Ion Trajectory Simulations Research Articles

Enhanced and correlated lattice vibrations of relaxed Cu(0 0 1) surface studied by high-resolution medium energy ion scattering

The relaxed Cu(001) surface was analyzed by high-resolution medium energy ion scattering (MEIS) using 120keV He+ ions in a layer-by-layer fashion. We found the top-layer contraction of 1.6% and the 2nd-layer expansion of 0.9%, quite different from the close-packed (111) surface. Then enhanced thermal vibration amplitudes (TVAs) and the correlations between the 1st and 2nd nearest neighbor atoms in the [101]- and [001]-string were also determined simultaneously by MEIS spectrum analysis combined with Monte Carlo simulations of ion trajectories considering the surface relaxation and enhanced TVAs as well as correlations. We obtained the TVAs of the top-layer atoms strongly enhanced by 1.67±0.06 and 1.55±0.04 times that of the bulk (0.085Å) in the lateral and surface normal direction, respectively and the correlation coefficients of +0.33±0.04 and +0.28±0.04, respectively for Cu atoms in the [101]- and [001]-axis oscillating perpendicular to each string. The correlation between the 2nd nearest neighbor atoms in the [101]-string is small probably less than +0.2. The results obtained here are compared with the other experimental reports and the Debye approximation as well as molecular dynamics simulations using the embedded atom method.

PGAS‐FMM: Implementing a distributed fast multipole method using the X10 programming language

SUMMARYThe fast multipole method (FMM) is a complex, multi‐stage algorithm over a distributed tree data structure, with multiple levels of parallelism and inherent data locality. X10 is a modern partitioned global address space language with support for asynchronous activities. The parallel tasks comprising FMM may be expressed in X10 by using a scalable pattern of activities. This paper demonstrates the use of X10 to implement FMM for simulation of electrostatic interactions between ions in a cyclotron resonance mass spectrometer. X10's task‐parallel model is used to express parallelism by using a pattern of activities mapping directly onto the tree. X10's work stealing runtime handles load balancing fine‐grained parallel activities, avoiding the need for explicit work sharing. The use of global references and active messages to create and synchronize parallel activities over a distributed tree structure is also demonstrated. In contrast to previous simulations of ion trajectories in cyclotron resonance mass spectrometers, our code enables both simulation of realistic particle numbers and guaranteed error bounds. Single‐node performance is comparable with the fastest published FMM implementations, and critical expansion operators are faster for high accuracy calculations. A comparison of parallel and sequential codes shows the overhead of activity management and work stealing in this application is low. Scalability is evaluated for 8k cores on a Blue Gene/Q system and 512 cores on a Nehalem/InfiniBand cluster. Copyright © 2013 John Wiley & Sons, Ltd.

Skimming-trajectory effect for energy loss of medium-energy He ions passing along major crystal axes of KI(001) and RbI(001)

The energy loss of an ion passing along a major crystal axis before and/or after undergoing a large-angle collision is strongly enhanced, because its path is close to a lattice-site atom located at the crystal axis; this is the so-called skimming effect. One may find this effect in high-resolution medium-energy ion scattering (MEIS) spectra from submonolayers of single crystals. In the present study, the MEIS spectra were observed for medium-energy He${}^{+}$ ions backscattered from KI(001) and RbI(001) crystals at various scattering geometries. The observed surface peaks were decomposed into scattering components from top-, second-, and third-layer atoms considering the hitting probabilities, which were derived from Monte Carlo simulations of ion trajectories, taking account of the enhanced and correlated thermal vibrations. The results obtained here demonstrate that the energy loss of the ions which move skimming trajectories is expressed reasonably well by the impact-parameter-dependent energy loss calculated using the nonperturbative coupled-channel method.

Overtone mobility spectrometry: part 5. Simulations and analytical expressions describing overtone limits.

Mathematical expressions for the analytical duty cycle associated with different overtones in overtone mobility spectrometry are derived from the widths of the transmitted packets of ions under different instrumental operating conditions. Support for these derivations is provided through ion trajectory simulations. The outcome of the theory and simulations indicates that under all operating conditions there exists a limit or maximum observable overtone that will result in ion transmission. Implications of these findings on experimental design are discussed.

