Development of High spectral resolution Coherent Raman microscopy for deciphering Biomineralisation Pathways in Corals

Development of High spectral resolution Coherent Raman microscopy for deciphering Biomineralisation Pathways in Corals Réf ABG-131726 Sujet de Thèse 06/05/2025 Autre financement public Institut Fresnel Lieu de travail MARSEILLE - Provence-Alpes-Côte dAzur - France Intitulé du sujet Development of High spectral resolution Coherent Raman microscopy for deciphering Biomineralisation Pathways in Corals Champs scientifiques

• Physique

Mots clés optique non linéaire, microscopie, biominéralisation Description du sujet Scientific context Biomineralisation is the capability developed by some living organisms to produce hard (often crystallized) tissues to answer their fundamental needs, such as e.g., protection, light capture, space orientation, or buoyancy. Remarkably, those hierarchically structured crystals (Figure 1a-d) are formed under non-conventional physico-chemical conditions [1] involving a high level of biological control through the mediation of specific organic molecules produced by the animal. This process, which is only partly understood (Figure 1e), would open exciting perspectives in many application domains, such as CO2 capture, 3D printing, chirurgical implant or dental prosthesis, to cite only a few [1]. Among biominerals, calcium carbonate attracts a lot of attention for its spread in various animal species like mollusc shells, sea urchins, or corals. A general biomineralisation mechanism is proposed, involving the production of amorphous calcium carbonate, which further crystallizes in calcite or aragonite. Major questions to be addressed are: what is the structural and chemical nature of the amorphous precursor(s)? What mechanisms govern the amorphous to crystalline transition? What are the role and nature of the organic molecules involved along the mineralization cycle? At Fresnel Institute, we are addressing these questions by developing novel optical applied to the biomineralisation question. They respectively allow us to provide structural chemical information (optical coherent Raman, Figure 1f), at a high resolution and high sensitivity level. Furthermore, we exploit the capability of these instruments to image well-defined regions, representative of the early stage of biomineralisation, i.e., where the temporal imprint of the biomineral formation and growth is clearly visible. This PhD thesis project aims at focusing on the development of coherent Raman microscopy, which will be further applied on coral species samples, ideally in vivo. Coherent Raman microscopy Amorphous calcium carbonate precursors present vibrational signatures, which are significantly different from their crystalline counterparts. They also vary as a function of their exact chemical composition, making them invaluable tools to progress on some of the major biomineralisation questions listed above. In order to image the amorphous to crystalline transition, Raman coherent microscopy is used at Institut Fresnel, based on an in-house developed set-up. It is based on a 4-waves mixing, in which two photons interact with the vibration of the targeted molecules. This imaging modality is fast, efficient and highly-spatially resolved, making it compatible with in vivo studies. However, the need to produce short laser pulses to activate the non-linear process results in a spectral broadening, limiting the spectral resolution. It makes the fine identification and characterization of the amorphous and crystalline phases difficult and limited. PhD Thesis objectives The PhD Thesis project is structured along two main objectives. First, the student will build an optical line allowing the increase of the spectral resolution. The approach is based on « spectral focusing » [3]: two laser pulses will be temporally stretched thanks to optical gratings and temporally recombined at the sample. This high-spectral resolution microscope will be tested and quantified on well-known samples. Second, the method will be applied to shed new light on the biomineralisation mechanisms occurring in corals samples. To reach this aim, post mortem and alive samples will be investigated. Thanks to collaboration with the team of Sylvie Tambutté at the Monaco Scientific Center, the student will have access to a unique set of samples, in which the early growth front is easily accessible with optical approaches including Coherent Raman microscopy. The experiments will allow to evidence the occurrence and transformation of different calcareous amorphous precursors in time and 3D space and to understand the role of the different compounds of the organic tissue in the building of the hard tissue. If successful, the in vivo experiments will be further conducted under different non-optimal growth conditions. Additional characterizations will be performed with electron microscopy and Raman spectroscopy. Finally the chemical results will be confronted to the physical results (x-ray diffraction) for a full description of the physico-chemical growth mechanism in corals. Prise de fonction : 01/10/2025 Nature du financement Autre financement public Précisions sur le financement MITI Présentation établissement et labo daccueil Institut Fresnel

Depuis sa création en 2000, lInstitut Fresnel na cessé de croitre et daffirmer son rayonnement scientifique dans des sujets très variés autour de la physique des ondes. Plus récemment, le laboratoire a élargi son périmètre scientifique vers la biologie, la biophysique et le biomédical, en fort lien avec limagerie. Les thèmes de recherche du laboratoire couvrent aujourdhui quatre grands axes : modélisation et simulation électromagnétiques, nanophotonique et composants optiques, traitement de linformation et ondes aléatoires et, enfin, imagerie avancée et vivant. Les synergies entre ces axes sont importantes et donnent naissance à des projets innovants, souvent aux frontières entre plusieurs disciplines. Ces projets peuvent être aussi bien fondamentaux quappliqués avec un fort potentiel dinnovation, que le laboratoire accompagne au travers de plusieurs plateformes technologiques. Le laboratoire est aujourdhui soutenu par les établissements de tutelle, Aix-Marseille Université, CNRS et Centrale Marseille. Près de deux cents personnes dont cent permanents travaillent à ce jour à lInstitut Fresnel avec un budget consolidé denviron 9 millions deuros.

Site web : https://www.fresnel.fr/wp/ Intitulé du doctorat Doctorat de physique Pays dobtention du doctorat France Etablissement délivrant le doctorat Aix-Marseille Universtié Ecole doctorale Physique et sciences de la matière Profil du candidat

Required skills: Physical background, optical experimental skills are mandatory, willing to work in an interdisciplinary area.

Date limite de candidature 28/06/2025