We seek to modify the deformation characteristics of bone through a pharmacological treatment. This project would demonstrate such a concept using animal bone. Treated and untreated bone will be made available for the interrogation of bone by x-rays. Students will be engaged in the data interpretation of x-ray scattering experiments on bone, not subjected to mechanical loads or subjected to mechanical loads.

Biological Characterization and Imaging, Biological Simulation and Technology, Material Modeling and Simulation, Material Processing and Characterization, Other

• Materials Engineering
• Mechanical Engineering
• Biomedical Engineering

Materials Characterization, X-ray techniques; Experience in lab work

School of Mechanical Engineering

Thomas Siegmund

Cell migration plays an important role in physiology and pathophysiology. Migrating cells are able to sense surrounding mechanical environments. For example, a number of experiments have demonstrated that nano- and micro-patterns can guide migration of cells. This migratory behavior is called the contact guidance and is of great importance in various physiological processes, such as cancer metastasis. In this research project, we aim to use a rigorous computational model and collaborate with experimentalists in order to investigate intrinsic mechanisms of the contact guidance. A participating student will run computer simulations and analyze data from the simulations to perform the research. If necessary, everything for this project can be done remotely.

Biological Simulation and Technology, Cellular Biology

• Mechanical Engineering
• Biomedical Engineering
• Biological Engineering - multiple concentrations
• Computer Engineering

Intermediate/Proficient C coding skills Sufficient experiences in MATLAB coding Basic knowledge of cell biology (optional)

Weldon School of Biomedical Engineering

Taeyoon Kim

Neurons convert biochemical information (through binding of a neurotransmitter) to electrical signal (via action potential) and back to biochemical signal (through the release of neurotransmitters). These distinct and separable processes can be reconstituted in a synthetic neuron by using natural and engineered proteins, and a synthetic neuron platform can be used to understand the rules governing the emergence of the present morphology of a neuron and the architecture of the neuronal system. This project thus aims to construct a synthetic neuron with a modular design and a programmable synthetic neuronal network capable of recapitulating basic functions of a natural neuronal system (e.g., action potential, synaptic communication, and basic computation) and with a long-term vision of incorporating more advanced computation and potentiation.

Biological Characterization and Imaging, Biological Simulation and Technology, Cellular Biology

• Chemical Engineering
• Biological Engineering - multiple concentrations
• Biomedical Engineering
• Neurobiology and Physiology

Chemical Engineering

Chongli Yuan

Spinal cord injury is a significant human health problem affecting about 300,000 people in the US. Better treatment options are needed to overcome the limited regeneration potential of the human spinal cord. Zebrafish larvae are an emerging model system for drug screening for several reasons including large number of embryos per breeding, genetics, and availability of behavioral assays for drug testing. Our lab is conducting a large scale drug screen with an FDA-approved library to identify novel compounds that enhance functional recovery following injury as assessed by a swimming assay. The student will be involved with fish breeding, spinal cord injury, drug treatment, and behavioral assay. We hope that this work will identify new compounds with translational potential.

Biological Characterization and Imaging, Biological Simulation and Technology, Cellular Biology, Medical Science and Technology

• Biology
• Cell Molecular and Developmental Biology
• Biochemistry
• Neurobiology and Physiology
• Genetics
• Microbiology

Cell Biology, Neurobiology, fine motor skills, working with zebrafish

Biological Sciences

Daniel Suter

EMBRIO

Biological Characterization and Imaging, Biological Simulation and Technology

• No Major Restriction

BIOL

Janice Evans

From leopards to fish, many animals sport patterns (like stripes or spots) on their bodies. My group takes a mathematical approach to understand how patterns form in the skin of zebrafish, which are small striped with important biomedical applications. Zebrafish development takes months, but simulating pattern formation takes minutes. In this project, I will mentor a student in building image-processing software to make simulated zebrafish patterns look more like real fish.

Big Data/Machine Learning, Biological Characterization and Imaging, Biological Simulation and Technology, Cellular Biology

• Mathematics
• Computer Science
• Biomedical Engineering
• Biological Engineering - multiple concentrations
• Engineering (First Year)
• Agricultural Engineering

Good team members who are excited about interdisciplinary research, have taken a course in linear algebra, and have strong programming skills.

Mathematics

Alexandria Volkening

Infectious diseases are a leading cause of economic burden on food production from animals. For example, bovine respiratory disease leads to a loss of ~$1 billion annually. Current methods for tackling these diseases includes the administration of antibiotics by trial-and-error. This approach leads to failure of treatment in up to one-third of the cases. In addition, it also leads to a proliferation of antibiotic resistance in pathogens.
Our research project focuses on developing a low-cost user-friendly biosensor based on paper that can detect which pathogen is causing the disease and whether it exhibits antibiotic resistance. Such a biosensor would provide a readout to the farmer or the veterinary physician and suggest which antibiotics are likely to be successful.
Lab members working in the team have three objectives: i) design, test, and optimize primers for detecting pathogens and genes associated with bovine respiratory diseases, ii) build and field-test a paper-based device for conducting loop-mediated isothermal amplification, and iii) build and field-test a heating/imaging device for conducting the paper-based assay in the field.
The SURF student will work on one of the objectives depending on their background and experience.

