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DOE OSTI2021

Early Drug Discovery and Development of Novel Cancer Therapeutics Targeting DNA Polymerase Eta (POLH)

Polymerase eta (or Pol η or POLH) is a specialized DNA polymerase that is able to bypass certain blocking lesions, such as those generated by ultraviolet radiation (UVR) or cisplatin, and is deployed to replication foci for translesion synthesis as part of the DNA damage response (DDR). Inherited defects in the gene encoding POLH (a.k.a., XPV) are associated with the rare, sun-sensitive, cancer-prone disorder, xeroderma pigmentosum, owing to the enzyme’s ability to accurately bypass UVR-induced thymine dimers. In standard-of-care cancer therapies involving platinum-based clinical agents, e.g., cisplatin or oxaliplatin, POLH can bypass platinum-DNA adducts, negating benefits of the treatment and enabling drug resistance. POLH inhibition can sensitize cells to platinum-based chemotherapies, and the polymerase has also been implicated in resistance to nucleoside analogs, such as gemcitabine. POLH overexpression has been linked to the development of chemoresistance in several cancers, including lung, ovarian, and bladder. Co-inhibition of POLH and the ATR serine/threonine kinase, another DDR protein, causes synthetic lethality in a range of cancers, reinforcing that POLH is an emerging target for the development of novel oncology therapeutics. Using a fragment-based drug discovery approach in combination with an optimized crystallization screen, we have solved the first X-ray crystal structures of small novel drug-like compounds, i.e., fragments, bound to POLH, as starting points for the design of POLH inhibitors. The intrinsic molecular resolution afforded by the method can be quickly exploited in fragment growth and elaboration as well as analog scoping and scaffold hopping using medicinal and computational chemistry to advance hits to lead. An initial small round of medicinal chemistry has resulted in inhibitors with a range of functional activity in an in vitro biochemical assay, leading to the rapid identification of an inhibitor to advance to subsequent rounds of chemistry to generate a lead compound. Importantly, our chemical matter is different from the traditional nucleoside analog-based approaches for targeting DNA polymerases.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Asymmetric linker generates intrinsically disordered metal–organic framework with local MOF-74 structure

Here, we report an intrinsically disordered MOF in the MOF-74 family, Mg 2−x (as-dobpdc) (as-dobpdc 4− = 3′,4-dioxidobiphenyl-3,4′-dicarboxylate). Despite the absence of crystallinity, this material exhibits local ordering consistent with that of its crystalline isomers, maintains porosity, and exhibits a high density of open metal sites. Metal–organic frameworks (MOFs) are typically valued for their combination of crystallinity, porosity, and tunability. However, amorphous MOFs can retain local order while introducing advantages, such as broader distribution of active sites types, reduced thermal conductivity, and emergent modes of tunability via control over the type of disorder. Conventional amorphization strategies rely on external stimuli including pressure, temperature, stress, electrical discharge, or fast precipitation. Recently, amorphous MOFs have been accessed directly using low symmetry organic linkers.

Dinakar, Bhavish [Massachusetts Institute of Techn↗

DOE OSTI2023

Band inversion-driven warping and high valley degeneracy

Band inversion is a physical phenomenon that can warp the band structure in topological insulators, generating multiple electronic valleys for conducting carriers. However, the conditions under which band inversion induces warping are not well understood. Here, we derive two general rules that must be satisfied for band warping to occur in centrosymmetric and non-magnetic topological insulators: (1) bands must be sufficiently inverted, and (2) secondary bands must have opposite parity and be close in energy to the band edges. We chart the valley degeneracies that can emerge from band inversion in each of the 11 centrosymmetric point groups, revealing that an increase in the valley degeneracy between 2- and 48-fold is possible from band inversion. The generalized rules offer a unique band engineering approach by capitalizing on the non-trivial electronic structures of topological insulators.

