Centrum voor Wiskunde en Informatica
Amsterdam, The NetherlandsCWI
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
DE
T
TE
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 structureIon 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 motionsDifferent ion motions
• Cyclotron motionCyclotron motion• Inside cloud motionInside cloud motion
Cloud-cloud interactions Frequency shifts Phase locking
Investigated Phenomena
Ion cloud structure Different ion motions
• Trapping motion• Inside cloud motion
Cloud-cloud interactionsCloud-cloud interactions Frequency shifts Phase locking
Interaction
Investigated Phenomena
Ion cloud structure Different ion motions
• Trapping motion• Inside cloud motion
Cloud-cloud interactions Frequency shiftsFrequency shifts Phase lockingPhase locking
Frqtheo ≠ Frqmeasured
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 icondephase icon
Dephasing of ion clusters
Frequency Icons
Frequency Icons
Ion dynamics in frequency/phase terms• frequency icon: actual oscillation
frequencies of ion clusters relative to theoretical frequencies
• dephase icondephase 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
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