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DOE OSTI2025

Diversity in the Common Fold: Structural Insights into Class D β-Lactamases from Gram-Negative Pathogens

Class D β-lactamases (DBLs) represent a major threat to antibiotic efficacy by hydrolyzing β-lactam drugs, including last-resort carbapenems, thereby driving antimicrobial resistance in Gram-negative bacteria. The enzymes share a structurally conserved two-domain α/β architecture with seven active-site motifs and three flexible extended loops (the P-loop, Ω-loop, and newly designated B-loop) that surround the active site. While each of these loops is known to influence enzyme function, their coordinated roles have not been fully elucidated. To investigate the significance of their interplay, we compared the sequences and crystal structures of 40 DBLs from clinically relevant Gram-negative pathogens and performed molecular dynamics simulations on selected representatives. Combined structural and dynamical analyses revealed a strong correlation between B-loop architecture and carbapenemase activity in the pathogens Klebsiella and Acinetobacter, particularly regarding loop length and spatial organization. These findings emphasize the B-loop’s critical contribution, in concert with the P- and Ω-loops, in tuning active site versatility, substrate recognition, catalytic activity, and structural stability. A deeper understanding of how these motifs and loops govern DBL function may inform the development of novel antibiotics and inhibitors targeting this class of enzymes.

antibiotic resistance↗

DOE OSTI2025

Strongly nonlinear wave propagation in elasto-plastic metamaterials: Low-order dynamic modeling

Nonlinear elastic metamaterials are known to support a variety of dynamic phenomena that enhance our capacity to manipulate elastic waves. Since these properties stem from complex, subwavelength geometry, full-scale dynamic simulations are often prohibitively expensive at scales of interest. Prior studies have therefore utilized low-order effective medium models, such as discrete mass-spring lattices, to capture essential properties in the long-wavelength limit. While models of this type have been successfully implemented for a wide variety of nonlinear elastic systems, they have predominantly considered dynamics depending only on the instantaneous kinematics of the lattice, neglecting history-dependent effects, such as wear and plasticity. Here, to address this limitation, the present study develops a lattice-based modeling framework for nonlinear elastic metamaterials undergoing plastic deformation. Due to the history- and rate-dependent nature of plasticity, the framework generally yields a system of differential-algebraic equations whose computational cost is significantly greater than an elastic system of comparable size. We demonstrate the method using several models inspired by classical lattice dynamics and continuum plasticity theory and explore means to obtain empirical plasticity models for general geometries, thereby gaining insight into the influence of microstructural plasticity on effective material performance, which can be used to improve the design of nonlinear mechanical metamaterials.

Dynamic simulation↗

DOE OSTI2024

eReaxFF force field development for BaZr 0.8 Y 0.2 O 3-δ solid oxide electrolysis cells applications

The use of solid-oxide materials in electrocatalysis applications, especially in hydrogen-evolution reactions, is promising. However, further improvements are warranted to overcome the fundamental bottlenecks to enhancing the performance of solid-oxide electrolysis cells (SOECs), which is directly linked to the more-refined fundamental understanding of complex physical and chemical phenomena and mass exchanges that take place at the surfaces and in the bulk of electrocatalysis materials. Here, we developed an eReaxFF force field for barium zirconate doped with 20 mol% of yttrium, BaZr 0.8 Y 0.2 O 3-δ (BZY20) to enable a systematic, large-length-scale, and longer-timescale atomistic simulation of solid-oxide electrocatalysis for hydrogen generation. All parameters for the eReaxFF were optimized to reproduce quantum-mechanical (QM) calculations on relevant condensed phase and cluster systems describing oxygen vacancies, vacancy migrations, electron localization, water adsorption, water splitting, and hydrogen generation on the surfaces of the BZY20 solid oxide. Using the developed force field, we performed both zero-voltage (excess electrons absent) and non-zero-voltage (excess electrons present) molecular dynamics simulations to observe water adsorption, water splitting, proton migration, oxygen-vacancy migrations, and eventual hydrogen-production reactions. Based on investigations offered in the present study, we conclude that the eReaxFF force field-based approach can enable computationally efficient simulations for electron conductivity, electron leakage, and other non-zero-voltage effects on the solid oxide materials using the explicit-electron concept. Moreover, we demonstrate how the eReaxFF force field-based atomistic-simulation approach can enhance our understanding of processes in SOEC applications and potentially other renewable-energy applications.

