analyzing complex ftms simulations: a case study in high-level visualization of ion motions

Centrum voor Wiskunde en Informatica

Amsterdam, The NetherlandsCWI

Wojciech BurakiewiczRobert 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 Spectrometrya) Mass spectrometryb) Simulations

2. Visualizationa) Standard techniquesb) Our visualization tools

3. Evaluation 4. Conclusions

Fourier Transform Mass SpectrometryMass 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