Monte Carlo Simulation of Ion Trajectories of Reacting Chemical Systems: Mobility of Small Water Clusters in Ion Mobility Spectrometry

For the comprehensive simulation of ion trajectories including reactive collisions at elevated pressure conditions, a chemical reaction simulation (RS) extension to the popular SIMION software package was developed, which is based on the Monte Carlo statistical approach. The RS extension is of particular interest to SIMION users who wish to simulate ion trajectories in collision dominated environments such as atmospheric pressure ion sources, ion guides (e.g., funnels, transfer multi poles), chemical reaction chambers (e.g., proton transfer tubes), and/or ion mobility analyzers. It is well known that ion molecule reaction rate constants frequently reach or exceed the collision limit obtained from kinetic gas theory. Thus with a typical dwell time of ions within the above mentioned devices in the ms range, chemical transformation reactions are likely to occur. In other words, individual ions change critical parameters such as mass, mobility, and chemical reactivity en passage to the analyzer, which naturally strongly affects their trajectories. The RS method simulates elementary reaction events of individual ions reflecting the behavior of a large ensemble by a representative set of simulated reacting particles. The simulation of the proton bound water cluster reactant ion peak (RIP) in ion mobility spectrometry (IMS) was chosen as a benchmark problem. For this purpose, the RIP was experimentally determined as a function of the background water concentration present in the IMS drift tube. It is shown that simulation and experimental data are in very good agreement, demonstrating the validity of the method.

Model of the dynamics of ion propagation through dielectric capillaries

In this paper, a model explanation for the angular oscillations of an ion beam transmitted through a capillary in the case of a nonzero ion entry angle into it is proposed. A “jet” model for charging capillary walls is developed; it is a good tool for the numerical solution of problems involving the Monte Carlo simulation of ion trajectories in the study of ion propagation through macrocapillaries in the case in which it is impossible to trace the number of trajectories equivalent to that of ions in experiments.

The influence of drift gas composition on the separation mechanism in traveling wave ion mobility spectrometry: insight from electrodynamic simulations

The influence of three different drift gases (helium, nitrogen, and argon) on the separation mechanism in traveling wave ion mobility spectrometry is explored through ion trajectory simulations which include considerations for ion diffusion based on kinetic theory and the electrodynamic traveling wave potential. The model developed for this work is an accurate depiction of a second-generation commercial traveling wave instrument. Three ion systems (cocaine, MDMA, and amphetamine) whose reduced mobility values have previously been measured in different drift gases are represented in the simulation model. The simulation results presented here provide a fundamental understanding of the separation mechanism in traveling wave, which is characterized by three regions of ion motion: (1) ions surfing on a single wave, (2) ions exhibiting intermittent roll-over onto subsequent waves, and (3) ions experiencing a steady state roll-over which repeats every few wave cycles. These regions of ion motion are accessed through changes in the gas pressure, wave amplitude, and wave velocity. Resolving power values extracted from simulated arrival times suggest that momentum transfer in helium gas is generally insufficient to access regions (2) and (3) where ion mobility separations occur. Ion mobility separations by traveling wave are predicted to be effectual for both nitrogen and argon, with slightly lower resolving power values observed for argon as a result of band-broadening due to collisional scattering. For the simulation conditions studied here, the resolving power in traveling wave plateaus between regions (2) and (3), with further increases in wave velocity contributing only minor improvements in separations.

Accelerated Simulation Study of Space Charge Effects in Quadrupole Ion Traps Using GPU Techniques

Space charge effects play important roles in the performance of various types of mass analyzers. Simulation of space charge effects is often limited by the computation capability. In this study, we evaluate the method of using graphics processing unit (GPU) to accelerate ion trajectory simulation. Simulation using GPU has been compared with multi-core central processing unit (CPU), and an acceleration of about 390 times have been obtained using a single computer for simulation of up to 10(5) ions in quadrupole ion traps. Characteristics of trapped ions can be investigated at detailed levels within a reasonable simulation time. Space charge effects on the trapping capacities of linear and 3D ion traps, ion cloud shapes, ion motion frequency shift, mass spectrum peak coalescence effects between two ion clouds of close m/z are studied with the ion trajectory simulation using GPU.

