7.1.1 Odin

• Name:
  Platform for advanced monitoring, control and optimisation of bioprocesses
• Keywords:
  Bioinformatics, Biotechnology, Monitoring, Automatic control
• Scientific Description:

  ODIN is a distributed application, whose graphical interface can be launched remotely through the Internet. The application, developed in Erlang, is architected around an MQTT broker. It is robust and tolerant to hardware failures in order to avoid that a wrong manipulation can have harmful consequences on the biotechnological process.

  Thus, the implementation of a new algorithm is done by a plugin written in Python language. Modifying one of these algorithms does not require recompiling the code.

• Functional Description:
  This application proposes a framework for on-line supervision of bioreactors. It gathers the data sampled from different on-line and off-line sensors. ODIN is a distributed platform, enabling remote monitoring as well as remote data acquisition. In a more original way, it enables researchers and industrials to easily develop and deploy advanced control algorithms, optimisation strategies, together with estimates of state variables or process state. It also contains a process simulator which can be harnessed for experimentation and training purposes. It is modular in order to adapt to any plant and to run most of the algorithms, and it can handle the high level of uncertainties that characterises the biological processes. The architecture is based on Erlang, and communication between modules through a MQTT Broker with Python for running the algorithms. ODIN is developed in collaboration with the INRIA Ibis research team.
• News of the Year:
  A diagnosis module was implemented to detect issues in the hardware or in the connection between the various modules. The calibration module was updated also allowing actuator calibration. Finally, the python module for managing the priorities accesses to the different elements of the platform was updated.
• URL:
  https://­team.­inria.­fr/­biocore/­software/­odin/
• Contact:
  Olivier Bernard
• Participants:
  Olivier Bernard, Nicolas Niclausse, Eugenio Cinquemani, Tamas Muszbek, Thibaud Kloczko, Nicolas Chleq, Jean-Luc Szpyrka, Pierre Fernique, Julia Elizabeth Luna, Come Le Breton, Jonathan Levy, Amine Lahouel, Tristan Cabel, François Caddet, Erwan Demairy, Riham Nehmeh, Marc Vesin, Carlos Zubiaga Pena

Participation in experimental campaigns.

R. Ranini took part to the Tara Europa campaign (30 days in Italian coastal waters aboard Tara), where he was in charge of the plankton net processing lab. The data recorded along the campaign will be used for the setup of his modeling on the particle size distribution in marine water determined by the local biotic and abiotic environment.

Modeling thermal adaptation in microalgae.

We studied a broad range of species and their response to temperature. Algorithms were developed to automatically calibrate the parameters of the CTMI (Cardinal Temperature Model with Inflexion) and the Hinshelwood models  42. It turns out that the optimal temperature, the minimal and the maximal temperature for growth are strongly correlated. Relationships between these cardinal temperatures and key parameters from the environment (sea surface temperature, solar flux, ...) were explored. Some of the relationships stay valid also for a broad range of microorganisms such as yeast and bacteria.

Use of AI for improving the oceanic carbon flux estimates.

The objective of this work is to provide a model describing the particle size distribution (PSD) as a function of the environmental conditions using Artificial Intelligence approaches, so as to better represent the amount of organic carbon which will be exported in the deep layers of the ocean. We introduced a more accurate model than Junge's law, aiming to reduce biases in vertical carbon flux assessments. It highlights limitations in state of the art modeling used to predict PSD distribution, particularly for slopes and convexity. The approach uses XGBoost (eXtreme Gradient Boosting) with 0D environmental snapshots for efficiency but sacrifices detailed temporal and spatial information. This work is carried out within the OceanIA Inria challenge, and is the core of the PhD thesis of Romain Ranini.

Modeling the coupling between photosynthesis and hydrodynamics.

We consider a coupled physico-biological model describing growth of microalgae in a raceway pond cultivation process, accounting for hydrodynamics. Our approach combines a biological model (based on the Han model) and shallow water dynamics equations that model the fluid dynamics into the raceway pond 28. We developed an optimization procedure dealing with the topography to maximize the biomass production over one lap or multiple laps with a paddle wheel. The results show that a flat topography is optimal in a periodic regime. We then studied the influence of mixing, assuming that a mixing device can redistribute the algae so that they can have access to light 30. A strategy to optimally mix the algae was derived especially by alternating high and low light 28.

Modeling temperature dynamics in bioreactors.

Temperature plays a key role in the microalgae dynamics. We developed a heat transfer model to simulate the temperature evolution in the process medium, depending on the meteorology, and its impact on algal productivity. We proposed a general framework to simulate these multiphysics systems, keeping a balanced degree of complexity between the biological and the physical models 34.

