"Biotransport" Syllabus

Introducing your Spring 2026 Learning Guide

This learning guide contains important information about the course. Start here when you have questions about the course.

Who is helping you learn?

Brian P. Helmke, PhD

helmke@virginia.edu

Office: MR4 1124

Graduate TA: --

Undergraduate TA: --

When do we meet?

Class meetings: Tue/Thu 9:30 am–10:45 am Eastern Time

Exam week: Thu, May 4, 2026, 2:00 pm–5:00 pm Eastern Time

Additional coaching:

• Office hours: check the post pinned at the top of your Piazza feed
• I have an open door policy: you may stop by and knock any time.
• If you can't drop by my office, send a private Piazza message to 'Instructors', and we'll find a time to zoom with you.
• Please post and answer questions using Piazza so everyone in the class benefits.

Resources to support your well-being

As your professor, I care about you and your well-being. We all have a responsibility to maintain a safe community on Grounds, and I promise to do my part to create a safe space that supports you in your personal journey. If you or a friend are feeling overwhelmed, stressed, or isolated, there are many individuals here who are ready and wanting to help. If you wish, you can make an appointment with me to talk in my office. I will listen, and I will help you find resources that may be helpful to you.

Alternatively, there are also other University and School resources available to you when you experience academic or personal stresses. The School of Engineering and Applied Science has staff members located in Thornton Hall who you can contact to help manage academic or personal challenges. Please do not wait until the end of the semester to ask for help!

The Center for Connection in Engineering (CCE) is a student space designed to help students succeed academically and beyond. It exists to connect students with the academic, financial, health, and community resources they need to thrive both at UVA and in the world. The CCE includes an open study area, event space, and staff members on site. For more information, contact Dr. Meara Habashi at mhabashi@virginia.edu. 

The Department of Student Health & Wellness offers support programs for students. Visit https://www.studenthealth.virginia.edu/support or call 434-243-5150 to get started and schedule an appointment. When scheduling, be sure to specify that you are an Engineering student. If you prefer to speak anonymously and confidentially over the phone, call Madison House’s HELP Line at any hour of any day: 434-295-TALK.

If you or someone you know has been affected by power-based personal violence, sexual or gender-based harassment or violence, bias, or hazing, then I encourage you to make a report of the incident either anonymously or in your own name through the university's Just Report It website. The Sexual Assault Resource Agency. (SARA), Shelter for Help in Emergency. (SHE), and UVA Women’s Center (434-982-2252) are also ready and eager to help. As a faculty member, I am a responsible employee, which means that I am required by University policy and by federal law to report certain kinds of conduct that you report to me to the University's Title IX Coordinator. The Title IX Coordinator's job is to ensure that the reporting student receives the resources and support that they need, while also determining whether further action is necessary to ensure survivor safety and the safety of the University community. The worst possible situation would be for you, your friend, or me to remain silent when there are so many here willing and able to help.

It is my goal to create a learning experience that is as accessible as possible. Please meet with me to explore your options if you anticipate any challenges meeting course requirements or interacting with the course materials. You may also wish to work with the Student Disability Access Center to discuss a range of options for removing barriers in this course. We are fortunate to have an SDAC advisor, Courtney MacMasters, physically located in Engineering. You may email her at cmacmasters@virginia.edu to schedule an appointment. If you have already been approved for accommodations through SDAC, please send me your accommodation letter and meet with me so we can develop an implementation plan together.

If your religious beliefs or observances conflict with academic requirements in this course, please post me a private message on Piazza, and I will do my best to reasonably accommodate you. You may also contact the University's Office for Equal Opportunity and Civil Rights with questions or concerns about academic accommodations for your religious beliefs or observances.

Why should you care about biotransport?

How can you deliver a drug to kill tumors without killing the patient? How can you harness nanotechnology to design inexpensive kits to diagnose diseases in low-resource countries? How do you create functioning blood vessels to repair an injury or keep artificial organs alive? How should you model motility and proliferation of bacteria during an infection? These are examples of “grand challenges” faced by practicing biomedical engineers that require us to design mathematical and experimental approaches for predicting, measuring, and interpreting transport phenomena quantitatively. In this course, you will combine your knowledge of applied mathematics and human physiology from the molecule to cell to whole body length scales to begin exploring how to answer grand challenge questions such as these.

How will this course help your career development?

