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Current Funded Positions
Master 2 Student to continue on a PhD thesis on Blood Rheophysics
We are recruiting a Master Student beginning 2027 (January-February 2027) for a 5 to 6 months internship on probing blood rheophysics at the local scale of the cells to produce a Numerical Twin. The internship will consist in develop a currently missing metrological building block: capacitive pressure microsensors, integrable into a microfluidic chip, able to resolve pressure differences on the order of 100 Pa (1 mbar) to finely quantify pressure losses in confined blood flows.
This internship is the gateway to a joint CBS/IES PhD, co-supervised by Manouk Abkarian (CBS) and Benoît Charlot (IES), starting in autumn 2027 and funded by the ANR (36 months). You will integrate pressure sensors and 2b-FCS into state-of-the-art rheology and microfluidics experiments to probe the extensional rheology of blood (cross-slot devices) and flows around obstacles, in direct confrontation with the consortium’s simulations — a topic with strong potential for publications in leading journals.
To apply, or for more details email Manouk :
Research Engineer (IR or IE): Optical instrumentation and custom microscopes
We are recruiting a research engineer (IE or IR) to design, build, optimize, and program new microscopy platforms. You will contribute to several ongoing and upcoming systems, including a phase-contrast plus fluorescence microscope with IR-based autofocus for highly stable, very long time-lapse measurements, an epifluorescence microscope integrated with optical tweezers (tweezers already built) with a focus on system integration, synchronization, and automated acquisition, a digital holographic microscope coupled with light sheet fluorescence, and a bioluminescence imaging setup for low-light measurements and long-term automated imaging. The role combines hands-on optical alignment and performance optimization (stability, SNR, drift), hardware integration (cameras, stages, illumination, shutters, autofocus, triggers), and development of control and acquisition software in LabVIEW and/or Python, along with documentation, calibration and diagnostic routines, and day-to-day support for instrument users. We are looking for a strong experimental optics/instrumentation profile (physics/optics training), with experience building and troubleshooting optical setups and an interest in writing robust, maintainable instrument-control code, and experience in microscopy, fluorescence, low-light imaging, hardware triggering/DAQ, and version control is a plus. This is a 1-year position, renewable. To apply, or for more details, email Ashley.
Postdoc or Research Engineer: Digital Holographic Microscopy
We are recruiting either a Postdoctoral Researcher or a Research Engineer (IR or IE) to develop the optical design, numerical reconstruction algorithms, and data analysis pipelines for digital holographic microscopy applied to flowing red blood cells and swimming bacteria, with opportunities to incorporate modern machine-learning approaches where relevant. The project combines experimental constraints with heavy computation, including forward and inverse modeling of hologram formation, robust phase and amplitude reconstruction, high-throughput processing of large datasets, and extraction of biophysical observables such as cell shape dynamics, flow-dependent deformation, trajectories, and swimming kinetics. The role includes implementing and validating reconstruction and analysis workflows (Python and/or similar scientific computing environments), improving speed and reliability (clean software architecture, reproducibility, testing, version control), and working closely with experimentalists to connect algorithmic outputs to ground-truth measurements and instrument parameters; experience in computational imaging, inverse problems, and scientific software is essential, and experience in optics and microscopy is a strong plus. Familiarity with machine learning for reconstruction, denoising, segmentation, or tracking (e.g., deep learning toolkits and GPU workflows) is highly valued, but not required if you have a strong physics/maths foundation and excellent coding skills. This is a 1-year position, renewable. To apply, or for more details, email Ashley.
Postdoc or Research Engineer: Physics of bacterial biofilm nucleation
We are looking for a Postdoc or Engineer with experience and/or a passion for digital holographic microscopy (DHM) and light sheet fluorescence microscopy. The project will build a microscope, from scratch, which combines the two modalities in order to i) track bacteria in 3D over large fields of view and with high spatial and time resolution, and ii) observe the swimming to surface-adhered transition that nucleates a biofilm and interogate surface-induced intracellular changes via fluorescent biomarkers. The ideal candidate may have a background in optics and/or in methods of numerical reconstruction. Experience in machine learning and programming GPUs would be a plus. Experience working with bacteria is not necessary, but welcome! To apply, or for more details, email Ashley.
Master Internship: Dynamic Regulation of Fungal Bioluminescence
Fungal bioluminescence is one of the few naturally occurring systems that allows cellular physiology to be observed non-invasively in real time. While the phenomenon has long fascinated scholars, it was only recently that the mechanism by which fungi bioluminescence, the Caffeic Acid Cycle, was uncovered. However, the core regulators of these enzymes, and indeed the evolutionary reason to produce light in the first place, remain unknown. While previous work has shown that fungal light emission follows a circadian rhythm, we recently discovered that bioluminescence can also respond to changes in light and temperature within minutes, suggesting the existence of rapid regulatory mechanisms that operate independently of the circadian clock. The physiological basis of these fast responses remains unknown. In this project, the Master's student will investigate how environmental perturbations influence the dynamics of mycelial bioluminescence of the Brazilian glowing fungus Neonothopanus gardneri. Using a custom-built incubator capable of automated time-lapse imaging under precisely controlled illumination and temperature, the student will culture fungal mycelium, perform perturbation experiments, and quantify the resulting changes in light emission. Image analysis will be performed in Python to quantify how rapidly fungal bioluminescence responds to environmental perturbations and to identify conditions that alter these dynamics. By combining experimental biology with quantitative image analysis, this project aims to uncover new mechanisms regulating fungal bioluminescence while providing the student with hands-on experience in microscopy, programming, data analysis, and fungal physiology. To apply, or for more details, email Peter or Ashley.