Prefocusing inside a linear ion beam guide—A SIMION study

A set of 14 stacked ring electrodes was studied by the SIMION ion trajectory simulation program under a pressure of 1Pa with different applied RF frequencies and RF voltage amplitudes when a classical DC gradient of 38V/cm is applied. Ion–neutral collision effects were considered by adopting a successful and integrated hard sphere, elastic, ion–neutral collision user program provided by SIMION. Mass dependent ion transmission efficiencies could be obtained. In the classical operation mode of the ion beam guide, a RF frequency of 2MHz was crucial to obtain very good ion transmission efficiency along a broad mass range. Lower RF frequencies (<1.5MHz) limited the good transmission efficiencies only to high masses with m/z>500amu. SIMION can reproduce expected efficiency curves which show that low m/z ions below 150amu represent a challenge for such linear ion beam devices even when high RF driving frequency of 2MHz is applied. The simulations also show that a DC gradient of at least 30V/cm is crucial to maintain good transmission efficiencies which are in agreement with previously published results. A new operation mode for running the same device is introduced for earlier ion focusing in between the second and fifth ring electrodes, prior to slight beam divergence after the focus point. This required a significant change of the applied DC voltages to alter the shape of the DC gradient curve along the central z axis. The newly identified operation mode allows enhancing the mass dependent ion transmission efficiency in a wide m/z range between 80 and 1000amu when an RF frequency of 2MHz is applied to the first ten ring electrodes.

Benchtop Energetics: Hyperthermal Species Detection

We propose a novel scheme for monitoring the transition between deflagration and “detonation-like” behavior of small-scale explosive samples-in-vacuum subjected to short duration shock stimuli. Our approach relies on measuring the chemical identities and velocity distributions of the gaseous species produced by such samples; e.g. the relatively low velocity expansion-quenched reaction intermediates produced by deflagration versus the hyperthermal thermodynamically stable molecules generated by the termination of a detonation wave at an explosive-vacuum interface. We demonstrate our ability to detect such species by time-of-flight mass spectrometry (TOFMS) using fast Al atoms produced by laser ablation of aluminum metal. Extensive SIMION simulations of ion trajectories in our mass spectrometer lead to a semi-quantitative model connecting the system operating parameters and the velocity-dependent neutral species detection efficiency. We present a method for correcting our data for these detection biases, and for transforming them into neutral species velocity and kinetic energy distributions. We also present preliminary TOFMS data of hyperthermal organic molecular species produced by direct laser ablation/ignition of thin-film nitrocellulose samples.

Plasma Polarization Around Dust Particle in an External Electric Field

AbstractThe effect of plasma polarization around a negatively charged dust particle is investigated with the help of Monte Carlo simulation of ion trajectories in the electric field of the dust particle and an external electric field. The induced dipole moment of such a system was estimated in a wide range of dust particle and plasma parameters. It is shown that the dipole moment is very large, and has a non‐monotonous dependence on the external electric field. For a small external electric field, it weakly depends on the charge of the dust particle. The dipole moment reduces with the decrease of ion mean free path (© 2011 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Construction of a Newly Designed Small-Size Mass Spectrometer for Helium Isotope Analysis: Toward the Continuous Monitoring Of 3He/4He Ratios In Natural Fluids

