microcalorimeter spectrometer, based on the spaceflight XRS instrument, at the Electron Beam Ion Trap (EBIT) facility at the Lawrence Livermore National Laboratory. Over the last decade, this highly successful partnership has made fundamental measurements in laboratory astrophysics including the measurements of the absolute cross sections of all the Fe L shell transitions from Fe XVII to Fe XXIV, line ratios in Fe and Ni L shell transitions, measurements of Fe K shell emission over a wide range of electron energies, and direct measurements of charge exchange emission from highly ionized Fe, O, N, and most recently L shell S, using a variety of donor gases. This work has resulted in the publication of over 30 peer-reviewed articles with many more either submitted or in preparation. The newest addition to the facility, the ECS microcalorimeter spectrometer, developed under this program, has performed flawlessly as a facility-class instrument since 2007. We propose here to continue our highly successful partnership and deploy new technology to resolve lines in the important 1/4 keV band that encompasses the M-shell iron emission and the L shell emission, including charge exchange, of many of the lower-Z elements, such as Si, S, Mg, Ne, Ca, and Ar. We thus propose completing a new spectrometer that will bring substantially improved performance to the laboratory astrophysics program at EBIT and will enable fundamentally new measurements. Thus, in addition to maintaining the current spectrometers, which will begin this work, a significant component of this proposal is the completion of a new spectrometer leveraged off of the substantial progress in high-resolution x-ray detectors developed for the International X-ray Observatory mission. The spectrometer will be composed of a detector system with unparalleled spectral resolution: 2 eV resolution across the 0.05-10 keV band. This will allow
Fig. 8 in Glucosinolate profiles and phylogeny in Barbarea compared to other tribe Cardamineae (Brassicaceae) and Reseda (Resedaceae), based on a library of ion trap HPLC-MS/MS data of reference desulfoglucosinolates
Fig. 8. The intraspecific diversity of Barbarea vulgaris and relations to other species in the genus analyzed by parsimony network analysis of ITS regions from Barbarea accessions using SplitsTree (Huson and Briant, 2006). The B. vulgaris ITS sequences are defined as seven groups and detailed accession information is found in Supplementary Table S1. The respective alignment is shown in Supplementary Table S2, and bootstrap values are provided for 1000 replicates.
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Allen Brain Atlas
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.