We describe an exciting new application domain for deep reinforcement learning (RL): droplet routing on digital microfluidic biochips (DMFBs). A DMFB consists of a two-dimensional electrode array, and it manipulates droplets of liquid to automatically execute biochemical protocols for clinical chemistry. However, a major problem with DMFBs is that electrodes can degrade over time. The transportation of droplet transportation over these degraded electrodes can fail, thereby adversely impacting the integrity of the bioassay outcome. We demonstrated that the formulation of droplet transportation as an RL problem enables the training of deep neural network policies that can adapt to the underlying health conditions of electrodes and ensure reliable fluidic operations. We describe an RL-based droplet routing solution that can be used for various sizes of DMFBs. We highlight the reliable execution of an epigenetic bioassay with the RL droplet router on a fabricated DMFB. We show that the use of the RL approach on a simple micro-computer (Raspberry Pi 4) leads to acceptable performance for time-critical bioassays. We present a simulation environment based on the OpenAI Gym Interface for RL-guided droplet routing problems on DMFBs. We present results on our study of electrode degradation using fabricated DMFBs. The study supports the degradation model used in the simulator.

Microfluidics-based biochips enable the precise control of nanoliter volumes of biochemical samples and reagents. They combine electronics with biology and integrate various bioassay operations, such as sample preparation, analysis, separation, and detection. Compared to conventional laboratory procedures, which are cumbersome and expensive, miniaturized biochips offer the advantages of higher sensitivity, lower cost, system integration, and less likelihood of human error. Because of these advantages, microfluidic biochips are being increasingly used for DNA sequencing, point-of-care clinical diagnostics, and immunoassays. This chapter describes three mainstream microfluidic technology platforms: (1) flow-based microfluidics, (2) digital microfluidics, and (3) microelectrode-dot-array biochips. The chapter presents recent advances in computer-aided design tools for simulation, synthesis, and chip optimization. These tools target modeling and simulation, scheduling, module placement, and droplet routing. With the help of these tools, biochip users can concentrate on the development of nanoscale bioassays, leaving details of chip optimization and implementation to software tools.

Microfluidic platforms have recently emerged as an invaluable component for studying synthetic biology as they are capable of emulating complex molecular networks of biological pathways (biocircuits) on a chip. A special type of biochemical assays, known as biocircuit-regulatory scanning (BRS) assays, is employed to regulate gene expression, enabling comprehensive exploration of related biocircuit parameters. Prior work has provided high-level design methodologies for implementing BRS; however, most of these methods are abstract and cannot be used in practice as they overlook the dynamics of interactions between the samples and the biochip. In this article, we address this limitation by providing a comprehensive framework that implements BRS assays. The proposed framework, named BioScan, includes: 1) a statistical method that selects suitable volumetric ratios of biochemicals used to execute a BRS assay; 2) a high-level synthesis method that generates the specifications of the target BRS assay; 3) a translation technique enabling implementation of BRS on a microelectrode-dot array (MEDA) biochip; and 4) a Dirichlet-regressor that constructs the parameter space of the associated biocircuit. Simulation results show that the proposed framework can efficiently perform parameter-space exploration (PSE) while significantly reducing completion time and reagent cost.

Epigenetics, the study of inheritable mechanisms that regulate gene expression, has clinical ramifications from cancer to autoimmune disorders to psychiatric pathologies. The main tool to study epigenetics is chromatin immunoprecipitation (ChIP), which probes the relationship between DNA and its structural nucleosome-forming histone proteins. Standard benchtop ChIP has three major drawbacks: (1) it requires a large input volume of cells, (2) it is very time consuming and work intensive, and (3) it is low throughput. Digital microfluidic biochips (DMFB) have proven to be successful at utilizing small volumes of reagents and samples to perform high throughput bioanalyses and assays of macromolecules. Their ease of configurability, automation, and high sensitivity make them an ideal platform for ChIP adaptation. Previously, we demonstrated the first step towards ChIP implementation on a DMFB by detecting specifically modified nucleosomes, the building blocks of chromatin, in a semi-quantitative nucleosome immunoprecipitation (NuIP) assay. Herein, we modify the prior 'sweep-through' DMFB design to enhance the capture and detection of analyte-bound magnetic beads. With this modification, we can increase both the level of detection and granularity when probing a sample. Furthermore, this new 'pull-through' design presents a novel method for bead collection using an on-chip magnetic source.

