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All sources NASA NTRS DOE OSTI

DOE OSTI2025

Mapping Local Dissipation and Entropy Production in Complex and Active Fluids

While global entropy production provides a measure of irreversibility, its partitioning into contributions from local regions is key to understanding the mechanisms underlying time-reversal symmetry breaking in complex systems and active matter. Here, by analyzing local heat flows and fluxes, we propose a framework that enables the mapping of local dissipation and entropy production in a nonequilibrium system. We test this approach in simulations of fluids driven through complex environments and active systems. We connect the results across the local and global scales by showing that local dissipation and entropy production satisfy a local version of the usual (global) fluctuation theorem, which accounts for the correlations between the local region and its surroundings. Interestingly, in the case of the active fluid, our analysis reveals that these correlations are of opposite signs for the active (stochastic) and passive (deterministic) contributions to local dissipation.

Entropy↗

DOE OSTI2020

Controlled Assembly of Upconverting Nanoparticles for Low-Threshold Microlasers and Their Imaging in Scattering Media

Micron-sized lasers fabricated from upconverting nanoparticles (UCNP) coupled to whispering gallery mode (WGM) microresonators can exhibit continuous-wave anti-Stokes lasing useful for tracking cells, environmental sensing, and coherent stimulation of biological activity. The integration of these microlasers into organisms and microelectronics requires even smaller diameters, however, which raises threshold pump powers beyond practical limits for biological applications. To meet the need for low lasing thresholds and high fidelity fabrication methods, we use correlative optical and electron microscopy to uncover the nanoparticle assembly process and structural factors that determine efficient upconverted lasing. We show that 5 μm microspheres with controlled submonolayer UCNP coatings exhibit, on average, 25-fold lower laser thresholds (1.7 ± 0.7 kW/cm 2 ) compared to the mean values of the lowest threshold UCNP lasers, and variability is reduced 30-fold. WGMs are observed in the upconversion spectra for TiO 2 -coated microspheres as small as 3 μm, a size at which optical losses had previously prevented such observations. Finally, we demonstrate that the WGM signatures of these upconverting microlasers can be imaged and distinguished through tissue-mimicking phantoms. These advances will enable the fabrication of more efficient upconverting lasers for imaging, sensing, and actuation in optically complex environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Redox active plant phenolic, acetosyringone, for electrogenetic signaling

Abstract Redox is a unique, programmable modality capable of bridging communication between biology and electronics. Previous studies have shown that the E. coli redox-responsive OxyRS regulon can be re-wired to accept electrochemically generated hydrogen peroxide (H 2 O 2 ) as an inducer of gene expression. Here we report that the redox-active phenolic plant signaling molecule acetosyringone (AS) can also induce gene expression from the OxyRS regulon. AS must be oxidized, however, as the reduced state present under normal conditions cannot induce gene expression. Thus, AS serves as a “pro-signaling molecule” that can be activated by its oxidation—in our case by application of oxidizing potential to an electrode. We show that the OxyRS regulon is not induced electrochemically if the imposed electrode potential is in the mid-physiological range. Electronically sliding the applied potential to either oxidative or reductive extremes induces this regulon but through different mechanisms: reduction of O 2 to form H 2 O 2 or oxidation of AS. Fundamentally, this work reinforces the emerging concept that redox signaling depends more on molecular activities than molecular structure. From an applications perspective, the creation of an electronically programmed “pro-signal” dramatically expands the toolbox for electronic control of biological responses in microbes, including in complex environments, cell-based materials, and biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

From machine learning to chemical insight: Darwinian chance and the stability of charge carriers in flow batteries

In chemistry, rationalizing and predicting reaction behavior in complex environments is challenging, but this knowledge is required for practical applications and materials advancement. Here, we focus on one such example that uses organic molecules as redox-active materials in electrochemical energy storage. In flow batteries, these molecules (also known as redoxmers) serve as charge carriers, and exceptional chemical stability in all states of charge is required for long-term use. Here, we show how machine learning combined with chemist's knowledge can be used to reveal patterns in the reactivity of charged redoxmers by providing mechanistically tractable clues.

