Teaching

(+) Undergraduate Quantitative Biology (UQ-bio) Summer School (Summer 2021)

The Undergraduate Quantitative Biology (UQ-bio) Summer School is an annual event intended to help undergraduate and first year graduate students acquire essential skills to advance predictive modeling of cellular regulatory systems.  Participants will be exposed to a survey of work in quantitative biology and provided with in-depth instruction in selected techniques. The emphasis of the 2021 program will be experimental and computational techniques useful to understand cellular regulatory networks at the single-cell level. 

The main focus of the program is to get students working together on small mentored projects. Participants will have access to several pre-recorded technical lecture videos each week (approximately 3 hours per week) and will attend daily live events including: research seminars from top scientists in the field (1-2 hours per week), mentored problem sessions (2 hrs per week), project-specific software tutorial sessions (2 hrs per week), career discussion forums (1 hr per week), student presentation sessions (2 hrs per week), and more. The summer school is designed for undergraduate students and early stage graduate students, or anyone with a quantitative background who is new to modeling cellular regulatory systems/networks.

More information about the 2021 UQ-bio Program is available at the course website: http://q-bio.org

(+) BIOM 421 - Transport Phenomena in Biomedical Engineering (Fall 2020)

2020FA-BIOM-421-001: Transport Phenomena in Biomedical Engineering

BIOM 421 – Transport Phenomena in Biomedical Engineering

Prerequisites:BMS 300, LIFE 210, CBE 330, CBE 332 (or MECH 344 and MECH 102)
Lecture Time:MW 4:15 – 5:30 p.m.
Location:Scott 229
Zoom Link:XXX
Zoom Passcode:105080
Instructor:Professor Brian Munsky (he/his/him)
Office:Scott 354
E-mail:munsky@colostate.edu
TA/Grader:William Raymond (wsraymon@rams.colostate.edu)

Texts and Resources:

Recommended:

  • Basic Transport Phenomena in Biomedical Engineering, 4th Edition, by R.L. Fournier, Taylor & Francis, 2018.

Optional:

  • Transport Phenomena in Biological Systems, 2nd Edition, by G.A. Truskey, F. Yuan, and D.K. Katz, Pearson Prentice Hall, 2009
  • An Introduction to Modeling of Transport Processes, Applications to Biomedical Systems, by A. Datta and V. Rakesh, Cambridge Texts in Biomedical Engineering, 2010. (Good place to look for examples of potential course projects).
  • Texts from CBE 210, 332 and 442.
  • Additional course materials will be posted on Canvas.
    •  

Course Description:

This course is intended for senior undergraduate biomedical engineering students who have already had courses in differential equations, numerical methods, basic cell biology, basic physiology, thermodynamics and transport phenomena. This course discusses in detail engineering models of active and passive mechanisms of momentum and mass transport in mammalian cell organelles, cells, tissues, organ systems, and organisms. Non-Newtonian properties of blood and biological fluids will be described. Mass transport concepts will include diffusion and thermodynamic partitioning at and across biological membranes, ion transport, oxygen transport, and mass transport coupled to biochemical reaction kinetics and reaction equilibria. Biomedical engineering applications of transport phenomena will include topics such as thermal regulation, drug delivery (targeted, controlled, and localized), pharmacokinetic models (for drug distribution and clearance, toxicology, and biomedical imaging), and design of extracorporeal devices such as blood oxygenators, kidney dialyzers, and bioreactors for tissue engineering. The course will emphasize the development and application of numerical methods to study transport problems.

Course Objectives:

Students who complete this course will be able to:

  1. Use equilibrium thermodynamics to describe driving forces for biological processes such as phase equilibria, interactions at mesophase interfaces (e.g. biological membranes), and partitioning across membranes.
  2. Apply engineering models of momentum and mass transport, including both analytical and numerical solutions, to phenomena in biological systems such as flow of biological fluids and active transport across membranes.
  3. Solve conservation equations that involve coupled biochemical reaction kinetics and transport phenomena.
  4. Discriminate among and numerically simulate different pharmacokinetic models including one-compartment and multiple-compartment models for drug and toxin distribution and clearance in organs and organisms.Use computational analyses of transport phenomena and thermodynamics to probe understanding of biological processes and to design and optimize biomedical devices.
  5.  

