Automated Design of Digital Microfluidic Lab-on-Chip under Pin-Count Constraints Tao Xu and Krishnendu Chakrabarty Department of Electrical and Computer Engineering Duke University, Durham, NC 27708, USA. E-mail: {tao,krish}@ee.duke.edu ABSTRACT the top plate is coated with a continuous ground electrode. A droplet Digital microfluidic biochips, as referred to as lab-on-a-chip, are rests on a hydrophobic surface over an electrode, as shown in Figure revolutionizing DNA sequencing, immunoassays, and clinical 1. It is moved by applying a control voltage to an electrode adjacent diagnostics. Bioassays steps are mapped to a sequence of to the droplet and, at the same time, deactivating the electrode just microfludic operations on a two-dimensional array of electrodes. under the droplet. This electronic method of wettability control The number of independent input pins used to control the electrodes creates interfacial tension gradients that move the droplets to the is an important cost-driver, especially for disposable PCB devices charged electrode. Using the electrowetting phenomenon, droplets that are being developed for clinical and point-of-care diagnostics. can be moved to any location on a two-dimensional array. By We review two design-automation methods for such varying the patterns of control-voltage activation, many pin-count-constrained biochips. The first design procedure relies on fluid-handling operations such as droplet dispensing, merging, a droplet-trace-based array partitioning scheme and an efficient pin splitting, mixing, localized heating, and incubation can be executed assignment technique, referred to as the “Connect-5 algorithm”. The on-chip in a programmable fashion. For example, mixing can be second pin-constrained design method relies on “cross-referencing” performed by routing two droplets to the same location and then addressing based on “rows” and “columns” to access electrodes. An turning them about some pivot points [9]. efficient droplet manipulation method is presented for this The rapid development of microfluidics technology has enabled cross-referencing technique based on a mapping of the the concurrently execution of complicated bioassays on digital droplet-movement problem to the clique-partitioning problem from microfluidic platforms [10, 11]. As a result of greater concurrency, graph theory. each individual bioassay requires more sophisticated control for resource management. Therefore there is a need to deliver the same Categories and Subject Descriptors level of design automation support to the biochip designers and users B.m MISCELLANEOUS that the semiconductor industry takes for granted. The increase in the system complexity and integration levels poses General Terms: Algorithms, Design additional challenges for electrode addressing and system control. Keywords: Array partition, Cross-referencing, Lab-on-Chip, Most prior work on biochips computer-aided-design (CAD) has Microfluidics, Pin-count constraints assumed a direct-addressing scheme, where each electrode is connected to a dedicated control pin; it can therefore be activated independently. This method provides the maximum freedom for 1. INTRODUCTION droplet manipulation, but it requires an excessive number of control Microfluidics technology has made great strides in recent years pins. For example, a total of 104 pins are needed to independently [1-6]. Promising applications of this emerging technology include control the electrodes in a 100×100 array. Multi-layer electrical high-throughput DNA sequencing, immunoassays, environmental connection structures and wire-routing solutions are complicated by toxicity monitoring, and point-of-care diagnosis of diseases [4]. the large number of independent control pins in such arrays. Product Microfluidics-based miniaturized devices, often referred to in the cost, however, is a major marketability driver due to the one-time-use literature as biochips or lab-on-chip, are being increasingly used for (disposable) nature of most emerging devices. Thus, the design of laboratory procedures involving molecular biology. Compared to pin-constrained digital microfluidic arrays is of considerable conventional laboratory experiment procedures, which are usually importance for the emerging marketplace. cumbersome and expensive, these miniaturized and automated In this paper, we review two recently published design techniques biochip devices offer a number of advantages such as higher for pin-constrained lab-on-chip. A droplet-trace-based sensitivity, lower cost due to smaller sample and reagent volumes, array-partitioning method is first described. This method is based on and less likelihood of human error. the concept of “droplet trace” [12], extracted from the scheduling and An especially