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

Polymers in Biology

Nuclei are stained blue with DAPIActin 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 - 100 m

40m

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-2D Quasi-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 nm 10 nm 100 nm 1 m 10 m 100 m

persistence length p radius of

gyration

Rg

contour length L

Atomistic

Coarse graining

MicrochannelsNanochannels

Capture essential physics : Polymers, Solvent, Confinement

Flow timescale ~ minutes => coarse-grained model

Ld

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.