08 HYDROGEN↗

DOE OSTI2025

A Hybrid Dynamic/Steady-State Tool With Protection Simulation for Cascading-Outage Analysis of Extreme Events in Power Systems

The bulk electric power grid is subject to vulnerabilities from component outages, which in certain combinations (extreme events) might lead to cascading outages. Some of these outages can be severe enough to trigger brownouts and blackouts. Much is known about mitigating the first few failures near the beginning of a cascade, but there are few established methods and tools for directly analyzing the risks of cascading component outages over a longer time scale. Current power system tools have limited ability to perform detailed and accurate cascading-outage analysis, which could be computationally intensive. The Dynamic Contingency Analysis Tool (DCAT) enables power system planning engineers to more realistically assess the consequences of extreme contingencies and potential cascading events across their systems and interconnections. DCAT has several unique features: (i) detailed hybrid dynamic and steady-state analysis of power systems to mimic real-world cascading outages, (ii) detailed modeling of protection systems embedded in the dynamic simulation, (iii) simulation of corrective action after transients, (iv) simulation of islanding , and (v) high-performance computing capability to simulate a large number of contingencies in a reasonable time. DCAT outputs will help find technically sound solutions to reduce the risk of cascading outages. This paper provides details of DCAT methodology and shows its capabilities with extreme events on real-world cases.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Diffuse scattering from dynamically compressed single-crystal zirconium following the pressure-induced α → ω phase transition

The prototypical α → ω phase transition in zirconium is an ideal test bed for our understanding of polymorphism under extreme loading conditions. After half a century of study, a consensus had emerged that the transition is realized via one of two distinct displacive mechanisms, depending on the nature of the compression path. However, recent dynamic-compression experiments equipped with diffraction diagnostics performed in the past few years have revealed new transition mechanisms, demonstrating that our understanding of the underlying atomistic dynamics and transition kinetics is in fact far from complete. We present classical molecular dynamics simulations of the α → ω phase transition in single-crystal zirconium shock compressed along the [0001] axis using a machine-learning-class potential. The transition is predicted to proceed primarily via a modified version of the two-stage Usikov-Zilberstein mechanism, whereby the high-pressure ω phase heterogeneously nucleates at boundaries between grains of an intermediate β phase. We further observe the fomentation of atomistic disorder at the junctions between β grains, leading to the formation of highly defective interstitial material between the ω grains. We directly compare synthetic x-ray diffraction patterns generated from our simulations with those obtained using femtosecond diffraction in recent dynamic-compression experiments, and show that the simulations produce the same unique, anisotropic diffuse scattering signal unlike any previously seen from an elemental metal. Our simulations suggest that the diffuse signal arises from a combination of thermal diffuse scattering, nanoparticlelike scattering from residual kinetically stabilized α and β grains, and scattering from interstitial defective structures. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗

