Course Title: BIOEN 327 Fluids and Materials Laboratory

Instructor: Christopher Neils
Credits: 2
UW Catalog Course Description: Practical exploration of 1) the behavior of fluids and soft materials that occur in biological systems and biomedical devices, and 2) the interaction between cells and their environment. Includes methods of measurement, analysis, and design. Laboratory only.

Prerequisites by Course: Requires concurrent registration with BIOEN 325 and BIOEN 326.

Prerequisites by Topic: Physics (mechanics and oscillatory motion), general chemistry, differential equations, MATLAB programming.

Overview: This course provides laboratory instruction in methods to measure, analyze and predict the behavior of fluids, solids and that occur in biological systems and biomedical devices. An emphasis is placed on the interaction between cells and their environment, and on the interaction of fluids and compliant solids to determine the behavior of a combined dynamic system. Examples include lung expansion and air flow, cardiac contraction to eject blood, and visceral expansion due to pulsatile blood flow. BIOEN 327 draws on content from the concurrent fluid and solid mechanics lecture courses, BIOEN 325 and 326. Lab projects are 50% in structured lab periods and 50% as self‐guided projects using laboratory facilities. Self‐guided projects include computational analyses using COMSOL, which is introduced via online and instructor‐guided tutorials.

Textbooks:  None.  Reading will be assigned from the BIOEN 325 and 326 textbook(s).  Each lab project will have a handout with background, procedure, and reference to appropriate texts and online journal articles.

Course Objectives: At the end of this course, students should be able to…

  • Set up and conduct experiments to evaluate material properties
  • Understand the limitations of basic analytical models of solid and fluid behavior Develop
  • computational models of simple mechanical and fluidic systems Predict the behavior of systems that
  • combine fluidic and structural components
  • Predict the response of cells and organisms to mechanical factors in their environment

Outcomes Addressed by this Course:

B. An ability to design and conduct experiments, as well as to analyze and interpret data.

  • Measure fluid and solid mechanical systems to determine their properties and behavior.

Students must generate, and record in their notebooks, an experimental procedure for each lab exercise. For example, lab 1 requires students to classify gels as solid or liquid, choose an appropriate method for analyzing the rheological properties (for a liquid) or shear strength (for solids) of the material, record results, and draw conclusions. Lab project 3 requires students to configure the mechanical and electronic portions of a tensile test device, generate a test procedure, record the data manually and/or via data acquisition hardware, record measurement uncertainties, convert length and elongation values into stress and strain values, and calculate derivative properties such as elastic modulus and Poisson’s ratio. Knowledge is assessed via a lab report recorded in the lab notebook.

D. An ability to function on multi‐disciplinary teams.

  • Work constructively in teams to solve bioengineering problems.

Most class exercises in BIOEN 327 require that students work in groups of 2‐4 students. In some complex projects, teams of 2‐3 contribute components of a larger system that is then used for data collection. The complex problem (tensile testing of tendons) presents an opportunity for peer evaluation of contributions to the team. Team performance will be assessed via a peer evaluation of the large‐group tendon test exercise.

K. An ability to use the techniques, skills, and modern engineering tools necessary for engineering practice (i.e. computer and analytical equipment).

  • A. Learn numerical methods to solve ODE systems. (MATLAB)

Students convert a second‐order differential equation that represents fluid oscillations into a system of 1st order differential equations and use MATLAB to find the transient solution. Knowledge is assessed via a written report that presents the solution and compares it to experimental measurements of the oscillatory system.

  • B. Learn to use numerical methods to solve PDE problems. (COMSOL)

Students use the COMSOL finite element analysis software to model transient thermal conduction through gels, problem, steady state fluid flow, and static stress distribution in beams of uniform and tapered profile. Knowledge is assessed by a homework assignment that includes the fluids and structures problems.

M. The capability to apply advanced mathematics (including differential equations and statistics), science, and engineering to solve the problems at the interface of engineering and biology.

  • Expand their understanding of static and dynamic system behavior.

In one exercise, students create a differential equation model of fluid oscillation that includes gravity, viscous drag, and inertial components. Knowledge may be assessed via the description and derivation of the differential equations for the fluid oscillation model, or via the use of statistics in the tendon tensile tests.

N. The ability to make measurements on and interpret data from living systems, addressing the problems associated with the interaction between living and non‐living materials and systems.

  • Apply  solid  and  fluid  mechanics  theory  to  the  interaction  of  two  bioengineering systems.