Master Internship: Decoding Bacterial Conversations: Quantitative Analysis of Intra- and Interstrain Quorum Sensing in Aliivibrio fischeri
Bacteria coordinate collective behaviors through quorum sensing, a cell-cell communication mechanism in which diffusible signaling molecules regulate gene expression according to population density. In the marine bacterium Aliivibrio fischeri, quorum sensing controls bioluminescence, providing an exceptionally quantitative and non-invasive readout of signaling activity. While the molecular components of this regulatory network have been extensively characterized, comparatively little is known about how communication differs between naturally occurring strains. This project will investigate the spatiotemporal dynamics of intra- and interstrain quorum sensing using two A. fischeri strains exhibiting markedly different luminescence phenotypes. Quantitative measurements of bacterial growth and bioluminescence in liquid and solid-state cultures will be used to compare signaling responses under self- and cross-signaling conditions. The resulting datasets will be analyzed using custom Python pipelines to characterize the emergence and evolution of collective bioluminescence across time and space, providing insight into differences in signal production, signal perception, and downstream regulatory processes. More broadly, this work will establish a quantitative framework for comparing bacterial communication networks and illustrate how dynamic phenotypic measurements can reveal principles governing information transfer between microbial populations. To apply, or for more details, email Peter or Ashley.
Master Internship: From Statistical Mechanics to Experiment- Decoding Switching in the Bacterial Flagellar Motor
The bacterial flagellar motor is a rotary molecular machine that enables bacteria to swim by switching stochastically between clockwise and counterclockwise rotation. This switching response is remarkably sensitive to chemical signals, allowing bacteria to rapidly change their swimming behavior during chemotaxis. Although several physical models have been proposed to explain how the many proteins of the motor switch collectively, the underlying mechanism remains debated. Existing theories range from equilibrium allosteric and Ising-like conformational-spread models to non-equilibrium models incorporating torque generation, stochastic fluctuations, and long-range mechanical coupling. These models can reproduce some of the same average behaviors but may differ in their predictions for the fluctuations and dynamics of individual motors.
In this project, the Master’s student will implement and systematically compare the principal theoretical models of bacterial flagellar motor switching. Using analytical calculations and stochastic simulations, including Monte Carlo or kinetic simulation methods, the student will determine which experimentally accessible signatures could distinguish between competing mechanisms. These signatures may include clockwise bias, switching frequency, distributions and correlations of clockwise and counterclockwise intervals, switching trajectories, sensitivity to mechanical load, and the relationship between motor torque and switching cooperativity. The theoretical predictions will then guide single-motor experiments in Escherichia coli. Microscopic beads attached to truncated flagellar filaments will provide a high-resolution readout of motor rotation, allowing switching events to be detected and their statistics compared directly with model predictions. Depending on progress, newly acquired measurements of switching in the sodium-driven motor of Vibrio alginolyticus may also be incorporated to investigate which features of switching are universal and which depend on motor architecture or bacterial species. By closely integrating statistical physics, computational modeling, and quantitative experiments, this project will provide training in stochastic processes, numerical simulation, Python data analysis, microscopy, and single-molecule biophysics.To apply, or for more details, email Francesco or Ashley.
Master Internship: Dynamics of Liquid Jet Retraction in Blood and Model Suspensions
The dynamics of liquid jet breakup and retraction are fundamental fluid mechanical processes that play important roles in applications ranging from inkjet printing to disease transmission. Especially measuring the speed at which a liquid jet retracts can give insight into the properties of the respective fluid. Although Newtonian liquid filaments are relatively well understood, complex fluids containing suspended particles or polymers are more difficult to understand. In particular the presence of red blood cells can alter the interfacial dynamics through their deformability, aggregation behavior or interaction with the surrounding fluid. Understanding how microscopic particle properties influence macroscopic jet dynamics could provide new insight into blood rheology and disease-related changes of blood cells.
This project will involve generating liquid jets using a piezo-driven drop-on-demand system and recording the resulting jet formation, breakup and retraction using a high speed camera. Experiments will be conducted on model suspensions as well as human blood samples, allowing direct comparison between simplified systems and biologically relevant fluids. The student will learn experimental techniques for sample preparation of suspensions, handling human blood and operating imaging equipment. Following the image acquisition, the student will develop numerical tools to process the image sequences and extract quantitative information such as the retraction velocity, filament geometry or characteristic time scales. Particular attention will be given to understanding why the filament retraction is accelerated in suspensions and how these effects may be linked to changes in the cell properties. To apply, or for more details, email Manouk or Ashley.
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Interested in any aspect of our work? Please get in touch to discuss the possibility of jointly applying for Masters, PhD, or postdoc funding.
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