Optimization of polymerase chain reaction on a cyberphysical digital microfluidic biochip

The amount of DNA strands available in a biological sample is a major limitation for many genomic bioanalyses. To amplify the traces of DNA strands, polymerase chain reaction (PCR) is widely used for conducting subsequent experiments. Compared to conventional instruments and analyzers, the execution of PCR on a digital microfluidic biochip (DMFB) can achieve short time-to-results, low reagent consumption, rapid heating/cooling rates, and high integration of multiple processing modules. However, the PCR biochip design methods in the literature are oblivious to the inherent randomness and complexity of bioanalyses, and they do not consider the interference among on-chip devices and the cost of droplet transportation. We present, for the first time, an integrated design method to optimize the complete PCR procedure, including (i) DNA amplification and termination control, (ii) resource placement that satisfies physical constraints needed to avoid interference, and (iii) droplet transportation needed for mixing and detection. We propose a statistical model for sensor feedback-driven (cyberphysical) on-line decision making in order to optimize and control the execution sequence for DNA amplification. Next, we present a geometric algorithm for layout design to avoid device interference and reduce the cost of droplet routing. Simulation results on three laboratory protocols demonstrate that the proposed design method results in a compact layout and produces an execution sequence for efficient control of PCR operations on a cyberphysical DMFB.

The amount of DNA strands available in a biological sample is a major limitation for many genomic bioanalyses. To amplify the traces of DNA strands, polymerase chain reaction (PCR) is widely used for conducting subsequent experiments. Compared to conventional instruments and analyzers, the execution of PCR on a digital microfluidic biochip (DMFB) can achieve short time-to-results, low reagent consumption, rapid heating/cooling rates, and high integration of multiple processing modules. However, the PCR biochip design methods in the literature are oblivious to the inherent randomness and complexity of bioanalyses, and they do not consider the interference among the neighboring devices and the cost of droplet transportation. We present an integrated design solution to optimize the complete PCR procedure, including: 1) DNA amplification and termination control; 2) resource placement that satisfies proximity constraints; and 3) droplet transportation. Based on the sensor feedback data, a statistical model is developed to optimize and control the DNA amplification sequence in real-time on a cyberphysical biochip. Next, we present a geometric algorithm for avoiding device interference and for reducing droplet routing cost. A novel optical sensing system is deployed based on the physical visibility of droplets. Simulation results for three laboratory protocols demonstrate that the proposed design method results in a compact layout and produces an execution sequence for efficient control of PCR operations on a cyberphysical DMFB.

For several genomic bioanalyses, the number of sample collection of nucleotide bases is a significant constraint. Polymerase chain reaction (PCR) is commonly used in further research to intensify the traces of DNA strands. The digital microfluidic biochip (DMFB) PCR system can achieve shorter results, low reagents usage, accelerated heating and air conditioning speeds, and high management of various modeling techniques compared to traditional experiments and analysis tools. Digital microfluidic biochips (DMFBs) are widely used in biomolecular interactions quantitatively, and the two phases of the PCR process are offered a convenient forum for the same chip configuration. Droplets in DMFBs, nanoliters or picoliters, can be manipulated with the electrical weaving-on-dielectric effect with the two-dimensional electrode array. The accurate monitoring of the gout volume and the response time of any study stage may be carried out utilizing DMFB-incorporated sensors. The DMFB platform provides several benefits in implementing PCR with traditional instruments and analyzers. It will smoothly execute the PCR protocol and reach short-term outcomes, low reagent intake, heating/cooling speeds, and use in multiple areas. The integration of multi-processing module PCR devices can also be minimized in size and power usage. A DMFB example enhances the DNA (i.e., the first stage of the PCR procedure). A warmed area is produced in thermal units (e.g., a heater). First, wastewater from the reservoir “PCR mix” is blended with the biological material of the required DNA streams. Numerous alternated heating and refraining steps can be taken through the well-conceived droplet. Each spawn is divided with a double siding, termed “DNA melting,” with each strand functioning as a synthesizer design for the new DNA strands, called “principal melting.” There are two stages in each thermal cycle to heat the drip. That’s the droplet’s cooling. Millions can then enhance the initial DNA ribs. As fluorescence marks the target DNA molecules in gout, the quantities of stranded DNA in gout may be monitored by calculating their antioxidant capacity using optic detectors built into the biochip. However, the literature’s PCR biochip modeling approaches are ignorant of the randomness and difficulty of bioanalysis and the interference between on-chip equipment and droplet transfer costs are not considered. For the first time, we have introduced an integrated design approach for optimizing the entire PCR process, including amplification and termination control for DNA location of resources that meet the physical limitations necessary for preventing interruption and transport through droplets required for mixing and detection. We suggest an online mathematical model for sensor-derived feedback (cyber-physical) decision- making to refine and to monitor the DNA amplification execution sequence. Next, we have a geometric interface modeling algorithm to prevent interaction with devices and increase droplet route costs. Simulated experiments on three laboratory protocols show that the design approach suggested results in a compact structure and provides an execution series for efficiently managing cyber-physical DMFB PCR operations.