Grand challenges are fundamental questions in biotransport with broad applications to science, engineering, and human health. In this course I will help you acquire a conceptual and practical framework that you can apply to solve complex grand challenges in your future research, engineering practice, or clinical practice. More simply stated, your goal is to build skills for designing and implementing a problem-solving process as a practicing biomedical engineer. By the end of the course, you will be able to answer the following questions:

1. How do I use math to figure out how, why, and where stuff flows in the body?
2. Some equations in physics and engineering are easy, like F = ma. When and how can I use simple common sense equations to approximate flows of stuff in my complicated biology models or medical device designs?
3. I’ve taken classes like differential equations and physiology, but I don’t know what those classes have to do with each other. How do I put stuff from other classes together to solve “real-world” medical problems or to design medical devices?
4. How can I use equations and answers that I found using tools like Google and Wikipedia to solve homework problems and to do engineering design?
5. How do I use equations and answers from this class to solve problems in research and medicine next year in my Senior Capstone Project or after I graduate?

Want to see learning goals and outcomes in the more formal language of academics and ABET?

What will we do in this course?

The bridge truss diagrams below illustrate how we will develop your framework for solving grand challenges in biotransport. The three conservation laws are like the basic shape of a king post truss bridge: they are required and sufficient to provide a stable foundation for any bridge truss design or to solve any biotransport problem. However, for more complicated or specialized problems, like longer bridge spans, heavier truck loads, or multi-lane highways, more complicated truss designs are required that use additional truss elements. Likewise, we will solve complex biotransport problems by adding elements to the basic conservation laws.

The calendar of class activities is published in the UVACanvas Modules. In order to help you plan, the due dates for assignments are fixed and are published to your UVACanvas Calendar. The rest of the course schedule is dynamic so I can adjust the activities and timing based on our progress and interests. I will update the calendar after each class to keep you informed.

How will we create a supportive and equitable learning environment?

I believe we should make it our goal to support and include each person in the room so we each have an equal opportuntiy to achieve our learning objectives. I invite you to consider the following guidelines for discussion in class and in our team-based activities during the course.

1. Recognize how our individual mix of identities inform our perspectives, assumptions, and actions.
2. Allow everyone's voice to be included and heard.
3. Be open to changing our perspectives based on what we learn from others.
4. Create a space that welcomes feedback. Critique ideas, not individuals.
5. Engage mindfully and be aware of how our words and actions may impact others.

How will you succeed in this course?

Participate. I expect you to participate actively in the course based on your own learning goals. We will regularly work in collaborative teams in class and through online office hours and discussions using Piazza. This approach facilitates our learning and mimics your future professional role as a member of interdisciplinary teams of engineers, clinicians, and business people. Since we all come from different backgrounds and experiences, our peers are valuable resources for learning. Don’t shortchange them and yourself by sitting by quietly during class discussions.

Communicate. This course may be unlike any of your previous courses, with increasingly complex content and new kinds of engineering challenges. Because I am committed to helping you address these new challenges, I have an open door policy in addition to class and office hours; I will meet with you or respond to your Piazza post within 24 hours whenever possible. You should let me know what ideas and tools are challenging to you and how you are doing in the class. If you start this habit early in the semester, then I will be able to better tailor our activities to help you learn.

Take risks. Engineering design often requires personal judgments about which references to include or ignore, which mathematical approaches to follow, and/or how to interpret complex data. Sometimes the “right” answer is unknown, incomplete, or even wrong! Nobel Prize breakthroughs have resulted from attempting to support a “best guess” with incomplete data or from finding evidence to explain an “experiment gone wrong”. My goal is to create a safe learning environment in which you will be rewarded for going out on a limb to defend your ideas. Do your best to make your assumptions and decision-making process transparent in your answers. If you’re not sure how to start a problem, don’t be scared to defend your assumptions and go for it!

Have fun. Sometimes we all need a mental break. During class, I often feel the need to pause and tell a joke. Feel free to share your own jokes (mine are awful!). The only rule is that it must not be a joke that will get me fired! Jokes are not graded; it’s just for fun!

Where can you look for important information?

Anywhere you want! Bring your favorite web-enabled device (with a fully charged battery!) to every class; we’ll use it often. “Real” biomedical engineers use handbooks, textbooks, online resources, peer-reviewed articles, personal communications with colleagues, etc. to learn what they need to know to answer complex questions like the ones listed above. As your colleague, I will recommend some resources and post my notes on the class UVACanvas site, but you should not feel limited to only the materials I suggest. In fact, you will probably need additional resources to complete the full story surrounding some of these challenging questions.

How will you and I evaluate your progress?

Helping yourself learn (10%). In order to evaluate your own progress in learning each day’s concepts, I will ask you to answer short concept check questions or practice problems before or during each class. Some questions help you review and check your understanding of key concepts. Other questions ask you to reflect on your learning process. Some may be submitted anonymously. Specific instructions will be provided each day. These answers will not be graded individually, but completing them thoughtfully will count towards your grade. In order to help you reflect on your own learning, we will discuss your answers together in class.

