Simulation as an Integrator in

an Undergraduate Biological
Engineering Curriculum
A. K. DATTA,1 V. RAKESH,1 D. G. WAY2
1
Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853
2
Center for Teaching Excellence, Cornell University, Ithaca, New York 14853

Received 29 September 2010; accepted 21 December 2010

ABSTRACT: A novel multifaceted elective course in Biological Engineering is described, along with the
experience in its instruction and development over 14 years. The course introduces modeling and simulation
to solve biological/biomedical problems to students with a background in transport processes but with no prior
experience in modeling. The critical elements needed to introduce such modeling to less experienced students are
discussed, such as simplifying a problem for problem formulation, case studies that build a clear bridge to their
preparation in fundamentals, and extracting important details from a simulation. The question of a black box versus
a white box approach to presenting simulations is addressed. Active learning practices such as think-pair-share and
distributed learning are introduced as enablers for this course. Student motivation has been increased by making
the course student-centered with the students themselves selecting and executing the modeling projects. The
authors describe how the same course can serve many purposes in a curriculum, including the introduction of a
state-of-the-art design tool, extending fundamental knowledge to solve realistic problems, enhancing the funda-
mentals, introducing teamwork, written and oral communication, and design concepts. Although we have discussed
the course in the context of biological/biomedical engineering, it can also be extended to other engineering
curricula such as Mechanical and Chemical Engineering. ß 2011 Wiley Periodicals, Inc. Comput Appl Eng Educ;
View this article online at wileyonlinelibrary.com; DOI 10.1002/cae.20519

Keywords: curriculum; design; modeling; transport processes; biomedical engineering

INTRODUCTION experience deemed increasingly important by engineers [4].

Inclusion of simulations into the engineering curriculum has been
How Simulation Is an Important Part of Engineering rapidly expanding in recent years, perhaps with the availability of
Education user-friendly software interfaces (e.g., see Refs. [5–7]), although
details of how to incorporate it into the undergraduate curriculum
Simulation is an important component of engineering design and
is very much an open question [3]. Employers have been expecting
research. For example, as illustrated in Figure 1, in several of the
the students to have exposure to computer-aided engineering tools.
biomedical engineering (BME) design stages (e.g., see Ref. [1]),
Need to develop appropriate simulation-based engineering content
simulation can speed up the process. Integration of simulation in
is felt more acutely in the emerging curricula of biological and
undergraduate engineering education (Fig. 2) in an appropriate
related engineering in comparison with more mature curricula
manner that can enhance fundamental principles and also provide
such as mechanical and chemical engineering.
students with a cutting-edge tool has been in the forefront of
discussions on the engineering curriculum, as evidenced by a
report from the US National Science Foundation [2]. A recent Biological and Related Engineering Curricula
workshop with a nationwide audience also emphasized the need to
Biological and related engineering curricula (such as bioengin-
integrate simulation into design courses and discussed ways to
eering and BME) reflect some of the newest innovations in engin-
accomplish it [3]. Properly carried out, simulation-based instruc-
eering and have been evolving, particularly in the last 15 years
tion can approach mimicking the hands-on, application-based
(e.g., see Ref. [8]). In one study [9] of BME and bioengineering
curricula, about 75% of the programs require a course in solid
mechanics and transport phenomena among other engineering
Correspondence to A. K. Datta (akd1@cornell.edu).
science and fundamentals courses. In another survey of biological
ß 2011 Wiley Periodicals, Inc. engineering, bio-resource engineering, and similarly named

1
2 DATTA, RAKESH, AND WAY
Figure 1 Various stages of biomedical engineering design and where
simulation (analysis) can play a significant role, for example, by reducing
the time involved.
departments, 22 out of 28 departments had a course on heat transfer
or heat and mass transfer and about 75% of these courses were on
heat and mass transfer [10]. Availability of transport courses in the
existing curricula can facilitate introduction of computing to them.
Appropriate introduction of computing in a biological engin-
eering curriculum can itself be a topic for discussion. For the
purposes of this paper, we can think of three ways of infusing
computing in a biological engineering curriculum. The first way is
Figure 2 Engineering curriculum with simulation integrating the various components, as suggested in this example
course.
to introduce the generic computing concepts (algorithmic think-
ing, program structure and organization, object oriented program-
ming, recursion, data structure, beyond just language skills). A
second way would be to include computing as an engineer’s
toolbox for modeling and simulation, either at a generic level
(MATLAB, fuzzy logic, neural networks, dynamical control proc-
esses, data acquisition, machine vision, expert systems) or inte-
grated with design and research (CFD, process design, e.g.,
SuperPro, computational neurobiology, integration of systems).
Finally, a third way to include computing would be through
bioinformatics and computational biology (function–structure
prediction, mechanisms of regulation, analysis of protein shapes,
protein folding).
The course discussed in this paper introduces computing in a
biological engineering curriculum as an engineer’s toolbox for
modeling and simulation (i.e., the second method listed above).
The chosen engineering fundamentals are the transport processes
since they are required in most such curricula, as mentioned above.
Thus an engineer’s toolbox for modeling and simulation is intro-
duced that is integrated with design and research on the one hand
and fundamentals of transport processes on the other hand.
Need for an Upper Level Course That Is Broad-Based
As the core of biological engineering has become more estab-
lished, there is a scarcity of broad-based (i.e., not too specialized)
upper level courses. Design is yet another area in the curriculum
that needs to be emphasized more. There is also the consideration
of the constraint of not adding another course in an already packed
curriculum. The authors will show that the course discussed here
serves the multiple purposes of incorporating computing, design,
upper level elective and written and oral communication, while
still holding clearly to the fundamentals course that is already part
of the curriculum, and extends to real world problem solving in
industry and academia. This course introduces the undergraduates
to physics-based simulation of biological processes. The use of

