PhD applications – Mirror doctoral contracts idil 2026

SUBJECT A – Life and Environmental Sciences, Science and Technology

Impact of the structure of bio-based gels on their ability to encapsulate and release therapeutic molecules in the colon

Desired student profile:

Master's degree or engineering degree in biochemistry, physical chemistry, or materials science. Plus points: an interest in or skills in soft matter physics.

Skills in enzymology and physical chemistry.

Interpersonal skills for teamwork. Proficiency in good laboratory practices.

Writing skills, spoken and written scientific English, independence, curiosity, rigor, and dynamism.

Research laboratory experience may be an asset but is not required to apply.

TOPIC B – Information, Structures, and Systems

Dynamic monitoring of the encapsulation and release of bioactive molecules in and by a bio-based gel bead.

Desired student profile:

Master's degree or engineering degree in physics, physical chemistry, or materials science. Knowledge of soft matter physics is a plus.

Interpersonal skills for teamwork. Proficiency in good laboratory practices.

Writing skills, spoken and written scientific English

Independence, curiosity, rigor, and dynamism.

Research laboratory experience may be an asset but is not required to apply.

Project summary:

The VEBIOCOL project aims to characterize the potential of feruloylated arabinoxylan (AXf) gels, the main non-starch polysaccharides in cereals, as targeted delivery vectors for local oral treatment of the colon. These biopolymers are unique in that they are resistant to digestive fluids and enzymes in the human gastrointestinal tract and are degraded in the colon by microbiota glycosyl hydrolases. The project evaluates the encapsulation and release capabilities of bioactive molecules in AXf gels under static in vitro digestive conditions simulating the different compartments of the gastrointestinal tract, up to the colon.This study is based on an interdisciplinary approach combining biochemistry and physics, enabling an integrated, multi-scale analysis of the "molecular structure/properties/functionalities" continuum of the gels.

Thesis 1 integrates various molecular structures of AXf and aims to understand, using biochemical and rheological approaches, the links between molecular structure, architecture, properties, and functionality of gels.

The physical approach of thesis 2, based on mapping molecular dynamics and fluorescence with spatial and temporal resolutions adapted to the scale of a millimeter-sized gel bead, aims to measure and model the coupled kinetics of polymers and molecules to be encapsulated during the encapsulation and release stages.

The same compounds will be used in both theses (AXf, model environments of the gastrointestinal tract and colon, and bioactive proteins), enabling constant and relevant dialogue between the two teams. The synergy between the two theses will make it possible to identify the parameters necessary for optimized and targeted delivery of bioactive molecules (in this case, immunomodulatory milk proteins) to the colon.

SUBJECT A – Life and Environmental Sciences, Science and Technology

Influence of the urban environment on the circadian rhythms of wild chickadees and mice

Desired student profile:

We are looking for a highly motivated individual who wishes to undertake a study straddling ecology and physiology. The candidate should have skills in animal physiology, behavior, and ecology, as well as in combining field and laboratory work. Previous experience in fieldwork with wild animals is desirable, as is a good command of statistical tools.

SUBJECT B – Chemical and Biological Sciences for Health

Influence of nocturnal exposure to artificial light on
the circadian pacemaker in laboratory mice

Desired student profile:

The candidate will hold a Master's degree in Neuroscience or Physiology, with a solid foundation in molecular biology, and a willingness to work with live animals (a license to conduct animal experiments would be an advantage). Fluency in English (B2) is necessary to thrive in an international environment.

Project summary:

The expansion of human activities into the nighttime raises issues both for public health (such as anxiety, depression, metabolic and cardiovascular disorders linked in particular to night work) and for the environment (disruption to many wild animal species, especially in large, constantly expanding urban centers).

The origin of these disorders lies in the fact that humans and wild animals have an autonomous rhythm, shaped over a long period of evolution, in line with our planet's 24-hour rotation. These circadian clocks are robust, but perhaps not completely rigid... offering the possibility of adapting natural rhythms to the functioning of our modern societies. To understand if and how such adaptations are possible, and if it is feasible
to help people with disorders, we must first study the extent to which our clocks and those of animals are adaptable. We therefore propose two theses that will address the physiological and behavioral impact of disturbances in the day-night cycle and the mechanisms involved at the cerebral level, in order to estimate the extent to which these effects could be reversible, and how.

In the first thesis, we will examine the consequences of alterations in day-night cycles on the behavior and physiology of two widespread wild species (the house mouse and the great tit).

In the second thesis, we will focus specifically on the suprachiasmatic nuclei, the cerebral seat of our internal clock. We will examine their modularity in the brains of laboratory mice when faced with physiological and pathological disturbances.

