From mass spectral features to molecules in molecular networks: a novel workflow for untargeted metabolomics.

In the context of untargeted metabolomics, molecular networking is a popular and efficient tool which organizes and simplifies mass spectrometry fragmentation data (LC-MS/MS), by clustering ions based on a cosine similarity score. However, the nature of the ion species is rarely taken into account, causing redundancy as a single compound may be present in different forms throughout the network. Taking advantage of the presence of such redundant ions, we developed a new method named MolNotator. Using the different ion species produced by a molecule during ionization (adducts, dimers, trimers, in-source fragments), a predicted molecule node (or neutral node) is created by triangulation, and ultimately computing the associated molecule calculated mass. These neutral nodes provide researchers with several advantages. Firstly, each molecule is then represented in its ionization context, connected to all produced ions and indirectly to some coeluted compounds, thereby also highlighting unexpected widely present adduct species. Secondly, the predicted neutrals serve as anchors to merge the complementary positive and negative ionization modes into a single network. Lastly, the dereplication is improved by the use of all available ions connected to the neutral nodes, and the computed molecular masses can be used for exact mass dereplication. MolNotator is available as a Python library and was validated using the lichen database spectra acquired on an Orbitrap, computing neutral molecules for >90% of the 156 molecules in the dataset. By focusing on actual molecules instead of ions, MolNotator greatly facilitates the selection of molecules of interest.

Wider Potential Windows of Cellulose Multiwall Carbon Nanotube Fibers Leading to Qualitative Multifunctional Changes in an Organic Electrolyte

The trend across the whole of society is to focus on natural and/or biodegradable materials such as cellulose (Cell) over synthetic polymers. Among other usage scenarios, Cell can be combined with electroactive components such as multiwall carbon nanotubes (CNT) to form composites, such as Cell-CNT fibers, for applications in actuators, sensors, and energy storage devices. In this work, we aim to show that by changing the potential window, qualitative multifunctionality of the composites can be invoked, in both electromechanical response as well as energy storage capability. Cell-CNT fibers were investigated in different potential ranges (0.8 V to −0.3 V, 0.55 V to −0.8 V, 1 V to −0.8 V, and 1.5 V to −0.8 V), revealing the transfer from cation-active to anion-active as the potential window shifted towards more positive potentials. Moreover, increasing the driving frequency also shifts the mode from cation- to anion-active. Scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy were conducted to determine the ion species participating in charge compensation under different conditions.

Effects of the Solar Wind Dynamic Pressure on the Martian Topside Ion Distribution: Implications on the Variability of Bulk Ion Outflow

With the aid of the ion densities measured by the Neutral Gas and Ion Mass Spectrometer and the solar wind dynamic pressures measured by the Solar Wind Ion Analyzer on board the Mars Atmosphere and Volatile EvolutioN, we investigate the modulation of a sequence of ion species in the Martian topside ionosphere by the upstream solar wind condition. Almost all ion species, except for CO 2 + and OCOH+, are very sensitive to the variation of the solar wind condition, and their densities decrease with increasing solar wind dynamic pressure. The response of the topside ion distribution to the variation of the solar wind condition is also found to be remarkably related to the magnetic field orientation, in that the solar wind modulation occurs mainly over regions with near-horizontal field lines. These observations imply substantially enhanced outflow velocities for all ion species under high solar wind dynamic pressures when the ambient magnetic fields are near-horizontal.

Mechanism of FIB-Induced Phase Transformation in Austenitic Steel

The transformation of unstable austenite to ferrite or α′ martensite as a result of exposure to Xe+ or Ga+ ions at room temperature was studied in a 304 stainless steel casting alloy. Controlled Xe+ and Ga+ ion beam exposures of the 304 were carried out at a variety of beam/sample geometries. It was found that both Ga+ and Xe+ ion irradiation resulted in the transformation of the austenite to either ferrite or α′ martensite. In this paper, we will refer to the transformation product as a BCC phase. The crystallographic orientation of the transformed area was controlled by the orientation of the austenite grain and was consistent with either the Nishiyama–Wasserman or the Kurdjumov–Sachs orientation relationships. On the basis of the Xe+ and Ga+ ion beam exposures, the transformation is not controlled by the chemical stabilization of the BCC phase by the ion species, but is a result of the disorder caused by the ion-induced recoil motion and subsequent return of the disordered region to a more energetically favorable phase.