simulation to reduce the time and effort in building physical
prototypes has improved productivity in many areas of engineer-
ing. Introducing such a course would provide the undergraduates
with a cutting edge tool in the field of biological engineering
design and research.
THE COURSE STRUCTURE AND CONTENT
This course at Cornell University is entitled ‘‘Computer-Aided
Engineering: Applications to Biomedical Processes’’ [11]. It is co-
listed in the Department of Biological Engineering and in the
School of Mechanical and Aerospace Engineering. It is a one
semester, three credit course intended for seniors and juniors in
engineering who have taken fluid mechanics and heat transfer,
preferably with mass transfer. No prior experience in modeling is
assumed. Student grades are made up of a class project (45%), two
exams that test some of the general principles of modeling (40%)
and the completion of homework and tutorials (15%). The course
has been taught continuously since 1996 and is organized around
modeling biomedical transport processes chosen by the students,
working in groups of four (Table 1). Typical class size is around 45.
For the first 11 years, the software FIDAP (Fluent, Inc., Evanston,
IL) was used and has since been replaced by the software COM-
SOL Multiphysics.
Goals for the Course
The primary goal for the course is to have the students think of
computer simulation as an important practical tool in design and
research projects in the industry as well as academia. By the
completion of the course, they should know the guts of a typical
computer-aided engineering software program and have realistic
ideas about the advantages (flexibility and power) and pitfalls (it is
easy to get a wrong answer; the tool is not a substitute of the
underlying fundamental knowledge) of such a tool. At the end,
they should be comfortable in solving less complex problems
themselves and working with experts in solving problems with
increasing complexity. The secondary goals for this course are to
include the relationships to design, written and oral communi-
cation, and exposure to the quantitative approach to solving bio-
medical problems involving but not limited to thermal therapy and
drug delivery. The course goals are not to (1) teach a software
program; (2) make the student an expert in computational fluid
Table 1 Projects During One (2010) Offering of the Course
Thermal effect on dermal layers following defibrillation of heart
Modeling treatment of P. aeruginosa biofilms in the lungs using
aerosolized tobramycin
Modeling of antibotic diffusion from implanted beads in localized injured
tissue
Peritoneal kidney dialysis
Controlled release of ciprofloxacin from PLGA-coated contact lenses to
treat eye infections
Modeling the flow and diffusion of lidocaine through gum and tooth
Optimizing combined laser treatment and cryogen spray cooling for the
removal of port wine stains
Modeling brain cooling helmets for ischemia patients
Optimization of transdermal drug delivery with microcapsules
Transient diffusion of chemotherapeutic agent through tumor
microspheroid
Long-term flux profile of implanon birth control implant
SIMULATION IN UNDERGRADUATE CURRICULUM 3
dynamics or any specific biomedical application; or (3) teach
numerical methods (although a small amount is included).
Contents of the Course
The course introduces computer prototyping using physics-based
simulation software that is used extensively in academia and
industry. To avoid potential misuse of the software as black
box, emphasis on the underlying theory is made in class in addition
to the discussion of various components of the software such as the
governing equations and numerical solution of the equations. The
aim of the course is to provide students with a hands-on appreci-
ation of the flexibility and power of such a tool while simul-
taneously getting a feel of the complexities and the need for the
user to stay on top of the physics. The student learns both how easy
it is to solve a complex problem as well as how easy it is to obtain a
wrong answer. Both biomedical processes based on fluid flow, as
well as heat and mass transfer problems are considered such as
cryosurgery, hyperthermia, laser surgery, and drug delivery. In
each case, a design issue is identified. The students learn about the
biological aspects of these processes as they formulate a math-
ematical problem from the physical process and interpret the
simulation results.
Organization of Lectures
Figure 3 shows the overall organization of the course in terms of its
three components—lectures, hands-on computer lab activities,