The two theses will finally converge in a final chapter in which we will use the lessons learned from our work on laboratory mice to describe, in a novel way, the brain mechanisms at work in our two wild species. This project, which concerns biology and health as well as ecology and evolution, will enable the two supervisors involved, Xavier Bonnefont (IGF, CBS2) and Samuel Caro (CEFE, GAIA), to initiate a brand new collaboration and pool their respective expertise on biological rhythms for the first time. These two theses not on
ly raise complementary questions, but also interdependent ones, enabling the two PhD students to work hand in hand to advance this integrative and innovative project.

SUBJECT A – Human Movement Sciences

The value of haptic feedback in learning how to use the hand for diagnostic and therapeutic purposes

Desired student profile:

Training or professional experience as a healthcare provider (medical, paramedical, manual therapy), Master's degree (research, education, humanities), desired experience (clinical examination skills, internship or experience in healthcare), interpersonal skills, strong written and oral communication skills (French and English), adaptability, availability.

TOPIC B – Information, Structures, and Systems

Design of a flexible haptic sensor suitable for monitoring the pressure exerted by the hand during palpation

Desired student profile: Engineering school or Master's degree (applied physics, electronics, mechatronics, applied mathematics), excellent interpersonal skills, strong written and oral communication skills (French and English), adaptability, desired experience (internship working on medical applications and/or AI).

Project summary:

The reform of medical studies in France, with the introduction of Structured Objective Clinical Examinations (ECOS), highlights the need to standardize the teaching of clinical skills. Palpation, an essential component of clinical examination, relies on haptic perception. The learner assesses the biomechanical properties of tissues by interpreting tactile and proprioceptive information perceived through their hands.

Today, learning palpation is mainly based on mentoring, without a standardized framework or appropriate teaching tools to structure the training. Modernizing the teaching of the sense of touch in healthcare is therefore a major educational challenge. Objective monitoring of the pressure exerted by the hand on tissue would allow learners to assess their clinical skills by comparing them with those of experienced clinicians. Furthermore, it will be possible to improve the accuracy of research in clinical practice for diagnostic (i.e., measurement of spasticity) and therapeutic (i.e., effectiveness of a manual medicine technique) purposes.

The HAPTIMED (HAPTique MEDical) project offers an interdisciplinary approach combining movement sciences, flexible electronics, and artificial intelligence to design an innovative educational tool dedicated to learning clinical palpation. The goal is to monitor the manual movements performed during the palpation exam using a haptic glove equipped with flexible electronic sensors capable of recording the pressure exerted by the clinician's hand on the anatomical structures being tested. A machine learning algorithm, trained on haptic data labeled by expert clinicians, will analyze these signals to provide individualized educational feedback (practical recommendations).

The project is based on two mirrored theses and a cross-cutting theme:

The first thesis focuses on standardizing the palpatory examination. Analyzing manual clinical procedures will enable us to define objective criteria for haptic competence and adapt educational feedback.

The second focuses on the design of a haptic glove adapted to monitoring the pressure exerted by the hand on the anatomical structures being tested.

These two aspects are consolidated by a cross-cutting approach to managing uncertainty based on the formalism of belief function theory. The modeling of a digital twin of haptic perception represents a significant advance in medical education. This innovative device will accelerate and optimize the acquisition of the sense of touch in healthcare, objectively evaluate clinical skills involving touch, and ensure longitudinal monitoring of the learning curve. HAPTIMED will enable the establishment of evidence-based educational recommendations, contributing directly to the standardization of OSCE.

SUBJECT A – Chemistry

Design and chemical synthesis of mono- and multi-capped RNA.

Desired student profile:

The ideal candidate will have a strong background in organic synthesis and a proven interest in nucleic acid chemistry and/or life sciences.

SUBJECT B – Biological Sciences for Health

Customized RNA styling and expression solutions for targeted gene therapy

Desired student profile:

RNA biology: in particular RNA extraction, mRNA purification

Mass spectrometry and analytical chemistry: knowledge of sample preparation and LC-MS/MS, mass spectrometry data analysis

Synthetic and molecular biology: knowledge/skills in epitranscriptomics would be an advantage

Cell culture and transfection: mammalian cell culture, electroporation, RNA delivery

Interdisciplinary and collaborative work: team spirit, willingness to collaborate between biology and chemistry

Project summary:

In recent years, RNA has attracted growing interest in therapeutic research, particularly for vaccine development, cell reprogramming, and protein production. Although mRNA vaccines have proven to be effective, safe, and versatile, their stability remains a challenge compared to DNA-based alternatives. To improve this stability and enhance ribosome binding, RNA is chemically modified via epitranscriptomics, a process that regulates post-transcriptional gene expression and key biological functions. These modifications fall into two categories: cap modifications and internal modifications, with the mRNA cap playing a crucial role in translation initiation. For example, the 5′ N7-methylguanosine (m7G) cap interacts with translation initiation factors, thereby influencing mRNA stability and translation. In addition, modifications such as 2′-O-methylation (2′OMe) and N6-methyladenosine (m6A) at the 5′ untranslated region (5′ UTR) further modulate translation and decapping activity. The diversity of cap modifications across cell types offers an opportunity for targeted gene expression, potentially improving RNA-based therapies.

