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