Abstraction Layers for Scalable Microfluidic Biocomputers (Extended Version)

Microfluidic devices are emerging as an attractive technology for automatically orchestrating the reactions needed in a biological computer. Thousands of microfluidic primitives have already been integrated on a single chip, and recent trends indicate that the hardware complexity is increasing at rates comparable to Moore's Law. As in the case of silicon, it will be critical to develop abstraction layers--such as programming languages and Instruction Set Architectures (ISAs)--that decouple software development from changes in the underlying device technology.Towards this end, this paper presents BioStream, a portable language for describing biology protocols, and the Fluidic ISA, a stable interface for microfluidic chip designers. A novel algorithm translates microfluidic mixing operations from the BioStream layer to the Fluidic ISA. To demonstrate the benefits of these abstraction layers, we build two microfluidic chips that can both execute BioStream code despite significant differences at the device level. We consider this to be an important step towards building scalable biocomputers

Towards a Theory of Droplet-Mixing Graphs in Microfluidics

In this work, we study the problem of fluid mixing in microfluidic chips. The motivation for studying this problem comes from the process of sample preparation for chemical, biological, medical and environmental experiments, which often require preparation of fluid mixtures with desired concentrations. We assume that fluids are manipulated in discrete units called droplets. The input set of droplets consist of two distinct fluids: the reactant, which is the fluid of interest, and the buffer fluid that is used to dilute it. The goal is to produce a target set of droplets with prespecified reactant concentrations. In the model we study, the mixing process in a microfluidic chip can be abstractly represented as a mixing graph. A mixing graph is a collection of micro-mixers (nodes) connected by micro-channels (edges) that converts an input set of droplets I into a set of output droplets T, by applying a sequence of 1:1 mixing operations. This graph may also produce some waste, which are superfluous droplets of fluid not used in the target set. Computational complexity of most natural questions regarding such mixing graphs remain open. For example, it is not even known whether it is decidable for a given target set to be produced without waste. Current work in the literature contains only heuristic approaches that compute mixing graphs while attempting to optimize certain objectives, including minimizing waste, reactant usage, the depth of the graphs, and more.Our first contribution is an efficient algorithm for computing mixing graphs for single-droplet targets. Our algorithm produces significantly less waste than state-of-the-art algorithms in an experimental comparison. We also provide a bound on its worst-case performance that is significantly better than those for earlier algorithms. Our second result concerns the variant of the problem where the objective is to design a mixing graph that perfectly mixes a collection of input droplets with arbitrary concentrations. We provide a complete characterization of input sets for which such graphs exist, and an efficient algorithm to construct these graphs. In addition, we provide several other results about properties of mixing graphs and the computational complexity of computing mixing graphs of fixed depth

Harvinaisten merkkaamattomien solujen kokoon perustuva erottelu mikrofluidistiikalla

