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

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Start date : 01/09/2021

offer n° IMEPLAHC-PHOTO-04-07-2021

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.

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.

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 – 04 56 52 95 31
Co-supervisor (30%): Davide BUCCI – 04 56 52 95 39

  • Keywords : Engineering sciences, Electronics and microelectronics - Optoelectronics, FMNT, IMEP-LaHc
  • Laboratory : FMNT / IMEP-LaHc
  • CEA code : IMEPLAHC-PHOTO-04-07-2021
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Dynamic sensing methods using microelectronic devices: from an experimental exploration to the development of a new ‘dynamic’ sensor

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Start date : 01/10/2021

offer n° IMEPLAHC-CMNE-03-26-2021

          Dynamic sensing methods using microelectronic devices:
    from an experimental exploration to the development of a new    ‘dynamic’ sensor

Deadline for application: the 1st of June 2021, beginning of contract: the 1st of Oct. 2021

Laboratory / group: IMEP-LAHC/CMNE
Advisors: – Christoforos THEODOROU (
–  Irina IONICA (

In the wide family of the bio-chemical sensors, the ISFETs (Ion Sensing Field Effect Transistors) occupy a place of honor thanks to their multiple advantages, for example in terms of miniaturization, sensitivity, co-integration with reading circuitry etc [1]. The working principle of such a device is based on the shift of the threshold voltage of the transistor, due to the intentional addition of charges-to-be-detected in the proximity of its channel [1]. The resulting conductivity modulation is then measured in (quasi)-static conditions, in which externally applied bias are slow enough and the device is assumed at equilibrium at
every measurement point. This is the principle of the so-called ‘charge-based sensors’ (CBS).
Despite their certain advantages and simplicity of operation, the CBS’ sensitivity is by definition limited by the amount of charge of the deposited particles with regards to the minimum detectable charge, which is in turn limited by the electrical parameters of the device and by biasing. Furthermore, the selectivity of CBS, i.e. the capacity of distinguishing between different types of particles, is almost non-existing (if the surface is not chemically functionalized), because many types of particles can have exactly the same amount of charge.
To overcome these two drawbacks of CBS (minimum sensitivity and no selectivity), various alternative approaches have been suggested in the recent literature, having a core element in common: they all use dynamic effects, instead of static, as a means for detection. This thesis will address two main methods of
dynamic sensing:

  1.  The ‘out-of-equilibrium potential’ method (co-developed by members of CMNE in IMEP-LAHC [2]):
    The interest of monitoring out-of-equilibrium instead of static current resides in the fact that the potential signature is very strong in a region where the current level is very small and noisy. This allows the creation of very low voltage/power sensors with potential sensitivity enhancement, thanks to the
    dynamic reading. The aim here will be to go from a simple proof-of-concept of such a response, to a realistic sensor design with improved figures of merit. From a more fundamental point of view the study involves a full understanding and modeling of the mechanisms that create the potential barriers at the
    contacts and that are responsible for the out-of-equilibrium response. This can be also an advantage for applications, since unlike most of the methods that need optimized ohmic contacts, for the out-ofequilibrium phenomena Schottky barriers provoke and enhance the potential response.
  2. The ‘fluctuation-enhanced sensing’ (FES) method: This principle is based on the effects of dynamic interaction between device surface traps and electrons of deposited molecules, leading to a unique characteristic low-frequency noise spectrum for each sensing target [3], hence enabling the selectivity
    aspect in ISFET sensing. In other studies [4], a similar concept is used, taking advantage of the modulation in a trap’s occupancy and/or electrostatic impact. This thesis aims to re-examine in a systematic way the claims of these publications, clearly identify the advantages of FES against CBS in order to avoid misconceptions, and test the feasibility of FES for a variety of microelectronic devices,both in-home fabricated ones (such as Pseudo-MOSETs on SOI) and from collaborators (such as Nanowire/NanoNet/NanoRibbon FETs, Si Nanogauges).
    A whole new field of alternative sensing applications using noise or out-of-equilibrium effects as means of detection is open for exploration, while at the same time fundamental research around these phenomena is needed, in order to scientifically prove the feasibility and innovation of every approach. This thesis aims to respond to these challenges and showcase/propose the development of novel ‘dynamic’ sensors.
    Additionally, a real bench mark of these methods will allow identifying the strength and best applications of each one.
    The candidate must have a very good background in semiconductor physics and characterization of semiconductor devices. Knowledge of concepts in bio-chemical sensing will be a plus. The research will cover fabrication and functionalization, electrical characterization methods, as well as modeling and simulation aspects. The thesis will benefit from a rich collaboration environment and possibility of benchmark with wide variety of methods and devices.
    The candidate must have very good academic record, with high grades.

