Big molecules in a small space : Macromolecules in Micro-confinement 陳彥龍 中央研究院物理研究所和應用科學中心 Entropy

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

Organ Printing Mironov et al. (2003) Boland et al. (2003) Forgacs et al. (2000) Organ printing and cell assembly 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)

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

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

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

Our Research 2 nm 3.4 nm 1 nm10 nm 100 nm 1  m10  m100  m persistence length  p radius of gyration R g contour length L Atomistic Coarse graining MicrochannelsNanochannels Capture essential physics : Polymers, Solvent, Confinement Flow timescale ~ minutes => coarse-grained model

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

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.