Homework problems (25%). Practicing by doing is often effective to help you learn common equation derivations and mathematical methods. These homework problems are designed to give you practice setting up and solving analytical equations that you will be able to apply to answer questions in specific biomedical engineering applications. Your learning facilitators are available in person and online (using Piazza) to help you when you get stuck. I can also help you with electronic submission and grading rubric.

Quiz problems (25%). In the role of professional consultant, biomedical engineers sometimes need to come up with common equations and solution methods on-the-fly. Being able to think on your feet to solve a problem quickly also generates fun conversations at cocktail parties. For these problems, you will act as consultants to solve new twists on problems that you have seen before.

Solving grand challenges (25%). In these projects, you will identify and set up a framework to solve grand challenges using biotransport. The challenge problem topics will be based on research and design challenges in the BME department, medical clinics, and other labs at UVa, current events in medicine and engineering, or even your suggestions. Your goal is to identify, to evaluate, and to integrate resources from class, in textbooks, in peer-reviewed literature, and online that you will use to develop a framework for addressing the grand challenge. In some cases (but not always), you may be able to propose a complete mathematical solution. Your grade will be based on a rubric (that I will share with you) that assesses criteria such as problem definition, evaluation of resources, quality and completeness of the solution framework, and discussion of the innovativeness and importance of your project.

Final exam (15%). The cumulative final exam will challenge you with a series of short questions and problems to assess your ability to integrate concepts and methods from class discussions and your grand challenge projects.

A word about professional and academic integrity

As practicing professionals, engineers are trusted to maintain the highest standards of ethics, integrity, and personal responsibility. Since you have joined this community of trust to prepare for your future career, I expect you to fully comply with all of the provisions of the UVa Honor System. In addition to pledging that you have neither received nor given aid on an assignment, your signature also affirms that you have not knowingly represented as your own any opinions or ideas that are attributable to another author in published or unpublished notes, study outlines, abstracts, articles, textbooks, or web pages. In other words, I expect that all assignments and reports are your original work and that references are cited appropriately. Breaking this trust agreement not only will result in zero credit for the assignment in question and referral to the Honor Committee but also will jeopardize your future as a professional engineer. Don’t let yourself down.

What about using GenAI?

Generative artificial intelligence (AI) tools—software that creates new text, images, computer code, audio, video, and other content—have become widely available. Well-known examples include ChatGPT for text and DALL•E for images. This policy governs all such tools, including those released during our semester together. You may use generative AI tools for work in this course however you see fit. If you do use generative AI tools on assignments in this class, you must identify the tool and which part of your work is attributable to the tool. Additionally, please include a brief description (a sentence or two) of how you used the tool and what strategy was effective or ineffective. Example uses include summarizing sources, generating draft text, or proofreading. If you choose to use generative AI tools, please remember that they are typically trained on limited datasets that may be biased or out of date. Additionally, generative AI datasets are trained on pre-existing material, including copyrighted material; therefore, relying on a generative AI tool may result in plagiarism or copyright violations. Finally, keep in mind that the goal of generative AI tools is to produce content that seems to have been produced by a human, not to produce accurate or reliable content; therefore, relying on a generative AI tool may result in your submission of inaccurate content. It is your responsibility—not the tool’s—to assure the quality, integrity, and accuracy of work you submit in any college course. Although you have wide latitude to determine how you use generative AI tools in this course, you must be wary of unintentional plagiarism or fabrication of data. You should always be guided by Honor and your sense of professional ethics. Please act with integrity, for the sake of both your personal character and your academic record.

More questions? Here's the FAQs.

Where can I find the Zoom links for class activities?

Class sessions are in-person, so attendance in Zoom is not available at this time. Sometimes it will be convenient to schedule additional coaching sessions or office hours using Zoom. Click on the 'Online Meetings' tool in our class UVACanvas page to find a meeting ID.

When and where are office hours?

Check out the Additional Coaching section under People & Places.

I'm on the Waitlist. What are my chances of getting in?

Ideally the course size is evenly distributed between fall and spring semesters so that everyone may benefit from in-class discussion and frequent interactions with instructors. Post a private message to me in Piazza with the reason that you must take biotransport this semester, and I'll respond as quickly as possible.

Am I allowed to have my laptop, tablet, and cell phone available during class?

Yes! In fact, you will need your web-enabled device to participate in activities during class.

How should I prepare for class?

Envision yourself as a professional engineer or clinician. No matter what your career path, it is likely that you will often be a member of an interdisciplinary problem-solving team. Since your peers in class come from all different backgrounds, you all can learn well by studying in teams. Don’t be scared to reach out to someone you haven’t worked with before.