Measurement of tendon tensile properties involves the challenge of handling and testing biological materials using mechanical tools. In another exercise, students assembled a liquid flow chamber and used it to observe the effect of fluid shear stress on bacterial adhesion. Student knowledge may be assessed via a final exam or a report on the flow chamber experiment.

Topics Covered:
1.   Documentation of designs and experiments in lab notebooks
2.   Stress testing of solids and gels
3.   Measurement of fluid flow, resistance, and oscillation
4.   Modeling of fluid oscillations as second‐order differential equations
5.   Computational solution of ODEs using MATLAB
6.   Degradation of implantable materials
7.   Design and utilization of flow cells for life science microscopy
8.   Effect of shear stress on cell development or adhesion
9.   Computation analysis of heat transfer, structures, and flow using COMSOL
10. Measurement of thermal properties using transient heat conduction experiments

Relationship to Program Educational Objectives: BIOEN 327 focuses on objectives 1,3, and 4, as follows:

  • PEO 1: This course develops specific technical skills including circuit building and programming in LabView, professional skill including team building and resume writing, and foundational knowledge of human physiology.
  • PEO 3: By developing a sense of laboratory etiquette and shared responsibility, this course inculcates a sense of community in our students.
  • PEO 4: Students in this course receive instruction and practice in record‐keeping. They are also guided through challenging experiments in which they create instrumentation and conduct experimental procedures, developing self‐reliance and creative problem‐solving abilities. As such, they develop the ability to perceive the need for new technical knowledge, as well as the skills to acquire it.

Course Schedule:  One formal three‐hour lab period, plus an additional 3 hours per week of in‐lab time at a time determined by each work team.

Computer Use: Requires word‐processing software for preparing homework assignments and the final report, and on‐line access to communicate via email and download materials from the course web site. Data analysis and simulation require use of spreadsheet software, COMSOL, and MATLAB, which are provided both in the student labs and via the bioengineering remote terminal server.

Course Grading:
40%     Informal  reporting  and  record‐keeping  in  lab  notebooks,  which  will  be  turned  in periodically.
40%     Formal written reports of the experiments and design testing performed in lab
10%     Class participation and lab skills
10%     Written Final Exam covering practical material gained from experience in the lab.

BIOEN 327 Weekly Schedule
Week Purpose Lab Handouts Deliverable
1. introduction to Labview Introduce the courseIntroduce LabView using a frequency analyzer example. Lab guideLabview Tutorial (sound)Labview Tutorial (DAQ) Demonstrate program for TA.
2. Tensile tester Prepare tensile tester for use later in the quarter.Examine material degradation over time. Build difference amplifiers and write Labview interface.Place suture materials (PGA, collagen, nylon) in liquid over range of pH. Record methods in your notebook. Have TA check notebook when you are done.
3. Respiration Explore quantitative respiratory physiology: lung volume & pressure, at rest and exercise. Background readingProcedure Typed report with 2‐3 authors.  Share data; each author writes one section.
4. Will it flow? Analyze structural properties of gels Background readingProcedure Handwritten report in lab notebook.
5. Resume Workshop Improve job‐related professional skills. Guests: Kelli Jayn Nichols & Victor Snyder Before lab: draft résumé to KJN.
6. Fluid Oscillations Improve understanding of laminar and turbulent flow by developing differential equations for oscillatory flow.Develop computation skills via MATLAB solution to the ODEs. Lab 4a Assignment: U-tube problem statement and guide to MATLAB’s ODE solver Typed, individually authored homework assignment.Rubrick
7. Tensile Tests Compare tensile properties of biological and non‐biological materials. Dissect rat tails; perform stress‐strain and stress‐relaxation tests on suture materials and tendons. Typed report with 3 authors.
8. Fluid Dynamics and Modeling Observe flow behavior and compare experiment to analytical solutions.Introduce COMSOL flow simulation; compare to  BIOEN 325 homework solutions. Lab 4b: Flow experimentsCOMSOL model of peristalsis Hand in worksheet with experimental results.  Upload COMSOL results.
9. Thanksgiving week
10. Heat transfer reate electronic thermometer; measure temperature distribution in heated/cooled gel.Observe thermal damage of albumin, and compare to MATLAB simulation. Prelab readingLab ProcedureHeat conduction in cylindrical coordinates Write formal handwritten report in lab notebook.
11. Heat Transfer II Create thermal models using COMSOL; compare to theory (homework).bserve thermal damage produced by HIFU. Background reading.COMSOL instructions.HIFU procedure. Hand in worksheet with experimental results.  Upload COMSOL results.Course evaluations
Finals Week Final exam covering practical material

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