Grading (100 pts + up to 5 pts E.C.):

  • 1 Mid-Term Exam  – 20 pts
  • 1 Final Exam (cumulative) - 20 pts
  • 3 Individual homework assignments – 15 pts (5 pts each)
  • 2 Individual Computer Assignment -- 10 points (5 pts each)
  • 3 Group Computer Assignments – 15 pts (5 pts each)
  • 4 Quizzes Based Upon Computer Assignments -- 20 pts (5 pts each)
  • Extra credit poster: up to 5 pts
  • Extra credit software tutorial: up to 5 pts

Grade Breakdown (out of 100 pts):

  • 81 – 100   A
  • 71 – 80     B
  • 61 – 70     C
  • 51 – 60     D
  • <50           F

Homework Policies:

  • Homework is due at the assigned times. Late homework will not be accepted.  However, if you need an extension, please ask at least 24 hours before the time the assignment is due.
  • Group Computer Assignments: You may choose groups of 2 or 3 for each computer assignment. You may form new groups for each assignment (self-enroll in canvas).  Each group will hand in a single assignment. Assignments should be submitted as .zip files on CANVAS.
  • Individual Assignments: You may discuss individual homework and computing assignments with other students, but each student must hand in their own individual assignment. If you discuss the assignments with other students, you must disclose this in writing in your submission.
  • Students may not use a solutions manual, the Internet, or copy any part of an assignment from another student or group, including those from previous years. Students may use the textbook, resources listed above, and class notes. If you want to use a resource not listed, ask in class or email Dr. Munsky for permission.
  • Homework solutions should be well organized with a logical structure. If the grader cannot follow your solution, you will not get credit for the problem. Final answers should be highlighted or boxed. Units have to be carried out all the way through the answer. In other words, all numbers must have the proper units. Work with algebraic expressions as far as possible before final computations.

Computer Assignments

  • Assigned codes should be written in MATLAB.
  • Each code assignment will require:
    • One or more codes in a specified format.
    • A script that runs this code and verifies results for specified test cases with known solution. These should be published as .doc, .txt, or .pdf documents;
    • A brief statement (in bullet points) as to why your solutions do or do not make sense.
  • It is CRUCIAL that you follow all instructions exactly, especially regarding required function name, inputs and outputs. If anything is unclear in a given assignment, make sure to contact the instructor as soon as possible.
  • All codes must be documented and include a description. Points will be taken off for poorly documented computer codes or unlabeled figures even if they work perfectly!
  • Codes will be graded according to the rubric or point list to be provided at the time of the assignment.
  • Several computational assignments will contain extra credit problems that will allow you to explore advanced topics in computational transport analysis.

Quizzes

  • There will be four short individual quizzes designed to test your use of the computational tools developed throughout the course. These will require the use of Matlab to complete.

The extra credit group tutorial :

  • Groups will create a video-recorded tutorial on a specific software tool for use in transport analysis.
  • Each group can have up to 3 students and will be worth up to 5 points for each student.
  • Choice of software is first-come-first-served with instructor approval.
  • Only one group is permitted to prepare their tutorial for any given software package.
  • Tutorial will contain:
    • A brief description of a computational tool, its authors, its history, and a survey of the kinds of transport problems this tool has been used to address in past studies.
    • A summary and link to a step-by-step guide for the acquisition and installation of the program.
    • A step-by-step, video-recorded tutorial on how the chosen computational tools can be applied to the analysis of the biological phenomenon under investigation. The object of this is not to develop new materials, but to boil down an existing tutorial from the product developer into a form that is easier for undergraduates in biomedical engineering to understand and implement. The focus models used in the tutorial should be related to transport in BME.

