Big molecules in a small space : Macromolecules in Micro-confinement

1. Big molecules in a small space : Macromolecules in Micro-confinement 陳彥龍 (yenglong@phys.sinica.edu.tw) 中央研究院物理研究所和應用科學中心 Entropy

2. Polymers in Biology Endothelial Cell Diameter: 7nm Persistence length : ~10 mm F-Actin DNA 3.4 nm Nuclei are stained blue with DAPI Actin filaments are labeled red with phalloidin Microtubules are marked green by an antibody Persistence length : ~ 50 nm

3. Organ Printing Mironov et al. (2003) Boland et al. (2003) Forgacs et al. (2000) • Cells deposited into gel matrix fuse when they are in proximity of each other • Induce sufficient vascularization • Embryonic tissues are viscoelastic • Smallest features ~ O(mm) Organ printing and cell assembly

4. Confining Macromolecules Fluid plug reactor from Cheng group, RCAS Advantages of microfluidic chips Channel dimension ~ 10nm - 100 mm Microfluidic washing machine, Schwartz group • High throughput • Low material cost • High degree of parallelization • High sensitivity 40mm Efficient device depends on controlled transport Theory and simulations help us understand dynamics of macromolecules

5. Expt H H Physics of confined polymers K. Jo, D.C. Schwartz Quasi-2D Quasi-1D Flow Direction 1cm How does macromolecule dynamics change as confinement becomes smaller ? 760 nm (w) x 160 nm (h)

6. What do we do ? Molecular Dynamics - Model atoms and molecules using Newton’s law of motion Monte Carlo - Statistically samples energy and configuration space of systems Cellular Automata - Complex pattern formation from simple computer instructions Large particle in a granular flow Polymer configuration sampling Sierpinksi gasket • If alive, dead in next step • If only 1 living neighbor, alive

7. 1 nm 10 nm 1 mm 10 mm 100 mm 100 nm Our Research Coarse graining Nanochannels Microchannels Atomistic contour length L persistence length xp radius of gyration Rg 3.4 nm 2 nm Capture essential physics : Polymers, Solvent, Confinement Flow timescale ~ minutes => coarse-grained model

8. Ld Some results and predictions DNA molecules migrate away from walls, they are pushed back out

9. Calculations are based on physics. Without physics, simulations are just numbers. Computer simulations allow us to perform extremely complex computation to imitate the real world and study microscopic and macroscopic systems. Theory and computation can make predictions before the experiment is (can be) done. Calculations can guide/confirm experiments / resolve controversies / predict new phenomenon.