Using printer ink color to control the behavior of paper microfluidics.

Paper microfluidic devices (including lateral flow assays) offer an excellent combination of utility and low cost. Many paper microfluidic devices are fabricated using the Xerox ColorQube line of commercial wax-based color printers; the wax ink serves as a hydrophobic barrier to fluid flow. These printers are capable of depositing four different colors of ink, cyan (C), magenta (M), yellow (Y), and black (K), plus 11 combinations of these colors (CM, CY, CK, MY, MK, YK, CMY, CMK, CYK, MYK, and CMYK), although most researchers use only black ink to print paper microfluidic devices. Recently, as part of a project to develop a computer-aided design framework for use with paper microfluidics devices, we unexpectedly observed that different colors of wax ink behave differently in paper microfluidics. We found that among the single colors of ink, black ink actually had the most barrier failures, and magenta ink had the fewest barrier failures. In addition, some combinations of colors performed even better than magenta: the combinations CY, MK, YK, CMY, CYK and MYK had no barrier failures in our study. We also found that the printer delivers significantly different amounts of ink to the paper for the different color combinations, and in general, the color combinations that formed the strongest barriers to fluid flow were the ones that had the most ink delivered to the paper. This suggests that by simply weighing paper samples printed with all 15 combinations of colors, one can easily find the color combinations most likely to form a strong barrier for a given printer. Finally, to show that deliberate choices of ink colors can actually be used to create new functions in paper microfluidics, we designed and tested a new color-based "antifuse" structure that protects paper microfluidic devices from a typical operator error (addition of too much fluid to the device). Our results provide a set of color choice guidelines that designers can use to control the behavior of their paper microfluidics

BioScript: programming safe chemistry on laboratories-on-a-chip

This paper introduces BioScript, a domain-specific language (DSL) for programmable biochemistry which executes on emerging microfluidic platforms. The goal of this research is to provide a simple, intuitive, and type-safe DSL that is accessible to life science practitioners. The novel feature of the language is its syntax, which aims to optimize human readability; the technical contributions of the paper include the BioScript type system and relevant portions of its compiler. The type system ensures that certain types of errors, specific to biochemistry, do not occur, including the interaction of chemicals that may be unsafe. The compiler includes novel optimizations that place biochemical operations to execute concurrently on a spatial 2D array platform on the granularity of a control flow graph, as opposed to individual basic blocks. Results are obtained using both a cycle-accurate microfluidic simulator and a software interface to a real-world platform

Optimistic chordal coloring: a coalescing heuristic forSSAform programs

The interference graph for a procedure in Static Single Assignment (SSA) Form is chordal. Since the k-colorability problem can be solved in polynomial-time for chordal graphs, this result has generated interest in SSA-based heuristics for spilling and coalescing. Since copies can be folded during SSA construction, instances of the coalescing problem under SSA have fewer affinities than traditional methods. This paper presents Optimistic Chordal Coloring (OCC), a coalescing heuristic for chordal graphs. OCC was evaluated on interference graphs from embedded/multimedia benchmarks: in all cases, OCC found the optimal solution, and ran, on average, 2.30× faster than Iterated Register Coalescin

Standardizing design performance comparison in microfluidic manufacturing

Microfluidic devices published in literature today lack sufficient information for automating the physical design process. Moreover, the constantly changing landscape of manufacturing and technological requirements poses a large problem in the physical design automation space. In this talk, we discuss some of the methodologies and standards formulated by CIDAR at BU and CARES at UC Riverside that allow not only allow the researchers in the physical design automation space to share and compare their results but also provide means for capturing the Specify, Design and Build lifecycle in microfluidic design

Chronoprints: Identifying Samples by Visualizing How They Change over Space and Time.