Acoustics-based tweezers provide a unique toolset for contactless, label-free, and precise manipulation of bio-particles and bioanalytes. Most acoustic tweezers rely on acoustic radiation forces; however, the accompanying acoustic streaming often generates unpredictable effects due to its nonlinear nature and high sensitivity to the three-dimensional boundary conditions. Here, we demonstrate acoustohydrodynamic tweezers, which generate stable, symmetric pairs of vortices to create hydrodynamic traps for object manipulation. These stable vortices enable predictable control of a flow field, which translates into controlled motion of droplets or particles on the operating surface. We built a programmable droplet-handling platform to demonstrate the basic functions of planar-omnidirectional droplet transport, merging droplets, and in situ mixing via a sequential cascade of biochemical reactions. Our acoustohydrodynamic tweezers enables improved control of acoustic streaming and demonstrates a previously unidentified method for contact-free manipulation of bioanalytes and digitalized liquid handling based on a compact and scalable functional unit.

The ability to precisely manipulate nano-objects on a large scale can enable the fabrication of materials and devices with tunable optical, electromagnetic, and mechanical properties. However, the dynamic, parallel manipulation of nanoscale colloids and materials remains a significant challenge. Here, we demonstrate acoustoelectronic nanotweezers, which combine the precision and robustness afforded by electronic tweezers with versatility and large-field dynamic control granted by acoustic tweezing techniques, to enable the massively parallel manipulation of sub-100 nm objects with excellent versatility and controllability. Using this approach, we demonstrated the complex patterning of various nanoparticles (e.g., DNAs, exosomes, ~3 nm graphene flakes, ~6 nm quantum dots, ~3.5 nm proteins, and ~1.4 nm dextran), fabricated macroscopic materials with nano-textures, and performed high-resolution, single nanoparticle manipulation. Various nanomanipulation functions, including transportation, concentration, orientation, pattern-overlaying, and sorting, have also been achieved using a simple device configuration. Altogether, acoustoelectronic nanotweezers overcome existing limitations in nano-manipulation and hold great potential for a variety of applications in the fields of electronics, optics, condensed matter physics, metamaterials, and biomedicine.

A digital microfluidic biochip (DMFB) enables the miniaturization of immunoassays, point-of-care clinical diagnostics, DNA sequencing, and other laboratory procedures in biochemistry. A recent generation of biochips uses a micro-electrode-dot-array (MEDA) architecture, which provides fine-grained control of droplets and seamlessly integrates microelectronics and microfluidics using CMOS technology and a TSMC fabrication process. To ensure that bioassays are carried out on MEDA biochips efficiently, high-level synthesis algorithms have recently been proposed. However, as in the case of conventional DMFBs, microelectrodes are likely to fail when they are heavily utilized, and previous methods fail to consider reliability issues. In this article, we first present a new microelectrode cell (MC) design such that the droplet-sensing operation can be enabled/disabled for individual MCs. Next, "partial update" and "partial sensing" operations are presented based on an IEEE Std. 1687 IJTAG network design. Finally, wear-leveling synthesis method is proposed to ensure uniform utilization of MCs on MEDA. A comprehensive set of simulation results demonstrate the effectiveness of the proposed hardware design and design automation methods.

A digital microfluidic biochip (DMFB) is an attractive platform for immunoassays, point-of-care clinical diagnostics, DNA sequencing, and other laboratory procedures in biochemistry. A recent generation of biochips uses a micro-electrode-dot-array (MEDA) architecture, which provides fine-grained controllability of droplets and seamlessly integrates microelectronics and microfluidics using CMOS technology. In order to ensure robust fluidic operations and high confidence in the outcome of biochemical experiments, chip testing, fault diagnosis, and fault recovery are critical for MEDA biochips. In this article, we present an effective fault-recovery solution based on the homogeneous structure of MEDA. Since the microelectrode cells (MCs) in an MEDA biochip are identical, we add multiplexers for reconfigurability, whereby an MC with faulty components can use the hardware resources in a neighboring MC. In addition, we use the IEEE 1687 (also known as IJTAG) network to reduce the number of control signals needed for the multiplexers, and to provide flexible subscan chain access for the fault-recovery control flow. A comprehensive set of simulation results demonstrates the effectiveness of the proposed fault-recovery solution for MEDA biochips.

