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LLNL SFA OBER FY23 Program Management and Performance Report: BioGeoChemistry at Interfaces

The focus of the BioGeoChemistry at Interfaces SFA has been to identify and quantify the biogeochemical processes and the underlying mechanisms that control actinide mobility in an effort to reliably predict and control the cycling and migration of actinides in the environment. The research approach has included: (1) Field Studies that capture actinide behavior on the timescale of decades (Research Thrust 1), and (2) Fundamental Laboratory Studies that isolate specific biogeochemical processes observed in the field (Research Thrust 2). These Research Thrusts are underpinned by the unique capabilities and staff expertise at Lawrence Livermore National Laboratory, allowing the BioGeoChemistry at Interfaces SFA to advance our understanding of actinide migration behavior in the environment, and serve as a resource for environmental radiochemistry research internationally (Figure 1). In FY23, our SFA research focused on transient redox gradients across stratified waters, sediment-water interfaces, and mineral-water interfaces to address processes controlling cycling of redox-sensitive metals. Nevertheless, Research Thrusts 1 and 2 are guided by the following broad central hypotheses that were developed during our last program review held at the end of FY18: Thrust 1 Hypothesis: Biogeochemical processes occurring on the timescale of years to decades lead to greater actinide recalcitrance in sediments and limits their migration in surface and groundwater. Thrust 2 Hypothesis: Long-term biogeochemical processes include mineral and surface alteration, which leads to stabilization of actinide surface associations or incorporation into mineral precipitates. Our strategic goal is to use the knowledge gained from our Science Plan to advance our understanding of the behavior of actinides and other radionuclides (e.g. Cs) and provide DOE with the scientific basis for remediation and long-term stewardship of DOE’s legacy sites. More broadly, we are improving our understanding of transport phenomena in environmental systems sciences with a particular emphasis on environmentally relevant (long-term) timescales. While we retained some of our historical focus on actinide biogeochemistry this past fiscal year, biogeochemical processes occurring at unique Test Bed locations associated with this SFA provide fundamental information on abiotic and biotic redox processes that control the cycling of redox sensitive metals under dynamic and transient conditions. Furthermore, in collaboration with SFA teams at Argonne National Laboratory, our SFA has begun to transition away from the current research focus and develop a new research program in terrestrial wetland systems. The Terrestrial Wetland Function and Resilience SFA program plan will be delivered to the Environmental System Science (ESS) program within BER at the end of FY23.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

BioGeoChemistry at Interfaces (LLNL SFA OBER FY22 Program Management and Performance Report)

The focus of the BioGeoChemistry at Interfaces SFA is to identify and quantify the biogeochemical processes and the underlying mechanisms that control actinide mobility in an effort to reliably predict and control the cycling and migration of actinides in the environment. The research approach includes: (1) Field Studies that capture actinide behavior on the timescale of decades (Research Thrust 1), and (2) Fundamental Laboratory Studies that isolate specific biogeochemical processes observed in the field (Research Thrust 2). These Research Thrusts are underpinned by the unique capabilities and staff expertise at Lawrence Livermore National Laboratory, allowing the BioGeoChemistry at Interfaces SFA to advance our understanding of actinide migration behavior in the environment, and serve as an resource for environmental radiochemistry research internationally. In the past year, our greater focus on transient redox gradients across stratified waters, sediment-water interfaces, and mineral-water interfaces extended our research beyond actinides to address processes controlling cycling of redox-sensitive metals more broadly. Nevertheless, Research Thrusts 1 and 2 are guided by the following broad central hypotheses that were developed during our last program review held at the end of FY18: Thrust 1 Hypothesis: Biogeochemical processes occurring on the timescale of years to decades lead to greater actinide recalcitrance in sediments and limits their migration in surface and groundwater. Thrust 2 Hypothesis: Long-term biogeochemical processes include mineral and surface alteration, which leads to stabilization of actinide surface associations or incorporation into mineral precipitates. Our strategic goal is to use the knowledge gained from our Science Plan to advance our understanding of the behavior of actinides and other radionuclides (e.g. Cs) and provide DOE with the scientific basis for remediation and long-term stewardship of DOE’s legacy sites. More broadly, we will enhance our understanding of transport phenomena in environmental systems sciences with a particular emphasis on environmentally relevant (long-term) timescales. While we retain our focus on actinide biogeochemistry, our increased focus on overall biogeochemical processes occurring at unique Test Bed locations associated with this SFA provides fundamental information on abiotic and biotic redox processes that control the cycling of redox sensitive metals under dynamic and transient conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Linking Community‐Climate Disequilibrium to Ecosystem Function