Biological Simulation and Technology, IoT for Precision Agriculture

• Biochemistry
• Biological Engineering - multiple concentrations
• Biomedical Engineering
• Agricultural Engineering
• Mechanical Engineering
• Electrical Engineering

Relevant skills for the project: • Wet lab skills and experience with molecular biology • Autodesk Fusion 360 for 3D Modeling/Printing and Laser Cutting • Python Programming Language for image processing and graphical user-interface using Raspberry Pi (or any other single board computer) To be successful at this position, you should have a GPA>3.5, prior experience working in a lab, and the ability to work in a team.

Agricultural and Biological Engineering

Mohit Verma

The increasing worldwide demand for vaccines along with the intensifying economic pressure on health care systems underlines the need for further improvement of vaccine manufacturing. In addition, regulatory authorities are encouraging investment in continuous manufacturing process to ensure robust production, avoid shortages, and ultimately lower the cost of medications for patients. The limitations of in-line process analytical tools are a serious drawback of the efforts taken in place. In line analysis of viral particles are very limited, due to the large time required for the current techniques for detection, qualitative and quantitative analysis. Therefore, there is a need for new process analytical technology. This project has both experimental and computation components and two students will be recruited for perform different tasks. The student focusing on experiments will fabricate devices and test them. The student focusing on computations will focus on developing machine learning codes.

Big Data/Machine Learning, Biological Characterization and Imaging, Biological Simulation and Technology, Biotechnology Data Insights, Cellular Biology, Computer Architecture, Deep Learning

• No Major Restriction

For the experimental portion of the project: fabrication, cell culture, microfluidics, microscopy For the computational portion of the project: Coding, Python

Mechanical Engineering

Arezoo Ardekani

Cancer is a major threat for humans worldwide, with over 18 million new cases and 9.6 million cancer-related deaths in 2019. Although most common cancer treatments include surgery, chemotherapy, and radiotherapy, unsatisfactory cure rates require new therapeutic approaches. Recently, adoptive cellular immunotherapies with chimeric antigen receptor (CAR) engineered T and natural killer (NK) cells have shown impressive clinical responses in patients with various blood and solid cancers. However, current clinical practices are limited by the need of large numbers of healthy immune cells, resistance to gene editing, lack of in vivo persistence, and a burdensome manufacturing strategy that requires donor cell extraction, modulation, expansion, and re-introduction per each patient. The ability to generate universally histocompatible and
genetically-enhanced immune cells from continuously renewable human pluripotent stem cell (hPSC) lines offers the potential to develop a true off-the-shelf cellular immunotherapy. While functional CAR-T and NK cells have been successfully derived from hPSCs, a significant gap remains in the scalability, time-consuming (5 or more weeks), purity and robustness of the differentiation methods due to the cumbersome use of serum, and/or feeder cells, which will incur potential risk for contamination and may cause batch-dependency in the treatment. This project thus aims to develop a novel, chemically-defined platform for robust production of CAR-T and CAR-NK cells from hPSCs.

Biological Characterization and Imaging, Biological Simulation and Technology, Cellular Biology, Genetics, Medical Science and Technology

• No Major Restriction
• Chemical Engineering
• Biological Engineering - multiple concentrations
• Biochemistry
• any related major

Previous experience with cell culture and molecular biology is a bonus, but NOT required.

Davidson School of Chemical Engineering

Xiaoping Bao

Two projects are available. One involves the investigation of enhancing optical imaging resolution using single photon counting techniques. Conventional optical imaging has a hard limit on its spatial resolution, to about one half of the wavelength, and many situations can benefit from higher resolution. In addition, it is challenging to image through scattering media. By way of example, being able to sense with light deeper in the brain would be of enormous benefit in neuroscience. The statistics of photons emitted by or transmitted through an object contain valuable information about the object which could be used to enhance image resolution and possibly see through substantial background scatter. Experiments will be conducted using laser light and with a set of single photon avalanche detectors (SPADs) to measure photon correlations in time, over wavevector (direction), and between detectors in various imaging configurations. Results from these experiments will be used to assess the effectiveness of various techniques for enhancing spatial resolution in imaging applications. This work has a diverse set of potential applications including biological imaging, sensing defects in semiconductors, and imaging through fog. The other project relates to optical forces on structured membranes induced by a laser. The modeling of the mechanical motion of a thin membrane deflected by laser light will be used to determine the membrane properties from experimental and simulated data. This will allow extraction of the mechanical material properties and more generally the validation of a theory for optomechanics that can then be used in design. The nascent field of optomechanics offers enormous impact scope, including remote actuation and propulsion, of importance in fields as diverse and molecular biology, communication, and transport. This project relates to attaining the underpinnings to move along such paths in engineering, as well as the basic physics of optical forces in material at small length scales.

Biological Characterization and Imaging, Biological Simulation and Technology, Deep Learning, Material Modeling and Simulation, Nanotechnology, Other

• Electrical Engineering
• Physics

Students with an interest in experimental work and a strong background in electromagnetics would be a good fit for this project. The undergraduate student will work with graduate students to perform experiments in an optics laboratory, perform modeling and data analysis using MATLAB or python, and review relevant literature to develop a working understanding of single photon measurement techniques and their applications to super-resolution imaging. This project would be suitable for students majoring in electrical engineering, physics, or a related discipline.

Electrical and Computer Engineering

Kevin Webb