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DOE OSTI2021

Revealing the etching process of water-soluble Au 25 nanoclusters at the molecular level

Etching (often considered as decomposition) is one of the key considerations in the synthesis, storage, and application of metal nanoparticles. However, the underlying chemistry of their etching process still remains elusive. Here, we use real-time electrospray ionization mass spectrometry to study the reaction dynamics and size/structure evolution of all the stable intermediates during the etching of water-soluble thiolate-protected gold nanoclusters (Au NCs), which reveal an unusual “recombination” process in the oxidative reaction environment after the initial decomposition process. Interestingly, the sizes of NC species grow larger and their ligand-to-metal ratios become higher during this recombination process, which are distinctly different from that observed in the reductive growth of Au NCs (e.g., lower ligand-to-metal ratios with increasing sizes). The etching chemistry revealed in this study provides molecular-level understandings on how metal nanoparticles transform under the oxidative reaction environment, providing efficient synthetic strategies for new NC species through the etching reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

An Adsorptive Membrane Platform for Precision Ion Separation: Membrane Design and First‐Principles Studies

One of the key challenges in separation science is the lack of precise ion separation methods and mechanistic understanding crucial for efficiently recovering critical materials from complex aqueous matrices. Herein, first-principles electronic structure calculations and in situ Raman spectroscopy are studied to elucidate the factors governing ion discrimination in an adsorptive membrane specifically designed for transition metal ion separation. Density functional theory calculations and in situ Raman data jointly reveal the thermodynamically favorable binding preferences and detailed adsorption mechanisms for competing ions. How membrane binding preferences correlate with the electronic properties of ligands is explored, such as orbital hybridization and electron localization. The findings underscore the importance of the phenolate group in oxime ligands for achieving high selectivity among competing transition metal ions. In-depth understanding on which specific atomistic site within the microenvironment of metal-ligand binding pockets governs the ion discrimination behaviors of the host will build a solid foundation to guide the rational design of next-generation materials for precision separation essential for energy technologies and environment remediation. In tandem, synthetic controllability is demonstrated to transform 3D micrometer-scale crystals to a 2D crystalline selective layer in membranes, paving the way for more precise and sustainable advances in separation science.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Efficient Capture and Release of the Rare-Earth Element Neodymium in Aqueous Solution by Recyclable Covalent Organic Frameworks

Rare-earth elements (REEs) are present in a broad range of critical materials. The development of solid adsorbents for REE capture could enable the cost-effective recycling of REE-containing magnets and electronics. In this context, covalent organic frameworks (COFs) are promising candidates for REE adsorption due to their exceptionally high surface area. Despite having attractive physical properties, COFs are heavily underutilized for REE capture applications due to their limited lifecycle in aqueous acidic environments, as well as synthetic challenges associated with the incorporation of ligands suitable for REE capture. Here, in this work, we show how the Ugi multicomponent reaction can be leveraged to postsynthetically modify imine-based COFs for the introduction of a diglycolic acid (DGA) moiety, an efficient scaffold for REE capture. The adsorption capacity of the DGA-functionalized COF was found to be more than 40 times higher than that of the pristine imine COF precursor and more than four times higher than that of the next-best reported DGA-functionalized solid support. This rationally designed COF has appealing characteristics of high adsorption capacity, fast and efficient capture and release of the REE ions, and reliable recyclability, making it one of the most promising adsorbents for solid–liquid REE ion extractions reported to date.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Enabling AI in synthetic biology through Construction File specification

The Construction File (CF) specification establishes a standardized interface for molecular biology operations, laying a foundation for automation and enhanced efficiency in experiment design. It is implemented across three distinct software projects: PyDNA_CF_Simulator, a Python project featuring a ChatGPT plugin for interactive parsing and simulating experiments; ConstructionFileSimulator, a field-tested Java project that showcases 'Experiment' objects expressed as flat files; and C6-Tools, a JavaScript project integrated with Google Sheets via Apps Script, providing a user-friendly interface for authoring and simulation of CF. The CF specification not only standardizes and modularizes molecular biology operations but also promotes collaboration, automation, and reuse, significantly reducing potential errors. The potential integration of CF with artificial intelligence, particularly GPT-4, suggests innovative automation strategies for synthetic biology. While challenges such as token limits, data storage, and biosecurity remain, proposed solutions promise a way forward in harnessing AI for experiment design. This shift from human-driven design to AI-assisted workflows, steered by high-level objectives, charts a potential future path in synthetic biology, envisioning an environment where complexities are managed more effectively.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Synthetic soils for ecological and synthetic biology applications