36 MATERIALS SCIENCE↗

DOE OSTI2023

A Perspective on Sustainable Computational Chemistry Software Development and Integration

The power of quantum chemistry to predict the ground and excited state properties of complex chemical systems has driven the development of computational quantum chemistry software, integrating advances in theory, applied mathematics, and computer science. The emergence of new computational paradigms associated with exascale technologies also poses significant challenges that require a flexible forward strategy to take full advantage of existing and forthcoming computational resources. In this context, the sustainability and interoperability of computational chemistry software development are among the most pressing issues. In this perspective, we discuss software infrastructure needs and investments with an eye to fully utilize exascale resources and provide unique computational tools for next-generation science problems and scientific discoveries.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Nanoparticle-Induced Disorder at Complex Liquid–Liquid Interfaces: Effects of Curvature and Compositional Synergy on Functional Surfaces

The self-assembly of surfactant monolayers at interfaces plays a sweeping role in tasks ranging from household cleaning to the regulation of the respiratory system. The synergy between different nanoscale species at an interface can yield assemblies with exceptional properties, which enhance or modulate their function. However, understanding the mechanisms underlying coassembly, as well as the effects of intermolecular interactions at an interface, remains an emerging and challenging field of study. Herein, we study the interactions of gold nanoparticles striped with hydrophobic and hydrophilic ligands with phospholipids at a liquid–liquid interface and the resulting surface-bound complexes. We show that these nanoparticles, which are themselves minimally surface active, have a direct concentration-dependent effect on the rapid reduction of tension for assembling phospholipids at the interface, implying molecular coassembly. Through the use of sum frequency generation vibrational spectroscopy, we reveal that nanoparticles impart structural disorder to the lipid molecular layers, which is related to the increased volumes that amphiphiles can sample at the curved surface of a particle. The results strongly suggest that hydrophobic and electrostatic attractions imparted by nanoparticle functionalization drive lipid–nanoparticle complex assembly at the interface, which synergistically aids lipid adsorption even when lipids and nanoparticles approach the interface from opposite phases. The use of tensiometric and spectroscopic analyses reveals a physical picture of the system at the nanoscale, allowing for a quantitative analysis of the intermolecular behavior that can be extended to other systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Interfacial Electromechanics Predicts Phase Behavior of 2D Hybrid Halide Perovskites

Quasi-two-dimensional (2D) mixed-cation hybrid halide perovskites (A' 2 A N–1 M N X 3N+1 ; A' = large organic molecule with cationic group, A = [Cs + , CH 3 NH 3 + , HC(NH 2 ) 2 + ], M = [Pb, Sn, Ge], X = [I – , Br – , Cl – ]) have rapidly emerged as candidates to improve the structural stability and device lifetime of 3D perovskite semiconductor devices under operating conditions. The addition of the large A' cation to the traditional AMX 3 structure introduces several synthetic degrees of freedom and breaks M–X bonds, giving rise to peculiar critical phase behavior in the phase space of these complex materials. In this work, we propose a thermodynamic model parametrized by first-principles calculations to generate the phase diagram of 2D and quasi-2D perovskites (q-2DPKs) based on the mechanics and electrostatics of the interface between the A' cations and the metal halide octahedral network. Focusing on the most commonly studied methylammonium lead iodide system where A' is n-butylammonium (BA; CH 3 (CH 2 ) 3 NH 3 + ), we find that the apparent difficulty in synthesizing phase-pure samples with a stoichiometric index N > 5 can be attributed to the energetic competition between repulsion of opposing interfacial dipole layers and mechanical relaxation induced by interfacial stress. Our model shows quantitative agreement with experimental observations of the maximum phase-pure stoichiometric index (N crit ) and explains the nonmonotonic evolution of the lattice parameters with increasing stoichiometric index (N). This model is generalizable to the entire family of q-2DPKs and can guide the design of photovoltaic and optical materials that combine the structural stability of the q-2DPKs while retaining the charge carrier properties of their 3D counterparts.

14 SOLAR ENERGY↗

DOE OSTI2020

Rapid Mineral Precipitation During Shear Fracturing of Carbonate-Rich Shales

Target subsurface reservoirs for emerging low-carbon energy technologies and geologic carbon sequestration typically have low permeability and thus rely heavily on fluid transport through natural and induced fracture networks. Sustainable development of these systems requires deeper understanding of how geochemically mediated deformation impacts fracture microstructure and permeability evolution, particularly with respect to geochemical reactions between pore fluids and the host rock. Here, a series of triaxial direct shear experiments was designed to evaluate how fractures generated at subsurface conditions respond to penetration of reactive fluids with a focus on the role of mineral precipitation. Calcite-rich shale cores were directly sheared under 3.5 MPa confining pressure using BaCl 2 -rich solutions as a working fluid. Experiments were conducted within an X-ray computed tomography (xCT) scanner to capture 4-D evolution of fracture geometry and precipitate growth. Three shear tests evidenced nonuniform precipitation of barium carbonates (BaCO 3 ) along through-going fractures, where the extent of precipitation increased with increasing calcite content. Precipitates were strongly localized within fracture networks due to mineral, geochemical, and structural heterogeneities and generally concentrated in smaller apertures where rock:water ratios were highest. The combination of elevated fluid saturation and reactive surface area created in freshly activated fractures drove near-immediate mineral precipitation that led to an 80% permeability reduction and significant flow obstruction in the most reactive core. While most previous studies have focused on mixing-induced precipitation, this work demonstrates that fluid–rock interactions can trigger precipitation-induced permeability alterations that can initiate or mitigate risks associated with subsurface energy systems.