Despite their therapeutic potential, the application of modified caps is limited by challenges related to synthesis methods. Current in vitro approaches for preparing capped mRNAs rely on co-transcriptional incorporation of cap analogs or post-transcriptional enzymatic capping, but these methods remain limited in terms of the types of modifications that can be incorporated. Recent advances in tri- and tetranucleotide cap analogs have enabled direct incorporation of modified caps, but these techniques are still limited.

To overcome these limitations, we have developed a strategy that allows both natural and unnatural chemical modifications to be incorporated at the 5′ end of mRNA. This modular approach, combining chemistry and enzymology, enables systematic screening of cap modifications to assess their impact on properties such as mRNA stability and translation capacity. This project aims to bring together the expertise of the IBMM and IRCM teams to develop solutions tailored to gene expression in specific cell subtypes with optimal efficiency, thus providing innovative tools for RNA-based therapeutic strategies. Objectives include the synthesis of natural and multi-capped oligonucleotides, the establishment of a detailed profile of cap modifications in immune cells, and the development of a screening method to identify the most effective capped oligonucleotides for specific cell subtypes.

SUBJECT A – Chemical and Biological Sciences for Health

Engineering and assembly of biohybrids for signal transduction integrating cellular biosensors with functional biopolymers

Desired student profile:

This doctoral contract focuses on the development of bacterial biosensors and the assembly of biohybrid systems capable of responding to radiofrequency (RF)-modulated stimuli. The ideal candidate should hold a Master's degree in bioengineering, molecular biology, synthetic biology, or biophysics, with a strong interest in interdisciplinary research.

The doctoral project involves engineering bacterial strains with customized biosensors, optimizing polymer-bacteria interfaces, and integrating biohybrids into electrogenic platforms. The student will acquire expertise in synthetic biology, microbiology, and advanced microscopy, and will work closely with the IES electronics partner on device integration and validation.

TOPIC B – Information, Structures, and Systems

Development and validation of conductive biopolymers for RFID interaction and integration with biohybrids

Desired student profile:

This position focuses on the design and characterization of conductive polymers for integration with biological systems. The ideal candidate should hold a Master's degree (M.Sc., Engineering School) with a specialization in electronics (from direct current to radio frequencies), materials science, or applied physics, with a strong interest in biosensors and biomedical applications.

The work will consist of developing conductive polymers (COPs) that are responsive to environmental stimuli and radiofrequency (RF) induction, designing new protocols for their electrical characterization (from kHz to GHz), and collaborating on their integration into functional bacterial biohybrids. The student will have access to state-of-the-art platforms for microfluidics and wireless system prototyping and will interact regularly with the CBS biology team.

Project summary:

The mirror doctoral project, BIOREACH, explores the design of bioelectronic systems capable of remote detection and response, integrating genetically modified bacteria with conductive organic polymers (COPs). These electrogenic biohybrids aim to revolutionize biomedical technologies by enabling bidirectional communication for therapeutic and diagnostic applications. This innovative initiative addresses the limitations of current cell control methods, such as optogenetics and sonogenetics, by exploiting RF technology, which offers deeper tissue penetration and non-invasive external control. It relies on biohybrids equipped with electrically conductive biopolymers coupled with biosensors integrated into bacterial chassis reprogrammed for signal integration and transmission.

BIOREACH exemplifies interdisciplinary synergy, combining expertise in biophysics, synthetic biology, soft matter, and electronics. The project brings together two leading research groups: the Synthetic Biology team at the Center for Structural Biology (CBS), which specializes in biohybrid engineering, and the RFID and Flexible Electronics team atthe Institute of Electronics and Systems (IES), renowned for its expertise in microtechnology and wireless communication. Their collaboration covers the design of biocompatible conductive polymers, bacterial biosensors, and functional biohybrids, while developing innovative methodologies for electrical characterization and system integration.

Two complementary doctoral projects form the basis of BIOREACH. The first focuses on engineering bacteria equipped with biosensors capable of responding to signals induced by POPs, enabling precise control of cellular functions. The second develops new POPs with adjustable properties, capable of interacting with electromagnetic waves and triggering cellular responses. Both projects emphasize strong interaction between biology and electronics, promoting advanced interdisciplinary training through international collaborations, including joint internships at the University of Tokyo.