Based on this heat-transfer model, we proposed an auto-adaptive heat-transfer model together with an autotuning procedure 12 that can predict the temperature evolution inside different type of raceway ponds or more complex cultivation systems (photobioreactors with complex geometries) using weather forecasts. We also considered the influence of a greenhouse on the medium temperature and the model training automatically adapted to accurately predict temperature 11. The model was tested under five different climatic conditions (Narbonne, Milan, Bonaire, Wageningen, Nice), and was even able to reproduce the dynamics of biofilm growth under a greenhouse, in collaboration with the Inalve start-up 23.

Modeling chemical speciation and pH in bioreactors

A robust chemical model that accurately describes ionic speciation is essential for understanding and optimizing the growth of microorganisms such as microalgae and bacteria. We developed a chemical model to simulate ionic equilibria in highly saline environments, considering activities rather than concentrations of ions, together with ionic strength, a key factor in ion pairing phenomena. The originality of the approach we developed consists in transforming the initial problem (algebraic equation system) in the solution of a differential equation system, reducing the unknows from 40 to 5. Using experimental data from Total energy pilot-scale applications and PHREEQC software, the most significant ion pairing products were identified and incorporated into the new chemical model in Matlab. On top of this, dedicated experiments and pH measurements were carried out at the Laboratory of Oceanography of Villefranche sur Mer. The experimental data and PHREEQC simulation results were used for validating the outcomes of the new chemical model. The model demonstrated good accuracy in predicting pH, ionic strength, ion pairing products, and ionic composition of saline solutions. This study was the main subject of Annalisa Reali's master thesis at Politecnico di Milano under the supervision of F. Casagli and O. Bernard, within the framework of the ANR BARRIER project.

A comprehensive hybrid modeling approach for predicting biological dynamics: application to algae-bacteria systems

Algae-bacteria systems are promising for wastewater remediation, but challenges exist in improving efficiency and reducing costs at an industrial scale. Mathematical models, particularly mechanistic models (MM), are useful for simulating biological processes, but they are complex and not suited for efficient process control. Artificial Neural Networks (ANN) have potential but may not preserve essential properties like mass conservation. Hybrid models combine MM and ANN, maintaining physical laws while adapting to data. This study presents a hybrid approach applied to the ALBA model, simulating algae-bacteria dynamics 20. The model was calibrated and validated on pilot-scale applications. The hybrid approach predicts key variables accurately, with performance dependent on the data used for training. A trade-off exists between generalization and accuracy, requiring consideration for each specific case. The hybrid model was developed in a Python package that is based on JAX.

Extending Algae-Bacteria Model for Predicting Microbial Communities in Wastewater Treatment

Bacteria and microalgae coexist and interact in wastewater treatment, exchanging oxygen, CO2, vitamins, and protection through allelopathy or toxin degradation . These interactions promote microbial symbiosis, diversity, and variability. Modeling these dynamics is challenging but aided by data from an experimental campaign carried out at the University of São Paulo State University (Brasil) who, on top of routine measurements, did omics analyses to estimate diversity. Including microbial structure improves predictability but increases model complexity, requiring a balance between detail and operability. This work 26 extends the ALBA model to include a refined desciption of the present microorganisms, improving microbial community predictability during wastewater treatment.

In addition, microalgae-bacteria systems for wastewater remediation, commonly applied in high-rate algal-bacteria ponds (HRABP), are limited by effluent clarification and load capacity, due to sub-optimal operational conditions. We studied the introduction of membrane filtration to address these issues by decoupling solid retention time (SRT) from hydraulic retention time (HRT). The M-ALBA model, an extension of the ALBA model with a membrane separation compartment, was developed to predict membrane-assisted HRABP performance (model developed in Matlab). Simulations showed that decoupling SRT and HRT improves nitrogen removal, reduces ammonia volatilization, and achieves better performances compared to the case where membrane were not applied. This work enhances understanding of microalgae-bacteria interactions in membrane systems. This work was done in collaboration with the Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso (Chile).

8.8.1 Control and Optimization of microalgae production

Participants: Olivier Bernard, Francesca Casagli, Ignacio Fierro, Ali Gharib, Walid Djema.

Environmental impact assessment.

We have studied the environmental impact of protein production from microalgae in an algal biofilm process, using a Life Cycle Assesment (LCA) approach and compared it to other sources (fisheries, soy,...). We have analyzed the updated version of the production system and proposed several optimizations to reduce the environmental impact. This study confirms the interest of microalgae for reducing the environmental impact 46 compared with other sources of proteins like fishmeal or soy. More generally, this work proposes a new approach to assess and reduce the environmental footprint of processes which use non mature technologies (PhD thesis of D. Penaranda in collaboration with M. Morales from the Norwegian University of Science and Technology).

