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 on
some Physical and Biological Problems
Communications in Excitable Networks
Institute of Physics
Academia 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 from
Soft-matters
Effects of Conformations of DNA on
some Physical and Biological Problems
Turbulent Drag Reduction by
Polymers
Drag Reduction = less dissipation by turbulence
Passive Drag Reduction 
Change of B.C.
Shark Skin Swimming Suit
Airplane Skin Coverage
Trans-Alaska Pipeline (internal flow)
1287 Km
5~25ppm
Injected every 100Km
25%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 h.
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)
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
(2)
(5)
Buffer solution
- 10mM tris-HCL (pH 7.8 at 25℃),
10mM NaCl and 1mM EDTA.
(1) Motor (2) Flexible couple ring (3) Torque sensor
(4) Fluid container (5) Rotating disk
(3)
(4)
Torque Measurement
Torque Variation
10,000
D ate : 2000. 2. 23
Sam ple :  -D N A (1.35ppm )
A pparatus : 370m l R D A
o
Tem p.: 25 C
R PM : 500~2500 R PM
Sw eep rate : 20rpm /sec
N R E =250000~1300000
9,000
8,000
Torque
7,000
6,000
5,000
4,000
B uffer solution
D N A 1.35ppm
3,000
2,000
500
1000
1500
2000
2500
RPM
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)
Only L/2 degradation
Electrophoresis
23.1Kp
The electrophoresis result of lambda DNA
after degradation for 1 hour at 1,980 rpm, 25℃.
Packing of DNA
What is Spermidine?
A,
three phosphates adjacent from the same B, intrastrand across the major groove.
strand of the major groove.
J Biol Chem. 2004 Oct 1;279(40):42041-54. Epub 2004 Jul 28.
Physiological role of polyamines
•
•
•
•
First discovered in human seminal fluid
Nucleic acid packaging, DNA replication
Transcription and translation
Ubiquitous in many cellular processes
Coil-to-Globule Transition in
duced by Spermidine (SPD)
Good Drag Reducer
Poor Drag Reducer
(N-[3-Aminopropyl]-1,4butanediamine)
Trihydrochloride
C7H19N3·3HCl FW 254.6
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(r/rcr) + 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
Highway
Poisson distribution
Exponential Network
Airlines
Power-law distribution
Scale-free Network
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