Turnover in species composition often lags behind the pace of climate change, resulting in mismatches between climate and communities. However, the impact of these community‐climate disequilibria on ecosystem functions is rarely considered, and current methods for measuring disequilibria assume that species ranges were, until recently, in equilibrium with climate. Here, in this work, we develop a simple theoretical model to address both of these problems by linking community‐climate disequilibrium with ecosystem functioning. We show how disequilibrium can impair functioning in the near‐term even when climate change is expected to enhance functioning in the long‐term. Responses are most likely to change over time in communities where turnover is slow, the impact of disequilibrium counteracts the direct effects of climate on ecosystem function, and pre‐existing disequilibrium is large. These findings emphasise the importance of precise and unbiased estimates of community‐climate disequilibria for improving ecological forecasts. By fitting our model to time series of both climate and ecosystem function from a metacommunity simulation, we show the potential for community‐climate disequilibrium to be inferred without direct knowledge about species' distributions or climatic tolerances. We end by outlining a research agenda to apply dynamic disequilibrium concepts and test novel hypotheses across diverse ecosystems.

climate change↗

Ecological acclimation: A framework to integrate fast and slow responses to climate change

Ecological responses to climate change occur across vastly different time-scales, from minutes for physiological plasticity to decades or centuries for community turnover and evolutionary adaptation. Accurately predicting the range of ecosystem trajectories will require models that incorporate both fast processes that may keep pace with climate change and slower ones likely to lag behind and generate disequilibrium dynamics. However, the knowledge necessary for this integration is currently fragmented across disciplines. We develop ‘ecological acclimation’ as a unifying framework to emphasize the similarity of dynamics driven by processes operating on dramatically different time-scales and levels of biological organization. The framework focuses on ecoclimate sensitivities, measured as the change in an ecological response variable per unit of climate change. Acclimation processes acting at different time-scales cause these sensitivities to shift in magnitude and even direction over time. We highlight shifting ecoclimate sensitivities in case studies from diverse ecosystems, including terrestrial plant communities, coral reefs and soil microbiomes. Models predicting future ecosystem states inevitably make assumptions about acclimation processes; these assumptions must be explicit for users to evaluate whether a model is appropriate for a given forecast horizon. Similarly, decision frameworks that clearly account for multiple acclimation processes and their distinct time-scales will help natural resource managers plan for ecological impacts of climate change from years to many decades into the future. We outline a synthetic research programme focused on the time-scales of ecological acclimation to reduce uncertainty in ecological forecasts.

climate adaptation↗

Nematic Colloidal Micro‐Robots as Physically Intelligent Systems

Abstract Physically intelligent micro‐robotic systems exploit information embedded in micro‐robots, their colloidal cargo, and their milieu to interact, assemble, and form functional structures. Nonlinear anisotropic fluids such as nematic liquid crystals (NLCs) provide untapped opportunities to embed interactions via their topological defects, complex elastic responses, and ability to dramatically restructure in dynamic settings. Here a four‐armed ferromagnetic micro‐robot is designed and fabricated to embed and dynamically reconfigure information in the nematic director field, generating a suite of physical interactions for cargo manipulation. The micro‐robot shape and surface chemistry are designed to generate a nemato‐elastic energy landscape in the domain that defines multiple modes of emergent, bottom‐up interactions with passive colloids. Micro‐robot rotation expands the ability to sculpt interactions; the energy landscape around a rotating micro‐robot is dynamically reconfigured by complex far‐from‐equilibrium dynamics of the micro‐robot's companion topological defect. These defect dynamics allow transient information to be programmed into the domain and exploited. Robust micro‐robotic manipulation strategies are demonstrated that exploit these diverse modes of nemato‐elastic interaction to achieve cargo docking, transport, release, and assembly of complex reconfigurable structures at multi‐stable sites. Such structures are of great interest to future developments of LC‐based advanced optical device and micro‐manufacturing in anisotropic environments.

