Analyzing Complex FTMS Simulations: a Case Study in High-Level Visualization of Ion Motions

Abstract

AmsterdamFigure 1: Three views of ion-motion: Left is a low-level direct rendering of an ion-cloud. Trajectories are used to show motion of a few ions. Middle image shows 'comet icons' which encode motion and density properties of clusters of related ions. The right image shows relative ion motions from a camera tethered to the center of the comet. ABSTRACTCurrent practice in particle visualization renders particle position data directly onto the screen as points or glyphs. Using a camera placed at a fixed position, particle motions can be visualized by rendering trajectories or by animations. Applying such direct techniques to large time dependent particle data sets often results in cluttered images in which the dynamic properties of the underlying system are difficult to interpret.In this case study we take an alternative approach for the visualization of ion motions. Instead of rendering ion position data directly, we first extract meaningful motion information from the ion position data and then map this information onto geometric primitives. Our goal is to produce high-level visualizations that reflect the physicists' way of thinking about ion dynamics. Parameterized geometric icons are defined to encode motion information of clusters of related ions. In addition, a parameterized camera control mechanism is used to analyze relative instead of only absolute ion motions.We apply the techniques to simulations of Fourier transform mass spectrometry (FTMS) experiments. The data produced by such simulations can amount to 5·10 4 ions and 10 5 time steps. This paper discusses the requirements, design and informal evaluation of the implemented system.

Fast image–charge calculations for multi-particle simulations in FT-ICR analyzer cells of arbitrary geometry

“…A simulated time domain transient was collected for each experiment and a frequency domain spectrum was derived using FOM-AMOLF's AWE software [25]. The ion cloud and the resulting image-charge distribution was visualized with inhouse software developed at FOM-AMOLF [2].…”

“…Multi-particle simulations provide a useful approach for studying collective ion motion in an FTICR analyzer cell, and to accurately model the influence of subtle effects such as spacecharge and ion-image charge interactions [1][2][3][4][5]. Simulations provide the ability to test the effects of parameters that are difficult to control experimentally such as the precise number and spatial distribution of ions in an analyzer cell [6].…”

“…The radially repulsive force of the trapping potential leads to magnetron motion of the ion, and a reduction in the observed orbital frequency from the ideal value given by Eq. (2). For most commonly used analyzer cells, there is a spatial gradient in the trapping field, leading to a change in magnetron frequency across the analyzer cell, and thus, a loss of coherence as ions undergo axial motion [8].…”

Comparison of particle-in-cell simulations with experimentally observed frequency shifts between ions of the same mass-to-charge in fourier transform ion cyclotron resonance mass spectrometry

“…For each computational experiment, a simulated time domain transient was acquired and a frequency domain spectrum was derived using the fast Fourier transform (FFT) incorporated in FOM-AMOLF’s AWE software [26]. Visualization of the simulated ion cloud was accomplished with in-house software developed at FOM-AMOLF [27]. …”

Visualization for the Physical Sciences

“…Multi‐field 2D data is visualized using a field [LFH08] or using time [YXG*10] as a third dimension. Multi‐field 3D data is visualized using glyphs and a variation in the glyph colour [SIG05] or shape [CFG*05, BvL06, JKM06, DMB*06, MDHB*07], using trajectories, vector glyphs or surfaces together with volume rendering [SYS*06, JCSB03], parallel coordinates [QCX*07] or multiple‐linked views and brushing [CFG*05, KLM*08].…”