Thrust 1 - Single Polymer and Interfacial Dynamics
The goal is to understand single molecule dynamics to develop techniques for biomolecular and materials processing at interfaces.
DNA dynamics in microfluidic mixed flows. Muller is developing both cross-slot and microfluidic four-roll mill devices to accomplish flow-enhanced, rapid single molecule DNA hybridization. These microfluidic devices will allow studies of the effects of stretching on DNA hybridization kinetics. These studies will permit rapid attachment of sequence-specific markers to create a sequence-specific sensor, provide benchmark data for extending simulation tools to include reaction kinetics, and make available an apparatus for bringing together vesicles or other supramolecular assemblies in a controlled way. The two microdevices, a cross-slot and a “microfluidic four-roll mill,” create stagnation-point flows that allow us to trap single DNA molecules. Through manipulation of the flow rates and geometry, the extension of the DNA chain and the flow type (rotation, shear, extension) can be controlled.
Figure 1 contains a schematic of both microdevices. At present, the microfluidic four-roll mill device can create mixed flows where polymer dynamics is qualitatively different than in the “standard” extensional or shear flows. One ramification of this is polymer chain length fluctuations that are flow-type dependent, as predicted in dynamic simulations using fast numerical algorithms with full intramolecular hydrodynamic interactions by Shaqfeh.
Prototypes of the cross-slot device, based on the design of Schroeder, Chu, and Shaqfeh have been fabricated using wax and PDMS soft lithography. A flow focuser has been added to allow probes to be introduced along a stagnation streamline, and steady, reproducible flow focusing has been demonstrated. These devices have been used to trap and stretch DNA in purely extensional flow. In parallel, we have designed probes that allow simultaneous visualization of the DNA backbone and the probe oligonucleotide.
In the next year, we plan to demonstrate hybridization under single molecule stretch, demonstrate analysis of ex-situ probe marking in the cross-slot trap, demonstrate probe design for sequence specific assays, demonstrate trapping with the four-roll mill, and understand flow type as a control variable in single molecule processes.
Figure 1. a) Schematic of microfluidic cross-slot with flow focusing, b) microfluidic four-roll mill. The stagnation (trapping) point is highlighted in yellow. c) Plot of the tumbling period as a function of Weissenberg number in the four-roll mill.
Stretching tethered DNA as a scaffold for organic wires. Shaqfeh and Bao have examined a stretching flow from a surface stagnation point as a means of stretching DNA between two electrodes. The surface extensional flow creates interesting dynamic properties as predicted by numerical simulation including conformational hysteresis, which is important to understand in the engineering of the stretching flow for this application. This is the first time that conformational hysteresis has been predicted in a nonlinear flow, and in this instance the interface creates the nonlinearity that drives the phenomenon. Numerical simulations are made possible because of a new algorithm for summing long range hydrodynamic intramolecular interactions (HI) including wall HI. Large scale simulation has proven invaluable as a probe for these hysteretic or “glassy” dynamics, and these findings have significant ramifications for microfluidics of complex fluids.
