BioDate 2023: 13 interdisciplinary MSc projects supported with 2,5k
In May 2023, Delft Bioengineering Institute organized the fifth edition of BioDate: the ‘speed date’ event where BEI PIs can meet and explore possibilities for collaboration. This year, the participating PIs have generated thirteen new interdisciplinary MSc projects! Three of the teams have already recruited a student for the project, the others will hopefully follow soon, so BEI can transfer the grant money of €2500 and the projects can start.
MSc Project | Supervisor #1 | Supervisor #2 | Student |
Sophinese Iskander-Rizk (3mE/PME) | Behrooz Fereidoonnezhad (3mE/BME) | To be recruited | |
Yanki Aslan (EWI/ME) | Jie Zhou (3mE/BME) | To be recruited (2 students) | |
Jovana Jovanova (3mE/MTT) | Joana Martins (IO/SDE) | To be recruited | |
Microfluidic downscaling for assessment of cell performance in dynamic environments | Cees Haringa (TNW/BT) | Volkert van Steijn (TNW/ChemE) | To be recruited |
Toward implantable and wearable devices capable of molecule detection | Filipe Cardoso (EWI/ME) | Baris Kumru (LR/ASM) | Amar Zouboye (MSc Biomedical Engineering) |
Havva Yoldas (EWI/DIAM) | Selene Pirola (3mE/BME) | To be recruited | |
Analysis of pattern formation in multi-species microbial aggregates | Havva Yoldaş (EWI/ DIAM) | Rebeca Gonzalez Cabaleiro (TNW/BT) | To be recruited |
Comparing omics techniques for predicting what your gut-bacteria can do | Thomas Abeel (EWI/INSY) | Mark van Loosdrecht (TNW/BT) | Bianca-Maria Cosma (MSc Computer Science – Bioinformatics) |
Smart super-resolution microscopy data acquisition using Deep Learning | Kristin Grußmayer (TNW/BN) | Nergis Tomen (EWI/INSY) | Gijs Schouw (MSc Applied Physics) |
Understanding the genetic network that governs the evolution of yeast | Liedewij Laan (TNW/BN) | Johan Dubbeldam (EWI) | To be recruited |
3D printing calcified arteries to understand blood flow dynamics in the brain | Selene Pirola (3mE/BME) | Kunal Masania (LR/ASM) | To be recruited |
>> Characterizing blood clots using photoacoustic imaging
Blood clots play a crucial role in several vascular diseases such as strokes. The exact composition of blood clots varies from patient to patient, and it is important that the doctors are aware of the specific properties in order to plan the best treatment for their patient. However, there is no method yet to obtain such detailed information on blood clots in a living patient. In this master thesis project, Sophinese Iskander-Rizk (3mE/PME) and Behrooz Fereidoonnezhad (3mE/BME) will supervise a student who will contribute to provide a proof-of-concept for characterization of blood clot composition, microstructure and mechanical properties by using photoacoustic imaging techniques.
Project: Characterization of tissue microstructure by photoacoustic imaging
Supervisors: Sophinese Iskander-Rizk (3mE/PME) and Behrooz Fereidoonnezhad (3mE/BME)
Student: to be recruited
>> Detecting infections in patients using implantable antennas
The lives of millions of patients are at risk every year due to surgical site infections. Only when visible signs appear, such as fever, pain or swelling, the complications are detected. Late treatment with antibiotics causes resistance of bacteria, thereby raising postoperative morbidity and mortality, and the associated healthcare costs increase substantially. Therefore, it is important to detect, track, and immediately react to post-surgical infections. In this double master thesis project, supervisors Yanki Aslan (EWI/ME), Jie Zhou (3mE/BME) and Clementine Boutry (EWI/ME) combine their expertise on materials, electronics and wireless operation to address two major challenges: detecting and tracking the degradation of the implant embedded deep inside the tissue, causing local pH changes, and the complex correlation between the implant degradation and the surrounding pH changes related to infection.
Project: DegRadar: Real-time RADAR Sensing of BioDEGRADABLE Implant Antennas for Infection Detection (two projects)
Supervisors: Yanki Aslan (EWI/ME), Jie Zhou (3mE/BME) and Clementine Boutry (EWI/ME)
Students: to be recruited
>> Exploring living materials for offshore industry
Climate change is threatening the health and sustainability of the world’s oceans through the rising of CO2 levels and ocean acidification. In order to preserve marine ecosystems, we need to find innovative solutions for this problem. Microbial biomineralization may offer a promising solution aiming at reducing the impacts of climate change, through its application in the production of more durable and sustainable materials. In this project, microbiologist Joana Martins (IO/SDE) and mechanical engineer Jovana Jovanova (3mE/MTT) combine their expertise to explore the potential of biomineralized materials for offshore applications. Under their supervision, a master’s student will integrate biology, design and engineering in order to develop a novel metamaterial with unique qualities to reduce environmental impact.
