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1. Engineering Genetic Circuits: Advancements in Genetic Design Automation Tools and Standards for Synthetic Biology

   https://doi.org/10.1016/j.mib.2022.102155  

   Buecherl, Lukas; Myers, Chris J. (May 2022, Current opinion in microbiology)

   Takano, Eriko; Breitling, Rainer (Ed.)

   Synthetic biology is a field at the intersection of biology and engineering. Inspired by engineering principles, researchers use defined parts to build functionally defined biological circuits. Genetic design automation allows scientists to design, model, and analyze their genetic circuits in silico before building them in the lab, saving time and resources in the process. Establishing synthetic biology’s future is dependent on genetic design automation, since the computational approach opens the field to a broad, interdisciplinary community. However, challenges with part libraries, standards, and software tools are currently stalling progress in the field. This review first covers re- cent advancements in genetic design automation, followed by an assessment of the challenges ahead, and a proposed automated genetic design workflow for the future. 

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2. Programmed Internal Reconfigurations in a 3D‐Printed Mechanical Metamaterial Enable Fluidic Control for a Vertically Stacked Valve Array

   https://doi.org/10.1002/adfm.202315419  

   Supakar, Tinku; Space, David; Mejia, Sophy; Tan, Rou_Yu; Alston, Jeffrey_R; Josephs, Eric_A (April 2024, Advanced Functional Materials)

   Abstract Microfluidic valves play a key role within microfluidic systems by regulating fluid flow through distinct microchannels, enabling many advanced applications in medical diagnostics, lab‐on‐chips, and laboratory automation. While microfluidic systems are often limited to planar structures, 3D printing enables new capabilities to generate complex designs for fluidic circuits with higher densities and integrated components. However, the control of fluids within 3D structures presents several difficulties, making it challenging to scale effectively and many fluidic devices are still often restricted to quasi‐planar structures. Incorporating mechanical metamaterials that exhibit spatially adjustable mechanical properties into microfluidic systems provides an opportunity to address these challenges. Here, systematic computational and experimental characterization of a modified re‐entrant honeycomb structure are performed to generate a modular metamaterial for an active device that allows us to directly regulate flow through integrated, multiplexed fluidic channels “one‐at‐a‐time,” in a manner that is highly scalable. A design algorithm is presented, so that this architecture can be extended to arbitrary geometries, and it is expected that by incorporation of mechanical metamaterial designs into 3D printed fluidic systems, which themselves are readily expandable to any complex geometries, will enable new biotechnological and biomedical applications of 3D printed devices. 

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3. A Generalized Residue Number System Design Approach for Ultralow-Power Arithmetic Circuits Based on Deterministic Bit-Streams

   https://doi.org/10.1109/TCAD.2023.3250603  

   Givaki, Kamyar; Khonsari, Ahmad; Gholamrezaei, M H; Gorgin, Saeid; Najafi, M Hassan (March 2023, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems)

   The peak power consumption has become an important concern in the hardware design process of some of today’s applications, such as energy harvesting (EH) and bio-implantable (BI) electronic devices. The limited peak harvested power in EH devices and heating concerns in BI devices are the main reasons for power control’s importance in these devices. This article proposes a generalized design approach for ultralow-power arithmetic circuits. The proposed circuits are based on residue number system (RNS) combined with deterministic bit-streams. The resulting circuits can be used in systems with a restricted power budget. We suggest several approaches to design generic hardware-efficient adders, multipliers, multiply-accumulate (MAC) unit, forward converters (FCs), and reverse converters (RCs). Using the proposed approach, designing these components for any moduli of the RNS can be performed through simple bit-width adjustments in the circuits. The synthesis results show that the proposed adder achieves, on average, 69% and 2% lower area compared to the bit-serial and a state-of-the-art RNS adder, respectively. Furthermore, the proposed multiplier outperforms the bit-serial, interleaved, and a state-of-the-art design for multiplying RNS numbers by, on average, 57%, 60%, and 77% in terms of power consumption, respectively. The efficiency of our approach is shown via two essential applications, digital signal processing, and machine learning. We implement an FFT engine using the proposed method. Compared to prior RNS implementations, our design achieves 47% lower power consumption. We also implement a CNN accelerator’s processing element (PE) with the proposed computation elements. Our design provides considerable speedup and lower power consumption compared to a state-of-the-art ultralower-power design. 

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4. Does logic locking work with EDA Tools

   Han, Zhaokun; Yasin, Muhammad; Rajendran, Jeyavijayan (April 2021, USENIX Security Conference 2021)

   Logic locking is a promising solution against emerging hardware security threats, which entails protecting a Boolean circuit using a “keying” mechanism. The latest and hitherto unbroken logic-locking techniques are based on the “corrupt-and-correct (CAC)” principle, offering provable security against input-output query attacks. However, it remains unclear whether these techniques are susceptible to structural attacks. This paper exploits the properties of integrated circuit (IC) design tools, also termed electronic design automation (EDA) tools, to undermine the security of the CAC techniques. Our proposed attack can break all the CAC techniques, including the unbroken CACrem technique that 40+ hackers taking part in a competition for more than three months could not break. Our attack can break circuits processed with any EDA tools, which is alarming because, until now, none of the EDA tools can render a secure locking solution: logic locking cannot make use of the existing EDA tools. We also provide a security property to ensure resilience against structural attacks. The commonly-used circuits can satisfy this property but only in a few cases where they cannot even defeat brute-force; thus, questions arise on the use of these circuits as benchmarks to evaluate logic locking and other security techniques. 

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5. Determination of the Empirical Electrokinetic Equilibrium Condition of Microorganisms in Microfluidic Devices

   https://doi.org/10.3390/bios10100148  

   Coll De Peña, Adriana; Hill, Nicole; Lapizco-Encinas, Blanca H. (October 2020, Biosensors)

   null (Ed.)

   The increased concern regarding emerging pathogens and antibiotic resistance has drawn interest in the development of rapid and robust microfluidic techniques to analyze microorganisms. The novel parameter known as the electrokinetic equilibrium condition (EEEC) was presented in recent studies, providing an approach to analyze microparticles in microchannels employing unique electrokinetic (EK) signatures. While the EEEC shows great promise, current estimation approaches can be time-consuming or heavily user-dependent for accurate values. The present contribution aims to analyze existing approaches for estimating this parameter and modify the process into an accurate yet simple technique for estimating the EK behavior of microorganisms in insulator-based microfluidic devices. The technique presented here yields the parameter called the empirical electrokinetic equilibrium condition (eEEEC) which works well as a value for initial approximations of trapping conditions in insulator-based EK (iEK) microfluidic systems. A total of six types of microorganisms were analyzed in this study (three bacteria and three bacteriophages). The proposed approach estimated eEEEC values employing images of trapped microorganisms, yielding high reproducibility (SD 5.0–8.8%). Furthermore, stable trapping voltages (sTVs) were estimated from eEEEC values for distinct channel designs to test that this parameter is system-independent and good agreement was obtained when comparing estimated sTVs vs. experimental values (SD 0.3–19.6%). The encouraging results from this work were used to generate an EK library of data, available on our laboratory website. The data in this library can be used to design tailored iEK microfluidic devices for the analysis of microorganisms. 

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