Ion Population Research Articles

Magnetospheric ion influence at the dayside magnetopause

AbstractMagnetospheric ions have the potential to affect magnetic reconnection at the magnetopause. The results of a survey of magnetospheric ions near the magnetopause are reported here. Composition measurements from the Magnetospheric Multiscale (MMS) mission are used to determine the total mass density of all magnetospheric ions and distinguish two populations of magnetospheric ions: the warm plasma cloak and the plasmaspheric drainage plume. The warm plasma cloak can contain substantial O+, and the plasmaspheric plume can contain substantial He+. The results of the survey show that, for nominal magnetospheric activity, the warm plasma cloak and plasmaspheric plume will reduce the normalized reconnection rate at the magnetopause by greater than 20% only a few percent of the time.

A feasibility study on obtaining d-orbital populations from aspherical-atom refinements on three spin crossover compounds

Although compounds undergoing thermally induced spin crossover have been widely studied, their experimental d-orbital populations from single-crystal X-ray diffraction have rarely been reported. Three pairs of structures of iron/manganese coordination compounds were re-evaluated. Least-squares refinements relied on aspherical scattering factors obtained from molecular quantum-mechanical DFT single-point computations of the respective solid-state conformation, initiated by accurate starting structures from preliminary invariom refinements of the ligand environment. Further evaluation concerned d-orbital populations of metal ions from (a) single-point computations projected onto the Hansen-Coppens multipole model and from (b) experimental refinements of the metal atoms only. The latter were successful for good-quality data, independent of temperature, and provided only one spin state was exclusively present in the crystal. Crystals that underwent light-induced excited spin state trapping were not showing the expected d-orbital populations.

Computation of Alfvèn eigenmode stability and saturation through a reduced fast ion transport model in the TRANSP tokamak transport code

Alfvénic instabilities (AEs) are well known as a potential cause of enhanced fast ion transport in fusion devices. Given a specific plasma scenario, quantitative predictions of (i) expected unstable AE spectrum and (ii) resulting fast ion transport are required to prevent or mitigate the AE-induced degradation in fusion performance. Reduced models are becoming an attractive tool to analyze existing scenarios as well as for scenario prediction in time-dependent simulations. In this work, a neutral beam heated NSTX discharge is used as reference to illustrate the potential of a reduced fast ion transport model, known as kick model, that has been recently implemented for interpretive and predictive analysis within the framework of the time-dependent tokamak transport code TRANSP. Predictive capabilities for AE stability and saturation amplitude are first assessed, based on given thermal plasma profiles only. Predictions are then compared to experimental results, and the interpretive capabilities of the model further discussed. Overall, the reduced model captures the main properties of the instabilities and associated effects on the fast ion population. Additional information from the actual experiment enables further tuning of the model’s parameters to achieve a close match with measurements.

Front-End Electron Transfer Dissociation Coupled to a 21 Tesla FT-ICR Mass Spectrometer for Intact Protein Sequence Analysis.

High resolution mass spectrometry is a key technology for in-depth protein characterization. High-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) enables high-level interrogation of intact proteins in the most detail to date. However, an appropriate complement of fragmentation technologies must be paired with FTMS to provide comprehensive sequence coverage, as well as characterization of sequence variants, and post-translational modifications. Here we describe the integration of front-end electron transfer dissociation (FETD) with a custom-built 21 tesla FT-ICR mass spectrometer, which yields unprecedented sequence coverage for proteins ranging from 2.8 to 29kDa, without the need for extensive spectral averaging (e.g., ~60% sequence coverage for apo-myoglobin with four averaged acquisitions). The system is equipped with a multipole storage device separate from the ETD reaction device, which allows accumulation of multiple ETD fragment ion fills. Consequently, an optimally large product ion population is accumulated prior to transfer to the ICR cell for mass analysis, which improves mass spectral signal-to-noise ratio, dynamic range, and scan rate. We find a linear relationship between protein molecular weight and minimum number of ETD reaction fills to achieve optimum sequence coverage, thereby enabling more efficient use of instrument data acquisition time. Finally, real-time scaling of the number of ETD reactions fills during method-based acquisition is shown, and the implications for LC-MS/MS top-down analysis are discussed. Graphical Abstract ᅟ.

