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Journal ArticleDOI

Fluid-level synthesis unifying reliability, contamination avoidance, and capacity-wastage-aware washing for droplet-based microfluidic biochips

01 May 2019-Iet Computers and Digital Techniques (The Institution of Engineering and Technology)-Vol. 13, Iss: 3, pp 166-177
TL;DR: A complete fluid-level synthesis considering all the essential goals together instead of dealing with them in isolation is proposed effectively handles the trade-off scenarios and provides flexibility to the designer to decide the threshold of the individual optimisation objective leading to the construction of a good-quality solution as a whole.
Abstract: Production of correct bioassay outcome is the foremost objective in digital microfluidic biochips (or DMFBs). In high-frequency DMFBs, continuous actuation of electrodes leads to malfunctioning or even breakdown of the system. The improper functioning of a biochip tends to produce erroneous results. On the other hand, while transporting droplets, the residues may get stuck to electrode walls and cause contamination to other droplets. To ensure proper assay outcome, washing becomes mandatory, whose incorporation may delay the bioassay completion time significantly. Furthermore, each wash droplet possesses a capacity constraint within which the residues can be washed off successfully. Evidently, the design objectives possess a large degree of trade-offs among themselves and must be attacked to prepare an efficient platform. Here, the authors propose a complete fluid-level synthesis considering all the essential goals together instead of dealing with them in isolation. The presented approach effectively handles the trade-off scenarios and provides flexibility to the designer to decide the threshold of the individual optimisation objective leading to the construction of a good-quality solution as a whole. The performance is evaluated over several benchmark bioassays.
Citations
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Journal ArticleDOI
TL;DR: The routing problem is identified as a dynamic path-planning problem and mixed path design problem under certain constraints, and an improved Dijkstra and improved particle swarm optimization (ID-IPSO) algorithm is proposed, which can accommodate more faulty electrodes for the same fault repair rate.
Abstract: Digital microfluidic biochips (DMFBs) are attractive instruments for obtaining modern molecular biology and chemical measurements. Due to the increasingly complex measurements carried out on a DMFB, such chips are more prone to failure. To compensate for the shortcomings of the module-based DMFB, this paper proposes a routing-based fault repair method. The routing-based synthesis methodology ensures a much higher chip utilization factor by removing the virtual modules on the chip, as well as removing the extra electrodes needed as guard cells. In this paper, the routing problem is identified as a dynamic path-planning problem and mixed path design problem under certain constraints, and an improved Dijkstra and improved particle swarm optimization (ID-IPSO) algorithm is proposed. By introducing a cost function into the Dijkstra algorithm, the path-planning problem under dynamic obstacles is solved, and the problem of mixed path design is solved by redefining the position and velocity vectors of the particle swarm optimization. The ID-IPSO routing-based fault repair method is applied to a multibody fluid detection experiment. The proposed design method has a stronger optimization ability than the greedy algorithm. The algorithm is applied to , , and fault-free chips. The proposed ID-IPSO routing-based chip design method saves 13.9%, 14.3%, and 14.5% of the experiment completion time compared with the greedy algorithm. Compared with a modular fault repair method based on the genetic algorithm, the ID-IPSO routing-based fault repair method has greater advantages and can save 39.3% of the completion time on average in the completion of complex experiments. When the ratio of faulty electrodes is less than 12% and 23%, the modular and ID-IPSO routing-based fault repair methods, respectively, can guarantee a 100% failure repair rate. The utilization rate of the electrodes is 18% higher than that of the modular method, and the average electrode usage time is 17%. Therefore, the ID-IPSO routing-based fault repair method can accommodate more faulty electrodes for the same fault repair rate; the experiment completion time is shorter, the average number of electrodes is lower, and the security performance is better.

6 citations


Cites methods from "Fluid-level synthesis unifying reli..."

  • ...The design methods of DMFBs are mainly divided into two types: modularization design [15] and droplet path design [16]....

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Journal ArticleDOI
TL;DR: In this article, the authors proposed an improved whale optimization algorithm (IWOA), which can reduce the excessive use of an electrode and reuse electrodes in an average manner to optimize the longest lifetime of digital microfluidic biochips.

1 citations

Journal ArticleDOI
TL;DR: In this paper , a routing-based synthesis method based on a digital microfluidic biochip (DMFB) platform is presented, which can ensure a much higher chip utilization factor by removing the virtual modules on the chip and the extra electrodes needed as guard cells.
Abstract: With the continuous application and development of the digital microfluidic technology in various fields, many researchers have studied the design of digital microfluidic chips. Module-based chip design methods greatly simplify the design process but waste resources, including through the inadequate use of electrodes within the module and guard cells. To address this problem, a routing-based synthesis method based on a digital microfluidic biochip (DMFB) platform is presented. Routing-based DMFBs ensure a much higher chip utilization factor by removing the virtual modules on the chip and the extra electrodes needed as guard cells. Many previous works focused only on the problems of synthesis completion times, bioassay completion times, and electrode utilization rates. However, the reliability of chips has not been fully studied, and this factor is extremely important because faulty chips affect the test results. Thus, the influence of chip reliability should be fully considered. This paper proposes a design method based on Bayesian decision-making (BBD) for routing-based DMFBs that can fully consider the reliability of chips during the DMFB design process. Simulated experimental results showed that the method can address the reliability problems of chips. The efficiency and convergence performance of the algorithm were very good. The proposed method can achieve an average assay completion time that is shorter than those of the moduleless synthesis (MLS) and modified-MLS (MMLS) methods. The electrode usage rate of the proposed method is better than that of the module-based and improved Dijkstra and improved particle swarm optimization (ID-IPSO) methods.

