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1. Optical coherence between atomic species at the second scale: improved clock comparisons via differential spectroscopy

   https://doi.org/10.48550/arXiv.2109.09540  

   Kim, M.E.; McGrew, W.F.; Nardelli, N.V.; Clements, E.R.; Hassan, Y.S.; Zhang, X.; Valencia, J.L.; Leopardi, H.; Hume, D.B.; Fortier, T.M.; et al (April 2022, ArXivorg)

   Comparisons of high-accuracy optical atomic clocks \cite{Ludlow2015} are essential for precision tests of fundamental physics \cite{Safronova2018}, relativistic geodesy \cite{McGrew2018, Grotti2018, Delva2019}, and the anticipated redefinition of the SI second \cite{Riehle2018}. The scientific reach of these applications is restricted by the statistical precision of interspecies comparison measurements. The instability of individual clocks is limited by the finite coherence time of the optical local oscillator (OLO), which bounds the maximum atomic interrogation time. In this letter, we experimentally demonstrate differential spectroscopy \cite{Hume2016}, a comparison protocol that enables interrogating beyond the OLO coherence time. By phase-coherently linking a zero-dead-time (ZDT) \cite{Schioppo2017} Yb optical lattice clock with an Al+ single-ion clock via an optical frequency comb and performing synchronised Ramsey spectroscopy, we show an improvement in comparison instability relative to our previous result \cite{network2020frequency} of nearly an order of magnitude. To our knowledge, this result represents the most stable interspecies clock comparison to date. 

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2. Convergent latitudinal erosion of circadian systems in a rapidly diversifying order of fishes

   https://doi.org/10.1101/2025.05.28.656707  

   Wright, Daniel B; Zhang, Yanfan; Daane, Jacob M (May 2025, bioRxiv)

   Abstract Biological clocks enable organisms to anticipate cyclical environmental changes. Some habitats, such as those at high latitudes or deep sea, experience seasonally diminished or absent diel cues upon which species entrain their circadian rhythms. Fishes of the order Perciformes have rapidly diversified and adapted to these arrhythmic ecosystems, raising the possibility that evolutionary modifications to their circadian biology contributes to their success as one of the most species-rich orders of vertebrates. Here, we used a comparative genomic approach to investigate patterns of biological clock gene loss and circadian rhythms across 33 perciform and six outgroup species. We found both widespread and lineage-specific loss and relaxed selection in core clock genes, particularly in the convergently evolving polar and deep-sea Notothenioidei and Cottioidei suborders. This trend of circadian gene loss was significantly correlated with latitude, with higher-latitude species showing greater loss. Whether these losses and relaxed selection lead to changes in circadian rhythms is unknown for most perciforms. To address this, we performed metabolic phenotyping on three notothenioid species and found no circadian metabolic oscillations during the late austral fall, including in the sub-AntarcticEleginops maclovinus, sister to the Antarctic adaptive radiation. We propose that diminished reliance on endogenous biological clocks may be an adaptive feature that facilitates the survival and diversification of perciform fishes in polar and arrhythmic environments. 

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3. Power Clocks: Dynamic Multi-Clock Management for Embedded Systems

   Holly Chiang, Hudson Ayers (February 2021, 6th Annual International Conference on Distributed Computing in Sensor Systems (DCOSS 2020))

   null (Ed.)

   This paper presents Power Clocks, a kernel-based dy- namic clock management system that reduces active en- ergy use in embedded microcontrollers by changing the clock based on ongoing computation and I/O requests. In Power Clocks, kernel hardware drivers asynchronously re- quest clocks, providing a set of constraints (e.g., maximum speed), which the kernel uses to dynamically choose the most efficient clock. To select a clock, Power Clocks makes use of the observation that though slower clocks use less power and are suited for fixed time I/O operations, faster clocks use less energy per clock tick, making them opti- mal for pure computation. Using Power Clocks, a networked sensing application consumes 27% less energy than the best static clock, and within 3% of an optimal hand-tuned dy- namic clock strategy. Power Clocks provides similar energy savings even when there are multiple applications. 

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4. The redox rhythm gates immune-induced cell death distinctly from the genetic clock

   https://doi.org/10.1073/pnas.2519251122  

   Karapetyan, Sargis; Mwimba, Musoki; Chen, Tianyuan; Yao, Zhujun; Dong, Xinnian (September 2025, Proceedings of the National Academy of Sciences)

   Organisms use circadian clocks to synchronize physiological processes to anticipate the Earth’s day-night cycles and regulate responses to environmental signals to gain competitive advantage. While divergent genetic clocks have been studied extensively in bacteria, fungi, plants, and animals, an ancient conserved circadian redox rhythm has been recently reported. However, its biological function and physiological outputs remain elusive. Here, we uncovered the coexistence of redox and genetic rhythms with distinct period lengths and transcriptional targets through concurrent metabolic and transcriptional time-course measurements in anArabidopsislong-period clock mutant. Analysis of the target genes indicated regulation of the immune-induced programmed cell death (PCD) by the redox rhythm. Moreover, this time-of-day-sensitive PCD was eliminated by redox perturbations and by blocking the signaling pathway of the plant defense hormones jasmonic acid/ethylene, while remaining intact in genetic clock-defective backgrounds. This study shows that compared to robust genetic clocks, the more sensitive circadian redox rhythm serves as a signaling hub in regulating incidental energy-intensive processes, such as immune-induced PCD involving reprogramming of chloroplast and mitochondria activities, to provide organisms a flexible strategy to mitigate metabolic overload during stress responses. 

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5. Discovering regulators in post transcriptional control of the biological clock of Neurospora crassa using Variable Topology Ensemble Methods on GPUs

   https://doi.org/10.1109/ACCESS.2018.2871876  

   Al-Omari, A.; Griffith, J.; Caranica, C.; Taha, T.; Schuttler, H.-B.; Arnold, J. (October 2018, IEEE access)

   In previous work we reconstructed the entire transcriptional network for all 2,418 clock-associated genes in the model filamentous fungus, N. crassa. Several authors have suggested that there is extensive post-transcriptional control in the genome-wide clock network (IEEE 3: 27, 2015). Here we have successfully reconstructed the entire clock network in N. crassa with a Variable Topology Ensemble Method (VTENS), assigning each clock-associated gene to the regulation of one or more of 5 transcription factors as well as to 6 RNA operons. The resulting network provides a unifying framework to explore the clock’s linkage to metabolism through post-transcriptional regulation, in which ~850 genes are predicted to fall under the regulatory control of an RNA operon. A unique feature of all of the RNA operons inferred is their functional connection to genes connected to the ribosome. We have been successful in distinguishing several hypotheses about regulatory topologies of the clock network through protein profiling of the regulators. 

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