Check the Modules in UVACanvas. Materials and activities to help you prepare for class will be posted regularly.

Complete the practice problems. These problems will be "lightly graded"—you get full credit for giving your best effort, whether or not you arrive at the correct answer. If you're not sure about your answer or are stuck, then write a short description of where you are stuck and what you would need to know to continue. The purpose of practice problems is to help you understand and reinforce key concepts in the study notes and other class materials.

Do I need to buy a textbook?

No. UVACanvas will contain links to readings and resources to support your learning, and I encourage you to seek out more resources on your own. I'm always happy to look at web pages, videos, and other things you find to help fit them into the context of our class.

What is Piazza?

Piazza is a class discussion tool designed to enable fast and efficient sharing of information among classmates, the TAs, and the instructors. Rather than emailing questions to the instructors, I encourage you to post your questions on Piazza. If you have a personal question, you may post a private message to 'Instructors'.

What is the best way to contact Dr. Helmke or a TA with questions?

Please post questions related to the course using Piazza. It's OK to post anonymously if you don't want to feel on the spot, and everyone can benefit from the discussion. If you have a personal issue, you may post a private message directed to 'Instructors'.

I sent an email to Dr. Helmke or a TA about the class. Why didn't anyone respond?

Please post questions related to the course using Piazza. We will respond to Piazza messages within 24 hrs (usually much faster than that!), but we will normally not respond to emails about class unless there are extenuating circumstances.

Why is using Piazza so much better than email?

1. Piazza organizes everything in the same site, so it's easy to share messages among students and instructors.
2. Piazza uses html, so it's easy to submit or share files and web links.
3. Piazza is a wiki, so it's easy to update and clarify question and answers.
4. When you share your question in Piazza with the class, everyone benefits; you're probably not the only one with that question (even though it might sometimes feel that way).
5. I regularly check Piazza with an app on my phone, so I can respond quickly. Emails rapidly get buried or forgotten. (My inbox accumulates up to 300 emails per day!)

Am I allowed to post answers to questions in Piazza?

Yes, please! The best way for all of us to learn is to interact continuously rather than to wait for office hours. If you know the answer to a posted question, please post it under Student Answer. Also note that Piazza is a wiki. You can and should revise previously posted questions and answers to improve their usefulness for everyone in the course. I love it when I can mark a student post as "Good Answer" because it's basically what I would have written anyway. It's a great way for you to test and build confidence in your new knowledge.

What should I do if I will miss a class?

Almost everyone misses a class now and then for a good reason. If you notify me before the class, then I will work with you to make sure your learning isn’t affected. A screenshot of notes from each class and a class recording will be posted each day. I will normally not schedule a make-up for missing in-class activities, since they are designed to encourage small group discussions about the class content. Concept Check questions are interactive and part of the discussions, so I don't think it really makes sense to turn them in later after class. Occasionally missing Concept Checks in class will not normally affect your grade. If you have special circumstances or are not sure what to do, just ask me (or post a private message to 'Instructors' on Piazza), and we'll figure it out.

What if I will miss a day with quiz problems?

I will normally not schedule a make-up for missing quiz problems without prior arrangements, since we discuss the solutions immediately in class. If you wake up feeling ill or if an emergency occurs, please do your best to contact me by private Piazza message before class. I will do my best to work out a fair compromise with you.

What if I need to turn in an assignment late?

If extenuating circumstances will prevent you from turning in an assignment on time, please do your best to contact me by private Piazza message before the deadline, and I'll do my best to work out a fair compromise with you. I will normally not accept late work without prior arrangements, since the deadlines are designed to inform instruction and allow us to discuss the assignments during the next class.

I clicked on the 'Class Recording' link in the Module calendar page, but it says I need permission to view the recording. What do I do?

Normally, you can click on the link in the Module calendar page, but first you will have to pass through a security “feature” in UVACanvas. The first time you try to view a class recording, click on the Panopto Video navigation tool on the left of the class UVACanvas page. This will pass your credentials to Panopto (the software add-in that manages the recordings) and take you to the class recordings list.

After the first time, you should be able to click through the links in the class activities calendar to go directly to the recordings. Post me a Piazza message if you still have problems or get some other unexpected permissions or login issue.

Where can I get help with Canvas?

If you experience any problems while using UVACanvas, the Canvas Support team is available to assist you 24/7/365. You can contact the team by direct chat, or by phone at (866) 897-5086. You can also explore the Canvas Student Guides (step-by-step instructions), Student Video Overviews, and other resources tailored specifically for students.