More Like this

1. Stochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINA

   https://doi.org/10.1021/acssynbio.1c00159  

   Buecherl, Lukas; Roberts, Riley; Fontanarrosa, Pedro; Thomas, Payton J.; Mante, Jeanet; Zhang, Zhen; Myers, Chris J. (October 2021, ACS synthetic biology)

   In synthetic biology, combinational circuits are used to program cells for various new applications like biosensors, drug delivery systems, and biofuels. Similar to asynchronous electronic circuits, some combinational genetic circuits may show unwanted switching variations (glitches) caused by multiple input changes. Depending on the biological circuit, glitches can cause irreversible effects and jeopardize the circuit’s functionality. This paper presents a stochastic analysis to predict glitch propensities for three implementations of a genetic circuit with known glitching behavior. The analysis uses STochastic Approximate Model-checker for INfinite-state Analysis (STAMINA), a tool for stochastic verification. The STAMINA results were validated by comparison to stochastic simulation in iBioSim resulting in further improvements of STAMINA. This paper demonstrates that stochastic verification can be utilized by genetic designers to evaluate design choices and input restrictions to achieve a desired reliability of operation. 

   more » « less
2. Optimized Entanglement Purification

   https://doi.org/10.22331/q-2019-02-18-123  

   Krastanov, Stefan; Albert, Victor V.; Jiang, Liang (February 2019, Quantum)

   We investigate novel protocols for entanglement purification of qubit Bell pairs. Employing genetic algorithms for the design of the purification circuit, we obtain shorter circuits achieving higher success rates and better final fidelities than what is currently available in the literature. We provide a software tool for analytical and numerical study of the generated purification circuits, under customizable error models. These new purification protocols pave the way to practical implementations of modular quantum computers and quantum repeaters. Our approach is particularly attentive to the effects of finite resources and imperfect local operations - phenomena neglected in the usual asymptotic approach to the problem. The choice of the building blocks permitted in the construction of the circuits is based on a thorough enumeration of the local Clifford operations that act as permutations on the basis of Bell states. 

   more » « less
3. 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. 

   more » « less
4. STAMINA in C++: Modernizing an Infinite-State Probabilistic Model Checker

   https://doi.org/10.1007/978-3-031-43835-6_7  

   Jeppson, Josh; Volk, Matthias; Israelsen, Bryant; Roberts, Riley; Williams, Andrew; Buecherl, Lukas; Myers, Chris J; Zheng, Hao; Winstead, Chris; Zhang, Zhen (September 2023, Lecture notes in computer science)

   Jansen, N; Tribastone, M (Ed.)

   Improving the scalability of probabilistic model checking (PMC) tools is crucial to the verification of real-world system designs. The STAMINA infinite-state PMC tool achieves scalability by iteratively constructing a partial state space for an unbounded continuous-time Markov chain model, where a majority of the probability mass resides. It then performs time-bounded transient PMC. It can efficiently produce an accurate probability bound to the property under verification. We present a new software architecture design and the C++ implementation of the STAMINA 2.0 algorithm, integrated with the STORM model checker. This open-source STAMINA implementation offers a high degree of modularity and provides significant optimizations to the STAMINA 2.0 algorithm. Performance improvements are demonstrated on multiple challenging benchmark examples, including hazard analysis of infinite-state combinational genetic circuits, over the previous STAMINA implementation. Additionally, its design allows for future customizations and optimizations to the STAMINA algorithm. 

   more » « less
5. The Soft Compiler: A Web-Based Tool for the Design of Modular Pneumatic Circuits for Soft Robots

   https://doi.org/10.1109/LRA.2022.3159858  

   Kendre, Savita V.; Whiteside, Lauryn; Fan, Tian Y.; Tracz, Jovanna A.; Teran, Gus T.; Underwood, Thomas C.; Sayed, Mohammed E.; Jiang, Haihui J.; Stokes, Adam A.; Preston, Daniel J.; et al (July 2022, IEEE Robotics and Automation Letters)

   Developing soft circuits from individual soft logic gates poses a unique challenge: with increasing numbers of logic gates, the design and implementation of circuits lead to inefficiencies due to mathematically unoptimized circuits and wiring mistakes during assembly. It is therefore practically important to introduce design tools that support the development of soft circuits. We developed a web-based graphical user interface, the Soft Compiler , that accepts a user-defined robot behavior as a truth table to generate a mathematically optimized circuit diagram that guides the assembly of a soft fluidic circuit. We describe the design and experimental verification of three soft circuits of increasing complexity, using the Soft Compiler as a design tool and a novel pneumatic glove as an input interface. In one example, we reduce the size of a soft circuit from the original 11 logic gates to 4 logic gates while maintaining circuit functionality. The Soft Compiler is a web-based design tool for fluidic, soft circuits and published under an open-source MIT License. 

   more » « less