November 11, 2020


ESR1: Multiscale modeling of flagellar beating, from waveforms to swimming

A theoretical model for the autonomous beating of cilia and eukaryotic flagella will be established. The simulation results for the beat pattern of single cilia will be tested with experimental observations to determine parameters for the description of a realistic beat. Emergent metachronal waves and (collective) swimming behavior of multi-ciliated microswimmers will be studied and compared with experimental results.

Contact: Gerhard Gompper

ESR2: Determination of visco-elastic properties of flagella

In this project the ESR will establish experimental protocols to study dynamic response of axonemes to externally imposed periodic shear. The flagellar response will be measured as a function of amplitude and frequency of the applied shear stress and the mechanical properties of the basal-bodies will be established.

Contact: Marco Polin

ESR3: Impact of ciliary flows on cell feeding

Unicellular nanoflagellates play a key role in microbial food webs, by eating microbes, and by themselves being prey to zooplankton. The action of their flagella generates feeding currents to enhance prey encounter rates but the feeding flows at the same time exposes the flagellates to theuir rheotactic (flow sensing) predation predators. The evolution of the highly diverse flagellar arrangements, beat patterns and kinematics found among flagellates in the ocean is the result of the often-conflicting needs to feed, survive, and move.

The project aims at exploring and quantifying foraging trade-offs in nanoflagellates with diverse flagellar arrangements. Depending on the expertise and interests of the candidate, the PhD project can focus on different aspects of this topic, from CFD modelling and quantification of feeding flows by particle tracking or μ-PIV, to microscopic observations of foraging behavior or assessment of predation risk by incubation experiments and observations.

Contact: Thomas Kiørboe

ESR4 – Bacterial dynamics in heterogeneous landscapes

The resource landscape of microbes in a range of environments is composed of nutrient pulses and filaments, as occurs for example for microbes in the ocean due to turbulence. This is a problem at the interface between fluid mechanics and the biophysics of searching, and has to date received very little attention despite being the ubiquitous situation in which chemotaxis unfolds in aquatic environments. Numerical models (based on Direct Numerical Simulations) predict that the benefit afforded by chemotaxis is affected by the intensity of turbulence, yet experimental tests are lacking, due largely to the difficult of generating nutrient filaments at the appropriate scales while simultaneously quantifying microbial responses. This project will focus on developing a new approach to tackle this question, by combining microfluidic technology with video-microscopy and advanced image analysis.

Contact: Roman Stocker

ESR5 – Driven motion in a complex environment

Many bacteria have the ability to move in their environment in order to respond to their needs, be they nutrients or oxygen. Strikingly, bacteria exhibit a rich repertoire of swimming patterns, from run-and-tumble to run-reverse-flick. Which benefits come with a particular pattern however remains an open question. Besides, bacteria often have to perform those moves under mechanical constraints such as hydrodynamics or geometric constraints for which our understanding of bacteria motion is currently limited. Our goal is to explore those issues, using both a theoretical approach and an experimental investigation of magnetotactic bacteria.

Contact: Cecile Cottin-Bizonne

ESR6 – Swimming in complex 3D structured environments

Swimming bacteria like E. coli achieve propulsion in a low Reynolds number environment by rotating a bundle of flexible helical flagella. Theoretical approaches usually treat the bundle as a thick and rigid effective helical filament. On the other hand, both direct observation of fluorescently labelled flagella and multiscale molecular dynamics simulations reveal that the bundle is a more dynamic and strongly interacting complex whose detailed behavior may have important effects on both single cell propulsion and interactions with neighboring cells and confining structures.

Contact: Roberto DiLeonardo

ESR7 – Dissecting bacterial cell-cell interactions and the emergence of collective movement

Suspensions of swimming bacteria display collective motion when the density of bacteria increases. These collective movements take the form of large groups of cells that transiently move in the same direction, which break up into swirls, forming intermittent vortex-like structures. The cell-cell interaction mechanisms that underlie the emergence of bacterial collective motion in two- and three-dimensional suspensions are unclear. Using genetics, we will modify bacterial cell-cell interactions, to study their involvement in collective movement, in close comparison to theoretical work.

Contact: Knut Drescher

ESR8 – Bacteria propulsion and interactions in monolayer biofilms

Flagellated bacteria exhibit a particular mode of locomotion denoted as swarming, where they migrate collective over surfaces and from stable aggregates, which can become highly mobile. Bacteria in swarms are distinctly different from planktonic cells as they assume different morphologies — they are more elongated and the number of flagella is significantly increased — and they are densely packed. This points toward the importance of cell shape and propulsion in swarming. Moreover, collective swarming is observed for other microswimmers, e.g., trypanosomes, which are propelled in a completely different fashion.

Contact: Gerhard Gompper

ESR9 – Evolution of microswimmer designs in distinct micro-environments

Microbial parasites thrive in or on most living beings. Their strategy is to persist, rather than to kill quickly. Among the prototypic parasites, the trypanosomes are most versatile and best studied examples. An enormous range of trypanosome species infect basically all animals, and in humans, they cause deadly diseases. We study the African trypanosomes that are transmitted by the infamous tsetse fly, and cause sleeping sickness. These trypanosomes undergo several genetically programmed stage transitions in the mammalian host and in the insect vector. All life cycle stages are basically variations over the same construction theme, as they feature a single flagellum, uniquely attached alongside the spindle-shaped cell body. The motion capabilities and properties, however, vary considerably between the trypanosome forms. We therefore hypothesize that evolution has shaped the individual parasite stages for maneuvering in distinct micro-environments, such as human skin and adipose tissues tissue spaces, blood circulation and brain, as well as the complex digestive system of the tsetse fly. We aim at reproducing these environments and measuring, manipulating and simulating the swimming behavior of evolutionary adapted and naïve parasites therein.

