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Bio-1 New developments of the geant4 Monte carlo simulation toolkit

Takashi Sasaki, Koichi Murakami – KEK, Japan Satoshi Tanaka, Kuoko Hasegawa – Ritsumeikan U., Japan Akinori Kimura – Ashikaga Inst. Of Tech., Japan Sébastien Incerti – CENBG, France. Bio-1 New developments of the geant4 Monte carlo simulation toolkit.

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Bio-1 New developments of the geant4 Monte carlo simulation toolkit

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  1. Takashi Sasaki, Koichi Murakami – KEK, Japan Satoshi Tanaka, Kuoko Hasegawa – Ritsumeikan U., Japan Akinori Kimura – Ashikaga Inst. Of Tech., Japan Sébastien Incerti – CENBG, France Bio-1New developments of the geant4 Monte carlo simulation toolkit TYL-FKPPL 2012, 28-30 May, Clermont-Fd, France

  2. Content • Bio-1 2011 collaboration activities • Development of specific applications at the Physics-Medicine interface • PTSim software for particle therapy simulation • Development of specific applications at the Physics-Biology interface : • the Geant4-DNA project • Development of a new visualization scheme • Efforts toward parallel Geant4 • Proposed workplan for 2012 • Collaboration matters

  3. The Geant4 toolkit

  4. The Geant4 toolkit: GEometry And Tracking 4 • A set of libraries to simulateinteractions of particleswithmatter • Initiated by CERN in 1994 for HEP (LHC), successor of Geant3 • R&D 44 1994-1998, 1st release in December 1998 • Nowdeveloped by an international collaboration (~100 members) • Object-orientedtechnology • Set of libraries : not a user code • Constantlyupdated (two public releases per year) • Entirelyopen source and free • Simulation of a particlephysicsexperiment • Define a flexible geometry • Model physical interactions : electromagnetic, hadronic • Generateprimaryparticles and simulatetheir interactions • Extractphysicalquantities and analyzethem • Capabilities • Visualization • Interactivity • Extensibility http://geant4.org SLAC 2011

  5. ATLAS, CMS, LHCb, ALICE @ CERN PET Scan(GATE) BaBar, ILC… Brachytherapy Medical linac Earth magnetosphere GLAST/FERMI(NASA) GAIA Physics-Biology DICOM dosimetry ISS Hadrontherapy

  6. PHYSICS-MEDICINEPTSIM

  7. New particle therapy clinics are opening in Japan • Proton/Carbon-ion Facilities in Japan • 11Proton/Carbon Therapy facilities in operation in Japan • U. of Tsukuba PMRC (1983) • NIRS (1979) (C) • National Cancer Center East Hospital (1988) • Shizuoka Cancer Center (2003) • Wakasa wan energy research center • Hyogo Ion Beam medical center (p/C) (2001) • Fukui Prefectural Hospital (2011) • Medipolis Medical Research Institute (2011) • Southern TOHOKU Proton Therapy Center (2008) • Gumma U. Heavy Ion Medical Center (2010) • Quality life 21 Jyohoku (Under Construction) Nagoya City • U. of Hokkaido (Under Construction) u * * * * * * * * u * * *

  8. KEK, TNCT, AIT, Rits, Naruto U., NIRS, HIBMC, NCC PTSIM: Particle Therapy Simulation based on Geant4 • Project “Development of a simulation framework for advanced radio-therapy” • Funded by the Japan Science and Technology Agency (JST) and Core Research for Evolutional Research and Technology (CREST) • Oct. 2003 – Mar. 2010 • Joint Project among Geant4 developers, physicists, and medical physicists • Use-cases were sampled from medical physicists at treatment facilities Software suite for simulating particle therapy Use-case => Modularization => Provided as a class library DICOM Handler Scorers gMocren Driver Primary Beam Material Definition Geometry Description Event Level Parallel Processing Optimized Physics Processes Main Program gMocren Visualization User interface commands (Input Macro File)

