Research Program
Cellular Microdynamics

Project #
CM6

Participating Faculty:	Robert Austin, David Lawrence, Ted Cox
NBTC Students/Postdocs:	Chih-kuan Tung
Other Students/Postdocs:	David Inglis, John Davis, Keith Morton, Peter Galajda

Objectives
Our basic mission for this project is to develop innovative, new ways to sort the contents of single cells using a deep understanding of hydrodynamics at the sub-micron scale.  As our sorting technology for subcellular objects develops, we will use this technique to track adaptation and evolution in cells.

Methods
One of the early lessons you learn when you cross over into real biological systems is that rarely are two biological objects identical, they are quite often different.  Any attempt to find patterns within a biological system must be designed to look at a large number of supposedly identical molecules which may have a large variance.

We have been aware of this from the start, and our original design used photolithography to make arrays of obstacles and channels, and standard photolithographic techniques remain a core technology in our work.   However, photolithography cannot be used to make sub-micron width objects easily, and electron-beam lithography is tedious and an expensive way to make nanochannels over large (cm x cm) areas.  One of our collaborators, Professor Steven Chou at Princeton University (Electrical Engineering), has developed ways to transfer patterns of nanochannels into substrates that be used as etching masks, Prof. Chou’s grad student keith Morton has developed ways narrow the channels and create arrays with feature sizes approaching 10 nm.

Another substantial problem in interfacing biological objects with cellular components is the interaction of cell components with the materials used in microlithography. Since interrogation of proteins and nucleic acids is done using various spectroscopic methods, it is necessary that the materials

out of which the observation windows on the microfabricated flow cell are made are transparent to the desired wavelengths.  At the same time it is important that the chosen materials can be

micromachined into structures that allow appropriate fluid manipulations such as fast mixing required for measurements of protein folding kinetics.   While silicon still remains the material of choice for high aspect ratio feature etching, materials traditionally used spectrograph cuvettes such as fused silica (also called quartz or amorphous quartz) or calcium fluoride are most desirable as the observation windows due to their low fluorescence and high transmittance in the UV, visible and IR range.  This creates challenges to bond dissimilar materials or to fabricate the structures in optical materials for which high aspect ratio etching is not so readily available.

As one moves into the nanofabrication  area one meets further problems:  sealing to nanostructures now must be truly hermetic at the molecular level, surface properties become ever more important as the surface/volume ratio rises, the pressures needed to maintain flow rates of interest rise to the kilobar level requiring very strong bonds.  Also, surface  defects in materials become more important as sizes shrink these defects can act as blockages in nanodevices.  Much or our recent work involves dealing with these questions.

Accomplishments

• Theoretical models and experimental tests made for the critical particle size of fractionation in deterministic arrays.
• New technology for probing adaptation and evolution using nano/microtechnology coupled with genomics and ecology.
• Scaling of array and nanochannels down to sub-100 nm sizes for true molecular fractionation.