Vanderbilt University
BME 272 Design of Biomedical Engineering Devices and Systems I
Application of Heterodyne Chemistry to Biochemical Processes
NCIIA Grant Proposal
Madeleine Durkee, Ryan Planchard, Kenneth Varner, and Shenali Wickramanayake
Introduction
Biochemical regulatory networks can be described as a complex integration of
cycles and cascades, controlled by positive and negative feedback loops to produce
reaction pathways that are linear, hyperbolic, sigmoidal and oscillatory. Such complex,
intertwined, dynamical systems occurring in and between cells can lead to
misinterpretation of results from perturbed biochemical networks and whole cell studies.
A more complete understanding of the dynamics of these regulatory networks can be
developed through mathematical and physical models of individual reactions occurring
within cell signaling pathways. Here we introduce an analytical method to delve deeper
into our understanding of nonlinear chemical and biochemical reactions, called
“heterodyne chemistry.” The term heterodyne originated in radio frequency processing
and refers to a method in which two oscillating signals are combined into a non-linear
mixer to shift the output frequency into a more desirable range. By applying this concept
to chemical reactions in a highly controlled microfluidic environment, we hope to unveil
the hidden complexities in seemingly simple biochemical reactions, and further
investigate the presence of highly unstable and otherwise undetectable intermediates.
In order to first develop this technique, we employ the use of the light-producing
peroxyoxalate chemiluminescence reaction as a model chemical system.
Biological processes, such as metabolic reactions, often involve complex steps
including reversible reactions that work towards maintaining homeostasis. Current
models of biochemical processes, like models of many chemical reactions, oversimplify
the process by which this occurs, making identification of the mechanism of action
impossible through the use of these models. Pharmaceutical companies need a process
to discover the intricate kinetics of the biological systems on the molecular level in order
to develop drugs that not only identify therapeutic target and treat the dysfunction
occurring in the body, but also avoid contraindications and dangerous side effects.
History and Context
Prior to biological and biochemical application, the heterodyne chemistry method
was applied to simpler, previously modeled chemical reactions. Simulated light output
from the fluorescein quenching reaction and the peroxyoxalate chemiluminescence
reaction was determined through the use of mathematical models. Rotary Planar
Peristaltic Micropumps (RPPMs) were used to conduct chemical solutions at sinusoidal
rates through peak tubing into a microfluidic channel. Light production was detected in
real time and analyzed using Fast Fourier Transforms (FFTs). The resulting spectra
were compared to model FFT spectra. Discrepancies between the model FFT spectrum
and the experimental FFT spectrum indicate a flaw in the pre-determined model of the
reaction, meaning that there are intermediates that exist that had not previously been
accounted for. Given the experimental FFT spectra, actual reaction kinetics can
hypothetically be back-calculated, but the process for doing so has yet to be defined.
Work Plan/Outcomes
The future clinical application of this design will result as an outgrowth of the use
of this technique in discovery and translational laboratories. With the ability to gain a
thorough understanding of biochemical pathways, investigators will be able to identify
the crucial reactants and intermediary products. This will further enhance knowledge of
metabolic pathways, and potential offer a more accurate identification process of
potential therapeutic targets. The current round of funding will be verifying the efficacy
of this methodology against standardized non-linear reactions from scientific literature.
Through the comparison of heterodyne experimental data with modeling consistent with
previously defined reaction kinetics, we hope to replicate the intricacies of several
chemical reactions (fluoroscein quenching, peroxyoxalate, and a fluorescent ATPase
reaction). The application of heterodyne chemistry to various biochemical pathways is a
natural outgrowth of this proposal. Currently photon emission is our only indicator of
product formation, but this phenomena is not consistent with the majority of chemical
processes. Other applications of this technique would require real-time tracking of a
single/multiple reaction product(s). The development of a microfluidic pH sensor “addon” to the current heterodyne chemistry set up offers a corollary to further verify the
efficacy of heterodyne chemistry. The compilation of these data sets will provide the
necessary evidence to test on a much larger scale. Future work will entail the tracking of
multiple products through the use of mass spectrometry. The development of this
system will have the widest applications, but will prove the outgrowth of the foundational
research.
Our final design product will include a sinusoidal concentration generator (RPPM
peristaltic pumps) in concert with a detection system (Either pH or photon detection).
These elements will be used to gather heterodyne data which will be directly processed
through MATLAB to derive a frequency spectra from the reaction. Translating this
spectra into reaction kinetics presents a unique challenge, but also provides the end
goal of using this technique to further understand the intricacies biochemical processes.
Evaluation/ Sustainability
The ultimate goal for this type of procedure would be to be able to accurately
model, predict the behavior of, and identify currently undetectable intermediate products
of higher order biochemical reactions. However, at this moment we would like to prove
the efficacy of this method for identifying all of the intermediates of a reaction by first
testing it on known chemical processes. Therefore it is our main concern to prove that
this heterodyne model is an accurate and reliable way to characterize these types of
reactions. The project will be considered a success if we are able to identify the
products and/or rates of the reactions through the detection of changes in both light
intensity and pH, as these are currently the simplest ways to track the reactions. The
focus reaction will be a fluorescently tagged ATP enzymatic reaction, but the specific
reaction has not yet been determined. This will then ensure that we have correctly
identified the system so that we can determine the level of accuracy of the current
model. Solving the reverse heterodyne chemistry problem, being able to determine
chemical equations from a heterodyne chemistry Fourier Transform spectrum, would be
considered the ultimate success, but thoroughly solving this problem may not be in the
scope of this project.
Team
Every member of the team has an understanding of reaction kinetics,
microfluidics, how to gather frequency measurements using LabView, and how to
calculate FFTs. Each member also brings specific knowledge that will be compiled to
result in the completion of this project. Kenneth Varner and Ryan Planchard will use
MatLab to produce computer models of the chemical reactions. Kenneth Varner will also
be constructing and updating a web-page, which will include updates on the design
process and images of the project. Ryan Planchard and Madeleine Durkee have
experience with similar experimental setups, experimental protocols and data analyses.
Madeleine Durkee will also provide specific knowledge on the heterodyne process and
provides experience in fabricating microfluidic device masks and microfluidic devices.
Shenali Wickramanayake will construct differential equations from the data gathered
and use knowledge of chemical kinetics combined with the ability to solve and interpret
differential equations to begin the process of solving the problem of reverse heterodyne
chemistry.
Gantt Chart
Madeleine Durkee
1921 Scarritt Place
Nashville, TN, 37203
702-506-6249
Madeleine.s.durkee@vanderbilt.edu
Education
Vanderbilt University
Bachelor of Engineering in Biomedical Engineering; May 2013
Engineering GPA- 3.08
Research Experience
Searle Systems Biology and Bioengineering Undergraduate Research Experience (SyBBURE) April 2011-present
Undergraduate Researcher