Project: Cyanobacterial Biomineralized Materials for Offshore Structures
Supervisors: Jovana Jovanova (3mE/MTT) and Joana Martins (IO/SDE)
Student: to be recruited
>> Microfluidic downscaling for assessment of cell performance in dynamic environments
While bioprocesses are rising in popularity as a production method for materials, scale-up of bioprocesses to enable large-scale production remains difficult. One of the main challenges is the emergence of highly dynamic cellular environments, with unforeseen impacts on cell performance. Microfluidic scale-down simulators are a promising approach to collect the data regarding cell-environment and cell-cell interactions that are needed for building numerical models that can mitigate scale-up risks. But current systems do not allow for amplitude control, and culture monitoring options are limited. Therefore, within this master thesis project, supervisors Cees Haringa (TNW/BT), Volkert van Steijn (TNW/ChemE) and Rinke van Tatenhove-Pel (TNW/BT) aim to create and characterize an improved scale-down system, and for the first time quantify the impact of rapid, continuous variations on cellular growth on a single-cell level.
Project: μWAVE: Microfluidic downscaling for assessment of cell performance in dynamic environments
Supervisors: Cees Haringa (TNW/BT), Volkert van Steijn (TNW/ChemE) and Rinke van Tatenhove-Pel (TNW/BT)
Student: to be recruited
>> Toward implantable and wearable devices capable of molecule detection
Wearable devices and implants for real-time monitoring have emerged as revolutionary technologies with the potential to transform healthcare and enhance individual well-being. However, only a few recently developed technologies allow real-time molecular detection at the wearable or implantable level (e.g., glucose monitoring). Especially in implants, real-time molecule detection relies on label-free strategies. These strategies usually lack specificity and reasonable detection limits because they measure physical characteristics common to several molecules. Also, non-specific molecules or cells in the environment may hinder the molecule of interest from reaching the sensor. In this master thesis project, Biomedical Engineering MSc student Amar Zouboye will work on tackling those problems. The expertise of supervisors Filipe Cardoso (EWI/ME) and Baris Kumru (LR/ASM) in biosensors and hydrogels, respectively, will help make the project a success.
Project: Hydrogel sensing layers for implantable and wearable devices
Supervisors: Filipe Cardoso (EWI/ME) and Baris Kumru (LR/ASM)
Student: Amar Zouboye (MSc Biomedical Engineering)
>> A new computational model to study vascular calcification
Vascular calcification is the abnormal build-up of calcium in the walls of arteries, leading to disrupted blood flow by hardening and narrowing them. Understanding arterial calcification and its systemic effects on blood flow is crucial for maintaining cardiovascular health. To study local and systemic perturbations in blood flow caused by calcified vessel walls, vascular 1D Reduced Order Models (ROMs) offer a computationally efficient solution. However, they do not allow to capture in detail the geometrical complexity of calcific lesions. In this project, Havva Yoldas (EWI/DIAM) and Selene Pirola (3mE/BME) will supervise a student who will pioneer a novel 2D ROM that effectively captures both geometric detail and vessel properties, while maintaining computational efficiency for analysing organ-level hemodynamic phenomena.
Project: Reduced order modelling of calcified vascular networks
Supervisors: Havva Yoldas (EWI/DIAM) and Selene Pirola (3mE/BME)
Student: to be recruited
>> Analysis of pattern formation in multi-species microbial aggregates
In multi-species microbial communities, the ecological interactions between different species lead to spatial segregation in aggregates such as granules and biofilms. To gain a comprehensive understanding of this complex process and control over the formation of microbial aggregates, it is necessary to study the principles governing the interactions between microorganisms, their environment and spatial arrangement. In this MSc project, supervisors Havva Yoldaş (EWI/DIAM) and Rebeca Gonzalez Cabaleiro (TNW/BT) will join their forces so that a student with a strong background in applied mathematics and an interest in interdisciplinary research can analyse mathematical the formation of specific spatial patterns that have been in silico predicted for multispecies microbial aggregates.