DOE OSTI2026

Effect of Lithium Doping on MgO Hydroxylation and Carbonation

Recovery of magnesium from brines can potentially be used to source MgO (periclase) as a CO 2 sorbent or for Mg-based cements. However, it is not clear how common impurities in brines, such as lithium, affect the resulting MgO reactivity. Here, to test the effect of lithium incorporation on MgO reactivity for hydration and carbonation, we combined computational simulations with experiments. Experimentally altered (Mg,Li)O with a low dopant concentration (0.012 ± 0.002% w/w Li) was characterized using synchrotron-based X-ray scattering and high-resolution electron microscopy to measure reaction layer formation on (Mg,Li)O. Single-crystal X-ray diffraction analysis of (Mg,Li)O demonstrates that the incorporation of lithium leads to the formation of oxygen vacancies. The presence of vacancies is likely causing faster hydroxylation rates as predicted by ab initio molecular dynamics simulations. However, the faster hydroxylation rates likely lead to faster passivation of the surface because we observe thinner reaction layers on (Mg,Li)O samples both over short time periods (30 days) and over long time periods (28 years). After 28 years, the reaction layer on the (Mg,Li)O sample was less than one-third of the thickness of that of the pure MgO sample. In addition, over 30 days, reaction layers on (Mg,Li)O samples primarily formed at steps rather than on terraces, in contrast to our previous observations on MgO. Based on our results, naturally occurring impurities in MgO modify its reactivity even at very low concentrations and need to be considered for accurate reaction rate prediction for application of MgO as a CO 2 sorbent or in cements.

MgO↗

DOE OSTI2025

Excess Density as a Descriptor for Electrolyte Solvent Design

Electrolytes mediate interactions between the cathode and anode and determine performance characteristics of batteries. Mixtures of multiple solvents are often used in electrolytes to achieve desired properties, such as viscosity, dielectric constant, boiling point, and melting point. Conventionally, multi-component electrolyte properties are approximated with linear mixing, but in practice, significant deviations are observed. Excess quantities can provide insights into the molecular behavior of the mixture and could form the basis for designing high-performance electrolytes. Here we investigate the excess density of commonly used Li-ion battery solvents such as cyclic carbonates, linear carbonates, ethers, and nitriles with molecular dynamics simulations. We additionally investigate electrolytes consisting of these solvents and a salt. The results smoothly vary with mole percent and are fit to permutation-invariant Redlich-Kister polynomials. Mixtures of similar solvents, such as cyclic-cyclic carbonate mixtures, tend to have excess properties that are lower in magnitude compared to mixtures of dissimilar substances, such as carbonate-nitrile mixtures. We perform experimental testing using our automated test stand, Clio, to provide validation to the observed simulation trends. We quantify the structure similarity using SOAP fingerprints to create a descriptor for excess density, enabling the design of electrolyte properties. To a first approximation, this will allow us to estimate the deviation of a mixture from ideal behavior based solely upon the structural dissimilarity of the components.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

Sienna Modeling Framework [Slides]

NREL's Sienna modeling framework effectively builds, solves, and analyzes the scheduling problems and dynamic simulations of quasi-static infrastructure systems. It uses a modular framework to answer different questions about future energy systems, fundamentally advancing the nation's ability to model individual and integrated infrastructure systems at a range of spatial and temporal scales. This presentation will include NREL power grid researcher Clayton Barrows.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

Effects of high-pressure hydrogen exposure on filler-elastomer adhesion

Elastomers are known to gain enhanced mechanical properties through compounding with nanosized filler particles such as silica or carbon black. Filler dispersion and filler-polymer interfacial strength are key contributing factors to this improvement. The interfacial strength is critical to part lifetime in pressurized gas sealing applications such as O-rings, where weak binding between the filler particle and polymer matrix can lead to internal void structures. With the aim to build a fundamental understanding of precursors to pressurized hydrogen-induced failure in elastomers, we use all-atom molecular dynamics simulations to study the impact of hydrogen oversaturation on filler-polymer interaction strength. We systematically study the interface between a commonly used elastomer, ethylene-propylene-diene monomer (EPDM) and silica by varying gas concentration, crosslink density, and surface chemistry. Our simulations predict that decompression leads to a localization of excess gas near the interface. In conclusion, we demonstrate that this localized gas can weaken interfacial adhesion and quantify the interaction using thermodynamic approaches.