58 GEOSCIENCES↗

DOE OSTI2025

Quantum description of wave dark matter

We outline a fundamentally quantum description of bosonic dark matter (DM) from which the conventional classical-wave picture emerges in the limit 𝑚 ≪10 eV. As appropriate for a quantum system, we start from the density matrix, which encodes the full information regarding the possible measurements we could make of DM and their fluctuations. Following fundamental results in quantum optics, we argue that for DM it is most likely that the density matrix takes the explicitly mixed form of a Gaussian over the basis of coherent states. Deviations from this would generate non-Gaussian fluctuations in DM observables, allowing a direct probe of the quantum state of DM. Our quantum optics–inspired approach allows us to rigorously define and interpret various quantities that are often only described heuristically, such as the coherence time or length. The formalism further provides a continuous description of DM through the wave-particle transition, which we exploit to study how density fluctuations over various physical scales evolve between the two limits and to reveal the unique behavior of DM near the boundary of the wave and particle descriptions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Redefining precision interferometry and spectroscopy with high-performance optical interference coatings

High-performance optical interference coatings have transformed precision interferometry and spectroscopy by enabling unparalleled control over light–matter interactions. This review explores recent innovations in ion-beam sputtered amorphous dielectric, as well as substrate-transferred crystalline coatings, and their impact on systems at the forefront of precision metrology. These state-of-the-art coating techniques generate multilayers with ultralow optical losses, yielding mirrors with exceptional reflectivity. Refinements in their noise performance push the ultimate limits of sensitivity, resolution, and stability in demanding laser-based metrology applications. These technologies underpin the most advanced timekeeping and spatial measurement tools, enabling high-finesse reference cavities for the world’s most precise optical atomic clocks and low-noise reflective test masses for km-baseline gravitational-wave detectors. Emerging hybrid designs combining these techniques expand access to the mid-infrared spectral region, enabling the first ultralow-optical-loss coatings in the 3000–5000 nm wavelength range for enhanced spectroscopy and trace-gas detection. We highlight how these technologies redefine coating performance metrics and set new benchmarks in quantum science, fundamental physics, and precision optical sensing.

Cole, Garrett D. [University of Arizona, Tucson, A↗

DOE OSTI2020

Updated Medical Waste Management Plans and Emergency Action Plans for the Lawrence Livermore National Laboratory Main Site

Attached are the updated Medical Waste Management Plans and Emergency Action Plans for Lawrence Livermore National Laboratory’s (LLNL) Biosafety Level 2 (BSL-2) facilities and Biosafety Level 3 (BSL-3) facility. A redline version of each document has also been provided. Minor changes such as facility personnel, contact information, and titles for those that support onsite Biosafety Labs at LLNL have been made to the document. It should be noted that the most recent versions of the Medical Waste Large Quantity Generator Registration Application Form and Medical Waste Management Plan were incorporated and sourced from the Alameda County Department of Environmental Health website.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Cybersecurity Resiliency of Marine Renewable Energy Systems Part 2: Cybersecurity Best Practices and Risk Management