A digital microfluidic biochip (DMFB) is an attractive technology platform for revolutionizing immunoassays, clinical diagnostics, drug discovery, DNA sequencing, and other laboratory procedures in biochemistry. In most of these applications, real-time polymerase chain reaction (PCR) is an indispensable step for amplifying specific DNA segments. To reduce the reaction time to meet the requirement of “real-time” applications, multiplexed PCR is widely utilized. In recent years, three-dimensional (3D) DMFBs that integrate photodetectors (i.e., cyberphysical DMFBs) have been developed, which offer the benefits of smaller size, higher sensitivity, and faster result generations. However, current DMFB design methods target optimization in only two dimensions, thus ignoring the 3D two-layer structure of a DMFB. Furthermore, these techniques ignore practical constraints related to the interference between on-chip device pairs, the performance-critical PCR thermal loop, and the physical size of devices. Moreover, some practical issues in real scenarios are not stressed (e.g., the avoidance of the cross-contamination for multiplexed PCR). In this article, we describe an optimization solution for a 3D DMFB and present a three-stage algorithm to realize a compact 3D PCR chip layout, which includes: (i) PCR thermal-loop optimization, (ii) 3D global placement based on Strong-Push-Weak-Pull (SPWP) model, and (iii) constraint-aware legalization. To avoid cross-contamination between different DNA samples, we also propose a Minimum-Cost-Maximum-Flow-based (MCMF-based) method for reservoir assignment. Simulation results for four laboratory protocols demonstrate that the proposed approach is effective for the design and optimization of a 3D chip for multiplexed real-time PCR.

A digital microfluidic biochip (DMFB) is an attractive technology platform for revolutionizing immunoassays, clinical diagnostics, drug discovery, DNA sequencing, and other laboratory procedures in biochemistry. In most of these applications, real-time polymerase chain reaction (PCR) is an indispensable step for amplifying specific DNA segments. In recent years, three-dimensional (3D) DMFBs that integrate photodetectors (i.e., cyberphysical DMFBs) have been developed. They offer the benefits of smaller size, higher sensitivity and quicker time-to-results. However, current DMFB design methods target optimization in only two dimensions, hence they ignore the 3D two-layer structure of a DMFB. Moreover, these techniques ignore practical constraints related to the interference between on-chip device pairs, the performance-critical PCR thermal loop, and the physical size of devices. In this paper, we describe an optimization solution for a 3D DMFB, and present a three-stage algorithm to realize a compact 3D PCR chip layout, which includes: (i) PCR thermal-loop optimization; (ii) 3D global placement based on Strong-Push-Weak-Pull (SPWP) model; (iii) constraint-aware legalization. Simulation results for four laboratory protocols demonstrate that the proposed approach is effective for the design and optimization of a 3D chip for real-time PCR.

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Digital micro fluidic (DMF) biochips are now being extensively used to automate several biochemical laboratory protocols such as clinical analysis, point-of-care diagnostics, and polymerase chain reaction (PCR). In many biological assays, e.g., in bacterial susceptibility tests, samples and reagents are required in multiple concentration (or dilution) factors, satisfying certain "gradient" patterns such as linear, exponential, or parabolic. Dilution gradients are usually prepared with continuous-flowmicrofluidic devices, however, they suffer from inflexibility, non-programmability, and from large requirement of costly stock solutions. DMF biochips, on the other hand, are shown to produce, more efficiently, a set of random dilution factors. However, all existing algorithms fail to optimize cost or performance when a certain gradient pattern is required. In this work, we present an algorithm to generate any arbitrary linear gradient, on-chip, with minimum wastage, while satisfying a required accuracy in concentration factors. We present new theoretical results on the number of mix-split operations and waste computation, and prove an upper bound on storage requirement. The corresponding layout design of the biochip is also proposed. Simulation results on different linear gradients show a significant improvement in sample cost over three earlier algorithms used for the generation of multiple concentrations.

The aim of this study was to compare the sensitivity and specificity of polymerase chain reaction (PCR) using two primer pairs and combined with blood culture, immunoglobulin M enzyme-linked immunosorbent assay (IgM ELISA), microscopic agglutination test (MAT) and slide agglutination test (SAT) in the diagnosis of human leptospirosis. We analysed 124 serum samples: 60 from patients with confirmed leptospirosis, 20 from patients with other diseases and 44 from healthy individuals. Analysing the first serum sample collected during the first 3-8 days of disease, the sensitivities of the four tests MAT, IgM ELISA, SAT and PCR were, respectively, 69.0%, 79.3%, 72.4% and 62%. In subsequent samples, those same sensitivities were, respectively, 95.4%, 100%, 100% and 72.7% in samples collected from days 9 to 14 and 88.9%, 88.9%, 77.8% and 44.4% in those collected from days 15 to 42. The most specific method (at 100%) was PCR and the least specific (at 89.1%) was IgM ELISA. Although we found PCR to be less sensitive than the serological tests over the course of the disease, our data indicate that PCR was the most sensitive in those initial serum samples presenting no specific antibodies detectable by any of the serological methods tested. We also recommend that PCR can be used in combination with serological tests as we found that this improves the sensitivity of the diagnosis of leptospirosis in the first phase of the disease (93.1-96.5%).