Separating and isolating rare cells with cheap methods and rapid prototyping is attractive in analysing DNA in foetal cells circulating in maternal blood with non-invasive methods. Inertial microfluidics as a separation method is based on equilibrium points or trajectories that the particles migrate during flow. In this work, three different separation devices and one with a main purpose is concentration of diluted solutions after separation were investigated. The purpose of the thesis is to gain inertial focusing and particle separation. The chips were fabricated by using soft-lithography process with SU-8 masters for transferring patterns on PDMS. After curing, the chips were cut, punched and treated with oxygen plasma to bond on microscope slides. Flow thru the devices was produced with syringe pumps. Devices were optimized first using de-ionized water, then investigated with different concentrations of polystyrene microparticles and finally with cells to gain preliminary results. Devices were tested within 0.006 ml/min to 10 ml/min range. Non-equilibrium inertial array chip (NISA chip) is based on wall induced inertial lift force and siphoning by geometry induced pressure difference. NISA chip was investigated to separate 8 µm from 10 µm particles. The device had optimization issues with back-flow to feed, particle attachment to islands and low concentration of output samples. Spiral chip is based on net inertial lift forces and Dean secondary flow induced by curvature of the device. The device was investigated with large throughput (above 4.9 ml/min flow rate) to separate 10 µm particles from 15 µm particles. Spiral chip had suboptimal outlet design, which let to large deviation in data. However, the results showed particle focusing during videoing of the flow although with low separation efficiency. Labyrinth chip is likewise based on net inertial forces and Dean secondary flow as well as alternating corner design that induces additional mixing of particles. The chip was investigated with reasonably high throughput (above 1.75 ml/min flow rate) to separate 10 µm particles from 15 µm particles. The device showed inertial focusing both in video results and the particle analysis. Separation was seen in particle analysis. Concentrator chip is based on inertial focusing and siphoning. Chip was investigated to concentrate solution of 10 µm 105 particles/ml tenfold. The device showed effective concentration using optimal flow rate with particles and using slightly slower flow rate with preliminarily cell experiments.Harvinaisten solujen erottelu ja eristäminen edullisilla menetelmillä ja nopealla prototypoinnilla on houkuttelevaa, kun analysoidaan verenkierrossa olevia kasvainsoluja tai DNA:ta sisältäviä sikiönsoluja äidin verestä ei-invasiivisesti. Inertiaalinen mikrofluidistiikka erottelumenetelmänä perustuu erikokoisten solujen taipumukseen asettua eri tasapainopisteisiin tai lentoradoille virtauksessa. Tässä työssä kolme erottelulaitetta sekä yksi solujen konsentrointiin erottelun jälkeen tähtäävä laite tutkittiin, jotta selvitettäisiin laitteiden kyky fokusoida ja erotella partikeleita. Sirut valmistettiin pehmyt-litografialla, jossa SU-8 mastereilla siirrettiin mikrofluidistiset kanavat PDMS:ään. Kovettumisen jälkeen sirut leikattiin, rei’itettiin, käytettiin happiplasmassa ja bondattiin mikroskooppilaseihin. Virtauskokeissa käytettiin ruiskupumppua. Laitteet tutkittiin ja optimoitiin alustavasti ensin deionisoidulla vedellä ja sitten erilaisilla polystyreeni mikropartikkeli liuoksilla ja lopuksi vielä alustavilla solukokeilla. Laitteet tutkittiin virtausnopeusvälillä 0.006 ml/min - 10 ml/min. Inertiaaliarray siru (NISA siru) perustuu kanavan saarien seinien aiheuttamaan inertiaalivoimaan ja lappoon, joka syntyy geometriasta johtuvista paine-eroista. Laite tutkittiin tarkoituksena erottaa 8 µm partikkelit 10 µm partikkeleista. Laitteen optimointi osoittautui haasteelliseksi johtuen nesteen takaisinvirtauksesta syötteeseen, partikkelien tarttumisesta saariin ja ulostulojen matalasta konsentraatiosta. Spiraali siru perustuu inertiaalivoimiin ja Deanin sekundaari virtauksiin, jotka johtuvat kanavan kaareutuvuudesta, sekä kanavan pylväiden virtausta supistavaan vaikutukseen. Laite tutkittiin korkeilla virtausnopeuksilla tarkoituksena erottaa 10 µm partikkelit 15 µm partikkeleista. Spiraali sirun ulostulon design aiheutti korkeaa hajontaa partikkelianalyysissa. Toisaalta, laitteen virtauksen videotuloksissa ja partikkelianalyysissa on nähtävissä selkeä inertiaalifokusointi. Labyrintti siru perustuu myös inertiaalivoimiin ja Deanin sekundaari virtoihin sekä laitteen designissa olevien kulmien partikkeleita sekoittavaan vaikutukseen. Laite tutkittiin korkeahkoilla virtausnopeuksilla keskittyen 10 µm ja 15 µm partikkelien erotteluun. Laitteen virtauksen videotuloksissa ja partikkelianalyysissa on selkeä fokusointi. Lisäksi erottelua oli havaittavissa partikkelianalyysissa. Konsentraattori siru perustuu inertiaalifokusointiin ja lappoon. Laite tutkittiin tarkoituksena konsentroida 10 µm 105 partikkelia/ml kymmenkertaisesti. Laitteessa oli havaittavissa selkeää konsentroitumista partikkeleilla optimaalisella virtausnopeudella ja alustavissa solukokeissa hieman matalammalla virtausnopeudella