Marine renewable energy (MRE) is an emerging source of power for marine applications, marine devices, and coastal communities. This energy source relies on industrial control systems and IT to support operations and maintenance activities, which create a pathway for an adversary to gain unauthorized access to systems and data and disrupt operations. Incorporating cybersecurity risk prevention measures and mitigation capabilities from inception, development, operation, to decommissioning of the MRE system and components is paramount to the protection of energy generation and the security of network architecture and infrastructure. To improve the resilience of MRE systems as a predictable, affordable, and reliable source of energy, cybersecurity guidance was developed to enable operators to assess cybersecurity risks and implement security measures commensurate with the risk. This publication is the second of a two-part series, with Part 1 addressing a framework to determine cybersecurity risk by assessing the vulnerability of an MRE system to potential cyber threats and the consequences a cyberattack would have on the end user. This Part 2 publication describes an approach to select appropriate cybersecurity best practices commensurate with the MRE system's cybersecurity risk. The guidance includes 86 cybersecurity best practices, which are associated with 36 cybersecurity domains and grouped into nine categories. The best practices follow the core functions of the National Institute of Science and Technology Cybersecurity Framework (e.g., identify, detect, protect, respond, and and recover) and insights from both maritime and energy industry guidance documents to identify security measures effective in protecting information and operational technology assets prevalent in MRE systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Discovering mechanisms for materials microstructure optimization via reinforcement learning of a generative model

Abstract The design of materials structure for optimizing functional properties and potentially, the discovery of novel behaviors is a keystone problem in materials science. In many cases microstructural models underpinning materials functionality are available and well understood. However, optimization of average properties via microstructural engineering often leads to combinatorically intractable problems. Here, we explore the use of the reinforcement learning (RL) for microstructure optimization targeting the discovery of the physical mechanisms behind enhanced functionalities. We illustrate that RL can provide insights into the mechanisms driving properties of interest in a 2D discrete Landau ferroelectrics simulator. Intriguingly, we find that non-trivial phenomena emerge if the rewards are assigned to favor physically impossible tasks, which we illustrate through rewarding RL agents to rotate polarization vectors to energetically unfavorable positions. We further find that strategies to induce polarization curl can be non-intuitive, based on analysis of learned agent policies. This study suggests that RL is a promising machine learning method for material design optimization tasks, and for better understanding the dynamics of microstructural simulations.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Emergence of nosocomial associated opportunistic pathogens in the gut microbiome after antibiotic treatment

Introduction: According to the Centers for Disease Control’s 2015 Hospital Acquired Infection Hospital Prevalence Survey, 1 in 31 hospital patients was infected with at least one nosocomial pathogen while being treated for unrelated issues. Many studies associate antibiotic administration with nosocomial infection occurrence. However, to our knowledge, there is little to no direct evidence of antibiotic administration selecting for nosocomial opportunistic pathogens. Aim: This study aims to confirm gut microbiota shifts in an animal model of antibiotic treatment to determine whether antibiotic use favors pathogenic bacteria. Methodology: We utilized next-generation sequencing and in-house metagenomic assembly and taxonomic assignment pipelines on the fecal microbiota of a urinary tract infection mouse model with and without antibiotic treatment. Results: Antibiotic therapy decreased the number of detectable species of bacteria by at least 20-fold. Furthermore, the gut microbiota of antibiotic treated mice had a significant increase of opportunistic pathogens that have been implicated in nosocomial infections, like Acinetobacter calcoaceticus/baumannii complex, Chlamydia abortus, Bacteroides fragilis, and Bacteroides thetaiotaomicron. Moreover, antibiotic treatment selected for antibiotic resistant gene enriched subpopulations for many of these opportunistic pathogens. Conclusions: Oral antibiotic therapy may select for common opportunistic pathogens responsible for nosocomial infections. In this study opportunistic pathogens present after antibiotic therapy harbored more antibiotic resistant genes than populations of opportunistic pathogens before treatment. Our results demonstrate the effects of antibiotic therapy on induced dysbiosis and expansion of opportunistic pathogen populations and antibiotic resistant subpopulations of those pathogens. Follow-up studies with larger samples sizes and potentially controlled clinical investigations should be performed to confirm our findings.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Material Design Strategies for Recovery of Critical Resources from Water

Population growth, urbanization, and decarbonization efforts are collectively straining the supply of limited resources that are necessary to produce batteries, electronics, chemicals, fertilizers, and other important products. Securing the supply chains of these critical resources via the development of separation technologies for their recovery represents a major global challenge to ensure stability and security. Surface water, groundwater, and wastewater are emerging as potential new sources to bolster these supply chains. Recently, a variety of material-based technologies have been developed and employed for separations and resource recovery in water. Judicious selection and design of these materials to tune their properties for targeting specific solutes is central to realizing the potential of water as a source for critical resources. Here, the materials that are developed for membranes, sorbents, catalysts, electrodes, and interfacial solar steam generators that demonstrate promise for applications in critical resource recovery are reviewed. In addition, a critical perspective is offered on the grand challenges and key research directions that need to be addressed to improve their practical viability.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Trajectory Ensemble Methods Provide Single-Molecule Statistics for Quantum Dynamical Systems

