Model-based systems engineering for life-sciences instrumentation development

Next‐generation genome sequencing machines and Point‐of‐Care (PoC) in vitro diagnostics devices are precursors of an emerging class of Cyber‐Physical Systems (CPS), one that harnesses biomolecular‐scale mechanisms to enable novel "wet‐technology" applications in medicine, biotechnology, and environmental science. Although many such applications exist, testifying the importance of innovative life‐sciences instrumentation, recent events have highlighted the difficulties that designing organizations face in their attempt to guarantee safety, reliability, and performance of this special class of CPS. New regulations and increasing competition pressure innovators to rethink their design and engineering practices, and to better address the above challenges. The pace of innovation will be determined by how organizations manage to ensure the satisfaction of aforementioned constraints while also streamlining product development, maintaining high cost‐efficiency and shortening time‐to‐market. Model‐Based Systems Engineering provides a valuable framework for addressing these challenges. In this paper, we demonstrate that existing and readily available model‐based development frameworks can be adopted early in the life‐sciences instrumentation design process. Such frameworks are specifically helpful in describing and characterizing CPS including elements of a biological nature both at the architectural and performance level. We present the SysML model of a smartphone‐based PoC diagnostics system designed for detecting a particular molecular marker. By modeling components and behaviors spanning across the biological, physical‐nonbiological, and computational domains, we were able to characterize the important systemic relations involved in the specification of our system's Limit of Detection. Our results illustrate the suitability of such an approach and call for further work toward formalisms enabling the formal verification of systems including biomolecular components

Lab-on-a-Chip Fabrication and Application

The necessity of on-site, fast, sensitive, and cheap complex laboratory analysis, associated with the advances in the microfabrication technologies and the microfluidics, made it possible for the creation of the innovative device lab-on-a-chip (LOC), by which we would be able to scale a single or multiple laboratory processes down to a chip format. The present book is dedicated to the LOC devices from two points of view: LOC fabrication and LOC application

Integrated modular microfluidic system for forensic Alu DNA typing

Driven by the numerous applications of genome-related research, fully integrated microfluidic systems have been developed that have advanced the capabilities of molecular and, in particular, genetic analyses. A brief overview on integrated microfluidic systems for DNA analysis is given in Chapter 1 followed by a report on micro-capillary electrophoresis (µCE) of Alu elements with laser-induced fluorescence (LIF) detection, in which the monomorphic Alu insertions on the X and Y chromosomes were utilized to detect male DNA in large female DNA background (Y: X = 1:19) without cell sorting prior to the determination. The polymorphic Alu loci with known restricted geographical distribution were used for ethnicity determination. A valveless integrated microsystem that consists of three modules is discussed as well: (1) A solid-phase extraction (SPE) module microfabricated on polycarbonate, for DNA extraction from whole cell lysates (extraction bed capacity ~209 ±35.6 ng/cm² of total DNA). (2) A continuous-flow polymerase chain reaction (CFPCR) module fabricated in polycarbonate (Tg ~150 ºC) in which selected gene fragments were amplified using biotin and fluorescently-labeled primers accomplished by continuously shuttling small packets of PCR reagents and template through isothermal zones. (3) µCE module fabricated in poly(methylmethacrylate), which utilized a bioaffinity selection and purification bed (2.9-µL) to preconcentrate and purify the PCR products generated from the CFPCR module prior to µCE. Biotin-labeled CFPCR products were hydrostatically pumped through the streptavidin-modified bed where they were extracted onto the surface of the poly(methylmethacrylate) micropillars (50-µm width; 100-µm height; total surface area of ~117 mm²). This SPE process demonstrated high selectivity for biotinylated amplicons and utilized the strong streptavidin/biotin interaction (Kd =10-15M) to generate high recoveries. The SPE selected CFPCR products were thermally denatured and single stranded DNA released for size-based separations and LIF detection. The multiplexed SPE-CFPCR-µCE yielded detectable fluorescence signal (S/N≥3; LOD ~75 cells) for Alu DNA amplicons for gender and ethnicity determinations with a separation efficiency of ~1.5 x105 plates/m. Compared to traditional cross-T injection procedures typically used for µCE, the affinity preconcentration and injection procedure generated signal enhancements of 17-40 fold, critical for CFPCR thermal cyclers due to Taylor dispersion associated with their operation

