Sarmishtha Ghoshal

Accelerated Functional Testing of Digital Microfluidic Biochips

Structural testing of digital microfluidic biochips targets the detection of physical defects, but it does not guarantee robust execution of target bioassays or the integrity of assay outcomes. Functional testing is needed to detect fluidic malfunctions. Such tests ensure whether or not, the elementary fluidic operations, such as droplet transportation, mixing, incubation, and splitting are reliably executed on the microfluidic array. Routing test and mixing/splitting test are two important steps in functional testing. We present two procedures for optimal bidirectional routing test and accelerated mixing/splitting test. Compared to previous methods, these procedures need significantly fewer droplet manipulation steps and reduced execution time. The proposed method of functional testing in an N x N microfluidic array requires only a constant number of mixing/splitting steps. Further, the test outcome is free from boundary errors related to droplet size that may arise during mixing/splitting test.

On residue removal in digital microfluidic biochips

Multiplexing several assays in time on the same digital microfluidic biochip is often needed in several biochemical applications. Contamination may lead to undesirable mixing of the residue left by one assay with the droplets of the subsequent assay. Hence, cleaning the droplet pathways of such a biochip by wash droplets between successive assays is required. Since a wash droplet may have a finite capability of residue removal, one has to design an efficient route planning for wash droplet(s) that minimizes the washing time and/or electrode actuation. In this paper, we formulate the problem in terms of graph Eulerization and Capacitated Chinese Postman Problem. We also propose efficient solutions and report some simulation results.

Superparamagnetic iron oxide nanoparticle attachment on array of micro test tubes and microbeakers formed on p-type silicon substrate for biosensor applications

A uniformly distributed array of micro test tubes and microbeakers is formed on a p-type silicon substrate with tunable cross-section and distance of separation by anodic etching of the silicon wafer in N, N-dimethylformamide and hydrofluoric acid, which essentially leads to the formation of macroporous silicon templates. A reasonable control over the dimensions of the structures could be achieved by tailoring the formation parameters, primarily the wafer resistivity. For a micro test tube, the cross-section (i.e., the pore size) as well as the distance of separation between two adjacent test tubes (i.e., inter-pore distance) is typically approximately 1 μm, whereas, for a microbeaker the pore size exceeds 1.5 μm and the inter-pore distance could be less than 100 nm. We successfully synthesized superparamagnetic iron oxide nanoparticles (SPIONs), with average particle size approximately 20 nm and attached them on the porous silicon chip surface as well as on the pore walls. Such SPION-coated arrays of micro test tubes and microbeakers are potential candidates for biosensors because of the biocompatibility of both silicon and SPIONs. As acquisition of data via microarray is an essential attribute of high throughput bio-sensing, the proposed nanostructured array may be a promising step in this direction.

Testing of Digital Microfluidic Biochips Using Improved Eulerization Techniques and the Chinese Postman Problem

Digital micro fluidic technology is now being extensively used for implementing a lab-on-a-chip. Micro fluidic biochips are often used for safety-critical applications, clinical diagnosis, and for genome analysis. Thus, devising effective and faster testing methodologies to warrant correct operations of these devices after manufacture and during bioassay operations, is very much needed. In this paper, we propose a technique to obtain the route plan of a test droplet for the purpose of structural testing of biochips. The technique is applicable to fully reconfigurable arrays and application specific biochips. We propose an improved eulerization technique to implement the test plan based on a graph model of the chip. The optimal eulerization can be abstracted in terms of the classical Chinese postman problem. The Euler tour can then be identified using a cycle decomposition method, which is easy to implement. This can also be used in phase-based test planning leading to significant savings in testing time. The method provides a unified approach towards unidirectional structural testing and can be easily adapted to design an improved droplet routing procedure for bidirectional functional testing of digital micro fluidic biochips.

