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.
Download ReportTranscript 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.
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 T em p.: 25 C R PM : 500~2500 R PM Sw eep rate : 20rpm /sec N R E =250000~1300000 9,000 8,000 T orque 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