Development of the Fast Gamma Radiation Detectors for the Time-of-Flight Positron Emission Tomography

Innovative functional imaging technologies are a key component of the "Medicine for the Future" program, one of the main strategic priorities of the CEA. We are seeking a highly motivated PhD student to join our team and contribute to the next generation of Positron Emission Tomography (PET) systems. PET is a powerful nuclear medical imaging technique widely used in oncology and neurobiology. It involves the decay of a radioactive tracer, which emits positrons that annihilate with electrons, producing two 511 keV photons. These photons are detected in coincidence and used to reconstruct the spatial distribution of the tracer within the patient's body. Accurate timing of these coincidence signals, known as Time-of-Flight (TOF) information, is crucial for enhancing image quality by localizing the annihilation point along the line of response. The development of ultra-fast detectors is a central challenge in modern PET technology.
This PhD thesis offers an exciting opportunity to contribute to the development of cutting-edge technologies for TOF-PET within the ClearMind project. In this innovative detector concept, Cherenkov and scintillation photons are produced in a monolithic lead tungstate (PbWO4) crystal. These photons are converted into electrons by a photoelectric layer and multiplied in a microchannel plate. The opposite surface of the crystal is instrumented with a matrix of silicon photomultipliers. The resulting electrical signals are amplified by gigahertz bandwidth amplifiers and digitized by fast SAMPIC acquisition modules. Advanced machine-learning techniques are applied to the complex acquired signals to reconstruct the time and coordinates of the gamma interaction in the crystal. In addition, the thesis will investigate the potential of alternative fast scintillating crystals and study their timing, light yield, and compatibility with the photodetectors, to push the performance of future TOF-PET systems even further.

Biomimetic 3D Materials for More Predictive Intestinal Toxicity Testing

Assessing the toxicity of chemical substances to human health requires reliable experimental models that accurately reflect human physiology. The intestine represents a major interface between the human body and its environment, yet current cellular models fail to fully reproduce its structural organization and physical properties. This PhD project aims to develop advanced intestinal models using three-dimensional biomimetic materials (BAM). Through 3D printing technologies, these materials will reproduce key architectural features of the intestine, including its crypts and villi. An innovative, patented coating, whose mechanical properties can be tuned independently of scaffold geometry, will mimic essential characteristics of the intestinal extracellular matrix. Intestinal organoid-derived cells will be cultured on these scaffolds to develop models that more closely resemble human intestinal physiology. The project will investigate how microenvironmental geometry and stiffness influence intestinal cell organization, differentiation, and function. The resulting models will then be exposed to reference chemicals with known toxicological effects. Cellular responses will be analyzed and compared with those obtained using conventional culture models. The objective is to determine whether better reproducing the intestinal microenvironment can improve the sensitivity, reproducibility, and physiological relevance of toxicity testing. This interdisciplinary project will combine biomaterials engineering, cell biology, mechanobiology, and toxicology. Ultimately, these advanced intestinal models could also contribute to reducing the reliance on animal experimentation.

Optimization of CotA bacterial laccases (Bacillus subtilis) and their Pseudomonas homologs for the biodegradation of PFAS under biofilm growth conditions: an integrated approach combining enzyme engineering and microbial ecophysiology

PFAS comprise a family of more than 6,000 virtually indestructible fluorinated compounds that are now subject to European regulations. Existing treatment processes are costly, energy-intensive, or waste-generating, and biological approaches face a major hurdle: effectively defluorinating PFOA and PFOS quickly and at high concentrations remains impossible to date. Among the candidate enzymes, laccases stand out: functioning in the open air, they break down PFOA in the presence of mediators. However, the literature remains dominated by fungal enzymes, which are effective in acidic environments, whereas the water to be treated is neutral to basic. The project therefore focuses on the CotA laccase from Bacillus subtilis—which is heat-stable, active in basic environments, naturally bound to the spore, and easily optimizable—as well as on Pseudomonas strains capable of forming pollutant-tolerant biofilms. During sessile growth, the biofilm matrix traps PFAS, protects the enzyme, and creates conditions favorable for co-metabolism. Since this approach has never been quantified, it opens up an unexplored scientific niche.