Online Lectures and Course Modules

Many course lectures will be pre-recorded and posted on Canvas at the beginning of each module. Slides will also be provided at that time. Lectures will be organized into several course modules and sub-modules including: (1) learning objectives, (3) required or suggested reading,  (2) links to lectures and notes, and (4) homework and study problems.  Students are strongly encouraged to view these course modules regularly. Course attendance is not required – all lectures, exercises, assignments, and exams will be available online.

In-Person and Synchronous Exercises

Most in-person meetings (MW, 4:15pm-5:30pm) will be devoted example problems, computation exercises, and office hour style questions and discussions. These will be live-streamed on Zoom and posted on Canvas. Updates to notes will be posted after each lecture.

All synchronous sessions will be held on Zoom.

Please use the Zoom 'raise hand' or chat window features to ask questions during synchronous exercises.

Canvas

All course-related materials (e.g., handouts, homework assignments, exams, etc.) will be available through Canvas (Links to an external site.) only. All assignments will be submitted through Canvas. Please also make sure that you can receive the instructor’s announcements made on Canvas in a timely manner; click here (Links to an external site.) for help using Canvas.

Matlab

Students will require a working installation of Matlab (version R2020) to complete several homework assignments, quizzes, and exams. A full version of Matlab is available to all CSU students, and can be downloaded following the instructions at: https://www.engr.colostate.edu/ets/matlab/ (Links to an external site.)

Any student who has trouble installing Matlab for use at home should contact the instructor in the first week of class.

COVID-19 Public Health Precautions

All students must follow all public health precautions as outlined at COVID 19 - public health precautions.  These precautions will be strictly followed in this course. Any failure to uphold these precautions will lead to an immediate dismissal from the class with a report made to the CSU administration.

All students should fill out a student-specific symptom checker each day before coming to class (https://covidrecovery.colostate.edu/daily-symptom-checker/ (Links to an external site.)). In addition, please utilize the symptom checker to report symptoms, if you have a positive test, or exposed to a known COVID contact. If you know or believe you have been exposed or are symptomatic, it is important for the health of yourself and others that you report it through this checker. You will not be in trouble or penalized in any way for reporting. If you report symptoms or a positive test, you will receive immediate instructions on what to do and CSU’s Public Health Office will be notified. Once notified, that office will contact you and most likely conduct contact tracing, initiate any necessary public health requirements and/or recommendations and notify you if you need to take any steps. For the latest information about the University’s response, please visit the CSU COVID-19 site (https://covidrecovery.colostate.edu/ (Links to an external site.)). 

Academic Integrity Policy:

  • The engineering profession is founded upon an expectation of utmost integrity among practicing engineers. Because of the trust placed in engineers by society, the college of engineering at Colorado State University expects its students to live up to a high standard of academic integrity. There is a zero tolerance policy in this class for violations of university academic integrity policies.
  • Furthermore, to achieve the best possible learning experience, students must work on, and fully understand the solutions for, all of the course assignments. If a student fails to complete their own work and/or copies from an unauthorized source, they are cheating themselves out of their education and are committing plagiarism.
  • This course will adhere to the CSU Academic Integrity Policy as found in the General Catalog - 1.6, pages 7-9 (Links to an external site.) and the Student Conduct Code (Links to an external site.). At a minimum, violations will result in a grading penalty in this course and a report to the Office of Conflict Resolution and Student Conduct Services. In addition, a copy of the report will be sent to David Dandy and will be placed in your student file.
  • If you have questions about academic integrity at CSU see the following web resource… http://learning.colostate.edu/integrity/index.cfm (Links to an external site.)
  • On homework assignments, students may not use a solutions manual or copy any part of an assignment from another student, including those from previous years. Both the student who copied and who allowed the copying of material will receive the same penalty.
  • For open book exams, you may use your textbook and course notes. No electronic devices are allowed during exams. Talking to other students is not allowed during the exam. 
  • Homework and exams may not be shared with future students or on the Internet.

Accommodations:

Please let the instructor know as soon as possible if you have a disability, which may require some modification of seating, testing or other class requirements so that appropriate arrangements may be made.