The construction of a small-size, magnetic sector, single focusing mass spectrometer (He-MS) for the continuous, on-site monitoring of He isotope ratios ((3)He/(4)He) is described. The instrument is capable of measuring (4)He/(20)Ne ratios dissolved in several different types of natural fluids of geochemical interest, such as groundwater and gas from hot springs, volcanoes and gas well fields. The ion optics of He-MS was designed using an ion trajectory simulation program "TRIO," which permits the simultaneous measurement of (3)He and (4)He with a double collector system under a mass resolution power (M/ΔM) of >700. The presently attained specifications of He-MS are; (1) a mass resolving power of ca. 430, sufficient to separate (3)He(+) from interfering ions, HD(+) and H3 (+), (2) ultra-high vacuum conditions down to 3×10(-8) Pa, and (3) a sufficiently high sensitivity to permit amounts of (3)He to be detected at levels as small as 10(-13) cm(3) STP (3×10(6) atoms). Long term stability for (3)He/(4)He analysis was examined by measuring the (3)He/(4)He standard gas (HESJ) and atmospheric He, resulting in ∼3% reproducibility and ≤5% experimental error for various amounts of atmospheric He from 0.3 to 2.3×10(-6) cm(3) STP introduced into the instrument. A dynamic range of measurable (3)He/(4)He ratios with He-MS is greater than 10(3) which was determined by measuring various types of natural fluid samples from continental gas (with a low (3)He/(4)He ratio down to 2×10(-8)) to volcanic gas (with a high (3)He/(4)He ratio up to 3×10(-5)). The accuracy and precision of (3)He/(4)He and (4)He/(20)Ne ratios were evaluated by comparing the values with those measured using well established noble gas mass spectrometers (modified VG5400/MS-III and -IV) in our laboratory, and were found to be in good agreement within analytical errors. Usefulness of the selective extraction of He from water/gas using a high permeability of He through a silica glass wall at high temperature (700°C) is demonstrated.

Optimization of Extraction System for Cold Cathode Ion Source

We have simulated ion trajectories with the SIMION 3D, version 7.0, package to optimize the extraction system of a cold-cathode ion source and compared the results with experimental data collected under the same operational conditions. The simulation determined the negative voltage applied to the extractor electrode and the extraction gap widths that maximize the ion-beam current for singly charged nitrogen ions with low emittance and small diameter. The experiment measured the input electrical discharge and output ion beam characteristics of the source at different nitrogen pressures. The extractor electrode voltage and the extraction gap width were determined at 8 × 10−4 Torr nitrogen. The results of the simulation agreed well with the experimental data.

Separation principle and Monte Carlo studies for differential mobility spectrometry

independent of the field. Therefore, a net displacement toward either electrode of the gap is generated during one cycle of the asymmetric RF waveform. Since different type of ions experiences a different net displacement, the ion can be separated by adjusting the bias between the two electrodes to compensate the displacement, namely compensation voltage, VC. In this work, we examine the relation between nonlinear mobility coefficient, α, and the compensation voltage. In our previous work Monte-Carlo simulation of ion trajectories in DMS [13] was reported. However, the previous simulation was restricted by three conditions. First the RF asymmetric waveform was a square function, which is hardly used in practical DMS spectrometers. Second, ion clustering in low electric field and declustering in high electric field, which result in different ion identities, were not considered. Third, polarization effects were not considered. Due to these limitations, it was difficult to compare Monte-Carlo simulation result with experimental data. In this work, we considered a more realistic waveform used in DMS experiments, field-induced clustering and de-clustering, and the effect of polarization on the cross section calculation. In order to compare with simulated results, some specific DMS experiments were done for typically known reactant ions, H + (H2O)n.

Computer investigation of ion beam optics for a Freeman type ion source system

The present work investigates the computer analysis of the ion beam properties produced by a Freeman type system. The extraction for such system is composed of four electrodes that permit to keep a fixed output energy by means of two accelerating gaps and one decelerating gap. The latter allows reducing the beam divergence angle. The combination of the acceleration/deceleration sections provides to keep a low beam emittance at the source outlet. The simulation of single charged argon ion trajectories for a plasma concave of curvature 4 mm was first studied with and without space charge effect using acceleration/deceleration extraction system with the aid of the SIMION computer program. The voltage applied to the accelerating electrode was optimized to accomplish the suitable ion trajectories without hitting the extraction electrode. Then, two additional studies were performed: the influence of the acceleration voltage and extraction voltage on the beam emittance and beam diameter; and the effect of the extraction gap width (distance between the plasma emission surface and the acceleration electrode) on the shape of the ion beam envelope and the position of the ion beam waist. Last, the influence of the space charge on the ion beam envelope was also investigated.

Overtone mobility spectrometry: part 3. On the origin of peaks.

