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PHY 3903 version 2003

Gary W. Slater 31.oct.2003

gslater@science.uottawa.ca

613-562-5800 x6775

MCD 222

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Writing = 40%– your topic = 5%– PRL format = 20%– seminar = 15%

Physique = 10%– Biographies=3%– Abstract=3%– scholarship$=4%

%%%%%%Approx.%%%%%%

Maple = 50%– 6 weeks– 5 assignments– 1 longer

problem/project– Assigments minus

worst one above 50% = 40%

– projet = 10%

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Schedule October 3

Non-Maple 3Maple 3

October 10Maple 4

October 17UofO open house

October 24– Absent

October 31Non-MapleMaple 5

November 7Maple6=finNon-Maple=fin

November 14, 21, 28Séminaires!!!!!

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Séminaires Seminar: 8+2 min + 3 min Q

transparencies -or-PowerPoint

Will take place in the last 3 weeks of the semester

• 14, 21, 28 novembre

Le département sera invité Vous devez préparer le texte de 4 pages

format PRL pour le séminaire, et je les metterai sur le site W3

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14 novembreGascon : Video speed electronic paper Lefebvre : L’effet CasimirBertrand : C60Kelly : Space travelZhang : Wolfram’s Computational Equivalence

Parent : Dark matterCienak : Strong nuclearforce

Les séminaires 8+2+3 minutes

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Les séminaires 8+2+3 minutes

21 novembre

Stone : Fractals Kamran : Cosmologie M Lalonde : Sonoluminescence Meunier : Matérialisme scientifique O’Byrne : Superfluidity Vachon : Astronomie expérimentale Miranda : Quantum Cryptography

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Les séminaires 8+2+3 minutes

28 novembre

J Lalonde : SNO Pinet : Parallel computing & HPCCorrigan : The anthropic principleComeau : Particle acceleratorsDumouchel : Thermonuclear synthesisD’Eca : String TheoryWong : Quantum dots

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PLAN: Maple 9 Getting started (Chapters 1-4) Polynomials (Chapters 5-7, 13, 14) Functions (Chapter 8) Calculus (Chapters 9-11, 17) List, set, array (Chapter 12) Linear Algebra (Chapters 18, 19) Solving equations (Chapter 16) Graphics (Chapter 15)

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30 october – 1 november

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PGS Master’s and Doctoral Check List:

Form 200

Outline of proposed research (1 page)

Awards, Contributions and Statement (2 pages)

Support letters for location of tenure (if applicable) All official academic transcripts (undergraduate and graduate)

Appendix 1, Report on the Applicant, in a sealed envelope (two required)

Appendix 2, Departmental/University Evaluation

Signed cover page

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Physics as a profession 1. Science et vérité 2. La recherche et

sa société 3. M. Sc. & Ph. D. 4. Information 5. Publishing 6. Éthique 7. Journalism, etc.

8. PresentationFigs, tables, fits…

9. SéminairesSlides, plan, …

10. $Grants, costs…

11. Canadagranting agencies…

12. Physicist ?

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9. Seminars Modes

transparencies/acétates~standard in physics

slidesmedical sciences

PowerPointgrowing, + movies!

blackboardmaths!

Durationstypically 10-20 mininvited speaker will

have about X2-3~10% for questionsin a conference, you

MUST stopin a seminar, taking

too much time is a sign of a poor speaker

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Parts[introduce the group]plan

1 slide

introduction to the topic

what are the questions to be investigated

methodsresultsconclusions & future

1-2 slides

Postersnow very commonposter sessions can

have 10s or even 100s of posters

surface area ~ 2 m2

will last a few hoursbusiness cards and

reprints/preprints are exchanged

main problem: too much, too small

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The ABSTRACT(for a conference)titlenames of authors,

with the speaker being the first author

addresses (brief) 10 lines or somaybe 1-2 referencesmay have

acknowledgmentsoften vague because

results are not known 6 months ahead of time!