A study was carried out to assess the environmental benefit of using microalgae-bacteria to process wastewater, and in particular digestates from anaerobic digestion 458. Various scenarios were simulated using the ALBA model 32 assuming an industrial plant located in Rennes (Brittany, France) dealing with an actual climatology and for various conditions of Hydraulic and Solid retention times, alkalinity addition and biomass valorization for generating energy. In total, 72 different scenarios were explored, for which LCA was carried out. The results were compared to scenarios where the digestates are classically treated in a wastewater treatment plant. It results that the microalgae approach makes sense from an environmental point of view 46.

This work is the result of a collaboration with Arnaud Helias of INRAE-LBE (ITAP, Technologies et méthodes pour les agricultures de demain, Montpellier).

8.12.1 Optimal therapeutic control in cancer

Participants: Walid Djema, Pauline Mazel.

Generalized versions of Lotka-Volterra models were analyzed to represent interactions between cancerous and healthy cells, facilitating the design of strategies for chemotherapy and targeted therapies. By employing Pontryagin's Maximum Principle (PMP), the proportion of healthy cells was maximized under specific constraints 25. This project, which involves ongoing advancements in modeling, analysis, and control, is being conducted in collaboration with RWTH Aachen University Uniklinik in Germany. This is the main subject of the PhD thesis of Pauline Mazel. In a different context, another type of competition between cell populations was investigated, focusing on the issue of resistance developed by certain cells to treatments. The study aimed to explore strategies to overcome this resistance through optimized drug administration protocols that activate distinct cell death pathways. In this regard, in collaboration with J. Roux and M. Péré from the MACBES team at Inria, a novel model was developed and calibrated: this model provides promising applications and future perspectives in the domain of therapeutic control.

8.12.2 Optimal resource allocation for metabolite production.

Participants: Walid Djema, Javier Innerarity Imizcoz.

Strategies for resource allocation in bacteria under periodic and time-varying environmental conditions were investigated using a dynamic ODE model and PMP. The results revealed that optimal control can yield complex structures with higher-order singular arcs (Chattering phenomena). These findings demonstrate that maximum growth can be achieved under periodic conditions, emphasizing the crucial role of a key molecule (named ppGpp) in regulating protein precursors in E. coli (13, 24). This is the main subject of the PhD thesis of Javier Innerarity Imizcoz. J.-L. Gouzé (Inria MACBES) and F. Mairet (IFREMER) are also involved in this work.

8.12.3 Optimal control of algae-bacteria consortia.

Participants: Walid Djema, Olivier Bernard.

An algae-bacteria consortium was optimized to maximize biomass production in a bioreactor in collaboration with MICROCOSME and within the framework of the ANR project (Ctrl_AB) 18. In a new project supported by Idex-UniCA (OPTI-ABh), in collaboration with Ifremer Nantes (F. Mairet), we explore pollutant removal approaches that favor algae growth while activating bacterial mechanisms to neutralize more resistant pollutants. Numerical tools were utilized to determine microbial strategies for bioprocess control. This is the main subject of the PhD thesis of Rand Aswad, Grenoble, in collaboration with E. Cinquemani (Microcosme). J.-L. Gouzé (Inria MACBES) is also involved in this work.

8.12.4 Agroecosystem optimization.

Participants: Suzanne Touzeau, Frédéric Grognard, Frank Kemayou Mangwa, Walid Djema.

Bananas are major staple foods in many tropical countries. These plants are affected by burrowing nematodes (Radopholus similis) that create root lesions and induce great damages. As part of a collaboration with the MACBES Team (F. Grognard, S. Touzeau and F. Kemayou Mangwa) with their EPITAG associate team with Cameroon, we developed a model of plant-pest interactions with the original feature that infestation intensity may vary within the root. We did a bifurcation analysis and solved an optimal control against the pest, consisting in maximizing profit thanks to the application of biostimulants. The optimal control obtained is pseudo-periodic, suggesting an overyielding phenomenon. This work, carried out in collaboration with F. Mairet (IFREMER), is part of Frank Kemayou's ongoing PhD thesis.

10.2.1 Visits of international scientists

• In the framework of the ITN DigitAlgaesation, we had the visit of Lars Stegemüller from DTU (April 20th to 20th, 2024), and Giovanni Consoli (Univ. Padova) (September 2nd to 6th, 2024)
• Mustafa Hani Khammash visited us in March 2024.
• Rolf Findeisen gave a seminar in November 29th, 2024.