and group projects. Under the constraints of one semester duration
and no prior background of the students with the software, many
changes have been made over the years both to the contents of each
component and their relative timing in the semester, depending on
the software, hardware, and the text material developed for the
class, and the balance between lectures and hands-on compu-
tational activities. With the user-friendliness of the software COM-
SOL Multiphysics and the availability of a text [12], it is now
possible to have the three components be almost independent
activities.
Lectures can be thought of as having two parts: (1) problem
formulation and generic issues in analysis; and (2) theory and
background material. In the first and perhaps the most important
part of problem formulation, the students learn how to start with a
physical process and develop its mathematical analog in terms of
governing equations, boundary conditions, etc. They also learn
how to decide on a computational domain, its dimensions (1D/2D/
3D), size, and so on. Here guidelines are provided for intelligent
simplification of a physical process, most of which are generic
concepts, applicable to contexts beyond the biomedical one used in
the course. Pre-processing aspects such as choosing the best mesh
and time step size for a problem and post-processing features such
as how to compute the parameter of interest are covered next.
Guidelines toward model validation and simple optimization are
provided. A short introduction to design in the context of bio-
medical processes is provided with topics such as criteria for
design, design specifications, design evaluation, design verifica-
tion, design validation, regulatory agencies, and how simulation
fits into the design process. The advantages of simulation-based
engineering as opposed to prototype-based engineering are
introduced.
In the second part of the lectures, background, or theory is
provided, starting with simple derivation of governing equations,
followed by source terms and their biomedical origins such as laser
4 DATTA, RAKESH, AND WAY
Figure 3 Schematic showing the structure of the course. Items in the three columns proceed simultaneously. Typically,
the items in the first column end a couple of weeks before the semester ends.
and radiofrequency heating and reactions, boundary conditions,
and material properties. Since a course in heat transfer (preferably
heat and mass transfer) is a prerequisite, most of this material is
review, except that within the context of biomedical processes. A
complete overview of the finite difference method and the one-
dimensional finite element method to solve the governing
equations is presented, including some numerical aspects such
as linearization, direct and iterative methods to solve the linear set
of equations, errors, convergence, and accuracy. Discussions of
these topics, albeit not in detail, ensure that the computational
software is not used as a black-box and the students are aware of the
underlying theory and the need for validation.
Organization of Computation Laboratory Using the
Developed Tutorials
The primary purpose of the computation laboratory is for the
students to learn the implementation of the problem and its
solution in the software. There are two parts to the computation
laboratory—(1) an in-class, hands-on demonstration of the soft-
ware for just one lecture period, using one of the tutorials and (2)
the students’ completion of four different simulations using step-
by-step tutorials that have been developed.
A critical component of this course has been to develop
tutorials that provide step-by-step, easy to follow instructions
using extensive illustrations that solve a problem from start to
finish using the particular software. The typical structure of a
tutorial is shown in Figure 4. The students are introduced to the
software in the only hands-on session with a tutorial on drug
delivery, where the students follow the step-by-step procedure.
All of the tutorials are followed-up with software and theory-
related questions that the students need to answer as part of the
completion report on that tutorial. This is one of the many ways of
ensuring the students are not relating to the software as a black box.
The software-related questions include changing parameter values
and re-running the simulation, doing additional post-processing,
and performing mesh convergence analysis. The four tutorials are
designed so that by the time students complete them they have a
 SIMULATION IN UNDERGRADUATE CURRICULUM 5

