Introduction to the Laboratories of Bio and Soft-matters

陳志強中央研究院物理研究所

中央大學生物物理研究所

Content

• Overview of Biophysics in Academia Sinica (15 min)

• Laboratory of Soft and Biomatter (30 min)

Effects of Conformations of DNA onsome Physical and Biological Problems

Communications in Excitable Networks

Institute of PhysicsAcademia Sinica

• Theory / High Energy• Nano/Surface• Complexity

Research Opportunities in Academia Sinica

• 李世炳 - System Biology• 梁鈞泰 - Flocking• 周家復 - Nano/Bio devices• 林耿慧 - Self-Assembly• 阮文滔 - Single molecule DNA• 陳彥龍 - Single DNA in Microfluidics• 李定國 - Protein folding• 胡進錕 - Protein folding, DNA and etc

Laboratory of Bio and Softmatters

• Softmatter -- de Gennes in the 90s• Energy comparable to KT, many degree of

freedom (complexity)• Nonlinearity and Cooperativity

• Polymers - proteins, DNA• Networks - polymers, bio-chemical reactions, cells and neurons

People Involved

陳志強 * 黎璧賢 ( 中大 )

賈魯強 ( 元培 )

• Lab: 519 (NCU)

Lab: 320 (Academia Sinica)

Nonlinear Phenomena fromSoft-matters

Effects of Conformations of DNA onsome Physical and Biological Problems

Turbulent Drag Reduction by Polymers

Passive Drag Reduction Change of B.C.

Drag Reduction = less dissipation by turbulence

Shark Skin Swimming Suit Airplane Skin Coverage

Trans-Alaska Pipeline (internal flow)

1287 Km5~25ppm Injected every 100Km25%DR up to D=1.2m

Why DNA ?

Structure of DNA

Why DR with DNA ?

1.DNA is very long - can be much longer than

2. DNA processes secondary structure

- elastic properties different from polymers

3. Structure can be changed by pH or temperature

- Good probe for turbulence ?

Setup

(1) Motor (2) Flexible couple ring (3) Torque sensor(4) Fluid container (5) Rotating disk

(1)

(2) (3)

(5)(4)

Lambda DNA

- Promega Corporation / U.S.A.

- Size: 48,502bp

- Commonly used substrate in

restriction enzyme activity assay.

- Storage: –20℃- Concentration of stock solution: 515

g/ml

Buffer solution

- 10mM tris-HCL (pH 7.8 at 25 ), ℃10mM NaCl and 1mM EDTA.

Torque Measurement

The Shaft torque measurement for buffer solution and 1.35 wppm solution of lambda DNA in continuous mode rpm sweep at 25℃. (sweep rate;

20rpm/sec)

500 1000 1500 2000 25002,000

3,000

4,000

5,000

6,000

7,000

8,000

9,000

10,000

Date : 2000. 2. 23Sample : -DNA (1.35ppm)Apparatus : 370ml RDA

Temp.: 25oCRPM: 500~2500 RPMSweep rate : 20rpm/secN

RE=250000~1300000

Buffer solution DNA 1.35ppm

To

rqu

e

RPM

Torque Variation

Only L/2 degradation

The electrophoresis result of lambda DNA after degradation for 1 hour at 1,980 rpm, 25℃.

Electrophoresis

23.1Kp

Packing of DNA

What is Spermidine?

J Biol Chem. 2004 Oct 1;279(40):42041-54. Epub 2004 Jul 28.

A,three phosphates adjacent from the samestrand of the major groove.

B, intrastrand across the major groove.

Physiological role of polyamines

• First discovered in human seminal fluid

• Nucleic acid packaging, DNA replication

• Transcription and translation

• Ubiquitous in many cellular processes

(N-[3-Aminopropyl]-1,4-butanediamine)

Trihydrochloride

C7H19N3·3HCl FW 254.6

Coil-to-Globule Transition in

duced by Spermidine (SPD)

NH3H3N NH2

NH3H3N N

H2

NH3H3N N

H2

Spermidine (SPD)

NH3H3N NH2

NH3H3N N

H2

NH3H3N N

H2

NH3H3N N

H2

NH3H3N N

H2

NH3H3N N

H2

Spermidine (SPD)

Poor Drag ReducerGood Drag Reducer

Summary of DR

• Only a few %DR by improvement of wall properties

• a few ppm of additive of long chain polymers in turbulent flow can produce a max of 80% DR

• Polymers broken (degraded) by turbulence

• NO BASIC UNDERSTANDING YET !

• DNA might provide a good probe for turbulence

Summary

• Many nonlinear effects induced by the conformation of DNA

• Turbulent Drag Reduction

• Coil-Globule Transition

• Structure and Packing of DNA

• Effect of conformation of the transcription of DNA

Complexity from Bio-matters

Communications in Excitable Networks

Life Cycle of Slime Mold

Aggregation of dicty

Chemotaxi and cAMP

Waves of cAMP

Periodic Motion of Cells

The Physics of Excitable Systems

What are excitable systems?

• Unstable state with respect to large perturbations

• Excitatory and Inhibitory states

• Examples:– BZ reactions– Slime molds– Heart muscles– Neurons

Scaling in Slime Mould ?

High density

Low density

Distribution of Slugs

- Culture with different densities

- Harvest after 36 hour

-Digital pictures

- Population Regulation self-similar shape V = A*L but A = aL

V = bA3/2

Density dependence of Slug size

Upper critical size

Lower critical size

V ~ Alog(cr)V0

Exponential Distribution at high density

Power law distribution in low density?

Leo Glass, Physics Today ， Aug. 1996。

Spiral Waves

Spirals in Cardiac cell cultures

Lee et al PRL, 92, 198103, 2005

Cardiac Cultures

Early Beatings

Synchronized Traveling Wave

Cardiac-Neuron Co-culture

Cardiac-Neuron Co-culture

Cardiac-Neuron Co-culture

Scale-free network

Poisson distribution

Exponential Network

Power-law distribution

Scale-free Network

AirlinesHighway

Summary

• Biophysics Understanding of Biological Nonlinearity and Complexity in terms of Physical Principles

• Physics of Polymers and Networks of Excitable Systems

• DNA Slime Mould Heart Brains

• Both fundamental and applied problems

• NCU/Academia Sinica Best Combination in Taiwan