Yao, Tianyi↗

Ultrafast radiographic imaging and tracking: An overview of instruments, methods, data, and applications

Ultrafast radiographic imaging and tracking (U-RadIT) use state-of-the-art ionizing particle and light sources to experimentally study sub-nanosecond transients or dynamic processes in physics, chemistry, biology, geology, materials science and other fields. These processes are fundamental to modern technologies and applications, such as nuclear fusion energy, advanced manufacturing, communication, and green transportation, which often involve one mole or more atoms and elementary particles, and thus are challenging to compute by using the first principles of quantum physics or other forward models. One of the central problems in U-RadIT is to optimize information yield through, e.g. high-luminosity X-ray and particle sources, efficient imaging and tracking detectors, novel methods to collect data, and large-bandwidth online and offline data processing, regulated by the underlying physics, statistics, and computing power. We review and highlight recent progress in: (a.) Detectors such as high-speed complementary metal-oxide semiconductor (CMOS) cameras, hybrid pixelated array detectors integrated with Timepix4 and other application-specific integrated circuits (ASICs), and digital photon detectors; (b.) U-RadIT modalities such as dynamic phase contrast imaging, dynamic diffractive imaging, and four-dimensional (4D) particle tracking; (c.) U-RadIT data and algorithms such as neural networks and machine learning, and (d.) Applications in ultrafast dynamic material science using XFELs, synchrotrons and laser-driven sources. Hardware-centric approaches to U-RadIT optimization are constrained by detector material properties, low signal-to-noise ratio, high cost and long development cycles of critical hardware components such as ASICs. Interpretation of experimental data, including comparisons with forward models, is frequently hindered by sparse measurements, model and measurement uncertainties, and noise. Alternatively, U-RadIT make increasing use of data science and machine learning algorithms, including experimental implementations of compressed sensing. Machine learning and artificial intelligence approaches, refined by physics and materials information, may also contribute significantly to data interpretation, uncertainty quantification and U-RadIT optimization.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Revealing functional insights into ER proteostasis through proteomics and interactomics

The endoplasmic reticulum (ER), responsible for processing approximately one-third of the human proteome including most secreted and membrane proteins, plays a pivotal role in protein homeostasis (proteostasis). Dysregulation of ER proteostasis has been implicated in a number of disease states. As such, continued efforts are directed at elucidating mechanisms of ER protein quality control which are mediated by transient and dynamic protein-protein interactions with molecular chaperones, co-chaperones, protein folding and trafficking factors that take place in and around the ER. Technological advances in mass spectrometry have played a pivotal role in characterizing and understanding these protein-protein interactions that dictate protein quality control mechanisms. Here, we highlight the recent progress from mass spectrometry-based investigation of ER protein quality control in revealing the topological arrangement of the proteostasis network, stress response mechanisms that adjust the ER proteostasis capacity, and disease specific changes in proteostasis network engagement. We close by providing a brief outlook on underexplored areas of ER proteostasis where mass spectrometry is a tool uniquely primed to further expand our understanding of the regulation and coordination of protein quality control processes in diverse diseases.

60 APPLIED LIFE SCIENCES↗

Remarkably Weak Anisotropy in Thermal Conductivity of Two-Dimensional Hybrid Perovskite Butylammonium Lead Iodide Crystals

Two-dimensional (2D) hybrid organic-inorganic perovskites consisting of alternating organic and inorganic layers are a new class of layered structures. They have attracted increasing interest for photovoltaic, optoelectronic, and thermoelectric applications, where knowing their thermal transport properties is critical. In this study, we carry out both experimental and computational studies on thermal transport properties of 2 D butylammonium lead iodide crystals and find their thermal conductivity is ultralow (below 0.3 W m( -1 ) K -1 ) with very weak anisotropy (around 1.5) among layered crystals. Further analysis reveals that the unique structure with the preferential alignment of organic chains and complicated energy landscape leads to moderately smaller phonon lifetimes in the out-of-plane direction and comparable phonon group velocities in in-plane and out-of-plane directions. These new findings may guide the future design of novel hybrid materials with desired thermal conductivity for various applications.

