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Welcome to Physics 498Bio Understanding biology using “simple” ideas from physics. You must know enough biology to have a sense of what to study!. Monday, Wednesday, 10:30 am- 12 pm: 158 Loomis. Your host: Professor Paul Selvin Office: 365 Loomis

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Welcome to physics 498bio understanding biology using simple ideas from physics

Welcome to Physics 498Bio

Understanding biology using “simple” ideas from physics.

You must know enough biology to have a sense of what to study!

Monday, Wednesday, 10:30 am- 12 pm: 158 Loomis

Your host:

Professor Paul Selvin

Office: 365 Loomis

Office Hr: after class or 10:30-11:30 am Friday.

(Can anyone NOT make it?)

[email protected]: 244-3371

Your co-host (TA):

Anne Cai, 2nd year physics student doing biophysics

Office: 328 Loomis

Office Hrs: Sunday 1-2:30pm OR Tuesday 3:30-5pm

depending on whether HW due on Mon. or Wed.

[email protected]: 305-282-9398

HW due 1 week from date of assignment

Course Info:

Online.physics.uiuc.edu/courses/physics498bio/spring08

Or

people.physics.uiuc.edu/Selvin/PRS/PRS.html

then physics498bio Spr10

Or

physics.uiuc.edu, Courses, Intro to Biophysics Research (next to 498Bio)


Welcome to physics 498bio understanding biology using simple ideas from physics

Course Information Physics 498Bio

Introduction to Biological Physics

You’ve (hopefully) made a good choice!

Prerequisites

Physics 111, 112 (or equivalent)

Some knowledge of Statistical Mechanics Gibb’s Free Energy, entropy: DG = DH-TDS

Boltzmann’s Constant, kB

Boltzmann Factor: exp(-Ei/kT)

ATP: Adenosine TriPhosphate (universal energy currency)

(Remember in useful units:

[kBT = 4 pN-nm; ATP = 80-100 pN-nm ~ 25 kT])

Some elementary calculus.

No previous biology assumed. I teach it in course.

Required Reading

Essential Cell Biology, 3rd edition:

by Bruce Alberts et al.

Excellent introduction to biology. Chpt 1-5, 11-13

Read Chpt 1: Quiz next Wednesday.

Need to know biology in order to do biophysics!

Using physics to understand biology!

Not biology to understand physics!


Welcome to physics 498bio understanding biology using simple ideas from physics

Goals of course

1. Learn some basic molecular biology.

Language of Life: 4 key components

DNA (PCR, sequencing)

Proteins...can do everything!

2.Learn how to apply basic physics to biology.

Mechanics, Electricity & Light, Statistical Mechanics

(Example today – What planets are life possible on?)

3.Learn about/type problems biophysicists work on.

Biology...

Molecular motors (chemical  mechanical)

Ion Channels (chemical Ion Gradients electrical)

[Photosynthesis (light  electricalchemical energy)]

Stochastic Nature of gene expression,

Magnetic Navigation, Vision...

4.Learn“back of the envelope”type calculations.

Example today: Strength of animals

5.Learn experimental (bio)physics

How to measure (nm distances, pN forces),

Single molecules (Fluorescence, Optical Tweezers

Magnetic Traps, Patch Clamp Techniques)

Some guest lecturers– people doing the stuff!

Klaus Schulten

How do birds know which way is North?


In singulo biophysics

In singulo Biophysics

Single molecules, single cells, single species, single planets…

Heterogeneity is the norm

Men vs. women: height, sex organs

Important to understand (prostate cancer, ovarian cancer

It is only in last 10 (20) years that single molecule detection has been possible!


Welcome to physics 498bio understanding biology using simple ideas from physics

Course Schedule

DNA (& Proteins…)

1) Jan. 20th : Intro; King Kong; Temp. of Earth; Evolution & Modern Biology

2) Jan 25th : Central Dogma of Biology; Partition Function

3) Jan 27th : The 4 class of macromolecules; Entropy

4) Feb 1st : DNA Technology : FISH, PCR, Forensics

5) Feb 3rd : DNA Technology : Gene Chips

6) Feb 8th : DNA as Spaghetti: Magnetic Traps

7) Feb 10th : Magnetic Traps, Part II

8) Feb 15th : Carbohydrates and Lipids

Fluorescence

9) Feb 17th : ATPase Operates at near 100% Efficiency

10) Feb 22nd : [I’m gone]: Alternative make-up day?

11) Feb 24th : Microscopes and Resolution; X-ray Diffraction

12) March 1st : Super-Accuracy, Super-resolution techniques: FIONA, SHREC,

13) March 3rd : More super-accuracy: PALM, STORM

14) March 8th : STED, FRET, Part I

15) March 10th : FRET Part II and DNA helicase—TJ Ha’s Science magazine article.

Students Teach!

16) March 15th : Student Presentations

17) March 17th : Student Presentations

March (22, 24) Vacation

Optical Traps allow you to see Angstrom & Nanometer distance.

18) March 29th : Optical Traps- theory and Experiment

19) March 31st : Optical traps, Part II

Diffusion: Inertia doesn’t mean anything!

Diffusion and Bacteria Moving

20) April 5th :How E. coli swim and tread water Diffusion: Inertia doesn't mean anything

21) April 7th :Magnetic Orientation? Klaus Schulten.

Vision & Ion Channels

22) April 12th : Ion Channels – Voltage-sensitve (nerves, neuromuscular)

23) April 14th : Ion Channels – Ligand sensitive (your brain)

24) April 19th : Vision

Single Cells: Most Genes are few in Number—some surprising results

25) April 21st : Studying Gene Activity in Individual Cells.

