Droplet-trace-based array partitioning and a pin assignment algorithm for the automated design of digital microfluidic biochips
Summary (2 min read)
Keywords:
- Connect-5 algorithm, droplet-based microfluidics, droplet trace, pin-constrained biochip design, synthesis 1.
- Currently, most commercially-available biochips are either based on microarrays [4] or they rely on continuous fluidic flow in etched microchannels [1].
- Automated design therefore becomes necessary for this emerging marketplace.
- Multi-layer electrical connection structures and wire routing solutions are complicated by the large number of independent control pins in such arrays.
2. Digital Microfluidic Biochips
- A digital microfluidic biochip utilizes the phenomenon of electrowetting to manipulate and move microliter or nanoliter droplets containing biological samples on a two-dimensional electrode array [5].
- A unit cell in the array includes a pair of electrodes that acts as two parallel plates.
- By varying the patterns of control voltage activation, many fluid-handling operations such as droplet merging, splitting, mixing, and dispensing can be executed in a similar manner.
- To address the need for low-cost, PCB technology has been employed recently to inexpensively mass-fabricate digital microfluidic biochips.
- A large number of independent control pins necessitates multiple PCB layers, which adds significantly to the product cost.
4. Array Partitioning and Pin Assignment
- The authors first review the problem of electrode interference in microfluidic arrays.
- This problem can be solved by addressing each electrode and its neighbors with distinct pins.
- Recent experimental studies have shown that five independent pins are adequate to route a droplet to any place on the chip for single droplet manipulation [17].
- Since both Pin 3 and Pin 8 are charged, Dj will be split unintentionally.
- Therefore, for the partitioned array, the number of droplets that can be simultaneously transported without stall cycles is equal to the number of partitions, and the total number of control pins needed is equal to five times the number of partitions.
4.1. Trace-Based Partitioning Algorithm
- As discussed above, partitioning can effectively avoid electrode interference if each partition includes only one droplet.
- Note that droplet traces may have spatial overlap, i.e., they may intersect at one or more unit cells on the array.
- Again, time-division pin-sharing (TDPS) can be used to reduce the number of pins since pin sets of the other (non-overlapping) partitions can be candidates for direct-addressing in the overlapping partition.
- Next the time spans for Partitions 1 and 4 are checked and it is seen that their time spans do not overlap with that for Partition 23.
- Depending on the outcome of this procedure, a spatial overlap region can be then divided into two groups—a spatially overlapping but temporally non-overlapping (SOTN) region, and a spatially overlapping as well as temporal overlapping (SOTO) region.
4.2. Extended Partitioning Algorithm
- The authors present an extension of the partitioning algorithm that does not require module placement information.
- In Section 4.1, the authors needed the placement information for modules that handle multiple droplets, such as mixers and splitters to determine the droplet traces.
- The mixing operation can be viewed as two droplets being routed together along an identical path simultaneously with the start point in the mixer region.
- Note that splitting and mixing can both be viewed as deliberate electrode interference.
- The number of pins can be further reduced.
4.3. Pin assignment using the Connect-5 algorithm
- In Section 4.1 and Section 4.2, the authors have described an automated partitioning method for digital microfluidic arrays.
- This approach allows us to use a regular distribution of pins, a layout feature that is not directly obtained from graph coloring.
- The tiling using Bagua repetitions forms the basis for the Connect-5 algorithm.
- Recall that the shifting direction, once chosen, must remain fixed during the assignment procedure for a given partition.
- Since this is true for any Bagua repetitions and any partition can be tiled by five copies of Bagua repetitions, the “cross constraint” is automatically met for every cell in their pin assignment method.
6. Conclusions
- The authors have presented an efficient algorithm for array partitioning and pin assignment in pin-constrained digital microfluidic biochips.
- The proposed partitioning algorithm is based on the concept of droplet trace, which is extracted from the scheduling and droplet routing results produced by a synthesis tool.
- The array partitioning and pin assignment methods have been evaluated using a set of multiplexed bioassays.
- By drastically reducing the number of control pins with minimal impact on assay throughput, the proposed design technique is expected to reduce cost and lead to further miniaturization of disposable biomedical devices for the emerging healthcare market.
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Cites background from "Droplet-trace-based array partition..."
...Electrodes are connected to control pins for electrical actuation....
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...Hence this technology is referred to as digital microfluidics [1]....
