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

Scheduling and Fluid Routing for Flow-Based Microfluidic Laboratories-on-a-Chip

Microfluidic laboratories-on-a-chip (LoCs) are replacing the conventional biochemical analyzers and are able to integrate the necessary functions for biochemical analysis on-chip. There are several types of LoCs, each having its advantages and limitations. In this paper we are interested in flow-based LoCs, in which a continuous flow of liquid is manipulated using integrated microvalves. By combining several microvalves, more complex units, such as micropumps, switches, mixers, and multiplexers, can be built. We consider that the architecture of the LoC is given, and we are interested in synthesizing an implementation, consisting of the binding of operations in the application to the functional units of the architecture, the scheduling of operations and the routing and scheduling of the fluid flows, such that the application completion time is minimized. To solve this problem, we propose a list scheduling-based application mapping (LSAM) framework and evaluate it by using real-life as well as synthetic benchmarks. When biochemical applications contain fluids that may adsorb on the substrate on which they are transported, the solution is to use rinsing operations for contamination avoidance. Hence, we also propose a rinsing heuristic, which has been integrated in the LSAM framework

One dimensional photonic crystal for label-free and fluorescence sensing application

The development of more sensitive and more reliable sensors aids medical applications in many fields as diseases detection or therapy progress. This thesis threats the development of an optical biosensor based on electromagnetic modes propagating at the interface between a finite one-dimensional photonic crystal (1DPC) and a homogeneous external medium, also named Bloch Surface Waves (BSW). BSW have emerged as an attractive approach for label-free sensing in plasmon-like sensor configurations. Besides label-free operation, the large field enhancement and the absence of quenching allow the use of BSW to excite fluorescent labels that are in proximity of the 1DPC surface. This approach was adapted to the case of angularly resolved resonance detection, thus giving rise to a combined label-free/labelled biosensor platform. BSW present many degrees of design freedomthat enable tuning of resonance properties. In order to obtain a figure of merit for an optimization, I investigated the measurement uncertainty depending on resonance width and depth with different numericalmodels. This has led to a limit of detection that can assist the choice of the best design to use. Two tumor biomarkers, such as vascular endothelial growth factor (VEGF) and Angiopoietin-2 (Ang2), have been considered to be detected with the BSW biosensing platform. For this purpose the specific antibodies for the two tumor biomarkers were immobilized on the 1DPC biochip surface. The conclusive experiments reported in this work demonstrated the successful detection of the VEGF biomarker in complex matrices, such as cell culture supernatants and human plasma samples. Moreover, the platformwas used to determinate Ang2 concentration in untreated human plasma samples using low volumes, 300 μL, and with short turnaround times, 30 minutes. This is the first BSW based biosensor assay for the determination of tumor biomarker in human plasma samples at clinically relevant concentrations

Fluigi: an end-to-end software workflow for microfluidic design

One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications with implications in health, materials, and sensing. Computational design methodologies allow for increased performance and reliability of these circuits. Major challenges that remain include increasing the scalability and robustness of engineered biological systems and streamlining and automating the synthetic biology workflow of “specify-design-build-test.” I summarize the advances in microfluidic technology, particularly microfluidic large scale integration, that can be used to address the challenges facing each step of the synthetic biology workflow for genetic circuits. Microfluidic technologies allow precise control over the flow of biological content within microscale devices, and thus may provide more reliable and scalable construction of synthetic biological systems. However, adoption of microfluidics for synthetic biology has been slow due to the expert knowledge and equipment needed to fabricate and control devices. I present an end-to-end workflow for a computer-aided-design (CAD) tool, Fluigi, for designing microfluidic devices and for integrating biological Boolean genetic circuits with microfluidics. The workflow starts with a ``netlist" input describing the connectivity of microfluidic device to be designed, and proceeds through placement, routing, and design rule checking in a process analogous to electronic computer aided design (CAD). The output is an image of the device for printing as a mask for photolithography or for computer numerical control (CNC) machining. I also introduced a second workflow to allocate biological circuits to microfluidic devices and to generate the valve control scheme to enable biological computation on the device. I used the CAD workflow to generate 15 designs including gradient generators, rotary pumps, and devices for housing biological circuits. I fabricated two designs, a gradient generator with CNC machining and a device for computing a biological XOR function with multilayer soft lithography, and verified their functions with dye. My efforts here show a first end-to-end demonstration of an extensible and foundational microfluidic CAD tool from design concept to fabricated device. This work provides a platform that when completed will automatically synthesize high level functional and performance specifications into fully realized microfluidic hardware, control software, and synthetic biological wetware

