BME 418 Quantitative Cell Biology

BME 418 Quantitative Cell Biology
Course Description:
In this course students will learn the fundamentals of cell structure and function
from a quantitative or physical perspective. The goal is to provide a general
background in cell biology with a physical perspective that is of particular interest
and importance to biomedical engineers. The students will master the basic skills
of quantitative or semi-quantitative analysis applicable to a broad number of
topics. First, the students will learn how to make scientific “guestimations” to
compute proteins and gene numbers useful for model building. After learning the
general principles of the functions of a cell, the students will investigate specific
models of DNA random walks, ion- channel dynamics and electrostatics of
protein molecules. Through discussion of a collection of important and relevant
problems in cell biology, the course adopts a central notion best described by the
authors in the preface of the textbook: “an appropriate application of a relatively
small number of fundamental physical models can serve as the foundation of
whole bodies of quantitative biological intuition, broadly useful across a wide
range of biological problems.” At the end of the semester the students will
present a scientific project on one concept they feel most passionate about and
has the strongest connection to their scientific career.
This year I will be adopting a variety of engaged learning techniques developed
by Prof. Eric Mazur (MIT) and Prof. Steve Yalisove (UMich, MSE). You are
invited (and encouraged) to visit their website and learn more about Engaged
We will meet twice a week for 1.5 hours, Tuesdays and Thursdays 3:30 -5pm in
FXB 1024. The GSI for this course is Quan Zhou ( and
the IA is Eric Waselewski ( The office hours will be
announced at the beginning of the term.
There will not be any formal lecture but rather group work and guided inquiry
work. Homework will not be graded. Your only homework will be the assigned
reading from the textbook. Most of the reading will be assigned on Thursday
followed by a short quiz first thing Tuesday. On the last day of the term (April
21st, Tuesday) you will present a group project. I will not hold a midterm or a
final exam. Instead, after finishing several chapters from the textbook the
students will complete a Readiness Assurance Assessment (RAA). These will
be a short (15-20 questions) set of LearningCatalytics questions, very similar to
the problems solved during the class work. Each student will answer the
questions individually, followed by a group solution. The grade will be combined
of the individual effort and the group effort.
Groups: We will assign the students into groups of 5 at the beginning of the
course and switch the groups after the second RAA. During class time, the
students will sit with their groups at separate tables. Each table will have an
access to an adjacent whiteboard. Each student will be asked to bring a Wi-Fi
enabled device that can access a web browser (Chrome, Safari, or Netscape).
All materials will be sent to the student devices via a web-based product called
We will present questions, problems and examples that were traditionally
delivered during lecture, via LearningCatalytics. In all cases, students will first
answer the question and then spend time discussing it with their groups and
answering again. These answers will not be graded, and the students can review
the questions later. This year the BME 418 students will receive a free account
with LearningCatalytics. We will use LC just about every day our class meets
and also for the Readiness Assurance Assessments (which are 60% of the
grade). Click here for instructions.
Textbook and Assigned Reading
Physical Biology of the Cell (PBoC) (1st or 2nd edition), Rob Philips, Jan Kondev,
Julie Theriot, Hernan G. Garcia, GarlandScience.
Here are the current e-book options:
Vitalbook E-Book:
The VitalBook e-book is available for purchase in its entirety or by chapter, or to
rent for 1 year or 180 days, in the US and Canada from VitalSource. In this
course we will cover 10 chapters.
Purchase or rent in North America.
Physical Biology of the Cell will also be available on Amazon Kindle Print
The final component of the course is the problem-based learning. Each group of
the students will prepare one project that focuses on a concept related to the
topics covered in the course. We will post the list of topics, but students are
encouraged to identify topics by themselves as well. These are open-ended
group based projects that will culminate in a short video (3-5 min). Feel free to
use Khan academy or Youtube videos from the University as examples.
Everyone in the group will get the same grade. An example of a grading rubric
for presentations is shown below.
Rubric for the Video (12 points)
Project Completeness (1 points)
Clean and free from distracting information (2)
Balanced number of words and equations (1)
Clear diction, smooth delivery (1)
Told a story (the audience could tell what the point of the presentation was) (2)
Identified an interesting topic (2)
Utilized at least 2 of 4 core concepts (1)
Talked about relevance for BME or potential application (1)
Peer assessment (1)
Class structure
A typical week will start with a short individual quiz (10-15min) on the assigned
reading material. After the quiz, I will follow up with a short (10 min, max) lecture
to summarize the concepts in the textbook and will answer students’ questions
related to the text they read at home. At the remaining time the students will
solve problems and derive equations as a group, with the instructor, GSI and IA
present in the class to answer questions. On Thursdays, we will start again with
an overview of the current text and answering questions, followed by problem
solving. At the end of the class on Thursday the students will have to submit all
the group assignments in the LC. The work will not be graded for correctness,
but for the effort.
3 credits, TOTAL
RAAs (4 x14=56 points, 1x4 peer assessment, total 60 points)
Quiz (9 x 2=18 points, there will be 10 quizzes, but only your top 9 scores will be
Project (12 points)
Insightful reading of the textbook (10 points)
Late assignments after the due date will be discounted 50%.
Honor Code.
All students are presumed to be decent and honorable, and all students in the
class are bound by the College of Engineering Honor Code. You may not seek to
gain an unfair advantage over your fellow students. It is acceptable to discuss
general solution strategies with peers, but you may not allow any classmate to
copy your solution. Note that creating an unfair advantage for another student is
an Honor Code violation. Login in under someone else username is a violation of
the Honor Code. According to the Family Educational Rights and Privacy Act
(FERPA) students are only allowed to pick up their own work, and not the work of
friends or classmates (even if they have a written approval from their