27 research outputs found
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BioScript: programming safe chemistry on laboratories-on-a-chip
This paper introduces BioScript, a domain-specific language (DSL) for programmable biochemistry which executes on emerging microfluidic platforms. The goal of this research is to provide a simple, intuitive, and type-safe DSL that is accessible to life science practitioners. The novel feature of the language is its syntax, which aims to optimize human readability; the technical contributions of the paper include the BioScript type system and relevant portions of its compiler. The type system ensures that certain types of errors, specific to biochemistry, do not occur, including the interaction of chemicals that may be unsafe. The compiler includes novel optimizations that place biochemical operations to execute concurrently on a spatial 2D array platform on the granularity of a control flow graph, as opposed to individual basic blocks. Results are obtained using both a cycle-accurate microfluidic simulator and a software interface to a real-world platform
A Design of Digital Microfluidic Biochip along with Structural and Behavioural Features in Triangular Electrode Based Array
AbstractDigital microfluidic based biochip manoeuvres on the theory of microfluidic technology, having a broad variety of applications in chemistry, biology, environmental monitoring, military etc. Being concerned about the technological advancement in this domain, we have focused on equilateral triangular electrodes based DMFB systems. Accepting the associated design issues, here, we have addressed many facets of such electrodes regarding their structural and behavioural issues in comparison to the existing square electrodes. As the requisite voltage reduction is a key challenging design issues, to implement all the tasks using triangular electrodes that are possible in square electrode arrays as well, is a tedious job. Furthermore, to deal with this new design deploying triangular electrodes, we have analyzed all the necessary decisive factors including fluidic constraints to ensure safe droplet movements and other modular operations together with mixing and routing. Moreover, an algorithm has been developed to find a route for a given source and destination pair in this newly designed DMFB. Finally, we have included a comparative study between this new design and the existing one while encountering the above mentioned issues
Droplet routing for digital microfluidic biochips based on microelectrode dot array architecture
A digital microfluidic biochip (DMFB) is a device that digitizes fluidic samples into tiny droplets and operates chemical processes on a single chip. Movement control of droplets can be realized by using electrowetting-on-dielectric (EWOD) technology. DMFBs have high configurability, high sensitivity, low cost and reduced human error as well as a promising future in the applications of point-of-care medical diagnostic, and DNA sequencing. As the demands of scalability, configurability and portability increase, a new DMFB architecture called Microelectrode Dot Array (MEDA) has been introduced recently to allow configurable electrodes shape and more precise control of droplets.
The objective of this work is to investigate a routing algorithm which can not only handle the routing problem for traditional DMFBs, but also be able to route different sizes of droplets and incorporate diagonal movements for MEDA. The proposed droplet routing algorithm is based on 3D-A* search algorithm. The simulation results show that the proposed algorithm can reduce the maximum latest arrival time, average latest arrival time and total number of used cells. By enabling channel-based routing in MEDA, the equivalent total number of used cells can be significantly reduced. Compared to all existing algorithms, the proposed algorithm can achieve so far the least average latest arrival time
Strategic Optimization Techniques For FRTU Deployment and Chip Physical Design
Combinatorial optimization is a complex engineering subject. Although formulation often depends on the nature of problems that differs from their setup, design, constraints, and implications, establishing a unifying framework is essential. This dissertation investigates the unique features of three important optimization problems that can span from small-scale design automation to large-scale power system planning: (1) Feeder remote terminal unit (FRTU) planning strategy by considering the cybersecurity of secondary distribution network in electrical distribution grid, (2) physical-level synthesis for microfluidic lab-on-a-chip, and (3) discrete gate sizing in very-large-scale integration (VLSI) circuit.
First, an optimization technique by cross entropy is proposed to handle FRTU deployment in primary network considering cybersecurity of secondary distribution network. While it is constrained by monetary budget on the number of deployed FRTUs, the proposed algorithm identi?es pivotal locations of a distribution feeder to install the FRTUs in different time horizons. Then, multi-scale optimization techniques are proposed for digital micro?uidic lab-on-a-chip physical level synthesis. The proposed techniques handle the variation-aware lab-on-a-chip placement and routing co-design while satisfying all constraints, and considering contamination and defect. Last, the first fully polynomial time approximation scheme (FPTAS) is proposed for the delay driven discrete gate sizing problem, which explores the theoretical view since the existing works are heuristics with no performance guarantee. The intellectual contribution of the proposed methods establishes a novel paradigm bridging the gaps between professional communities
Microfluidic Communications Protocol Design and Transmission Performance Analysis
The new field of nanocommunications aims to develop communication systems at the nanoscale. It has developed into two main communication directions: molecular communications andelectromagnetic communications. Microfluidic communications is a subtype of molecular communications. Existing liquid based microfluidics applications are the main target for the integration of a communication feature.
Currently, there are still no standards for microfluidics communications protocol. The protocols should consider particular phenomena such as noise, transmission access priorities, and probability of coalescence between microdroplets. Those phenomena bring challenges in protocol development of microfluidics communications.
In this thesis, the protocol stack for microfluidics communications is developed. Starting from the physical layer, feasible modulation schemes for data transmission suitable for microfluidics communications is examined. Later, medium access control layer protocols is discussed in order to optimize transmission medium access for the network entities. This is done to avoid droplet coalescence. Specification of the addressing and routing methods is defined to ensure data submission to the destination point. Finally, the performance of the proposed schemes and numerical comparison to viable alternatives are analyzed.
The results of the evaluation are reached through MATLAB software simulations. This work concentrates on Communication through Silence (CtS) where the payload is represented as distance between two droplets. Two schemes of CtS (decimal and hexadeximal) are investigated. Both CtS schemes with particular optimum amount binary payload outperforms OOK in throughput performance. The fairness of the transmission system can be achieved for a decentralized system by combining slotted (TDMA) scheme and a probability-based algorithm