A digital microfluidic biochip (DMB) is an attractive platform for automating laboratory procedures in microbiology. To overcome the problem of cross-contamination due to fouling of the electrode surface in traditional DMBs, a contactless liquid-handling biochip technology, referred to as acoustofluidics, has recently been proposed. A major challenge in operating this platform is the need for a control signal of frequency 24 MHz and voltage range ±10/±20 V to activate the IDT units in the biochip. In this paper, we present a hardware design that can efficiently activate/de-activated each IDT, and can fully automate an bio-protocol. We also present a fault-tolerant synthesis technique that allows us to automatically map biomolecular protocols to acoustofluidic biochips. We develop and experimentally validate a velocity model, and use it to guide co-optimization for operation scheduling, module placement, and droplet routing in the presence of IDT faults. Simulation results demonstrate the effectiveness of the proposed synthesis method. Our results are expected to open new research directions on design automation of digital acoustofluidic biochips.

A digital microfluidic biochip (DMFB) enables miniaturization of immunoassays, point-of-care clinical diagnostics, and DNA sequencing. A recent generation of DMFBs uses a micro-electrode-dot-array (MEDA) architecture, which provides fine-grained control of droplets and real-time droplet sensing using the CMOS technology. However, microelectrodes in a MEDA biochip degrade when they are charged and discharged frequently during bioassay execution. In this article, we first make the key observation that the droplet-sensing operations contribute up to 94% of all microelectrode actuation in MEDA. Consequently, to reduce the number of droplet-sensing operations, we present a new microelectrode cell (MC) design as well as a selective-sensing method such that only a small fraction of microelectrodes perform droplet sensing during bioassay execution. The selection of microelectrodes that need to perform the droplet sensing is based on an analysis of experimental data. A comprehensive set of simulation results show that the total number of droplet-sensing operations is reduced to only 0.7%, which prolongs the lifespan of a MEDA biochip by 11× without any impact on bioassay time-to-response.

Advances in lab-on-a-chip technologies are driven by the pursuit of programmable microscale bioreactors or fluidic processors that mimic electronic functionality, scalability, and convenience. However, few fluidic mechanisms allow for basic logic operations on rewritable fluidic paths due to cross-contamination, which leads to random interference between "fluidic bits" or droplets. Here, we introduce a mechanism that allows for contact-free gating of individual droplets based on the scalable features of acoustic streaming vortices (ASVs). By shifting the hydrodynamic equilibrium positions inside interconnected ASVs with multitonal electrical signals, different functions such as controlling the routing and gating of droplets on rewritable fluidic paths are demonstrated with minimal biochemical cross-contamination. Electrical control of this ASV-based mechanism allows for unidirectional routing and active gating behaviors, which can potentially be scaled to functional fluidic processors that can regulate the flow of droplets in a manner similar to the current in transistor arrays.

The IEEE Std. 1687 facilitates flexible access to on-chip instruments through the JTAG test-access port. This flexibility enables the minimization of the overall access time (OAT), and a number of techniques have been proposed in the literature to achieve this goal. However, the OAT is still high for instruments that require a large amount of test data if this data is shifted through the scan chain serially. In order to further reduce the OAT, we present an efficient test-scheduling method that exploits broadcast and hardware parallelism for instrument access. A broadcast scheduling method is synergistically combined with three parallel IJTAG designs. We show that under different cost criteria, we can select the most efficient parallel IJTAG design such that the equivalent access time (EAT) is minimized. In addition, an interconnect fabric design and an integer-linear-programming method is used to balance the lengths of multiple scan chains. Two industry chip designs and three IJTAG benchmarks are used to evaluate the effectiveness of the proposed method.

