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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Modeling FLEX Human Actions Using the EMRALD Dynamic Risk Assessment Tool

Most current efforts have modified and applied existing human reliability analysis (HRA) methods to treat human actions related to beyond-design-basis external events in which diverse and flexible coping strategies (FLEX) equipment would be deployed. However, many questions remain regarding the suitability of legacy HRA methods to address FLEX human actions, sparking the need for a new method of reasonably evaluating them. In this context, Idaho National Laboratory (INL) researched a relatively new approach to treating FLEX human actions via Event Modeling Risk Assessment Using Linked Diagrams (EMRALD) software. EMRALD was developed to support the increasing need for dynamic probabilistic risk assessment (PRA) models that can respond to evolving plant conditions during simulations. A couple benefits were identified when analyzing FLEX human actions through this software. In general, it is especially useful for evaluating a strategy’s feasibility, including FLEX human actions that require a relatively long time to perform. In this paper, we suggest how FLEX human actions can be modeled using the EMRALD software. Two different HRA modeling approaches using EMRALD are introduced: (1) procedure-based modeling and (2) PRA/HRA-based modeling. The former approach was introduced in the authors’ previous paper, whereas this paper mainly discusses how the latter approach works for an extended loss of AC power (ELAP) scenario with relevant procedures and PRA models. A hybrid method combining the two modeling approaches is introduced at the paper’s conclusion.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Water foraging with dynamic roots in E3SM; The role of roots in terrestrial ecosystem memory on intermediate timescales (Final Technical Report)

Terrestrial ecosystems can show sustained responses to stress events that may last for years after the initial perturbation. This phenomenon is referred to as legacy or memory and it emerges from a set of ecosystem processes that are poorly captured by Earth System and Land Surface Models. Consequently, these models struggle to predict the impact that extreme climate events have on surface energy, carbon and hydrological exchange once a stressor such as drought has relaxed or in response to repeated exposure to stress. In this project, we set out to test how the addition of dynamic root profiles in land surface models impact the capacity for Earth System Models, such as the Department of Energy’s E3SM, to capture realistic legacy effects. Observations have shown that vegetation shifts their root profiles during stress events to forage for water and these altered root profiles may take years to relax back to the initial state. We hypothesized that the alteration of the belowground root structures may be a source of terrestrial ecosystem legacy that is missing from models. To test this idea we undertook three core activities. (1) We developed a global-scale analysis of the impact of dynamic roots on ecosystem legacy building from a recently developed dynamic root module. (2) We developed new root dynamics in the DOE’s Energy Land Model (ELM) that allowed not only root profiles to shift their profile but also simultaneously alter carbon allocation to fine root pools. We then tested the impact of these new dynamics with intensive sensitivity analysis at four long-term AmeriFlux sites. (3) We undertook detailed isotopic analysis of tree rings from these AmeriFlux sites to assess ecophysiological and ecohydrological legacy to stress events that can be used to benchmark the sensitivity experiments with ELM. From these core activities, we report the following key findings. Firstly, on a global scale, the addition of dynamic roots led to chronically water-stressed ecosystems recovering faster to climate stress while wetter ecosystem showed enhanced legacy. This is because across ecosystems, stress events were almost universally associated with water shortages that led to the development of deeper root profiles. These deeper root profiles proved beneficial for recovery from drought stress. While the root dynamics did not universally improve the modeled representation of legacy it showed complex transient dynamics that emerge from the addition of dynamic roots. Secondly, the sensitivity analysis illustrated long term shifts in rooting depths away from the prescribed default profile suggesting that initializing of root profiles could benefit from spin-up simulations that converge on locally optimized root profiles. In addition, by enabling dynamic allocation some of the sites predicted unrealistically low allocation to roots (and high allocation to leaves). While these changes did not dramatically alter modeled gross primary productivity, they illustrated that without more sophisticated root processes in models, there is little penalty to dramatically disinvest in roots. Thirdly, the isotopic analysis of tree rings showed highly distinct legacy responses across species and sites. For example, T. canadensis showed reduced transpiration the year after stress events illustrated by sustained elevated $\delta^{18}$O. In contrast, A saccharum displayed elevated $\delta^{13}$C associated with reduced stomatal conductance in response to the previous years’ stress event. These geochemical signatures of legacy were present despite tree growth returning to normal the year after the stress. The results show the importance of species-level dynamics in legacy that are absent in modeling that assumes common traits within plant functional types. In summary, the work here established new avenues to explore root dynamics in models while illustrating how additional root processes are needed before dynamic carbon allocation can be implemented. Lastly, this project provided mentorship to a postdoctoral fellow, training for an early career scientist and multiple undergraduate students recruited from a minority serving institution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Informing the planning of rotating power outages in heat waves through data analytics of connected smart thermostats for residential buildings

