Mathematics, Physics and Basic Programming for the Structural Biologist
|Offered||Study Year 2, Semester 2|
|Course Coordinators||Mu Yuguang (Assoc Prof)||YGMu@ntu.edu.sg||6316 2885|
|Lescar, Julien (Assoc Prof)||Julien@ntu.edu.sg||6908 2208|
|Contact hours||Lectures: 24, Tutorials: 12, Laboratories: 9|
|Approved for delivery from|
|Last revised||17 Mar 2020, 14:38|
This course aims to introduce concepts of mathematics and physics required in the day to day practice of structural biology. After learning signal analysis and image formation theory, you will learn mathematical modeling and computer programming to solve problems in structural biology.
Upon successfully completing this course, you should be able to:
Complex numbers and vector calculus
Fourier coefficients and calculating Fourier transforms
Wave propagation including Electromagnetic waves
Analysis of interference experiments like Young two slits experiments
Simple diffraction experiments
Huygens, Malus and Fermat principles
Basics of lasers and some of their biomedical applications
Python coding principles
|Component||Course ILOs tested||SBS Graduate Attributes tested||Weighting||Team / Individual||Assessment Rubrics|
|Assignment||1, 2, 3, 4||1. b |
|100||both||See Appendix for rubric|
These are the relevant SBS Graduate Attributes.
1. Recognize the relationship and complexity between structure and function of all forms of life, resulting from an academically rigorous in-depth understanding of biological concepts
b. Explain the relationship between structure and function of all forms of life at the molecular level
2. Critically evaluate and analyze biological information by applying the knowledge, scientific methods and technical skills associated with the discipline
g. Evaluate the results of their own experiments and decide on the next step
3. Develop and communicate biological ideas and concepts relevant in everyday life for the benefit of society
e. Discuss current critical questions in the field of biology
4. Acquire transferable and entrepreneurial skills for career development
a. Demonstrate innovative approaches to solving problems in biological science, leading to new approaches or techniques
5. Develop communication, creative and critical thinking skills for life-long learning
c. Demonstrate critical thinking skills such as analysis, discrimination, logical reasoning, prediction and transforming knowledge
6. Develop codes of social responsibility and scientific ethics, particularly in relation to biological advancement and applications
c. Respect regulations involving plagiarism and copyright
7. Demonstrate information literacy and technological fluency
b. Work effectively with common technologies in biology
The lectures will use the ResponseWare system to provide feedback in class on concepts and details for each lecture and hence, you will receive regular feedback on your understanding of the details and concepts being taught. (This helps you to achieve intended learning outcomes 1-4).
In the tutorials, you will receive feedback in the following ways:
- By direct feedback for each answer given during the course of the tutorial.
- The class will discuss key answers at the end of each tutorial. (a. and b. helps you to achieve intended learning outcomes 1 & 2).
- You will discuss with the tutors selected research papers (This helps you to achieve intended learning outcomes 3).
In the labs, you will receive feedback on proper programming practices. (This helps you to achieve intended learning outcomes 4).
The concepts will be introduced during the lectures and illustrated by examples. Further examples will be worked out together during the tutorials. Notes and the key concepts of each lecture will be uploaded to NTULearn at least 3 days before the lecture.
1. We will post questions one week before each tutorial so you can work on answering them.
1. We will introduce Python, a high level programing language.
For Maths/Physics for the Biophysicist:
- Grant R. Fowles, Introduction to Modern Optics, 2nd Edition, Dover, 1989. ISBN-13: 978-0486659572
- Eugene Hecht, Optics, Fifth edition, Pearson, ISBN-10:0-133-97722_6
- Igor N. Serdyuk, Nathan R. Zaccai, Giuseppe Zaccai, Methods in Molecular Biophysics 1st edition, Cambridge University Press, 2007 ISBN: 0-521-81524-X
- John D. Jackson, Classical Electrodynamics, 3rd Edition, John Wiley & Sons, 1998. ISBN: 978-0-471-30932-1
- M. Born & E. Wolf, Principles of Optics, 7th Edition Cambridge University Press, 1999 ISBN: 0 521 64 2221
- Frank J (2006) Three-dimensional electron microscopy of macromolecular assembly. Oxford University Press
- Murphy DB (2001) Fundamentals of light microscopy and electric imaging. Wiley-Liss ISBN 0-471-25391-X
- Vretblad A (2003) Fourier Analysis and Its Applications. Springer-Verlag ISBN 0-387-00836-5
For Scientific Programming:
- Wentworth, P., Elkner, J., Downey, A. B., & Meyers, C. (2012). Learning with Python 3 (RLE). Retrieved from http://openbookproject.net/thinkcs/python/english3e/
To be successful in this course, it is expected that you put in a significant amount of effort into preparation (via the readings), and coding practice, in addition to attending the classes/tutorials/labs.
Good academic work depends on honesty and ethical behaviour. The quality of your work as a student relies on adhering to the principles of academic integrity and to the NTU Honour Code, a set of values shared by the whole university community. Truth, Trust and Justice are at the core of NTU’s shared values.
As a student, it is important that you recognize your responsibilities in understanding and applying the principles of academic integrity in all the work you do at NTU. Not knowing what is involved in maintaining academic integrity does not excuse academic dishonesty. You need to actively equip yourself with strategies to avoid all forms of academic dishonesty, including plagiarism, academic fraud, collusion and cheating. If you are uncertain of the definitions of any of these terms, you should go to the Academic Integrity website for more information. Consult your instructor(s) if you need any clarification about the requirements of academic integrity in the course.
|Lescar, Julien (Assoc Prof)||LKC 06-10||6908 2208||Julien@ntu.edu.sg|
|Mu Yuguang (Assoc Prof)||04s-46a||6316 2885||YGMu@ntu.edu.sg|
|Week||Topic||Course ILO||Readings/ Activities|
|1, 2, 3|
|1, 2, 3|
|1, 2, 3|
Basic optics and image formation
|1, 2, 3|
Lasers and biomedical applications
|1, 2, 3|
The way of the program
Hello, little turtles!
|1, 2, 3, 4|
There are four graded assignments that form the Continuous Assessment, each assignement is worth 25 marks.
Graded assignments are based on
1-Graded Report on Scientific programming in Python
Graded report on the computer practical session displaying the code you have written and and an example of its application.
|16 to 20||Well-articulated coding supported by appropriate comments explaining the logic behind the code|
|10 to 15||The code works efficiently but explanations are not detailed enough.|
|Less than 10||Confusing code with little or no explanations and comments|
2, 3 and 4: Exercises and assays (covering e.g. vectors, complex numbers, Fourier series, waves, polarization, interference, image formation, lasers ... )
Points will be awarded as follows for each assignment:
|16 to 20||Sound and/or cogent answers supported with appropriate scientific |
reasoning and explanations related to biomedical structural biology.
|10 to 15||Generally acceptable answers but not adequately supported with |
appropriate scientific reasoning and explanations related to biomedical
|Less than 10||Majority of the answers are unsound or not cogent, with little or unacceptable explanations.|
Total: The total mark for each part will be scaled to 25, giving a total of 100 for the four assignments.
As a result of this course, it is expected you will develop the following "big picture" attributes:
Have enhanced critical thinking ability
Awareness of the importance of mathematics, physics and programming skills in the practice of biology
Willingness to diligently debug scripts