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1. ARCH-COMP20 Repeatability Evaluation Report

   https://doi.org/10.29007/8dp4  

   Johnson, Taylor T (September 2020, EPiC Series in Computing)

   This report presents the results of the repeatability evaluation for the 4th International Competition on Verifying Continuous and Hybrid Systems (ARCH-COMP’20). The competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020, affiliated with the IFAC World Congress. In its fourth edition, twenty-eight tools submitted artifacts through a Git repository for the repeatability evaluation, applied to solve benchmark problems for seven competition categories. The majority of participants adhered to the requirements for this year’s repeatability evaluation, namely to submit scripts to automatically install and execute tools in containerized virtual environments (specifically Dockerfiles to execute within Docker), and several categories used performance evaluation information from a common execution platform. The repeatability results represent a snapshot of the current landscape of tools and the types of benchmarks for which they are particularly suited and for which others may repeat their analyses. Due to the diversity of problems in verification of continuous and hybrid systems, as well as basing on standard practice in repeatability evaluations, we evaluate the tools with pass and/or failing being repeatable. 

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2. Using Electromagnetic Transient Program (EMTP) for accurate prediction of faults location

   https://doi.org/10.1109/naps50074.2021.9449751  

   Carr, Christopher; Lavrova, Olga; Ranade, Satish (April 2021, 2020 52nd North American Power Symposium (NAPS))

   null (Ed.)

   Electrical power systems are sophisticated networked grids, which need to function with high reliability to provide electricity to customers. With high number of interconnected busses and devices in both transmission and distribution networks, electrical power systems need powerful programs to perform high speed calculations. This paper describes the Electromagnetic Transient Program - Alternative Transient Program (EMTP-ATP) and its usage in modeling of faults behavior in complex electric power systems. The results from EMTP-ATP modeling were compared to models in PSCAD to validate developed models. EMTP-ATP is further used in this paper to show steps in designing a system with a Single-Line-Ground fault (SLG) to analyze high frequency composition of SLG faults. 

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3. SAR11 bacteria have a high affinity and multifunctional glycine betaine transporter

   https://doi.org/doi:10.1111/1462-2920.14649  

   Noell, Stephen; Giovannoni, Stephen (May 2019, Environmental microbiology)

   Marine bacterioplankton face stiff competition for limited nutrient resources. SAR11, a ubiquitous clade of very small and highly abundant Alphaproteobacteria, are known to devote much of their energy to synthesizing ATP-binding cassette periplasmic proteins that bind substrates. We hypothesized that their small size and relatively large periplasmic space might enable them to outcompete other bacterioplankton for nutrients. Using uptake experiments with 14C-glycine betaine, we discovered that two strains of SAR11, Candidatus Pelagibacter sp. HTCC7211 and Cand. P. ubique HTCC1062, have extraordinarily high affinity for glycine betaine (GBT), with half-saturation (Ks) values around 1 nM and specific affinity values between 8 and 14 L mg cell−1 h−1. Competitive inhibition studies indicated that the GBT transporters in these strains are multifunctional, transporting multiple substrates in addition to GBT. Both strains could use most of the transported compounds for metabolism and ATP production. Our findings indicate that Pelagibacter cells are primarily responsible for the high affinity and multifunctional GBT uptake systems observed in seawater. Maximization of whole-cell affinities may enable these organisms to compete effectively for nutrients during periods when the gross transport capacity of the heterotrophic plankton community exceeds the supply, depressing ambient concentrations. 

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4. Transforming an ATP-dependent enzyme into a dissipative, self-assembling system

   https://doi.org/10.1038/s41589-024-01811-1  

   Li, Yiying; Zhu, Jie; Zhang, Zhiyin; Wei, Jiapeng; Wang, Fengbin; Meisl, Georg; Knowles, Tuomas_P J; Egelman, Edward H; Tezcan, F Akif (January 2025, Nature Chemical Biology)

   Nucleoside triphosphate (NTP)-dependent protein assemblies such as microtubules and actin filaments have inspired the development of diverse chemically fueled molecular machines and active materials but their functional sophistication has yet to be matched by design. Given this challenge, we asked whether it is possible to transform a natural adenosine 5′-triphosphate (ATP)-dependent enzyme into a dissipative self-assembling system, thereby altering the structural and functional mode in which chemical energy is used. Here we report that FtsH (filamentous temperature-sensitive protease H), a hexameric ATPase involved in membrane protein degradation, can be readily engineered to form one-dimensional helical nanotubes. FtsH nanotubes require constant energy input to maintain their integrity and degrade over time with the concomitant hydrolysis of ATP, analogous to natural NTP-dependent cytoskeletal assemblies. Yet, in contrast to natural dissipative systems, ATP hydrolysis is catalyzed by free FtsH protomers and FtsH nanotubes serve to conserve ATP, leading to transient assemblies whose lifetimes can be tuned from days to minutes through the inclusion of external ATPases in solution. 

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5. System Description : JGXYZ An ATP System for Gap and Glut Logics

   https://doi.org/10.1007/978-3-030-29436-6_31  

   Sutcliffe, G.; Pelletier, F.J. (July 2019, Lecture notes in computer science)

   This paper describes an ATP system, named JGXYZ, for some gap and glut logics. JGXYZ is based on an equi-provable translation to FOL, followed by use of an existing ATP system for FOL. A key feature of JGXYZ is that the translation to FOL is data-driven, in the sense that it requires only the addition of a new logic’s truth tables for the unary and binary connectives in order to produce an ATP system for the logic. Experimental results from JGXYZ illustrate the dierences between the logics and translated problems, both technically and in terms of a quasi-real-world use case. 

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