REU Research Projects

Development of Hand-Held Devices for Pathogen Detection

Faculty Mentor: Z. Hugh Fan

Project Description: Viruses are a global public health problem, evidenced from the pandemic of coronavirus disease 2019 (COVID-19). It is highly desirable to have a device that can detect viruses for transmission control and differentiate various viruses for disease-specific clinical care. To meet the need, the objective of this project is to develop a rapid and cost-effective platform for detecting pathogens at the point of care. The platform will disintegrate pathogens (a process called lysis) and perform isothermal amplification of enriched nucleic acids, followed by colorimetric detection by naked eye or a smartphone camera.  Innovation is needed in the device miniaturization, sequential reagent delivery, and operation in the field without power and laboratory equipment.  The project is a part of the lab’s efforts on microfluidics, which is an interdisciplinary field involving engineering, sciences, and medicine.  

What the Participant Will Do: This project is experimentally focused.  The student will be trained to fabricate devices, including 3D printing, lamination, and integration.  The devices will then be tested by the student while being trained on valving control, assays, and detection.  Various detection schemes and conditions will be investigated, and their effects on detection sensitivities will be studied.  The student is encouraged to test their own ideas after training and understanding the challenges associated with the project.

New Classes of Fluid Instabilities in 3D Printing of Soft Matter

Faculty Mentor: Thomas E. Angelini

Project Description: Technology for 3D printing with hard materials is in a very mature state; hobbyists can 3D print hard thermoplastics with high precision at low costs.  Many important applications in healthcare require the use of soft materials, like hydrogels and elastomers, which have the feel of Jell-O or soft rubber.  The recent invention of a soft matter 3D printing technique at UF has opened the door to 3D printing precise objects made from soft matter.  However, the new combinations of complex soft materials involved in this 3D printing technique have generated unanticipated fluid instabilities.  The physical principles that control these instabilities have not yet been determined, limiting the ability to advance the technology.

What the Participant Will Do: The REU student will 3D print a diversity of different shapes like lines, spheres, cylinders, and planes and study their evolution under destabilizing forces.  The shapes will be made from a viscous or viscoelastic liquid and suspended in 3D space without any support apart from an embedding continuum.  The embedding material is a granular-gel based liquid-like solid, which is a solid from a thermodynamic perspective yet also possesses many of the properties of a liquid.  The student will perform time-lapse microscopy and photography and learn digital image processing techniques for data analysis.​

Development of New Tools for Cell Mechanics Studies

Faculty Mentor: Xin Tang

Project Description: Mechanical signaling strongly influences embryological development, differentiation, morphogenesis, tissue patterning, and aging as well as various other biological functions. When mechanosensing, mechanotransduction, and mechanoresponse are misregulated, diseases usually occur or progresses. For example, cancer deaths are mostly caused by metastasis of malignant cells, not by the tumor itself. During metastasis, cancer cells detach from the primary tumor, spread to different body locations via the lymph system and/or blood circulatory system, reattach to invade the target organs and form the secondary malignant tumors. Interestingly, in contrast to healthy organs, primary tumors are often mechanically stiffer. This stiffened mechanical milieu has been identified as one of the promoting signals to enhance metastasis. The invention of new technologies generally enables the dissection and manipulation of basic operating principles underlying these biological and pathological processes, leading to new potential therapeutics to improve health.

What the Participant Will Do: What the Participant Will Do: This multidisciplinary project contains both experimental (70%) and computational  (30%) components. The participant will be provided with training on live-cell imaging, design of novel biomaterials, and numerical simulation for biomechanics and mechanobiology research. The student will apply these skills to investigate how biophysical signals influence the function and behavior of cancer and normal cells. 

