Astronauts are exposed to a unique radiation environment during space missions. This environment is dominated by high charge and energy (HZE) ions with sources that include solar energetic particles (SEPs), galactic cosmic rays (GCRs), and trapped electrons and protons around planetary bodies with substantial magnetic fields. Traditional shielding strategies aim to reduce astronaut radiation exposure by increasing vehicle mass, but this is ineffective for the extremely penetrating GCRs. Use of electromagnetic fields has been investigated previously, but these studies have been limited to single point designs. The NASA Active Shielding project has instead developed a workflow that includes a fast and accurate particle propagation code (Active Shielding Particle Pusher), which can be used to rapidly evaluate the shielding efficacy of many different permutations of electromagnetic shielding designs. While some validation of the code has been previously done, additional validation is needed to increase user confidence in simulation results involving more complicated electrostatic conductor configurations. In the present study, we evaluated shielding properties of spherical electrode arrays and planar grid structures against 2 MeV or 6 MeV H+ and 22.5 MeV Fe6+ ions using ASPP, SIMION, and COMSOL, and compared these results to laboratory-based measurements. Many numerical experiments were conducted to reproduce experimental ion beam tests that measure the consequential particle reduction rate in a safe zone compared to the initial number of ions. The experimental visualizations were also compared with the present numerical results and found to be in close agreement with each other for all considered voltage combinations applied to electrode structures. This comparison allows us to use numerical models to predict the behavior of complex shielding structures at much larger scales not feasible in a laboratory environment.

The Spacecraft Atmosphere Monitor (SAM.) is a scientific payload, which includes a Paul quadrupole ion trap (QIT) mass spectrometer and has been continuously operated onboard the International Space Station (ISS) between August 2019 and July 2021. S.A.M. measures the chemical composition of ISS cabin air and reports on major constituents (N-2, O-2, Ar, CO2, and CH4) once every 2 s. Each second, S.A.M. measures one hundred individual mass spectra stored in 4800 ins-long channels. This report presents the autonomous onboard data analysis software that calibrates the mass spectrum, removes the residual gas background signal, identifies species of interest, and reports relevant abundances. In addition, we describe a ground-based analysis of downloaded S.A.M.'s data to extract the H, C, N, O, and Ar isotope ratios. We also describe experiments, requested by the ISS Vehicle office, to ascertain if benzene was present in the ISS cabin air (it was not). We demonstrate that S.A.M. instrument measures isotope ratios with precision and accuracy comparable to the state-of-the-art laboratory-size magnetic sector mass spectrometers. (C) 2022 Elsevier B.V. All rights reserved.