Punch Card Programmable Microfluidics

Small volume fluid handling in single and multiphase microfluidics provides a promising strategy for efficient bio-chemical assays, low-cost point-of-care diagnostics and new approaches to scientific discoveries. However multiple barriers exist towards low-cost field deployment of programmable microfluidics. Incorporating multiple pumps, mixers and discrete valve based control of nanoliter fluids and droplets in an integrated, programmable manner without additional required external components has remained elusive. Combining the idea of punch card programming with arbitrary fluid control, here we describe a self-contained, hand-crank powered, multiplex and robust programmable microfluidic platform. A paper tape encodes information as a series of punched holes. A mechanical reader/actuator reads these paper tapes and correspondingly executes a series of operations onto a microfluidic chip coupled to the platform in a plug-and-play fashion. Enabled by the complexity of codes that can be represented by a series of holes in punched paper tapes, we demonstrate independent control of fifteen on-chip pumps with enhanced mixing, on-off valves and a novel on-demand impact-based droplet generator. We demonstrate robustness of operation by encoding a string of characters representing the word "PUNCHCARD MICROFLUIDICS" using the droplet generator. Multiplexing is demonstrated by implementing an example water quality test utilizing colorimetric assays for pH, ammonia, nitrite and nitrate content in different water samples. With its portable and robust design, low cost and ease-of-use, we envision punch card programmable microfluidics will bring complex control of microfluidic chips into field-based applications in low-resource settings and in the hands of children around the world bringing microfluidics and low-Reynolds number hydrodynamics to everyday classrooms.Comment: 29 pages, 6 figure

Advances in Microfluidics Technology for Diagnostics and Detection

Microfluidics and lab-on-a-chip have, in recent years, come to the forefront in diagnostics and detection. At point-of-care, in the emergency room, and at the hospital bed or GP clinic, lab-on-a-chip offers the potential to rapidly detect time-critical and life-threatening diseases such as sepsis and bacterial meningitis. Furthermore, portable and user-friendly diagnostic platforms can enable disease diagnostics and detection in resource-poor settings where centralised laboratory facilities may not be available. At point-of-use, microfluidics and lab-on-chip can be applied in the field to rapidly identify plant pathogens, thus reducing the need for damaging broad spectrum pesticides while also reducing food losses. Microfluidics can also be applied to the continuous monitoring of water quality and can support policy-makers and protection agencies in protecting the environment. Perhaps most excitingly, microfluidics also offers the potential to enable entirely new diagnostic tests that cannot be implemented using conventional laboratory tools. Examples of microfluidics at the frontier of new medical diagnostic tests include early detection of cancers through circulating tumour cells (CTCs) and highly sensitive genetic tests using droplet-based digital PCR.This Special Issue on “Advances in Microfluidics Technology for Diagnostics and Detection” aims to gather outstanding research and to carry out comprehensive coverage of all aspects related to microfluidics in diagnostics and detection

Recent Advances on Sorting Methods of High-Throughput Droplet-Based Microfluidics in Enzyme Directed Evolution

Droplet-based microfluidics has been widely applied in enzyme directed evolution (DE), in either cell or cell-free system, due to its low cost and high throughput. As the isolation principles are based on the labeled or label-free characteristics in the droplets, sorting method contributes mostly to the efficiency of the whole system. Fluorescence-activated droplet sorting (FADS) is the mostly applied labeled method but faces challenges of target enzyme scope. Label-free sorting methods show potential to greatly broaden the microfluidic application range. Here, we review the developments of droplet sorting methods through a comprehensive literature survey, including labeled detections [FADS and absorbance-activated droplet sorting (AADS)] and label-free detections [electrochemical-based droplet sorting (ECDS), mass-activated droplet sorting (MADS), Raman-activated droplet sorting (RADS), and nuclear magnetic resonance-based droplet sorting (NMR-DS)]. We highlight recent cases in the last 5 years in which novel enzymes or highly efficient variants are generated by microfluidic DE. In addition, the advantages and challenges of different sorting methods are briefly discussed to provide an outlook for future applications in enzyme DE