2D Material Nano-Laminates for Selective Transport and/or Adsorption of Species

Faculty Mentor: Saeed Moghaddam

Project Description: The objective of this research is to determine the effect of different synthesis conditions on transport characteristics of a bilayer Graphene Oxide (GO) structure as the active layer of a Nano-Filtration (NF) membrane.  The proposed structure is an order of magnitude thinner than the active layer of existing NF membranes (100-200 nm).  Preliminary results on a membrane (prepared without optimizations) show 3-4 times less energy consumption compared to the state-of-the-art NF and Reverse Osmosis (RO) membranes.  This new membrane can be a viable solution for low-cost removal of Endocrine Disrupting Chemicals (EDCs) from water resources, as recent scientific reports have provided evidence of adverse reproductive outcomes (infertility, cancers, and malformations) from exposure to EDCs.  Although the existing NF and RO membranes have been shown to separate organic micropollutants effectively, they suffer from high energy use. To realize the potential of GO-based NF membranes in energy-efficient cleaning of drinking water, it is essential to develop a comprehensive understanding of the effect of physicochemical properties of the GO nanoplatelets and their interlinking molecules on transport characteristics of the GO bilayer.  The effects of oxidation process, nanoplatelets size, defects size and density, and the interlinking molecule on water permeation and EDCs rejection rates will be studied.The student will be trained on the science of species transport through nanostructures and testing methods.

Solar Thermochemical Water Splitting to Produce H2 Fuel

Faculty Mentor: Jonathan Scheffe

Project Description: Conversion of solar energy to chemical fuels, such as molecular hydrogen (H2) or synthesis gas (syngas), via a thermochemical process provides a potential pathway towards clean renewable energy that can be stored for long periods of time and transported over large distances. The metal-oxide based thermochemical redox cycle is one such method of solar fuel production. A typical metal-oxide based redox cycle is characterized by two reactions occurring in separate steps. The first step, driven by solar energy, involves endothermic reduction of the metal-oxide, resulting in the evolution of oxygen from the crystal structure of the metal-oxide. In the exothermic second step, the reduced metal-oxide is oxidized with steam (H2O) to produce H2 or with a mixture of H2O and carbon dioxide (CO2) to produce syngas.

What the Participant Will Do: The main purpose of this research project to experimentally evaluate and compare the performance of candidate metal oxide materials that are hypothesized to produce greater H2 yields isothermally compared to the state of the art oxide, nonstoichiometric ceria. This is part of a larger Department of Energy sponsored project entitled “A New Paradigm for Materials Discovery and Development for Lower Temperature and Isothermal Thermochemical H2 Production” and will involve collaboration with computational and materials synthesis experts in Materials Science and Engineering at UF.

Interaction between Needle Surfaces and Tissues during Biopsy

Faculty Mentor: Hitomi Greenslet

Project Description: Needle biopsy procedures are used to extract tissue samples for cancer diagnosis.  It has been hypothesized that the combination of lower needle insertion force, including friction between the tissue and needle surface, and less needle deflection leads to a more effective biopsy procedure, such as one that more accurately extracts a larger amount of tissue from a lesion with less damage.  Based on this hypothesis, a new coaxial needle system was created to enable the extraction of more tissue with less damage.  The preliminary study found that the clearance between the inner stylette and outer needle and the needle insertion speed are the key factors affecting the needle insertion force and amount of tissue extracted.  This project aims to clarify the mechanism behind that trend by analyzing the interaction between the needle surface and tissue during a biopsy

What the Participant Will Do: The student will run biopsy tests using chicken breast and phantom tissue (e.g., gelatin and polymers) and collect data (including needle-insertion force, in situ tissue movement during biopsy, and extracted tissue weight, geometry and condition).  The student will learn how to design experiments, collect and analyze data, and summarize the findings. The student will clarify the relationships between the movement of tissue on the needle surface, friction between the tissue and needle surface, and amount and condition of the extracted tissue, which will result in the discovery of fundamental knowledge related to the tissue–needle interaction and tissue-damaging mechanisms during biopsy.

Control Development and Testing using Functional Electrical Stimulation

Faculty Mentor: Warren Dixon

Project Description: Functional electrical stimulation (FES) is a rehabilitation technique in which an electric current is applied across a muscle group to activate motor neurons and induce muscle contractions to perform a functional task such as cycling.  Motorized FES induced cycling is a common rehabilitative treatment since it involves repetitive low impact coordination of the limbs.  By switching the stimulation across different muscle groups so that each muscle contributes only to the forward motion of the cycle’s crank angle, a nonlinear state-dependent switched system arises. Since there are unstable regions of the crank cycle in which the legs are inefficient at producing torque, the control strategy can intermittently switch between different muscle groups and a motor to help reduce fatigue, allowing for more repetitions.During the first week of the program, the students will be introduced to the Institutional Review Board (IRB) process and the protocol and procedures for performing control experiments on people.  The following weeks they will learn how to interface the computer and software with the electrical stimulator and electrodes, and observe experimental procedures being performed.  Students will be given tutorial information about the basic switching control structure and will be provided software that encodes such algorithms.  Students will then perform experiments on volunteers using the buddy system while adhering to safety policies and practices.  They will also perform statistical analysis tests to determine cause effect relationships and correlations in the experimental data.