Foundation models for the hierarchical representation and reconstruction of particle collision events

Precision measurements at the Large Hadron Collider (LHC) require a detailed understanding of the particles produced in each collision and the relationships between them. However, reconstructing the underlying physics process remains extremely challenging. Different decay chains can produce similar experimental signatures, several particle assignments may be compatible with the same event, and undetected particles leave incomplete information. A representation connecting these observations to different possible physical interpretations could improve reconstruction and provide a common basis for multiple analyses.
In this project, we propose to develop a hierarchical representation of collision events within the HEP Foundry programme led by the supervisors. This representation will connect reconstructed particles, composite objects, and possible decay chains within a unified machine-learning model. The model will first be trained on a diverse range of simulated processes and then adapted to specific reconstruction tasks. The objective is to retain several physically compatible interpretations of an event and quantify their uncertainties. Higgs boson pair production (HH), particularly in the four-bottom-quark final state, will serve as the main physics case study. This process probes the Higgs self-coupling and the shape of the Higgs potential, making it a major objective of the LHC physics programme. Its challenging reconstruction and large backgrounds will provide a stringent test of the proposed framework.
This PhD project will naturally fit within the ScienceFace initiative, notably by contributing to the development of shared software tools for scientific data curation and the construction of scientific foundation models.

Conformational dynamics of single molecules using atomic force microscopy

Molecular biology emerged in the 1940s with the goal of understanding biological activity at the molecular level. Since the discovery of the DNA double helix, structural biology has focused primarily on determining the precise atomic structure of molecules. However, conventional high-resolution techniques such as cryo-electron microscopy or X-ray crystallography provide only static snapshots. Although nuclear magnetic resonance and computer simulations incorporate the dynamic dimension, no experimental method allows for the direct observation of a single, isolated molecular structure.
The major challenge currently facing the field is therefore to precisely link structural dynamics to biological function. To achieve this, integrated structural biology now combines several experimental approaches, chemical data, and computational tools. In this context, high-speed atomic force microscopy stands out by enabling the direct, time-resolved visualization of macromolecular motion. Nevertheless, the link between the topography obtained through this dynamic microscopy and the underlying atomic structures has yet to be fully exploited.
This research project therefore aims to use the computational pipeline called AFM-Assembly to translate dynamic microscopy data into structural information. The work will involve adapting and optimizing this set of algorithms—which have already been validated on static images—to process large sets of dynamic data. The selected candidate will be responsible for modifying the code for this pipeline, which runs on Linux, requiring a basic understanding of Shell and C programming. Finally, the study will rely on high-performance computers as well as experimental data that is either already available or acquired in collaboration with specialists in Marseille.

Preequilibrium dilepton production in Oxygen - Oxygen collisions with LHCb

At the Large Hadron Collider (LHC) at Geneva, collisions of nuclei are used to create a thermodynamic system described by fluid dynamics under extreme conditions of temperature and energy density. The temperature of the short-lived system is sufficiently
high in order to release the building blocks of matter at a subnucleonic scale, quarks and gluons. This state of matter is commonly called Quark Gluon Plasma (QGP). The space-time evolution of heavy-ion and light-ion collisions at the LHC is described by close-to-ideal hydrodynamics after a short pre-equilibrium lapse of time. However, key features of the
early stages of these collisions are largely unknown. These characteristics are crucial tounderstand the applicability limits of hydrodynamics as well as the thermalization process of a strongly interacting system.
In recent publications, it was pointed out that the dilepton production in the intermediate mass scale between 1.5 and 5 GeV/c² is highly sensitive to the ´thermalisation´ time scale towards the equilibrium QGP. In 2025, the LHC collided for the first time oxygen nuclei. In these collisions, the background conditions are less challenging than in lead-lead collisions
and the experimental sensitivity to the preequilibrium dileptons is enhanced.
The principal goal of this thesis is to perform the first preequilibrium dilepton production measurement at the LHC in Oxygen
-Oxygen collisions using the LHCb apparatus.
This measurement will be based on novel background rejection techniques exploiting the forward geometry of LHCb.
In parallel, the discrimination between the preequilibrium signal and other sources of dileptons, most notably the Drell
-Yan process, will be studied thanks to theoretical calculations and simulations. In a second part, the measurement feasibility will be studied with the current and the future LHCb detector. Depending on the result, a measurement in heavy
-ion collisions could be envisaged.

Molecular Mechanisms of IRE1a Regulation in Stress Signaling

The endoplasmic reticulum supports the biogenesis and maturation of approximately one-third of the human proteome, including most secreted proteins and many membrane proteins. The accumulation of improperly folded proteins can activate the stress sensor IRE1a, initiating adaptive stress response (UPR). Dysregulation of this response is implicated in several diseases, including cancer and metabolic disorders. IRE1a also responds to changes in membrane lipids, but the underlying molecular mechanisms remain poorly understood. This PhD project aims to understand how the membrane environment influences IRE1a structure and dynamics. It will focus on its membrane-spanning region and the flexible linker connecting it to the signaling domains. The work will involve producing protein fragments and studying them in membranes with controlled lipid compositions. Solution and solid-state nuclear magnetic resonance (NMR) spectroscopy will provide atomic-level information about these regions. Complementary biochemical and biophysical approaches will characterize their self-association and interactions with lipids. The aim is to identify how lipids affect the organization of the membrane-spanning region and the mobility of the flexible linker. Studying fragments containing both regions will help test how these effects are transmitted between them. The results will provide a structural basis for understanding IRE1a regulation and its role in stress responses.

