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

TYL-FKPPL 2012, 28-30 May, Clermont-Fd, France

Takashi Sasaki, Koichi Murakami – KEK, JapanSatoshi Tanaka, Kuoko Hasegawa – Ritsumeikan U., JapanAkinori Kimura – Ashikaga Inst. Of Tech., Japan

Sébastien Incerti – CENBG, France

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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

The Geant4 toolkit

The Geant4 toolkit: GEometry And Tracking 4

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A set of libraries to simulate interactions of particles with matter Initiated by CERN in 1994 for HEP (LHC), successor of Geant3 R&D 44 1994-1998, 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

http://geant4.org

SLAC 2011

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Earth magnetosphere

ISS

GAIA

GLAST/FERMI

(NASA)

Brachytherapy

PET Scan(GATE)

Hadrontherapy

DICOM dosimetry

Medical linac

ATLAS, CMS, LHCb, ALICE @ CERN

BaBar, ILC…

Physics-Biology

PHYSICS-MEDICINEPTSIM

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)

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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

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Software suite for simulating particle therapy

Geometry Descript

ion

Geometry Descript

ion

Material

Definition

Material

Definition

Optimized Physics Processes

Optimized Physics Processes

Scorers

Scorers

Event Level

Parallel Processi

ng

Event Level

Parallel Processi

ng

gMocren Visualiza

tion

gMocren Visualiza

tion

Main ProgramMain Program

User interface commands(Input Macro File)

DICOM Handle

r

DICOM Handle

r

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

DICOMServer

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)

GRIDCLOUDSGRIDCLOUDS

Generally, simulation of 1 billion proton events need about 240 CPU hours

RTP completes dose calculation within 2 ~ 5 minutes Large scale

computing environmentis necessary

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PTSIM web interface10

A PTSIM web interface has been

developed to make easier

for submitting jobs on Grid or Cloud

LCG NAREGI (Toyama NCT site)

WMSWMS

UIUI

PXPX

CECE

SESE

CECE

WNWN

WNWN

WNWN

WNWN

WNWN

WNWN

LFCLFC

kek2-ce05OS: RedHatWN(*): 48 (x8core)Memory: 4GB/WN

kek2-ce05OS: RedHatWN(*): 48 (x8core)Memory: 4GB/WN

VOMSVOMS

kek2-ce01OS: RedHatWN(*): 2 (x8core) Memory: 4GB/WN

kek2-ce01OS: RedHatWN(*): 2 (x8core) Memory: 4GB/WN

*)Number of WNs used in this research.

WNWN

Machine:2 CPU x 6 Core x 2 threadsMachine:2 CPU x 6 Core x 2 threads

WNWN

WNWN

WNWN

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

WNWN

Machine:2 CPU x 6 Core x 2 threadsMachine:2 CPU x 6 Core x 2 threads

WNWN

WNWN

WNWN

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 threadsMachine:2 CPU x 6 Core x 2 threads

Machine:2 CPU x 6 Core x 2 threadsMachine:2 CPU x 6 Core x 2 threads

GRID performance11

See talk by Pr. Sasaki on Tuesday

GRID performance12

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-BIOLOGYGeant4-DNA

How can Geant4-DNA model radiation biology ?

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Physics stagestep-by-step modelling

of physical interactions of

incoming & secondary ionising radiation with

biological medium (liquid water)

Physics stagestep-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 stageDNA strands, chromatin fibres, chromosomes, whole cell

nucleus, cells… for the prediction of damages resulting from direct and

indirect hits

Geometry stageDNA 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 DIRECT DNA damages

Biology stageINDIRECT DNA damages (dominant @ low

LET)

Biology stageINDIRECT DNA damages (dominant @ low

LET)

t=0 t=10-15s t=10-6s

FJPPLFJPPL

Geometrical stage - 115

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 - 216

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 - 317

46 chromosomes are built from a random walk approach

Each chromosome has a selectable overall shape Sphere, cylinder, box 5.4x104 voxels

46 chromosomes

Geometrical stage - 418

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

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

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New visualization scheme

On behalf of

Satoshi Tanaka – Ritsumeikan U., JapanKuoko Hasegawa – Ritsumeikan U., JapanAkinori 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

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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

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ATLAS

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ATLAS

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Dose

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Dose

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Geant4 Example

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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

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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

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Cost effects

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

Belle II CPU requirement provided by Prof. Hara.

1 CPU is almost 10 HEPSpec

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PROPOSED WORKPLAN

Workplan - 135

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 - 236

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 - 337

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

Participants39

France Japan

V. Breton LPC Clermont K. Amako KEK

C. Champion U. Metz / CENBG

T. Aso TNCMT

S. Elles LAPP Y. Hirano NIRS

S. Incerti CENBG G. Iwai KEK

J. Jacquemier LAPP A. Kimura Ashikaga IT

L. Maigne LPC Clermont K. Murakami KEK

I. Moreau CENBG C. Omachi Nagoya city

Y. Perrot LPC Clermont T. Sasaki KEK

C. Seznec CENBG S. Tanaka Ritsumeikan U.

M. Verderi LLR H. Yoshida Shikoku U.

Budget request for 201240

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 much41