Master projects available in the Stocker lab

Tomographic imaging of Diatoms using digital holographic microscopy

An important group of unicellular organisms in the oceans are diatoms, ubiquitous photosynthetic eukaryotes. Diatoms are at the base of marine food webs carrying out ~20% of the yearly photosynthesis on Earth[1]. They are responsible for the conversion of large amounts of inorganic carbon into organic matter, serving as food for many other marine organisms.

Based on recent work [2]–[5], we want to use a Digital holographic camera attached to an inverted microscope(available in the lab) to image singular living diatoms in high temporal (on the order of minutes) and spatial resolution (on the order of microns) and investigate the topics listed below. Digital Holography Microscopy (DHM) quantifies the optical path difference of a sample compared to the surrounding media based on refractive index differences and allows the extraction of density and dry mass measurements. Figure 1 shows how QPI allows the measurement and tomographic reconstruction of chloroplasts in a T.rotula cell. The eight chloroplasts (shown in red) are detected based on their refractive index differences compare to the rest of the cell, their volume can be extracted (V_chl) and their 3D position within the cell can be determined.

We aim at developing a new method to visualize and track subcellular structures such as organelles in 3-D in single-cell diatoms. The diatoms might be fixed at the end of a glass capillary, inside a capillary, or rotated by flow to extract a full 3D scan of cells. (see [2]). The target is to image Thalassiosira pseudonana, Thalassiosira rotula, and Ditylum brightwellii.

A prospective student will develop the tomographic imaging setup in the lab, automating the image acquisition and the tomographic reconstruction. By staining different organelles and using fluorescent imaging, we will establish protocols how to image and differentiate the various organelles.

You can do this project as a semester or master thesis. The scope of the project will vary accordingly.

For more information, please see here or contact Dieter Baumgartner (baumgartner@ifu.baug.ethz.ch) or Oliver Müller (mueller@ifu.baug.ethz.ch).

Impact of chemokinesis on bacteria-particle encounters

Processes controlling biogeochemical cycles are characterized by tight interactions between recycling organisms and their substrate and are therefore highly dependent on encounters between the organisms and the substrate. For example, the encounter rate between marine bacteria and sinking particles of organic matter in the ocean is of particular importance for the ocean carbon cycle. Bacteria are responsible for recycling of 50 Gt of particulate organic carbon in the ocean every year, leaving behind only 1% of the particles that sink and reach the oceans’ sediment where they remain buried and stored for millennia. To enhance particle consumption in the ocean, bacteria evolved a sophisticated toolbox, which includes hydrolytic enzymes, attachment appendages and chemokinesis (i.e. the ability of bacteria to increase their swimming speed in response to high nutrient levels). Yet, the ability of bacteria to sense plumes in the wakes of sinking particles that leak organic matter and use them to increase their encounters and therefore the consumption of organic particles requires further investigation (illustration below).

FigVision

In this thesis, the student will explore the response of bacteria exposed to chemical plumes generated in a controlled manner in a microfluidic device with the goal to evaluate if chemokinetic behavior can increase the encounter rate between bacteria and leaky sinking particles. The student will also use an existing bacteria-particle encounter model to explore the parameter space beyond the experimentally accessible range.

During the project, the student will learn how to culture bacteria, analyze their motile behavior, build microfluidic devices, master imaging techniques, and rationalize experimental observations with a model.

Knowledge of Matlab is recommended but not required.

The thesis will be supervised by Dr. Uria Alcolombri, Dr. Jonasz Słomka and Prof. Roman Stocker.
For more information, please contact Dr. Uria Alcolombri (alcolombri@ifu.baug.ethz.ch) or Dr. Jonasz Słomka (slomka@ifu.baug.ethz.ch).

Assessing groundwater–river interaction at the Kappelen experimental site

Most quaternary aquifers in the Swiss Plateau are in dynamic interaction with a river. In losing stream sections, river water passes through the ecologically relevant hyporheic zone and infiltrates into the underground, where it eventually reaches the saturated zone. In gaining stream sections, on the other hand, groundwater exfiltrates into the river and becomes surface water. The exchange between surface water and groundwater is typically highly dynamic. As a consequence, contamination of either resource threatens the quality of the other. Adequate characterization of river–aquifer interaction is thus paramount, in particular for the planning and management of well protection zones.

