Numerical modeling of pressure-driven flow in a complex microfluidic-actuation network | Great project for a Design Portfolio!
Amy Herr, Professor
Bioengineering
Applications for Spring 2025 are closed for this project.
We are addressing a major blocker in microfluidic design: the macro-to-micro interface. Here, we consider how to precisely move and situation an array of single nuclei (from single mammalian cells). We have a vacuum-driven manifold that does the job, but we need to understand best operating parameters, and know that an awesome numerical simulation (e.g., Comsol) can help us do that design optimization more quickly.
Consequently, You will design and develop a numerical model and simulation framework for optimization of our vacuum-driven microfluidic system (lovingly called "VacTrap"). VacTrap is designed for high-throughput single-nucleus RNA sequencing (snRNA-seq). Briefly, we use vacuum to generate a pressure difference to drive fluids through a branching microfluidic system, ensuring uniform delivery of biological material and reagents to several hundred (or even thousands) microwells.
When you are wildly successful, you will be assisting use with the identification of ideal operating conditions, optimization of microfluidic system geometry, and prediction of the forces and time scales required to perform all stages of the study efficiently.
In this role, the selected candidate will receive one-on-one mentoring from a Visiting Professor and feedback from your BioE faculty member.
Role: Tasks & Learning Outcomes
Gain an Understanding and Design Experience with Microfluidic Systems
- Learn the principles behind vacuum-driven microfluidic systems, in a passive, branched fluidic channel network.
- Study and then tune key parameters influencing system efficiency, such as vacuum pressure, channel geometry, and flow rates.
2. Develop a Computational Model
- Use of computational fluid dynamics (CFD) software (e.g. ANSYS Fluent, COMSOL Multiphysics) to model the conditions in the VacTrap system (simulate vacuum-driven flow and analyze shear stress and flow uniformity as a function of different channel dimensions and biological samples properties).
3. Validation of Simulation with Empirical Results
- Validation & Verification of simulation results through comparison to experimental data from fluid flow in the VacTrap system. This is a key skill set for any engineering seeking to use or command simulation tools.
- While you will not be conducting wet-lab engineering research in this project, you will become quite familiar with experimental design, data analysis, and interpretation, with your mentor.
4. Documentation and Presentation of Results
- Collection and analysis of simulation data, documenting findings to improve system efficiency and design changes.
- Communication of results in a short talk and an opportunity to present research findings as a college-wide poster session. Great experience, good for feedback, and awesome on your resume.
Qualifications: Undergraduate or Master’s student in Mechanical Engineering (ME), Bioengineering (BioE), or a related field. Strong computational background and experience with computational fluid dynamics (CFD) software (e.g., ANSYS Fluent, COMSOL Multiphysics) and AutoCAD software. Desirable but not essential: knowledge of microfluidic systems, fabrication methods, and applications in biological research. Self-driven, serious, meticulous engineer with a collaborative and curious attitude.
Day-to-day supervisor for this project: Patrycja Baranowska , Post-Doc
Hours: 9-11 hrs
Related website: https://herrlab.berkeley.edu
Biological & Health Sciences Engineering, Design & Technologies