Abstract With climate change, heat waves have become more frequent and intense. Rotating power outages happen when the power supply is unable to meet the cooling demand increase resulting from extreme high temperatures. Power outages during heat waves expose residents to high risks of overheating. In this study, we propose a novel data-driven inverse modelling approach to inform decision makers and grid operators on planning rotating power outages. We first infer the building thermal characteristics using the connected smart thermostat data, and used the estimated thermal dynamics to simulate the thermal resilience during a heat wave event. Our proposed method was tested for the California power outage in August 2020 by using the open source Ecobee Donate Your Data dataset. We found in California the power outage should not last more than two hours during heat waves to avoid overheating risks. Informing the residents in advance so they can prepare for it through pre-cooling is a simple but effective strategy to expand the acceptable power outage duration. In addition to assisting power outage planning, the proposed method can be used for other applications, such as to evaluate a building energy efficiency policy, to examine fuel poverty, and to estimate the load shifting potential of building stocks.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

Atmospheric and oceanic energy transport during North Atlantic freshening events: influences of moisture transport and hydrologic cycle feedbacks

Analogs of present-day rapid ice melt can be found in episodic discharges of icebergs that occurred during glacial periods called Heinrich events. This introduces excess meltwater into the North Atlantic and weakens the Atlantic thermohaline circulation (AMOC), triggering a hydrologic cycle–AMOC collapse feedback as the atmospheric energy transport compensates for reduced northward heat transport. Here we employ a novel series of 100-year North Atlantic “hosing” simulations to investigate atmospheric and oceanic energy transport response from freshwater forcing, focusing in particular on the role of atmospheric rivers (ARs) within atmospheric energy transport. Importantly, we use an “overwriting” methodology that allow us to attribute AMOC weakening to added North Atlantic meltwater and subsequent hydrologic cycle responses, respectively. In contrast to far-reaching response of transient eddies, our results show a substantial increase in moisture convergence from ARs that is geographically constrained to the North Atlantic midlatitudes. Such AR changes nevertheless comprise an important component of net precipitation changes over the Euro-Atlantic sector, with the amount being comparable to that from transient eddies over the subpolar Atlantic. Over the course of the century-long simulations, we demonstrate that hydrologic cycle responses to North Atlantic freshening and subsequent feedbacks, including those from ARs, account for approximately half of the simulated AMOC collapse. Furthermore, our work highlights the dynamics of atmospheric moisture transport response to North Atlantic freshening events and elucidates how intensifying moisture transport may accelerate AMOC collapse in the future.

Atmospheric Science↗
DOE OSTI2024

Data for: Time to anoxia: Observations and predictions of oxygen drawdown following coastal flood events

This dataset contains data and code associated with the paper Patel et al. "Time to anoxia: Observations and predictions of oxygen drawdown following coastal flood events".The coastal terrestrial-aquatic interface (TAI) is a highly dynamic system characterized by strong physical, chemical, and biological gradients. In particular, shifting soil redox conditions and consumption of terminal electron acceptors, due in part to dynamic hydrologic conditions, is a strong driver of carbon availability and transformations across TAIs. However, while redox dynamics are well described, our ability to quantitatively forecast rates of oxic to anoxic shifts in soils with different characteristics and inundation regimes is limited. We integrated field measurements, laboratory incubations, and model simulations to improve mechanistic understanding of oxygen consumption dynamics in coastal soils. Continuous in situ monitoring unexpectedly revealed that flooding caused temporary spikes in subsurface dissolved oxygen followed by rapid consumption in the wetlands. To further investigate these mechanisms in a controlled setting, we performed laboratory incubations using surface and subsurface soils from a TAI gradient (defined here as upland forest to transitional forest to wetland) in Western Lake Erie to measure oxygen consumption rates in TAI soils during flood events. In our experiments, wetland soils reached anoxia the fastest, in ∼ 9 h on average, whereas upland soils turned anoxic in ∼ 18 h. Subsurface upland soils did not turn anoxic even after two weeks of saturation in the lab, and their oxygen consumption patterns suggested carbon and/or nutrient limitation. These results are consistent with in-situ groundwater redox and oxygen measurements in the field, where wetland soils exhibited the highest rates of oxygen consumption along the TAI. Model simulations of oxygen consumption suggested that oxygen consumption had stronger abiotic controls in wetland soils but stronger biotic controls in upland soils, providing a useful framework for future incubation experiments. Microbial activity is a strong driver of oxygen consumption in TAI soils, although it is constrained by the availability of dissolved carbon in subsurface soils.This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv format, which can be accessed and processed using MS Excel or R. This archive can also be accessed on GitHub at https://github.com/COMPASS-DOE/cmps-time_to_anoxia (DOI: 10.5281/zenodo.10815374).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Analysis of Narrow Bipolar Events Using Mode Decomposition Methods

