Lab Focus: Biological Engineering

Lab Website:

Project Name: Programmable Human Induced Pluripotent Stem Cells Using RNAi-based Logic Circuitry

Project Description: Synthetic biologists aim to engineer life by taking biological “parts”– for example, a protein that cleaves a specific RNA sequence, or a protein that blocks translation of a specific RNA transcript– and composing them into “circuits”. These circuits cause cells to behave differently than they would naturally. In order to design our biological circuits, we are developing modeling approaches that can be used to predict how well a potential circuit design will work in human cells. This project involves CRISPR, genome engineering, biological circuit design, mathematical modeling, and coding in MATLAB.

Weiss Lab Mentors:

Noreen Wauford – Graduate Student

Katherine Ilia – Graduate Student

Professor Roger Kamm

Lab Focus: Biological Engineering

Lab Website:

Project Name: Developing a microfluidic recirculating in vitro cell culture platform for drug screening

Project Description: Drug development has surged over the years but very few drugs reach the final approval stage. As many as 90% of drugs have failed in clinical trials, showcasing the need for a better early-stage drug screening platform. Organ-on-a-chip technology is a promising avenue for studies such as drug screening but it currently lacks enough physiological relevance. The development of a fluid recirculating system will enable long term cell culture of these microphysiological systems under forces and flows similar to those found in the body. The student will be introduced to several techniques including microfluidic device fabrication, CAD/CAM, numerical simulations, cell culture, immunostaining, and fluorescent microscopy.

Kamm Lab Mentors:

Marie Anna Floryan – Graduate Student (Mechanical engineering, device design, cancer)

Georgios Pavlou – Post Doc (Bioengineering, Neurological disease models )

Professor Mathias Kolle

Lab Focus: Mechanical Engineering

Lab Website:

Project Name: Musical color synesthesia: a touch-responsive, bio-inspired, photonic synthesizer

Project Description:

Standard musical synthesizers rely on translating a user’s selection of button states and lever positions into the amplification of selected acoustic frequency bands and sound signatures to create a desired audio signal. Typically, synthesizers look very technical, clunky and at best have a nerdy, engineered aesthetic. By contrast, notable efforts in the arts have long explored the relations between musical signals and colors; some humans even have the sensory ability to couple sound signals directly to visual perception, sensing sounds as swirls of color, a condition that is called synesthesia. In this project, we aim to explore a technological approach to generate a tighter coupling between visual input stimuli and acoustic responses, translating colors directly into music with the aid of a new “magical” material that changes color, when it is deformed (a bit like a cuttlefish, when you cuddle it too tightly). Combined with an imaging sensor that in real-time captures color patterns generated by a user via local mechanical perturbations of the material (for instance achieved by pushing a finger into it) and computational infrastructure that associates the detected patterns with specific sound features, this material forms the foundation for a musical color synthesizer. We anticipate that the proposed opto-acoustic device will allow artists and users far greater freedom in expressing their creativity than anything that’s currently available as synthesizer technology. Frankly, once this sense-bridging gem has been built

Kolle Laboratory Mentors:

Benjamin Miller – PhD Candidate

Hannah Feldstein – Graduate Student

Professor Asegun Henry

Lab Focus: Mechanical Engineering

Lab Website:

Project Name: Sonification of the Periodic Table

Project Description: Atomic vibrations are present at any temperature above 0K. These atomic vibrations are unique to any material and they determine many of their properties. For decades, researchers have studies the vibration of atoms by making frequency dependent plots out of them. In this project, our focus will be to sonify these atomic vibrations and for the first make them audible to human ear. The ultimate goal will be to study the correlation between the generated sounds from each material and the properties that the material exhibits. After generating the sounds for all the elements in the periodic table, and making a website for these generated sounds, which will be accessible in our group website soon, we will focus on the following goal for the remaining of the project:

Henry Lab Mentors:

Kiarash Gordiz – PhD

Andrew Rohskopf – PhD Candidate

Professor Ming Guo 

Lab Focus: Mechanical Engineering

Lab Website:

Project Name: Geometric features of cells on a sphere

Project Description:

There are many beautiful geometries that we can find in nature, such as the spiral on shells, the hexagons in honeycomb etc. These structures are initially formed by cells migrating and packing in a nicely organized way. Indeed, when we grow many cells to form a layer on a spherical surface, the cells also exist unique cell shape distributions. Are you interested to know why they naturally self-organize into well-regulated geometries? In this one-year-long project, we are going to specifically focus on the geometric features of cells growing on a spherical surface and to study how the cell shape plays a role in regulating different cell migratory behaviors. For example, when one cell divides into two cells, the cell shape defined by the number of neighbor cells actively changes that affect how they move. Furthermore, we are interested to study how cell shape changes as sphere curvature changes. In the end, this study will provide an understanding of the relation between cell geometric feature and physiological processes.

Guo Lab Mentors:

Yu Long Han – PhD

Wenhui Tang – PhD Candidate

Professor Alex Shalek

Lab Focus: Biological Engineering

Lab Website:

Project Description: Single-cell RNA sequencing is a technique that scientists use to identify cell types in the body and understand how they work. For example, single-cell RNA sequencing can help define the molecular differences between a muscle cell and a skin cell. In the Shalek lab’s Summer 2020 project, we will use chemistry to invent more advanced methods for single-cell RNA sequencing.

Shalek Lab Mentors:

Samuel Jonathan Allon – PhD Candidate

Mike Vilme

Professor Wim van Rees

Lab Focus: Computational Applied Science & Engineering

Lab Website:

Project Title: Flow trapping with a cylinder pair at low Reynolds numbers

Project Description: Flow trapping in a highly viscous fluid (i.e, low Reynolds flows) is of interest for both fundamental science and applied engineering. For example, in certain studies of biological cells, capturing the target cells is often a crucial step in experiments. Meanwhile, filtration and transportation of particles in solutions also require efficient flow trapping methods. In this project we intend to numerically study a pair of rotating bodies as a flow trapping device using MATLAB. We will start with simulating a pair of rotating cylinders in two dimensional flows at low Reynolds numbers and then carry the study over to a pair of spheres or spheroids in three dimensions. We intend to find out the flow patterns and trapping efficiencies for such devices. Further, we could also consider controlling these devices with a reinforcement learning algorithm. This will enable the pair of cylinders or spheres to dynamically adjust their rotation rates depending on the concentration fields or density of particles to be filtered in the surrounding fluids. Overall, this project will involve learning fluid mechanics and numerical methods at low Reynolds numbers.

Van Rees Lab Mentors:

Lingbo Ji – Graduate Student

Xinjie Ji – Graduate Student

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