The aim of the proposed Master thesis is the characterization of the river–aquifer interaction near the Kappelen (BE) well field using hydraulic (water levels) and chemical indicators, and by numerical modelling at different scales. The student will, supported by LUIW, complement the existing sensor network of the IfU groundwater field lab by installing two piezometers near the Alte Aare River and equip them with pressure sensors. A third sensor will be installed within the river. Based on existing datasets and measures collected during the project, the river–aquifer interaction will be modelled using state-of-the-art groundwater modelling software. In addition to characterizing the river–aquifer interaction, the following questions will be addressed:

  • What are the advantages and disadvantages of using river discharge measurements as opposed to measurements of water chemistry in the river and in the aquifer for the characterization of the river–aquifer interaction?
  • How does model resolution impact the simulated river–aquifer interaction, and what recommendations can be given to applied groundwater modelers for implementing river–aquifer interaction in regional groundwater models?

The student will have the opportunity to perform Acoustic Doppler Current Profiler (ADCP) measurements in the Alte Aare River, install and equip piezometers, refine their understanding of river–aquifer interaction and develop their applied groundwater modelling capacity.

The thesis will be supervised by Dr. Beatrice Marti, Dr. Marius Floriancic, Dr. Joaquin Jimenez-Martinez and Prof. Roman Stocker.

For more information, please contact Beatrice Marti (martib@ethz.ch)

Mimicking capillary fringe dynamics in a microfluidic chip to study the impact on biofilm formation

The shallow subsurface is a highly fluctuating environment with regard to phase saturation (i.e., air and water content) and hydrodynamic conditions (such as fluid flow velocities and the presence of multiphase flow). Events such as rainfall or irrigation and processes of infiltration, evaporation and groundwater level fluctuation can lead to a transient change in the velocities and phase saturation in the pore space. The capillary fringe lies at the interface between the vadose zone (partially saturated in water) and the saturated zone, and its position is highly dependent upon fluctuations of the groundwater level. Shifting saturation in this zone is also responsible for varying physicochemical conditions. This fluctuating interface has been shown to be a hotspot of biogeochemical activity. The local microbial community is often found living as biofilms (i.e., multicellular aggregates within an extracellular matrix), which are crucial for their survival in this complex environment. The impact of wetting and drying cycles associated with capillary fringe movement on biofilm development, and therefore on the biogeochemical cycles that they influence, is a current matter of debate.

The aim of the proposed Masters project is to develop a method to mimic capillary fringe dynamics. Microfluidics represents an extremely powerful tool to study these interactions at laboratory scale, offering the ability to precisely control fluid flow and mimic natural micro-environmental conditions, while allowing optical access to observe and quantify the interactions at high spatial and temporal resolution. The project will include development of an experimental system including a microfluidic porous medium allowing reproducible imbibition and drainage cycles as well as bacterial growth. In addition to development of the device, the project has the following aims:

  1. Hydraulic characterization, including water saturation and pressure profiles;
  2. Characterization of the flow field;
  3. Optimization of imbibition and drainage cycles to allow observations on timescales relevant for biofilm development.

The student will have the opportunity to gain experience in microfluidic methods and the use of image analysis tools.

For more information, please contact Dorothee Kurz (dkurz@ethz.ch) or Joaquin Jimenez-Martinez (jjimenez@ethz.ch).

Hydraulic resistance of membrane biofilms: effect of extracellular polymeric substances

Bacteria inevitably colonize membrane filtration systems to form biofilms. These biofilms on membrane surfaces reduce permeate flux due to the increased hydraulic resistance, but practical experience indicates that avoiding their formation is almost impossible. Eawag has thus developed a new paradigm for the operation of membrane systems, which consists in taking advantage of biofilms formed on membrane surfaces to assist in the control of both the quantity and quality of the permeate.

The main objective of the proposed master thesis is thus to identify the causal link between the EPS composition (especially bacterial cells and polysaccharides) and the hydraulic resistance of membrane biofilms. Usually, the main challenge in determining the causality of this relationship results from the complex composition of the EPS matrix of natural biofilms. We thus propose to use Bacillus subtilis, a model organism, to study biofilm formation on membrane surfaces and to understand the effect on filtration performance. The use of model organisms allows the formation of model biofilms with a controlled composition, a crucial resource in determining the link between chemical composition and mechanical properties of the biofilm.