Semester Long Class Project

The third component of the course—the semester long project—is
the most important component and accordingly, almost half of the
course grade is assigned to it. The students are required to work in
small groups (
4 students). All projects are chosen by the indi-
vidual groups with the only constraints that the primary physics of
the project is transport phenomena (fluid flow, heat and mass
transfer) and its application area is medicine. They follow the
procedure outlined in the lectures: deciding on a goal, simplifying
to the right geometry, formulating the governing equation, and
boundary conditions, implementing them in COMSOL, meshing,
solving, and performing sensitivity analysis for design and optim-
ization. The TA and the instructor work very closely with the
groups in each of these steps. For example, they ensure that the
problems chosen are neither too simple nor too complex and the
governing equations appropriately represent the physics. A com-
prehensive written report and an oral presentation of the work are
required from each group.

Examples of Projects
Close to 100 biomedical projects in this course from the past can be
seen at http://courses.cit.cornell.edu/bee4530/ under Past Projects.
A quick glimpse of one of these projects is provided below, along
with another one in the bioenvironmental applications area.

Vaporization of Prostatic Tissue to Treat Benign Prostatic

Hyperplasia. The prostate is a key component of the male repro-
ductive system (Fig. 5a). Often, due to age, the prostate becomes
enlarged resulting in a condition known as benign prostatic hyper-
plasia (BPH). While pharmacological options are generally the
first choice, surgery is sometimes necessary to treat this condition.
Laser procedures are ideal because of the decreased risks to the
patient, but complications arise when the layer of coagulated tissue
created by the laser becomes too thick. An ideal laser wattage and
application time must be determined in order to minimize the
coagulation layer while achieving an effective level of vaporiza-
tion. This can be achieved by having a computer model of the
physical process [13].
As part of problem formulation, Figure 5b shows a
schematic of the process. The governing heat transfer equation
is given by
@T 1 @ @T @2 T
rcP ¼ k½ ðr Þ þ 2  þ Q (1)
@t r @r @r @z
where
Q ¼ ma f (2)

Here ma is the absorption coefficient and f is the laser fluency.

Figure 4 Typical layout of the tutorials developed for the course. A light diffusion formulation from the literature was used to
compute laser fluency, f
@f
Dr2 f þ c ma f ¼ 0 (3)
@t
comprehensive understanding of the software and are comfortable
where
working with the software independently. This enables them to
work on their class project independently with minimal help from D ¼ c ½3ðma þ ð1gÞms Þ1 (4)
the instructor and the teaching assistant (TA). The instructor and
the TA are, however, available at all times to help students if they Here ms is the scattering coefficient. To account for the effect
have any implementation problems in the software once they start of vaporization on the heat source term, the effect of moisture
working on their project. content, m, on the absorption and scattering coefficients was
6 DATTA, RAKESH, AND WAY

Figure 5 (a) Anatomy of the prostate and (b) simplified axisymmetric (about z-axis) model schematic of the prostate and
surrounding tissue with the prostate approximated as a cylinder surrounding the urethra. (c) Contour plot of prostate region
at 1 s at 80 W, showing contours at 333, 338, and 373 K, which correspond to coagulation and vaporization temperatures.
(d) Trends in the depth of the coagulation zone of the prostate as the laser wattage and run time parameters are varied [12].

modeled as combination that produces the desired level of vaporization while

 
m
ma ¼ ma0
m0
The moisture change was modeled using the simple evapor-
ation model
 bio-resource engineering curriculum, such as soil and water,
@m Q=l when T  373
¼ (6)
@t T < 373
The material properties needed for the solution are provided
in Currie et al. [13]. The mathematical model was solved using
COMSOL Multiphysics. Using this simulation, the vaporization
and coagulation thicknesses in prostatic tissue were determined, as
shown in Figure 5c. The results indicated that increasing laser
wattage and/or application time increases the thickness of vapor-
ized tissue and decreases the thickness of coagulation. Further-
more, the results suggested that the thickness of the coagulation
zone converges to a minimum value as wattage and/or application
time is increased, as illustrated in Figure 5d. This simulation could
be used to determine an ideal laser wattage-application time
minimizing tissue coagulation.
(5)
Extending to Other Biological Processes: Bioenvironmental
Engineering. Due to the physics-based structure of the course,
it can easily accommodate various interests within a biological or
environmental engineering, food and bio-processing, plant and
animal systems, in addition to BME. Retaining the framework of
the course, that is, transport processes, the course can easily be
extended to include these applications to students in biological
engineering departments. We have developed some course
materials in the form of tutorials for such processes that will allow
instructors to jump-start such a course. An example of such a
process for which a tutorial has been developed is now presented.
Secondary Treatment of Swine Wastewater in Duckweed
Pond An efficient method of recovery of nutrients such as nitro-
gen from swine wastewater is the use of a plant-based system such
as duckweed. Duckweed (shown in Fig. 6a) can easily grow on the
surface of a swine lagoon due to favorable pH conditions and
uptake ammonium ions (NH4þ), which is the predominant form of
 SIMULATION IN UNDERGRADUATE CURRICULUM 7

Figure 6 (a) Example of a real world process (pond covered with duckweed). (b) A simplified schematic of the process,
as part of problem formulation. Ammonium ions diffuse toward the top of the pond and are removed from the top surface by
the duckweed. Pond picture from http://pond.dnr.cornell.edu/Pond/Images/Pond%20covered%20with%20duck-
weed%202.jpg. (c) Ammonium ion concentration profiles at different times. (d) Effect of change in different parameters
(diffusivity and reaction rate) on nitrogen removal by the duckweed.

nitrogen in swine wastewater, in large quantities. The movement of Figure 6b), the nutrient uptake by the duckweed is given by a first
ammonium ions in the static pond and absorption by the duckweed order reaction with a rate constant k:
on the pond surface can be modeled to gain insight on the process
@c
of nitrogen recovery [14]. D ¼ kc (8)
Problem Formulation Figure 6b shows the schematic of the @x x¼L

process. The pond has an initial concentration of ammonium ion

There is no movement of the nutrient through the bottom
that can be taken up by the duckweed covering the top surface of
surface of the pond
the static pond. Ammonium ions move through the pond due to
diffusion. The movement of the nutrient, ammonium ion, is gov- @c
D ¼0 (9)
erned by the transient diffusion equation. @x x¼0

