Department of Physics - Term Paper Objectives and Instructionsphyweb.physics.nus.edu.sg/~Biophysics/GEM1521K/Term Paper... · Web viewYour readings must reflect your understanding

GEK 1521 / PC1326 Special semester 2005 guidelines for Term Paper

Term Paper: Objectives, Instructions and Topics

The term paper is a very important component of the course, making up 40% of the total assessment.

I. OBJECTIVES

To provide an opportunity for you to go deeper into a topic of your choice, related to the physical aspects of life science. It may be a topic you are interested in or one that may be relevant to your major. A list of suggestions may be found in the final part of this document.

II. INSTRUCTIONS

A group size of 3-5 persons is recommended (need not be from the same tutorial group). To form groups would lessen the work for each member, and more importantly, it will help in developing a team working spirit, which is an important element in the 21st century education. Apart from this, discussing with friends would facilitate learning, and may even lead to some creative brainstorming.

If you can not find the proper team members yourself, please email to the

teaching Assistant Mr. Lim Zhi Han (Email: [email protected] ) the topic you prefer. He will help you with the grouping.

When deciding on a topic, your group must try to gain at least a basic understanding /overview of the chosen topic and start looking around for suitable references.

Find your information from one or two main sources, with several ancillary ones. Please do not obtain your information solely from the Internet as the material found there often lacks scientific depth and rigor. If you do use information from the Internet, you should ensure that your sources are reliable and scientifically sound.

Once your group has finalized a topic, a representative must send an email to Mr. Lim Zhi Han with the following information:

o Selected topico Names and matriculation numbers of every group member o An abstract of less than 100 words

The deadline for this is May 25, 2006, but you are encouraged to do this as early as possible so that you can get started on the project.

Your readings must reflect your understanding of the chosen topic. It should give an overview of the topic. It should be pitched at a level that your fellow classmates can understand, and written in an interesting manner.

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mailto:[email protected]

mailto:[email protected]


Please feel free to contact Mr. Lim Zhi Han or myself at any stage during the project, if you encounter any difficulty, have a query, or need some suggestions.

The final report

o It should be about 15 to 25 pages long. Detailed guidelines to the format of the report is given in Appendix 1.

o It should consist of ~ 15 (3 person group), ~ 20 (4 person group), and ~ 25 (5 person group) pages, respectively.

o In any case, your report should not exceed 25 pages (inclusive of everything).

o A title page consisting of the subject title, the names and matriculation numbers of all members of your group should be attached. See Appendix 2.

o Abstract (less than 250 words) and a Table of contents should be provided.

o The report must be properly typed and printed (double-sided). It can either be stapled or bound. Pages must be numbered.

o It may contain figures, graphs and equations, if you think that they can help illustrate the points you wish to make. Figures and graphs are recommended rather than equations. Do not put any equations which you don’t really understand.

All sources of the arguments, data, figures and facts from literature and Internet must be referenced properly. All references should be listed at the end of your report (e.g., author, title, publisher and year, for a book). See Appendix 1 for more details.

The final report must be handed in directly by June 13, 2006.

Reports received after this date will not be considered.

The assessment criteria are as follows: o Content: Does the essay cover the important aspects of the

subject? How much breadth and depth is there? Were figures and illustrations used appropriately? (50%)

o Originality and creativity: Does your essay stand out from the others on the same topic? Is there evidence of trying to rewrite in your own words? Was the topic presented in an interesting or creative way? (30%)

o Overall considerations: Was the essay clearly written? Was it well organized and presented? (20%)

o All group members will receive the same grade. In certain special cases, you may be required to come for an interview as

part of the assessment (e.g., when it is not sure whether you understand what you are writing about).

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IMPORTANT WARNING

Everybody is expected to complete and hand in a term paper. If you do not, you would almost certainly fail the course.

