Overview of research in Biophysics Institute @NCU. 中央大學生物物理所

1. Overview of research in Biophysics Institute @NCU. 中央大學生物物理所 From DNA to collective behavior of organisms http://www.phy.ncu.edu.tw/~ibp/

2. Graduate Institute of BioPhysicsat NCU 國立中央大學 生物物理所 Biophysics Life Science 生命科學系 Inst. Systems Biology & Bioinformatics 系統生物與生物資訊所 Brain Research Center,UST 聯合大學腦科學中心 Institute of Phys., Academia Sinica 中研院物理所 Soft Condensed Matter Physics Dept. Center for Complex Systems 複雜系統中心

3. What is Biophysics? Biophysical Society defines as: "that branch of knowledge that applies the principles of physics and chemistry and the methods of mathematical analysis and computer modeling to understand how the mechanisms of biological systems work” . • Why BioPhysics ? • Material Nature of Bio-substances affect Biological properties. (Evolution made use of the physical properties of bio-materials) • Physical principles & Laws holds from microscopic level  macroscopic level • Traditional Biology is descriptive, non-quantitative

4. Why BioPhysics ? • Physics is universal. • Rise of molecular biology: DNA, RNA, protein are universal in all living matters • Universality in Central Dogma: DNARNAproteinBiological functions… • New, interesting, exciting & useful. • Lots of unsolved important problems. • Techniques & Methodology in physics can probe the fundamental principles in bio-systems of a wide spectrum of scales in a quantitative way.

5. Physics is vital in breakthrough in life sciences • Breakthrough in physical instrument: optical microscope (Hooke, 1665), amplifier, X-ray, electron microscope, MRI, SPM, mass spectrometer, Single molecule microscopy,…. Nobel laureates in physiology/medicine that were physicists/had physics training: • Georg von Békésy (physical mechanism of the cochlea, 1961) • Francis Crick (DNA, 1962) • Alan Hodgkin (nerve cell ,1963) • Haldan Hartline (visual processes in the eye, 1967) • Max Delbrück (bacteriophage l, 1969) • Rosalyn Yalow (radio-immunoassays of peptide hormones, 1977) • Werner Arber (restriction enzymes , 1978) • Erwin Neher (single ion channels in cells ,1991) • Peter Mansfield (NMR, 2003)……

6. Wide Spectrum • Length Scales: nm  mm  mm  cm  m  km DNA,RNA,protein, intracellular, virus, bacteria, Intercellular, collective motion, insects, animals/plants, migration • Time Scales: fs  ps  ms  ms  s e transfer,H-bonding,water DNA,RNA,protein rearrangement , protein folding DNA transcription  hr  day  year  Byr cell division Earth organisms , animal migration evolution • Knowledge: Interdisciplinary 跨越各學科領域 MathematicsPhysicsChemistryBiologyMedical • Biophysicist is a TRUE Scientist ! Explore to the maximum freedom for doing science! • 需要物理與非物理背景人材加入!

7. 國立中央大學 生物物理研究所 • Officially established in 2004(碩士班),博士班(2008) • 教授: 6 副教授: 1 助理教授 2 • 合聘教授: 3 合聘助理教授: 2 • 現有從事生物物理領域在學研究生(含物理所) 碩士班：23 博士班：7 • 博士後: 6 • 以物理之技術或方法去探討生物系統中存在之基本原理，從而對生物過程提供深入及定量之了解。 • 「5年500億發展國際一流大學及頂尖研究中心計畫」 經費建立 生物物理共用核心設施 • 歡迎物理與非物理背景同學加入.中大及中研院提供獎學金

9. BioPhysics Theory Groups at NCU Soft matters • 陳培亮Peilong Chen: bio-hydrodynamics, mechanics of propulsion in living organisms,pattern formation in biology • 陳宣毅Hsuen-Yi Chen:complex fluids, cell adhesion, collective motion in flocks • 黎璧賢Pik-Yin Lai:DNA physics, biomolecular chain models, neurons, biological networks • 李紀倫Chi-Lun Lee:protein folding, charged biomolecules • 梁鈞泰Kwan-tai Leung: self-propelling motion in organisms, flocking, non-equilibrium bio-processes • 高仲明Chung-ming Ko:Evolution models, astrobiology • 王敏生Min-Sheng Wang:Neural Networks, brain wave & MEG analysis • 李弘謙Hoong-Chien Lee:Bioinformatics, protein physics, genome/DNA sequence analysis Biophysics