EPDM↗

DOE OSTI2025

Transport Mechanisms of Hydrogen Gas and Ions in Poly(potassium acrylate) Electrolytes

Poly(potassium acrylate) (PAAK) in high concentration KOH solutions is a promising electrolyte for use in alkaline zinc batteries. Atomistic molecular dynamics simulations are used to investigate the transport mechanisms of hydrogen gas and zincate ions through both KOH solutions and PAAK solutions with comparable concentrations of KOH. Hydrogen molecules do not interact with the ions or the polymer, and simply diffuse through the system. Furthermore, their diffusion constant decreases with both increasing KOH concentration and when in the polymer, due to the increased viscosity of the solution. By contrast, zincate ions form long-lived clusters with the PAAK chains which significantly slow their diffusion.

Batteries↗

DOE OSTI2025

Pressure induced irreversible phase transformation in an ordered high-entropy alloy

We report on a pressure induced irreversible phase transformation in an ordered eutectic high-entropy alloy (EHEA) AlCoCrFeNi2.1. The suction cast sample was synthesized by arc melting of raw elements resulting in an ordered B2 and FCC phase mixture for eutectic AlCoCrFeNi2.1 alloy. This phase mixture was confirmed by transmission electron microscopy (TEM) where superlattice reflections corresponding to ordered B2 phase were observed while the FCC phase remains disordered. The B2 phase was observed to be enriched in Nickel and Aluminum while the surrounding FCC phase is enriched in Fe, Cr and Co. The suction-cast EHEA sample was studied by X-ray diffraction under high pressure in a diamond anvil cell with platinum pressure marker to 73 GPa at ambient temperature. The B2 to FCC phase transformation is completed by 3 GPa in sharp contrast to BCC to FCC phase transition of 21 GPa in additively manufactured EHEA samples. The X-ray diffraction and TEM studies of pressure recovered samples show presence of only FCC grains without any specific orientation with respect to starting sample. These results are consistent with molecular dynamics simulations that the presence of B2 phase aids in the formation of the B2 to FCC phase transition under high pressures.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Rotation of Crystal Seed During Early Stages of Growth Reveals the Anisotropy of Glass Matrix

Glass-ceramics are a highly valuable class of materials that are needed for realizing many high-tech as well as consumer products. They are made by controlling crystallization of glass. Theoretical atomistic insights obtained using molecular dynamics simulations in this work reveal that crystal seeds can spontaneously rotate within glass at high temperatures due to anisotropic forces at the glass-crystal interface. This rotation challenges the long‐held view of glass as isotropic solid, and highlights how atomic‐scale inhomogeneities influence crystal growth and microstructure, hence the physical properties glass‐ceramics.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Macroscale properties and atomic-scale mechanisms of ash removal in low-temperature hydrothermal carbonization

Biogenic ash is a significant impediment to the utilization of agricultural residues in biofuel production. Such challenge can be addressed by various treatments, as demonstrated in this study on the experimental and computational mechanisms involved in the hydrothermal treatment (HT) of wheat straw. A combination of classical (all-atom) molecular dynamics simulations of cellulose carrying silica and calcium species, along with first principles quantum chemical calculations, indicates the dissociation of inorganics from the cellulose with increased HT temperature. Here, this observation is confirmed by experimental evidence of effective ash removal by HT, showing at least 50% removal of sulfur, chlorine, potassium, and calcium, and 12.5% of silica, leading to a reduced total ash content (from 6.7% to 4.2%).Changes in structural features upon HT, such as surface cellular structure and porosity, were revealed, accompanied by an increased specific surface area (from 1.17 to 6.34 m 2 /g). Our simulations suggest that silica binds tightly to the hydrophobic face of cellulose at room temperature, but HT significantly reduces the binding free energy of association with both hydrophobic and hydrophilic surfaces. Most significantly, ash removal leads to an increased calorific value, rising from approximately 16 MJ/kg to about 19 MJ/kg, along with improved thermal behavior. The improved integration combustion index parameter S indicates that the combustion properties improve with ash removal efficiency. The proposed atomic-level mechanism for the observed removal of inorganics during mild HT underscores the potential of such treatment in producing energy-dense wheat straw, a widely available agricultural residue.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Molecular understanding of ion transport in a zwitterionic electrolyte

