Project type: Explore Project

Methodologies for scheduling and routing droplets in digital microfluidic biochips

Summary

The overall purpose of this project is to define, investigate, and provide preliminary methodologies for scheduling and routing microliter-sized liquid droplets on a planar surface in the context of digital microfluidics.

The main idea is to use a holistic approach in the design of scheduling and routing methodologies that takes into account real-world physical, topological, and behavioral constraints. Thus, producing solutions that can immediately find use in practical applications.

Value Creation

DMF biochips have been in the research spotlight for over a decade. However, the technology is still not mature at a level where it can deliver extensive automation to be used in applied biochemistry processes or for research purposes. One of the main reasons is that, although rather simple in construction, DMF biochips lack a clear automated procedure for being programmed and used. The existing methodologies for programming DMF biochips require an advanced level of understanding of software programming and of the architecture of the biochip itself. These skills are not commonly found in potential target users of this technology, such as biologists and chemists.

A fully automated compilation pipeline able to translate biochemical protocols expressed in a high-level representation into the low-level biochip control sequences would enable access to the DMF technology by a larger number of researchers and professionals. The advanced scheduling and routing methodologies investigated by this project are one of the main obstacles towards broadly accessible DMF technology. This is particularly relevant for researchers and small businesses which cannot afford the large pipetting robots commonly used to automate biochemical industrial protocol. One or more DMF biochips can be programmed to execute ad-hoc repetitive and tedious laboratory tasks. Thus, freeing qualified working hours for more challenging laboratory tasks.

In addition, the scheduling and routing methodologies targeted by this project enable for online decisions, such as controlling the flow of the biochemical protocols depending upon on-the-fly sensing results from the processes occurring on the biochip. This opens for a large set of possibilities in the biochemical research field. For instance, the behavior of complex biochemical protocols can be automatically adapted during execution using decisional constructs (if-then-else) allowing for real-time protocol optimizations and monitoring.

From a scientific perspective, this project would enable cross-field collaboration, develop new methodologies, and potentially re-purpose those techniques that are well known in one research field to solve problems of another field. For the proposed project, interesting possibilities include adapting advanced routing and
graph-related algorithms or applying well-known online algorithms techniques to manage the real-time flow control nature of the biochemical protocol. The cross-field nature of the project has the potential of providing a better understanding of how advanced scheduling and routing techniques can be applied in the context of a strongly constrained application such as DMF biochips. Thus, laying the ground for novel solutions, collaborations, and further research.

Finally, it should be mentioned that the outcome of this project, or of a future larger project based on the proposed explorative research, is characterized by a concrete business value. Currently, some players have entered the market with DMF biochips built to perform a specific biochemical functionality [12,13]. A software stack that includes compilation tools supporting programmability and enabling the same DMF biochip to perform different protocols largely expands the potential market of such technology. This is not the preliminary aim of this research project, but it is indeed a long-term possibility.

Participants

Project Manager

Luca Pezzarossa

Assistant Professor

Technical University of Denmark
DTU Compute

E: lpez@dtu.dk

Eva Rotenberg

Associate Professor

Technical University of Denmark
DTU Compute

Lene M. Favrholdt

Associate Professor

University of Southern Denmark
Department of Mathematics and Computer Science