Theory and analysis of generalized mixing and dilution of biochemical fluids using digital microfluidic biochips

Digital microfluidic (DMF) biochips are recently being advocated for fast on-chip implementation of biochemical laboratory assays or protocols, and several algorithms for diluting and mixing of reagents have been reported. However, all methods for such automatic sample preparation suffer from a drawback that they assume the availability of input fluids in pure form, that is, each with an extreme concentration factor (CF) of 100%. In many real-life scenarios, the stock solutions consist of samples/reagents with multiple CFs. No algorithm is yet known for preparing a target mixture of fluids with a given ratio when its constituents are supplied with random concentrations. An intriguing question is whether or not a given target ratio is feasible to produce from such a general input condition. In this article, we first study the feasibility properties for the generalized mixing problem under the (1:1) mix-split model with an allowable error in the target CFs not exceeding 1 2d, where the integer d is user specified and denotes the desired accuracy level of CF. Next, an algorithm is proposed which produces the desired target ratio of N reagents in ONd mix-split steps, where N ( ≥ 3) denotes the number of constituent fluids in the mixture. The feasibility analysis also leads to the characterization of the total space of input stock solutions from which a given target mixture can be derived, and conversely, the space of all target ratios, which are derivable from a given set of input reagents with arbitrary CFs. Finally, we present a generalized algorithm for diluting a sample S in minimum (1:1) mix-split steps when two or more arbitrary concentrations of S (diluted with the same buffer) are supplied as inputs. These results settle several open questions in droplet-based algorithmic microfluidics and offer efficient solutions for a wider class of on-chip sample preparation problems.

Test Planning in Digital Microfluidic Biochips Using Efficient Eulerization Techniques

Digital microfluidic technology is now being extensively used for implementing a lab-on-a-chip. Microfluidic biochips are often used for safety-critical applications, clinical diagnosis, and for genome analysis. Thus, devising effective and faster testing methodologies to warrant correct operations of these devices after manufacture and during bioassay operations, is very much needed. In this paper, we propose an Euler tour based technique to obtain the route plan of a test droplet for the purpose of structural testing of biochips. The method is applicable to various digital microfluidic biochip architectures, e.g., fully reconfigurable arrays, application specific biochips, pin-constrained irregular geometry biochips, and to defect-tolerant biochips. We show that in general, the optimal Eulerization and subsequent determination of an Euler tour in the graph model of a biochip can be abstracted in terms of the classical Chinese postman problem. The Euler tour can be identified by running the classical Hierholzer’s algorithm, which relies on a simple cycle decomposition and splicing method. This improved Eulerization technique leads to an efficient test plan for the chip. This can also be used in phase-based test planning that yields savings in testing time. The method provides a unified approach towards structural testing and can be easily adopted to design a droplet routing procedure for functional testing of digital microfluidic biochips.

Low-Cost Dilution Engine for Sample Preparation in Digital Microfluidic Biochips

Recently developed digital microfluidic biochips can implement biochemical laboratory assays (protocols) on a small size chip for automatic and reliable analysis of biochemical fluid samples. Dilution of a sample fluid is the basic step required in almost all bioassays. We propose a dilution engine for sample preparation that can produce multiple (a stream of) droplets of the target fluid with the same concentration level and present a scheduling scheme for mapping the dilution steps into the dilution engine. Our proposed architecture for dilution engine uses one (

On-Line Error Detection in Digital Microfluidic Biochips

1:1

Error-Correcting Sample Preparation with Cyberphysical Digital Microfluidic Lab-on-Chip

) mix-split microfluidic module (mixer) and a constant number of storage units. Its performance is compared with another layout of only one mixer with no storage unit. Simulation results show that the proposed scheme can efficiently reuse the waste droplets of earlier steps and hence utilizes less amount of expensive biochemical fluids. Moreover, the scheme generates multiple target droplets with the same concentration level in less number of dilution steps (i.e., time) and at a relatively lower cost.

High-throughput dilution engine for sample preparation on digital microfluidic biochips

Digital microfluidic technology is being increasingly used for implementing a lab-on-a-chip with many life-critical applications. Testing of these biochips is thus indispensable not only after manufacture, but also during in-field operation. To keep the product cost (including both design and test) low for disposable biochips, efficient on-line test techniques are desirable. All previous on-line test mechanisms interleave testing and the target bioassay protocol, but they involve overhead such as use of separate test droplet(s) and increased completion time. In this paper, we propose a simple on-line error-detection methodology that can be performed concurrently with the normal operation of the system with no or little extra effort. The proposed procedure does not require any test droplet. In the case of incorrect operation, the error is detected on or before the completion of the bioassay. The main objective of the proposed strategy is to ensure the correctness of the executed assay on-chip and not to guarantee the absence of a defect in the chip. The given assay protocol is assumed to be executed correctly if the on-line procedure finishes with success. The assay is aborted as soon as an error is detected, thereby saving costly sample/reagents. Moreover, the scheme can be easily adopted to enhance diagnosis.