Diamond MEMS Biosensors: Development and applications

This research focuses on the development a dielectrophoresis-enhanced microfluidic impedance biosensor (DEP-e-MIB) to enable fast response, real-time, label-free, and highly sensitive sensor for bacterial detection in clinical sample. The proposed design consists of application of dielectrophoresis (DEP) across a microfluidic channel to one of the impedance spectroscopy electrodes in order to improve the existent bacterial detection limits with impedance spectroscopy. In order to realize such a design, choice of electrode material with a wide electrochemical potential window for water is very important. Conventional electrode material, such as gold, are typically insulated for the application of DEP, and they fail when used open because the DEP voltages avoiding electrolysis do not provide enough force to move the bacteria. First, the use of nanodiamonds (ND) seeding gold surface to widen the electrochemical potential window is examined, since diamond has a wider potential window. ND seed coverage is a function of sonication time, ND concentration, and solvent of ND dispersion. Examining these parameters allowed us to increase the ND surface coverage to ~35%. With the highest ND coverage achievable, such electrodes are still susceptible to damage from electrolysis, however yield a unique leverage for impedance biosensing. When NDs is seeded at a 3x3 interdigitated electrode array, which act as electrically conductive islands between the electrodes and reduce the effective gap between the electrodes, thus allowing to perform impedance spectroscopy in solutions with low electrical conductivity such as ITS. The changes obtained in resistance to charge transfer with bacterial capture is nearly twice than that obtained with plain electrodes. Secondly, the feasibility of using boron-doped ultra nanocrystalline diamond (BD-UNCD) to apply DEP is tested without constructing a 3x3 IDE array. BD-UNCD electrodes can be used for DEP through tagging of the bacteria with immunolatex beads. This allows applying a larger DEP force on the bacteria. Since historically bead based assays are plagued with problems with non-specific binding, the role of different parameters including bead bioconjugation chemistry, bead PEGylation, BD-UNCD surface PEGylation, and DEP on specific and non-specific binding are tested. Most importantly DEP increases the specific binding and PEGylation of beads decreases the specific binding. Finally, a 3x3 IDE array with BD-UNCD was fabricated, and used impedance spectroscopy to test the suitability of BD-UNCD IDEs for impedance biosensing. The huge electrode resistance and the charge transfer resistance at BD-UNCD IDEs poses a problem for impedance biosensing as it will lead to lower sensitivity. BD-UNCD is the material of choice for applying DEP at open electrodes however gold is the choice of material for designing the chip interconnects. So the BD-UNCD layer should be as thin as possible and the interface between gold IDEs and the solution phase during DEP. The findings in this dissertation put us closer to realizing a DEP-eMIB

Microfluidics for Biosensing

There are 12 papers published with 8 research articles, 3 review articles and 1 perspective. The topics cover: Biomedical microfluidics Lab-on-a-chip Miniaturized systems for chemistry and life science (MicroTAS) Biosensor development and characteristics Imaging and other detection technologies Imaging and signal processing Point-of-care testing microdevices Food and water quality testing and control We hope this collection could promote the development of microfluidics and point-of-care testing (POCT) devices for biosensing

Cellulose-Based Biosensing Platforms

Cellulose empowers measurement science and technology with a simple, low-cost, and highly transformative analytical platform. This book helps the reader to understand and build an overview of the state of the art in cellulose-based (bio)sensing, particularly in terms of the design, fabrication, and advantageous analytical performance. In addition, wearable, clinical, and environmental applications of cellulose-based (bio)sensors are reported, where novel (nano)materials, architectures, signal enhancement strategies, as well as real-time connectivity and portability play a critical role

Laser-induced forward transfer (LIFT) of water soluble polyvinyl alcohol (PVA) polymers for use as support material for 3D-printed structures

The additive microfabrication method of laser-induced forward transfer (LIFT) permits the creation of functional microstructures with feature sizes down to below a micrometre [1]. Compared to other additive manufacturing techniques, LIFT can be used to deposit a broad range of materials in a contactless fashion. LIFT features the possibility of building out of plane features, but is currently limited to 2D or 2½D structures [2–4]. That is because printing of 3D structures requires sophisticated printing strategies, such as mechanical support structures and post-processing, as the material to be printed is in the liquid phase. Therefore, we propose the use of water-soluble materials as a support (and sacrificial) material, which can be easily removed after printing, by submerging the printed structure in water, without exposing the sample to more aggressive solvents or sintering treatments. Here, we present studies on LIFT printing of polyvinyl alcohol (PVA) polymer thin films via a picosecond pulsed laser source. Glass carriers are coated with a solution of PVA (donor) and brought into proximity to a receiver substrate (glass, silicon) once dried. Focussing of a laser pulse with a beam radius of 2 µm at the interface of carrier and donor leads to the ejection of a small volume of PVA that is being deposited on a receiver substrate. The effect of laser pulse fluence , donor film thickness and receiver material on the morphology (shape and size) of the deposits are studied. Adhesion of the deposits on the receiver is verified via deposition on various receiver materials and via a tape test. The solubility of PVA after laser irradiation is confirmed via dissolution in de-ionised water. In our study, the feasibility of the concept of printing PVA with the help of LIFT is demonstrated. The transfer process maintains the ability of water solubility of the deposits allowing the use as support material in LIFT printing of complex 3D structures. Future studies will investigate the compatibility (i.e. adhesion) of PVA with relevant donor materials, such as metals and functional polymers. References: [1] A. Piqué and P. Serra (2018) Laser Printing of Functional Materials. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA. [2] R. C. Y. Auyeung, H. Kim, A. J. Birnbaum, M. Zalalutdinov, S. A. Mathews, and A. Piqué (2009) Laser decal transfer of freestanding microcantilevers and microbridges, Appl. Phys. A, vol. 97, no. 3, pp. 513–519. [3] C. W. Visser, R. Pohl, C. Sun, G.-W. Römer, B. Huis in ‘t Veld, and D. Lohse (2015) Toward 3D Printing of Pure Metals by Laser-Induced Forward Transfer, Adv. Mater., vol. 27, no. 27, pp. 4087–4092. [4] J. Luo et al. (2017) Printing Functional 3D Microdevices by Laser-Induced Forward Transfer, Small, vol. 13, no. 9, p. 1602553