All sources that you use must be properly referenced. Any direct copying of material from your sources must be acknowledged, by placing quotes around the excerpted material and referring to the source in the footnotes or reference section. The direct use of material from any source without such acknowledgement constitutes plagiarism, and, if discovered, would result in your term paper receiving a fail grade.

Direct copying entire paragraphs or sections from a source with only minor paraphrasing is not allowed.

In view of the preceding warning, it is your responsibility to ensure that your group members do not plagiarize any material.

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III. ESSAY TOPICS

Note: the references provided in the following subjects just serve as a starting point for the paper. In order to complete the term paper, you may have to go beyond the provided references to search for more comprehensive information either from Internet or other sources.

Subject 1: Anomalous properties of water

Description: Life depends on anomalous properties of water; for e.g., large heat capacity, high thermal conductivity and high water content in organisms contribute to thermal regulation and control of body temperature. The high latent heat of evaporation prevents dehydration and provides evaporative cooling. Water is an excellent solvent and has unique hydration properties towards biological macromolecules which stabilize their structures, and hence their functions, in solution. Water has properties at low temperatures that are quite different from its properties at high temperatures. In this essay you are encouraged to discuss the structure of water and its important properties that support life on earth.

References:

Martin Chaplin, http://www.lsbu.ac.uk/water/anmlies.html#1a and references therein.

Subject 2: Molecular self-assembly of amphiphilic molecules and the structure and functionalities of biomembrane.

Description: In preparing this essay, you should at least cover the following points:

Intermolecular interactions between amphiphilic molecules and molecular packing parameter

The formation of molecular bilayers Cell and biomembrane The structures and biological functions of biomembranes The role of biomembrane in transporting materials and bio-signals

between cells and their environment. The formation of biomembranes and artificial biomembranes. The applications of biomembranes in other areas of life science.

References: D.F. Evans, and H. Wennerstrom, The Colloidal Domain, where Physics, Biology, and

Technology Meet, (VCH, 1994). Biophysics, An Introduction, by R. M. J. Cotterill, John Wiley & Sons (2002).

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http://www.lsbu.ac.uk/water/anmlies.html#1a


Subject 3: Freezing and anti freeze protein

Description: When freezing occurs in cells of a biological system, formation of ice crystals may damage the cell. Nevertheless, some plants, fish and insects can survive at temperatures well below zero. The secret is that they have certain proteins, the so-called anti-freeze proteins, which prevent the formation of ice even at subzero temperatures. These proteins have some important applications in food processing, and life sciences such as the preservation of organs. You should at least cover the following points in your essay:

How does freezing take place? Physical principles of ice crystallization. How do anti-freeze proteins stop the formation of ice? How can we produce anti-freeze proteins artificially? The applications of anti-freeze proteins in life sciences.

References: N. Du and X.Y. Liu, Appl. Phys. Lett. 81, 445-448 (2002). D. Rosenfeld and W. L. Woodley, Nature (London) 405, 440 (2000). P. L. Davies, G. L. Fletcher, and C. L. Hew, in Environmental Stress and Gene

Regulation (BIOS Scientific, Oxford, 1999), p. 61. C. A. Knight, Nature (London) 406, 249 (2000).

Subject 4: Bioelectricity

Description: In preparing this essay, the following points should be covered Physical principles of bioelectric signals. How are bioelectric signals produced, and transmitted in human bodies? Bioelectric signals and receptors The imaging of bioelectric signals and disease diagnoses.

References: Life (5th edition) by R. Lewis, D. Gaffin, M. Hoefnagels and D. Parker, McGraw Hill

(2004). John D.Cutnell and Kenneth W. Johnson, Physics, Wiley, 6th edition. Biophysics, An Introduction, by R. M. J. Cotterill, John Wiley & Sons (2002). Biology in Physics – Is Life Matter? by Konstantin Bogdanov, Academic Press

(2000).