Characterization by laser-induced photodetachment of anions formed during dust particle growth in a magnetically confined very low-pressure argon–acetylene plasma

Anions in low-pressure magnetically confined Ar–C2H2 plasmas were investigated using the laser-induced photodetachment technique. In particular, the influence of the magnetic field (B) was studied. We observed that the density of negatively-charged species n– increases with B and slightly decreases when the C2H2 percentage grows. These phenomena are the result of changes in the plasma kinetics. We also observed that n– decreases as the pressure increases from 2 to 10 mTorr due to the corresponding rise of the collision frequency, which leads to enhanced losses of the negatively-charged species. In parallel, the photodetachment cross-section was deduced from the energy dependence of the photodetachment signal and was found to be close to that of C2H− anions, which indicates that these anions are likely to dominate the negative ion population.

The Validity of 21 cm Spin Temperature as a Kinetic Temperature Indicator in Atomic and Molecular Gas

Abstract The gas kinetic temperature (T K ) of various interstellar environments is often inferred from observations that can deduce level populations of atoms, ions, or molecules using spectral line observations; H i 21 cm is perhaps the most widely used, and has a long history. Usually the H i 21 cm line is assumed to be in thermal equilibrium and the populations are given by the Boltzmann distribution. A variety of processes, many involving Lyα, can affect the 21 cm line. Here we show how this is treated in the spectral simulation code Cloudy, and present numerical simulations of environments where this temperature indicator is used, with a detailed treatment of the physical processes that determine level populations within H0. We discuss situations where this temperature indicator traces T K , cases where it fails, as well as the effects of Lyα pumping on the 21 cm spin temperature. We also show that the Lyα excitation temperature rarely traces the gas kinetic temperature.

Quantitative Shotgun Proteomics Unveils Candidate Novel Esophageal Adenocarcinoma (EAC)-specific Proteins

Esophageal cancer is the eighth most common cancer worldwide and the majority of patients have systemic disease at presentation. Esophageal adenocarcinoma (OAC), the predominant subtype in western countries, is largely resistant to current chemotherapy regimens. Selective markers are needed to enhance clinical staging and to allow targeted therapies yet there are minimal proteomic data on this cancer type. After histological review, lysates from OAC and matched normal esophageal and gastric samples from seven patients were subjected to LC MS/MS after tandem mass tag labeling and OFFGEL fractionation. Patient matched samples of OAC, normal esophagus, normal stomach, lymph node metastases and uninvolved lymph nodes were used from an additional 115 patients for verification of expression by immunohistochemistry (IHC).Over six thousand proteins were identified and quantified across samples. Quantitative reproducibility was excellent between technical replicates and a moderate correlation was seen across samples with the same histology. The quantitative accuracy was verified across the dynamic range for seven proteins by immunohistochemistry (IHC) on the originating tissues. Multiple novel tumor-specific candidates are proposed and EPCAM was verified by IHC.This shotgun proteomic study of OAC used a comparative quantitative approach to reveal proteins highly expressed in specific tissue types. Novel tumor-specific proteins are proposed and EPCAM was demonstrated to be specifically overexpressed in primary tumors and lymph node metastases compared with surrounding normal tissues. This candidate and others proposed in this study could be developed as tumor-specific targets for novel clinical staging and therapeutic approaches.