promising category of microfluidic lab-on-chip relies droplet routing results produced by a synthesis tool. An efficient on “digital microfluidics”, which is based on the principle of pin-assignment method, referred to as the “Connect-5 algorithm”, is electrowetting-on-dielectric [1, 5, 7, 8]. A typical digital microfluidic combined with array partitioning to address electrode arrays with biochip consists of a two-dimensional electrode array [1]. A unit cell limited number of control pins. The second pin-constrained design in the array includes a pair of electrodes that acts as two parallel method is based on a “cross-referencing” chip structure, which plates. The bottom plate contains a patterned array of electrodes, and allows control of an N×M grid array with only N+M control pins [13]. An efficient droplet manipulation method has been proposed to Permission to make digital or hard copies of all or part of this work for achieve high throughput on “cross-referencing” based chips. We personal or classroom use is granted without fee provided that copies are not evaluate the proposed method using a multifunctional chip designed made or distributed for profit or commercial advantage and that copies bear to execute a set of multiplexed bioassays and the polymerase chain this notice and the full citation on the first page. To copy otherwise, or reaction. republish, to post on servers or to redistribute to lists, requires prior specific The organization of the rest of the paper is as follows. In Section 2, permission and/or a fee. we discuss related prior work on biochip design-automation and ISPD’08, April 13–16, 2008, Portland, Oregon, USA. Copyright 2008 ACM 978-1-60558-048-7/08/04...$5.00. 190 pin-constrained chip design. Section 3 describes the array 3.1 Impact of Droplet Interference -partitioning method. Section 4 presents the grouping-based droplet A pin-constrained layout may result in unintentional droplet manipulation method for cross-referencing-based chips. Section 5 movement when multiple droplets are present in the array. Figure 2 evaluates the proposed method using a biochip for multiplexed shows a 4×4-array in which the 16 electrodes are controlled by only bioassay. Conclusions are drawn in Section 6. 9 input pins. The pin numbers are indicated in the figure. Droplet 2. RELATED PRIOR WORK interference occurs if we attempt to move droplet Di while keeping droplet Dj at its current location. Suppose Di is at coordinate location Recent years have seen growing interest in CAD tools for digital (0,0) and Dj is at coordinate location (3,2). To move Di to (1,0), we microfluidics [14-17]. One of the first published methods for biochip need to activate electrode (1,0) and deactivate (0,0). This implies that synthesis decouples high-level synthesis from physical design [15]. It a high voltage must be applied to Pin 8 while a low voltage must be is based on rough estimates for placement costs such as the areas of applied to Pin 1. Note however that a high voltage on Pin 8 also the microfluidic modules. These estimates provide lower bounds on activates electrode (3,3). This results in the inadvertent stretching of the exact biochip area, since the overheads due to spare cells and droplet Dj across electrodes (3,2) and (3,3). cells used for droplet transportation are not known a priori. The sharing of control pins can also affect a single droplet. An However, it cannot be accurately predicted if the biochip design example is shown in Figure 3. To move droplets Di one electrode to meets system specifications, e.g., maximum allowable array area and the left requires Pin 8 to be activated. However, the electrode on the upper limits on assay completion times, until both high-level right of the droplet is also connected to Pin 8; it is therefore also synthesis and physical design are carried out. [18] proposed a unified activated. As a result, Di is pulled from both sides and it undergoes system-level synthesis method for microfluidic biochips based on inadvertent splitting. The above example shows that the sharing of parallel recombinative simulated annealing (PRSA). control pins can lead to unintentional operations such as droplet splitting and inadvertent movement due to droplet interference. This Top glass Ground problem therefore must be avoided in any practical pin assignment. plate electrode Droplet Filler Fluid Hydrophobic layer Control Bottom plate electrodes (a) (b) (a) (b) Figure 2. An example to illustrate droplet interference due to the Figure 1. A digital microfluidic array: (a) 2-D electrode array (b) sharing of control pins by the electrodes: (a) coordinate locations unit cell side view. for the electrodes; (b) pin-assignment for the electrodes. The top-down synthesis flow method unifies architecture