A digital microfluidic biochip (DMFB) enables miniaturization of immunoassays, point-of-care clinical diagnostics, DNA sequencing, and other laboratory procedures in biochemistry. A recent generation of biochips uses a microelectrode-dot-array (MEDA) architecture, which provides fine-grained control of droplets and seamlessly integrates microelectronics and microfluidics using CMOS technology. To ensure that bioassays are carried out on MEDA biochips efficiently, high-level synthesis algorithms have recently been proposed. However, as in the case of conventional DMFBs, microelectrodes are likely to fail when they are heavily utilized, and previous methods fail to consider reliability issues. In this paper, we present the design of an IEEE Std. 1687 (IJTAG) network and a block-aware high-level synthesis method that can effectively alleviate reliability problems in MEDA biochips. A comprehensive set of simulation results demonstrate the effectiveness of the proposed method.

A digital microfluidic biochip (DMFB) is an attractive platform for immunoassays, point-of-care clinical diagnostics, DNA sequencing, and other laboratory procedures in biochemistry. A recent generation of biochips uses a micro-electrode-dot-array (MEDA) architecture, which provides fine-grained controllability of droplets and seamlessly integrates microelectronics and microfluidics using CMOS technology. In order to ensure robust fluidic operations and high confidence in the outcome of biochemical experiments, chip testing, fault diagnosis and fault recovery are critical for MEDA biochips. In this paper, we present an effective fault- recovery solution based on the homogeneous structure of MEDA. Since the microelectrode cell (MCs) in a MEDA biochip are identical, we add multiplexers for reconfigurability, whereby an MC with faulty components can use the hardware resources in a neighboring MC. In addition, we use the IEEE 1687 (a.k.a. IJTAG) network to reduce the number of control signals need for the multiplexers, and to provide flexible sub-scan chain access for the fault-recovery control flow. A comprehensive set of simulation results demonstrates the effectiveness of the proposed fault-recovery solution for MEDA biochips.

A digital microfluidic biochip (DMB) is an attractive platform for automating laboratory procedures in microbiology. However, a major problem associated with today's DMBs is the risk of cross-contamination due to undesirable fouling of the electrode surface, i.e., droplet materials stick to the surface. To overcome the above problem, a contactless liquid-handling biochip technology referred to as acoustofluidics has recently been proposed, and droplet manipulations on acoustofluidic biochips have also been experimentally demonstrated. In order to ensure robust fluidic operations and high confidence in the outcome of biochemical experiments, acoustofluidic biochips must be adequately tested before they are used for bioassay execution. This paper presents the first approach for testing of an acoustofluidic biochip that includes an array of interdigital transducers (IDTs). We first present structural test techniques to evaluate the pass/fail status of each IDT, and identify the type of fault if it fails. In order to ensure correct operation of functional units, e.g., mixers and routers, we also present functional test techniques to address fundamental acoustofluidic operations such as droplet transportation and droplet mixing. We evaluate the proposed test methods using experiments on fabricated acoustofluidic biochips.

Sample preparation is an important application for the digital microfluidic biochips (DMFBs) platform, and many methods have been developed to reduce the time and reagent usage associated with on-chip sample preparation. However, errors in fluidic operations can result in the concentration of the resulting droplet being outside the calibration range. Current error-recovery methods have the drawback that they need the use of on-chip sensors and further re-execution time. In this paper, we present two dilution-chain structures that can generate a droplet with a desired concentration even if volume variations occur during droplet splitting. Experimental results show the effectiveness of the proposed method compared to previous methods.

A digital microfluidic biochip (DMB) is an attractive platform for automating laboratory procedures in microbiology. To overcome the problem of cross-contamination due to fouling of the electrode surface in traditional DMBs, a contactless liquid-handling biochip technology, referred to as acoustofluidics, has recently been proposed. A major challenge in operating this platform is the need for a control signal of frequency 24 MHz and voltage range ±10/ ±20 V to activate the inter-digital-transducer (IDT) units in the biochip. A preliminary solution based on amplifiers, mechanical relays, and jump wires introduces signal loss (at least 6dB), signal coupling, and waveform distortion. In this paper, we present a new IDT-driver design that offers three major advantages: smaller form factor and lower cost, effective and high-quality signal generation and transmission, and fully-automated and flexible biochip control. Experimental demonstrations of droplet routing and a simple bioassay highlight the effectiveness of our hardware design.