Magneto-thermal reconnection processes, related mode momentum and formation of high energy particle populations

In the context of a two-fluid theory of magnetic reconnection, when the longitudinal electron thermal conductivity is relatively large, the perturbed electron temperature tends to become singular in the presence of a reconnected field component and an electron temperature gradient. A finite transverse thermal diffusivity removes this singularity while a finite ‘inductivity’ can remove the singularity of the relevant plasma displacement. Then (i) a new ‘magneto-thermal’ reconnection producing mode, is found with characteristic widths of the reconnection layer remaining significant even when the macroscopic distances involved are very large; (ii) the mode phase velocities can be both in the direction of the electron diamagnetic velocity as well in the opposite (ion) direction. A numerical solution of the complete set of equations has been carried out with a simplified analytical reformulation of the problem. A sequence of processes is analyzed to point out that high-energy particle populations can be produced as a result of reconnection events. These involve mode-particle resonances transferring energy of the reconnecting mode to a superthermal ion population and the excitation of lower hybrid waves that can lead to a significant superthermal electron population. The same modes excited in axisymmetric (e.g. toroidal) confinement configurations can extract angular momentum from the main body of the plasma column and thereby sustain a local ‘spontaneous rotation’ of it.

Design of a TW-SLIM Module for Dual Polarity Confinement, Transport, and Reactions.

Here we describe instrumental approaches for performing dual polarity ion confinement, transport, ion mobility separations, and reactions in structures for lossless ion manipulations (SLIM). Previous means of ion confinement in SLIM, based upon rf-generated pseudopotentials and DC fields for lateral confinement, cannot trap ions of opposite polarity simultaneously. Here we explore alternative approaches to provide simultaneous lateral confinement of both ion polarities. Traveling wave ion mobility (IM) separations experienced in such SLIM cause ions of both polarities to migrate in the same directions and exhibit similar separations. The ion motion (and relative motion of the two polarities) under both surfing and IM separation conditions are discussed. In surfing conditions the two polarities are transported losslessly and non-reactively in their respective potential minima (higher absolute voltage regions confine negative polarities, and lower absolute potential regions are populated by positive polarities). In separation mode, where ions roll over an overtaking traveling wave, the two polarities can interact during the rollovers. Strategies to minimize overlap of the two ion populations to prevent reactive losses during separations are presented. A theoretical treatment of the time scales over which two populations (injected into a DC field-free region of the dual polarity SLIM device) interact is considered, and SLIM designs for allowing ion/ion interactions and other manipulations with dual polarities at 4Torr are presented. Graphical Abstract ᅟ.

Compression Ratio Ion Mobility Programming (CRIMP) Accumulation and Compression of Billions of Ions for Ion Mobility-Mass Spectrometry Using Traveling Waves in Structures for Lossless Ion Manipulations (SLIM).

We report on the implementation of a traveling wave (TW) based compression ratio ion mobility programming (CRIMP) approach within structures for lossless ion manipulations (SLIM) that enables both greatly enlarged trapped ion charge capacities and also efficient ion population compression for use in ion mobility (IM) separations. Ion accumulation is conducted in a SLIM serpentine ultralong path with extended routing (SUPER) region after which CRIMP compression allows the large ion populations to be "squeezed". The SLIM SUPER IM module has two regions, one operating with conventional traveling waves (i.e., traveling trap; TT region) and the second having an intermittently pausing or "stuttering" TW (i.e., stuttering trap; ST region). When a stationary voltage profile was used in the ST region, ions are blocked at the TT-ST interface and accumulated in the TT region and then can be released by resuming a conventional TW in the ST region. The population can also be compressed using CRIMP by the repetitive merging of ions distributed over multiple TW bins in the TT region into a single TW bin in the ST region. Ion accumulation followed by CRIMP compression provides the basis for the use of larger ion populations for IM separations. We show that over 109 ions can be accumulated with high efficiency in the present device and that the extent of subsequent compression is only limited by the space charge capacity of the trapping region. Approximately 5 × 109 charges introduced from an electrospray ionization source were trapped for a 40 s accumulation period, more than 2 orders of magnitude greater than the previously reported charge capacity of an ion funnel trap. Importantly, we show that extended ion accumulation in conjunction with CRIMP compression and multiple passes through the serpentine path provides the basis for a highly desirable combination of ultrahigh sensitivity and SLIM SUPER high-resolution IM separations.

