plateforme de calcul pour les sciences du vivant interdisciplinary activities v. breton cnrs-in2p3,...
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Plateforme de Calcul pour les Sciences du Vivant
http://clrpcsv.in2p3.fr
Interdisciplinary activities
V. Breton
CNRS-IN2P3, LPC Clermont-Ferrand
RECFA open day, May 12 2006
Credits: A. Billebaud, M. Farizon, J-M Fontbonne, S. Incerti, P. Le Dû, S. Leray, E. Suraud
Introduction
• Our core activity is to understand the universe at small and at cosmological distances
• Competences acquired to support core projects can benefit other scientific domains– Accelerators– Detectors– Computing
• We are called upon to contribute our scientific competence to other fields of science and to solve certain problems raised by the society
• Development of interdisciplinary research on two main fronts– Interface with life sciences (on the steps of Marie Curie)– Processing of nuclear wastes
Interdisciplinary research at IN2P3
IN2P3
Life sciences - Medical imaging - Hadron therapeutic cancer treatment - DNA Sequencing - Study of Low doses
Chemistry - Radiochemistry - Detection of trace elements - Waste treatment
MIPPU (mathematics, computer science, physics and universe) - Theoretical physics - Materials for detectors - Solid state physics - Behavior of irradiated materials - Aggregates - Telecommunications - Grids
Social sciences - Dating - Risk Perception - History of sciences
Engineering - Microelectronics - Highly stable lasers - Waste treatment
Environment - Waste treatment - Oceanography - Low level radioactivity
Sciences of the universe - Astrophysics and cosmology - Oceanography - Waste treatment - Low-level radioactivity - Dating
Physics and chemistry for nuclear energy and environment
• Nuclear energy is probably going to regain momentum in the close future– Awareness of the impact of fossil energy on greenhouse effect– Growing need of emerging countries– Limited reserves and foreseeable exhaustion of fossil energy– Limited capacity of renewable energies
• In this perspective, convincing answers must be found to issues related to– Waste management– Security– Non-proliferation
• New types of reactors, new methods for characterizing nuclear material are under study
Research activities at IN2P3 and DAPNIA
• Radiochemistry: Physics and Chemistry of radioactive materials produced in the present and future nuclear energy sector, in the environment (waste storage sites) and in medecine– Resources: 5 IN2P3 laboratories, 45 permanent staff + 30 non
permanent staff
• Metrology: measurement and monitoring of radioactivity in the environment– Resources: 20 staff + 8 NP staff
• Study of physics and scenarios for future reactors– Resources: 15 staff + 8 NP staff
• Nuclear physics for future reactors and other applications– Resources: 27 staff + 16 NP staff
Organization of work and perspectives
• Organization of work– CNRS interdisciplinary program PACE (Nuclear Cycle Post
Processing program)– CNRS Research Groups : PRACTIS, NOMADE, GEDEPEON– European FP6 projects: ACTINET6, IP-EUROTRANS, …– Collaboration with CEA and industry (EDF, ANDRA,
FRAMATOME, COGEMA)
• Scientific prospects for the next 10 years: carry out upstream research in the electro-nuclear field– Acquisition of fundamental data (spallation, captures, fission)– Study hybrid systems for transmutation– Contribute to the study of innovating systems for the future
nuclear energy
Interaction of particles with matter
• Interdisciplinary research on accelerators and ion beams
• Main research areas– Collision processes– Understanding energy deposit by polyatomic projectiles such as
aggregates or molecules in solids– Simulation of particle interaction with materials– Experimental simulation of material aging under irradiation– Use of structural changes induced by ion and aggregate beams
• Resources: > 4 laboratories, ~ 34 staff in IN2P3 laboratories (20% of the french research community)
Organization of work and perspectives
• Organization of work– Natural collaboration with the scientific communities using accelerators
and ion beams– Lack of organization around the different levels of interaction between
particle and matter Community of 170 researchers spread in 24 laboratories
• Perspectives– Creation of a Research Group (GDR) “fundamental research on particle
– matter interaction”– Identified common topics of interest
Elementary collision processes Fragmentation paths, energy and excitation transfer mechanisms in
molecules and aggregates Relaxation paths for materials under irradiation Modeling of matter energy transfer and relaxation phases Impact of different levels of disorder on biological, physical and chemical