STUDY OF THE NUCLEAR COLLECTIVE PROPERTIES OF 232TH WITH THE AGATA SPECTROMETER

The study of so-called ‘deformed’ atomic nuclei with a non-spherical charge distribution is essential for testing nuclear interactions and structural models. These deformed nuclei exhibit a very particular pattern of excited states, known as ‘rotational bands’. These bands can be constructed on states with different deformations or different intrinsic structures (shape coexistence). The subject of the thesis is the experimental study of the macroscopic and microscopic properties of the nucleus 232Th. This nuclide exhibits a wide variety of rotational bands that are thought to be due to vibrations of the nuclear surface known as quadrupole and octupole vibrations. In particular the latter have attracted a great deal of interest recently, as octupolar deformed nuclei can be used to determine nuclear electric dipole moments, a fundamental question in physics in general. In our particular case, the aim is to characterise for the first time the quadruplet of octupole bands expected in a strongly deformed nucleus. Furthermore, this nucleus is the only example with a rotational band built on a double quadrupole vibration. A comprehensive characterisation of the excitation scheme of 232Th will also be of interest with regard to its gamma emissions as a possible future reactor fuel.

We will study these various shapes using the powerful technique of Coulomb excitation, which is the most direct method for determining the shape of nuclei in their excited states. The experiment will be carried out using AGATA, a new-generation gamma spectrometer consisting of a large number of finely segmented germanium crystals, which can identify each point of interaction of a gamma ray inside the detector and then, using the innovative concept of ‘gamma-ray tracking’, reconstruct the energies of all the gamma rays emitted and their emission angles with unprecedented precision. A complementary experiment will be carried out at HIL Warsaw, which will enable better interpretation of the highly complex data provided by AGATA.

An event generator for hard probes of the preequilibrium stages of ion collisions at the LHC

At the Large Hadron Collider (LHC) at Geneva, collisions of nuclei are used to create a thermodynamic system described by fluid dynamics under extreme conditions of temperature and energy density. The temperature of the short-lived system is sufficiently high in order to release the building blocks of matter at a subnucleonic scale, quarks and gluons. This state of matter is commonly called Quark Gluon Plasma (QGP). The space-time evolution of heavy-ion and light-ion collisions at the LHC is described by close-to-ideal hydrodynamics after a short pre-equilibrium lapse of time. However, key features of the early stages of these collisions are largely unknown. These characteristics are crucial to understand the applicability limits of hydrodynamics as well as the thermalization process of a strongly interacting system.
In recent publications, it was pointed out that the dilepton production in the intermediate mass scale between 1.5 and 5 GeV/c² is highly sensitive to the ´thermalization´ time scale towards the equilibrium QGP.
This thesis is dedicated to the development of an event generator based on state-of-the-art theoretical calculations for the production of charm quarks from the preequilibrium in hadronic collisions at the LHC. The generator will allow to generate simulations adapted for the usage in the LHC experiment and to simulate the preequilibrium signal within general purpose event generators. Machine learning methods will be used for the tool optimisation.

Structure and reactions of light and medium mass nuclei with the Gamow Shell Model with Coupled Channels

This project investigates the structure and reactions of exotic atomic nuclei near the limits of stability, where nuclei may be weakly bound or unbound. Recent advances in radioactive-ion-beam technology enable experimental study of these rare systems, which often exhibit unusual features such as extended “halo” structures. Traditional nuclear models, effective for stable nuclei, fail to capture the complexities of these open quantum systems. To address this, the project develops and applies the Gamow Shell Model (GSM) and its extension to coupled-channel (GSM-CC) approaches, which treat nuclei as open systems able to exchange particles and energy with their environment. This enables a unified description of both nuclear structure and reactions, including the effects of the quantum continuum that become significant near the driplines. These models yield accurate predictions that align with experimental data, guide future research, and remain flexible enough to apply to areas such as hypernuclei, atomic anions, and engineered quantum systems. A key innovation is integrating structure and reaction theories, overcoming traditional divisions in the field. The frameworks are designed for computational efficiency and scalability, leveraging supercomputing resources and incorporating uncertainty quantification for reliable predictions. The project also fosters international collaborations with leading experimental facilities and contributes to the training of young scientists. By bridging gaps between theory and experiment, structure and reactions, and across quantum sciences, this research advances understanding of matter under extreme conditions, with broad implications for fundamental science and emerging technologies.

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