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REU Research Projects

Engineered Microchannel Surfaces for Tumor Cell Isolation

Faculty Mentor: Z. Hugh Fan

Project Description: Circulating tumor cells (CTC) in the peripheral blood are potential biomarkers for cancer diagnosis and prognosis.  However, CTCs are extremely rare in the bloodstream, making their detection very challenging.  Microfluidics is a unique platform to address this challenge because: (i) a significant decrease in the diffusion distance, from mm in a conventional container to microns in a microfluidic device, results in an increase in the interaction opportunities between CTCs and capture agents, and (ii) the higher surface-to-volume ratio in a microchannel results in higher loading density of capture agents and accordingly higher capture efficiency.  Multiple schemes have been integrated into microfluidic devices to further enhance the efficiency, including micropillars, micromixers, nanoparticles, and multivalent capture agents.  The objective of this project is to engineer surfaces and fabricate microfluidic devices that could advance tumor cell capture efficiency and selectivity.  Specifically, biomimetic surfaces will be created on the microchannels to enhance their interactions with tumor cells. The student will be trained to fabricate microfluidic devices.  The devices will then be tested by the student while being trained on micropumps and microscopic observation.  Unique surface designs and various microchannel geometries will be assessed, and their effects on tumor cell capture efficiency will be investigated.

 

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.  The REU student will 3D print simple platonic 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.

 

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.

 

Safe Drinking Water through Solar Distillation to Prevent Disease

Faculty Mentor: Jonathan Scheffe

Project Description: According to the World Health Organization, unsafe water, poor sanitation and inadequate hygiene account for 9.1% of the world’s disease and 6.3% of all deaths.  Solar distillation for water desalination provides a renewable and straightforward approach for producing high purity water from contaminated sources.  This project will introduce undergraduate students to basic solar engineering principles that they will then use to design a solar still for the production of high purity, potable drinking water.  The objective of the project is for the student to design, construct and test a prototype solar still manufactured from cheap and plentiful materials.  First, the students will assess different designs in an effort to maximize solar energy conversion efficiency.  This will be accomplished by performing steady state mass and energy balances that couple all relevant modes of heat transfer (conduction, convection and radiation).  Students will then construct the solar still and measure performance over a two week time period and compare results to their model.  Performance will be predicted for various global locations over a time period of a year.  The underlying design principles and solar engineering skills acquired during this project will prepare the student for more advanced and cutting edge solar engineering applications.  These include the development of photovoltaic cells, artificial photosynthetic techniques for producing fuels and thermal power production technologies. 

 

Photonic Based Methods for Cancer Screening

Faculty Mentor: David Hahn

Project Description: The proposed research seeks to develop novel photonic-based sensing methodologies that provide improved sensitivity and/or specificity for in situ and/or in vivo tissue cancer screening, as well as to aid in the diagnosis and treatment of other chronic diseases of the skin and tissue [13,14].  Such an approach has the ultimate potential to increase the percentage of curable cancer cases by promoting detection of the disease at early stages.  The full clinical potential of biophotonic sensing schemes has not yet been realized, and the slow maturation process for point-of-care biophotonics can be attributed to several limiting factors inherent to the complexities of the clinical setting, including significant patient-to-patient variability in optical response.  The proposed research seeks to add a novel new dimension to the optical spectroscopy space (i.e., beyond traditional fluorescence and Raman).  In addition, the project also functions to educate and train students in the important technology crosscutting areas of biomedical photonics and advanced analytical schemes.  Students will learn laser spectroscopy; hence, they will learn operation of laser systems, data acquisition via spectroscopy and imaging, and they will use data processing schemes including chemometric analysis such as PCA and PLS methodologies.  Opportunities may arise for participation in IRB approved studies.  The emphasis of the proposed research is on a novel approach to basic laser-biomaterial interactions toward enhanced disease detection and screening, a complex problem given the nature of biomolecular materials undergoing irradiation with deep UV light sources and the complexities and variations of real biological systems (e.g. human tissue).

 

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 biopsyThe 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 weight, geometry and condition of the extracted tissue.  Clarifying the relationships between the movement of tissue on the needle surface, friction between the tissue and needle surface, and amount and conditions of the extracted tissue 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 (see Fig. 5 for the existing testbed) 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.

 

Mechanobiology of Wound Healing

Faculty Mentor: Chelsey Simmons

Project Description: While many amphibians can regrow entire limbs and organs, examples of mammalian regeneration are very limited.  Recently, the Simmons group has identified a remarkable mammal that has regenerative ability: The African Spiny Mouse (Acomys).  Preliminary data from collaborations between the Simmons group and medical and biology researchers across UF are exciting and intriguing: Acomys tissues do not exhibit fibrosis (scarring) when repairing damage.  Understanding fibrosis is thus the key to unlocking the secrets of regeneration.  The REU Participant will perform research to test the hypothesis that mechanical stimuli can direct regeneration by providing controlled mechanical stimulation of cells from regenerative (Acomys) and normal (Mus) mice.  During the first two weeks of the program, the student will learn how to fabricate hydrogels and run wound healing assay, along with receiving pertinent hands-on safety training.  With the Acomys model and an innovative suite of tunable mechanical microenvironments, this research enables a complete system to identify the role of mechanical strain on scar-free wound healing.

 

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 behavior of hydrogel materials during dynamic loading conditions using classical atomistic simulations.  Specifically, Monte Carlo methods will be employed to construct computational models of hydrogel samples with different water volume fractions, and molecular dynamics simulations will be employed to study wave propagation, void initiation and void growth during shock loading conditions.  Molecular dynamics simulation is particularly well-suited to study shockwave behavior in materials, as the fundamental deformation mechanisms associated with shock occur on nanosecond timescales and nanometer length scales.  During the first two weeks of the program, the student will be provided with an account on the University of Florida high-performance computing system (HiPerGator) and will use the examples provided with the atomistic simulation codes LAMMPS and MCCCS Towhee as exercises to learn how to create input files, submit jobs, and analyze the results of atomistic simulations.

 

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.