10.2.2 Visits to international teams

• Walid Djema was a recipient of the 2024 Franco-German Program by DAAD for research visits in Germany. The project, titled Integrative Mathematical Modeling for Understanding and Controlling Hematopoietic Stem Cell Dynamics and Acute Leukemia, was carried out from November 30th, 2024, to January 1st, 2025, at the Institute for Computational Biomedicine - Disease Modeling, RWTH Aachen University. A collaboration was established with Dr. Thomas Stiehl's team, focusing on the modeling, analysis, and control of acute myeloid leukemia.

10.3.1 H2020 projects

10.4.1 National programmes

• ANR PhotoBioFilm Explorer: The first objective of the PhotoBioFilm project (2021-2024) is to explore the activity of the molecules produced within a microalgae biofilm, and explaining its resistance to contamination. The second objective is to identify, characterize and produce novel biocompounds with benefits for human or animal health. The target is antibiotics, but other activities will be tested, especially antiviral activities. Biocore will be in charge of the biofilm modeling and the optimization of the production of the molecules of interests. Project coordinated by O. Bernard.
• ANR Ctrl-AB: The objectives of the Ctrl-AB project (2021-2024) are (i) to develop new control methods for the optimization of the productivity of a microbial community, and (ii) to demonstrate the effectiveness of these methods on a synthetic algal-bacterial consortium. Interestingly, co-culturing of E. coli with Chlorella leads to higher biomass and lipid productivity. Improved growth of Chlorella occurs despite competition of E. coli for the same substrates. On top of its ability to produce molecules like vitamins, which are necessary for algal growth, bacteria also produce carbon dioxide (CO${}_2$), which is the substrate of the photosynthesis of the algae. The algae can produce oxygen (O${}_2$) fueling bacterial growth, thus giving rise to a mutualistic pattern of interactions giving rise to several challenges for modeling and controlling this artificial ecosystem. Project coordinated by J.-L. Gouzé.
• ANR Barrier: This proof of concept project (2023-2027) with multidisciplinary expertise is willing to demonstrate, from the laboratory to a pilot process, that selected bacteria can protect microalgae when growing in contaminated wastewaters, providing higher algal resilience, productivity and bioremediation efficiency in wastewater treatments. It is coordinated by O. Pringault (IRD, Mediterranean Institute of Oceanography).
• SIGNALIFE: Biocore was part of this Labex (scientific cluster of excellence, 2nd period 2020-2024) whose objective is to build a network for innovation on Signal Transduction Pathways in Life Sciences, and is hosted by the University Côte d'Azur.

10.4.2 Inria funding

• Inria Startup Studio, DareWin: (2022-2024). The DareWin project is consolidating the bases of a startup which will develop Darwinian selection approaches in highly controlled bioreactors to naturally select and improve microalgal strains of industrial interest.

11.1.1 Scientific events: organisation

• We organize a monthly scientific seminar together with the MACBES project-team in which external guests and collaborators are regularly invited.
• We also organize a yearly four day-retreat together with the MACBES project-team where we share our work of the year; this year, it took place mid-October in Peyresq.
• Francesca Casagli is co-chair in the Task Group of IWA (International Water Association) on modeling phototrophic systems.
• F.Casagli and O.Bernard took part to the organization of a workshop on modeling phototrophic systems during the The 1st International Conference on Novel Photorefineries for Resource Recovery in Valladolid, Spain 21 .
• F.Casagli and O. Bernard are involved in the coordination and writing of a position paper for the IWA Task Group.

11.1.2 Member of the organizing committees

O. Bernard was in the organizing committee of the AlgoReseau in Nice "Focus on micro- and macro-algae work in the Mediterranean " which took place in July 11th and 12th, 2024, in Nice and Villefranche-sur-mer.

11.1.3 Chair of conference program committees

O. Bernard was the head of the academic scientific committee of the AlgaEurope conference which took place in December 10th to 13th, 2024 in Athens.

11.1.4 Member of the conference program committees

O. Bernard was in the scientific committee of 1st International Conference on Novel Photorefineries for Resource Recovery (Valladolid, September 2024).

11.1.5 Reviewer

• All BIOCORE members have been reviewers for the major 2024 conferences in our field: Conference on Decision and Control, European Control Conference, International Federation of Automatic Control ...
• The team is reviewing articles for the main journals of Automatic Control (Automatica, IEEE Transactions on Automatic Control, Journal of Process Control), for mathematics applied to biology (Journal of Mathematical Biology, Mathematical Biosciences), and for biology or biotechnology journals (Algal Research, Plos computational Biology, Bioresource Technology, ... ).

