Proceedings of IMECE04

2004 ASME International Mechanical Engineering Congress and Exposition

November 13-20, 2004, Anaheim, California USA

IMECE2004-62303

Buoyancy Driven Microfluidics

Z. Chen, S. Qian, J. Wang, and H. H. Bau1
Dept. Mechanical Engineering and Applied Mechanics
University of Pennsylvania, Philadelphia, PA 19104-6315

It is not surprising that the use of buoyancy as a driving force in microfluidic systems has
attracted little or no attention. Buoyant forces are proportional to the volume and do not scale
favorably as the device size is reduced. Nevertheless, in certain biotechnological applications,
one can produce sufficiently large buoyancy forces to generate fluid motion at velocities on the
order of mm/s even in conduits with equivalent diameters of a few hundreds of microns. One
example is the thermal polymerase chain reaction (PCR) for DNA amplification. In this process,
the reagents’ temperature varies from about 55°C to 94°C. Such large temperature variations can
induce significant buoyant forces. Another class of systems that can be driven by buoyant forces
is rotating laboratories on a chip (lab on a CD). In such laboratories, large centrifugal
accelerations may induce significant buoyant forces even when the temperature variations are
relatively small. These temperature variations can be used to propel and control fluid flow.

In this presentation, we describe a successful demonstration of a self-actuated, continuous

flow (SAFC) PCR reactor for DNA amplification. The common PCR process requires one to
cycle the sample’s temperature from about 94C (denaturation) to 55°C (annealing) to 72°C
(extension). In most bench-top PCR reactors, the sample is maintained stationary while the
temperature is repetitively alternated, which makes it necessary to heat and cool both the
reagents and the heating block. This process results in considerable thermal inertia, and it is a
relatively slow and energy-intensive process. Some of these shortcomings can be overcome
through miniaturization and the use of continuous flow reactors. In continuous flow PCR
reactors, the temperatures of the three thermal zones are maintained fixed while the reagents are
circulated continuously through these thermal zones. Continuous flow reactors allow for
significantly shorter heating and cooling times with reduced energy consumption since it is not
necessary to combat the thermal inertia of the apparatus. The continuous flow reactors require,
however, a means for propelling the sample. In recent years, various means for propelling the
fluid, ranging from pressure to peristalsis to magneto-hydrodynamics, have been proposed. Here,
we put forward an intriguing alternative.

1
Corresponding author, bau@seas.upenn.edu

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 The relatively large temperature variations needed for PCR induce significant variations
in the fluid’s density, which we use to generate fluid motion. We constructed a closed loop
having a triangular shape and placed in the vertical plane (Fig. 1). The vertical leg was heated to
94°C (denaturation zone), part of the diagonal leg was maintained at 55°C (annealing zone), and
the horizontal leg was maintained at 72°C (extension zone). The upper part of the tube was
exposed to the ambient temperature to facilitate cooling from 94°C to 55°C. The closed loop
formed a thermosyphon, and the fluid’s density variations facilitated counter-clockwise
circulation. Flow velocities as high as 5mm/s were attained in a conduit with a 700µm diameter.
Interestingly, since for a given loop geometry both the buoyant and viscous forces are
proportional to the length of the loop, the flow velocity is only weakly dependent on the actual
length of the loop, and the loop can be readily scaled down in length with only moderate impact
on the fluid velocity. This assertion was demonstrated through experiments and theoretical
calculations.

The reagents circulated continuously among the various heated zones as required for
DNA amplification. Successful amplifications of 700-bp and 305-bp fragments of Bacillus
cereus genomic DNA have been demonstrated. Fig. 2 depicts gel images of the PCR products
compared with DNA amplification in bench top machines. The actual experimental data was
collected from a scaled up version of the apparatus depicted in Fig. 12.

We speculate that by judiciously heating various branches of a network (Fig. 3), we can
use buoyant forces to direct the flow to follow a desired path without the need for mechanical
valves. Work to prove the concept is ongoing, and the results will be described.

In summary, the paper describes our theoretical analysis and experimental verification of
a microfluidic system driven with buoyant forces. As an example of an application, a self-
driven, PCR machine was modeled, constructed, and successfully tested.

Acknowledgments: We enjoyed helpful discussions with Drs. D. Malamud, W. Abrams,

and Z. Wu (University of Pennsylvania, School of Dental Medicine) and P. Corstjens (Leiden
University). Ms. C. Davis and Mr. G. Tong (University of Pennsylvania, School of Dental
Medicine) assisted with the PCR experiments. The experimental and theoretical works were
supported, respectively, by NIH grant U01DE014964 and DARPA grant N66001-01-C-8056 to
the University of Pennsylvania.

2
Chen, Z., Qian, S., Abrams, W., R., Malamud, D., and Bau, H., H., 2004, Thermosyphon-based PCR Reactor:
Experiment and Modeling, Analytical Chemistry, 76, 3707-3715.

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 Annealing
Fig. 1: A self-actuated PCR machine. The device zone (55°C)
was fabricated with polycarbonate using layered Denaturation
Conduit Heaters zone (94°C)
manufacturing. The heaters were fabricated by
vapor deposition of metal on the polycarbonate
and standard photolithographic processing.
Extension
zone (72°C)

Fig. 2: Images of ethidium bromide stained

DNA products in a 1% agarose gel. A) Initial
denaturation of the self-actuated PCR was
performed outside the SAFC loop. Lanes A1-5:
700 bp fragment; lane A1- positive control I,
0.05 U/µL Taq and 27 ng/µL DNA template;
lane A2- positive control II, 0.1 U/µL Taq and
13.5 ng/µL DNA template; lanes A3 and 4-
SAFC PCR products using the same mixtures as
for controls I and II, respectively; Lane A5:
negative control using the same mixture as
control II without any DNA. Lanes A6-10: 305
bp DNA fragment; lane A6- positive control III,
0.05 U/µL Taq and 27 ng/µL DNA template; lane A7- positive control IV, 0.1 U/µL Taq and
13.5 ng/µL DNA template; lanes A8 and 9- SACF PCR products using the same mixtures as for
controls III and IV, respectively; Lane A10: negative control using the same mixture as control
IV without any DNA.
B) Initial denaturation of SAFC PCR was performed in the SAFC loop with all three heating
blocks maintained at 95 °C. Lane B1: positive control, 0.1 U/µL Taq and 13.5 ng/µL DNA
template. Lane B2: SAFC PCR products using the same mixture as the positive control.

Fig. 3: A device fabricated with polycarbonate to demonstrate the concept

of controlling fluid flow without the need for mechanical valves. Each of
the network branches is equipped with an individually controlled heater.
The flow path can be adjusted by judiciously adjusting the power input to
individual heaters.

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