  9. CT.MR Images MR images (DICOM3.0) MR Scanner Treatment planning Treatment parameters (DICOM-RTPlan) CT images (DICOM3.0) Treatment parameters (DICOM-RTPlan) DICOM Server CT Scanner Dose disp (DICOM-RTDose) RT Parameters (DICOM-RTPlan) G4 as a Dose engine Proton machine PTSIM in Radiation Treatment Planning RTP completes dose calculation within 2 ~ 5 minutes Large scale computing environment is necessary GRID CLOUDS Generally, simulation of 1 billion proton events need about 240 CPU hours

  10. PTSIM web interface A PTSIM web interface has been developed to make easier for submitting jobs on Grid or Cloud

  11. GRID performance NAREGI (Toyama NCT site) LCG VOMS WMS CE UI SE CE WN PX WN WN LFC WN WN WN kek2-ce05 OS: RedHat WN(*): 48 (x8core) Memory: 4GB/WN kek2-ce01 OS: RedHat WN(*): 2 (x8core) Memory:4GB/WN Machine:2 CPU x 6 Core x 2 threads See talk by Pr. Sasaki on Tuesday WN OS: RedHat VM: 24(Scientific Linux) WN: 26 Memory:2.6 GB/WN WN *)Number of WNs used in this research. WN WN Machine:2 CPU x 6 Core x 2 threads Machine:2 CPU x 6 Core x 2 threads Machine:2 CPU x 6 Core x 2 threads OS: RedHat VM: 24(Scientific Linux) WN: 23 Memory:2.6 GB/WN WN WN WN WN

  12. GRID performance Full simulation including beamline Fractions of initialization times (physics in blue, geometry in red) and simulation times Time consumeduntil all jobs are finished

  13. PHYSICS-BIOLOGYGeant4-DNA

  14. How can Geant4-DNA model radiation biology ? Physics stage step-by-stepmodelling of physical interactions of incoming & secondaryionising radiation withbiological medium (liquid water) • Excited water molecules • Ionised water molecules • Solvated electrons • Physicochemistry/chemistry stage • Radicalspecies production • Diffusion • Mutual interactions FJPPL Geometry stage DNA strands, chromatin fibres, chromosomes, whole cell nucleus, cells… for the prediction of damages resulting from direct and indirect hits Biology stage DIRECT DNA damages Biology stageINDIRECT DNA damages (dominant @ low LET) t=0 t=10-15s t=10-6s

  15. Geometrical stage - 1 • The FJPPL activity was focused on the geometrical stage of Geant4-DNA • Objective : develop a cellular phantom including chromosome territories down to DNA bases • Dr C. Omachi (KEK) visited CENBG for a month in 2011 • Developed a realistic cellular phantom obtained from confocal microscopy of HaCat keratinocyte line, including an ellipsoid cytoplasm and voxellized nucleus ~20μm Image of akeratinocyte (HaCaT/(H2B-GFP)Tg) nucleus

  16. Geometrical stage - 2 • Eachvoxelcontains a chromatine fiberelement • Eachchromatine fiberelementis made of 6 nucleosome • Eachnucleosome has 2 DNA 100-base pair loops • DNA is in the B-DNA conformation • The B-DNA sequencefollows the ratio 6:4 (A-T VS G-C)

  17. Geometrical stage - 3 • 46 chromosomes are built from a random walk approach • Each chromosome has a selectable overall shape • Sphere, cylinder, box 5.4x104voxels 46 chromosomes

  18. Geometrical stage - 4 • Geometrical model was extended to a skin-like tissue • Top view of three layers of skin-like tissue. • One layer consists 100 voxels with 100 x 100 x 10 micrometer µm3 volume each. • Each voxel contains one nucleus shown as a green sphere that includes the 46 choromosomes. • These results have been presented at the IBA 2011 conference