Zwitterions (ZIs) are unique molecules that carry both positive and negative charges, resulting in overall charge neutrality and high dielectric constants. These distinctive properties have enabled broad applications of zwitterionic functionality, including the emerging use of ZIs in lithium-ion battery electrolytes. As a contribution to this developing field, we use all-atom molecular dynamics simulations to investigate the ion transport mechanisms in amorphous mixtures of a zwitterionic liquid containing a range of LiTFSI salt concentrations. Furthermore, the local coordination environment around the Li + ions plays a strong role in governing ionic conductivity, as well as the enhancement of Li + transport numbers with increasing salt concentration. Addition of small amounts of water leads to increased conductivity and ion mobilities due to the water coordinating with the Li + ions, which reduces direct interactions with larger charged species.

Classical molecular dynamic simulations↗

DOE OSTI2026

Mechanism of ion pairing–induced co-ion penetration into the stern layer

In classical electric double layer (EDL) theory, co-ions—ions carrying the same charge as the electrode—are assumed to be excluded from the Stern layer because of electrostatic repulsion. However, ion pairing with adsorbed counterions may enable co-ions to access the EDL, a phenomenon that remains underexplored. Key questions therefore remain unresolved, including how deeply co-ions penetrate, how ion-specific properties govern them, and how ion pairing within the EDL differs from bulk solution. Here, in this study, we employ molecular dynamics simulations combined with well-tempered metadynamics to quantify co-ion penetration and ion-pairing thermodynamics at positively charged Mg-Al layered double hydroxide interfaces (σ = +20.6 μC/cm 2 ) in aqueous chloride electrolytes across 0.005–3 M range. We reveal a concentration-driven crossover: at dilute conditions, counterion–co-ion contact ion pairing (CIP) is thermodynamically unfavorable or only weakly favorable (ΔG CIP = +0.12 kcal/mol for Li + to −0.42 kcal/mol for K + ), leading to co-ion exclusion. As concentration increases (≥0.5 M), enhanced screening reduces surface repulsion and stabilizes CIP thermodynamics (ΔG CIP = −0.89 kcal/mol for Li + to −1.05 kcal/mol for K + at 3 M), enabling monovalent co-ions to penetrate the Stern layer following the hydration hierarchy K + > Na + > Li + , while divalent co-ions (Mg 2+ , Ca 2+ ) remain in the diffuse layer, forming only solvent-separated pairs. Comparison with bulk solution shows interfacial ion pairing is suppressed at low concentrations but converges to bulk-like thermodynamics at high concentrations, indicating surface effects vanish under strong screening. These results establish a quantitative framework linking ion-pairing thermodynamics to co-ion penetration and providing strategies to design electrochemical interfaces.

Co-ion penetration↗

DOE OSTI2025

Probing Nanorod Assembly and Dynamics in Polymer Nanocomposites in Equilibrium and Shear

Coarse-grained molecular dynamics simulations are used to examine the structure and dynamics of nanorod assemblies in polymer melts under equilibrium and simple shear. We show that as the concentration of nanorods increases, there is a transition from an isotropic phase to a two-phase region in which the nanorods phase separate into a dilute phase and dense bundles of hexagonally packed nanorods. The onset of the two-phase region is below that predicted by Onsager theory, which we attribute to an effective increase in the diameter of nanorods due to a layer of polymer bound to the rod surfaces. Equilibrium simulations show that increasing polymer chain length N enhances nanorod bundling at fixed nanorod concentration. Simulations of systems undergoing simple shear show that flow enhances nanorod alignment and bundling relative to those of equilibrium systems with similar properties. Finally, simulations reveal that increasing nanorod length enhances nanorod alignment under shear at equivalent shear rates but not at equivalent Péclet numbers. Overall, our simulations highlight that polymer matrix-nanorod attraction (i.e., chemistry), shear rate, and matrix chain length are desirable design variables to control the structure of nanorod-containing soft materials under simple shear.