properties of materials
Life sciences
• Main research areas– Physical and chemical characterization of
living organisms– Radiobiology– Radiotherapy – Medical and biological imaging– Informatics for life sciences
• Resources– 10 laboratories (including CEA)– 70 staff members (50 researchers, 20
technical staff)• A significant scientific production
– 29 thesis, 65 papers, 14 patents• Partners
– Hospitals, universities, CEA (life science department), CNRS (life science, engineering departments), INSERM (national institute for medical research), FP6 European projects
Physical and chemical characterization of living organisms
• Tools: accelerators of light / polyatomic ions
• Techniques used: imaging, chemical analysis, local irradiation
• Resources: 4 laboratories, 13 staff + 11 NP staff
• 3 research areas– Characterization of interfaces
between biomaterials and living tissues
– Characterization of biomolecules for bacteriology and environment
– Chemical exploration of cells to study exposure to nanoparticles and metals
Radiobiology
• Radiobiology is about characterizing and quantifying irradiation effects on biological systems
• Tools: 4 accelerator facilities (neutron, proton and ion beams)
• Resources: 4 laboratories, ~ 8 staff and 5 NP staff• Research areas
– Intermolecular dynamics under irradiation– Search for molecules or nano-objects increasing or
inhibiting radio sensitivity– DNA lesions and genomic instabilities induced by
irradiation– Irradiation of Intracellular targets – intra and extra cellular messaging after irradiation
Direct and indirect impact of radiations on DNA
Radiotherapy
• Radiotherapy is about using ionizing particles to kill cancerous cells
• Resources: 4 laboratories, 8 staff and 10 NP staff
• Research areas– Treatment planning– Development of accelerators for
radiotherapy treatment– Quality control (beam dosimetry,
on-line monitoring)
Simulation of an electron accelerator using GATE
Medical and biological imaging
• Development of imaging systems based on technological expertise
• Resources: 10 laboratories, 35 staff + 20 NP staff
• Research areas cover imaging devices from molecule to man– In vitro imaging– In vivo imaging (PET, SPECT, MRI)– Multi-modal imaging– Per-operative imaging
• Highlight: creation of a laboratory dedicated to brain functional imaging– Location: Orsay– Joint IN2P3-CNRS Life Science
Department laboratory
Per-operative compact imager, IPN Orsay
Activities in medical imaging at IN2P3 and DAPNIA
I magerie
in vitro
Cellulaire
Coupe anatomique
Micro CT
Micro SPECT
Micro TEP
Autres instruments
Peropératoire
TEP hadron
TEP corps entier
I RM
Petit
Animal
Homme
Curatif
Homme
diagnostic
recherche
I magerie
in vitro
xTal LXe
LXeSIC
TOHR
POCI
AIF
Modélisation Reconstruction
Informatics for life sciences
• Resources: – 7 laboratories– 6 staff + 20 NP staff
• Research areas – Simulation for dosimetry
and imaging (GATE) – Simulation for
radiobiology (Geant4)– Grids for life sciences and
healthcare
Simulation Modeling
Data handlingand analysis
Fundamental research in nuclearand particle physics
Detectors
GEANT4GATE Grids
Innovating technologies
Nuclear MedecineRadiobiologyRadiotherapy
Life sciencesHealthcare
Medical andBiological imaging
Grid-enabled in silico drug discovery
• Goal: reduce time and cost to develop new drugs by selecting the best drug candidates– Particularly relevant to neglected and
emerging diseases• Strategy: deploy virtual screening on
grids– Screening = selection of molecules active
on a given protein target– Grid added value: access to huge
computing resources• Successful deployment on EGEE
against malaria and bird flu– Malaria: 46 millions docking probabilities
computed in 6 weeks in the summer 2005– Bird flu: 100 CPU years to find new drugs
against mutated neuraminidase N1• Role of IN2P3: coordination of the grid
deployments
Countries contributing to EGEE Biomedical Virtual Organization
Number of malaria related jobs waiting and running on EGEE vs time
Organization of work at the interface with life sciences
• Interface with life sciences has been loosely structured in the last millennium– Local collaboration with hospitals or university groups– Transfer of expertise for technical developments
• Life sciences are moving into “big science”– Molecular biology experimental platforms produce very large volumes
of data studied by international collaborations – Research equipments become national (NeuroSpin, Hadrontherapy
centre)– Europe has developed large scale projects (NoE, IP) in FP6
• Interface with life sciences is being structured– Appointment of “chargés de mission” at CEA-DAPNIA (P. Le Dû, P.
