DNA Dynamics in Mixed Flows and in Micro- and Macro- Devices

 (Funded by the Center of Polymer Interfaces and Molecular Assemblages, 

CPIMA and the NSF Chemical and Thermal Sciences Division;
Collaboration with Prof. Steve Chu, Director of Lawrence Berkeley Laboratories)

The dynamics of DNA, as both a probe for polymer dynamics in flow and as a research area of great importance to industries associated with biosensors and lab-on-a-chip devices, has been an ongoing theme in our research group for more than seven years. The research begins with the development of detailed Brownian dynamic models for DNA dynamics in a variety of well-characterized flow fields which are validated with single molecule flourescence microscopy originating in the Chu group. This combination has allowed the description of new physical principles governing these dynamics under highly nonequilibrium conditions, including the tumbling dynamics and fluctuation dynamics of molecules in a wide range of planar flows with varying ratios of strain and vorticity. These flows designated as "mixed" flows span the behavior from purely vortical flow to purely straining motion. In purely straining flows, we have now demonstrated that the coil-stretch transition is hysteretic with two kinetically separate bistable states simultaneously existing. The dynamics is also interesting near the "critical point" known as simple shear flow where the straining and vorticity are exactly balanced. For flows near this point the conformational "phase transition" is associated with large fluctuations that can be examined in a detailed manner both computationally and experimentally. Finally, in our latest work, we are moving to examine fluorescently decorated synthetic polymers and entangle polymer systems as well.

] Our materials center known as CPIMA is focussed on the interfacial properties of polymers as well as their interfacial dynamics. Our developing DNA model has thus been applied to understand new DNA microdevices including post arrays for separation, Brownian ratchets and the rheology in ultrathin gaps. Simulating these nonequilibrium processes where the statistical mechanics of unbound molecules is not applicable, allows for the understanding of the new important physical principles that govern these processes. Two primary examples we have examined include "hairpin" dynamics associated with the unravelling of chains around posts as they interact. These dynamics are critical to understanding the relative mobilities of molecules as they are passed through post arrays and this mobility difference can allow for separation under certain conditions. Remarkably these dynamics are very similar to drop breakup in fixed fiber beds, where in this example, the dynamics of a drop wrapping around a fiber is key to understanding the breakup mechanism. (This is another project in our group which is examined via dynamic simulations using boundary integral techniques).A second interesting piece of physics is that associated with the change in nonequilibrium chain dynamics when a polymer is constrained to a gap of thickness comparable to its radius of gyration or tethered near a stagnation point on a solid surface. The latter can create conformation hysteresis of a wholly new kind which we examine again via detailed simulation and experiment.