11.1.6 Invited talks

• W. Djema was invited as a speaker at the Optimal Control Day organized by the FRUMAM in Marseille, in June 2024.
• F. Casagli was invited to give a talk within the INRAE workshop "Journée scientifique SPE NUM: les Approches hybrides IA - Systèmes dynamiques", on December 3rd, 2024 in Montpellier. Title of the talk "Hybrid modeling of biological processes: application to microalgae/bacteria systems".

11.1.7 Master theses and internships

• W. Djema supervised the master intership of Dominique Y. Lagos, through the Inria-Chile internship program (3 months visit). Dominique worked on species selection in competition for two substitutable substrates.
• W. Djema supervised Baptiste Boerkmann (Univ. Lyon) during a summer internship (M1 level) lasting 2 months, starting on July 1, 2024. Baptiste explored the application of the hybrid Pontryagin's Maximum Principle (PMP) to a biotechnological model.
• W. Djema supervised Théo Séminara (MIAGE Sophia Antipolis), an undergraduate student (L3 level), during a 2-month internship starting on July 1, 2024. Théo focused on creating scientific content and managing digital communication.
• O. Bernard and T. Sari supervised the master thesis of Pablo Rademacher and his 3 months stay "Global warming effect on competition: Modeling the effects of global warming on competition of species on a chemostat", University of Chile.
• O. Bernard co-supervised the master thesis of Miguel Antonio González Serrano (Unam, Mexico)
• F. Casagli and O. Bernard supervised the master thesis of Analisa Reali (Politecnico de Milano, Italy) on modeling chemical speciation in saline reactors.
• In the framework of thr ITN Digitalgaesation, O. Bernard supervised the secondments stays of Lars Sebastian Stegemüller (DTU, Denmark) , Giovanni Consoli (Imperial College, London) and, together with F. Casagli, R. Nordio (Univ. of Almeria, Spain).

11.1.8 Scientific expertise

• W. Djema has been appointed as a member of the Scientific Council of Academy 4 "Complexity and Diversity of Life," Université Côte d'Azur (since 2023), representing Inria within the council.
• O. Bernard is in the Scientific Advisory Board of the "Ferment du futur" Grand challenge of France 2030. O. Bernard is a member of the scientific committe of IRD (Institute of Research for the Development) in the CSS5 section (models and data). He participated to the recruitement juries for researchers and research directors at IRD.
• O. Bernard was in the Scientific and Pedagogic committee of the UniCA- EUR LIFE and in the steering committee of Federal Recherche Institut (IFR) Marine Ressources (MARRES).
• O. Bernard is member of the scientific committees of Inalve and Darewin Evolution.

11.1.9 Research administration

• W. Djema has been appointed as a member of the Scientific Council of Academy 4 "Complexity and Diversity of Life," Université Côte d'Azur (since 2023), representing Inria within the council.
• W. Djema has been elected as a member of the Inria center's committee, Centre Inria d'Université Côte d'Azur (since January 2024).

11.2.1 Teaching

• Licence: W. Djema (40h ETD), P. Mazel (20h ETD); “Mathématiques pour Biologistes: Analyse et Modélisation", L1 Université Côte d'Azur UniCA, France.
• Licence: W. Djema (32h ETD); “Math0: Enjeux", L1 Université Côte d'Azur UniCA, France.
• Licence: W. Djema (12h ETD), P. Mazel (32h ETD); “Statistiques pour les Biologistes", L1 Université Côte d'Azur UniCA, France.
• Licence: O. Bernard (35h ETD), “Use and optimization of photobioreactors”, Université de Pau et des pays de l'Adour, France.
• Licence: P. Mazel (16h TD), “Fondements mathématiques 1 - partie algèbre linéaire”, L1, Portail Sciences et Technologies, Université Côte d'Azur, France
• Licence: W. Djema (12h ETD), J. Innerarity (30h EDT), “Mathematical Analysis”: Ecole Centrale Méditerranée Nice.
• Master: O. Bernard (4.5h ETD), “Bioenergy from microalgae”, M2, Master International Energy Management : alternatives pour l'énergie du futur, Ecole Nationale Supérieure des Mines de Paris, France.
• Master: O. Bernard (36h ETD), “Modeling biotechnological processes”, M2, Ecole CentraleSupelec, Saclay, France.
• Master: O. Bernard (18h ETD), “Automatic Control applied to biotechnological processes”, M2, Ecole CentraleSupelec, Saclay, France.
• Master: O. Bernard (6h ETD), “Cultivation and use of Microalgae”, Master Mares, Université Côte d'Azur, France.
• Master: O. Bernard (24h ETD) and W. Djema (24h ETD), “Enseignement d’Intégration – “Automatic Control applied to biotechnological processes”, CentraleSupélec, Paris-Saclay, France.
• Master: W. Djema (12h ETD) M. Chaves (8h ETD), “Biology of Systems” – Lectures, Master BIM, Valrose, Nice
• Master: W. Djema (15h ETD), F. Grognard (15h), “Elements of Mathematics” – Lectures on mathematics and programming Python, and modeling in ecology, Master RISK, IMREDD, UniCA, Nice