Mangeot) and a scientific deputy director in charge of interdisciplinary activities at IN2P3 (E. Suraud)
– Research Group (GDR) “Instrumentation and simulation for biomedical imaging” started in 2005
– Involvement in european projects (CELLION, MAESTRO, EGEE, Embrace, BioinfoGRID)
– Bilateral collaborations with Germany, Austria, Korea,Taïwan, …
Scientific prospects for the next 10 years
• Objective 1: contribute to the next generation of FEL and to the R&D on the cold technology of the e+e- linear collider (TESLA)
• Objective 2: Contribute to the design and building of proton- and hadron-therapy centres
• Objective 3: Develop innovating imaging techniques in biology and medecine
• Objective 4: Contribute to emergence in France of multidisciplinary platforms based on ion beams for the irradiation and the modification of materials coupled with electron microscopes techniques or imaging systems
From Quarks to cosmos, scientific prospects of the next 10 years for nuclear and high energy physics of the
IN2P3-CNRS and the DAPNIA-DSM-CEA, November 2005
Highlight within objective 2 : the ETOILE project
• Goal: build a national centre for light-ion hadrontherapy in France
• Location: Lyon, Rhone-Alpes region • Budget:
– 90M€ to build the centre– A routine flux of 1000 patients per year
will be reached after 3 years with an operation cost of 15 M Euro.
• Status: approved by the french government in May 2005
• Research areas involving IN2P3 laboratories: – design of an in-beam PET detector– simulation of the interaction of carbon
ions with tissues– radiobiological studies on the
radiosensitivity and tolerance of normal tissues and on the radioresistance of tumours
Online PET at GSI hadrontherapy facility
Nanobeam High resolution analysis
TomographyLocalized irradiation
Local induction of charges
MicrobeamExtracted beam
Radiobiology
CharpaCharacterization and analysisAutomatized lineAtmospheric dusts Physics line
Production of neutrons
Extracted beamAir analysis
Archeological samples
Highlight within objective 4: the AIFIRA platform
AIFIRALocation: Bordeaux
Budget: 2,8M€Energy stability E/E ~ 2.5 10-5Spatial resolution up to 100 nm
Funding
• Funding is almost strictly going to projects– Staff recruited for project duration
• Regions are very supportive of infrastructures– Accelerators (AIFIRA, Etoile)– Grid infrastructures (Auvergrid)
• Newly created National Research Agency (ANR) supports multidisciplinary research projects– Several projects led by IN2P3 laboratories already
supported– ANR will play a growing role as a funding agency for
interdisciplinary activities
• European projects – IN2P3 involved in several European projects– Important resource for grid related activities
Conclusion
• Interdisciplinary activities involve a significant fraction of IN2P3 staff– Growing involvement of researchers and engineers– Growing budget (National Research Agency, European projects)
• Main interfaces– Physics and chemistry for nuclear energy and environment – Life sciences– But also interaction of particles with matter, …
• Perspectives– IN2P3 and CEA are ready to carry out upstream research in the electro-
nuclear field Nuclear energy is now part of nuclear physics program at IN2P3
– Structuring of interface with life sciences is underway Etoile hadron therapy centre in Lyon and AIFIRA multidisciplinary platform
in Bordeaux will be important centers of gravity for the future Emergence of bioinformatics in relation to grids