10. BioPhysics Experimental Labs at NCU • Bio-Soft Core Facilities Lab. : BioAFM, Confocal microscopy, Wet Labs, Bio samples, fast imaging systems, fluorescence microscopy, rheometer… • Complex System Lab.伊林Lin I:micro-motion of bio- and soft materials in confined spots, dynamics of neuronal system, laser pulse-soft matter interaction • Biophysics Lab.陳方玉Fang Yu Chen:Biomembrane, Membrane-active Peptides, Effect of peptide-forming pore on neuron function • Bio-membrane Lab.薛雅薇Ya-Wei Hsueh:lipid rafts in cell membranes, NMR spectroscopy, AFM measurement • Bio-Soft Matters Lab.黎璧賢 Pik-Yin Lai, 陳志強 C.K. Chan: • interactions in cells, neuronal networks, DNA mechanics & hydrodynamics, biomaterials • Soft-condensed Matter Lab.陳培亮Peilong Chen: bio-hydrodynamics, mechanics of propulsion in living organisms • Soft-Matter Lab. 林耿慧 K.H.Lin,阮文滔 W.T.Juan: bio-soft materials, colloids, single-molecule DNA

11. E

12. Biophysics/Soft-matter Theory & Experimental Group Bio-Soft Matters Lab. & Simulational Physics Lab. Principal Investigators: Pik-Yin Lai , C.K. Chan Graduate Institute of BioPhysics & Center for Complex Systems, NCU Bio-Soft Matters Lab. Recent experimentalresearch topics include single-molecule experiments on biomolecules、complex network of neuron/cardiac cells、synchronized firing of neuronal networks、dynamical/collective behavior of cells、DNA under flow、molecular motors、ion-channels. Drag reduction 。

13. Biophysics/Soft-matter Bio-Soft Matters Lab. & Simulational Physics Lab. Principal Investigators: Pik-Yin Lai , C.K. Chan Graduate Institute of BioPhysics & Center for Complex Systems, NCU Simulational Physics Lab. Simulations & analytical studies in close connection with expts. in Bio-Soft Matters Lab. Biological networks、structure & dynamics of biomolecules 、DNA elasticity/hydrodynamics、physics & topological interactions in knots、phase transitions in polymeric systems、 grafted polymer layers、 polymer adsorption 、charged polymers。

14. Play (Torture) with DNA • DNA stretching, elasticity • DNA drag reduction • DNA thermo-phoresis • DNA condensation • DNA under external fields • DNA jamming • DNA fibers • ………

15. B-form to S-form Transition under a Stretching force Lai & Zhou, J. Chem. Physics 118, 11189 (2003) • Force Experiments • Stretching a single end-grafted DNA • S-form • B-form • Abrupt increase of 1.7 times in contour length of dsDNA near 65pN. • Thermal fluctuations unimportant near onset of transition.

16. DNA transcription by RNA polymerase T7 DNA polymerase • effect of template tension polymerase activity • Pausing & arrest during polymerase • Mechanism of polymerization kinetics • Tune rate of DNA replication with external stresses

17. Classical mechanics approach • (thermal effects can be neglected since the DNA is quite straight near the onset of BS) • All lengths in units of R, energy in units of k/R f=fz, dimensionless forceb=fR /2k, t=(sinqcosf,sinq,sinf,cosq) • Minimizing Ebs: Euler Lagrange eqns. • B.C.s: 2

18. First order phase transition at bt First-order elongation:Stretch by untwisting b=0.073 b=0.075 • Untwisting upon stretching • Untwist per contour length from BS, DTw/Lo~-100 deg. /nm; • Almost completely unwound ~ 34deg./bp • Torque ~ 60 pN nm

19. Direct observation of DNA rotationduring transcription by Escherichia coli RNA polymeraseHarada et al., Nature 409 , 113 (2001) • DNA motor: untwisting gives rise to a torque • BS transition provides a switch for such a motor. G > 5 pN nm from hydrodynamic drag estimate

20. IR laser DNA thermophoresis (Soret effect) Migration of single DNA molecule towards under temperature gradient. Dyed DNA in micropipette channel (3mm~30mm) Soret effect in microchannel • may be used in bio-microfluidics, DNA separation process • Possible mechanism to achieve high DNA conc. for • pre-biotic life emergence in sea

21. DNA condensation & packing Complex competition of DNA elasticity, charge interactions, volume interactions, solvent effects…..