Soils are heterogeneous and dynamic systems characterized by complex physical, chemical, and biological interactions. Understanding these interactions is critical, as they influence plant productivity, global biogeochemical cycles, and ecosystem resilience. While ecologists have long studied soils in field, greenhouse, and laboratory settings, their complexity and heterogeneity make it challenging to pinpoint key properties driving biological processes and derive mechanistic insights. Advancements in synthetic biology, which seeks to engineer and control biological processes in soils, have increased the demand for standardized and controllable experimental platforms. These platforms, referred to here as ‘synthetic soils’, are systems designed to reproduce selected physicochemical characteristics of natural soils in a simplified and defined format, allowing scientists to systematically change soil physicochemical properties (i.e. texture, mineralogy, pH) to study how biological components (i.e. microbes, plants, soil fauna, etc.) respond to, modify, or interact within these controlled environments. This review explores existing synthetic soils, their advantages, limitations, and applications in ecology and synthetic biology, and discusses potential directions for their future development.

artificial soils↗

DOE OSTI2023

Soil microbiome engineering for sustainability in a changing environment

Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth’s soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

In Situ Methods for Metal-Flux Synthesis in Inert Environments

Flux growth synthesis is an advantageous synthetic method as it allows for the growth of single crystals of both congruently melting and metastable phases. The determination of synthetic parameters for the flux growth of new crystalline phases is complex as many factors and parameters need to be considered, such as purity and morphology of starting material and heating profile variables including maximum temperature, dwell time, cooling rate and flux removal temperature. In situ monitoring of crystallite growth can lead to elucidation of reaction intermediates and growth mechanisms. The determination of pivotal reaction parameters can revolutionize the way growth parameters are selected. In this work, we report a new sample environment and furnace apparatus for synchrotron in situ synthesis of crystalline materials, including flux grown intermetallics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

A Solvatochromic Near Infrared Fluorophore Sensitive to the Full Amyloid Beta Aggregation Pathway

Alzheimer's disease has long been associated with the aggregation of amyloid beta peptides (Aβ42) into macroscale plaques, although specific neurodegenerative agents have not been definitively identified. Much evidence has pointed to the soluble nanoscale oligomers that form early in the Aβ42 aggregation pathway, but there is little understanding of these structures, their mechanisms of formation, or how they grow into plaques. Here, we show that a solvatochromic fluorophore with near-infrared (NIR) emission can track synthetic Aβ42 aggregation through environment-sensitive spectral shifts from the earliest time points through plaque formation. This azide-functionalized phosphine oxide azetidine rhodol (Phazr-N3) shows large polarity-dependent changes in fluorescence emission, with maxima shifting from 630 nm in toluene to 703 nm in aqueous buffer, and a maximum quantum yield of 62%. Upon induction of Aβ42 aggregation, we observe immediate solvatochromic changes in Phazr-N3 fluorescence, with multiple apparent phases over 12 h, and which culminate before the onset of any major fluorescence changes of conformation-specific aggregation fluorophore thioflavin T. Solution anisotropy measurements show a low micromolar affinity of Phazr-N3 for disordered, free Aβ42 in solution, and real-time measurements are consistent with rapid liquid-liquid phase separation and slow dehydration of the growing aggregate. Spectral imaging of synthetic plaques stained in the presence of live cells and lipid-binding protein albumin shows over 4000-fold Phazr-N3 fluorescence intensity above background under no-wash conditions, and over 100-fold intensity above coplated microglial cells or a large excess of albumin. This use of a solvatochromic probe with structure-independent binding to free Aβ42 offers real-time, minimally invasive insight into the full Aβ42 aggregation pathway.

Wang, Zeming↗

DOE OSTI2023

Machine Learning Automated Analysis of Enormous Synchrotron X-ray Diffraction Datasets

X-ray diffraction (XRD) data analysis can be a time-consuming and laborious task. Deep neural network (DNN) based models trained with synthetic XRD patterns have been proven to be a highly efficient, accurate, and automated method for analyzing common XRD data collected from solid samples in ambient environments. However, it remains unclear whether synthetic XRD-based models can be effective in solving micro(μ)-XRD mapping data for in situ experiments involving liquid phases, which always have lower quality and significant artifacts. In this study, we collected μ-XRD mapping data from a LaCl 3 -calcite hydrothermal fluid system and trained two categories of models to analyze the experimental XRD patterns. Here, the models trained solely with synthetic XRD patterns showed low accuracy (as low as 64%) when solving experimental μ-XRD mapping data. However, the accuracy of the DNN models significantly improved (90% or above) when we trained them with a data set containing both synthetic and a small number of labeled experimental μ-XRD patterns. This study highlights the importance of labeled experimental patterns in training DNN models to solve μ-XRD mapping data from in situ experiments involving liquid phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

On the Limits of EM Based Detection of Control Logic Injection Attacks In Noisy Environments