(+) CBE 331 - Momentum Transport and Mechanical Separations (Fall 2020)

Course Syllabus

Colorado State University

Department of Chemical and Biological Engineering

CBE 331: Momentum Transfer and Mechanical Separations

PrerequisitesCBE 210 and MATH 340
Online LecturesPre-recorded lectures will be posted on Sunday evening.
Recitation / Office Hours

MWF 10:00 to 10:50am

 

InstructorDr. Brian Munsky (he/his/him)
    Office354 Scott Bioengineering
    Phone970-492-4863
    E-mailbrian.munsky@colostate.edu   
TAMichael May (michaelpmay@live.com)
GraderRachel Keating (keatirac@rams.colostate.edu)

Textbook

  • Gerhart, Gerhart, and Hochstein, Munson, Young, and Okiishi’s Fundamentals of Fluid Mechanics, 8th Ed., Wiley, 2016.

Reference Book (not required)

  • Bird, Stewart, and Lightfoot, Transport Phenomena, Revised 2nd Ed., Wiley, 2006.

Learning objectives

A student successfully completing this course will be able to:

  1. Determine the variation of pressure in a static fluid and calculate forces on submerged surfaces in a static fluid;
  2. Derive and apply the Bernoulli equation, and explain its limitations;
  3. Describe fluid flow using Eulerian and Lagrangian frames of reference;
  4. Apply the Reynolds transport theorem and material derivative;
  5. Apply conservation of mass and energy and Newton’s second law to a macroscopic control volume and solve the resulting ordinary differential equations to calculate velocity profiles, flow rates, pressure drops, and forces;
  6. Apply the Navier-Stokes equations to solve flow problems under steady-state conditions;
  7. Apply the Buckingham Pi theorem to deduce dimensionless relationships for data analysis, and apply the concept of similitude;
  8. Identify main characteristics of the different regimes of flow in pipes and conduits;
  9. Explain the concept of boundary layer and calculate its properties explicitly by analyzing flow over a flat plate.

For more detailed learning objectives, please see Modules posted on Canvas.  These can also be used as the study guide for quizzes/exams.

Online Lectures and Course Modules

All course lectures will be pre-recorded and posted on Canvas at the beginning of each week. Slides will also be provided at that time. Lectures will be organized into several course modules and sub-modules including: (1) learning objectives, (3) required or suggested reading,  (2) links to lectures and notes, and (4) homework and study problems.  Students are strongly encouraged to view these course modules regularly. Course attendance is not required – all lectures, exercises, assignments, and exams will be available online.

In-Person and Synchronous Exercises

In-person meetings (MWF, 10:00am-10:50am) will be devoted example problems and office hour style questions and discussions.  These will be live streamed on Zoom (see below for invite and password) and posted on Canvas. Notes will be posted after each lecture.

CBE 331 classes will be Online-Only for the first two weeks of the semester.

The reason for this decision is to increase social distancing and give the university sometime to get used to new policies put in place to minimize initial spread of the pandemic at the beginning of the semester. In-Person meetings will resume after Labor Day provided that the infection rates in Larimer county remain within acceptable limits.

All synchronous sessions will be held on Zoom.

Please use the Zoom 'raise hand' or chat window features to ask questions during synchronous exercises.

In-Person Attendance

Unfortunately, due to the ongoing COVID 19 pandemic and social distancing requirements, only 1/3 of the class can attend in-person class exercises each day. Each student has been assigned a specific day Monday, Wednesday or Friday. All in-person exercises will be live-streamed synchronously (on both Echo 360 and Zoom), and videos will be posted asynchronously on Canvas.

COVID-19 Public Health Precautions

All students must follow all public health precautions as outlined at COVID 19 - public health precautions.  These precautions will be strictly followed in this course. Any failure to uphold these precautions will lead to an immediate dismissal from the class with a report made to the CSU administration.