Multi-resolution analysis methods can reveal the underlying physical dynamics of nonstationary signals, such as those from lightning. In this paper we demonstrate the application of two multi-resolution analysis methods: Ensemble Empirical Mode Decomposition (EEMD) and Variational Mode Decomposition (VMD) in a comparative way in the analysis of electric field change waveforms from lightning. EEMD and VMD decompose signals into a set of Intrinsic Mode Functions (IMFs). The IMFs can be combined using distance and divergence metrics to obtain noise reduction or to obtain new waveforms that isolate the physical processes of interest while removing irrelevant components of the original signal. We apply the EEMD and VMD methods to the observations of three close Narrow Bipolar Events (NBEs) that were reported by Rison et al. The ΔE observations reveal the occurrence of complex oscillatory processes after the main NBE sferic. We show that both EEMD and VMD are able to isolate the oscillations from the main NBE, with VMD being more effective of the two methods since it requires the least user supervision. The oscillations are found to begin at the end of the NBEs' downward fast positive breakdown and appear to be produced by a half-wavelength standing wave within a weakly-conducting resonant ionization cavity left behind in the wake of the streamer-based NBE event. In conclusion, additional analysis shows that one of the NBEs was likely initiated by an energetic cosmic ray shower, and also corrects a misinterpretation in the literature that fast breakdown is an artifact of NBE-like events in interferometer observations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Highly Altered State of Proton Transport in Acid Pools in Charged Reverse Micelles

Transport mechanisms of solvated protons of 1 M HCl acid pools, confined within reverse micelles (RMs) containing the negatively charged surfactant sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) or the positively charged cetyltrimethylammonium bromide (CTABr), are analyzed with reactive force field simulations to interpret dynamical signatures from TeraHertz absorption and dielectric relaxation spectroscopy. We find that the forward proton hopping events for NaAOT are further suppressed compared to a nonionic RM, while the Grotthuss mechanism ceases altogether for CTABr. We attribute the sluggish proton dynamics for both charged RMs as due to headgroup and counterion charges that expel hydronium and chloride ions from the interface and into the bulk interior, thereby increasing the pH of the acid pools relative to the nonionic RM. For charged NaAOT and CTABr RMs, the localization of hydronium near a counterion or conjugate base reduces the Eigen and Zundel configurations that enable forward hopping. Thus, localized oscillatory hopping dominates, an effect that is most extreme for CTABr in which the proton residence time increases dramatically such that even oscillatory hopping is slow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Evaluating the Aftershock Duration of Induced Earthquakes

As the carbon sequestration community prepares to scale up the number and size of commercial operations, the need for tools and methods to assess and mitigate risks associated with these operations becomes increasingly important. One outstanding question is whether aftershocks of induced events decay quickly after injection operations cease or if aftershock activity persists for hundreds of years before returning to background levels more akin to tectonic events (Stein and Liu, 2009). Appropriate estimates of the aftershock duration impact several operational management decisions including mitigation strategies and post-injection monitoring for seismic activity. It is hypothesized that induced earthquake rates may diminish more quickly after injection is stopped, owing to higher stressing rates from injected fluids. Alternatively, it is plausible that only the first event in the sequence is induced by increased fluid overpressures, whereas subsequent events (e.g., aftershocks) respond to the stored tectonic stresses and static and dynamic stress changes due to the mainshock (Keranen et al., 2013). Further, if the aftershock duration can be linked to stressing rates due to injection, then it follows that operational strategies to reduce seismic hazard by reducing injection rates or volumes may be successful. However, if aftershocks of induced events are relieving stored tectonic stresses, then altering injection volumes may not alleviate ongoing seismic activity. Furthermore, knowledge of an aftershock duration could aid in the determination of an appropriate post-injection monitoring period for ongoing seismicity, which is a factor in overall operational costs. In this study, we model induced seismicity sequences in Oklahoma with a coupled Coulomb rate–state earthquake rate model (Dieterich, 1994; Kroll et al., 2017) to estimate aftershocks durations. Results for the current study indicate that elevated rates of aftershock activity following induced mainshocks return to background seismicity rates in less than five years, contrary to the tens to hundreds of years observed for tectonic aftershocks.