25 ENERGY STORAGE↗

DOE OSTI2022

Partially polaron-transformed quantum master equation for exciton and charge transport dynamics

Polaron-transformed quantum master equation (PQME) offers a unified framework to describe the dynamics of quantum systems in both limits of weak and strong couplings to environmental degrees of freedom. Thus, the PQME serves as an efficient method to describe charge and exciton transfer/transport dynamics for a broad range of parameters in condensed or complex environments. However, in some cases, the polaron transformation (PT) being employed in the formulation invokes an over-relaxation of slow modes and results in premature suppression of important coherence terms. A formal framework to address this issue is developed in the present work by employing a partial PT that has smaller weights for low frequency bath modes. In this work, it is shown that a closed form expression of a second order time-local PQME including all the inhomogeneous terms can be derived for a general form of partial PT, although more complicated than that for the full PT. All the expressions needed for numerical calculation are derived in detail. Applications to a model of a two-level system coupled to a bath of harmonic oscillators, with test calculations focused on those due to homogeneous relaxation terms, demonstrate the feasibility and the utility of the present approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Phosphorus chemistry in plant charcoal: interplay between biomass composition and thermal condition

Background Vegetation fire may change Phosphorus (P) cycling in terrestrial ecosystems through converting biomass into fire residues. Aim The aim of this study was to understand the chemistry and mobility of P in fire residues to help reveal P thermochemistry during biomass burning and post-fire P cycling. Methods A combination of sequential extraction, liquid 31P NMR and P K-edge XANES was used to obtain quantitative P speciation and explain P solubilisation behaviours of charcoal. Key results Despite varying diverse P species existing in raw biomass, only two P structural moieties – orthophosphate and pyrophosphate – were identified in charcoal. However, relative abundance of pyrophosphate differs greatly among charcoal samples from different biomass types, ranging between 0 and 40% of total extractable P. Although P K-edge XANES data indicates abundant soluble phosphate minerals, most P (70–90%) is likely occluded physically in the charcoal. The bicarbonate-extractable P (the Olsen-P) varies significantly and cannot be explained by surface P concentration or elemental stoichiometry alone. Conclusion and implications The results suggest the importance of starting biomass P speciation (i.e. molecular structure and complexation environment) and thermal conditions in controlling P speciation and availability in charcoal. The different P chemistry between charcoal and ash suggests the importance of fire types and severity in disturbing the P cycle.

Forestry↗

DOE OSTI2020

A broad-host-range event detector: expanding and quantifying performance between Escherichia coli and Pseudomonas species

Modern microbial biodesign relies on the principle that well-characterized genetic parts can be reused and reconfigured for different functions. However, this paradigm has only been successful in a limited set of hosts, mostly comprised from common lab strains of Escherichia coli . It is clear that new applications such as chemical sensing and event logging in complex environments will benefit from new host chassis. This study quantitatively compared how the same chemical event logger performed across four strains and three different microbial species. An integrase-based sensor and memory device was operated by two representative soil Pseudomonads— Pseudomonas fluorescens SBW25 and Pseudomonas putida DSM 291. Quantitative comparisons were made between these two non-traditional hosts and two benchmark E. coli chassis including the probiotic Nissle 1917 and common cloning strain DH5α. The performance of sensor and memory components changed according to each host, such that a clear chassis effect was observed and quantified. These results were obtained via fluorescence from reporter proteins that were transcriptionally fused to the integrase and downstream recombinant region and via data-driven kinetic models. The Pseudomonads proved to be acceptable chassis for the operation of this event logger, which outperformed the common E. coli DH5α in many ways. This study advances an emerging frontier in synthetic biology that aims to build broad-host-range devices and understand the context by which different species can execute programmable genetic operations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A structural description of the evolution of stakeholders and risk communication in the Department of Energy's defense nuclear facilities: Historical perspective, major stakeholders, and external events