11.2.2 Supervision

• PhD: I. Fierro Ulloa. “Development and analysis of a digital twin for monitoring, control and optimization applications in microalgae: the Microalgae Model”, since September 2021, UniCA. Defended on October 29th, 2024 Supervisor: O. Bernard.
• PhD: A. Gharib. “Robust control of microalgae processes accounting for future meteorology”, since September 2021. (UniCA, ITN Digitalgaesation). Defended on November 29th, 2024. Supervisors: O. Bernard (director) and W. Djema (co-director).
• PhD: D. Penaranda Sandoval. “Environmental impact assesment of technologically immature processes”, Université Côte d'Azur (UniCA), since September 2021. Defended on March 15th, 2024. Supervisor: O. Bernard. Supervisor: O. Bernard.
• PhD in progress: R. Ranini. "Deep learning approaches for enhancing models in oceanography", UniCA, since 2022. Supervisors: L. Guidi and O. Bernard.
• PhD in progress: Pauline Mazel. “Modeling and control of cancer cell population dynamics", since October 2023. Supervisors: F. Grognard (director, Macbes) and W. Djema (co-director, Biocore).
• PhD in progress: Javier Innerarity Imizcoz. “Optimal bacterial resource allocation for metabolite production", since November 2023. Supervisors: Jean-Luc Gouzé (director, Macbes), Francis Mairet (co-director, Ifremer Nantes) and W. Djema (co-supervisor, Biocore).
• PhD in progress: Manon Pugnet. "Optimal Control of the competition within microbial communities", Université Côte d'Azur, since 2024. Supervisor: O. Bernard and W. Djema.

11.2.3 Juries

• O. Bernard was member of the Individual monitoring Committee of Alexandre PETTI (Mines ParisTech).
• F. Casagli participated to the Individual monitoring Committee of the Ph.D. Irene MARTíNEZ MENÉNDEZ, from the Doctoral School EDSEVAB n°458. Title of the thesis: "Digital twins for the optimization of bioprocesses", Thesis director: César Arturo ACEVES-LARA, Thesis co-director: TONDA Alberto.
• O. Bernard was reviewer of the PhD thesis of Alberto Saccardo, University of Padova.
• O. Bernard was president of the PhD jury of MA Leca "Development of innovative strategies for the valorization of methanization digestates via Spirulina cultivation " at University of Pau, June 11th, 2024.
• O. Bernard was reviewer of the PhD thesis of Andriamahefasoa RAJAONISON "Environmental Life Cycle Assessment of time dependent microalgal-based energy production systems", PSL University (prepared at Mines ParisTech), directed by T. Ranchin and P. Lopez-Pérez, September 3rd, 2024.
• O. Bernard participated to the PhD jury of D. Penaranda as PhD Director ("Extrapolation of the environmental impact of low TRL environmental processes: Application to microalgae-based processes") on March 15th, 2024 (University of Nice Côte d'Azur).
• O. Bernard participated to the PhD jury of I. Fierro Ulloa. “Development and analysis of a digital twin for monitoring, control and optimization applications in microalgae: the Microalgae Model”, Defended on October 29th, 2024. Supervisor: O. Bernard.
• O. Bernard and W. Djema participated to the PhD jury of A. Gharib. “Robust control of microalgae processes accounting for future meteorology”, UniCA. Defended on November 29th, 2024. Supervisors: O. Bernard (director) and W. Djema (co-director).
• O. Bernard was jury member of the PhD thesis of Julien Lopez, "Search for bioactive compounds and study of the effect of nitrogen substrate on the metabolism of Tetraselmis suecica in biofilms", Sorbonne University, December 5th, 2024.

11.3.1 Productions (articles, videos, podcasts, serious games, ...)

• O. Bernard contributed to the Inria website Digital technology and the oceans: towards a better understanding of marine ecosystems;
• O. Bernard was interviewed by Mediapart for an article "Study phytoplankton to better understand oceans";
• The TedX Cannes conference given by F. Casagli in September 2023 When AI reveals Wastewater’s hidden treasures was published on YouTube (5100 views in 2024).

