Jeffrey McDaniel

An open-source compiler and PCB synthesis tool for digital microfluidic biochips

This paper describes a publicly available, open source software framework designed to support research efforts on algorithms and control for digital microfluidic biochips (DMFBs), an emerging laboratory-on-a-chip (LoC) technology. The framework consists of two parts: a compiler, which converts an assay, specified using the BioCoder language, into a sequence of electrode activations that execute out the assay on the DMFB; and a printed circuit board (PCB) layout tool, which includes algorithms to reduce the number of control pins and PCB layers required to drive the chip from an external source. The framework also includes a suite of visualization tools for debugging, and a collection of front-end algorithms that generate mixing/dilution trees for sample preparation.

Design and verification tools for continuous fluid flow-based microfluidic devices

This paper describes an integrated design, verification, and simulation environment for programmable microfluidic devices called laboratories-on-chip (LoCs). Todays LoCs are architected and laid out by hand, which is time-consuming, tedious, and error-prone. To increase designer productivity, this paper introduces a Microfluidic Hardware Design Language (MHDL) for LoC specification, along with software tools to assist LoC designers verify the correctness of their specifications and estimate their performance.

A Low-Cost Field-Programmable Pin-Constrained Digital Microfluidic Biochip

This paper introduces a field-programmable pin-constrained digital microfluidic biochip (FPPC-DMFB), which offers general-purpose assay execution at a lower cost than general-purpose direct addressing DMFBs and highly optimized application-specific pin-constrained DMFBs. One of the key cost drivers for DMFBs is the number of printed circuit board (PCB) layers, onto which the device is mounted. We demonstrate a scalable single-layer PCB wiring scheme for several FPPC-DMFB variations, for PCB technology with orthogonal routing capacity of at least three; for PCB technology with orthogonal capacity of two, more PCB layers are required, but the FPPC-DMFB retains its cost advantage. These results offer new insights on the relationship between PCB layer count, pin count, and cost. Additionally, to reduce the execution time of assays on the FPPC-DMFB, we present efficient algorithms for droplet routing, with and without contamination removal via wash droplets.

Simulated annealing-based placement for microfluidic large scale integration (mLSI) chips

Microfluidic large-scale integration (mLSI) chips comprise hundreds or thousands of microvalves integrated into a chemically inert elastomeric substrate. The design of these chips is time-consuming, error-prone, and presently performed by hand. To enhance design automation, a routability-oriented placement algorithm based on simulated annealing is introduced. This paper investigates relevant issues including: (1) grid representation; (2) perturbation operations; (3) objective function; (4) uniform vs. heterogeneous component sizes; (5) spacing rules and their effect on routability; and (6) random vs. directed initial placement. Our results show how the above issues affect both the pre-routing estimate on the routability of the chips, the number of flow channel intersections (each of which requires the insertion of several microvalves), and total channel distance as reported by our router.

Automatic synthesis of microfluidic large scale integration chips from a domain-specific language

BioCoder is a domain-specific language by which chemists and biologists can express experimental protocols in a manner that is unambiguous and clearly repeatable. This paper presents a software toolchain that converts a protocol specified in a restricted subset of BioCoder to a technology-specific description of the protocol, targeting flow-based microfluidic large-scale integration (mLSI) chips. The technology-specific description can then be used to either: (1) execute the protocol on a capable chip; or (2) to derive the architecture of a new mLSI chip that can execute the protocol.

Flow-Layer Physical Design for Microchips Based on Monolithic Membrane Valves

This article introduces a software toolchain for physical design and layout for the flow layer of microfluidic LoCs based on integrated microvalve technology. A case study shows that it can automatically produce layouts for the Mars Organic Analyzer LoC to detect biomolecules in soil on Mars.

Multi-terminal PCB escape routing for digital microfluidic biochips using negotiated congestion

This paper introduces a multi-terminal escape routing algorithm for the design of Printed Circuit Boards (PCBs) that control Digital Microfluidic Biochips (DMFBs). The new algorithm is based on the principle of negotiated congestion, which has been applied in the past to problems including FPGA routing and PCB escape routing for single-terminal nets. PCBs designed for Pin-constrained DMFBs, in which one control pin may drive multiple electrodes, require multi-terminal escape routing solutions. Experimental results indicate that negotiated congestion is more effective for multi-terminal escape routing than existing techniques, which are based on maze routing coupled with rip-up and re-route, yielding an overall reduction in the number of PCB layers in most the test cases that were tried.

PCB Escape Routing and Layer Minimization for Digital Microfluidic Biochips

This paper introduces a multiterminal escape routing algorithm for the design of printed circuit boards (PCBs) that control digital microfluidic biochips (DMFBs). The new algorithm extends a negotiated congestion-based single-terminal escape router that has been shown to be superior to previous methods. It relaxes the pin assignment to allow pin groups to be broken up when doing so can reduce the number of PCB layers. Experimental results indicate that the improved method can reduce both the number of PCB layers and average wirelength compared to existing DMFB escape routers.

The case for semi-automated design of microfluidic very large scale integration (mVLSI) chips

In recent years, significant interest has emerged in the problem of fully automating the design of microfluidic very large scale integration (mVLSI) chips, a popular class of Lab-on-a-Chip (LoC) devices that can automatically execute a wide variety of biological assays. To date, this work has been carried out with little to no input from LoC designers. We conducted interviews with approximately 100 LoC designers, biologists, and chemists from academia and industry; uniformly, they expressed frustration with existing design solutions, primarily commercially available software such as AutoCAD and Solidworks; however, they expressed limited interest and considerable skepticism about the potential for “push-button” end-to-end automation. In response, we have developed a semi-automated mVLSI drawing tool that is designed specifically to address the pain points elucidated by our interviewees. We have used this tool to rapidly reproduce several previously published LoC architectures and generate fabrication ready specifications.

Scheduling and Fluid Routing for Flow-Based Microfluidic Laboratories-on-a-Chip

Microfluidic laboratories-on-a-chip (LoCs) are replacing the conventional biochemical analyzers and are able to integrate the necessary functions for biochemical analysis on-chip. There are several types of LoCs, each having its advantages and limitations. In this paper we are interested in flow-based LoCs, in which a continuous flow of liquid is manipulated using integrated microvalves. By combining several microvalves, more complex units, such as micropumps, switches, mixers, and multiplexers, can be built. We consider that the architecture of the LoC is given, and we are interested in synthesizing an implementation, consisting of the binding of operations in the application to the functional units of the architecture, the scheduling of operations and the routing and scheduling of the fluid flows, such that the application completion time is minimized. To solve this problem, we propose a list scheduling-based application mapping (LSAM) framework and evaluate it by using real-life as well as synthetic benchmarks. When biochemical applications contain fluids that may adsorb on the substrate on which they are transported, the solution is to use rinsing operations for contamination avoidance. Hence, we also propose a rinsing heuristic, which has been integrated in the LSAM framework.