@c @2 c
¼D 2 (7) Initially the concentration of ammonium ions in the pond was
@t @x c0. The values of diffusivity (D), reaction rate constant (k), and
where D is the diffusivity of the nutrient in the static pond. At initial ammonium concentration (c0) were 7.0452  106 m2/h,
the duckweed surface (top boundary of the pond as shown in 0.906  103 m/h, and 64 mg N/L, respectively. The depth of the
8 DATTA, RAKESH, AND WAY
pond was 0.46 m. Simulations were run for a 6-day period of waste
treatment.
Numerical Solution and Results The mathematical model was
solved using COMSOL Multiphysics and the concentration of
ammonium ion as a function of distance from the bottom of the
pond was plotted at different times (Fig. 6c). It can be observed that
the concentration of the ammonium ions at the surface of the pond
falls rapidly due to the uptake by duckweed. Due to this decrease in
concentration, a concentration gradient is set up that helps in the
movement of the ions from the bottom of the pond to the surface. It
can also be observed that the rate of removal of ammonium ions by
the duckweed is faster than the diffusion of ammonium ions as the
ions at deeper locations of the pond remain at initial concentration.
The computational model, therefore, provides insight on the mech-
anism that determines the rate of the nitrogen removal process,
which in this case is diffusion since it is the slower process.
Sensitivity Analysis The computational model can also be used
to test different scenarios for the process. To determine how the
amount of nitrogen absorbed by the duckweed changes with the
change in the different parameters, the model was solved for
different values of diffusivity and reaction rate. As shown in Figure
6d, a 10-fold increase in the diffusivity leads to the fastest rate of
nitrogen removal. Increasing reaction rate 10 times also increases
the nitrogen removal, although it is not as fast as the case when the
diffusivity increases. Sensitivity analysis can serve several import-
ant purposes including identifying the most important parameters,
optimization, and the possible need to obtain more accurate prop-
erties data.
INSTRUCTIONAL CHALLENGES AND
HOW THEY WERE MET
In introducing simulation technology to the undergraduates, sev-
eral challenges had to be overcome during the 13 years of develop-
ment of the course. These challenges have been met through the
development of an appropriate course text [12] that bridges
between real world problems and engineering fundamentals, a
databank of Case Studies (tutorials) for distributed learning, and
the introduction of various other educational concepts that are now
described.
Introduction to the Software
Instruction to the computational software (Fig. 3) has evolved with
software and hardware over the years. We had to move away from
using live, simultaneous instruction to many students. Initially,
when using a mainframe computer years ago, simultaneous
instruction would not work simply because one computer got
too slow when that many memory intensive processes were sim-
ultaneously started. Live instruction is also quite difficult in that
learners can get stuck at any random step, independent of each
other, either slowing down the entire class or demanding more
attention than can be given by one or two instructors. This has been
resolved through the development of step-by-step tutorials that the
individual students can use at their own pace, using the concept
known as distributed learning [15]. Students are now active
‘‘doers,’’ and not listeners, with the teacher being the facilitator
and motivator. Only a minimal live lecture is provided, followed by
individual students working through visual-based tutorials. The
software interface has also evolved to become quite user-friendly
over time, making it considerably easier for the first-time learner.
Problem Formulation
For this learning group of undergraduate students who are the first
time modelers, perhaps nothing is more challenging than the step
of problem formulation—transforming a real world problem into
its mathematical equivalent (geometry, governing equations,
boundary conditions, and so on). This is a step we take for granted
for the more experienced student or modeler but cannot do so for
this group. The simplification process (e.g., see Ref. [16]), charac-
terized by ‘‘as simple as possible, but no simpler,’’ requires a mode
of thinking that is not present in an undergraduate or a graduate text
or taught in an undergraduate engineering fundamentals course. To
overcome this, generic guidelines to problem formulation were
developed. For example, to decide on geometry, they should ask
questions such as (1) what all regions are needed in the domain of
computation; (2) How many dimensions are really needed? (3)
When can we consider a problem axi-symmetric (geometry, gov-
erning equations, boundary condition, material properties, all have
to be axi-symmetric)? (4) How to implement an infinite domain in
the software (large enough domain where the far end is not affected
by the solution process)? Classroom instruction to assist in the
problem formulation step is discussed in the following section. In
addition to this generic instruction on problem formulation, stu-
dents have access to almost 100 problem formulations from proj-
ects completed in this class over the years. Numerous problem
formulation examples and ten complete case studies are included
in the text [12]. These instructional resources on problem formu-
lation are novel and critical for the undergraduate first time
modeler.
Building Interactivity
Even after developing the resources on problem formulation,
classroom instruction on problem formulation poses the challenge
of keeping the student engaged, as such content tends to be
abstract. Using the practice of a think-pair-share (http://
olc.spsd.sk.ca/DE/PD/instr/strats/think/) approach in a classroom,
generic instruction on a subtopic is followed by student group
application (in-class) of the generic concept to their individual
modeling projects. The instructor goes around the lecture room
answering questions to as many groups as possible. This serves the
dual purpose of making progress toward the individual project
while making the lectures interactive and engaging.
Relating to Prior Knowledge
The most painless and effective manner in which we can introduce
an advanced topic such as simulation of real world processes is to
show the clear relationship to prior learning, in this case to
fundamentals of fluid flow and heat and mass transfer. An effort
has been made to make this obvious at many stages throughout the
lectures and in the text material that has been developed. The
lectures go back to the governing equations that the students have
already seen in their fundamentals course, showing the limitations
on physical processes that had to be imposed to use the analytical
solutions they learned. We then contrast showing how a more
general version of the same momentum, energy or species trans-
port equation, that can describe a far more realistic process, can be
solved using simulations. Relating to equations they already know
makes it less daunting, especially for the students challenged by
mathematical aspects. Although the course depends on the fun-
damentals learned in the earlier classes, those fundamentals are