This project will produce major advances, including programmable biohybrid systems for real-time monitoring and therapy, high-impact publications, and patentable innovations. Beyond biomedical applications, BIOREACH will train its doctoral students in cutting-edge skills at the interface between biology and electronics, preparing them for leadership roles in academia and industry. This partnership not only enriches student training, but also establishes a strong and lasting collaboration between CBS andIES, paving the way for innovative advances in remotely accessible biohybrid technologies.

SUBJECT A – Life and Environmental Sciences, Science and Technology

Isotopic composition of collagen extracted from archaeological artifacts from the western Mediterranean basin

Desired student profile:

Prerequisites:

The candidate must hold a Master's degree (or engineering degree) in biogeochemistry, bioarchaeology, paleoclimatology, paleoenvironments, continental surface geosciences, environmental sciences, or related disciplines. Candidates with dual or interdisciplinary skills in these fields are particularly welcome.

A solid understanding of stable isotope geochemistry is required, particularly as applied toorganic matrices.

Required skills:

• Theoretical mastery of isotopic fractionation, particularly of carbon and nitrogen isotopes in living organisms (fauna/flora).
• Proficiency in data processing and statistical tools (R, SIAR, SIBER).
• Autonomy, creativity, and the ability to commit to an ambitious research project.
• Ability to work in a team, in an interdisciplinary environment (archeology, bioarcheology, geochemistry).
• Respect and kindness toward the work environment and colleagues.
• Collaborative spirit and openness to diverse scientific approaches.
• Interest in fieldwork and openness to international collaborations.
• Motivation to publish in peer-reviewed scientific journals.

Desired skills:

• Experience in extracting collagen from biological waste.
• A good knowledge of stable isotopes of sulfur, oxygen, and hydrogen.
• Theoretical and/or practical knowledge of isotope ratio mass spectrometry techniques – Knowledge of GC-IRMS – AMS (radiocarbon ¹⁴C).
• Skills in preparing samples for isotopic analysis (collagen, lipids, etc.).
• Experience or theoretical knowledge in archaeological protein analysis (ZooMS, CSIA-AA).
• Good level of scientific English (written and spoken)

We are looking for someonewho is curious and open-minded, with a stronghumanistic outlook, capable of bringing a new perspective to the interdisciplinary nature of the project. Analtruistic person who respects the values of collaboration and sharing, and who will be able to integrate the project into a network of international collaborations.

SUBJECT B – Chemical Sciences

Chiral analysis by mass spectrometry for archaeology

Desired student profile:

Prerequisites:

Graduate/future graduate with a Master's degree (or engineering degree) in the field of analytical sciences.

The candidate must have solid knowledge of mass spectrometry and separation techniques.

Required profile:

Knowledge/experience in high-resolution mass spectrometry, tandem mass spectrometry, ion mobility, and separation techniques such as liquid chromatography and capillary electrophoresis are required to develop analytical methods for characterizing peptides/proteins.

Knowledge of peptide and protein chemistry will be an asset, particularly for sample preparation. Experience in protein analysis using proteomic strategies will be appreciated.

The ability to work independently, creativity, and motivation to tackle complex scientific challenges within a multidisciplinary project are expected.

Project summary:

Collagen chirality alteration, a result of amino acid epimerization from the L to the D form over time, has significant perspectives in bioarchaeology. This project explores the potential of chiral analyses by mass spectrometry to analyze collagen in archaeological remains, aiming to refine dating techniques and improve our understanding of preservation processes.

The analytical strategy represents a major challenge. Indeed, the determination of the configuration of stereogenic centers constitutes the highest level of characterization for an organic molecule. In order to tackle such demanding structural identification levels of the biomolecules of interest (collagen proteins), we aim to implement fragmentation experiments in high-resolution tandem mass spectrometry (HR-MS/MS) coupled with liquid chromatography (LC) and ion mobility (IM-MS) on non-covalent diastereoisomeric species generated in the gas phase between a metal and the chiral peptide issued from tryptic digestion of extracted collagen samples. Such LC-IM-HR-MS/MS method development will be carried out on modern samples to study abundant and non-precious collagen material, which will
.

Our approach integrates collagen extraction, purification, and isotopic analyses (¹³C, ¹⁵N, 34S) to assess environmental and climate changes and agriculture and farming practices in Holocene Human Societies of the Western Mediterranean Basin. The method is validated using reference samples of known age, establishing a robust framework for applying amino acid epimerization as a chronological tool. By combining chiral analysis with 14C dating and multi-isotopic data, we propose a multi-parameter model that enhances the accuracy of organic material dating and paleo-ecological and paleo-climate indicators; the method
also creates a counterbalance to 14C dating and all the risks that this method brings.

Beyond archaeology, this research has broader applications in analytical chemistry and life sciences, where amino acid epimerization serves as a biomarker for tissue aging. This interdisciplinary approach thus provides an innovative pathway for studying protein longevity, with potential technological transfer to biomedicine and conservation sciences.