Enhancement of multiple parallel assay operations with cross contamination avoidance in a given biochip
08 Sep 2014-pp 1-7
About: The article was published on 2014-09-08. It has received 1 citations till now. The article focuses on the topics: Biochip.
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TL;DR: In this paper , a cross-referencing digital microfluidic biochips (DMFBs) with an efficient module placement design can be declared as a multifunctional chip or not, and a chip design which incorporates parallelism for enhancing performance in terms of assay completion time while performing multiple types of bioassays.
Abstract: Digital Microfluidic Biochips (DMFBs) perform many biochemical reactions requiring relatively less cost and very less amount of space. DMFBs that use cross-referencing addressing requires less number of pins, therefore, less manufacturing cost. However, it suffers from a problem called electrode interference, i.e., unwanted droplet operation because of an extra activated cell. DMFBs also suffer from a problem called cross-contamination, i.e., mixing of droplets with unwanted residues of droplets containing different chemicals which results in incorrect diagnosis. In this article, our objective is whether a cross-referencing DMFB with an efficient module placement design can be declared as a multifunctional chip or not. We propose a chip design which incorporates parallelism for enhancing performance in terms of assay completion time while performing multiple types of bioassays. We also propose a novel method, which automatically selects a new cross-contamination free path while routing from the source to the sink. We have included an on-chip washing scheme. The whole method ensures no Electrode Interference.
1 citations
References
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TL;DR: This work proposes a system design methodology that attempts to apply classical high-level synthesis techniques to the design of digital microfluidic biochips and develops an optimal scheduling strategy based on integer linear programming and two heuristic techniques that scale well for large problem instances.
Abstract: Microfluidic biochips offer a promising platform for massively parallel DNA analysis, automated drug discovery, and real-time biomolecular recognition. Current techniques for full-custom design of droplet-based “digital” biochips do not scale well for concurrent assays and for next-generation system-on-chip (SOC) designs that are expected to include microfluidic components. We propose a system design methodology that attempts to apply classical high-level synthesis techniques to the design of digital microfluidic biochips. We focus here on the problem of scheduling bioassay functions under resource constraints. We first develop an optimal scheduling strategy based on integer linear programming. However, because the scheduling problem is NP-complete, we also develop two heuristic techniques that scale well for large problem instances. A clinical diagnostic procedure, namely multiplexed in-vitro diagnostics on human physiological fluids, is first used to illustrate and evaluate the proposed method. Next, the synthesis approach is applied to a protein assay, which serves as a more complex bioassay application. The proposed synthesis approach is expected to reduce human effort and design cycle time, and it will facilitate the integration of microfluidic components with microelectronic components in next-generation SOCs.
172 citations
07 Nov 2004
TL;DR: A system design methodology is proposed that attempts to apply classical architectural-level synthesis techniques to the design of digital microfluidics-based biochips and develops an optimal scheduling strategy based on integer linear programming and two heuristic techniques that scale well for large problem instances.
Abstract: Microfluidics-based biochips offer a promising platform for massively parallel DNA analysis, automated drug discovery, and real-time biomolecular recognition. Current techniques for full-custom design of droplet-based "digital" biochips do not scale well for concurrent assays and for next-generation system-on-chip (SOC) designs that are expected to include fluidic components. We propose a system design methodology that attempts to apply classical architectural-level synthesis techniques to the design of digital microfluidics-based biochips. We first develop an optimal scheduling strategy based on integer linear programming. Since the scheduling problem is NP-complete, we also develop two heuristic techniques that scale well for large problem instances. A clinical diagnostic procedure, namely multiplexed in-vitro diagnostics on human physiological fluids, is used to evaluate the proposed method.
155 citations
08 Jun 2008
TL;DR: A broadcast-addressing-based design technique for pin-constrained multi-functional biochips that provides high throughput for bioassays and it reduces the number of control pins by identifying and connecting control pins with "compatible" actuation sequences.
Abstract: Recent advances in digital microfluidics have enabled lab-on-a-chip devices for DNA sequencing, immunoassays, clinical chemistry, and protein crystallization. Basic operations such as droplet dispensing, mixing, dilution, localized heating, and incubation can be carried out using a two-dimensional array of electrodes and nanoliter volumes of liquid. The number of independent input pins used to control the electrodes in such microfluidic "biochips" is an important cost-driver, especially for disposable PCB devices that are being developed for clinical and point-of-care diagnostics. However, most prior work on biochip design-automation has assumed independent control of the electrodes using a large number of input pins. Another limitation of prior work is that the mapping of control pins to electrodes is only applicable for a specific bioassay. We present a broadcast-addressing-based design technique for pin-constrained multi-functional biochips. The proposed method provides high throughput for bioassays and it reduces the number of control pins by identifying and connecting control pins with "compatible" actuation sequences. The proposed method is evaluated using a multifunctional chip designed to execute a set of multiplexed bioassays, the polymerase chain reaction, and a protein dilution assay.
137 citations
22 Oct 2006
TL;DR: A partitioning algorithm based on the concept of "droplet trace", which is extracted from the scheduling and droplet routing results produced by a synthesis tool, is proposed and an efficient pin assignment method, referred to as the "Connect-5 algorithm", is combined with the array partitioning technique based on droplet traces.
Abstract: Microfluidics-based biochips combine electronics with biology to open new application areas such as point-of-care medical diagnostics, on-chip DNA analysis, and automated drug discovery. Bioassays are mapped to microfluidic arrays using synthesis tools, and they are executed through the manipulation of sample and reagent droplets by electrical means. Most prior work on CAD for biochips has assumed independent control of electrodes using a large number of (electrical) input pins. Such solutions are not feasible for low-cost disposable biochips that are envisaged for many field applications. A more promising design strategy is to divide the microfluidic array into smaller partitions and use a small number of electrodes to control the electrodes in each partition. We propose a partitioning algorithm based on the concept of "droplet trace", which is extracted from the scheduling and droplet routing results produced by a synthesis tool. An efficient pin assignment method, referred to as the "Connect-5 algorithm", is combined with the array partitioning technique based on droplet traces. The array partitioning and pin assignment methods are evaluated using a set of multiplexed bioassays.
127 citations
16 Apr 2007
TL;DR: A droplet manipulation method based on a "cross-referencing" addressing method that uses "row" and "columns" to access electrodes that allows simultaneous movement of a large number of droplets on a microfluidic array is proposed.
Abstract: Digital microfluidic biochips are revolutionizing high-throughput DNA sequencing, immunoassays, and clinical diagnostics. As high-throughput bioassays are mapped to digital microfluidic platforms, the need for design automation techniques for pin-constrained biochips is being increasingly felt. However, most prior work on biochips CAD has assumed independent control of the underlying electrodes using a large number of (electrical) input pins. The authors propose a droplet manipulation method based on a "cross-referencing" addressing method that uses "row" and "columns" to access electrodes. By mapping the droplet movement problem to the clique partitioning problem from graph theory, the proposed method allows simultaneous movement of a large number of droplets on a microfluidic array. This in turn facilitates high-throughput applications on a pin-constrained biochip. The authors use random synthetic benchmarks and a set of multiplexed bioassays to evaluate the proposed method
86 citations