  19. Update on Geant4-DNA developments • New physics models upcoming • Elastic scattering for light ions in liquid water • Proton and hydrogen physics models for DNA material • First time in a public MC code • Multi-combination • With photon Physics (Standard, Livermore, Penelope) • With other EM processes and models • In different regions and energy ranges • Including atomic deexcitation • Prototype for water radiolysis simulation was released in Dec. 2011 in Geant4 • A user advanced example (« dnachemistry ») is in preparation • Variable density feature

  20. On behalf of Satoshi Tanaka – Ritsumeikan U., Japan Kuoko Hasegawa – Ritsumeikan U., Japan Akinori Tanaka – Ashikaga Inst. Of Tech., Japan New visualization scheme

  21. Conventional opaque visualization • The conventional schemes are not good at visualizing very complicated geometry • Tend to be fuzzy • No clear images • Needs sorting of polygons • Computing time is proportional to N log N • N: num. of polygons • Artifact because of failure of sorting • It is impossible to visualize opaquely polygon data, volume data and line data at the same time

  22. Latest scheme based on point-base rendering method • Groups of 3-D points allows very high precise visualization opaquely • Sorting operations are not necessary because of a stochastic algorithm • This solved the problems coming from sort operations in conventional schemes • Polygon data, volume data and line data can be visualized simultaneously • Will be applicable for visualizing DNA structure also

  23. ATLAS

  24. ATLAS

  25. Dose

  26. Dose

  27. Geant4 Example

  28. PARALLEL Geant4

  29. Efforts toward parallel Geant4 • Computation speed of Geant4 is a big issue in many application fields • HEP, medical, space, etc. • In parallel, the computer industry is going to many-core CPU • Integration of accelerator chips on CPU will be soon available • Intel and NVIDIA

  30. Trends of CPU • Many cores • 10 or more cores / CPU • Intel MIC (pronounced like “Mike”) • 50 or more simplified x86 cores • To be available in 2012 as a PCI-e card • Will be integrated with CPU (2015 ?) • Solve the bus neck • NVIDIA • ARM and GPGPU will be integrated • Solve the bus neck • ARM is a CPU mostly used for mobile devices

  31. Cost effects Belle II CPU requirement provided by Prof. Hara. 1 CPU is almost 10 HEPSpec • Case of Belle II experiment at super B factory at KEK • needs 40 000 cores needed for MC production • You may guess how much we can save if we speed up Geant4 • Much to do

  32. PROPOSED WORKPLAN

  33. Workplan - 1 • The KEK & CENBG teams met at IN2P3 headquarters on March 12, 2012 in Paris • 3 main activities • Activity 1: Physics-Medicine • Continue effort of validation of Geant4 physicsprocesses for hadrontherapy • PTSimwillbeextended to upcoming new Japanesefacilities • Promotion of PTSim in France

  34. Workplan - 2 • Activity 2 : Physics-Biology • Finalize the development & publication of Dr C. Omachi’s et al. cellular phantom model including DNA bases up to chromosome territories • Dr C. Omachi got a new position at new Nagoya’s protontherapy center • Will be performed by Dr Hirano (NIRS, Japan) • Make it available as a Geant4 public example

  35. Workplan - 3 • Activity 3 : parallel Geant4 • Re-design of Geant4 kernel will be done • Geant4 collaboration wide discussion is necessary • Only EM will be processed in parallel • We forget hadronic interactions for a while • A toy model will be implemented • A start point for the discussion • Outreach • Geant4 & Geant4-DNA tutorial • Much interest in understanding biological effects of radiation at the cellular scale after the nuclear accident at Fukushima • Japanese team deeply involved the Geant4/GATE tutorial at KISTI in Seoul, Oct. 31 – Nov. 4, 2011 • Continue this common teaching effort between Japan, Korea and France

  36. COLLABORATION MATTERS

  37. Participants

  38. Budget request for 2012 • Request from France • Visit CENBG team to KEK & NIRS • end of summer 2012 • Possibly participate to a Geant4 tutorial • Request from Japan • 3 japanese visits to CENBG

  39. Thank you very much

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