actually enhanced as they apply to real world processes where
students can focus on the process rather than the solution technique
(as would be true for analytical solutions which is generally not
their favorite topic).
‘‘Black,’’ ‘‘White,’’ or ‘‘Gray’’ Box Approach to
Simulation?
The potentials of misusing computational software are great. From
this standpoint, a total ‘‘black’’ box approach, where all of the
background for governing equations, boundary conditions and
numerical methods are hidden, is not recommended. At the same
time, a ‘‘white’’ box approach, that is, going through all the
relevant theory is obviously not feasible in this one semester
undergraduate course. Thus, a ‘‘gray’’ box approach is sometimes
recommended. This is indeed how the course has developed over
the years. Since the modeling in this course is based primarily on
transport processes, the students are required to have courses in
fluid mechanics, heat transfer, and mass transfer (at the under-
graduate level) before taking this course. Short derivations of
governing equations, detailed discussion on property values,
and the derivation of the one-dimensional finite-element method
is included, showing the relationship between theory and software
implementation. Using a multiphysics software such as COMSOL
Multiphysics, students are also able to include simpler formu-
lations of electromagnetic heating such as radiofrequency or laser,
and the governing equations for these are also included without
straying significantly from the student’s prior knowledge. The
students are also sensitized on the topic of model validation
and on how to trust a simulation.
Detailed Help in the Software
Students get their introduction to the software through the tuto-
rials, as discussed earlier. As they dig deeper into the simulation,
they can be expected to get into some fairly complex aspects of the
physics or its software implementation. How complex the physics
they get into is carefully controlled at the problem formulation
stage in the beginning of the semester when the students choose
their problems, making sure that overly complicated physics,
particularly those involving complex fluid flow, are avoided.
Any instructor with transport phenomena background would typ-
ically be able to provide such feedback to the students. It is
important that the TA also has enough experience in transport
phenomena. It is not necessary for the TA to have very detailed
knowledge of the software or a strong background in numerical
computation in the beginning. The TA can learn as needed—this is
certainly true for a user-friendly software interface such as that of
COMSOL Multiphysics and the availability of a number of solved
tutorials.
Learning and Communicating the Simulation Results
As most of the students are introduced to simulation concepts for
the first time, they are often thinking primarily in terms of how
homework was laid out in an engineering science course such as
one on heat transfer. Aside from the problem formulation issues
already discussed, extracting knowledge or analyzing results (as
opposed to just computing results) is not a skill that beginners
typically possess. For example, whether it is the point concen-
tration, average concentration, or the non-uniformity in concen-
tration that is the most relevant for the given situation, is not
obvious to them. The software simply provides numbers that
are the primary computed variables and it is up to the user to
SIMULATION IN UNDERGRADUATE CURRICULUM 9
extract the needed information. Even in a software program such as
the COMSOL Multiphysics, where secondary quantities such as
flux are readily available, the undergraduate student is often not
certain as to which one of these secondary quantities is the most
relevant for the situation. This was resolved by developing generic
text material with examples (tutorials/case studies) that provide
guidelines for various situations, in relation to the final goal for the
simulation.
Monitoring Progress Through the Semester
With 10–12 new projects (40–48 students), it is challenging to
ensure that continuous progress is made in the projects throughout
the semester. Perhaps the most critical component is the detailed
timeline that has been developed over the years that requires
students’ demonstration of progress every two weeks. Because
each project is different, the timelines are for generic components,
such as schematic, governing equation, and boundary conditions,
that are true for all projects. Some flexibility has to be built into
these deadlines since different projects may have a different
component as the major source of difficulty, that is, for some,
the geometry may be too complex and hard to decide, whereas for
another project boundary conditions may be the most difficult part.
The important criterion used here is to ensure students are making
progress toward the overall project.
Ensuring Individual Contribution in a Group
Since the project is accomplished in a group of four and the entire
group gets the same grade, another challenge has been to ensure an
effective group dynamics where everyone is contributing at a
comparable level. While almost all the groups are motivated in
this elective course where each group chooses its modeling topic,
and their accomplishment generally exceeds the minimum
requirement for the course, there are typically one or two groups
every year where group dynamics are not effective. In addition to
the instructor meeting with individual groups several times during
the semester and getting feedback from the TA who is in contact
with the groups, the most effective tool to measure group dynamics
