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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Phonons reveal coupled cholesterol-lipid dynamics in ternary membranes

Experimental studies of collective dynamics in lipid bilayers have been challenging due to the energy resolution required to observe these low-energy phonon-like modes. However, inelastic X-ray scattering (IXS) measurements — a technique for probing vibrations in soft and biological materials — are now possible with sub-meV resolution, permitting direct observation of low energy, phonon-like modes in lipid membranes. Here, in this study, IXS measurements with sub-meV energy resolution reveal a low-energy optic-like phonon mode at roughly 3 meV in the liquid-ordered (L o ) and liquid-disordered (L d ) phases of a ternary lipid mixture. This mode is only observed experimentally at momentum transfers greater than 5 nm -1 in the L o system. A similar gapped mode is also observed in all-atom molecular dynamics (MD) simulations of the same mixture, indicating that the simulations accurately represnt the fast, collective dynamics in the L o phase. It’s optical nature and the Q range of the gap together suggest that the observed mode is due to the coupled motion of cholesterol-lipid pairs, separated by several hydrocarbon chains within the membrane plane. Analysis of the simulations provide molecular insight into the origin of the mode in transient, nanoscale substructures of hexagonally packed hydrocarbon chains. This nanoscale hexagonal packing was previously reported based on molecular dynamics simulations and later by NMR measurements. Here, however, the integration of IXS and MD simulations identifies a new signature of the L o substructure in the collective lipid dynamics, thanks to the recent confluence of IXS sensitivity and MD simulation capabilities.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural dynamics and rejuvenation during cryogenic cycling in a Zr-based metallic glass

Subjecting metallic glasses repeatedly to liquid nitrogen temperature has become a popular method to homogeneously rejuvenate the material. Here in this paper we reveal the atomic-scale structural dynamics using in-situ x-ray photon correlation spectroscopy (XPCS) during and after cryogenic cycling of a Zr-based metallic glass in two structural states (plate and ribbon). Heterogeneous structural dynamics is observed at 300 K that changes to monotonic aging at 78 K. It is found that cryogenic cycling homogenizes the relaxation time distribution. This effect is much more pronounced in the ribbon, which is the only structural state that rejuvenates upon cycling. We furthermore reveal how fast atomic-scale dynamics is correlated with long-time structural relaxation times irrespective of the structural state, and that the ribbon exhibits unexpected additional fast atomic-scale relaxation in comparison to the plate material. A structural picture emerges that points towards heterogeneities in the fictive temperature as a requirement for cryogenic energy storage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Data-Driven Discovery of Linear Molecular Probes with Optimal Selective Affinity for PFAS in Water

Approaches to tackle the wide and growing variety of highly persistent per- and polyfluoroalkyl substances (PFAS) are of pressing global need because of their detrimental human health effects, such as cancer, birth defects, and hormone imbalance. Sensitive, selective, and easy-to-use real-time sensors to monitor and detect PFAS and sorbents to extract them are critical to meeting government-mandated environmental concentrations. In this work, we combine all-atom molecular dynamics simulations, enhanced sampling, deep representational learning, and Bayesian optimization to perform high-throughput virtual screening for highly sensitive and selective molecular probes. Our molecular design space consists of 3850 linear hydrocarbon chains with varying degrees of halogenation with and without amine- and phosphine-based headgroups. By employing a data-driven search process, we efficiently explore the molecular design space to optimize the sensitivity to perfluorooctanesulfonic acid (PFOS) as a prototypical PFAS analyte and selectivity relative to a sodium dodecyl sulfate (SDS) interferent. We calculate 504 Gibbs free energies of probe-analyte and probe-interferent interactions and identify probes with PFOS association free energies of up to (-ΔG PFOS ) = 9.8 ± 0.2 kJ/mol and selectivities relative to SDS of (-ΔΔG PFOS–SDS ) = 3.1 ± 1.5 kJ/mol. A C 11 Br 23 P(CH 3 ) 2 probe containing 11 backbone brominated carbons and a tertiary phosphine headgroup possesses the most sensitive binding constant to PFOS within the defined search space of K b PFOS = 177.4 ± 12.7, and a semibrominated probe C 5 H 11 C 7 Br 14 N(CH 3 ) 2 containing 12 backbone carbons and a tertiary amine headgroup possesses the highest selectivity relative to SDS of K b PFOS /K b SDS = 4.6 ± 1.7. A retrospective analysis of our data to extract interpretable design rules reveals that the sensitivity of linear hydrogenated probes increases by approximately 1 kJ/mol per C–C bond. The addition or removal of halogen atoms and amine or phosphine headgroups produces nonmonotonic changes in both sensitivity and selectivity with changes to the sensitivity of up to 2.5 kJ/mol. Finally, this work places empirical limitations on the performance of a wide range of linear probes for PFOS detection and offers a generic strategy for high-throughput computational screening to promote selective and sensitive binding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Hydrophilic and Apolar Hydration in Densely Grafted Cationic Brushes and Counterions with Large Mobilities