58 GEOSCIENCES↗
DOE OSTI2023

Inherent-state melting and the onset of glassy dynamics in two-dimensional supercooled liquids

Below the onset temperature T o , the equilibrium relaxation time of most glass-forming liquids exhibits glassy dynamics characterized by a super-Arrhenius temperature dependence. In this supercooled regime, the relaxation dynamics also proceeds through localized elastic excitations corresponding to hopping events between inherent states, i.e., potential-energy-minimizing configurations of the liquid. Despite its importance in distinguishing the supercooled regime from the high-temperature regime, the microscopic origin of T o is not yet known. Here, we construct a theory for the onset temperature in two dimensions and find that an inherent-state melting transition, described by the binding–unbinding transition of dipolar elastic excitations, delineates the supercooled regime from the high-temperature regime. The corresponding melting transition temperature is in good agreement with the onset temperature found in various two-dimensional (2D) atomistic models of glass formers and an experimental binary colloidal system confined to a water–air interface. Additionally, we find the predictions for the renormalized elastic moduli to agree with the experimentally observed values for the latter 2D colloidal system. We further discuss the predictions of our theory on the displacement and density correlations at supercooled conditions, which are consistent with observations of the Mermin–Wagner fluctuations in experiments and molecular simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Granger causal inference for climate change attribution

Abstract Climate change detection and attribution (D&A) is concerned with determining the extent to which anthropogenic activities have influenced specific aspects of the global climate system. D&A fits within the broader field of causal inference, the collection of statistical methods that identify cause and effect relationships. There are a wide variety of methods for making attribution statements, each of which require different types of input data and focus on different types of weather and climate events and each of which are conditional to varying extents. Some methods are based on Pearl causality (direct experimental interference) while others leverage Granger (predictive) causality, and the causal framing provides important context for how the resulting attribution conclusion should be interpreted. However, while Granger-causal attribution analyses have become more common, there is no clear statement of their strengths and weaknesses relative to Pearl-causal attribution and no clear consensus on where and when Granger-causal perspectives are appropriate. In this prospective paper, we provide a formal definition for Granger-based approaches to trend and event attribution and a clear comparison with more traditional methods for assessing the human influence on extreme weather and climate events. Broadly speaking, Granger-causal attribution statements can be constructed quickly from observations and do not require computationally-intesive dynamical experiments. These analyses also enable rapid attribution, which is useful in the aftermath of a severe weather event, and provide multiple lines of evidence for anthropogenic climate change when paired with Pearl-causal attribution. Confidence in attribution statements is increased when different methodologies arrive at similar conclusions. Moving forward, we encourage the D&A community to embrace hybrid approaches to climate change attribution that leverage the strengths of both Granger and Pearl causality.

Risser, Mark D. (ORCID:0000000319561783)↗
DOE OSTI2025

Dynamic probabilistic risk assessment and game theory for cyber security risk analysis in nuclear power plants

Nuclear Power Plants and energy systems have become more prone to cyber-attacks with their digitalization and the increased use of smart equipment. Hence, it is important to quantify the risk associated with cyber-attacks in such systems. Dynamic Probabilistic Risk Assessment which involves studying the evolution of a system due to random events and operator and attacker actions during a cyber-attack by employing a physics-based model of the system is a suitable framework to quantify cybersecurity risk in nuclear power plants. In addition to the plant dynamics, it is also important to model the strategies of the attackers and plant operators for an effective cybersecurity risk assessment. Game theory provides a set of necessary tools to model such strategic interactions. In this research, a framework that integrates dynamic probabilistic risk assessment with game theory for cybersecurity risk analysis in nuclear power plants is presented. The mathematical formulation is derived based on the theory of continuous event trees. We propose a game theory based action model, that utilizes physics-based rewards to define the strategies of attackers and operators at every decision epoch. As a case study, the risk associated with cyber-attacks on the digital components in the secondary side of a pressurized water reactor is studied using a reduced order model. A set of attacker actions and a set of operator actions are defined for the system. The operator and attacker interactions were modelled using simultaneous game, their action policies were computed using the concept of mixed strategy Nash equilibrium and the evolution of the system was studied.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Remote Sensing Detection of Growing Season Freeze-Induced Defoliation of Montane Quaking Aspen (Populus tremuloides) in Southern Utah, USA