The modern tools of chemistry excel at identifying a sample, but the cost, size, complexity, and power consumption of these instruments often preclude their use in resource-limited settings. In this work, we demonstrate a simple and low-cost method for identifying a sample based on visualizing how the sample changes over space and time in response to a perturbation. Different types of perturbations could be used, and in this proof-of-concept we use a dynamic temperature gradient that rapidly cools different parts of the sample at different rates. We accomplish this by first loading several samples into long parallel channels on a "microfluidic thermometer chip." We then immerse one end of the chip in liquid nitrogen to create a dynamic temperature gradient along the channels, and we use an inexpensive USB microscope to record a video of how the samples respond to the changing temperature gradient. The video is then converted into several bitmap images (one per sample) that capture each sample's response to the perturbation in both space (the y-axis; the distance along the dynamic temperature gradient) and time (the x-axis); we call these images "chronological fingerprints" or "chronoprints" of each sample. If two samples' chronoprints are similar, this suggests that the samples are the same chemical substance or mixture, but if two samples' chronoprints are significantly different, this proves that the samples are chemically different. Since chronoprints are just bitmap images, they can be compared using a variety of techniques from computer science, and in this work we use three different image comparison algorithms to quantify chronoprint similarity. As a demonstration of the versatility of chronoprints, we use them in three different applications: distinguishing authentic olive oil from adulterated oil (an example of the over $10 billion global problem of food fraud), identifying adulterated or counterfeit medication (which represents around 10% of all medication in low- and middle-income countries), and distinguishing the occasionally confused pharmaceutical ingredients glycerol and diethylene glycol (whose accidental or intentional substitution has led to hundreds of deaths). The simplicity and versatility of chronoprints should make them valuable analytical tools in a variety of different fields

SSI Revisited

The static single information (SSI) form, proposed by Ananian, then in a more general form by Singer, is an extension of the static single assignment (SSA) form. The latter is a well-established compiler intermediate representation that has been successfully used for numerous compiler analysis and optimizations. Several interesting results have also been shown for SSI concerning liveness analysis and representation of live-ranges of variables, which could make SSI appealing for just-in-time compilation. Unfortunately, previous literature on the SSI form is sparse and appears to be partly incorrect. Our paper corrects some of the mistakes that have been made. Our main result is a complete proof that, even for the most general definition of SSI, basic blocks, and thus program points, can be totally ordered so that live-ranges of variables correspond to intervals. This corrects the erroneous proof of Brisk and Sarrafzadeh

Finding the optimal design of a passive microfluidic mixer.

The ability to thoroughly mix two fluids is a fundamental need in microfluidics. While a variety of different microfluidic mixers have been designed by researchers, it remains unknown which (if any) of these mixers are optimal (that is, which designs provide the most thorough mixing with the smallest possible fluidic resistance across the mixer). In this work, we automatically designed and rationally optimized a microfluidic mixer. We accomplished this by first generating a library of thousands of different randomly designed mixers, then using the non-dominated sorting genetic algorithm II (NSGA-II) to optimize the random chips in order to achieve Pareto efficiency. Pareto efficiency is a state of allocation of resources (e.g. driving force) from which it is impossible to reallocate so as to make any one individual criterion better off (e.g. pressure drop) without making at least one individual criterion (e.g. mixing performance) worse off. After 200 generations of evolution, Pareto efficiency was achieved and the Pareto-optimal front was found. We examined designs at the Pareto-optimal front and found several design criteria that enhance the mixing performance of a mixer while minimizing its fluidic resistance; these observations provide new criteria on how to design optimal microfluidic mixers. Additionally, we compared the designs from NSGA-II with some popular microfluidic mixer designs from the literature and found that designs from NSGA-II have lower fluidic resistance with similar mixing performance. As a proof of concept, we fabricated three mixer designs from 200 generations of evolution and one conventional popular mixer design and tested the performance of these four mixers. Using this approach, an optimal design of a passive microfluidic mixer is found and the criteria of designing a passive microfluidic mixer are established

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

Thermal-Aware Data Flow Analysis

This paper suggests that the thermal state of a processor can be approximated using data flow analysis. The results of this analysis can be used to evaluate the efficacy of thermal-aware compilation strategies, or as input to thermal-aware optimizations that occur in the early stages of back-end compilation. We propose different ways how the exploitation of thermal behavior knowledge can be included in the different compilation phases. Copyright 2009 ACM