2D hybrid perovskite↗

Structural basis for autoinhibition by the dephosphorylated regulatory domain of Ycf1

Yeast Cadmium Factor 1 (Ycf1) sequesters glutathione and glutathione-heavy metal conjugates into yeast vacuoles as a cellular detoxification mechanism. Ycf1 belongs to the C subfamily of ATP Binding Cassette (ABC) transporters characterized by long flexible linkers, notably the regulatory domain (R-domain). R-domain phosphorylation is necessary for activity, whereas dephosphorylation induces autoinhibition through an undefined mechanism. Because of its transient and dynamic nature, no structure of the dephosphorylated Ycf1 exists, limiting understanding of this R-domain regulation. Here, we capture the dephosphorylated Ycf1 using cryo-EM and show that the unphosphorylated R-domain indeed forms an ordered structure with an unexpected hairpin topology bound within the Ycf1 substrate cavity. This architecture and binding mode resemble that of a viral peptide inhibitor of an ABC transporter and the secreted bacterial WXG peptide toxins. We further reveal the subset of phosphorylation sites within the hairpin turn that drive the reorganization of the R-domain conformation, suggesting a mechanism for Ycf1 activation by phosphorylation-dependent release of R-domain mediated autoinhibition.

59 BASIC BIOLOGICAL SCIENCES↗

Relevance of structural defects to the mechanism of mechanical deformation in metallic glasses

Abstract It is known that deformation in disordered materials such as metallic glasses and supercooled liquids occurs via the cooperative rearrangement of atoms or constituent particles at dynamical heterogeneities, commonly regarded as point-like defects. We show via molecular-dynamics simulations that there is no apparent relationship between atomic rearrangements and the local atomic environment as measured by the atomic-level stresses, kinetic and potential energies, and the per-atom Voronoi volume. In addition, there is only a weak correlation between atomic rearrangements and the largest and smallest eigenvalues of the dynamical matrix. Our results confirm the transient nature of dynamical heterogeneities and suggest that the notion of defects may be less relevant than that of a propensity for rearrangement.

36 MATERIALS SCIENCE↗

Ionization dynamics of intense laser-produced argon plasmas revealed by NLTE modeling

The ionization dynamics and transient behavior of under-dense plasma irradiated by an intense laser are investigated. We report two significant effects in the ionization behavior: (1) a surprisingly large delay in ionization response and (2) a stepwise ionization process which involves collisional and laser-driven photoionization (LDP) processes. Ionization induced by intense lasers can exhibit delayed responses due to rapid changes in conditions, particularly when atomic transition processes occur more slowly than the relevant time scales. Furthermore, modeling reveals that the two-step ionization process—collisional excitation followed by LDP—plays an important role in this ionization delay, with collisional excitation acting as the bottleneck. Even low-energy photons (∼3.5 eV) can predominantly ionize plasmas, challenging the conventional belief that such energies are insufficient to overcome the binding energy of bound electrons. These findings underscore the necessity of including such processes into plasma simulations for various laser-plasma experiments.

Collisional excitation↗

Machine learning for continuous quantum error correction on superconducting qubits

Abstract Continuous quantum error correction has been found to have certain advantages over discrete quantum error correction, such as a reduction in hardware resources and the elimination of error mechanisms introduced by having entangling gates and ancilla qubits. We propose a machine learning algorithm for continuous quantum error correction that is based on the use of a recurrent neural network to identify bit-flip errors from continuous noisy syndrome measurements. The algorithm is designed to operate on measurement signals deviating from the ideal behavior in which the mean value corresponds to a code syndrome value and the measurement has white noise. We analyze continuous measurements taken from a superconducting architecture using three transmon qubits to identify three significant practical examples of non-ideal behavior, namely auto-correlation at temporal short lags, transient syndrome dynamics after each bit-flip, and drift in the steady-state syndrome values over the course of many experiments. Based on these real-world imperfections, we generate synthetic measurement signals from which to train the recurrent neural network, and then test its proficiency when implementing active error correction, comparing this with a traditional double threshold scheme and a discrete Bayesian classifier. The results show that our machine learning protocol is able to outperform the double threshold protocol across all tests, achieving a final state fidelity comparable to the discrete Bayesian classifier.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Self-consistent and detailed opacities from a non-equilibrium average-atom model

