prof liu xiang yangprof liu xiang yang physics, nusphyweb.physics.nus.edu.sg/~biophysics/pc3267/a-pc...
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![Page 1: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/1.jpg)
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Prof Liu Xiang YangProf Liu Xiang YangPhysics, NUS
![Page 2: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/2.jpg)
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Course Home Pagehttp://www.physics.nus.edu.sg/~Biophysics/pc3267/indexa.htmlP d Password: pc3267Please familiarize yourselves with the information there especially with respect to the tutorials and other there, especially with respect to the tutorials and other matters
![Page 3: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/3.jpg)
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Wh i bi h i i t t?Why is biophysics important?
Many breakthroughs in biology are based on biophysicalprinciples and techniques Biophysical techniquesprinciples and techniques. Biophysical techniquescontinue to play an important role in biological andbiomedical science:X‐ray, NMR images, Electron microscopy, AFM,S i b iScanning probe microscopy, …To explore physical principles and underlyingmechanisms of many phenomena and problemsassociated with life sciences.To assist you to construct the overall picture that at firstsight appears to consist of many disconnected facts.To establish “physics” thinking ‐ “Does this hypothesismake sense given what is known about the dynamics ofmake sense, given what is known about the dynamics ofthis biological system?”, “Can I obtain a betterunderstanding based on exact physical principles?”
![Page 4: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/4.jpg)
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Virus and cellus a d ceHIV, SARS
![Page 5: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/5.jpg)
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C Vi l t iCase: Viral protein
Low pH
![Page 6: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/6.jpg)
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Case: SNARE proteinThe protein works like a nanomachine.The mechanism is pH the process is driven by a
Case: SNARE protein
The mechanism is pH, the process is driven by a hydrophilic/hydrophobic force
![Page 7: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/7.jpg)
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Fusion peptide
Physics can be applied to examine y ppmembrane fusion
![Page 8: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/8.jpg)
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Ai f thiAim of this course
By delivering general knowledgeconcerning the basic principles andi t f h i i lif i thimportance of physics in life sciences, theaim is to establish the interconnectednessof knowledge between human life andof knowledge between human life andactivity and basic physics.To establish the essential knowledge andTo establish the essential knowledge andpractical skills in modern life sciences.
![Page 9: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/9.jpg)
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Course OutlineBio‐molecular thermodynamics/statistics
First law of thermodynamics; molecular interpretation f h d of thermodynamic quantities;
Second law of thermodynamics in biological systems; Statistical complications in modeling macromolecular Statistical complications in modeling macromolecular structure; Molecular mechanics; bonding and non‐bonding g gpotentials; stabilizing interactions in macromolecules.
![Page 10: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/10.jpg)
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C O liCourse OutlineBiophysical description of Biophysical description of MacromoleculesPhysical and structural characteristics of yproteins and amino acidsPhysical environment in the cell Physical and symmetry relationships between molecules
l l h l d Molecular physical interactions and macromolecular structures
![Page 11: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/11.jpg)
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What is to be gained at the end of the Course?
You would be able to obtain essential knowledge of bio‐physical principles which play a very important part in many fields of life sciences.It will help you take other advanced modules in life sciences related subjects.You should be equipped with the basic q ppknowledge/skills to carry out life sciences related research
![Page 12: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/12.jpg)
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Reference Texts: CompulsoryReference Texts: Compulsory
Principles of Physical Biochemistry, K. Van Holde , W. Johnson , Pui Shing Ho, , J , g ,Prentice‐Hall, ISBN: 0‐13‐720459‐0 Biological Physics, Philip g y , pNelson, W.H. Freeman and CompanyISBN: 0‐7167‐4372‐87 7 437
![Page 13: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/13.jpg)
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f lReference Texts: Supplementary
Biophysics, An Introduction, C. Sybesma, Kluwer Academic Publishers, ISBN: 0‐7923‐0029‐7
Biophysics, Roland Glaser, Springer, ISBN: 3‐540‐6 8867088‐2
![Page 14: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/14.jpg)
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Biophysics Teaching Web: http://www.physics.nus.edu.sg/%7EBiophysics/
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Module Structure/AssessmentModule Structure/Assessment
Biophysics IIBiophysics IIp y(PC3267)
p y(PC3267)
~ 26 Lectures,(2.5 hrs/wk)
~ 26 Lectures,(2.5 hrs/wk)
15 hours Experiments
(20%)
15 hours Experiments
(20%)( )( )
~5 Tutorials~5 Tutorials 1 Test (10%)1 Test (10%)5 Tutorials(10%)
5 Tutorials(10%)
Short projectShort projectFinal Exam (50%)Final Exam (50%) (10%)(10%)
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Term paper/presentatione pape /p ese tat o
To provide the opportunity for you to get in touch with some get in touch with some frontiers in biophysics.Team spirit: Several (~3) p ( 3)students to work together as a Team
lActive‐learningPresentation skill
Teamwork
Scripps Res. Inst.
![Page 17: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/17.jpg)
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Project/presentation (cont )Project/presentation (cont.)
Group size: 3 studentsChoose a topic and submit an abstract (~100 words) to
Topic:To be chosen by yourself from the ( )
me by Feb. 8, 2008Carry out readings on this topic, and write a 10‐15 page
yourself from the list provided in the web.S th b f
p 5 p gessay and prepare the presentation.Deadline of submission: A il
See the web for more details
April 11, 2008
![Page 18: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/18.jpg)
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Expt Arrangements3 experiments.Start at the end of Jan (to be announced). J ( )
![Page 19: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/19.jpg)
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& i lTerm Test & Final Exam Test: Test – Tue, Mar 4, 2008
Venue: S1A‐0212
Duration: 1 hour (8:15‐9: 15am).
EXAM
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Official Lecture Time
1.5 times a week
T F i 8 S ATue, Fri., 8:00‐9:30 am, S1A‐0212
Format: Lecturing, and misc/videog
![Page 21: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/21.jpg)
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L A ti l D i L tLearn Actively During Lectures
T t d t d th Try to understand the key concepts during the lecture itself, as details can be filled in afterwards
Please do not hesitate to stop me to ask questions if things are not clear to you, or if I am going too fastast
![Page 22: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/22.jpg)
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Taking NotesJust jot down key points, or something that strikes you
Slides will be made available on the web a few days before each lecture (which you may want to print out beforehand)beforehand)
![Page 23: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/23.jpg)
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ExpectationsPl b l f l i i Please be punctual for lectures, as missing even a small portion might make it harder to follow at a later stage
Attendance is very important, as slides will deliberately be kept brief, and only elaborated y p , yupon in the lectures
Students should take the initiative to read up Students should take the initiative to read up further on the lecture material to enhance their understanding
![Page 24: Prof Liu Xiang YangProf Liu Xiang Yang Physics, NUSphyweb.physics.nus.edu.sg/~Biophysics/pc3267/A-PC 3267... · 2008. 1. 13. · yProf. Dr. Xiang Yang LIU yTel: 6516 2812 yEmail:](https://reader033.vdocuments.us/reader033/viewer/2022051900/5fef48d6c24be66b480fe063/html5/thumbnails/24.jpg)
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Contact InformationContact Information
Prof. Dr. Xiang Yang LIUTel: 6516 2812Email: phyliuxy@nus edu sgEmail: [email protected]: S13, M01‐4
Teaching Assistant (experiment): Dr.Office: S11‐02‐03, Lab: S7‐01‐17Tel: 6516 6598 (office)Email: [email protected]