Regulators and policymakers are routinely challenged with explaining complex concepts concerning risk. Part of the challenge is helping external and internal stakeholders to understand the context behind risk-related information and decisions. Here, this paper will describe the historical evolution of the safety and regulatory framework for an important category in the nuclear industry—defense nuclear facilities owned and operated by the US Department of Energy. In parallel with describing this evolution, three major events which occurred external to the complex of defense nuclear facilities will be summarized, and their impact on the maturation of the Department's safety and regulatory framework will be discussed. Finally, integrated with these two threads of discussion will be a chronicle of the changing set of involved organizations and the expanding set of external stakeholders involved in risk decisions—and therefore, the risk communications ecosystem surrounding defense nuclear facilities. It will be noted that this system was once describable as a classic “iron triangle,” but now has progressed to a complex network of federal and state organizations, numerous congressional committees, and expanding sets of external stakeholders. It is hoped that a comprehensive discussion of the context of risk assessment in the defense nuclear facilities complex—addressing historical insights, organizational evolution, and the maturing structure of regulation—will provide enhanced opportunities for building trust and understanding in this complex environment.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2021

Transient recovery problem in acoustics: A multichannel model-based deconvolution approach

Critical acoustical systems operating in complex environments contaminated with disturbances and noise offer an extreme challenge when excited by out-of-the-ordinary, impulsive, transient events that can be undetected and seriously affect their overall performance. Transient impulse excitations must be detected, extracted, and evaluated to determine any potential system damage that could have been imposed; therefore, the problem of recovering the excitation in an uncertain measurement environment becomes one of multichannel deconvolution. Recovering a transient and its initial energy has not been solved satisfactorily, especially when the measurement has been truncated and only a small segment of response data is available. The development of multichannel deconvolution techniques for both complete and incomplete excitation data is discussed, employing a model-based approach based on the state-space representation of an identified acoustical system coupled to a forward modeling solution and a Kalman-type processor for enhancement and extraction. In conclusion, synthesized data are utilized to assess the feasibility of the various approaches, demonstrating that reasonable performance can be achieved even in noisy environments.

42 ENGINEERING↗

DOE OSTI2025

Topology-imprinting in nonlinear metasurfaces

Flat optical components, or metasurfaces, have transformed optical imaging, data storage, information processing, and biomedical applications by providing unprecedented control over light-matter interactions. These nano-engineered structures enable compact, multidimensional manipulation of light’s amplitude, phase, polarization, and wavefront, producing scalar and vector beams with unique properties such as orbital angular momentum and knotted topologies. This flexibility has potential applications in optical communication and imaging, particularly in complex environments such as atmospheric turbulence and undersea scattering. However, designing metasurfaces for shorter wavelengths, such as visible and ultraviolet light, remains challenging due to fabrication limitations and material absorption. Here, we introduce an innovative concept called topology imprinting using judiciously designed all-dielectric nonlinear optical metasurfaces to replicate desired waveforms at fundamental and harmonic frequencies, opening promising avenues for advanced photonic applications.

42 ENGINEERING↗

DOE OSTI2025

Mapping structures and dynamics with frequency-correlated diffusion exchange

Understanding molecular motion in diffusion-driven complex environments is critical for designing sustainable materials and improving chemical processes. Here, we introduce a multidimensional nuclear magnetic resonance (NMR) method that captures how molecular populations exchange across different dynamic regimes. By extending the modulated gradient spin-echo technique to include frequency-frequency correlations, our approach reveals diffusion pathways that are otherwise obscured in heterogeneous systems. Implemented on a unilateral NMR magnet, the method eliminates gradient pulsing constraints and accesses dynamics in the kilohertz regime. We apply this technique to swelling and acid-catalyzed deconstruction of cross-linked and linear polymers to observe how structural heterogeneity evolves over time. By linking molecular motion to topology and chemical state, we extract physical metrics such as fractal surface dimensionality and reaction wavefront velocity, properties inaccessible with standard diffusion measurements. This work expands the capabilities of NMR for probing soft matter, with implications for polymer recycling and materials design.