26) April 26th : Gene Activity Part II

Students Teach!

27) May 3rd : Student Presentation

28) May 5th : Students Presentation


Welcome to physics 498bio understanding biology using simple ideas from physics

Grading

30%: Homework (Must do all of them): Mostly weekly assignments, but occasionally to write up something

Work together, but turn in separately.

Hand in at start of class– in class! (Do not be late.)

25% Mid-term Oral and written report

Oral & Written—the same subject

-- 12.5% on written report: 8 pg report.

-- 12.5% on oral report: 10-12 min plus 3-5 min for questions.

25%: Final Written Project & Oral Project– Same topic

-- 12.5% on written report: 10 pg report.

-- 12.5% on oral report: 10-12 min plus 3-5 min for questions.

No regular mid-term or final exams.

10% Quizzes (~1% on each)

--5 min quizzes making sure that you’ve done readings

10% on classroom participation /class evaluation


Welcome to physics 498bio understanding biology using simple ideas from physics

Yes, you get to evaluate class!Three (or 4) questions:

1. What was the most interesting thing you learned in class today?

2. What are you confused about?

3. Related to today’s subject, what would you like to know more about?

4. Any helpful comments.

Answer, and turn in at the end of class.

(I’ll give you ~5 minutes.)

I’ll typically start class with some of your questions.


Welcome to physics 498bio understanding biology using simple ideas from physics

Plagiarism

Not allowed! You will flunk the course.

In written project…

Something has always been written…

(unless you have truly come up with something new.)

Usually what’s written will be clearer than you can write it.

But you want to independently understand it.

And show me that you independently understand it.

So…

Read book/article, then close it,

Then write your own version. This way you know you understand it, and can explain it in your own words.

Also, when you “steal” a picture from somewhere, write in your paper where you got it from. A picture is worth a thousand words, but give credit where due.


Welcome to physics 498bio understanding biology using simple ideas from physics

Mass?

(density is the same):

10 x 10 x 10 = 103

Strength?

a Cross-sectional area (rope):

10 x 10 = 102.

1/10… 1/dimension

Strength/Mass ratio?

King Kong is proportionally speaking

is 10x weaker than regular gorilla!

Regular gorilla with 10 gorilla’s on him—couldn’t walk.


Welcome to physics 498bio understanding biology using simple ideas from physics

In water– held up by buoyant force.

Bones do not need to support weight

If have to, have super big bones– would sink.

If whale stranded on the beach?

Bones break; also overheat (because warm-blooded and water is going at conducting away heat, whereas air is not.)


Is there water based life on other planets example of physical limits to life

How much light?

1 meter

1 meter

Is there water-based life on other planets?Example of physical limits to life.

Idea: For water-based life, 0º < Tave < 100ºC

Can we calculate Tave of planets in our solar system?

Earth

What determines (surface) temp?

Answer: Heat (photons) from sun

Ie= 1.35 kW/m2

How many (flood)lights?

# Floodlight ~ 30 (1 meter away)

(Incandescent light 3% efficient)


Welcome to physics 498bio understanding biology using simple ideas from physics

Why determines earth temperature?

Why can life exist?

Temp of earth constant

Heat in = Heat out

Heat out

Heat in

Heatin = ??

Heatin = IinpRe2

(1-a)

  • = reflectivity of object

  • The albedo of the earth, i.e. the amount of light which is reflected (a) is about 0.3 (depending on cloud cover, the amount of snow, etc.) The remainder of sunlight is absorbed, transferred into random thermal vibrations.

Iin= 1.35 kW/m2

Assume the earth is a black-body.

(Stefan-Boltzmann Law)

Kittel, Thermal Physics pg 91-96

Heatout = 4pRe2σ T4

σ = const (=5.7 x 10-8 W/m2K4)

T = absolute Temp.

We balance the incoming energy flux from the Sun and the outgoing flux due to black-body radiation.

pRearth2(1- a)Iin = 4pRearth2sT4

Therefore: sT4= (1-a)Iin/4

T = 253°K


Welcome to physics 498bio understanding biology using simple ideas from physics

According to this (simple) model, TEarth should be 253°K.

In reality, it’s more like 280°K?

What happened?

Greenhouse Effect: 280°K (Homework)

When you change the balance, you get REAL effects!

Add CO2, you get an artificial Greenhouse Effect


Welcome to physics 498bio understanding biology using simple ideas from physics

Physics is about great laws

Some examples…

Newton’s 3 Laws (Mechanics)

(Electricity & Magnetism)

Maxwell’s 4 Equations

Isaac Newton

1642-1727

(Thermodynamics)

Gibb’s Free Energy

James Clerk Maxwell 1831-1879

(Quantum Mechanics)

Schrodinger’s Eq’n

J. Willard Gibbs

1839-1903

(Stat. Mechanics

of Entropy)

S= k·log W

Erwin Schrödinger

1887-1961

Ludwig Boltzmann 1844-1906


Does biology have any great theories laws

--One of the best tested scientific theories around

Evolution is a series of tricks/random events

Build complex beings from simpler parts

Often many ways of doing this

Our life form is just one.

Does Biology have any great theories/laws?

Charles Darwin, Age 51, 1860, On the Origin of Species

Evolution

-- Life evolved from simpler forms


Welcome to physics 498bio understanding biology using simple ideas from physics

Evaluate class

1. What was the most interesting thing you learned in class today?

2. What are you confused about?

3. Related to today’s subject, what would you like to know more about?

4. Any helpful comments.

Put your name in upper right-corner.

Then tear off your name before turning in. (That way you can be brutally honest!)

Answer, and turn in at the end of class.

(I’ll give you ~5 minutes.)


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