Stagnant low-energy ions in the near cusp region observed by Cluster

Measuring the low-energy ions in the Earth’s magnetotail lobes is difficult, because a spacecraft becomes positively charged in a sunlit and tenuous plasma environment. Recent studies have introduced a new method, making use of the positive electric potential on the Cluster spacecraft, to measure the low-energy ions (less than a few tens of electronvolts) in the polar caps/magnetotail lobes in the years 2001–2010. With the measured velocities, we are able to study the trajectories of these low-energy ions. Particle tracing has been used in previous studies, confirming that ions of ionospheric origin are the dominant contributor to the ion population in the Earth’s magnetotail lobes. In this work, we continue to study the source of low-energy ions measured in the lobes. We found that not all of the low-energy ions in the lobes come directly from the ionosphere. Particle tracing infers that some of the low-energy ions start to move tailward from the cusp/near-cusp region with a zero parallel velocity. In the following, we refer to these low-energy ions as stagnant low-energy ions. On the other hand, the in situ measurements by Cluster show a population of low-energy ions in the cusp/near-cusp region with pitch angles near 90° (i.e., no significant parallel velocity). The locations of stagnant low-energy ions are determined by particle tracing and in situ measurements. Similar ion energies and spatial distributions determined by these two methods confirm the presence of the stagnant low-energy ion population.

Plasma waves confined to the diamagnetic cavity of comet 67P/Churyumov–Gerasimenko

Ion acoustic waves were observed in the diamagnetic cavity of comet 67P/Churyumov– Gerasimenko by the Rosetta spacecraft on 2015 August 3, when the comet was 1.25 au from the Sun. Wave spectra recorded by the Langmuir probe (RPC-LAP), peak near 200 Hz, decrease for higher frequencies and reach the noise floor at approximately 1.5 kHz. These waves were observed only when the spacecraft was in the diamagnetic cavity or at its boundary, which is identified as a sharp drop in magnetic field magnitude, measured by RPC-MAG. The plasma, on both sides of the boundary, is dominated by a cold (a few hundred K) water group ion population, one cold (k B T e ∼ 0.1 eV) and one warm (k B T e ∼ 10 eV) electron population. The observations are interpreted in terms of current-driven ion acoustic waves, generated by currents that flow through bulges on the boundary of the diamagnetic cavity.

Gadolinium cation (Gd+) reaction with O2: Potential energy surface mapped experimentally and with theory.

Guided ion beam tandem mass spectrometry is used to measure the kinetic energy dependent cross sections for reactions of the lanthanide metal gadolinium cation (Gd+) and GdO+ with O2 and for collision-induced dissociation (CID) of GdO2+ with Xe. Gd+ reacts with O2 in an exothermic and barrierless reaction to form GdO+ and O. GdO2+ is also formed in this reaction, but this product ion is formed in a sequential reaction, as verified by pressure dependent measurements and comparison with the results for the reaction of GdO+ with O2. The CID experiments of GdO2+ indicate the presence of two GdO2+ precursor ion populations, assigned to a weakly bound oxygen molecule adduct (Gd+-O2) and an inserted cyclic Gd+ dioxide species (O-Gd+-O). Analysis of the resulting product ion cross sections yields bond dissociation energies (BDEs, D0) for Gd+-O2 and OGd+-O, where the latter BDE is also independently measured in an exchange reaction between GdO+ and O2. The CID experiments also provide the energy of the barrier for the rearrangement of the Gd+-O2 adduct to the inserted O-Gd+-O structure (as identified by loss of a single oxygen atom). The thermochemistry measured here yields D0(OGd+-O) = 2.86 ± 0.08 eV, D0(Gd+-O2) = 0.75 ± 0.11 eV, and a barrier height relative to Gd+-O2 of 0.31 ± 0.07 eV. These data are sufficient to characterize in some detail the potential energy surface of the Gd+ reaction with O2 entirely from experiment. Theoretical calculations are performed for comparison with the experimental energetics and for further insight into the reaction mechanisms.