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117 citations
114 citations
References
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6,255 citations
1,471 citations
"Droplet-trace-based array partition..." refers background or methods in this paper
...A digital microfluidic biochip utilizes the phenomenon of electrowetting to manipulate and move microliter or nanoliter droplets containing biological samples on a two-dimensional electrode array [5]....
[...]
...The “digital” structure also offers reconfigurability and a scalable system architecture based on a two-dimensional array [5, 6]....
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1,124 citations
"Droplet-trace-based array partition..." refers background in this paper
...Pin-constrained design of digital microfluidic biochips was recently proposed and analyzed in [3]....
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...They combine electronics with biology, and they integrate various bioassay operations, such as sample preparation, analysis, separation, and detection [1, 2, 3], in a single miniaturized platform....
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...These assays have been demonstrated recently [3]....
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...In addition to electrodes, optical detectors such as LEDs and photodiodes are also integrated in digital microfluidic arrays to monitor colorimetric bioassays [3]....
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...It has been predicted that, by providing miniaturization, automation and integration, microfluidic biochips will revolutionize laboratory procedures in molecular biology with applications to point-of-care diagnostics, DNA analysis, and automated drug discovery [2, 3]....
[...]
491 citations
"Droplet-trace-based array partition..." refers background in this paper
...They combine electronics with biology, and they integrate various bioassay operations, such as sample preparation, analysis, separation, and detection [1, 2, 3], in a single miniaturized platform....
[...]
...Currently, most commercially-available biochips are either based on microarrays [4] or they rely on continuous fluidic flow in etched microchannels [1]....
[...]
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Frequently Asked Questions (16)
Q2. What are the two main types of electrodes used for driving a droplet?
In order to drive a droplet along the X-direction, electrode rows on the bottom plate serve as driving electrodes, while electrode rows on the top serve as reference ground electrodes.
Q3. How can you solve the problem of electrode interference?
Electrode interference can be solved by “virtually” partitioning the array into regions, with each of them having only one activated cell at any point in time.
Q4. What are the main applications of microfluidics biochips?
Microfluidics-based biochips combine electronics with biology to open new application areas such as point-of-care medical diagnostics, on-chip DNA analysis, and automated drug discovery.
Q5. What is the way to reduce the number of control pins?
Although the multi-phase bus method is useful for reducing the number of control pins, it is only applicable to a one-dimensional (linear) array.
Q6. What can be done to reduce the number of control pins?
The concept of TDPS can also be applied in the spatial dimension to the operations inside the overlapping region to further reduce the number of control pins.
Q7. How many sets of pins are used for electrode control in different partitions?
By using different sets of five pins for electrode control in different partitions, electrode interference among partitions can be avoided.
Q8. What is the disadvantage of the ad-hoc partitioning method?
microfluidic modules such as mixers, splitters, and detectors are not considered in the ad-hoc partitioning method; an additional design step is needed to handle these modules separately.
Q9. how to reduce the number of control pins?
By drastically reducing the number of control pins with minimal impact on assay throughput, the proposed design technique is expected to reduce cost and lead to further miniaturization of disposable biomedical devices for the emerging healthcare market.
Q10. How many pins do two-dimensional arrays need to ensure full control of a single?
Recall that regardless of size, a two-dimensional array only needs five independent pins to ensure full control of a single droplet.
Q11. How many pins can be used to address the nine electrodes in Partition 23?
Hence the two set of pins (a total of 2x5=10 pins) in Partitions 1 and 4 can be used to directly address the nine electrodes in Partition 23.
Q12. How many independent pins are sufficient to route a droplet to any place on the chip?
Recent experimental studies have shown that five independent pins are adequate to route a droplet to any place on the chip for single droplet manipulation [17].
Q13. What is the last step in system synthesis?
Since the authors view pin assignment as the last step in system synthesis, information about module placement and droplet routing is available a priori.
Q14. How many copies of the same partition can be tiled?
Since this is true for any Bagua repetitions and any partition can be tiled by five copies of Bagua repetitions, the “cross constraint” is automatically met for every cell in their pin assignment method.
Q15. What is the problem with multi-layer electrical connection structures?
Multi-layer electrical connection structures and wire routing solutions are complicated by the large number of independent control pins in such arrays.
Q16. How can the authors determine the time spans for all the partitions?
The time spans for all the partitions can be easily calculated from the operation schedule, module placement and droplet routing results [19]; the overlaps can then be readily determined.