Growing season freeze events pose a threat to quaking aspen (Populus tremuloides Michx.), leading to canopy defoliation, reduced vigor, and increased mortality, especially for declining montane populations western North America. Detecting the spatial distribution and progression of this damage is challenging due to limited in situ observations in this region. This study represents the first attempt to comprehensively resolve the spatial extent of freeze-induced aspen canopy damage in southern Utah using multispectral remote sensing data. We developed an approach to detect the spatial and temporal dynamics of freeze-damaged aspen stands, focusing on a freeze event from 8–9 June 2020 in southern Utah. By integrating medium- (~250 to 500 m) and high-resolution (~10 m) satellite data, we employed the Normalized Difference Vegetation Index (NDVI) to compare post-freeze conditions with historical norms and pre-freeze conditions. Our analysis revealed NDVI reductions of 0.10 to 0.40 from pre-freeze values and a second flush recovery. We introduced a pixel-based method to evaluate freeze vulnerability, establishing a strong correlation (R values 0.78 to 0.82) between the onset of the first flush (NDVI > 0.50) and the accumulation of 100 growing degree days (GDD). These methods support the potential for retrospective assessments, proactive forest monitoring, and forecasting future risks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Regional Inertia Estimation Using Actual Event Measurements: Florida Case

As inverter-based resources’ integration in power grids increases, their uneven distribution across the electrical network leads to the formation of local regions that are weakly coupled to the larger interconnection. This signifies the necessity of regional frequency dynamics investigation and analyzing various inertia metrics. This paper presents a practical methodology for estimating regional rate-of-change of frequency (RoCoF) using actual event recordings, which is then used to evaluate regional inertia. Florida (FL) is selected as the region of interest due to its distinct regional frequency dynamics and the rising levels of solar generation. We identify and analyze confirmed events from 2017 to 2024 that occurred in FL. The results indicate that FL contributes about 14% to the total inertia of the US Eastern Interconnection, which approximately matches its share of generation capacity. Results also highlight seasonal fluctuations in energy generation, which play a significant role in influencing inertia and thus the RoCoF levels. This emphasizes the importance of estimating regional inertia to enhance grid operations for a future that focuses on distributed generation.

Dulal, Saurav [University of Tennessee, Knoxville ↗
DOE OSTI2022

Respiration regimes in rivers: Partitioning source–specific respiration from metabolism time series

Respiration in streams is controlled by the timing, magnitude, and quality of organic matter (OM) inputs from internal primary production and external fluxes. Here, we estimated the contribution of different OM sources to seasonal, annual, and event-driven characteristics of whole-stream ecosystem respiration (ER) using an inverse modeling framework that accounts for possible time-lags between OM inputs and respiration. We modeled site-specific, dynamic OM stocks contributing to ER: autochthonous OM from gross primary production (GPP); allochthonous OM delivered during flow events; and seasonal pulses of leaf litter. OM stored in the sediment and dissolved organic matter (DOM) transported during baseflow were modeled as a stable stock contributing to baseline respiration. We applied this modeling framework to five streams with different catchment size, climate, and canopy cover, where multi-year time series of ER and environmental variables were available. Overall, the model explained between 53% and 74% of observed ER dynamics. Respiration of autochthonous OM tracked seasonal peaks in GPP in spring or summer. Increases in ER were often associated with high-flow events. Respiration associated with litter inputs was larger in smaller streams. Time lags between leaf inputs and respiration were longer than for other OM sources, likely due to lower biological reactivity. Model estimates of source-specific ER and OM stocks compared well with existing measures of OM stocks, inputs, and respiration or decomposition. Our modeling approach has the potential to expand the scale of comparative analyses of OM dynamics within and among freshwater ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Using Dissipative Particle Dynamics to Model Effects of Chemical Reactions Occurring within Hydrogels

