Piyali Datta

Bio: Piyali Datta is an academic researcher from University of Calcutta. The author has contributed to research in topics: Biochip & Simple polygon. The author has an hindex of 4, co-authored 33 publications receiving 65 citations. Previous affiliations of Piyali Datta include Heritage Institute of Technology.

A technology shift towards triangular electrodes from square electrodes in design of Digital Microfluidic Biochip

Abstract: Digital Microfluidic Biochip (DMFB) is a ground-breaking invention in many areas of Microelectronics, Biochemistry, and Biomedical sciences. It is also known as ‘Lab-on-a-Chip’ for its performance as an alternative for laboratory experiments. Various types of diagnosis procedures are performed on it through a sequence of modular operations like sample preparation, mixing, and detection. Mixing is the most important operation of DMFB as the outcome of the experiment is almost dominated by mixing. A good mixing of corresponding sample and reagent gives proper result while an improper mixing leads to erroneous result, which may be the reason to discard the assay. So, our objective is the betterment of mixing operation. In this paper, we have proposed a design using equilateral triangular electrodes instead of square electrodes, maintaining all the constraints required to ensure safe droplet movement and other modular operations, while improvement of the mixing operation is the key design issue.

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

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.

Design Optimization at the Fluid-Level Synthesis for Safe and Low-Cost Droplet-Based Microfluidic Biochips

Abstract: Droplet-based Digital Microfluidic Biochips (or DMFBs) are now being the prime platform for a number of point of care diagnostics, clinical studies, and sample preparations. Several design optimization methods exist at the fluid-level that automate the tasks of a DMFB. However, in high frequency applications, its performance heavily deteriorates in the order of degrading electrodes producing incorrect outcomes. Vague results may also be generated if cross contamination during droplet routing is not avoided. We define a DMFB to be safe if it is capable of handling reliability and also free from cross contamination. Alongside, as the fluid-level of DMFBs comprises several tasks that altogether introduces design cycles and leads to higher cost, a low-cost platform is urgently required. This paper proposes a fluid-level design for DMFBs that considers the above facts together. A graph model has been used to tackle them. An exact algorithm is presented. The obtained results are validated with several benchmarks.

A Capacity-Aware Wash Optimization for Contamination Removal in Programmable Microfluidic Biochip Devices

Abstract: Flow-based microfluidic biochips have emerged as a potential lab-on-chip platform for numerous biochemistry operations. Among various flow-based biochips, Programmable Microfluidic Devices (PMDs) receive much attention due to its capability of performing functionalities on a single platform with no hardware modifications. High precision control and production of correct outcomes are the urgent needs in the PMDs. While sharing the micro-channels, a fluid-flow may be contaminated by the residues stuck on the channel. Washing of the microchannels with buffer fluid is an immediate solution for safe execution of biochemistry. However, each wash fluid has a finite washing capacity and can wash only a limited number of contaminated spots. In this paper, we propose a wash optimization model that aims to remove all the contaminations while minimizing washing time and total capacity wastage. The effectiveness of the proposed approach has been evaluated considering a number of baseline methods and the previous works.

A 2D Guard Zone Computation Algorithm for Reassignment of Subcircuits to Minimize the Overall Chip Area

Abstract: The guard zone computation problem finds vast applications in the field of VLSI physical design automation and design of embedded systems, where one of the major purposes is to find an optimized way to place a set of 2D blocks on a chip floor. In VLSI layout design, the circuit components (or the functional units/modules or groups/blocks of different subcircuits) are not supposed to be placed much closer to each other in order to avoid electrical (parasitic) effects among them (http://en.wikipedia.org/wiki/Curve_orientation, [13]). The (group of) circuit components on a chip floor may be viewed as a set of polygonal regions on a two-dimensional plane. Each (group of) circuit component(s) C i is associated with a parameter δ i such that a minimum clearance zone of width δ i is to be maintained around C i . The regions representing the (groups of) circuit components are in general isothetic polygons, but may not always be limited to convex ones. The location of the guard zone (of specified width) for a simple polygon is a very important problem for resizing the (group of) circuit components. In this paper, we have developed an algorithm to compute the guard zone of a simple polygon as well as to exclude the overlapped regions among the guard zones, if any. If the number of vertices in the given polygon is n, then our algorithm requires O(n log n + I log n) time, where I is the number of intersections among the guard zones. So, it is output sensitive in nature that depends on the value of δ i . The algorithm developed in the paper is proved to report a preferred guard zone of the given simple polygon excluding all the intersections, if any.

Triangulating a simple polygon in linear time

Abstract: We give a deterministic algorithm for triangulating a simple polygon in linear time. The basic strategy is to build a coarse approximation of a triangulation in a bottom-up phase and then use the information computed along the way to refine the triangulation in a top-down phase. The main tools used are the polygon-cutting theorem, which provides us with a balancing scheme, and the planar separator theorem, whose role is essential in the discovery of new diagonals. Only elementary data structures are required by the algorithm. In particular, no dynamic search trees, of our algorithm.

Advances in Testing Techniques for Digital Microfluidic Biochips

Abstract: With the advancement of digital microfluidics technology, applications such as on-chip DNA analysis, point of care diagnosis and automated drug discovery are common nowadays. The use of Digital Microfluidics Biochips (DMFBs) in disease assessment and recognition of target molecules had become popular during the past few years. The reliability of these DMFBs is crucial when they are used in various medical applications. Errors found in these biochips are mainly due to the defects developed during droplet manipulation, chip degradation and inaccuracies in the bio-assay experiments. The recently proposed Micro-electrode-dot Array (MEDA)-based DMFBs involve both fluidic and electronic domains in the micro-electrode cell. Thus, the testing techniques for these biochips should be revised in order to ensure proper functionality. This paper describes recent advances in the testing technologies for digital microfluidics biochips, which would serve as a useful platform for developing revised/new testing techniques for MEDA-based biochips. Therefore, the relevancy of these techniques with respect to testing of MEDA-based biochips is analyzed in order to exploit the full potential of these biochips.

Role of Digital Microfluidics in Enabling Access to Laboratory Automation and Making Biology Programmable

Abstract: Digital microfluidics (DMF) is a liquid handling technique that has been demonstrated to automate biological experimentation in a low-cost, rapid, and programmable manner This review discusses the role of DMF as a "digital bioconverter"-a tool to connect the digital aspects of the design-build-learn cycle with the physical execution of experiments Several applications are reviewed to demonstrate the utility of DMF as a digital bioconverter, namely, genetic engineering, sample preparation for sequencing and mass spectrometry, and enzyme-, immuno-, and cell-based screening assays These applications show that DMF has great potential in the role of a centralized execution platform in a fully integrated pipeline for the production of novel organisms and biomolecules In this paper, we discuss how the function of a DMF device within such a pipeline is highly dependent on integration with different sensing techniques and methodologies from machine learning and big data In addition to that, we examine how the capacity of DMF can in some cases be limited by known technical and operational challenges and how consolidated efforts in overcoming these challenges will be key to the development of DMF as a major enabling technology in the computer-aided biology framework

Development of advanced operators for enhanced on-chip biosensing in digital microfluidic platforms

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