Cardiovascular Engineering

Faculty Mentor: Roger Tran-Son-Tay and Dr. Scott Berceli (Dept. of Surgery)

Project Description: Cardiovascular disease is the number one cause of death and disability in the world. Cardiovascular Engineering is a multi-disciplinary field aims to improve our understanding and the treatments of cardiovascular diseases.  The goal of our laboratory is to develop new methods to study, diagnose and treat cardiovascular diseases. Projects include, for example, creating mathematical models to evaluate vessel remodeling after vein graft or stent implantation, understanding the fluid dynamics of diseases, like thrombosis and aneurysms, and developing tools to evaluate cell damage in blood dialysis and transfusion.  There are two projects (one more theoretical and the other more experimental) that students can choose from.  In the first one, students will learn advanced endografting techniques used for the treatment of aortic arch aneurysms.  They will learn how computational fluid mechanics modeling can be used to assess the impact of device design features (e.g., stent size and shape) on hemodynamic parameters using patient-based anatomical and hemodynamic data.  In the second project, students will design and fabricate a flow system made of tissue phantoms with perfusable capillary structures to better simulate in vivo blood circulation in order to assess cell damage that might occur in blood transfusion or dialysis. The designed structures will be fabricated using 3D printing by either directly printing soft matrix materials in air for structures with small diameter lumens (<100 µm) and embedding printing for structures with large diameter lumens (>100 µm). In addition, students will learn the fundamental of hemodynamics and mechanisms of red blood cell damage.

Atomistic Modeling of the Dynamic Behavior of Hydrogels

Faculty Mentor: Douglas Spearot

Project Description: Hydrogels are comprised of a mechanically or chemically cross-linked hydrophilic polymer network immersed in a matrix of absorbed water molecules.  Hydrogels are biocompatible and have been used extensively in advanced biomedical applications such as in tissue scaffolds, in vivo studies of traumatic brain injury, and repair or replacement of damaged tissue.  The objective of this project is to investigate the mechanical and/or thermodynamic behavior of hydrogels during dynamic loading conditions using classical atomistic simulations.  Specifically, computational methods will be employed to construct hydrogel models with different water contents, molecular weights or defect contents.  Molecular dynamics simulations will then be employed to study shock or shear wave propagation, void initiation and void growth.

What the Participant Will Do: This project is computationally focused. The participant will be provided access to the University of Florida high-performance computing system (HiPerGator) and will learn how to conduct atomistic simulations of hydrogel behavior. The student will use an existing simulation code — no programming experience is required although familiarity with Matlab or Python for data analysis is recommended.

Medical Image-based Modeling of Brain Flows

Faculty Mentor: Malisa Sarntinoranont

Project Description: The brain is buoyant within and surrounded by cerebrospinal fluid.  This fluid has similar properties to water, protects the brain from impacts, and acts to transport molecules into and out of the brain. In the fields of Alzheimer’s disease and sleep, there is increasing interest in how interior brain flows contribute to waste clearance into cerebrospinal fluid.  The objective of this project is to investigate drivers of interior brain flows that include capillary loss and vascular pulsations.  Magnetic resonance images will be used to develop brain models that include blood vessels, perivascular spaces (fluid-spaces around vessels) and surrounding tissues.  The REU Participant will perform computational fluid dynamics (CFD) models to study the roles of perivascular channel width, pulsation frequency, and tissue porosity on perivascular flows within brain tissues.  Tissue flows within the perivascular space are too slow to be measured non-invasively.  Physiologically based CFD simulations provide one way to understand better the physics driving these flows.During the first two weeks of the program, the participant will use examples from existing imaging data sets.  They will learn to use image-processing software (FIJI) to segment structures of interest from magnetic resonance images.  In the following weeks, 2D CFD (FLUENT) models will be developed that simulate flows within perivascular channels.While recent animal studies show dramatic uptake along these spaces into the brain, the contribution of pulsatile flows and its potential effect on dispersion and mixing are not well characterized.