11.3.2 Participation in Live events

• F. Casagli, W. Djema and O. Bernard participated to the cinéscience TEDx evening ("TEDxCannes fait son cinéma") (cinema CINEPLANET Antibes) for discussing and commenting the projection of the Tedex Video from F. Casagli;
• O. Bernard gave public conferences on "Introduction of LCA" in Science for All 06 outreach presentations in Cagnes-sur-mer (March 15th, 2024) and Beaulieu-sur-mer (March 21st, 2024);
• O. Bernard gave a public conference on the potential of microalgae at Saint Laurent University for All, February 22nd 2024.

11.3.3 Others science outreach relevant activities

• W. Djema served as an Inria messenger for the Tournée du Climat et de la Biodiversité during its stop at Parc Phoenix in Nice from May 16th to 18th, 2024.

International journals

• 8 articleD.D. Carecci, A.A. Catenacci, S.S. Rossi, F.Francesca Casagli, G.G. Ferretti, A.A. Leva and E.E. Ficara. A plant-wide modelling framework to describe microalgae growth on liquid digestate in agro-zootechnical biomethane plants.Chemical Engineering Journal485April 2024, 149981HALDOIback to text
• 9 articleO.Othman Cherkaoui-Dekkaki, W.Walid Djema, N.Nadia Raissi, J.-L.Jean-Luc Gouzé and N.Noha El Khattabi. Optimal control of waste recovery process.International Journal of Dynamics and Control2024HALDOIback to text
• 10 articleY.Yan Gao, O.Olivier Bernard, A.Andrea Fanesi, P.Patrick Perré and F.Filipa Lopes. The effect of light intensity on microalgae biofilm structures and physiology under continuous illumination.Scientific Reports141January 2024HALDOIback to text
• 11 articleA.A. Gharib, W.Walid Djema, F.Francesca Casagli and O.Olivier Bernard. Adaptive temperature model for microalgae cultivation systems.Journal of Process Control141September 2024, 103280HALDOIback to textback to textback to text
• 12 articleA.Ali Gharib, W.W. Djema, P. M.P. Moñino Fernández, R.R. Chin-On, M.M. Janssen and O.Olivier Bernard. Validation of an Adaptive Temperature Model for Closed Microalgae Cultivation Systems.Algal Research - Biomass, Biofuels and BioproductsJanuary 2025, 103838In press. HALDOIback to textback to textback to text
• 13 articleJ.Javier Innerarity Imizcoz, W.Walid Djema, F.Francis Mairet and J.-L.Jean-Luc Gouzé. Optimal resource allocation in micro-organisms under periodic nutrient fluctuations.Journal of Theoretical Biology2024. In press. HALDOIback to text
• 14 articleD.David Morgado, A.Andrea Fanesi, T.Thierry Martin, S.Sihem Tebbani, O.Olivier Bernard and F.Filipa Lopes. Exploring the dynamics of astaxanthin production in Haematococcus pluvialis biofilms using a rotating biofilm‐based system.Biotechnology and BioengineeringMarch 2024HALDOIback to text
• 15 articleD.David Morgado, A.Andrea Fanesi, T.Thierry Martin, S.Sihem Tebbani, O.Olivier Bernard and F.Filipa Lopes. Non-destructive monitoring of microalgae biofilms.Bioresource Technology398April 2024, 130520HALDOIback to textback to text
• 16 articleR.Rebecca Nordio, E.Enrique Rodríguez-Miranda, F.Francesca Casagli, A.Ana Sánchez-Zurano, J. L.José Luis Guzmán and G.Gabriel Acién. ABACO-2: a comprehensive model for microalgae-bacteria consortia validated outdoor at pilot-scale.Water Research248January 2024, 120837HALDOIback to textback to text
• 17 articleB. A.Bruno Assis Pessi and O.Olivier Bernard. Dynamical Metabolic Model for Optimizing Biotin-Regulated Lipid Production in Microalgae-Bacteria Symbiosis.IFAC-PapersOnLine58142024, 151-156HALDOIback to text

