Integrated photonic sensor on glass for detecting bacterial viability in polluted water

Sujet de thèse pour contrat doctoral fléché EEATS

Integrated photonic sensor on glass for detecting bacterial viability in polluted water

The adverse effects of technological and industrial accidents on health and environment lead public  authorities and the private sector to develop solutions able to measure the generated pollution.
The fire of the Lubrizol factory in Rouen has for instance highlighted that the currently available techniques are slow. Indeed, it took several days to analyze the first samples of contaminated water and soil. The development of portable and robust sensors able to characterize the toxicity of pollutants in real time  in a liquid phase is therefore a major challenge. Solutions based on a functionalization of the detection  region are in general proposed. However, exploiting chromogenic markers, expensive and potentially  dangerous for the environment¹ greatly penalizes the durability and the environmental footprint of  those detectors. The objective is therefore to design an integrated sensor that is robust, easy to clean  and that does not require any functionalization of the sensitive region.

In this context, the IMEP-LaHC, specialist of integrated photonic²,³ and optofluidic devices4, has  teamed up with laboratories offering complementary skills. The goal is to propose an integrated  solution based on a detection of bacterial viability, where bacteria play the role of sentinels for pollution of the analysed medium. Specialists in microbiology (laboratories LMSM, IGE, COBRA) and integrated sensors (IMEP-LaHC, G2Elab) compose the consortium. The ambition is to develop a solution on a glass substrate, well known and widely exploited by biologists, thanks to its mechanical and chemical robustness.
The sensor will co-integrate two detection functions, optical and electrical. They will measure  independently and redundantly the viability of bacterial solutions contaminated with pollutants.
The goal of this PhD is to work on the design and optimization of the optical sensing function.
The  innovative approach will exploit the advantages of integrated optics on glass and the  dielectrophoresis (DEP). A set of electrodes integrated on the sensor will allow applying a dielectrophoresis force, trapping bacteria to be sensed without exploiting any additional functionalization technique.

To obtain this goal, the three following points will be addressed during the PhD:

•  Design of a DEP function trapping the bacteria in vicinity of the optical signal. It will deal with
  the tailoring of the 2D (or even 3D) geometry of electrodes allowing the control of the electric field gradients.
• Sort bacteria according to their viability. The intensity and the direction of the DEP force
  depend on many parameters such as the frequency of the electrical signal, the permittivity of
  the medium and the particles as well as the shape of the latter. An equivalent electromagnetic
  model of bacteria will be defined to exploit those effects and spatially separate viable a nonviable cells. The PhD student will also work on the experimental validation of the model,
  exploiting polystyrene micro beads displaced by DEP.
• Model and optimize electromagnetic interaction of a guided optical signal with bacteria trapped on the surface of a waveguide. The study will identify and treat the parameters affecting thoverlap between the optical signal and the cellular model.

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1 Barik, A., Otto, L. M., Yoo, D., Jose, J., Johnson, T. W., & Oh, S. H. (2014). Dielectrophoresis- enhanced plasmonic sensing with gold nanohole arrays. Nano letters, 14(4), 2006-2012.
2 Broquin, J. E. (2007). Glass integrated optics: state of the art and position toward other technologies.In Integrated Optics: Devices, Materials, and Technologies XI (Vol. 6475, p. 647507). International Society for Optics and Photonics.
3 Jordan, E., Geoffray, F., Bouchard, A., Ghibaudo, E., & Broquin, J. E. (2015). Development of Tl+/Na+ ion-exchanged single-mode waveguides on silicate glass for visible-blue wavelengths applications. Ceramics International, 41(6), 7996-8001.
4 Allenet, T., Geoffray, F., Bucci, D., Canto, F., Moisy, P., & Broquin, J. E. (2019). Microsensing of plutonium with a glass optofluidic device. Optical Engineering, 58(6), 060502.
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The detection limit and the reliability of the optical sensor are key points to be considered, too. The
work will thus include:

• Designing the interaction surfaces between the optical signal and bacteria and calculating the refractive index change due to the variation of bacterial concentration.
•  Choosing the best approach among different interferometric functions, to compensate the drifts of the bacteria nutrient medium.
• Determining the goals for the optimal choice of the working point and the linearity range of the sensor.

The work to be done in the PhD will also include a microfabrication challenge, related to the cointegration of optical, electric and microfluidic functions on the same glass substrate. The work will thus lead to a final task of integration and characterization of a complete device by means of microbeads simulating the dielectric behaviour of bacteria. A strong ambition is to build a prototype that will allow the first tests with environmental samples in collaboration with the laboratories of the consortium.

To successfully complete the PhD, the student will work during the first year on the theoretical background of integrated photonics and DEP. A bibliographic study will notably be carried-out to review the state of the art of integrated bacterial sensing. Training on microfabrication tools in clean room and on simulation softwares will be scheduled, too. The goal will be to calculate the interaction of the DEP forces and/or the optical signal with bacterial models. The second year will start with the fabrication of the first prototypes, co-integrating DEP electrodes and optical functions. This will require training on the photonic characterization techniques available at the IMEP-LaHC. Those first prototypes will be sent to the partner laboratories, to validate the detection principle on biological samples. The feedback will be useful to optimize the design of the interferometric function. The cointegration of the three functions (electrical, optical and microfluidic) will be tackled between the second and the third year. The third year of the PhD will be devoted to the fabrication and calibration of a final prototype, in partnership with our colleagues specialists in biochemistry. The final PhD manuscript and publications associated to the work will then be written.

This PhD subject has been considered as a priority by the scientific council of the laboratory and the EEATS doctoral school. The subject has thus been highlighted as a “sujet fléché” by the doctoral school, which means that it is given priority in the allocation of a doctoral PhD research grant.
PhD supervisor (70%): Elise GHIBAUDO elise.ghibaudo@grenoble-inp.fr – 04 56 52 95 31
Co-supervisor (30%): Davide BUCCI davide.bucci@phelma.grenoble-inp.fr – 04 56 52 95 39

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