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

1. Analyzing Complex FTMS Simulations:a Case Study in High-Level Visualization of Ion Motions Wojciech Burakiewicz Robert van Liere Centrum voor Wiskunde en Informatica Amsterdam, The Netherlands CWI

2. Create new tools Clarify images Show physical phenomena Data properties: Large datasets Complex phenomena Visualization tools available: Point clouds Trajectories/Animation Motivation Study the dynamics of complex phenomena in particle simulations

3. Outline • Study subject: Fourier Transform Mass Spectrometry • Mass spectrometry • Simulations • Visualization • Standard techniques • Our visualization tools • Evaluation • Conclusions

4. 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

5. B D ~ 1 in vacuum 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 T E E T D

6. FTMS Datasets • 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

7. Investigated Phenomena • Ion cloud structure • Different ion motions • Trapping motion • Inside cloud motion • Cloud-cloud interactions • Frequency shifts • Phase locking

8. Investigated Phenomena • 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

9. Investigated Phenomena • Ion cloud structure • Different ion motions • Cyclotron motion • Inside cloud motion • Cloud-cloud interactions • Frequency shifts • Phase locking

10. Investigated Phenomena • Ion cloud structure • Different ion motions • Trapping motion • Inside cloud motion • Cloud-cloud interactions • Frequency shifts • Phase locking Interaction

11. Investigated Phenomena • Ion cloud structure • Different ion motions • Trapping motion • Inside cloud motion • Cloud-cloud interactions • Frequency shifts • Phase locking • Frqtheo≠ Frqmeasured • Clusters oscillate together

12. Visualization: Standard tools • 2D or 3D point clouds, • Dynamics: Trajectories/Animation • Problems • Image cluttering • Phenomena difficult to discern

13. Visualization: Standard tools • 2D or 3D point clouds, • Dynamics: Trajectories/Animation • Problems • Image cluttering • Phenomena difficult to discern

14. Our visualization tools • Comet icon • Ion cloud structure • Camera control • Ion and cloud motions • Frequency icons • Cloud frequency perturbations

15. 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

16. 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

17. Comet Icon • Cloud evolution

18. 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

19. 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

20. 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

21. 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

22. 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

23. Frequency Icons • Ion dynamics in frequency/phase terms • frequency icon: actual oscillation frequencies of ion clusters relative to theoretical frequencies • dephase icon: dephasing of each ion cluster • Frequency shifts • Phase locking

24. Frequency Icons • Ion dynamics in frequency/phase terms • frequency icon: actual oscillation frequencies of ion clusters relative to theoretical frequencies • dephase icon • Dephasing of ion clusters

25. Frequency Icons • Ion dynamics in frequency/phase terms • frequency icon: actual oscillation frequencies of ion clusters relative to theoretical frequencies • dephase icon

26. 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 Resume

27. Clarity of image Visibility of physical phenomena Evaluation (1)

28. Clarity of image Visibility of physical phenomena Evaluation (1)

29. 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

30. 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

31. The end