International peer-reviewed conferences

• 18 inproceedingsR.Rand Asswad, W.Walid Djema, O.Olivier Bernard, J.-L.Jean-Luc Gouzé and E.Eugenio Cinquemani. Optimization of microalgae biosynthesis via controlled algal-bacterial symbiosis.CDC 2024 - 63rd IEEE Conference on Decision and ControlMilan, ItalyIEEEOctober 2024, 1-6HALback to text
• 19 inproceedingsO.Olivier Bernard, M.Mickael Bestard, T.Thierry Goudon, L.Leo Meyer, S.Sebastian Minjeaud, F.Florent Noisette and B.Bastien Polizzi. Numerical schemes for mixture theory models with filling constraint: application to biofilm ecosystems.ESAIM: PROCEEDINGS AND SURVEYSCEMRACS 2022 - Transport in physics, biology and urban traffic77Marseille, France, FranceEDP Sciences, SMAI2024, 249 - 266HALDOIback to text
• 20 inproceedings O.Olivier Bernard, F.Francesca Casagli, B.Benoît Chachuat and F.Fabrizio Bezzo. Will machine learning (finally) contribute to the microalgae sector? Algaeurope 2024 Athens, Greece December 2024 HAL back to text
• 21 inproceedings F.Francesca Casagli, O.Olivier Bernard and J.-P.Jean-Philippe Steyer. Why modelling phototrophic systems? 1st International Conference on Novel PhotoRefineries for Resource Recovery PHOTOREFINERIES 2024 Valladolid (Spain), Spain September 2024 HAL back to text
• 22 inproceedingsI.Ignacio Fierro, B.Benoît Chachuat and O.Olivier Bernard. Optimal control of photobioreactor accounting for photoinhibition and photoacclimation.ADCHEM 2024 - 12th IFAC Symposium on Advanced Control of Chemical ProcessesToronto ( CA ), CanadaJuly 2024HALback to text
• 23 inproceedingsA.Ali Gharib, W.Walid Djema, P. M.P. Moñino Fernández, R.R. Chin-On, M.M. Janssen, F.Francesca Casagli and O.Olivier Bernard. A breakthrough in the temperature prediction of microalgal processes.AlgaEurope 2024Athen, GreeceDecember 2024HALback to text
• 24 inproceedingsJ.Javier Innerarity Imizcoz, W.Walid Djema, F.Francis Mairet and J.-L.Jean-Luc Gouzé. Optimal cell growth under periodic environment.MTNS 2024 - 26th International Symposium on Mathematical Theory of Networks and SystemsCambridge (Angleterre), United KingdomAugust 2024HALback to text
• 25 inproceedingsP.Pauline Mazel, W.Walid Djema and F.Frédéric Grognard. Optimal control for a combination of cancer therapies in a model of cell competition.CDC 2024 - 63rd IEEE Conference on Decision and ControlMilan, ItalyDecember 2024HALback to text

Conferences without proceedings

• 26 inproceedingsB. A.Bruno Assis Pessi, G.Gustavo Ribeiro Silva, C.C.M.E Pompei, O.Olivier Bernard and F.Francesca Casagli. Extending algae-bacteria model to dynamically predict microbialcommunity composition during sanitary wastewater treatment.The 1st International Conference on Novel Photorefineries for Resource RecoveryValladolid, FranceSeptember 2024HALback to text

Scientific book chapters

• 27 inbookH.Hubert Bonnefond, C.Charlotte Combe, J.-P.Jean-Paul Cadoret, A.Antoine Sciandra and O.Olivier Bernard. Potential of Microalgae.Green Chemistry and Agro-food Industry: Towards a Sustainable BioeconomySpringer Nature SwitzerlandApril 2024, 133-153HALDOIback to text

Doctoral dissertations and habilitation theses

• 28 thesisJ. I.Joel Ignacio Fierro Ulloa. Modelling and control of photobioreactors under dynamic light regimes.Université Côte d'AzurOctober 2024HALback to textback to textback to textback to text

Reports & preprints

• 29 reportA.André Abreu, D.David Johns, H.Haimanti Biswas, A.Andrew Knoll, H.Hubert Bonnefond, X.Xiamen Lin Xin, C.Chris Bowler, T.Thulani Makhalanyane, J.-P.Jean-Paul Cadoret, A.Abigail McQuatters-Gollop, R.Roberto Casati, B.Bettina Meyers, G.Grace Cawley, R.Ron Milo, F.Fiona Cumming Jane, A.Aditee Mitra, M.Minhan Dai, H.Hiroyuki Ogata, C.Colomban de Vargas, I.Ian Probert, C.Carlos Duarte, E.Emma Rocke, P.Paul Falkowski, A.Ali Sow Bamol, C.Camila Fernandez, M.Maris Stulgis, K.Kevin Flynn, H.Haruko Takeyama, L.Lionel Guidi, P.Paul Tett, G.Gustaaf Hallegraeff, M.Monica Thukral, K.Koji Hamasaki, R.Ruth Tiffer-Sotomayor, P.-A.Pierre-Alain Hoffmann, F.Flora Vincent, D.Daniele Iudicone and S.Samuel Wang. PLANKTON-BASED SOLUTIONS TO SUPPORT LIFE ON OUR PLANET: 4 CO2 Sink carbon and mitigate climate change.UN Compact2024HAL