Computational models that reveal the structural response of polymer gels to changing, dissolved reactive chemical species would provide useful information about dynamically evolving environments. However, it remains challenging to devise one computational approach that can capture all the interconnected chemical events and responsive structural changes involved in this multi-stage, multi-component process. Here, we augment the dissipative particle dynamics (DPD) method to simulate the reaction of a gel with diffusing, dissolved chemicals to form kinetically stable complexes, which in turn cause concentration-dependent deformation of the gel. Using this model, we also examine how the addition of new chemical stimuli and subsequent reactions cause the gel to exhibit additional concentration-dependent structural changes. Through these DPD simulations, we show that the gel forms multiple latent states (not just the “on/off”) that indicate changes in the chemical composition of the fluidic environment. Hence, the gel can actuate a range of motion within the system, not just movements corresponding to the equilibrated swollen or collapsed states. Moreover, the system can be used as a sensor, since the structure of the layer effectively indicates the presence of chemical stimuli.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Modeling the Solvation and Acidity of Carboxylic Acids Using an Ab Initio Deep Neural Network Potential

Formic and acetic acid constitute the simplest of carboxylic acids, yet they exhibit fascinating chemistry in the condensed phase such as proton transfer and dimerization. The go-to method of choice for modeling these rare events have been accurate but expensive ab-initio molecular dynamics simulations. Here, we present a deep neural network potential trained using accurate ab-initio data that can be used in tandem with enhanced-sampling methods to perform an efficient exploration of the free-energy surface of aqueous solutions of weak carboxylic acids. In particular, we show that our model captures proton dissociation and provides a good estimate of the pK a , as well as the dimerization of formic and acetic acid. This provides a suitable starting point for applications in different research areas where computational efficiency coupled with the accuracy of ab-initio methods is required.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Marine phytoplankton downregulate core photosynthesis and carbon storage genes upon rapid mixed layer shallowing

Marine phytoplankton are a diverse group of photoautotrophic organisms and key mediators in the global carbon cycle. Phytoplankton physiology and biomass accumulation are closely tied to mixed layer depth, but the intracellular metabolic pathways activated in response to changes in mixed layer depth remain less explored. Here, metatranscriptomics was used to characterize the phytoplankton community response to a mixed layer shallowing (from 233 to 5 m) over the course of two days during the late spring in the Northwest Atlantic. Most phytoplankton genera downregulated core photosynthesis, carbon storage, and carbon fixation genes as the system transitioned from a deep to a shallow mixed layer and shifted towards catabolism of stored carbon supportive of rapid cell growth. In contrast, phytoplankton genera exhibited divergent transcriptional patterns for photosystem light harvesting complex genes during this transition. Active virus infection, taken as the ratio of virus to host transcripts, increased in the Bacillariophyta (diatom) phylum and decreased in the Chlorophyta (green algae) phylum upon mixed layer shallowing. A conceptual model is proposed to provide ecophysiological context for our findings, in which integrated light limitation and lower division rates during transient deep mixing are hypothesized to disrupt resource-driven, oscillating transcript levels related to photosynthesis, carbon fixation, and carbon storage. Our findings highlight shared and unique transcriptional response strategies within phytoplankton communities acclimating to the dynamic light environment associated with transient deep mixing and shallowing events during the annual North Atlantic bloom.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection

The substrate for ribosomes actively engaged in protein synthesis is a ternary complex of elongation factor Tu (EF-Tu), aminoacyl-tRNA (aa-tRNA), and GTP. EF-Tu plays a critical role in mRNA decoding by increasing the rate and fidelity of aa-tRNA selection at each mRNA codon. Here, using three-color single-molecule fluorescence resonance energy transfer imaging and molecular dynamics simulations, we examine the timing and role of conformational events that mediate the release of aa-tRNA from EF-Tu and EF-Tu from the ribosome after GTP hydrolysis. Our investigations reveal that conformational changes in EF-Tu coordinate the rate-limiting passage of aa-tRNA through the accommodation corridor en route to the peptidyl transferase center of the large ribosomal subunit. Experiments using distinct inhibitors of the accommodation process further show that aa-tRNA must at least partially transit the accommodation corridor for EF-Tu∙GDP to release. aa-tRNAs failing to undergo peptide bond formation at the end of accommodation corridor passage after EF-Tu release can be reengaged by EF-Tu∙GTP from solution, coupled to GTP hydrolysis. These observations suggest that additional rounds of ternary complex formation can occur on the ribosome during proofreading, particularly when peptide bond formation is slow, which may serve to increase both the rate and fidelity of protein synthesis at the expense of GTP hydrolysis.

59 BASIC BIOLOGICAL SCIENCES↗