Subject 5: Gel Electrophoresis and DNA finger Printing

Description: Electrophoresis is a technique used to separate charged molecules in an electric field based on their sizes. DNA (deoxyribonucleic acid) is a negatively charged molecule having a uniform charge distribution. In agarose gel electrophoresis, DNA molecules move through the agarose gel pores toward the

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positive terminal. The DNA molecules are separated by size because the smaller molecules can move through the pores in the gel faster than larger ones.

In preparing this essay, the following points should be covered: Basic theory of electrophoresis Agarose gel – preparation and properties Preparation of DNA sample DNA specific dye to visualize the DNA bands. DNA finger printing, a technique widely used in crime detection, medical

laboratories etc.

References:

David Sheehan, “Physical Biochemistry: Principles and Applications”, Wiley, 2000. Methods and techniques in virology, Eds. Pierre Payment and Michel Trudel; Marcel

Dekker, New York, 1993. The nucleic acid protocols handbook, ed. Ralph Rapley, Humana Press, N. J, 2000. Life (5th edition) by R. Lewis, D. Gaffin, M. Hoefnagels and D. Parker, McGraw Hill

(2004).

Subject 6: Optics and vision

Description: In preparing this essay, you should at least cover the following points

The structure of eyes Physics principles of imaging in human eyes Eye defects. Principles and techniques of improving vision Lasers: Principles of production and properties Use of laser technology in ophthalmology

References:

J.H. Postlethwait & J.L. Hopson, The Nature of Life (the 3d edition), McGraw-Hill, Inc. John D.Cutnell and Kenneth W. Johnson, Physics, Wiley, 6th edition.

Subject 7: The structure of protein and protein crystallization

Description: In preparing this essay, you should at least cover the following points

Structures and types of proteins Bio functionalities of proteins Methods of determination of protein structures Principles of X-ray diffraction Principles and methods of protein crystal growth

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Protein crystallography

References: A. Ducruix, and R.Giege, Crystallization of Nucleic Acid and Proteins, (Oxford Press,

Oxford, 1999). M. Daune, Molecular Biophysics, (Oxford Press, Oxford,1993). David Sheehan, “Physical Biochemistry: Principles and

Applications”, Wiley, 2000.

Subject 8: Biosensors

Description: Biosensor is a new high-tech which concerns biology, material science, IT, physics, chemistry, medicine and environment. Bio-sensing technologies play a very important role in life sciences and other important fields closely related to our life. In the report on this subject, the following points should be covered:

Transmission of Information in a biological system Artificial biosensors and technologies. Bio-sensing and transduction elements and devices. Applications of biosensors Future prospects of biosensors.

References

A.P. Turner et.al, Biosensors: Fundamentals and Applications, (Oxford University Press, 1987).

Brian Eggins, Biosensors: an introduction, John Wiley & sons, 1996.

Subject 9: Photosynthesis

Description: Photosynthesis is the process by which the energy of sunlight is captured and used to sustain life on earth. Green plants, algae and some bacteria are capable of carrying out this process which takes place in the thylakoid membranes of the organelle called chloroplast. Light is absorbed by the pigment molecules (carotenoids, chlorophylls and phycobillins) in these membranes and is transferred to the so called photosynthetic reaction centers. The light energy is converted into chemical energy at these centers.

In the report on this subject, the following points should be covered:

Basic principles of photosynthesis Structure of photosynthetic reaction centre Fluorescence and resonance energy transfer Reaction center protein and prosthetic molecules Electron transfer in the reaction centre

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Light and carbon reactions

Reference:

Biochemistry by Garrett & Grisham 2nd Ed. Life (5th edition) by R. Lewis, D. Gaffin, M. Hoefnagels and D. Parker, McGraw Hill

(2004). Biophysics, An Introduction, by R. M. J. Cotterill, John Wiley & Sons (2002).