[1] N. Moser, et al,, P. Bergveld,
[2] L. Benea, et al,
[3] L. B. Kish et al,, S. Rumyantsev, et al,
[4] J. Li, et al, Y. Kutovyi et al.,

  • Keywords : Engineering science, Engineering sciences, Electronics and microelectronics - Optoelectronics, FMNT, IMEP-LaHc
  • Laboratory : FMNT / IMEP-LaHc
  • CEA code : IMEPLAHC-CMNE-03-26-2021
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Integration of scalable arrays of quantum dots on silicon

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Start date : 01/09/2021

offer n° SL-DRT-21-0883

  • Keywords : Engineering sciences, Technological challenges, Electronics and microelectronics - Optoelectronics, Emerging materials and processes for nanotechnologies and microelectronics, DCOS, Leti
  • Laboratory : DCOS / Leti
  • CEA code : SL-DRT-21-0883
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novel integrated circuit topologies using innovative capacitive components on silicon

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Start date : 01/10/2021

offer n° SL-DRT-21-0814

The objective of this thesis is to assess the potentiel of hybrid silicon capacitors developed at LETI as components in novel architectures of integrated energy conversion circuits. The hybrid capacitors exhibit a combination of unique properties in terms of energy density (ionic storage of the order of 40 mJ / mm3) and frequency response (dielectric storage demonstrated up to 30 GHZ), in addition to a technological realization on 200 mm silicon wafers.

Within the framework of this project, it is proposed to design energy conversion circuits (eg. DC-DC converters)exploiting the intrinsic properties of the hybrid capacitors developed at LETI.

  • Keywords : Engineering sciences, Technological challenges, Electronics and microelectronics - Optoelectronics, Emerging materials and processes for nanotechnologies and microelectronics, DCOS, Leti
  • Laboratory : DCOS / Leti
  • CEA code : SL-DRT-21-0814
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Innovative hydrogels for “minibrain-on-chip ” development to study Alzeimer’s disease

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Start date : 01/10/2021

offer n° SL-DRT-21-0633

Organ-on-chip approaches tackle the limitations of two-dimensional (2D) classic cellular cultures and animal models of neurodegenerative diseases. DRF/JACOB/SEPIA has developed “mini brains”, i.e. 3D cerebral organoids generated from iPSCs (induced pluripotent stem cells), presently cultivated using Matrigel, a commercial matrix derived from mouse tumor. The objective of the PhD thesis will be to investigate new 3D culture scaffolds, based on hyaluronic acid (HA) hydrogels presenting tunable stiffness and electrical conductivity, developed at DRT/LETI/DTBS. The cell-loaded hydrogels will additionally be formulated as bioinks for advanced printing technologies (extrusion combined with UV/visible photo-crosslinking). The expected outcome of the PhD is an improved “mini brain” model to study the development of neurodegenerative diseases, which could be applied to therapeutic strategies.

  • Keywords : Life Sciences, Technological challenges, Cellular biology, physiology and cellular imaging, Health and environment technologies, medical devices, DTBS, Leti
  • Laboratory : DTBS / Leti
  • CEA code : SL-DRT-21-0633
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