Kinetic simulation of asymmetric magnetic reconnection with cold ions

AbstractAt the dayside magnetopause, the magnetosphere often contains a cold ion population of ionospheric origin. This population is not always detectable by particle instruments due to its low energy, despite having an important contribution to the total ion density and therefore an impact on key plasma processes such as magnetic reconnection. The exact role and implications of this low‐temperature population are still not well known and has not been addressed with numerical simulation before. We present 2‐D fully kinetic simulations of asymmetric magnetic reconnection with and without a cold ion population on the magnetospheric side of the magnetopause, but sharing the same total density, temperature, and magnetic field profiles. The comparison of the simulations suggests that cold ions directly impact signatures recently suggested as a good marker of the X line region: the Larmor electric field. Our simulations reveal that this electric field, initially present all along the magnetospheric separatrix, is related to the bounce of magnetosheath ions at the magnetopause magnetic field reversal through Speiser‐like orbits. Once reconnection widens the current sheet away from the X line, the bouncing stops and the electric field signature remains solely confined near the X line. When cold ions are present, however, their very low temperature enables them to E × B drift in the electric field structure. If their density is large enough compared to other ions, their contribution to the momentum equation is capable of maintaining the signature away from the X line. This effect must be taken into account when analyzing in situ spacecraft measurements.

IMF dependence of energetic oxygen and hydrogen ion distributions in the near‐Earth magnetosphere

AbstractEnergetic ion distributions in the near‐Earth plasma sheet can provide important information for understanding the entry of ions into the magnetosphere and their transportation, acceleration, and losses in the near‐Earth region. In this study, 11 years of energetic proton and oxygen observations (> ~274 keV) from Cluster/Research with Adaptive Particle Imaging Detectors were used to statistically study the energetic ion distributions in the near‐Earth region. The dawn‐dusk asymmetries of the distributions in three different regions (dayside magnetosphere, near‐Earth nightside plasma sheet, and tail plasma sheet) are examined in Northern and Southern Hemispheres. The results show that the energetic ion distributions are influenced by the dawn‐dusk interplanetary magnetic field (IMF) direction. The enhancement of ion intensity largely correlates with the location of the magnetic reconnection at the magnetopause. The results imply that substorm‐related acceleration processes in the magnetotail are not the only source of energetic ions in the dayside and the near‐Earth magnetosphere. Energetic ions delivered through reconnection at the magnetopause significantly affect the energetic ion population in the magnetosphere. We also believe that the influence of the dawn‐dusk IMF direction should not be neglected in models of the particle population in the magnetosphere.

Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow.

Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions together with their precursor ions. This precursor-fragment ion map in a comprehensive MS/MS spectral library is crucial for relative quantification of fragment ions uniquely representative of each precursor ion. However, existing reference libraries are not sufficient for this purpose since the fragmentation patterns of small molecules can vary in different instrument setups. Here we developed a bioinformatics workflow called MetaboDIA to build customized MS/MS spectral libraries using a user's own data dependent acquisition (DDA) data and to perform MS/MS-based quantification with DIA data, thus complementing conventional MS1-based quantification. MetaboDIA also allows users to build a spectral library directly from DIA data in studies of a large sample size. Using a marine algae data set, we show that quantification of fragment ions extracted with a customized MS/MS library can provide as reliable quantitative data as the direct quantification of precursor ions based on MS1 data. To test its applicability in complex samples, we applied MetaboDIA to a clinical serum metabolomics data set, where we built a DDA-based spectral library containing consensus spectra for 1829 compounds. We performed fragment ion quantification using DIA data using this library, yielding sensitive differential expression analysis.