Contact: Markus Engstler

ESR10 – Imaging in 2020 – Integration, high throughput, automation

The optical microscope has evolved in the 20th century to become a workhorse of cell and microbiology research, as an instrument for direct human visualization. Modern integration with digital video acquisition, and current developments of super-resolution and optical manipulation, are still often integrated into an instrument design that is sub-optimal. The cost of many components (e.g. optical parts) is very high and again comes from layout constraints. While some laboratories have replaced traditional chassis, there have been few attempts at completely redesigning the imaging system to make use of the vast improvements in low cost sensor and optical components driven by mass markets. Furthermore, very little has been done in real-time analysis aiming to integrate feedback control into the experiments. These aspects could deliver a revolution in experimental practice of imaging living systems, particularly single cell experiments or conditions that require triggers based on cell/cell contact or other rare events, or in applications that require autonomous decisions (remote untethered sensing).

Contact: Allen Donald

ESR11 – Collective dynamics of microbial parasites

Parasites thrive in the ocean, and there are plenty of hosts for them to choose from. In marine planktonic ecosystems, the important role played by parasitism has long been underestimated, despite the enormous range of parasite life cycles and life styles. In particular, very little is known about the physical cues and the biophysical mechanisms involved in the complete infection cycle of marine parasites. Fundamental questions regarding the prevalence of parasitoids over the course of phytoplankton blooms, how they find a host to infect, and how the hosts defend against infection remain mostly unresolved.

Contact: Idan Tuval

ESR12 – Role of microflows in communities: laboratory ecology experiments

Previous work in our group has explored the interactions between two species in various contexts of host/pathogen interactions (we studied adhesion of malaria parasites to red blood cells; adhesion of bacteria to immune system cells and epithelium) and of symbiosis (bacteria/algae co-cultures). In all these systems, there are weak binding forces that are competing against shear stresses from external laminar flows (and in many cases there is actively generated micro-flows, via cilia and flagella beating). We will focus here on

bacteria/eukaryotic interactions, building laboratory communities towards model systems that correspond to two important biological situations: bacteria growing colonies adhered to epithelial cell layers; bacteria growing colonies around single cell algae.

Using new microfluidic structure designs we will test the role of external and internally generated flows on the growth of bacteria colonies, as well as environmental confinement, and investigate the inter-dependencies between the pairs of species. This understanding has general importance in both infectious disease and many ecological situations where flows exert forces that have to be overcome for cell/cell adhesion.

Contact: Pietro Cicuta

ESR13 – Transport of bacteria in disordered and complex environments

Transport of bacteria in disordered and complex environments – either by their geometry or stemming from the nature of the carrier fluid- is key to many innovative processes such as bioremediation or bacteria assisted drug delivery. In narrow biological conducts or soils, bacteria evolve in complex confined environments, leading to particularly complex and still not fully understood transport dynamics.

Contact: Anke Lindner

ESR14 – Jamming in active suspensions

The projects currently developed at the PMMH, in the “active fluids group” are oriented toward applying the concepts of “active matter” to the dynamics and hydrodynamics of bacterial populations. Active matter is a subject at the crossing point between statistical physics, hydrodynamics and biology. In this context, the group is currently assessing the swimming properties of motile bacteria exploring, individually or collectively, different controlled environmental situations. In the lab, we are using soft-lithography microfluidics to design micro- channels with different levels of geometrical complexity. Varying the chemical and the rheological properties of the suspending fluid, we currently seek to determine the emergent transport properties of a bacterial suspension and relate individual swimming properties to the large scale transport processes.

When the concentration of bacteria is large, one observes the emergence of collective motion which coincides with the appearance a “critical fluid behavior i.e. undergoing macroscopically a transition to a zero viscosity regime and also one can observe the emergence of large scale vortices spanning the size of the systems.

In this thesis project, we will seek to understand the influence of the collective effects on the transport processes and on the constitutive properties of the fluid. We will seek to investigate to which extend, “jamming” processes occurring naturally with passive particles at high concentration, would be maintained or eventually suppressed, in the case of such active suspensions flowing in various geometrical conditions, for example through porous system or constrictions.

Contact: Eric Clement

ESR153D tracking of microbes in multiple gradients

Digital Holography Microscopes (DHM) record time-sequences of the wave field transmitted through a measurement chamber. Processing of this information provides for each organism its 3D trajectory.  The objective of using DHM is to improve the understanding of the interaction between microbes and their environment: partners knowledge of 3D tracking will be shared and combined for various type of organisms and paradigms. In particular, we will use DHM in collaboration with the group of Roman Stocker (ETH) to track bacteria in 3D in order to study their response to multiple gradients by resolving for the first time the response of individual cells for long times. In nature, bacteria often encounter multiple cues simultaneously. For example, at the ocean-sediment interface gradients of oxygen and nutrients are frequent. In the body, gradients of oxygen and nutrients are similarly pervasive. The response to multiple chemicals implies the ability of bacteria to integrate their response, a topic almost entirely unexplored. The Stocker lab has developed microdevices that expose bacteria to multiple, controlled chemical gradients simultaneously. Quantification of the bacterial response, however, has faltered, due to the impossibility of tracking single bacteria for long times. DHM provides the ideal means to overcome this barrier.

Contact: Yves Emery