The Science behind the BioPen

The concept of recirculation


The BioPen® pipette tip is an open channel microfluidic device utilizing confined flow recirculation to enable high-resolution spatial control of the solute concentration in a confined liquid volume, very close to selected objects, such as single cells.

It is essentially a flow chamber, where a small volume of fluid is spatially confined within another, significantly larger fluid volume. The two miscible or immiscible liquids are physically in contact, separated only by means of a virtual boundary. Mixing between the two zones are largely defined by diffusion. The experimental conditions necessary to achieve efficient confinement, while inhibiting diffusion across the virtual boundary, are characterized by low Reynolds and high Péclet numbers.

A central channel serves as injection port or output channel (positive pressure), where liquid is introduced into the open volume, and two adjacent channels function as aspiration port or input channels (negative pressure), through which liquid is removed from it (see figure below). It creates a small perfusion volume at this end of the tip-to-open-volume interface, where the injected solution reaches a certain distance into the open volume.

To generate a stationary perfusion volume, the flow rate of the aspiration flow has to be higher than the flow rate of the injection flow, such that all fluid leaving the outlet will flow entirely into the neighboring inlet. Flow recirculation provides a mean to maintain a stationary concentration pattern, which would otherwise rapidly fade by spreading.


Animation movie showing flow recirculation:


Layout of the pipette tip

The pipette tip is made from a flexible medical grade elastomer material PDMS so that unlike glass pipettes it won’t break upon contact with a hard surface.

The pipette includes eight wells. Four wells for containing four different solutions and four wells for collecting wastes. Each well can contain up to 35 μl of solution. The use of integrated wells completely overcomes the typical problem of the dead volume of external tubing, which is significantly larger than the volume of the microchannels.

The pipette has a complex structure, which allows fast switching between four different solutions.

Two levels of pneumatic pressure are supplied by the attached pressure controller and fast switching is achieved through the use solenoid valves (see figure below).


Pon: positive pressure applied to the well of solution 1 to push solution 1 into the output channel
Poff: pressure applied to the other solution wells for maintaining the flow
Vswitch: vacuum applied to the switching point
Vrecirc: vacuum applied to the recirculation point

The software enables facile configuration and use of the BioPen® system. The Windows-based BioPen® software allows independent control of each pressure line and solution delivery (see figure below).


The perfusion volume itself is defined by the size, number and spacing of the channel outlets as well as the flow rates.

Video showing the control of the perfusion zone size:

View paper 1

View paper 2