Fricke, Sophia N. [University of California, Berke↗

DOE OSTI2024

FiberFlex: Real-time FPGA-based Intelligent and Distributed Fiber Sensor System for Pedestrian Recognition

In recent years, security monitoring of public places and critical infrastructure has heavily relied on the widespread use of cameras, raising concerns about personal privacy violations. To balance the need for effective security monitoring with the protection of personal privacy, we explore the potential of optical fiber sensors for this application. This article proposes FiberFlex, an intelligent and distributed fiber sensor system. Ultizing Field Programmable Gate Arrays (FPGA) high-level synthesis (HLS) acceleration, FiberFlex offers real-time pedestrian detection by co-designing the entire pipeline of optical signal acquisition, processing, and recognition networks based on the principles of optical fiber sensing. As a promising alternative to traditional camera-based monitoring systems, FiberFlex achieves pedestrian detection by analyzing the vibration patterns caused by pedestrian footsteps, enabling security monitoring while preserving individual privacy. FiberFlex comprises three modules: First , fiber-optic sensing system: A fiber-optic distributed acoustic sensing (DAS) system is built and used to measure the ground vibration waves generated by people walking. Second , algorithms: We first collect the training data by measuring the ground vibration waves, label the data, and use the data to train the neural network models to perform pedestrian recognition. Third , hardware accelerators: We use HLS tools to design hardware modules on FPGA for data collection and pre-processing and integrate them with the downstream neural network accelerators to perform in-line real-time pedestrian detection. The final detection results are sent back from FPGA to the host CPU. We implement our system FiberFlex with the in-house built DAS system and AMD/Xilinx Kintex7 FPGA KC705 board and verify the whole system using the real-world collected data. We conduct recognition tests on five test subjects of varying ages, heights, and weights in a fixed sensing area. Each subject experienced 20 real-time recognition tests using their daily walking habits, and the subjects were given adequate rest between tests. After 100 tests on five test subjects, the overall real-time recognition accuracy exceeded \(88.0\%\) . The whole system uses 55 W of power, 33 W in the optical DAS system and 22 W in the FPGA. Relying on its end-to-end interdisciplinary design, FiberFlex seamlessly combines fiber-optic sensors with FPGA accelerators to enable low-power real-time security monitoring without compromising privacy, making it a valuable addition to the existing security monitoring network. According to FiberFlex, more valuable research can be conducted in the future, such as fall monitoring for the elderly, migration of identification networks between different application scenarios, and improvement of anti-interference performance in more complex environments. In future perception networks, where the “eyes” are not feasible, let’s use fiber optic touch instead.

Distributed↗

DOE OSTI2021

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike’s full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Equivalent Point Sources for Simulating Nuclear/Radiological Search Operations

Modeling and simulation can be used to estimate the detection of different types and strengths of radioactive sources. Simulations of shielded gamma-ray sources in complex environments, such as searches in urban areas using vehicle-mounted detectors, can demonstrate what source strengths and shielding combinations should be able to be detected. For faster calculations, gamma-emitting sources that could have different shielding layers can be simulated ahead of time, resulting in equivalent point source emission distributions that can be used in larger simulation models. Larger-scale models will then run faster using equivalent point sources because the shielding layers around the sources have already been accounted for. Accompanying this paper are 260 equivalent point source emission files for 72 sources with different shielding layers, formatted for three different Monte Carlo codes. Users wanting to request versions of the SCALE and/or MCNP software can find details here: https://rsicc.ornl.gov/

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Markov Decision Processes for Intelligent, Risk-Informed Asset-Management Decision-Making

Advanced nuclear reactors are a promising option for aiding the world in achieving its net-zero carbon emission goals, however, there are significant challenges to attaining and maintaining economic competitiveness with other sources of electricity. To improve the economic competitiveness of advanced reactor designs, a project was initiated to explore the use of Markov Decision Processes (MDPs) to guide asset-management decision-making during advanced reactor operation. MDPs are a powerful tool for optimizing decision-making in complex environments and their application to advanced reactors can aid in planning maintenance and repair activities to minimize downtime and maximize generation. The described approach expands on previous work regarding the use of MDPs for operational decision-making through the direct incorporation of real-time plant information. The integral MDP analysis includes information from online component diagnostic tools and the plant’s real-time generation risk assessment (GRA) and probabilistic risk assessment (PRA), which evaluate plant risk from both an economic and safety perspective. The result is an asset-management optimization framework that is based on real-time data regarding plant component status and the current best-estimate of plant risk. The paper presents an overview of the theoretical framework to incorporate the different information pathways into an integral MDP analysis, along with example analyses.