The difficulty in applying traditional security mechanisms in Industrial Control System (ICS) environments makes a large portion of these mission-critical assets vulnerable to cyber attacks. Therefore, there is a dire need for the development of novel security mechanisms specifically designed to protect such critical systems. Recently a lot of attention has been given to mechanisms that exploit the EM emanations of devices for defense purposes. Such practices may lead to the development of robust external and non-intrusive anomaly detection systems. Nevertheless, the majority of current work in the area neglects to consider the implications of real-life environments, particularly environmental noise. In this work, we explore the limits of EM-based anomaly detection towards identifying injection attacks in control logic software in noisy environments. Our study conducted upon both synthetically generated and real signals identified that indeed environmental noise might significantly degrade the accuracy of the anomaly detection process. Experiments done upon synthetic data indicated that assuming that signals are captured with high sampling rates, even minor code injections can be detected with above-90% accuracy in noisy environments where SNR is up to -2dB. This is true even if naive detection methods are considered. Moreover, experiments done using a real-life testbed attest that even single-instruction injections can be detected with near-perfect accuracy in relatively clean environments. Finally, noise-elimination techniques can drastically improve the reliability of the detection mechanism even in noisy environments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Electrostatic Barriers to Nanoparticle Accessibility of a Porous Matrix

Translocation from one cavity to another through a narrow constriction (i.e., a “hole”) represents the fundamental elementary process underlying hindered mass transport of nanoparticles and macromolecules within many natural and synthetic porous materials, including intracellular environments. This process is complex and may be influenced by long-range (e.g., electrostatic) particle–wall interactions, transient adsorption/desorption, surface diffusion, and hydrodynamic effects. In this study, we used a three-dimensional (3D) tracking method to explicitly visualize the process of nanoparticle diffusion within periodic porous nanostructures, where electrostatic interactions were mediated via ionic strength. The effects of electrostatic interactions on nanoparticle transport were surprisingly large. For example, an increase in the Debye length of only a few nanometers (in a material with a hole diameter of ~100 nm) increased the mean cavity escape time 3-fold. A combination of computational and experimental analyses indicated that this hindered cavity escape was due to an electrostatic energy barrier in the region of the hole, which was quantitatively explained using DLVO theory. These findings explicitly demonstrate that the cavity escape process was barrier-limited and dominated by electrostatic effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Evaluation of KDP Estimation Algorithm Performance in Rain Using a Known-Truth Framework

Accurate estimation of specific differential phase ( K DP ) is necessary for rain rate estimation, attenuation correction, and hydrometeor classification algorithms. There are numerous published methods to process polarimetric radar observations of propagation differential phase shift (Φ DP ) and estimate K DP , but the corresponding K DP estimate uncertainty is unquantified. This study provides guidance on how commonly used K DP estimation algorithms perform in various environments. Here, we create numerous synthetic (“true”) K DP profiles, integrate over them to obtain “smoothed” Φ DP , and then add noise typical of S-band operational weather radar measurements. Each algorithm is applied to our noisy Φ DP profiles and compared to the true K DP profile such that the errors and uncertainty are quantified. The synthetic K DP profiles are Gaussian in shape, which allows systematic variations in their magnitude and width to determine how each algorithm performs in smooth, slowly changing K DP profiles, as well as steep profiles. Results demonstrate that algorithm performance is dependent on the Φ DP field received. These results are further supported by an error analysis of each algorithm for two more complicated synthetic K DP profiles. Some K DP algorithms allow users to change various tuning parameters; a subset of these tuning parameters is tested to provide guidance on how changing these parameters impacts algorithm performance. We then provide evidence that our known-truth framework provides insight into algorithm performance in observed data through two case studies.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Polymer nanoparticle photocatalysts realized in non-aqueous solvents

Colloidal organic nanoparticles (oNPs) have emerged as a promising category of photocatalyst, thanks to their long-lived surface-bound charges, electronic tunability, and strong absorption in the visible spectrum. Our previous research has established a direct correlation between charge generation in oNPs and their photocatalytic activity, highlighting their effectiveness as a framework for stable, long-lived free carriers. However, oNPs have been restricted to use only in aqueous environments as a result of being synthesized via either nano-emulsion or nano-precipitation procedures. Herein, we present a method for transferring oNP photocatalysts from water into polar non-aqueous solvents while retaining their long-term colloidal stability. We observed that the polymer chains in the solvent-transferred oNPs rearrange from a predominantly H-aggregate structure in water to a combination of H- and J-aggregate characteristics in N,N-dimethylformamide, suggesting a dynamic rearrangement in response to the new solvent environment. Importantly, transient absorption and time-resolved microwave conductivity measurements confirm that the solvent-transferred oNPs maintain their ability to generate free charges at an internal heterojunction. This development opens unique opportunities for eventually leveraging light-generated, long-lived electrons and holes in synthetic redox chemistry across diverse solvent environments, a direction that will be explored in future studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Choreographing root architecture and rhizosphere interactions through synthetic biology

Abstract Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Multi-scale Dynamics of Water Regulation by Bacteria in Synthetic Soil Microsystems (Final Technical Report)

The objective of this project was to develop a multifunctional in situ platform to link gene expression, regulation, and function with the spatiotemporal context of the whole cell environment. In particular, we focus on a synthetic rhizosphere microhabitat and spatial regulation of genes encoding production of exopolysaccharides, or EPS. We have fully met this objective and report results that support the hypothesis: microbial EPS production, acting at pore throats, limits water evaporation and promotes resilience of terrestrial soil systems.