To date a variety of different types of Mass Spectrometers has been utilized on missions to study the composition of atmospheres of many solar system bodies including Venus, Mars, Jupiter, Titan, the moon and several comets. For in-situ exploration of ice giant atmospheres, the highest priority composition measurements are helium and the other noble gases, noble gas isotopes, and other key isotopes including 3He/4He and D/H. Other important but lower priority composition measurements include abundances of volatiles C, N, S, and P, isotopes 13C/12C, 15N/14N, 18O/17O/16O and disequilibrium species PH3, CO, AsH3, GeH4, and SiH4. Required measurement accuracies are largely defined by the accuracies achieved by the Galileo (Jupiter) probe Neutral Mass Spectrometer and Helium Abundance Detectors, and current measurement accuracies of solar abundances[1]. The Jet Propulsion Laboratory’s Quadrupole Ion Trap Mass Spectrometer (QITMS)[2] is a compact, wireless instrument with a mass of only 7.5 kg, designed to meet these requirements and challenges specific to the planetary probe missions. It is currently the smallest flight MS available, capable of making measurements of all required constituents in the mass range 1-600Da, with a sensitivity of up to 1013 counts/mbar/sec and resolution of m/∆m=12000 at 40Da. During a fly-by or a descent mission, the time available to perform an in-situ measurement is usually short. This makes it challenging to measure the abundances of minor constituents for which long integration times are needed. Mass spectrometers largely employ a non-discriminatory electron impact ionization of sampled gas mixtures for creating ions, which means the probability to create and trap ion fragments of trace species is very low and further destabilized by space charge effects due to an excessive number of ions from dominant species. A selective resonant ejection technique was employed to lower the amount of major constituent species, while keeping the minor constituents intact, which resulted in higher accuracy measurements of minor species. Another inherent challenge of planetary entry probe mass spectrometers is the introduction of material to be sampled into the instrument interior, which operates at vacuum. Atmospheric entry probe mass spectrometers typically require a specially designed sample inlet system, which ideally provides highly choked, nearly constant mass-flow intake over a large range of ambient pressures. An ice giant descent probe would have to operate over a range of atmospheric pressures covering 2 or more orders of magnitude, 100 mb to 10+ bars, in an atmospheric layer of ~120 km at Neptune to ~150 km at Uranus. The QITMS features a novel MEMS based inlet system driven by a piezo-electric actuator that continuously regulates gas flow at inlet pressures of up to 100 bar. In this paper, we present an overview of the QITMS capabilities including instrument design and characteristics of the inlet system, as well as the most recent results from laboratory measurements in different modes of operation. [1] Mousis, O., et al., Pl. Sp. Sci., 155 12–40, 2018. [2] Madzunkov, S.M., Nikolic, D., J. Am. Soc. Mass Spectrom. 25(11), 2014.

A quadrupole ion trap mass spectrometer measures precisely the abundance and isotopic composition of small amounts of noble gases.

Introduction: Noble gases are powerful tracers of physical processes such as the delivery of volatile elements to planetary atmospheres through meteoritic/cometary bombardment [1,2], atmospheric escape, degassing from the silicate parts of planets, etc. In this context, understanding the isotopic composition of Xe in planetary atmospheres is a high priority since Xe isotope ratios can answer fundamental questions such as i) What is the delivery mix (Chondritic/Solar/Cometary) to planetary atmospheres?; ii) To what extent is the silicate portion of a planet degassed?; iii) How much of the atmosphere was lost through atmospheric escape and what is the timing of this process? While recent results from space missions contributed substantially to our knowledge of the elemental and isotopic composition of noble gases on Mars [e.g. 3] and in comets [e.g. 4], some planetary reservoirs remain to be sampled and analyzed. For example, the composition of the atmosphere of Venus is still a missing piece of the noble gas puzzle [5]. Compact mission concepts to sample the Venus atmosphere below the homopause and to measure noble gases with the JPL Quadrupole Ion Trap Mass Spectrometer (JPL-QITMS) have recently been proposed [6]. QITMS or Paul traps were invented 6 decades ago [7], but their potential use as a mass spectrometer for noble gases was explored only recently. For example, in the 1990's, a team at JPL developed a QITMS and demonstrated its ability to measure the abudances and isotopic composition of noble gases [eg. 8]. Another study demonstrated the ability of the JPL-QITMS to measure at high precision the composition of various artificial isotopic mixtures of Xe in dynamic mode [9]. In many mission scenarii, a dynamic measurement is not envisageable. For example, a mission to the Venus atmosphere would collect a sample below the homopause (where gas atoms are well mixed) with ppm to ppb levels of noble gases and measure it only afterwards. Ability to measure gas in static mode would thus be required. Here we show that recent developments of the instrument allow measurement of Kr and Xe isotopes in static mode with a sensitivity and precision meeting the analytical requirements for characterization of the Venus atmosphere. Instrumentation and calibration: Description of the QITMS. The JPL-QITMS consists of three electrodes. In the current configuration, the top and bottom (end-cap) electrodes are grounded whereas the ring electrode receives a high-voltage radiofrequency signal (1-2 kV). Gas neutrals are ionized by electron-impact in the mm-sized space between electrodes via a side-mounted electron gun composed of a Ta cathode and an Einzel lens. A voltage ramp applied to the ring electrode ejects ions along the zaxis (Fig. 1). Ions are detected with a MAGNUM Channeltron electron multiplier operated in pulsecounting mode. The whole system is placed in a vacuum chamber permanently pumped via a turbomolecular pump (pressure lower than 10 torr) except when a sample of gas is to be analyzed. During "static mode" analysis the chamber is isolated from the turbopump and a SAES NP10 getter in the chamber removes residual gases and reduces the partial pressure of hydrogen.

