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

Content 2  Bio 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

THE GEANT4 TOOLKIT

The Geant4 toolkit: GEometry And Tracking 4 4  A set of libraries to simulate interactions of particles with matter  Initiated by CERN in 1994 for HEP (LHC), successor of Geant3  R&D , 1st release in December 1998  Now developed by an international collaboration (~100 members)  Object-oriented technology  Set of libraries : not a user code  Constantly updated (two public releases per year)  Entirely open source and free  Simulation of a particle physics experiment  Define a flexible geometry  Model physical interactions : electromagnetic, hadronic  Generate primary particles and simulate their interactions  Extract physical quantities and analyze them  Capabilities  Visualization  Interactivity  Extensibility SLAC 2011

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

PHYSICS-MEDICINE PTSIM

New particle therapy clinics are opening in Japan  Proton/Carbon-ion Facilities in Japan  11 Proton/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) 7 * * * * * * * * * * * u u

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 – Mar  Joint Project among Geant4 developers, physicists, and medical physicists  Use-cases were sampled from medical physicists at treatment facilities 8 Software suite for simulating particle therapy Geometry Description Material Definition Optimized Physics Processes Scorers Event Level Parallel Processing gMocren Visualization Main Program User interface commands (Input Macro File) DICOM Handler Primary Beam Primary Beam gMocren Driver gMocren Driver Use-case => Modularization => Provided as a class library KEK, TNCT, AIT, Rits, Naruto U., NIRS, HIBMC, NCC

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

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

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

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

PHYSICS-BIOLOGY GEANT4-DNA

How can Geant4-DNA model radiation biology ? 14 Physics stage step-by-step modelling of physical interactions of incoming & secondary ionising radiation with biological medium (liquid water) Physics stage step-by-step modelling of physical interactions of incoming & secondary ionising radiation with biological medium (liquid water) Physicochemistry/chemistry stage Radical species production Diffusion Mutual interactions Physicochemistry/chemistry stage Radical species production Diffusion Mutual interactions Geometry stage DNA strands, chromatin fibres, chromosomes, whole cell nucleus, cells… for the prediction of damages resulting from direct and indirect hits Geometry stage DNA strands, chromatin fibres, chromosomes, whole cell nucleus, cells… for the prediction of damages resulting from direct and indirect hits Excited water molecules Ionised water molecules Solvated electrons Biology stage DIRECT DNA damages Biology stage INDIRECT DNA damages low LET) t=0t= st=10 -6 s FJPPL

Geometrical stage  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 a keratinocyte (HaCaT/(H2B-GFP)Tg) nucleus

Geometrical stage  Each voxel contains a chromatine fiber element  Each chromatine fiber element is made of 6 nucleosome  Each nucleosome has 2 DNA 100-base pair loops  DNA is in the B-DNA conformation  The B-DNA sequence follows the ratio 6:4 (A-T VS G-C)

Geometrical stage  46 chromosomes are built from a random walk approach  Each chromosome has a selectable overall shape  Sphere, cylinder, box 5.4x10 4 voxels 46 chromosomes

Geometrical stage  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 µm 3 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

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 in Geant4  A user advanced example (« dnachemistry ») is in preparation  Variable density feature 19

NEW VISUALIZATION SCHEME On behalf of Satoshi Tanaka – Ritsumeikan U., Japan Kuoko Hasegawa – Ritsumeikan U., Japan Akinori Tanaka – Ashikaga Inst. Of Tech., Japan

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 21

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 22

ATLAS 23

ATLAS 24

Dose 25

Dose 26

Geant4 Example 27

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PARALLEL GEANT4

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 31

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 32

Cost effects  Case of Belle II experiment at super B factory at KEK  needs cores needed for MC production  You may guess how much we can save if we speed up Geant4  Much to do Belle II CPU requirement provided by Prof. Hara. 1 CPU is almost 10 HEPSpec 33

PROPOSED WORKPLAN

Workplan  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 physics processes for hadrontherapy PTSim will be extended to upcoming new Japanese facilities Promotion of PTSim in France

Workplan  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

Workplan  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

COLLABORATION MATTERS

Participants 39 FranceJapan V. BretonLPC ClermontK. AmakoKEK C. ChampionU. Metz / CENBGT. AsoTNCMT S. EllesLAPPY. HiranoNIRS S. IncertiCENBGG. IwaiKEK J. JacquemierLAPPA. KimuraAshikaga IT L. MaigneLPC ClermontK. MurakamiKEK I. MoreauCENBGC. OmachiNagoya city Y. PerrotLPC ClermontT. SasakiKEK C. SeznecCENBGS. TanakaRitsumeikan U. M. VerderiLLRH. YoshidaShikoku U.

Budget request for  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

Thank you very much 41