The emergence of experiments capable of probing quantum dynamics at the single-molecule level requires the development of new theoretical tools capable of simulating and analyzing these dynamics beyond an ensemble-averaged description. In this article, we present an efficient method for sampling and simulating the dynamics of the individual quantum systems that make up an ensemble and apply it to study the nonequilibrium dynamics of the ubiquitous spin-boson model. We generate an ensemble of single-system trajectories, and we analyze this trajectory ensemble using tools from classical statistical mechanics. Our results demonstrate that the dynamics of quantum coherence is highly heterogeneous at the single-system level due to variations in the initial bath configuration, which significantly affects the transient exchange of coherence between the system and its bath. Here, we observe that single systems tend to retain coherence over time scales longer than that of the ensemble. We also compute a novel thermodynamic entanglement entropy that quantifies a thermodynamic driving force favoring system–bath entanglement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Is more better? Polyploidy in crops with diverse end uses and the potential for future applications

Increasing the number of chromosome sets can increase cell size and improve yields in some crops. Breeding polyploid crops introduces unique challenges compared to diploid species, which has deterred many from exploring the potential benefits. Despite this, recent technological advancements have alleviated some of the challenges related to complex genomes and enabled the improvement of many polyploid crops. Given these advancements, there is a need to review the use of higher ploidy crops and explore potential opportunities for increased chromosome number. Many of the leading bioenergy crops are polyploids and there may be additional opportunities to further diversify feedstocks for emerging bioenergy markets. Such diversification would help to meet the anticipated increase in renewable and sustainable energy demands. Here, in this perspective review, we review polyploid crops and the extent to which ploidy level impacts improvement and production. The advantages and disadvantages of each crop are discussed in the context of their ploidy level and end-use. Particular emphasis is given to the current role and potential of polyploidy in creating the next generation of bioenergy feedstocks. Polyploids present challenges to crop improvement due to their complex genomes, but many of these difficulties can and have been overcome with technological advancements. Approaches that facilitate the use of higher ploidy crops open a path to capturing the many benefits of polyploidy, such as increased fruit and seed size, vigour, diversity, biomass and yield quality. However, these benefits are not observed across all species. This further emphasizes the need to study higher ploidy in traditionally diploid crops.

bioenergy↗

DOE OSTI2020

Chiral Instabilities and the Onset of Chiral Turbulence in QED Plasmas

We present a first principles study of chiral plasma instabilities and the onset of chiral turbulence in QED plasmas with strong gauge matter interaction ( e 2 N f = 64 ), far from equilibrium. By performing classical-statistical lattice simulations of the microscopic theory, we show that the generation of strong helical magnetic fields from a helicity imbalance in the fermion sector proceeds via three distinct phases. During the initial linear instability regime the helicity imbalance of the fermion sector causes an exponential growth (damping) of magnetic field modes with right- (left-) handed polarization, for which we extract the characteristic growth (damping) rates. Secondary growth of unstable modes accelerates the helicity transfer from fermions to gauge fields and ultimately leads to the emergence of a self-similar scaling regime characteristic of a decaying turbulence, where magnetic helicity is efficiently transferred to macroscopic length scales. Within this turbulent regime, the evolution of magnetic helicity spectrum can be described by an infrared power spectrum with spectral exponent κ = 10.2 ± 0.5 and dynamical scaling exponents α = 1.14 ± 0.50 and β = 0.37 ± 0.13 .

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Field Validation of Electrocoagulation Treatment for Oily Wastewater at Cleveland-Cliffs Steel Mill in Cleveland, OH

The Industrial Technology Validation (ITV) program aims to identify and demonstrate the performance of new, emerging, and underutilized technologies in the industrial sector to help inform decisions towards accelerating commercialization and deployment. This initiative aims to identify, validate, and showcase new, emerging, and underutilized technologies in the industrial sector to expedite their commercialization and widespread deployment. By conducting thorough validations and demonstrating the efficacy of these technologies, the ITV program facilitates informed decision-making among industry stakeholders, contributing to the transition towards more sustainable and efficient industrial processes. This ITV demonstration involved the testing of an electrocoagulation (EC) treatment system at a steel plant in Ohio. The system was designed to treat oily wastewater generated from cold rolling operations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