All students should fill out a student-specific symptom checker each day before coming to class (https://covidrecovery.colostate.edu/daily-symptom-checker/ (Links to an external site.)). In addition, please utilize the symptom checker to report symptoms, if you have a positive test, or exposed to a known COVID contact. If you know or believe you have been exposed or are symptomatic, it is important for the health of yourself and others that you report it through this checker. You will not be in trouble or penalized in any way for reporting. If you report symptoms or a positive test, you will receive immediate instructions on what to do and CSU’s Public Health Office will be notified. Once notified, that office will contact you and most likely conduct contact tracing, initiate any necessary public health requirements and/or recommendations and notify you if you need to take any steps. For the latest information about the University’s response, please visit the CSU COVID-19 site (https://covidrecovery.colostate.edu/ (Links to an external site.)). 

Canvas

All course-related materials (e.g., handouts, homework assignments, exams, etc.) will be available through Canvas (Links to an external site.) only.   All assignments will be submitted through Canvas. Please also make sure that you can receive the instructor’s announcements made on Canvas in a timely manner; click here (Links to an external site.) for help using Canvas.

Matlab

Students will require a working installation of Matlab (version R2020) to complete several homework assignments, quizzes, and exams. A full version of Matlab is available to all CSU students, and can be downloaded following the instructions at: https://www.engr.colostate.edu/ets/matlab/ (Links to an external site.)

Any student who has trouble installing Matlab for use at home should contact the instructor in the first week of class.

Homework and Quizzes

There will be 8 to 10 homework assignments and quizzes. Homework assignments will be collected electronically and checked for completeness and for plagiarism.  Students are required to disclose if they worked with others on each assignment.

Each homework assignment will be combined with a short electronic quiz related to that assignment. Students must submit a homework assignment to be eligible to take the quiz. Quizzes will be graded on a 4-point scale as follows (rounded up to nearest 25%):

  • More than 75% correct: 4pts
  • Between 50-74% correct: 3pts
  • Between 25-49% correct: 2pts
  • Attempted but <24% correct: 1pt

All homework and quizzes are open book and open notes. Students may not work together or discuss quizzes. There will be no makeup quizzes.

Exams

There will be one mid-term exam, and one final exam. Both will designed to be completed in 90 minutes, and students will have a window of 7 hours (11am – 5pm) to download, complete, and submit their completed exams. Both the mid-term and the final exam will be cumulative. 

All quizzes and exams will be open book and open notes. All will require the use of Matlab. Students may not work together or discuss quizzes or exams.

There will be no makeup quiz/exam, and students will receive 0 credit for any quiz/exam they fail to take, unless the absence is excused.  Requests for an excused absence from a quiz/exam must be submitted in writing to the instructor prior to the next scheduled lecture following the quiz/exam.  All re-grades must be submitted to the instructor via email with a clear description of the student’s concern.  These can be at any time prior to the last day of classes.  

For students with learning disabilities, please e-mail the instructor a copy of your letter issued by the Student Disability Center (Links to an external site.), and the allotted time for quizzes and exams will be adjusted accordingly.

Extra Credit

Students can earn up to 5% extra credit by creating a Matlab GUI (using Matlab’s ‘appdesigner’) to visualize and solve an assigned or unassigned homework problem.  The GUI should allow for user to change all physical properties needed in the problem. Examples and instructions to create such GUIs will be presented throughout the semester. No two students can receive extra credit for the same problem. Students can create GUIs for at most two problems for a total of up to 10% extra credit.

Grading

Homework/Quizzes40%
Midterm exam            30%
Final exam                    30%
Extra Credit                     write up to two Matlab GUI to solve homework problems and earn up to (2 x 5%) extra credit.

Academic Integrity Policy

This course will adhere to the Academic Integrity Policy (Links to an external site.) of the Colorado State University General Catalog and the Student Conduct Code (Links to an external site.).  The policy is zero tolerance.  The minimum action taken for academic dishonesty will be a failing grade for the course.  In particular:

  • Students may not copy any part of a homework/quiz/exam from other students, including those in previous years. The student who knowingly provides his/her homework/ quiz/ exam to be copied is also in violation of the CSU policy. 
  • Discussing the content of a quiz/exam with someone who has not taken it is not allowed.
  • Students are expected to report incidents of academic dishonesty to the instructor.