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<sec>Compared with traditional communication technologies such as electrical interconnection, optical interconnection technology has the advantages of large bandwidth, low energy consumption, anti-interference, etc. Therefore, optical interconnection is becoming an important approach and development trend of short distance and very short distance data terminal communication. As the chip level optical interconnection is implemented, silicon on insulator (SOI) based on-chip optical interconnection has been widely utilized with the support of a series of multiplexing technologies. In recent decades, many on-chip optical interconnection devices have been developed by using conventional design methods such as coupled-mode, multimode interference, and transmission line theories. However, when used in device design, these conventional methods often face the problems such as complex theoretical calculations and high labor costs. Many of the designed devices also encounter the problems of insufficient compactness and integration, and single function.</sec><sec>Intelligent design method has the advantages such as pellucid principle, high freedom of optimization, and good material compatibility, which can solve the problems of conventional design methods to a large extent. With the widespread use of intelligent design methods in the design of on-chip optical interconnection devices, three main trends have emerged. Firstly, the size of on-chip optical interconnect device is gradually developing towards ultra compact size. Secondly, the number of intelligently designed controllable on-chip optical interconnect devices is increasing. Thirdly, on-chip optical interconnect devices are gradually developing towards integration and systematization. This paper summarizes the most commonly used intelligent design methods of photonic devices, including intelligent algorithms based intelligent design methods and neural networks based intelligent design methods. Then, the above three important research advances and trends of intelligently designed on-chip optical interconnection devices are analyzed in detail. At the same time, the applications of phase change materials in the design of controllable photonic devices are also reviewed. Finally, the future development of intelligently designed on-chip optical interconnection devices is discussed.</sec>

To evaluate three non-invasive assays for the diagnosis of schistosomiasis mansoni in an Egyptian village. Urine was collected for the detection of circulating cathodic antigen (CCA) and cell-free parasite DNA (cfpd) by Point-of-contact (POC)-cassette assay and PCR, respectively. These tests were compared to Kato-Katz (KK) faecal thick smear for detection of Schistosoma mansoni eggs. Disease prevalence by POC-CCA assay was 86%; by PCR it was 39% vs. 27% by KK. Compared to KK, the sensitivity of POC-CCA reached 100%, but its specificity was only 19.2% with 41% accuracy. Sensitivity of the PCR assay for cfpd was 55.56%, and specificity was 67.12% with 64% accuracy. A new end point was calculated for combined analysis of KK, POC-CCA assay and PCR. Sensitivity for the three tests was 52.94%, 90.2% and 76.47%; specificity was 100% for KK and PCR and 18.37% for POC-CCA. The accuracy calculated for the three tests at the end point was 76% for KK, 55% for POC-CCA assay and 88% for PCR. Conventional PCR assay for detection of cfpd provides a potential screening tool for intestinal schistosomiasis with reliable specificity, reasonable accuracy and affordable financial and technical cost.

In last one decade, Digital Microfluidic Biochips (DMFBs) are providing a well-organized platform in field of biochemical study. Particularly in the area of clinical diagnostic related applications, DMFBs provides low priced, movable and disposable tools. In a large section of DMFBs, actuation of droplet is accomplished by the method of electro wetting-on-dielectric, where nano-liter volume liquid or droplet can be controlled and manipulated on two-dimensional array of electrode. A most important design automation concern in DMFBs is the parallel transportation of droplet in a time multiplexed way inside a 2D array of electrode. The requirement of droplet routing is to organize the transportation of droplets in parallel by minimizing resource usage by satisfying maximum allowed time for routing. A droplet can be either homogeneous or heterogeneous. For routing of homogeneous type droplets, main aim is to share same electrodes between several route paths of different droplets for minimizing cell usage. In other words, our aim is to maximizing the cross contaminations. For heterogeneous type droplets our main aim is to eliminate or minimize the cross contamination. In most of the previous works, algorithm has been proposed either for homogenous or for heterogeneous droplet routing. In this work, we proposed an algorithm for combined routing. Our algorithm as input takes a sub-problem consists with a set of homogeneous droplets and a set of heterogeneous droplets. Then our algorithm applies homogeneous routing for homogeneous droplets where it will maximize contaminations and for heterogeneous droplets it will minimize contaminations by applying heterogeneous routing. We have applied our algorithm on a test12_12_2 present in bench mark suite I. In test12_12_2 sub-problem, we have 12 droplets. We have assumed six droplets are homogeneous and remaining is heterogeneous.