We present improved fits to our treatment of suppression of dielectronic recombination at intermediate densities. At low densities, most recombined excited states eventually decay to the ground state, and therefore the total dielectronic recombination rate to all levels is preserved. At intermediate densities, on the other hand, collisions can lead to ionization of higher-lying excited states, thereby suppressing the dielectronic recombination rate. The improved suppression factors presented here, although highly approximate, allow summed recombination rate coefficients to be used to intermediate densities. There have been several technical improvements to our previously presented fits. For H-through B-like ions the activation log densities have been adjusted to better reproduce existing data. For B-, C-, Al-, and Si-like ions secondary autoionization is now included. The treatment of density discontinuity in electron excitations out of ground state H-, He-, and Ne-like ions has been improved. These refined dielectronic recombination suppression factors are used in the most recent version of the plasma simulation code Cloudy. We show how the ionization and emission spectrum change when this physics is included. Although these suppression factors improve the treatment of intermediate densities, they are highly approximate and are not a substitution for a complete collisional-radiative model of the ionization balance.

This study identifies dynamical properties of maltose-binding protein (MBP) useful in unveiling active site residues susceptible to ligand binding. The described methodology has been previously used in support of novel topological techniques of persistent homology and statistical inference in complex, multi-scale, high-dimensional data often encountered in computational biophysics. Here we outline a computational protocol that is based on the anisotropic elastic network models of 14 all-atom three-dimensional protein structures. We introduce the notion of dynamical distance matrices as a measure of correlated interactions among 370 amino acid residues that constitute a single protein. The dynamical distance matrices serve as an input for a persistent homology suite of codes to further distinguish a small subset of residues with high affinity for ligand binding and allosteric activity. In addition, we show that ligand-free closed MBP structures require lower deformation energies than open MBP structures, which may be used in categorization of time-evolving molecular dynamics structures. Analysis of the most probable allosteric coupling pathways between active site residues and the protein exterior is also presented.

Introduction: There is a particular need for the development of miniaturized, high-G load tolerant, low-mass, low-power instruments for in situ studies of trace organic compounds, small inorganic molecules and their isotopes in planetary materials. Presented herein are the latest achievements in developing an instrument with the same analytical performance of commercial GCMS systems but approximately an order of magnitude smaller and optimized for space missions. The Jet Propulsion Laboratory (JPL) Planetary Surface Instruments (PSI) group has developed an instrument consisting of a quadrupole ion trap (QIT) Mass Spectrometer (MS), integrated with a Micro-Electro-Mechanical Systems (MEMS) Gas Chromatograph (GC), developed for human spaceflight applications for NASA Advanced Exploration Systems (AES).

In this paper, we report a MEMS preconcentrator (PC) -gas chromatograph (GC) that is a crucial part of the Spacecraft Atmosphere Monitor (S.A.M.).The S.A.M. is a highly miniature gas chromatograph -mass spectrometer (GC-MS) for monitoring the atmosphere of crewed spacecraft for both trace organic compounds and the major constituents of the cabin air.The S.A.M. instrument is the next generation of GC-MS, based on JPL's Vehicle Cabin Air Monitor (VCAM), which was launched to the International Space Station (ISS) in April 2010 and successfully operated for two years [1,2].The S.A.M. employs a unique MEMS PC-GC technology that replaces the macro PC-GC unit in the VCAM.We report herein the current progress of the MEMS PC-GC for the S.A.M. instrument.