has been the use of a web-based free software program CATME
(https://engineering.purdue.edu/CATME). The software CATME
(Comprehensive Assessment of Team Member Effectiveness) was
developed [17] exactly for a situation as this: one where teams are
used to accomplish work and peer evaluations and self-evaluations
can be used to assess how effectively each team member contrib-
utes to the team. Mandatory peer evaluation has definitely
improved the group dynamics and participation of group members
to the point of having very few (1–2) students attempting to get a
free ride.
MULTIPLE BENEFITS TO THE STUDENTS
Simulation as a Tool
Perhaps the single major benefit of the course is that by the end of
the course students see simulation as a versatile tool that is used
routinely to solve real world problems in both design and research.
They are made aware that similar tools exist for other types of
physics (e.g., electromagnetics, solid mechanics) and are a critical
part of today’s design process in most industries. During students’
hands-on experience with the tool, they develop a realistic impres-
sion of the tool—the level of subject matter expertise needed to use
the tool, the extent to which the tool can be trusted (or how to trust
10 DATTA, RAKESH, AND WAY
the results), and the array of real world situations where such a tool
can be used.
Extending Fundamentals to Solving Realistic Problems
The course allows students to explore situations at a substantially
higher level of complexity than is possible in a fundamentals
course where the physics has to be often drastically simplified
to be able to use simple analytical solutions. The course thus
provides a bridge between fundamentals they learn and the situ-
ations they see in real world, thus providing real world problem
solving skills. The students’ own selection and execution of proj-
ects makes the course student-centered and helps convince them of
the realistic nature of the problems that can be solved.
Enhancement of Fundamentals
Although not the primary intended goal of this course, the process
of simplifying a complex real world situation to setup a model,
implementing the solution process, and interpreting the results
enhances the student’s fundamental understanding (of transport
processes in this case). As mentioned earlier, enhancing funda-
mentals is indeed one of the goals of introducing computing in a
curriculum and the course contributes to that goal fairly well.
Group Work (Teamwork)
Being able to work in a group effectively is essential in an
engineering career and therefore is considered one of the critical
elements of engineering education. The process outcome in the
class related to team skills and participation is as important as the
product outcome (the final project report) of the class. However,
individual participation in the group project cannot be assumed or
left to informal encouragement. Thus, we include formal, web-
based, peer evaluation every two weeks during the semester, using
a freely available tool (CATME from Purdue University). Using
this tool, the group members evaluate each other on several aspects
of participation: (1) fair share of the work; (2) effective interaction
with teammates; (3) expecting quality; and (4) having relevant
knowledge skills and abilities. Instituting this survey tool has
provided continuous feedback on the team dynamics over the
semester and, more importantly, has definitely prevented the
occasional lack of contribution or other related teamwork diffi-
culties. Although we have not done so at this point in the course
history, it may be possible to also explicitly teach team skills and to
design assignments that support team skills in the class.
Design
Undergraduate engineering curricula are continually challenged to
include more design aspects, including: (1) solving open-ended
problems; (2) solving problems closer to the real world; (3) being
aware of constraints; (4) requiring interdisciplinary expertise; (5)
being a culminating experience; (6) involving group work; (7)
introducing variability; (8) introducing optimization; (9) inclusion
of presentation (oral and written). Students in this course must state
their projects in terms of a design objective: product, process, or
procedure. From the details already provided about this course,
these design topics are included in a very natural way. The projects
are certainly open-ended with no clear solution and start from a
real world situation. In their report, students need to address
physical, financial, environmental, or ethical constraints of the
design solution they are proposing. Their interdisciplinary exper-
tise in basic biology, physiology, and engineering sciences is often
integrated, leading to the final design outcome (a culminating
experience). Variability, inherent in design, can be very naturally
included through simulation of the physics over a range of design
parameters using either point data or assumed distributions of the
parameter (Monte-Carlo), which is the essence of simulation-
based design. In the process of studying variability, the concept
of optimization is automatically introduced. A slightly more for-
mal optimization process, such as defining an objective function, is
also introduced and case studies from literature demonstrating the
optimization process are shared.
Communication (Written, Oral)
Written and oral communications for engineering graduates are
areas that often beg more attention. Both of these forms of com-
munication are naturally included in this course. The final project
report at the end of the course serves to enhance written com-
munications. Since a simulation can produce many different
results with lots of details, it requires a special effort to distill