Ion behavior in low-power magnetically shielded and unshielded Hall thrusters

Magnetically shielded Hall thrusters achieve a longer lifespan than traditional Hall thrusters by reducing wall erosion. The lower erosion rate is attributed to a reduction of the high energy ion population impacting the walls. To investigate this phenomenon, the ion velocity distribution functions are measured with laser induced fluorescence at several points of interest in the magnetically shielded ISCT200-MS and the unshielded ISCT200-US Hall thrusters. The center of the discharge channel is probed to highlight the difference in plasma positioning between the shielded and unshielded thrusters. Erosion phenomena are investigated by taking measurements of the ion velocity distribution near the inner and outer wall as well as above the magnetic poles where some erosion is observed. The resulting distribution functions show a displacement of the acceleration region from inside the channel in the unshielded thruster to downstream of the exit plane in the ISCT200-MS. Near the walls, the unshielded thruster displays both a higher relative ion density as well as a significant fraction of the ions with velocities toward the walls compared to the shielded thruster. Higher proportions of high velocity ions are also observed. Those results are in accordance with the reduced erosion observed. Both shielded and unshielded thrusters have large populations of ions impacting the magnetic poles. The mechanism through which those ions are accelerated toward the magnetic poles has so far not been explained.

Infrared Multiple-Photon Dissociation Action Spectroscopy of the b2+ Ion from PPG: Evidence of Third Residue Affecting b2+ Fragment Structure.

Infrared multiple-photon dissociation (IRMPD) action spectroscopy was performed on the b2+ fragment ion from the protonated PPG tripeptide. Comparison of the experimental infrared spectrum with computed spectra for both oxazolone and diketopiperazine structures indicates that the majority of the fragment ion population has an oxazolone structure with the remainder having a diketopiperazine structure. This result is in contrast with a recent study of the IRMPD action spectrum of the PP b2+ fragment ion from PPP, which was found to be nearly 100% diketopiperazine (Martens et al. Int. J. Mass Spectrom. 2015, 377, 179). The diketopiperazine b2+ ion is thermodynamically more stable than the oxazolone but normally requires a trans/cis peptide bond isomerization in the dissociating peptide. Martens et al. showed through IRMPD action spectroscopy that the PPP precursor ion was in a conformation in which the first peptide bond is already in the cis conformation and thus it was energetically favorable to form the thermodynamically-favored diketopiperazine b2+ ion. In the present case, solution-phase NMR spectroscopy and gas-phase IRMPD action spectroscopy show that the PPG precursor ion has its first amide bond in a trans configuration suggesting that the third residue is playing an important role in both the structure of the peptide and the associated ring-closure barriers for oxazolone and diketopiperazine formation. Graphical Abstract ᅟ.

Ion Trapping by Dust Grains: Simulation Applications to the Enceladus Plume.

Using a particle-in-cell electrostatic simulation, we examine the conditions that allow low energy ions, like those produced in the Enceladus plume, to be attracted and trapped within the sheaths of negatively-charged dust grains. The conventional wisdom is that all new ions produced in the Enceladus plume are free to get picked up (i.e., accelerated by the local E-field to then undergo vB acceleration). However, we suggest herein that the presence of submicron charged dust in the plume impedes this pickup process since the local grain electric field greatly exceeds the co-rotation E-fields. The simulations demonstrate that cold ions will tend to accelerate toward the negatively charged grains and become part of the ion plasma sheath. These trapped ions will move with the grains, exiting the plume region at the dust speed. We suggest that Cassini's Langmuir probe is measuring the entire ion population (free and trapped ions), while the Cassini magnetometer detects the magnetic perturbations associated with pickup currents from the smaller population of free ions, with this distinction possibly reconciling the ongoing debate in the literature on the ion density in the plume.

Shock-induced mix across an ideal interface

According to particle-in-cell and multi fluid simulations, as a planar shock propagates across an unperturbed classical interface, significant amounts of rearward shocked material are predicted to advect with the shock front over distances that are much larger than an ion-ion collisional mean free path of a shocked ion. This novel mechanism of interface mixing is found to scale strongly with the Mach number (∼M4) and produces an ion population bunch that penetrates the upstream material at nearly the shock speed. Possible implications for ignition capsule designs are conjectured.