Subject 10: Optical and electron microscopy

Description: You should at least cover the following points in your essay: Eye and the need for microscopy Types of microscopy Resolving power of optical microscopy and electron microscopy and the

governing physics Imaging principles of optical, electron, and atomic force microscopy The applications of microscopy in biological specimens Comparison of the applications of different types of microscopy.

References:

J.H. Postlethwait & J.L. Hopson, The Nature of Life (the 3rd edition), (McGraw-Hill, Inc.). John D.Cutnell and Kenneth W. Johnson, Physics, Wiley, 6th edition. Biophysics, An Introduction, by R. M. J. Cotterill, John Wiley & Sons (2002).

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Appendix 1

Guidelines for Term Paper

Please read these pages carefully. Meticulous attention to these instructions will benefit you in the careful preparation of the report.

1. General Instructions

a. An abstract consisting of less than 250 words should be given at the beginning.

b. Including the title page, the report should not exceed 25 pages.

c. The original printout of the report including all the necessary references, tables, artwork, photographs, line drawings, etc., must be submitted to the lecturer in charge.

d. The report must be printed in the font size of 11pt, 1.5-SPACE on double side of good-quality white or near-white A4 paper, approximately, with margins of at least one inch on all sides. Illustrations and tables must be prepared as specified in Sections 2 and 3.

e. The first page of the report should give the title of the essay and the FULL name(s) and

MATRICULATION NUMBER (s) of the author(s).

f. Figures and tables (detailed, single-spaced) should be inserted in the proper places in the report.

g. Footnotes should be used only if it is not possible to incorporate the thought into the text without disrupting the flow of the argument. The placement of footnotes is indicated in the text by asterisks (or daggers, double daggers, etc., if there is more than one footnote on a page).

h. Current American spelling should be used. Webster's Third New International Dictionary should be used as final authority for spelling and hyphenation.

2. Illustrations

a. Original inked drawings, high-quality (300 dpi) laser printouts, or high-quality ink jet prints

(minimum 600 dpi on high-quality/photo paper) yield the best results and should be

submitted with the report.

b. The illustrations should be fully lettered, and the lettering must be large enough to remain

legible.

c. ILLUSTRATIONS SHOULD BE FREE OF UNNECESSARY DETAIL. Graphs should be prepared with

ticks on the axes rather than grid lines. Shading should be avoided if it is not essential to the

understanding of the illustration.

d. Photographs should be used conservatively.

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e. Generally, the illustrations should be numbered in a single sequence of Arabic numbers

throughout the report, in the order in which they are mentioned in the text. All text references

should employ the word “figure” rather than such varied designations as “diagram,” “chart,”

“photograph,” etc.

3. Tables

a. All tables should be numbered consecutively throughout the report, using Arabic numbers.

The sequence of table numbers should be independent of those used for figures or other

sequentially numbered elements.

b. Each table should be mentioned in the text, the reference being made by number and not by

such words as “above” or “below.”

4. Numbers, Units, Symbols, and Equations

a. Numbers up to ten should generally be spelled out, but numerals should be used for numbers

from 11 up, except that numerals are always used in conjunction with symbols and units of

measurement. Commas should separate groups of three digits in numbers of FIVE or more

digits (12,583) but no commas should be used in numbers of four digits (5837) unless they

are aligned in a column with numbers that do contain commas:1,356,789

78,652 5,382

Numbers between zero and one should be written with a cipher in front of the decimal point

(0.5—never .5).

b. The International System (SI) of units should be used. Units should be abbreviated when used

with numerals but written out when they occur in the text without numerals. The

abbreviations listed below should be employed. Note that these abbreviations are used

without periods:

ampere A meter mcalorie cal mho spell outcandela cd micrometer mcoulomb C microliter lcubic meter m3 milligram mgcurie Ci milliliter mldecibel db millimeter mmdegree Centigrade C millimeter of mercury mm Hgdegree Kelvin K million electron volts MeVdegree (angle) millivolt mVdyne dyn mole mol