the results and relate them to the design goals. How to do this is far
from obvious to a junior/senior undergraduate. The Engineering
Writing Program at Cornell University believes in helping students
in writing in context, and that program has become a partner in this
class. The program provides clear directions to the students to
relate the writing to its intended goal, and critiques individual
project reports. In going through this writing process, the students
satisfy the engineering writing requirement at Cornell University.
The oral communication is also built in naturally to this class as the
group project reports need to be presented at the end of the
semester.
FOLLOW-UP: LINKAGES TO THE OUTSIDE WORLD
Students in this course have gone on for higher studies in BME, to
medical school and to industry. On several occasions, exposure to
the benefits of modeling was carried over to the follow-up steps in
the student’s career. Thus, students introduced these to their
medical school colleagues, introduced as part of higher studies
in BME, and in industry.
SUMMARY
This course is an example of how simulation can be effectively
included, serving multiple purposes in an undergraduate engin-
eering curriculum in an integrated manner. Such purposes include
introduction to a cutting-edge tool such as computer-aided engin-
eering, development of teamwork, design, and oral and written
communication skills. At the same time, it is possible to sensitize
the students to the pitfalls of such simulation software so that they
use it more cautiously. By allowing undergraduate students to
develop real-life projects starting from a substantially higher level
of complexity compared to conventional homework problems, a
course that integrates simulation can boost student confidence. By
applying the fundamental engineering concepts such as heat and
mass transfer to more realistic problems without devoting much
time and energy to the mathematics behind the solution process,
the fundamentals are enhanced, while at the same time preparing
students more effectively for careers in design and research in
industry or higher education.
 SIMULATION IN UNDERGRADUATE CURRICULUM
The course discussed here is highly flexible in terms of its
place in the engineering curriculum. It is more readily an elective
course dealing with a particular application. Although the bio-
medical applications were the focus here, this developed frame-
work can be easily extended to other applications such as
bioprocess engineering and bioenvironmental engineering, and
to other engineering curricula such as mechanical or chemical.
The course can also be more broad-based with applications of
transport processes from more than one area (i.e., bioenvironmen-
tal and bioprocess) within the same curriculum. Finally, concepts
of introducing simulation, as presented here that build on heat and
mass transfer can be extended to other engineering fundamentals
such as solid mechanics and electromagnetics.
ACKNOWLEDGMENTS
Authors gratefully acknowledge departmental and university pro-
grams that supported the development of this course over the years.
In particular, the Cornell Innovation in Teaching Program helped
improve the distributed learning concept using the case studies.
Discussions with Dr. Lance Collins of the School of Mechanical
and Aerospace Engineering in this context is also appreciated.
Dr. Richard Felder’s suggestion to use CATME for peer evaluation
in improving the group dynamics is also appreciated.
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BIOGRAPHIES
Ashim Datta is a Professor in the Department of
Biological and Environmental Engineering at
Cornell University, where he has developed
and taught modeling of biomedical transport
processes as a course since 1996. He is the
recipient of the State University of New York
Chancellor’s Award for Excellence in Teaching
(2010) and he has authored a textbook, authored
and co-authored over 85 technical papers and
book chapters, and also co-edited three books on
biological heat and mass transfer.
Vineet Rakesh is a Research Scientist in the
Computational Medicine and Biology Division
of a biomedical research company. His research
includes development of novel multiscale
models of human/animal physiology, pathology,
injury, and pharmacology. He received his Ph.D.
in Biological Engineering from Cornell Univer-
sity. He has also worked as a teaching assistant
for the biomedical process modeling course at
11
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Cornell for three years and has been presented with the Outstanding
Teaching Assistant award. His Ph.D. research has included modeling of
airflow in the upper airway and drug transport in cancer therapy.
David Way has been at Cornell University for
30 years. During that time, Dr. Way has helped
initiate college-wide graduate teaching devel-
opment programs in four colleges, developed
faculty development materials used throughout
the university, assisted several colleges to rede-
sign their student evaluation of teaching sys-
tems, initiated and published the first university-
wide newsletter on undergraduate education,
consulted with over 30 departments and aca-
demic fields on instructional and faculty development, encompassing eight
schools and colleges on the Ithaca campus, and has been instrumental in the
design and development of an annual faculty retreat on teaching and
learning. He teaches Nutritional Sciences 6170, Teaching Seminar and
ALS 6015, The Practice of Teaching in Higher Education. He is author of
the Cornell Teaching Evaluation Handbook. He currently serves on the Vice
Provost’s Core Assessment Committee.