Dielectronic recombination (DR) is the dominant recombination process for most heavy elements in photoionized clouds. Accurate DR rates for a species can be predicted when the positions of autoionizing states are known. Unfortunately such data are not available for most third- and higher-row elements. This introduces an uncertainty that is especially acute for photoionized clouds, where the low temperatures mean that DR occurs energetically through very low-lying autoionizing states. This paper discusses S2+ → ?> S+ DR, the process that is largely responsible for establishing the [S iii]/[S ii] ratio in nebulae. We derive an empirical rate coefficient using a novel method for second-row ions, which do have accurate data. Photoionization models are used to reproduce the [O iii]/[O ii]/[O i]/[Ne iii] intensity ratios in central regions of the Orion Nebula. O and Ne have accurate atomic data and can be used to derive an empirical S2+ → ?> S+ DR rate coefficient at ∼104 K. We present new calculations of the DR rate coefficient for S2+ → ?> S+ and quantify how uncertainties in the autoionizing level positions affect it. The empirical and theoretical results are combined and we derive a simple fit to the resulting rate coefficient at all temperatures for incorporation into spectral synthesis codes. This method can be used to derive empirical DR rates for other ions, provided that good observations of several stages of ionization of O and Ne are available.

We present a method of DPD simulation based on a coarse-grained effective pair potential obtained from the DRISM-KH molecular theory of solvation. The theory is first used to calculate the radial distribution functions of all-atom solute monomers in all-atom solvent and then to invert them into an effective pair potential between coarse-grained beads such that their fluid without solvent accounts for molecular specificities and solvation effects in the all-atom system. Bonded interactions are sampled in relatively short MD of the all-atom system and modeled with best multi-Gaussian fit. Replacing the heuristically defined conservative force potential in DPD, the coarse-grained effective pair potential is free from the artificial restrictions on potential range and shape and on equal volume of solute and solvent blobs inherent in standard DPD. The procedure is flexible in specifying coarse-grained mapping and enormously increases computational efficiency by eliminating solvent. The method is validated on polystyrene chains of various length in toluene at finite concentrations for room and polystyrene glass transition temperature. It yields the chain elastic properties and diffusion coefficient in good agreement with experiment and all-atom MD simulations. DPD with coarse-grained effective pair potential is capable of predicting both structural and dynamic properties of polymer solutions and soft matter with high accuracy and computational efficiency.

Protein-protein and protein-ligand recognition plays an essential role in many biomolecular processes. Understanding the mechanisms of protein-ligand binding is also crucial for designing new and optimizing existing therapeutic agents, and in different biotechnological applications. It is well known that solvation effects, including hydrophobicity and solvent mediated hydrogen bonding, are major factors implicated in biomolecular processes. Such processes often involve slow conformational changes and exchange of solvent and ligand molecules between bulk solution and biomolecular cavities. We develop new approaches for accurate account of molecular solvation effects in protein-ligand recognition and binding, which further extend the ligand mapping protocols based on the molecular theory of solvation, a.k.a. the three-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH). Based on statistical mechanics, this theory provides a natural link between different levels of coarse-graining details in a multiscale description of solvation structure and thermodynamics, from highly localized structural solvent and bound ligand molecules to effective desolvation potentials and self-assembling nanoarchitectures in solvents of different composition in a range of thermodynamic conditions. Implemented in the new 3D-RISM-Dock protocol, the theory provides a quantitative estimate of binding affinities, based on a detailed physical description of hydrogen bonding, hydrophobicity, and solvation entropic effects, with full account for molecular specificities, thermodynamic conditions, and concentration effects. The theory accurately predicts the solvation structure of biomolecules. This allows us to incorporate the 3D-RISM-KH description of structural solvation in a new docking protocol. The latter has been successfully applied to predict the binding modes of the periplasmic binding proteins in situations when structural solvation and desolvation effects are of importance. We also show that the 3D-RISM-KH theory provides valuable information on the role of the solvation entropic effects in the ligand binding and large scale conformation dynamics of proteins.

Density-dependent effective dielectronic recombination rate coefficients are determined in order to explore finite-density effects on the ionization balance of plasmas.