diffusion↗

DOE OSTI2026

Substrate-Directed Dimensional and Phase Control of Peptide Assemblies on Two-Dimensional van der Waals Materials

Understanding and controlling biomolecular self-assembly on van der Waals (vdW) materials has the potential to advance hybrid bioelectronic devices by enabling precise tuning of the interface and modulation of the resulting electronic properties of the biomolecule-vdW heterostructure. However, how surface properties of vdW materials direct biomolecule assembly remains poorly understood. To fill this knowledge gap, we investigated the assembly of a peptide known to assemble into two-dimensional (2D) crystalline films on MoS 2 on three representative vdW surfaces: WS 2 , MoS 2 , and highly oriented pyrolytic graphite (HOPG). Using in situ atomic force microscopy (AFM), we find that assembly is substrate-dependent, resulting in multilayers on WS 2 , monolayers on MoS 2 , and multiple coexisting phases on HOPG. WS 2 exhibits a higher negative charge, strong long-range electrostatic interactions, and extensive hydration layering that may promote multilayer stacking. In contrast, MoS 2 has stronger short-range interactions with the peptides but much weaker long-range interactions and hydration structure, which may favor monolayer formation. Molecular dynamics simulations predict a corresponding switch from monolayer to multilayer aggregates of the adsorbed monomers, reflected in their relative mobilities. On hydrophobic HOPG, the peptides bind most strongly and remain as monomers with high surface mobility. The peptide dimers comprising the basic unit of the crystals are more compact on HOPG, which has a smaller lattice constant than WS 2 or MoS 2 , suggesting strain contributes to stabilizing multiple phases. Our results provide mechanistic insights into how surface charge and hydration structure, and the lattice structure of the substrates governs peptide assembly on vdW materials, offering a framework to rationally control the 2D peptide-vdW heterostructures.

Molecular dynamics simulations↗

DOE OSTI2025

Binding and Translocation of Substrate Allosterically Promotes Functional Interactions Within the AlkB–AlkG Electron Transfer Complex

The alkane monooxygenase AlkB and rubredoxin AlkG form an electron transfer complex that hydroxylates terminal alkanes to produce alcohols. The recent cryoEM study of Fontimonas thermophila AlkB-AlkG complex revealed its architecture, including a dodecane (D12) substrate at the active site. However, FtAlkBG molecular mechanism of action of remains unknown. Here, in this study, we examined its dynamics and interactions by multiscale computations, including molecular dynamics simulations, elastic network models, and QM/MM of the oxygen activation mechanism at the AlkB catalytic site. D12 maintained stable interactions within the catalytic site during two MD runs, coordinated by hydrophobic residues L263-L264, I267, I133. A third extended run revealed that D12 could translocate to a membrane-exposed site near S49/F46 along a hydrophobic channel gated by I54. During this translocation, D12 was temporarily stabilized at intermediate sites IS1 (lined by I27/L30-G31/G50/L53-I54/P59/S124/A127-V128) and IS2 (I33-G34/L37/L45-F46/S49) before nearly exiting the protein, and diffused back to the active site, assisted by L30. Substrate binding and translocation across those intermediate sites affects the coupling between the iron centers in AlkBG, and interfacial interactions between AlkB-AlkG. The channel was further connected to the cytosol, near two surface-exposed arginines, potentially allowing for O 2 passage. The allosteric effects between D12 putative entry site, catalytic site and AlkB-AlkG interface were analyzed by ENM-based methods which confirmed the cooperative perturbation-responses and strongly correlated movements of residues belonging to those distal regions. Our study provides new mechanistic insights into key sites and their interactions that could be targeted for developing AlkB-variants with desirable alkane conversion functions.

59 BASIC BIOLOGICAL SCIENCES↗