Quantitative Analysis of Nitrogen by Atom Probe Tomography Using Stoichiometric γ′-Fe4N Consisting of 15N Isotope

The nitrogen deficiency in steels measured by atom probe tomography (APT) is considered to arise from the obscurement of singly charged dimer nitrogen ions (N2+) by the iron-dominant peak (56Fe2+) at 28 Da. To verify this by quantifying the amount of N2+ ions, γ′-Fe4N consisting of the 15N isotope was prepared on iron substrates by plasma nitriding using a nitrogen isotopic gas (15N2). Although considerable amounts of 15N2+ were observed at 30 Da without overlap with any iron peak, the observed nitrogen concentrations of γ′-Fe4N were clearly lower than the stoichiometric composition (19–20 at%), using both pulsed voltage and pulsed laser atom probes. The origin of the missing nitrogen, excluding nitrogen obscured by other ion species, was predicted to be the occurrence of neutral nitrogen or nitrogen gas molecules in field evaporation. The generation rate of iron nitride ions (FeN2+) for 15N was significantly lower than that for 14N in γ′-Fe4N, which affected the amount of the missing nitrogen. The isotope effect suggests that the isotopic ratio cannot always be determined from only one ion species among the multiple species observed in the APT analysis. We discuss the mechanism of the isotope effect in FeN2+ formation by field evaporation.

Effect of non-uniform magnetic field on two ion species plasma-wall transition

Fluid theory has been employed to investigate the magnetized plasma-wall transition properties for two ion species plasmas with a uniform background of neutral gas density in the presence of an external magnetic field. The external applied magnetic field is parallel to the surface and its magnitude varies in the direction perpendicular to the surface. The governing equations of ion and electron fluids include ionization and collision with neutral atoms. A comparative study of transition parameters for non-uniform and uniform magnetic fields is performed at equal values of the magnetic flux density at $x = 0$. This study shows that the sheath region shrinks for the non-uniform magnetic field case, essentially in reason of the lower value of the average magnetic field intensity in the plasma-wall transition region. We introduce a figure of merit to quantify the non-uniformity of the magnetic field $(B_{\mathrm{max}}-B_{\mathrm{min}})/B_{\mathrm{max}}$, and show that for its value 0.21 it is possible to model the plasma-wall transition region considering the magnetic field as uniform and equal to its average value. Furthermore, we find that the density distribution of electrons close to the surface deviates from the Boltzmann distribution due to the influence of a strong magnetic field.

Ion Dynamics in the Meso-scale 3-D Kelvin–Helmholtz Instability: Perspectives From Test Particle Simulations

Over three decades of in-situ observations illustrate that the Kelvin–Helmholtz (KH) instability driven by the sheared flow between the magnetosheath and magnetospheric plasma often occurs on the magnetopause of Earth and other planets under various interplanetary magnetic field (IMF) conditions. It has been well demonstrated that the KH instability plays an important role for energy, momentum, and mass transport during the solar-wind-magnetosphere coupling process. Particularly, the KH instability is an important mechanism to trigger secondary small scale (i.e., often kinetic-scale) physical processes, such as magnetic reconnection, kinetic Alfvén waves, ion-acoustic waves, and turbulence, providing the bridge for the coupling of cross scale physical processes. From the simulation perspective, to fully investigate the role of the KH instability on the cross-scale process requires a numerical modeling that can describe the physical scales from a few Earth radii to a few ion (even electron) inertial lengths in three dimensions, which is often computationally expensive. Thus, different simulation methods are required to explore physical processes on different length scales, and cross validate the physical processes which occur on the overlapping length scales. Test particle simulation provides such a bridge to connect the MHD scale to the kinetic scale. This study applies different test particle approaches and cross validates the different results against one another to investigate the behavior of different ion species (i.e., H+ and O+), which include particle distributions, mixing and heating. It shows that the ion transport rate is about 1025 particles/s, and mixing diffusion coefficient is about 1010 m2 s−1 regardless of the ion species. Magnetic field lines change their topology via the magnetic reconnection process driven by the three-dimensional KH instability, connecting two flux tubes with different temperature, which eventually causes anisotropic temperature in the newly reconnected flux.