introduction to the laboratories of bio and soft-matters 陳志強 中央研究院物理研究所...
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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