Centrum voor Wiskunde en Informatica Amsterdam, The Netherlands CWI Wojciech Burakiewicz Robert van Liere Analyzing Complex FTMS Simulations: a Case Study in High-Level Visualization of Ion Motions
Create new tools Clarify images Show physical phenomena Motivation Data properties: Large datasets Complex phenomena Visualization tools available: Point clouds Trajectories/Animation Study the dynamics of complex phenomena in particle simulations
Outline 1.Study subject: Fourier Transform Mass Spectrometry a)Mass spectrometry b)Simulations 2.Visualization a)Standard techniques b)Our visualization tools 3.Evaluation 4.Conclusions
Fourier Transform Mass Spectrometry Mass Spectrometry: Determine chemical composition of substances at very low concentrations Investigate chemical properties of molecules Computer simulations: Understand physical phenomena Increase resolution and accuracy
D D E T T E Fourier Transform Mass Spectrometry Investigated substance: Ionized Trapped in electromagnetic field Oscillation frequency ~ mass Signal induced by oscillating ions measured on the detection plates. By studying the signal we discover the substance composition B ~ 1 in vacuum
Simulations: Up to 10^6 ions simulated over 10^5 time steps Experimental timescale: 100ms – 1s Output: Detected signal – similar to the real experiment Ion positions for each time step: File size: in Giga Bytes FTMS Datasets
Investigated Phenomena Ion cloud structure Different ion motions Trapping motion Inside cloud motion Cloud-cloud interactions Frequency shifts Phase locking
Ion cloud structure Ion cloud structure Different ion motions Trapping motion Inside cloud motion Cloud-cloud interactions Frequency shifts Phase locking Ion density m/z distribution Cloud dephasing Investigated Phenomena
Ion cloud structure Different ion motions Different ion motions Cyclotron motion Cyclotron motion Inside cloud motion Inside cloud motion Cloud-cloud interactions Frequency shifts Phase locking Investigated Phenomena
Ion cloud structure Different ion motions Trapping motion Inside cloud motion Cloud-cloud interactions Cloud-cloud interactions Frequency shifts Phase locking Interaction Investigated Phenomena
Ion cloud structure Different ion motions Trapping motion Inside cloud motion Cloud-cloud interactions Frequency shifts Frequency shifts Phase locking Phase locking Frq theo Frq measured Clusters oscillate together Investigated Phenomena
Visualization: Standard tools 2D or 3D point clouds, Dynamics: Trajectories/Animation Problems Image cluttering Phenomena difficult to discern
Visualization: Standard tools 2D or 3D point clouds, Dynamics: Trajectories/Animation Problems Image cluttering Phenomena difficult to discern
Our visualization tools Comet icon Ion cloud structure Camera control Ion and cloud motions Frequency icons Cloud frequency perturbations
Comet icon Partition the ion group along the center of gravity trajectory Count ions in each partition Choose partition size according to number of ions
Comet Icon m/z of ions in the group - color ion density in the comet - shape + saturation dephase state of the comet - shape detailed m/z distribution in the comet - color bar
Comet Icon Cloud evolution
Camera Control We postion the camera according to data properties in each frame: find cluster's center of gravity trajectory obtain local coordinate frame by computing the Frenet frame for this trajectory position the camera in this local coordinate frame
Camera Control Adjust camera in local coordinates: Camera positioned in the XY plane Camera viewing along the Z axis Camera placed arbitrarily Trapping motion of the ions
Camera Control Adjust camera in local coordinates: Camera positioned in the XY plane Camera viewing along the Z axis Camera placed arbitrarily Relative cloud motions
Camera Control Adjust camera in local coordinates: Camera positioned in the XY plane Camera viewing along the Z axis Camera placed arbitrarily Relative ion motions inside the cloud
Camera Control Adjust camera in local coordinates: Camera positioned in the XY plane Camera viewing along the Z axis Camera placed arbitrarily Relative ion motions inside the cloud
Ion dynamics in frequency/phase terms frequency icon: frequency icon: actual oscillation frequencies of ion clusters relative to theoretical frequencies dephase icon: dephasing of each ion cluster Frequency shifts Phase locking Frequency Icons
Ion dynamics in frequency/phase terms frequency icon: actual oscillation frequencies of ion clusters relative to theoretical frequencies dephase icon dephase icon Dephasing of ion clusters Frequency Icons
Ion dynamics in frequency/phase terms frequency icon: actual oscillation frequencies of ion clusters relative to theoretical frequencies dephase icon dephase icon
Resume Ion cloud structure Different ion motions Trapping motion Inside cloud motion Cloud-cloud interactions Frequency shifts Phase locking Dephasing Comet icon Camera control Frequency icons
Evaluation (1) Clarity of image Visibility of physical phenomena
Evaluation (1) Clarity of image Visibility of physical phenomena
Evaluation (2) Our tool has been used by physicists: FOM Institute for Atomic and Molecular Physics, Amsterdam The Institute for Energy Problems of Chemical Physics, Moscow With our tool a number of discoveries were made: Dephasing and phase-locking are strongly influenced by the density of the ions in the trap Excitation profile has great influence on the instrument detection accuracy and resolution
Conclusions The standard visualization tools do not suffice: Image cluttering Phenomena difficult to discern Our visualization tools explicitly show important phenomena Users apply this tool to do science
The end