Developed a novel technique for determining true biochemical and chemical reaction kinetics

Fabricated microfluidic device masks and microfluidic devices

Collaborated with Cornell University and Hofstra University on various aspects of project development

Analyzed Fast Fourier Transform spectrums for frequency content of chemical signals
Professional Membership
Biomedical Engineering Society February 2010-present

President of Vanderbilt chapter May 2011-present
o Organized meetings with potential employers
o Hosted student information sessions about research

Treasurer of Vanderbilt chapter May 2010-May 2011
o Monitored society budget and spending
Society of Women Engineers September 2009-July 2010

Member-Helped organize fund raising events for Vanderbilt University chapter
Volunteer work/Community Service
Children’s Miracle Network

Dance Marathon: Raised $150 and attended events with miracle children

Miss America/Miss Las Vegas Organization: Raised $200 and visited children in CMN hospitals
Project C.U.R.E.

Organized medical supplies to send to hospitals in third world countries

Recruited Vanderbilt biomedical engineering students to come to Project C.U.R.E. events
Technology Access Center

Adapted toys for handicapped children

Adjusted circuitry in toys by soldering
Work Experience
Nashville Predators July 2011-present
Public and Fan Relations
Nashville Parks & Recreation January 2010-present
Figure Skating/ Hockey Instructor
Vanderbilt University January 2010-present
Aerobics Instructor
Relative Coursework



Biomaterials/mechanics
Organic Chemistry
Physiology


Instrumentation
Neuromuscular
mechanics


BioTransport
Therapeutic
Bioengineering
Ryan Planchard
2301 Vanderbilt Place PMB 355615, Nashville, TN 37235/ 615-973-9951/ ryan.f.planchard@vanderbilt.edu
Education
Vanderbilt University
Aug. 2009 - Present
Nashville, TN
Major(s): Biomedical Engineering & Economics
Minor(s): Chemistry

Completed Coursework: Organic Chemistry, Statistics, Multivariable Calculus, Differential Equation, Linear
Algebra, Systems Physiology, Bioorganic Chemistry, Medicinal Chemistry, Biomaterials, Biomechanics,
Physiological Transport Phenomena, Biomedical Instrumentation
 Current Cumulative GPA: 3.854
Biomedical Engineering GPA: 3.930
Work Experiences
Vanderbilt University – Ingram Cancer Center
Aug. 2010 - Present
Nashville, TN
Lab Technician / Undergraduate Researcher
 Lab technician in the Oncology Department through the Vanderbilt University work-study program. Participates in
research projects under Dr. Utpal Davé, in addition to cleaning and maintaining lab equipment.
Vanderbilt University School of Medicine Summer 2012
Nashville, TN
Clinical Intern / Undergraduate Researcher
 Students are provided the opportunity to pursue a research project in an area of interest, allowing for my continued
participation in the Davé Lab. Students round with hospital based general medicine residents, and attend weekly
seminars to discuss patients seen on rounds, learn about the process of medical education, and discuss issues in
health care.
Undergraduate Clinical Research Internship Program
Vanderbilt University School of Engineering Summer 2011
Nashville, TN
Undergraduate Researcher
 Participated in research projects under Dr. John Wikswo, which required the fabrication and use of microfluidic
devices. Project included intensive computer modeling utilizing both MATLAB and COMSOL. Students attended
weekly seminars to develop critical research skills including topics such as AutoCAD, Photolithography, Journal
Databases, etc.
Summer Undergraduate Research Program
Honors and Awards
Fred J. Lewis Scholarship - Vanderbilt
Awarded: 2011-2012/2012-2013