Project: Analysis of pattern formation in multi-species microbial aggregates
Supervisors: Havva Yoldaş (EWI/ DIAM) and Rebeca Gonzalez Cabaleiro (TNW/BT)
Student: to be recruited
>> Comparing omics techniques for predicting what your gut-bacteria can do
By identifying the bacteria present in a person’s intestinal tract and understanding their capabilities, we can predict conditions from cancer to metabolic and neurological disorders. Using modern techniques, we can analyze their presence and functionality at various molecular levels. For instance, metagenomics can be used at the DNA level, metaproteomics at the protein level, and metabolomics at the metabolic level. In this project, Thomas Abeel (EWI/INSY) and Mark van Loosdrecht (TNW/BT) join forces to supervise MSc Computer Science – Bioinformatics student Bianca-Maria Cosma in her master’s thesis project. This project aims to evaluate the effectiveness and accuracy of predicting the molecular activity of specific bacterial species on the protein and metabolic level in the gut microbiome of humans by metagenomics, a DNA-level omic technique. This will pave the way for revolutionizing the analysis of microbiomes and for more cost-effective and comprehensive investigations.
Project: Comparative Analysis of Omics Techniques for Predicting Microbiome Functional Potential in Complex Systems
Supervisors: Thomas Abeel (EWI/INSY) and Mark van Loosdrecht (TNW/BT)
Student: Bianca-Maria Cosma (MSc Computer Science – Bioinformatics)
>> Smart super-resolution microscopy data acquisition using Deep Learning
Fluorescence microscopy has significantly contributed to our understanding of cellular processes in recent decades, and the development of advanced super-resolution microscopy techniques has allowed for the examination of cellular structures at the nanoscale. However, molecular insights obtained through a single super-resolution imaging method are still limited, mainly due to trade-offs between temporal and spatial resolution and manual microscope operation, leading to low throughput. In this master thesis project, super-resolution microscopy expert Kristin Grußmayer (TNW/BN) and computer vision specialist Nergis Tomen (EWI/INSY) will join forces and supervise MSc Applied Physics student Gijs Schouw, who will take on one of the specific challenges in this field: working on a universally applicable, objective method to determine the optimal density of emitters for achieving the best imaging results. Gijs will learn to execute state-of-the-art super-resolution microscopy experiments and gain more insight on deep learning methods and vision transformers for biomedical imaging.
Project: Smart Super-resolution Microscopy Data Acquisition Using Deep Learning
Supervisors: Kristin Grußmayer (TNW/BN) and Nergis Tomen (EWI/INSY)
Student: Gijs Schouw (MSc Applied Physics)
>> Understanding the genetic network that governs the evolution of yeast
In order to understand the evolution of cellular functions in budding yeast, S. cerevisiae, it is essential to better understand the genetic network that governs this process. For example, we would like to know which genes are important for developing different pathways to polarization and budding in yeast. In this master thesis project, Liedewij Laan (TNW/BN) and Johan Dubbeldam (EWI) will supervise a student who will combine methods from network science and nanobiology to make progress in the understanding and prediction of such genes.
Project: Using methods of complex network theory to understand fitness changes in genes between different yeast mutants
Supervisors: Liedewij Laan (TNW/BN) and Johan Dubbeldam (EWI)
Student: to be recruited
>> 3D printing calcified arteries to understand blood flow dynamics in the brain
Calcification in arterial walls and cerebrovascular disease leading to cognitive impairment and dementia are closely connected, possibly because of the changes in the blood flow dynamics in the brain. However, since it is very difficult to investigate brain blood flow dynamics in a living person, we do not know exactly how this works. Replications of a patient’s brain vasculature known as ‘phantoms’ are important tools for studying and understanding the complexities of blood flow dynamics. However, existing phantoms fail to capture the intricate mechanical behaviour of the vasculature. Therefore, in this master thesis project, Selene Pirola (3mE/BME), Kunal Masania (LR/ASM) and Behrooz Fereidoonnezhad (3mE/BME) will join forces to supervise a student who will develop a novel methodology to 3D print patient-specific brain artery phantoms that closely mimic the properties of the real brain vasculature affected by calcification.
Project: 3D Printing of Calcified Brain Vasculature Phantoms
Supervisors: Selene Pirola (3mE/BME), Kunal Masania (LR/ASM) and Behrooz Fereidoonnezhad (3mE/BME)
Student: to be recruited