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electron volt eV nanometer nmerg spell out newton Nfarad F ohm gauss G ohm-centimeter -cmgram g parts per million ppmhenry H percent %hertz Hz radian radhour h roentgen Rjoule J second (time) skiloelectron volt keV second (angle) "kilogram kg square meter m2kilometer km steradian srkilovolt kV tesla Tkilowatt kW torr Torrlambert L volt Vliter spell out watt Wlumen lm weber Wblux lx

c. The unit abbreviations listed above stand for the plural as well as the singular. Write 5 cm, not

5 cms.

d. The following prefixes may be combined with the basic unit abbreviations:

d deci (10-1) p pico (10-12)

k kilo (103)

c centi (10-2) f femto (10-15)

M mega (106)

m milli (10-3) da deka (10) G giga (109) micro (10-6) h hecto (102) T tera (1012

)n nano (10-9)

e. Display equations should be numbered using sequential Arabic numbers in parentheses in

the right margin. (Only one sequence should be used for both mathematical and chemical

equations.) In the text, equations should be referred to as Eq. (1), Eqs. (3)–(5); if the word

“Equation” begins a sentence, it should be written out in full. If a parenthetical reference to

an equation is made, the parenthesis around the number should be omitted, e.g., “A

relationship (Eq. 4) is derived….”

f. A displayed equation should be treated grammatically as part of a sentence, and THE TEXT

IMMEDIATELY PRECEDING a displayed equation punctuated according to the position of the

displayed equation in the sentence. (However, please note that PUNCTUATION SHOULD NOT

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BE USED WITHIN THE DISPLAY EQUATION.) Also, please remember, there should be a thin

space on both sides of an equals sign and any other operators.

g. The sequence of signs of aggregation should in general be {[( )]}, with due account taken

of the special meaning of the certain types of brackets.

h. Follow customary practice and do not use parentheses around simple arguments of

functions such as the sine, cosine, and logarithm, e.g., use sin 2ax, cos(2x/b), log2 2m.

i. Mathematical and symbolic material in display equations and in the body of the text must

be typed (or written) with great care. (If possible, avoid the handwriting of Greek letters and

other special symbols. If you cannot, they must be identified by name at their FIRST

occurrence.) If bold is unavailable, bold letters must be identified by a wavy underline at

EACH occurrence. If it is necessary to use symbols from fonts other than the usual italic or

bold (script, German, etc.), this may be indicated by color-coded underscores, but must

somehow be clearly identified.

j. Particular care must be taken to differentiate clearly between the letter l and the numeral 1,

the italic letter k and the Greek kappa, the italic w and the Greek omega, and also between

the capital and lower-case forms of such letters as c, k, o, p, s, u, v, w, x, and z.

k. Built-up fractions and other notation requiring more than one line of type (this does not

include subscripts and superscripts) should be avoided in the text proper, but if used, should

be displayed. Simple fractions can be converted to one-line form, using the solidus:

Parentheses must be used when ambiguities would otherwise result.

l. In text, the upper and lower limits on, e.g., summation symbols, should be placed to the right of the symbols in the sub-and superscript positions, e.g., i ai; they may be typed in

the customary position in displayed material, e.g., i ai.

m. The form exp (...) rather than e... should be used for complicated exponents, e.g., exponents

with sub-or superscripts; appropriate brackets should be used for the exp form following

point d above.

n. Instead of square root signs, the exponent 1/2 should be used with appropriate brackets.

o. Use forms such as ith rather than ith or ith.

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p. The chemical notation selected should avoid ring structures and vertical side chains

whenever possible. Cl OH may without loss of clarity be written as p-C1C6H4OH or CH3

| CH3-CH2-C-CH2-CH2-CH2-CH3 as CH3CH2C(CH3)2(CH2)3CH3 | CH3

Single bones are normally omitted. Indicate where long formulas may be broken.