Grabaskas, David↗

DOE OSTI2025

FlbB forms a distinctive ring essential for periplasmic flagellar assembly and motility in Borrelia burgdorferi

Spirochetes are a widespread group of bacteria with a distinct morphology. Some spirochetes are important human pathogens that utilize periplasmic flagella to achieve motility and host infection. The motors that drive the rotation of periplasmic flagella have a unique spirochete-specific feature, termed the collar, crucial for the flat-wave morphology and motility of the Lyme disease spirochete Borrelia burgdorferi. Here, we deploy cryo-electron tomography and subtomogram averaging to determine high-resolution in-situ structures of the B. burgdorferi flagellar motor. Comparative analysis and molecular modeling of in-situ flagellar motor structures from B. burgdorferi mutants lacking each of the known collar proteins (FlcA, FlcB, FlcC, FlbB, and Bb0236/FlcD) uncover a complex protein network at the base of the collar. Importantly, our data suggest that FlbB forms a novel periplasmic ring around the rotor but also acts as a scaffold supporting collar assembly and subsequent recruitment of stator complexes. The complex protein network based on the FlbB ring effectively bridges the rotor and 16 torque-generating stator complexes in each flagellar motor, thus contributing to the specialized motility and lifestyle of spirochetes in complex environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Constructing a High‐Resolution Aftershock Catalog for the 2017 Mw 8.2 Tehuantepec Earthquake Sequence Using a Machine Learning–Based Workflow

The 8 September 2017 Mw 8.2 Tehuantepec earthquake was the largest instrumentally recorded normal‐faulting earthquake in Mexico. The mainshock occurred offshore within the Tehuantepec seismic gap, generating >30,000 aftershocks in the following year. We applied an open‐source, machine learning (ML)–assisted workflow to construct a high‐resolution aftershock catalog using data from temporary and permanent seismic networks in southern Mexico. The workflow integrates PhaseNet for phase detection; GaMMA for phase association; and VELEST, HypoInverse, and HypoDD for velocity modeling and relocation. We processed seven months of continuous waveform data from 29 broadband stations, including a temporary rapid‐response deployment that improved station coverage of the offshore rupture zone. To evaluate performance, we compared our results against analyst‐reviewed picks and event locations from the Servicio Sismológico Nacional catalog. The resulting catalog contains 11,374 relocated earthquakes and represents the most comprehensive published dataset for this sequence, incorporating the first full use of the temporary network. Relocated hypocenters show improved depth control and align well with the Slab2.0 subduction geometry, revealing clearer separation between offshore slab events and onshore crustal seismicity. This study demonstrates that combining ML‐based detection with established methods provides a scalable and reproducible approach for constructing high‐quality earthquake catalogs in tectonically complex environments and offers practical guidance for adapting similar workflows to other earthquake sequences.

Garcia, Marc [The University of Texas at El Paso, ↗

DOE OSTI2025

Exploring Continuous Seismic Data at an Industry Facility Using Unsupervised Machine Learning

Seismic data recorded at industrial sites contain valuable information on anthropogenic activities. With advances in machine learning and computing power, new opportunities have emerged to explore the seismic wavefield in these complex environments. We applied two unsupervised machine learning algorithms to analyze continuous seismic data collected from an industrial facility in Texas, United States. The Uniform Manifold Approximation and Projection for Dimension Reduction algorithm was used to reduce the dimensionality of the data and generate 2D embeddings. Then, the Hierarchical Density-Based Spatial Clustering of Applications with Noise method was employed to automatically group these embeddings into distinct signal clusters. Our analysis of over 1400 hr (around 59 days) of continuous seismic data revealed five and seven signal clusters at two separate stations. At both stations, we identified clusters associated with background noise and vehicle traffic, with the latter’s temporal patterns aligning closely with the facility’s work schedule. Furthermore, the algorithms detected signal clusters from unknown sources and underline the ability of unsupervised machine learning for uncovering previously unrecognized patterns. Our analysis demonstrates the effectiveness of unsupervised approaches in examining continuous seismic data without requiring prior knowledge or pre-existing labels.

58 GEOSCIENCES↗