The origin of non-integer overtone peaks in overtone mobility spectrometry (OMS) spectra is investigated by ion trajectory simulations. Simulations indicate that these OMS features arise from higher-order overtone series. An empirically-derived formula is presented as a means of describing the positions of peaks. The new equation makes it possible to determine collision cross sections from any OMS peak. Additionally, it is extended as a means of predicting the resolving power for any peak in an OMS distribution.

Comparison of quadrupole mass filters with hyperbolic and cylindrical rods working in the third stability zone

The working point of a quadrupole mass filter is generally set in the first zone of stability. For applications that require higher resolutions other stability zones can provide a suitable alternative and in this article it is investigated the third zone in particular for applications in the low mass range. Ion trajectory simulations for 4He + have been carried out for cylindrical as well as hyperbolic rods and the results have been compared. For cylindrical rods the best mass resolution has been obtained with a ratio between rod radius and field radius of 1.120. For this value further simulations have been performed to determine the dependence of transmission on the injection regions and injection angle in the quadrupole field. The analysis of the transmission regarding low and high mass tails has shown that it is possible to get rid of the low mass tails for cylindrical rods by limiting the injection region, instead the high mass tails, which affect the transmission for both cylindrical and hyperbolic rods, can be reduced by increasing the frequency of the radio frequency applied to the rods. Therefore, although the mass resolution at 50% of the peak height for hyperbolic rods is always greater than for cylindrical ones, with a suitable (reduced) ion injection region, the maximum transmission and the baseline resolution of a filter equipped with cylindrical rods can be made to approach that of a hyperbolic rod filter.

Computer simulation of electron and ion trajectories in electron-impact ion sources of a quadrupole mass spectrometer

Electron and ion trajectories have been simulated in electron-impact ion sources of a quadrupole mass spectrometer. The ion trajectories in the conventional Nier-type ion source show poor extraction efficiency of the generated ions into the quadrupole. Based on the electron and ion trajectory simulation results, the Nier-type ion source has been modified to improve the ion extraction efficiency. The modified ion source exhibits much better ion extraction efficiency and smaller kinetic energy spread than the Nier-type ion source.

Pulsed ion extraction diagnostics in a quadrupole ion trap linear time-of-flight mass spectrometer

Pulsed extraction techniques are investigated for a quadrupole ion trap (QIT) interfaced to a linear time-of-flight (TOF) mass analyzer. A nonfocusing short-pulse mode of operation is developed and characterized. The short-pulse mode creates a near-monoenergetic ion packet, which is useful for reaction kinetics experiments and for making diagnostic measurements of the ion cloud size in the trap. Monopolar and bipolar pulsing modes, with the voltage pulses applied to one or both QIT endcaps to extract the ions into the TOF region, are compared. Ion TOF peak distributions are characterized experimentally and by ion trajectory simulations. Also, first-order spatial (Wiley-McLaren) focusing of ions is characterized for the conventional long-pulse extraction mode. The nonparallel fields in the QIT, which serves as the first acceleration region in the linear-TOF mass spectrometer, are shown to degrade spatial focusing and mass resolution.

Application of low energy ion blocking for adsorption site determination of Na Atoms on a Cu(111) surface

Ion blocking in the low keV energy range is demonstrated to be a sensitive method for probing surface adsorption sites by means of the technique of time-of-flight scattering and recoiling spectroscopy (TOF-SARS). Adsorbed atoms can block the nearly isotropic backscattering of primary ions from surface atoms in the outmost layers of a crystal. The relative adsorption site position can be derived unambiguously by simple geometrical constructs between the adsorbed atom site and the surface atom sites. Classical ion trajectory simulations using the scattering and recoiling imaging code (SARIC) and molecular dynamics (MD) simulations provide the detailed ion trajectories. Herein we present a quantitative analysis of the blocking effects produced by sub-monolayer Na adsorbed on a Cu(111) surface at room temperature. The results show that the Na adsorption site preferences are different at different Na coverages. At a coverage θ = 0.25 monolayer, Na atoms preferentially populate the fcc threefold surface sites with a height of 2.7 ± 0.1 Å above the 1st layer Cu atoms. At a lower coverage of θ = 0.10 monolayer, there is no adsorption site preference for the Na atoms on the Cu(111) surface.