Awarded to students in the School of Engineering with outstanding academic credentials and offering a positive impact
within the Vanderbilt community.
Tau Beta Pi
Initiated: Fall 2011
 Engineering Honors Fraternity recognizing Junior undergraduates ranking in the top eighth of their class. Invitation
is contingent on both academic achievement and a record of outstanding character. The organization is active
within the School of Engineering, and helps coordinate activities and events for undergraduate engineering students.
Dean’s List - Vanderbilt
Awarded: Fall: ’09 -‘11 Spring: ’10 - 12

Awarded to students achieving a 3.5 GPA or better over the course of a semester.
Kenneth Varner
Home Address
3025 Trellis Ln
Monroe, NC 28110
kenneth.a.varner@vanderbilt.edu
Home 704-282-4888
Cell 704-254-6451
Campus Address
Vanderbilt University, PMB
Nashville, TN 37235
Education
Vanderbilt University, Nashville, TN
Bachelor of Engineering, Biomedical Engineering, May 2013
Minor: Engineering Management
GPA: 3.276/4.0
University of New South Wales, Sydney, Australia
Study Abroad Program, July-November 2011
Charlotte Catholic High School, Charlotte, NC
High School Diploma, May 2009
Graduated First Honors
GPA: 4.32/5.0
Work Experience
Bank of America Stadium Concessions Charlotte, NC 2005-2008
Volunteer
• Sold concessions in the upper bowl during football games
• Met all sales goals
Harris Teeter Indian Trail, NC 2007-2011
Customer Service Clerk
• Supervised up to ten cashiers and baggers
• Dealt with customer complaints and problems
Relevant Coursework
Introductory Biomechanics
Biomedical Materials
Clinical Laboratory Sciences
Biomaterial Manipulation with Lab
Instrumentation
Systems Engineering
Program and Project Management
Activities
Best Buddies
2010-Present

College students are paired with those who have intellectual and developmental disabilities.

Activities Committee, 2012-2013
Biomedical Engineering Society
2010-Present

Vice President of Internal Affairs, 2012-2013
Skills
• FEMA Introduction to Emergency Program Management
• Proficient with Microsoft Office, MATLAB, and Mathematica
• Experience with ArcGIS
Strengths
• Strong communication and presentation skills
• Very methodical, thorough, and organized worker
Shenali D. Wickramanayake
6003 Heritage View Ct. • Hilliard, Ohio 43026 • (614) 282-7658
PMB 356189 • 2301 Vanderbilt Place • Nashville, TN 37235
Shenali.d.wickramanayake@vanderbilt.edu
EDUCATION
Vanderbilt University (May 2013)
Major: Biomedical Engineering
GPA: 3.165
Honors: Vanderbilt University School of Engineering Dean’s List (Spring 2012)
EXPERIENCE
Vanderbilt University Summer Undergraduate Research Experience, Optics Lab (2012)
 Image treated breast cancer cells using two-photon microscopy and fluorescence lifetime
imaging
 Quantify cell death differentiation via flow cytometry and microscopy assays
 Present research poster at poster session
Duke University Medical Center, Thoracic Surgery Department (2011)
 Analyze clinical esophagogastrectomy data
 Perform western blot, Q-PCR, ELSIA assay and cell culture
 Observe clinics and surgeries with Dr. Mark Onaitis
University of Ruhuna, Sri Lanka (2010)
 Sort and analyze data on Dengue fever
 Observe ward rounds and post-ops with Dr. Bhodinayake
Great Lakes Environmental Center, (2009)
 Perform basic tests on factory effluence samples
 Assist with the preparation and quantification of acute and chronic toxicity tests
Columbus Nationwide Children’s Hospital, Biopathology Center (2009)
 Prepare blood and tumor samples for testing
 Prepare microscope slides
ACTIVITIES
Manna Project (2011-present)
Vanderbilt One (2010-2011)
Inter-American Health Alliance (2009-2011)
VOLUNTEER/COMMUNITY SERVICE
OACS Zanzibar Service Project (2012), Teacher
 Teach Chemistry, Biology, and Math to secondary school students
 Advise secondary school teachers on improved teaching methods
 Prepare lesson plans
 Teach English to preschool students
Nashville Mobile Market (2011)
Salvation Army Soup Wagon (2010)
Tutoring Sudanese Refugees at the Lost Boys Center (2010)
COURSEWORK
Systems Physiology, Tissue Engineering, Biomaterials, Biomechanics, Neuromuscular
Mechanics and Physiology, Analysis of Biomedical Data, Logic