22. DNA condensed by spermidine Good turbulent drag Reducer Poor Drag Reducer

23. - + - + + - + - + - + - + - + - + - DNA+SPD E DNA 0.7% agarose gel Molecular Jamming of DNA in Gel Electrophoresis

24. E Single-λ DNA with [SPD]=20mM jamming when entering in 0.7% gel from 0.5X TBE buffer solution

25. DNA under external drive DNA in gel under AC electric field 

26. DNA fibers by Electro-spinning • DNA are negatively charged, SPD are added to bind to DNA to form aggregate  fiber • Understand how DNA can be packed into fibers  biological relevant for the packing of DNA in virus and nucleus • DNA are negatively charged, SPD are added to bind to DNA to form aggregate  fiber • Produce DNA fibers of special mechanical, electric, bio-chemical properties. Woven to DNA sheets… Bio-materials

27. Expt6: DNA + SPD No PEO (1%wt, 1mM) 1Day later

28. Simple to Complex: emerging properties of networks: Neurons & cardiac cells Hodgkin-Huxley Model (1952) Signal across synapses • Neuron Cell does not divide: number of neurons non-increasing. • Complex behavior/function determined by neurons • connections/synaptic strength. • Complex neuronal Network: • A single neuron in vertebrate cortex connects ~10000 neurons • Mammalian brain contains > 10**10 interconnected neurons • Signal & information convey via neuronal connections—coding • Coupled oscillator networks of Cardic cells: • nonlinear dynamics, spiral waves, spatiao-temporal patterns…

29. Hodgkin-Huxley model (1952) Expts. On giant axon of squid: time & voltage dependent Na, K ion channels + leakage current Ik = gNam3h (u - ENa) + gKn4 (u - EK) + gL (u - EL). gating variables: a, b: empirical functions

30. Experiments http://mouse.kribb.re.kr/mousehtml/kistwistar.htm Schematic procedures in preparing the sample of neuron cells from celebral cortex embryonic rats Embryos of Wistar rats E17~E18 breeding days

31. Growth of axon connection to form a network Typical confocal microscope pictures of cultures used in our experiments. Red: anti-MAP2 (neuronal marker); Green, anti-GFAP (glia marker). Black &white: phase contrast image; Merge of the three images above.

32. Optical recording of fluorescence signals from firing network Firing of the network is monitored by the changes in intracellular [Ca 2+] which is indicated by the fluorescence probe (Oregon Green). Non-synchronous Firing in early stage of growth

33. Synchronized Firing of Neuronal Network Culture Spontaneous firing of the cultures are induced by reducing [Mg2+] in the Buffered salt solution Firing  the changes in intracellular [Ca 2+] indicated by the fluorescence probe. Synchronized Firing at later stage of growth

34. Time dependence of the SF frequency for a growing network Phys. Rev. Lett. 93 088101 (2004) PRE (2006) • Critical age for SF, tc • SF freq. grows with time • f=fc+fo log(t/tc) tc

35. Coupling between neurons D • P(D)=mean prob. that 2 neurons initially separated by D • will be connected • Characteristic coupling length • Dc ~ 0.33mm ~ 2 rc

36. Biological implications • Active growth in early stage, retarded once goal is achieved. • Slowing down to maintain a long time span for function: homeostasis • Continuing fast growth used up energy • Too much connections may exceed information capacity for a single neuron

37. Many Spikes in one pulse: Bursting

38. Glia and neuron mixed culture (8DIV, 5X105) 0 -60 mV 2 s Electrophysiology measurement (whole-cell recording, current-clamp) Inter-burst synchronized , but intra-burst is NOT synchronized