This master thesis is a joint project between the groundwater and hydromechanics laboratories of ETHZ (Prof. R. Stocker) and Eawag (Prof. E. Morgenroth), and will mainly be conducted at ETHZ.

For more information, please contact Eleonora Secchi (secchi@ifu.baug.ethz.ch) or Nicolas Derlon (nicolas.derlon@eawag.ch).

 

Improving pipe-flow measurements with CFD calculations

Measuring water- and air-flow are key techniques for control and monitoring of environmental applications such as wastewater treatment plants or incineration plants. Although there are a variety of measurement techniques available, in practice many of these have poor to very poor accuracy. The main reason is that the most commonly used techniques for flow sensors only measure intensive parameters such as flow velocity, differential pressure or water level. As a consequence, the flow is calculated with a function that translates the intensive variable into flow. However, for the determination of this function it is important that the precise flow conditions are known, which is rarely the case. Most of the work to connect the intensive parameters to the flow was conducted between the 1930s and the early 2000s, and there are very few professional engineers nowadays with a deep understanding of the applied models.

New sensors with very high accuracy and the availability of computational fluid dynamic (CFD) calculations promise significant improvements in the precision and accuracy of pipe flow measurements.
In this project, the student will carry out:

  • Systematic calculations of pressure loss using the Darcy Weisbach equation;
  • Dimensioning of pipe flow measurements with standard methods for different flow sensors;
  • Modelling of pipe flow using CFD calculations;
  • Comparison of the results with calibration functions in the literature;
  • Optimization of sensor position and calibration for non-standard flow conditions;
  • Verification of the suggestions based on CFD calculations against field measurements;
  • Exclusion of potential error sources (e.g., sound waves).

Knowledge of a programming language (Matlab, Python) is required, and some knowledge of CFD calculations (Comsol) would be an advantage.

The project will be carried out under the supervision of Daniel Braun (Leiter Labor für Umweltingenieurwissenschaften), Professor R. Stocker, M. Hull (Product manager thermal flow measurements, Endress & Hauser), and Dr. M. Gresch (Hunziker-Betatech).

For more information, please contact Daniel Braun (braun@stab.baug.ethz.ch).

Improving open-channel flow measurements with CFD calculations

Measuring water flow in open channels is a key technique for monitoring and control of sewers and wastewater treatment plants, as well as continuous measurements of the runoff of rivers. Although there are a variety of measurement techniques available, in practice many of these have poor accuracy. The main reason is that the most commonly used techniques for flow sensors only measure intensive parameters such as flow velocity, differential pressure or water level. As a consequence, the flow is calculated with a function that translates the intensive variable into flow. However, for the determination of this function it is important that the precise flow conditions are known, which is rarely the case. Most of the work to connect the intensive parameters to the flow was conducted between the 1930s and the early 2000s, and there are very few professional engineers nowadays with a deep understanding of the applied models.

There are a variety of new sensors available that have very high accuracy and can measure multiple parameters. In addition, computational fluid dynamic (CFD) calculations promise significant improvements in precision and accuracy of open-channel flow measurements.
In this project, the student will:

  • Study the theory behind typical semi-empirical models, such as the Gauckler-Manning-Strickler equation, the Poleni equation and for venturi flumes;
  • Study the most commonly used measurement principles, such as venturi flume, ultrasonic flow meter, and ADCP;
  • Model open channel flow with CFD calculations;
  • Compare the results of CFD calculations with calibration functions in the literature;
  • Optimize sensor position and calibration for non-standard flow conditions;
  • Verify the suggestions based on CFD calculations with field measurements.

Knowledge of a programming language (Matlab, Python) is required, and some knowledge of CFD calculations (Comsol) would be an advantage.

The project will be carried out under the supervision of Daniel Braun (Leiter Labor für Umweltingenieurwissenschaften), Dr. M. Gresch (Geschäftsleitung Hunziker-Betatech), Professor R. Stocker, and Dr. B. Lüthi (Geschäftsführer Photrack AG).

For more information, please contact Daniel Braun (braun@stab.baug.ethz.ch).