Resultsusually, this is the

longest partcontains lots of

graphs, tables, etc.roughly 0.5-1/mingraphs of high qualitymake sure the labels

are readable

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STYLEwalk aroundmake jokes☺mention historyface the publicdo NOT block the

screen or the projector

speak upcheck the time or

follow the chair’s signs

english in most conferences

Before and afterbefore:

check your materialchair of the session will

introduce you, and mention the title

if it is a seminar, the chair will give a short biography

after:the chair will ask for

questions and usually chooses the order

the chair will decide when to terminate

the chair may ask you to stop immediately

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Recommended1 subtopic/slideuse easy-to-read

fonts and sizesdo not bring notesdo not read a textdo not try to answer a

question when you don’t know the answer

reduce the number of things to talk about but improve their presentation

Biggest mistakesexceed the timetoo much materialdoes not describe

the variables,the axesthe experiment

the goal of the work is not clear

no conclusions

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Examples of PowerPoint slides

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An Exact Numerical Approach to Calculating Diffusion Coefficients in Chemistry and Biology

Tuesday, November 7th, 2000 - University of Wisconsin - Madison

Physical Chemistry Seminar,

11:00 a.m., Room 8335 Chemistry Building.

Gary Slater, University of Ottawa, Canada

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My abstract Diffusion problems are common in the Natural Sciences and play an

important role in modern technology. Examples include the migration of macromolecular objects in gels and porous media, the lateral motion of proteins in biomembranes, the mixing of chemical species in stagnant liquids, etc. Standard theoretical methods focus on the diffusion equation and the relevant boundary conditions, but in practice this approach is usually rather limited. Computer simulations, based on the so-called Monte Carlo algorithm, are used extensively to understand how the structure of the system impacts the diffusion of mobile molecules. Our group has recently developed a numerical method that can replace Monte Carlo methods for a wide variety of systems. Typically, our method is faster than Monte Carlo simulations, uses only a Pentium processor, and provides results that are at least 6 to 9 orders of magnitude more precise. In this talk, I will first introduce the basic concepts of the theory of diffusion. Then, I will present our approach, how YOU can easily implemented it on a PC, and some results for various problems of interest in biology and chemistry.

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Random Walks: general aspects

Model for diffusion unbiased leads to non-

spherical patterns with isotropic mean properties

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http://polymer.bu.edu/java/

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Problems to be studied here

With constraints / obstacles No external field Simple particles Steady-state only 2D or 3D

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How to tackle such problems

Monte Carlo• lattice• obstacles• PBCs• generate random

numbers (1=+x, 2=-x, 3=+y, 4=-y)

• repeat ad nauseum• compute D=dx2/dt

as a slope, with its error bar

Our method• lattice• obstacles• PBCs• apply arbitrary field• compute exact

local probabilities and local velocities

• compute exact D in the limit where the field is zero

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Nernst-Einstein relation

C=concentration of obstacles

=external field =V/=mobility Valid only near

equilibrium

)0,(

)C,(

)0(D

)C(Dlim

0

It is much easier to compute a velocity (a “signal”) than a diffusion coefficient (a “fluctuation”)

Since 0, its value (& source) is arbitrary

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General local velocities

4 cases:• free V = /d• front blockade V = -(1-)/2d• rear blockade V = +(1+)/2d• blocked V = 0

LpLpV xxi )1()x(p d21

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Diffusion Coefficient

I1

II

0

nTTvvd

)0(

)C(lim)C(*)C(*D

)0(D

)C(D

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Examples...

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D*

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Gives rational fractions.

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(a) (b)

(c)

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Q: In the case of electrophoresis, should we worry about field lines?

Locke et al. recently claimed that the Ogston model actually work if we taken into account the curved field lines around non-conducting obstacles

Field lines could actually cancel some of the non-Ogston effects

However, that would violate the Einstein relation!

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CONCLUSIONS Our approach can replace Monte Carlo

methods for tons of applications Faster, simpler, more precise than Monte

Carlo, even on Pentiums!

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Acknowledgments Funded by: NSERC, Applied Biosystems Collaborators: Guy Drouin, Laurette

McCormick, Michel Gauthier