39. Bursting: role of inhibitory element • Continuous firing (over excited) is harmful--excitotoxicity • Inhibitors (Glia) suppress over-excited neurons • g=inhibitory field • Mean-field model • z=mean connectivity of a neuron to inhibitors FitzHugh-Nagumo model for neurons

40. Network of neurons & inhibitors Synchronized Bursting Intra-burst NOT synchronized

41. Experimental/Theoretical students Wanted • Experiments & Theories on bio-molecules, cells, neuronal/Cardiac physics, biological networks, bio-complex systems. • Non-physics background are welcome! • Interface bio/living system/molecules with materials. • Training on nano-bio-techniques Please contact黎璧賢: pylai@phy.ncu.edu.tw

42. Complex system Lab. 伊林Lin I • Bio/soft matter systems: • Micro-motion of bio- and soft materials in confined spots • dynamics of neuronal system • laser pulse-soft/bio matter interaction • Dusty plasma liquids: • effects of thermal excitation, external shear, finite size confinement, etc. on the micro-structure and micro-dynamics of dusty plasma liquid at the kinetic level

43. Biophysics Lab. 陳方玉Fang Yu Chen Membrane-active Peptides (NSC project) Anti-microbial peptides (AmP) is gene-encoded and is produced in innate immune system as the first-line defender to invading microbes and bacteria. There are three types of AmP -- -helix, -sheet and -ring. We have successfully proved the killing mechanism of -helix AmP - - stretching the target cell membrane to form pores on membrane, that leads the target cell to the death. We are now focusing at killing mechanism of those -sheet and -ring AMPs. Effect of peptide-forming pore on neuron function (UTS project) Gramicidin A (GA) is a small peptide, capable of forming trans-membrane ion channel which allows monovalent cations to pass. We are studying the effect of such GA channel on neuorn function.

44. Important Issues • The size of lipid rafts ? • Fraction of lipid rafts in cell membranes ? • The stabilityof lipid rafts ? • The origin of lipid rafts in cell membranes ? Techniques: Nuclear magnetic resonance) Atomic force microscopy (AFM) Ya-Wei Hsueh • Physical properties of biomembranes • Lipid-Protein interaction • applying solid-state NMR techniques in biological systems protein sphingolipid ● phospholipid cholesterol protein

45. Fluid Dynamics & Soft Matters 陳培亮Peilong Chen Statistical Mechanics of Electrolyte Solutions Distribution of electrolytes near interface, e.g., the cell membrane Fluid Dynamics in Soap Film Measuring friction at air-film interface Pattern Formation in Faraday Waves Pattern and mean flow interaction Block Copolymer Shear Alignment Derive the diffusion-stress coupled dynamics

46. Hsuan-Yi Chen Active membranes Pattern formation: inclusions in different states dislike each other. increasing activities

47. Computational Biology Laboratory HC Lee • Universality, Complexity & Self-Similarity in Complete Genomes • Molecular dynamics simulation of Protein Structure & Function

48. Wang, Min-Sheng (王敏生) Inverse problem of MEG (magnetoencephalography) Objective: To develop a method to determine the locations and strengths of synchronously activated neurons in the brain from the MEG data. Method: The brain is divided into blocks and a certain number of current dipoles are placed at the center of each block to represent the collective effect of synchronously activated neurons in that block. Assuming that the firing strength of all the current dipoles has the same Gaussian distribution of zero mean and large width prior to the knowledge of MEG data, the entropy of the whole system is minimized with respect to this Gaussian distribution (maximum entropy) under the constraint of MEG data.

49. BioPhysics Institute @NCU • Officially established in 2004 • Professors: 6 Assoc. Prof.: 1 Assist. Prof. 3 • Adj. Prof.: 2 Adj. assist.prof.: 2 • Graduate students working on areas in biophysics M.S.：23 Ph. D.：8 • Postdocs: 6 • aims at achieving some quantitative description of biological processes and search for the fundamental principles buried in these highly complex biological phenomena • 「5 years 500B」grant to support research & building of core facility labs. • Cross-disciplinary: researchers/students from physics & non-physics background