Beta 1


Title Synthesis of Biochemical Applications with Operation Variability on Digital Microfluidic Biochips
Author Sjøgreen, Christian Ejdal
Supervisor Pop, Paul (Embedded Systems Engineering, Department of Informatics and Mathematical Modeling, Technical University of Denmark, DTU, DK-2800 Kgs. Lyngby, Denmark)
Institution Technical University of Denmark, DTU, DK-2800 Kgs. Lyngby, Denmark
Thesis level Bachelor thesis
Year 2011
Abstract Digital microfluidic biochips are small devices promising to replace much of the equipment found in biochemical laboratories today. A digital biochip is composed of a two-dimensional array of electrodes. A small drop of liquid (a droplet) can occupy one electrode. The droplets can be manipulated on the biochip using a technique called electrowetting-on-dielectric. Any biochemical application (or bioassay), can be captured as a series of basic microfluidic operations performed using the droplets on a digital biochip. The bioassays are modeled using a directed graph, where each node is an operation. Apart from the operations themselves, the graph indicates the order in which they must be executed for the bioassay to be successful. Such a graph is called an application graph. In order for a digital microuidic biochip to execute the application graph of a bioassay the graph must be synthesized into a schedule for the biochip microcontroller. The schedule tells the biochip when and where to move the droplets to perform the bioassay. Errors can appear during the execution of an application, such as a stuck droplet or an imperfect split operation resulting in imbalanced volumes. A simple scheme has been proposed in literature, where several recovery schedules are produced at design time and are stored in the microcontroller. However, in this thesis we consider that the recovery schedules are produced during runtime, based on the observed errors. Researchers have proposed methods for schedule synthesis based on meta- heuristics, but they are very time-consuming. Hence, the existing methods cannot be used to synthesize a recovery schedule for the biochemical application at run time, as a reaction to errors. The objective of the thesis is to develop a fast and accurate heuristic for recovery schedule synthesis that can be applied online for fault-tolerance. We present the types of errors that can appear. Different approaches for the biochip controller to react to errors are discussed. The existing synthesis method is presented, and a fast but accurate heuristic algorithm for recovery schedule synthesis handling is proposed and implemented.
Imprint Technical University of Denmark (DTU) : Kgs. Lyngby, Denmark
Series IMM-B.Sc.-2011-02
Fulltext
Original PDF bac11_02.pdf (0.84 MB)
Admin Creation date: 2011-03-25    Update date: 2011-03-25    Source: dtu    ID: 275728    Original MXD