25-27 April 2012, Cannes, France ©EDA Publishing/DTIP 2012 ISBN: Droplet-Aware Module-Based Synthesis for Fault-Tolerant Digital Microfluidic Biochips Elena Maftei, Paul Pop, Jan Madsen Technical Univ. of Denmark, DK-2800 Kgs. Lyngby email: paul.pop@imm.dtu.dk Abstract—Microfluidic biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the basic functions for biochemical analysis. On a “digital” biochip liquids are manipulated as discrete droplets on a two- dimensional microfluidic array of electrodes. Basic operations, such as mixing and dilution, are performed on the array, by routing the corresponding droplets on a group of electrodes, forming a virtual device. Initially researchers have ignored the locations of droplets during operation execution, and have considered that all electrodes inside devices are occupied. We have recently proposed a droplet-aware approach for the execution of operations on the microfluidic array, in which the locations of droplets inside devices are known at each time step. In this article we extend the droplet-aware approach to consider the synthesis of biochips which contain defective electrodes on the microfluidic array. We show that for such biochips knowing the exact locations of droplets during operation execution leads to significant improvements in the completion time of applications. I. I NTRODUCTION Microfluidic biochips represent a promising alternative to conventional biochemical laboratories, and are able to integrate on-chip all the necessary functions for biochemical analysis such as, transport, splitting, merging, dispensing, mixing, and detection, using very small amount of fluids (micro- or nanoliters). Due to the lower cost per bioassay and increased automation and miniaturization compared to biochemical lab- oratories, biochips are expected to revolutionize areas such as clinical diagnosis, point-of-care diagnosis of diseases and DNA and protein analysis [1]. This article focuses on the synthesis of digital microfluidic biochips (DMBs). Such devices are based on the manipu- lation of discrete droplets using software-driven electronic control [2]. A typical digital microfluidic biochip is composed of a two-dimensional microfluidic array of identical cells, together with reservoirs for storing the samples and reagents, as shown in Figure 1a. Each cell is composed of two parallel glass plates, see Figure 1b. The top plate contains a single ground electrode, while the bottom plate has several control electrodes. The droplet moves between the two plates using an electri- cal method called electrowetting-on-dielectric (EWOD). With EWOD, the movement of droplets is controlled by applying voltages to the required electrodes. For example, turning off the middle control electrode and turning on the right control electrode in Figure 1b will force the droplet to move to the right. For the details on EWOD, the reader is directed to [3]. A. Operation Execution In order to perform a biochemical application on a biochip, its protocol must be known, that is the sequence of basic oper- ations (e.g., dispensing, mixing, dilution, detection) composing the application. Such a protocol will typically be provided by the users of the biochips, e.g., biochemists, and can be modeled using a sequencing graph. For example, Figure 1c describes part of a biochemical application which consists of seven input operations (O 1 –O 6 , O 10 ), during which droplets are created and dispensed on the array, three mixing operations (O 7 , O 8 and O 9 ) and one dilution operation (O 11 ). On a digital microfluidic biochip operations such as mixing and dilution are performed by repeatedly routing the droplets on a group of adjacent electrodes, forming a virtual module. Due to the fact that any electrodes on the chip can be used for such a purpose, we say that these operations are “reconfigurable”. A biochemical application may also contain “non-reconfigurable” operations, that are executed on real devices, such as reservoirs or optical detectors. The number and location of non-reconfigurable devices are decided during the design of the biochip and remain fixed after the fabrication of the device. Initially researchers have ignored the positions of droplets inside modules, considering them as black-boxes inside which operations are executed. In order to avoid the accidental merg- ing of droplets, it was considered that devices are surrounded by segregation areas, containing cells that cannot be used until the operations performing on the devices are completed. For example, the mixing operation O 7 in Figure 2b is executed inside the 2 × 3 module denoted by M 1 . However, due to the 1-electrode segregation area, the device occupies 4 × 5 electrodes. In [4] we have proposed a droplet-aware execution of mi- crofluidic operations, in which the exact positions of droplets inside devices are known at each time step. For example, in Figure 3b the mixing operations O 7 , O 8 and O 9 are performed by routing the droplets inside the virtual modules, according to the movement patterns described by the corresponding arrows. We avoid the accidental merging of droplets by maintaining a minimum distance between the executing operations, i.e., enforcing the fluidic constraints. The advantage of this ap- proach is a better utilization of the space on the microfluidic array. For example the M 1 device in Figure 3b occupies the same amount of space as the 2 × 3 M 1 device (4 × 5