Modern density functional theory (DFT) is a powerful tool for accurately predicting self-consistent material properties such as equations of state, transport coefficients and opacities in high energy density plasmas, but it is generally restricted to conditions of local thermodynamic equilibrium (LTE) and produces only averaged electronic states instead of detailed configurations. We propose a simple modification to the bound-state occupation factor of a DFT-based average-atom model that captures essential non-LTE effects in plasmas—including autoionization and dielectronic recombination—thus extending DFT-based models to new regimes. Finally, we then expand the self-consistent electronic orbitals of the non-LTE DFT-AA model to generate multi-configuration electronic structure and detailed opacity spectra. This article is part of the theme issue ‘Dynamic and transient processes in warm dense matter’.

36 MATERIALS SCIENCE↗

Photoinduced band renormalization effects in the topological nodal-line semimetal ZrSiS

Out-of-equilibrium effects provide an elegant pathway for probing and understanding the underlying physics of topological materials. In particular, controlling electronic band structure properties using ultrafast optical pulses has shown promise for creating exotic states of matter. Of recent interest is band renormalization in Dirac and Weyl semimetals as it leads to direct physical observables through the enhancement of the effective mass or in the shift of resonant energies. Here, in this work, we provide experimental and theoretical signatures of photoinduced renormalization of the electronic band structure in the topological nodal-line semimetal ZrSiS. Specifically, we show how the change in the transient reflectivity spectra under femtosecond optical excitations is induced by out-of-equilibrium effects that renormalize the kinetic energy of electrons. We associate the observed spectral features with an enhancement of the effective mass and to a redshift of the resonant frequency as a function of pump field strength. Finally, we show that the transient relaxation dynamics of the reflectivity is primarily an electronic effect with a negligible phononic contribution. Our study presents conclusive modifications of electronic properties in ZrSiS using ultrashort pulses and demonstrates the potential of this approach in creating photoinduced phases in topological quantum matter through an all-optical route.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A Participation Factor-Based Approach for Defining the EMT Model Boundary for Power System Simulations with Inverter-Based Resources

The increasing penetration of inverter-based resources (IBRs) introduces new challenges to power system simulations, particularly with the emergence of fast electromagnetic transient (EMT) dynamics and sub-synchronous oscillations (SSO) that require time-consuming EMT simulations. To reduce the time cost for simulating a large-scale power grid with IBRs, this paper proposes a novel participation factor-based approach for defining a critical zone for detailed EMT modeling and simulations, which includes the IBRs, synchronous generators, and the network components participating significantly in simulated contingencies. Both model-based and response-based methods are introduced for the estimation of participation factors (PFs). The case study on the 240-bus Western Electricity Coordinating Council (WECC) system demonstrates that the EMT zone determined by the proposed approach can effectively capture power system dynamics involving IBRs.

EMT simulation↗

High-Performance Computing Based EMT Simulation of Large PV or Hybrid PV Plants

Faults in the transmission grid have led to reduced power generation from power electronics resources that are typically not connected to the faulted transmission line. In many of the cases, partial loss of power is observed within the power electronics resources like large photovoltaic (PV) power plants. This phenomena is not captured in existing simulation models and/or simulators. High-fidelity switched system electromagnetic transient (EMT) dynamic models of PV power plants can improve the fidelity of models available for accurate analysis of the impact on PV plants during simulation of faults. However, these models are extremely computationally expensive and take a long time to simulate. Long simulation times limit the ability to use these models as larger regions are studied in EMT simulations with more power electronics resources. In this paper, numerical simulation algorithms are combined with high-performance computing techniques and applied to the high-fidelity switched system EMT model of PV plants. Using these techniques, a speed-up of up to 58x is obtained, while preserving the accuracy of the simulation at greater than 98%.

Debnath, Suman↗