5. References

a. You are responsible for the accuracy of your references. All names; dates; article, journal,

and volume titles; and volume and page numbers should be checked and double-checked

before the report is submitted.

b. References should be numbered in the order of their first mention in the text. The citation

may be used with or without the author’s name: “…it has been shown by Johnson17 that…”

or “…experiments with calcium,6 potassium,7 and strontium8 have shown….” Several

references may be cited together, the numbers being separated by commas and spaces:

“several recent investigations7, 9, 15 indicate….” If three or more consecutive references

are cited together, an en dash should be used between the lowest and highest reference

numbers: “…while others10–14, 17–19 show that….”

c. The reference list must be printed 1.5-SPACED with one extra line of space between each reference, in the style indicated by the following examples:

1. G. Bhatt, H. Grotch, E. Kazes, and D. A. Owen, Relativistic spin-dependent Compton

scattering from electrons, Phys. Rev. A 28(4), 2195–2200 (1983).

2. R. W. Arnett, K. A. Warren, and L. O. Muller, Optimum Design of Liquid Oxygen Containers,

Wright Air Development Center Technical Report No. 59-62 (August, 1961), pp. 118–120.

3. M. Wellner, Elements of Physics (Plenum Press, New York, 1991).

4. A. J. Duncan and Z. A. Sheikh, in: Polarized Electron/Polarized Photon Physics, edited by H.

Kleinpoppen and W. R. Newell (Plenum Press, New York, 1995), pp. 187–196.

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5. Kluwer Academic/Plenum Publishers (New York, January 1, 2000); http://www.wkap.nl.

The examples illustrate the following characteristic cases:

1. A journal article. ALL of the authors are given, initials with a space between, then

surname, followed by a comma. The full title of the article is given. Capitalize only the first

word of the title, the first word of the subtitle (if any), and proper nouns, proper adjectives,

or terms commonly capitalized. The abbreviated name of the journal follows (in the form

listed in Chemical Abstracts - List of Periodicals; names of journals or other periodical

publications not listed there should be spelled out). The volume number is bold and the first

and last page numbers are given (separated by an en dash), rather than just the first. For

journals with unnumbered volumes, the year takes the place of the volume number: J.

Chem. Soc. 1965, 2516–2522. For journals that start the pagination of each issue with 1, the

issue number must be given in parentheses following the volume number: Pribory i Tekhn.

Eksperim. 7(3), 53–57 (1962).

2. For pamphlets, bulletins, or any publications other than “regular” books or journals, give

all the information available and do not use abbreviations. Do not italicize the title. For

unpublished theses and dissertations, be sure to specify degree and institution (for

unpublished material, “unpublished” “paper,” “essay,” “report,” etc., or “personal

communication,” “in press,” etc., should be the final, PARENTHETICAL element in the

citation).

3. A single authored book reference.

4. A report in a multiauthored edited volume.

5. A website. The first element would be the individual or registered name (again, give as

much information as possible), then the affiliation/city, and the revision date (THE REVISION

DATE MUST BE GIVEN), the actual address is last.

An online journal would be as the above examples of journal citations with the addition of a

“(Online)” immediately following the journal title.

d. Do not use “ibid.,” “op. cit.,” or “loc. cit.” references, and do not use the abbreviation “et

al.” in the reference list, but list all authors, even when there are very many. However, the

text reference in such a case may take the form “…shown by Jones et al.7….”

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APPENDIX 2 THE FORMAT OF TITLE PAGE

GEM1521K: PHYSICS IN LIFE SCIENCES - TERM PAPER

Subject 6:

Optics and vision

By

Tan Yi Lin (Uxx066253)Ng Hoon Hwee (Uxx036250)

Chung Eric (Uxx077263)

June 12, 2006

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Documents

Department of Physics - Term Paper Objectives and Instructionsphyweb.physics.nus.edu.sg/~Biophysics/GEM1521K/Term Paper... · Web viewYour readings must reflect your understanding