42 ENGINEERING↗

DOE OSTI2026

Learning thermodynamic master equations for open quantum systems

The characterization of Hamiltonians and other components of open quantum dynamical systems plays a crucial role in quantum computing and other applications. Scientific machine learning techniques have been applied to this problem in a variety of ways, including by modeling with deep neural networks. However, the majority of mathematical models describing open quantum systems are linear, and the natural nonlinearities in learnable models have not been incorporated using physical principles. We present a data-driven model for open quantum systems that includes learnable, thermodynamically consistent terms. The trained model is interpretable, as it directly estimates the system Hamiltonian and linear components of coupling to the environment. We validate the model on synthetic two and three-level data, as well as experimental two-level data collected from a quantum device at Lawrence Livermore National Laboratory.

Mathematics and Computing↗

DOE OSTI2023

Synthetic Biology Toolbox for Nitrogen-Fixing Soil Microbes

The soil environment adjacent to plant roots, termed the rhizosphere, is home to a wide variety of microorganisms that can significantly affect the physiology of nearby plants. Microbes in the rhizosphere can provide nutrients, secrete signaling compounds, and inhibit pathogens. These processes could be manipulated with synthetic biology to enhance the agricultural performance of crops grown for food, energy, or environmental remediation, if methods can be implemented in these nonmodel microbes. A common first step for domesticating nonmodel organisms is the development of a set of genetic engineering tools, termed a synthetic biology toolbox. A toolbox comprises transformation protocols, replicating vectors, genome engineering (e.g., CRISPR/Cas9), constitutive and inducible promoter systems, and other gene expression control elements. Furthermore, this work validated synthetic biology toolboxes in three nitrogen-fixing soil bacteria: Azotobacter vinelandii, Stutzerimonas stutzeri (Pseudomonas stutzeri), and a new isolate of Klebsiella variicola. All three organisms were amenable to transformation and reporter protein expression, with several functional inducible systems available for each organism. S. stutzeri and K. variicola showed more reliable plasmid-based expression, resulting in successful Cas9 recombineering to create scarless deletions and insertions. Using these tools, we generated mutants with inducible nitrogenase activity and introduced heterologous genes to produce resorcinol products with relevant biological activity in the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Isotopic discrimination of natural and anthropogenic perchlorate sources in groundwater in a semi-arid region of northeastern Oregon (USA)

Perchlorate (ClO 4 - ) has synthetic and natural sources. Synthetic ClO 4 - is released to the environment from its use as an oxidant in military and aerospace applications, and from its presence in a variety of common commercial products, such as safety flares, chlorate herbicides, and fireworks. Natural sources of ClO 4 - in the environment include imported nitrate fertilizers derived from salt deposits in the Atacama Desert of Chile and indigenous natural ClO 4 - that accumulates in unsaturated soils and groundwaters in other arid and semi-arid environments, largely from atmospheric deposition. The stable isotope ratios of chlorine ( 37 Cl/ 35 Cl) and oxygen ( 18 O/ 16 O, 17 O/ 16 O) and the isotopic abundance of radioactive 36 Cl in ClO 4 - can be used to discriminate these different sources. Perchlorate was previously detected at relatively high concentrations (3.8–34.7 μg/L) in groundwater from many wells in the Boardman-Umatilla area near the Columbia River in northeastern Oregon, which is a semi-arid, highly agricultural, heavily irrigated area that includes several past and current military installations. Eight representative groundwater wells were sampled throughout this region and isotopic characteristics of ClO 4 - collected from each well were measured along with other chemical and isotopic parameters including tritium and other groundwater age indicators. We report isotopic data indicate that indigenous natural ClO 4 - was present in groundwater from all sampled wells and was the predominant source in five of the wells. Synthetic ClO 4 - was present in the three remaining wells with natural ClO 4 - , and a minor fraction of Atacama-fertilizer-derived ClO4- was indicated in one of the wells. Data from this study expand the geographic area of the USA in which indigenous natural ClO 4 - has been detected to include the semi-arid northwest. This study also illustrates the role of irrigation recharge as a mechanism for producing relatively high concentrations of indigenous natural ClO 4 - in groundwater by flushing accumulated salts from the unsaturated zone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