Detection of Pathogens in Water Using Micro and Nano-Technology

Detection of Pathogens in Water Using Micro and Nano-Technology aims to promote the uptake of innovative micro and nano-technological approaches towards the development of an integrated, cost-effective nano-biological sensor useful for security and environmental assays.  The book describes the concerted efforts of a large European research project and the achievements of additional leading research groups. The reported knowledge and expertise should support in the innovation and integration of often separated unitary processes. Sampling, cell lysis and DNA/RNA extraction, DNA hybridisation detection micro- and nanosensors, microfluidics, together also with computational modelling and risk assessment can be integrated in the framework of the current and evolving European regulations and needs. The development and uptake of molecular methods is revolutionizing the field of waterborne pathogens detection, commonly performed with time-consuming cultural methods. The molecular detection methods are enabling the development of integrated instruments based on biosensor that will ultimately automate the full pathway of the microbiological analysis of water

Detection of Pathogens in Water Using Micro and Nano-Technology

Detection of Pathogens in Water Using Micro and Nano-Technology aims to promote the uptake of innovative micro and nano-technological approaches towards the development of an integrated, cost-effective nano-biological sensor useful for security and environmental assays.  The book describes the concerted efforts of a large European research project and the achievements of additional leading research groups. The reported knowledge and expertise should support in the innovation and integration of often separated unitary processes. Sampling, cell lysis and DNA/RNA extraction, DNA hybridisation detection micro- and nanosensors, microfluidics, together also with computational modelling and risk assessment can be integrated in the framework of the current and evolving European regulations and needs. The development and uptake of molecular methods is revolutionizing the field of waterborne pathogens detection, commonly performed with time-consuming cultural methods. The molecular detection methods are enabling the development of integrated instruments based on biosensor that will ultimately automate the full pathway of the microbiological analysis of water

In Situ Preconcentration by AC Electrokinetics for Rapid and Sensitive Nanoparticle Detection

Reducing cost and time is a major concern in clinical diagnostics. Current molecular diagnostics are multi-step processes that usually take at least several hours or even days to complete multiple reagents delivery, incubations and several washing processes. This highly labor-intensive work and lack of automation could result in reduced reliability and low efficiency. The Laboratory-on-a-chip (LOC), taking advantage of the merger and development of microfluidics and biosensor technology, has shown promise towards a solution for performing analytical tests in a self-contained and compact unit, enabling earlier and decentralized testing. However, challenges are to integrate the fluid regulatory elements on a single platform and to detect target analytes with high sensitivity and selectivity. The goal of this research work is to develop an AC electrokinetic (ACEK) flow through concentrator for in-situ concentration of biomolecules and develop a comprehensive understanding of effects of ACEK flow on the biomolecule transport (in-situ concentration) and their impact on electronic biosensing mechanism and performance, achieving automation and miniaturization. ACEK is a new and promising technique to manipulate micro/bio-fluids and particles. It has many advantages over other techniques for its low applied voltage, portability and compatibility for integration into lab-on-a-chip devices. Numerical study on preconcentration system design in this work has provided an optimization rule for various biosensor designs using ACEK technique. And the microfluidic immunoassay lab-chip designed based on ACET effect has showed promising prospect for accelerated diagnostics. With optimized design of channel geometry, electrode patterns, and properly selected operation condition (ac frequency and voltage), the preconcentration system greatly reduced the reaction time to several minutes instead of several hours, and improved sensitivity of the assay. With the design of immunoassay lab-chip, one can quantitatively study the effect of ACET micropumping and mixing on molecular level binding. Improved sensors with single-chip form factor as a general platform could have a significant impact on a wide-range of biochemical detection and disease diagnostics including pathogen/virus detection, whole blood analysis, immune-screening, gene expression, as well as home land security