本课将教导你如何建构一个生物分子间反应的动力以及平衡数学模型，并应用这些定量分析解决横跨各式物种阶层的生物问题，且探讨内容将涵盖从独立分子间至分子族群间的相互作用。

教科书

Lauffenburger, Douglas A., and J. Jennifer Linderman，《受体：结合、循环以及讯息传递模型》，纽约: 牛津大学出版社, 1996. ISBN: 0195106636.

参考读物:

Hammes, Gordon G，《生物科学之热力学与动力学》，Hoboken, NJ: John Wiley and Sons, 2000. ISBN: 0471374911.

Creighton, Thomas E，《蛋白质：结构以及分子特性》，第二版. New York, NY: W. H. Freeman and Company, 1993. ISBN: 0716723174.

Bailey, James, and David F. Ollis，《生化工程纲要》，第二版. Burr Ridge, IL: McGraw Hill Higher Education, 1986. ISBN: 0070032122.

Steinfeld, Jeffrey I., J. S. Francisco, and W. L. Hase，《化学动力学》，第二版. E. Rutherford, NJ: Prentice Hall PTR, 1998. ISBN: 0137371233.

Cantor, Charles R., and Paul R. Schimmel，《生物物理化学》，New York, NY: Worth Publishers, 1980. ISBN: 0716711885, 0716711907, 0716711923.

Blanch, Harvey W., and D. S. Clark合辑，《生化工程》，New York, NY: Marcel Dekker, 1997. ISBN: 0824700996.

Shargel, Leon等人编著，《应用生物制药学与药物动力学》，New York, NY: McGraw-Hill Professional Publishing, 2004. ISBN: 0071375503.

Carberry, James J，《化学以及催化反应工程》，New York, NY: McGraw-Hill, 1976. ISBN: 0070097909.

Strogatz, Steven H，《非线性动力与混沌：于物理、生物、化学暨工程上之应用》，Cambridge, MA: Perseus Publishing, 2000. ISBN: 0738204536.

作业

总共有十二份作业。一开始的作业主要着重在课堂中所涵盖的数学模型与概念，并包含使用MatLab解题的内容。后半期的作业会更深入利用MatLab，执行课堂中所指定的研究论文中的模型。

Grading Scale for Model Implementations (PDF)

文献报告以及讨论

格式

• 每堂课进行两篇论文的报告以及讨论。（如有需要亦会提供额外之相关背景资料的论文）
• 每篇文章报告中应包括两部份，其报告的时间大致相同。
  1. 模型公式以及相关生物背景
     • 关键项目与简化自相关生物现象的基础概念（流览基础教科书里的图表可帮助你学习相关概念）
     • 该领域尚未解决的难题
     • 可能的技术或生物医学应用
     • 提出一个可用以描述本模型所有的必要构成要素的图形
     • 强调并讨论模型的相关公式，每一项式的出处以及为何使用该型态计算方式而舍其他公式的原因
     • 参数推算或回归计算的实验基础
     • 分析或数量化之解题方法
       
       
  2. 模型结论以及其它诠释
     • 该模型结果的分析报告
     • 该模型与目前已有的实验资料间的差异性比较
     • 其他可做的推论
       
       
• 上述每一段落由两位学生报告，并做出最终总结报告。

评分标准

In this course you will learn to construct kinetic and equilibrium mathematical models of biomolecular interactions, and apply these quantitative analyses to biological problems across a wide range of levels of organization, from individual molecular interactions to populations of cells.

Textbook

Lauffenburger, Douglas A., and J. Jennifer Linderman. Receptors: Models for Binding, Trafficking, and Signaling. New York: Oxford University Press, 1996. ISBN: 0195106636.

Supplemental Texts

Hammes, Gordon G. Thermodynamics and Kinetics for the Biological Sciences. Hoboken, NJ: John Wiley and Sons, 2000. ISBN: 0471374911.

Creighton, Thomas E. Proteins: Structures and Molecular Properties. 2nd ed. New York, NY: W. H. Freeman and Company, 1993. ISBN: 0716723174.

Bailey, James, and David F. Ollis. Biochemical Engineering Fundamentals. 2nd ed. Burr Ridge, IL: McGraw Hill Higher Education, 1986. ISBN: 0070032122.

Steinfeld, Jeffrey I., J. S. Francisco, and W. L. Hase. Chemical Kinetics and Dynamics. 2nd ed. E. Rutherford, NJ: Prentice Hall PTR, 1998. ISBN: 0137371233.

Cantor, Charles R., and Paul R. Schimmel. Biophysical Chemistry. New York, NY: Worth Publishers, 1980. ISBN: 0716711885, 0716711907, 0716711923.

Blanch, Harvey W., and D. S. Clark, eds. Biochemical Engineering. New York, NY: Marcel Dekker, 1997. ISBN: 0824700996.

Shargel, Leon, et al. Applied Biopharmaceutics and Pharmacokinetics. New York, NY: McGraw-Hill Professional Publishing, 2004. ISBN: 0071375503.

Carberry, James J. Chemical and Catalytic Reaction Engineering. New York, NY: McGraw-Hill, 1976. ISBN: 0070097909.

Strogatz, Steven H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering. Cambridge, MA: Perseus Publishing, 2000. ISBN: 0738204536.

Assignments

There will be a total of twelve assignments. Initial homework assignments will focus on mathematical modeling and concepts covered in class, including some work in MATLAB®. Later assignments will consist of more involved work in MATLAB®, implementing models described in assigned papers from the literature.

Grading Scale for Model Implementations (PDF)

Literature Paper Presentations and Discussion

Format

• 2 papers presented and discussed per class meeting (additional background papers may be provided).
• Each paper will be presented in 2 parts of roughly equivalent length.
  1. Biological background and model formulation
     • Key terms and simplified basic concepts of the relevant biology (scanned figures from basic textbooks might help).
     • Open questions in the field.
     • Potential technological and/or biomedical applications.
     • Present a schematic cartoon of the essential components of the model.
     • Highlight and discuss the model equations, origin of each term, and reason for rejection of alternative forms.
     • Experimental basis of parameter estimates or regression fits.
     • Method of solution, analytical or numerical.
       
       
  2. Model results and their interpretation
     • Critical presentation of the model outcomes.
     • Consistency with available experimental data.
     • Testable predictions.
       
       
• Two students will prepare to present each section above, and will make a joint presentation together.

Grading