Mechanics:
We will cover relevant topics in biological transport through analysis of key papers from the literature. One premise of this course is that the application of mathematical modeling and simulation to biological problems is an extremely useful tool for understanding complex behaviors observed in biology. Further, these approaches can play an important role in understanding, or determining, underlying mechanisms and can be used to motivate and propose new experiments.

Given this premise, we will approach material from an integrated biological / engineering / mathematical perspective. Specifically, we will structure the course into 3 major case studies along with a number of shorter exercises to highlight particular concepts. Topics to be covered are glucose-insulin dynamics, the role of gradients in developmental biology, the antibody binding site barrier in development of anti-tumor therapeutics, blood flow, and tumor vasculature. Said another way, we will discuss compartment models, simple diffusion systems, fluid dynamics, and combined convection-diffusion problems. For each module, we will focus on a paper or set of papers exemplifying the use of modeling/simulation to investigate a biological problem of interest. Through lecture, discussion, and supplemental reading (e.g. textbook, background papers), and guiding exercises, we will cover the fundamentals of the transport phenomena, biological background, and mathematical background to provide you with the tools to analyze the topic at hand.

Always bring your computers to class.

Deliverables:
The exercises are meant as preliminary exercises to orient you to the topic or methods at hand.

For each of the 4 case studies, you will work on implementing or analyzing the model at hand towards a final paper (1, 2, and 3) or presentation (4) on the module. Details provided in class.

To make this class enjoyable and rich for all of us, we expect you to actively participate in class discussions of the material.

Feedback and Assessment:
For each case study paper, you or your group will recieve feedback on your drafts. Each of the three case studies is worth 15% of your final grade. All authors will receive the same assessment and grade on a paper or presentation. Each paper will be assessed as if it were a submission to a journal for publication. It will receive a score from 1 to 5 which means:

5 - Absolutely no revisions necessary. Ready for publication. (Almost impossible to recieve this score)
4 - Excellent work - clearly thought out, analyzed, and presented. Minor revisions suggested, could be published.
3 - Very good work. However a major revision (or many minor revisions) are needed to make suitable for publication.
2 - Work requires major revisions. Not recommened for publication in current state.
1 - Unable to assess. Do not publish.

Papers for case studies 1, 2, and 3 should be written up using IEEE format. Templates for LaTeX (including the class) and Word are here.

Presentations for case study 4 should be technical, informative, and formal.

Case studies will be assessed based on the following breakdown:
4-5 = A
3-4 = B
2-3 = C
1-2 = D/F

Deliverables for the 5 Exercises are less formal and more individual. Exercises are each worth 5% of your grade. They will be assessed on a 0, 1, 2 basis corresponding to not completed, partially completed, and absolutely, beautifully complete.

The remaining 15% of your grade is discretionary and based on class participation and effort.

Teamwork:
As mentioned earlier, you may work with other members of the class during the case studies and you may work collaboratively for exercises. Teams can have no more than 3 members; in my experience 2 is better. If you decide to work in a team, it is important to bear the following points in mind:
- All team members are required to share with each other their various findings.
- All team members are required to share in the writing of the technical paper.
- You are never permitted to simply ``do'' things for other people.

While this is a very grey area, we would like you to consider the following question at moments of doubt: "Does this really help me learn?"

You may, of course, decide to work on your own, and this is perfectly acceptable.

Workload
In this course we will adopt the 12-hour rule as follows. As this is a 4 credit course, the student of typical preparation will spend roughly 12 hours per week on this course. Given the format of the course, you must monitor your own time usage, and I strongly encourage you to use your time efficiently. In addition, there will be times when working more will result in a better deliverable - you must assess this carefully and do not hesitate to cut your work short if need be. Another factor is teamwork, which can either help or hinder - please think about this carefully every time you arrange to meet as a team. One consequence of this rule is that in principle there are no peak periods of activity - this however is likely to prove false. It is very important that you provide me with continuous feedback on the workload issue.

Honor code
Unless otherwise stated in an assignment, you may consult with any member of the Olin community regarding any piece of work. You may also use any software and/or online resource. You must, however, accurately and completely acknowledge any assistance or resources that you use. We actively encourage teamwork and collaboration, but you must be able to defend any piece of work individually. If in doubt, ask yourself the question: Could I defend this work during an individual oral exam? If you have any questions about this policy please ask us as soon as possible.