1 citations

Journal ArticleDOI
TL;DR: With increasing effectiveness of flow-based microfluidic biochips in the field of biochemical experiments and point-of-care diagnosis, design automation demands enormous attention to integrate the technology into the design process.
Abstract: With increasing effectiveness of flow-based microfluidic biochips in the field of biochemical experiments and point-of-care diagnosis, design automation demands enormous attention to integrate the ...

1 citations

Proceedings ArticleDOI
23 Jul 2020
TL;DR: A proactive wash droplet routing that take wash capacity into account is proposed that shows improvement in washing time and total turn around time and a newwash droplet is moved in to replace the exhausted wash droplets.
Abstract: Contamination occurs when multiple droplets share few cells in their route. When the first droplet passes through a shared cell, it lefts a strain of residue on this cell. At later time cycle, when the second droplet traverses through this shared cell, the leftover residue contaminates it. This may leads to erroneous experimental outcome. To avoid this, wash droplets are used for cleaning the residue. The wash droplets are sandwiched in between two functional droplets. In this article, we propose a proactive wash droplet routing that take wash capacity into account. Here, every functional droplet is tailgated by a wash droplet. When wash droplet capacity is exhausted, a new wash droplet is moved in to replace the exhausted wash droplet. Experimental result shows improvement in washing time and total turn around time.

1 citations


Cites background from "Fluid-level synthesis unifying reli..."

  • ...[9]), this left ordinary contamination spots, which may leads to cross contamination spots in future sub problems....

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  • ...2019 [9] presents a fluid level synthesis considering wash droplet routing at the design level of the biochip....

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  • ...[9] takes wash capacity into consideration....

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  • ...Chakraborty et al. 2019 [9] presents a fluid level synthesis considering wash droplet routing at the design level of the biochip....

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  • ...[9] inserts wash droplets in between subproblems....

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References
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Book
01 Jan 1980
TL;DR: This classic introduction to artificial intelligence describes fundamental AI ideas that underlie applications such as natural language processing, automatic programming, robotics, machine vision, automatic theorem proving, and intelligent data retrieval.
Abstract: A classic introduction to artificial intelligence intended to bridge the gap between theory and practice, "Principles of Artificial Intelligence" describes fundamental AI ideas that underlie applications such as natural language processing, automatic programming, robotics, machine vision, automatic theorem proving, and intelligent data retrieval. Rather than focusing on the subject matter of the applications, the book is organized around general computational concepts involving the kinds of data structures used, the types of operations performed on the data structures, and the properties of the control strategies used. "Principles of Artificial Intelligence"evolved from the author's courses and seminars at Stanford University and University of Massachusetts, Amherst, and is suitable for text use in a senior or graduate AI course, or for individual study.

3,754 citations

Journal ArticleDOI
TL;DR: This paper presents an implementation of Yen’s algorithm, a classical algorithm for ranking the K shortest loopless paths between a pair of nodes in a network, and concludes that in practice this new implementation outperforms two other, Perko's implementation and a straightforward one.
Abstract: Yen’s algorithm is a classical algorithm for ranking the K shortest loopless paths between a pair of nodes in a network. In this paper an implementation of Yen’s algorithm is presented. Both the original algorithm and this implementation present ${\cal O}(Kn(m + n\log n))$ computational complexity order when considering a worst-case analysis. However, computational experiments are reported, which allow to conclude that in practice this new implementation outperforms two other, Perko’s implementation and a straightforward one.

301 citations

Proceedings ArticleDOI
13 Jun 2005
TL;DR: This work presents a synthesis methodology that unifies operation scheduling, resource binding, and module placement for such "digital" biochips and can also be used after fabrication to bypass defective cells in the microfluidic array.
Abstract: Microfluidic biochips promise to revolutionize biosensing and clinical diagnostics. As more bioassays are executed concurrently on a biochip, system integration and design complexity are expected to increase dramatically. This problem is also identified by the 2003 ITRS document as a major system-level design challenge beyond 2009. We focus here on the automated design of droplet-based microfluidic biochips. We present a synthesis methodology that unifies operation scheduling, resource binding, and module placement for such "digital" biochips. The proposed technique, which is based on parallel recombinative simulated annealing, can also be used after fabrication to bypass defective cells in the microfluidic array. A real-life protein assay is used to evaluate the synthesis methodology.

163 citations

Proceedings ArticleDOI
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

Journal ArticleDOI
TL;DR: A droplet-routing method that avoids cross-contamination in the optimization of droplet flow paths and targets disjoint droplet routes and minimizes the number of cells used for droplet routing is proposed.
Abstract: Recent advances in digital microfluidics have enabled droplet-based biochip devices for DNA sequencing, immunoassays, clinical chemistry, and protein crystallization. Since cross-contamination between droplets of different biomolecules can lead to erroneous outcomes for bioassays, the avoidance of cross-contamination during droplet routing is a key design challenge for biochips. We propose a droplet-routing method that avoids cross-contamination in the optimization of droplet flow paths. The proposed approach targets disjoint droplet routes and synchronizes wash-droplet routing with functional droplet routing, in order to reduce the duration of droplet routing while avoiding the cross-contamination between different droplet routes. In order to avoid cross-contamination between successive routing steps, an optimization technique is used to minimize the number of wash operations that must be used between successive routing steps. Two real-life biochemical applications are used to evaluate the proposed droplet-routing methods.

100 citations

Trending Questions (1)
How does the digital PCR impact the liquid biopcy?

The provided paper does not mention digital PCR or liquid biopsy. The paper is about fluid-level synthesis in droplet-based microfluidic biochips.