We employ all-atom molecular dynamics (MD) simulation framework to unravel water microstructure and ion properties for cationic [Poly(2-(methacryloyloxy)ethyl trimethylammonium chloride] (PMETAC) brushes with chloride ions as counterions. First, we identify locally separate water domains (or first hydration shells) each around the {N(CH 3 ) 3 } + and the C=O functional groups of the PMETAC chain and one around the Cl - ion. These first hydration shells around the respective moieties overlap and the extent of the overlap depends on the nature of the species triggering it. Second, despite the overlap, the water molecules in these domains demonstrate disparate properties dictated by the properties of the atoms/groups around which they are located. For example, the presence of the methyl groups make the {N(CH 3 ) 3 } + group trigger apolar hydration as evidenced by the corresponding orientation of the dipole of the water molecules around the {N(CH 3 ) 3 } + moiety. These water molecules around the N(CH 3 ) 3 } + group also have enhanced tetrahedrality as compared to the water molecules constituting the hydration layer around the C=O group and the Cl - counterion. Our simulations also identify that there is an intervening water layer between the Cl - ion and {N(CH 3 ) 3 } + group: this layer prevents the Cl - ion from coming very close to the {N(CH 3 ) 3 } + group. As a consequence, there is a significantly large mobility of the Cl - ions inside the PMETAC brush layer. Furthermore, the C=O group of the PE chain, due to the partial negative charge on the oxygen atom and the specific structure of the PMETAC brush system, demonstrates strongly hydrophilic behavior and enforces a specific dipole response of water molecules analogous to that experienced by water around anionic species of high charge density. As a result, our findings confirm that PMETAC brushes undergo hydrophilic hydration at one site, apolar hydration at another site, and ensures large mobility of the supported Cl- counterions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Atomic Evolution of Hydrogen Intercalation Wave Dynamics in Palladium Nanocrystals Revealed by Liquid-Phase Transmission Electron Microscopy

Solute-intercalation-induced phase separation creates spatial heterogeneities in host materials, a phenomenon ubiquitous in batteries, hydrogen storage, and other energy devices. Despite many efforts, probing intercalation processes at the atomic scale has been a significant challenge. By utilizing liquid-phase transmission electron microscopy (TEM), we study hydrogen (de)intercalation in palladium nanocrystals as a model system and have achieved unprecedented atomic-resolution imaging of hydrogen intercalation wave dynamics. Our observations reveal that intercalation wave mechanisms, instead of shrinking-core mechanisms, prevail at ambient temperature for palladium nanocubes ranging from ∼60 nm down to ∼10 nm. Systematic image analysis uncovers the atomic evolution of the hydrogen intercalation wave, transitioning from nonplanar and inclined boundaries to those closely aligned with {100} planes. Our kinetic Monte Carlo simulations demonstrate that the observed intercalation wave dynamics correspond to sorption pathways minimizing the lattice mismatch strain at the phase boundary. In conclusion, unveiling the atomic intercalation pathways holds profound implications for engineering intercalation-mediated devices and advancements in energy sciences.

Lee, Daewon [Lawrence Berkeley National Laboratory↗
DOE OSTI2025

Designing Physicochemically‐Ordered Interphases for High‐Performance Composites

To enhance the mechanical properties of carbon fiber‐reinforced polymer composites, a physicochemical scaffold is designed incorporating microscopically architected chemically reactive nanofibers that act as a multiscale bridge between the carbon fibers and the matrix. Thermally activated nanofibers leverage their morphologically driven mechanochemical properties to form covalent bonds with adjacent polymer molecules, creating a co‐continuous network that dramatically enhances fiber‐matrix load transfer. By meticulously controlling the nanofiber architecture through variable surface area, functional group availability, and polymer chain alignment effects, the extent of covalent bonding between nanofibers and the matrix is manipulated ultimately resulting in improved carbon fiber‐matrix adhesion. Further, the concept was validated using polyacrylonitrile nanofibers within an acrylonitrile butadiene styrene matrix in a discontinuous carbon fiber‐reinforced composite system. Nanomechanical studies using atomic force microscopy and low‐field nuclear magnetic resonance spectroscopy confirmed immobilized, chemically transferred, and ordered nanostructures at the interphase. The resulting composites demonstrated ≈56% and ≈175% improvements in tensile strength and toughness, respectively, compared to composites without nanofiber. Comprehensive thermal, rheological, and X‐ray scattering analyses, along side all‐atomic molecular dynamics simulations, revealed the fundamental mechanisms behind these improvements in mechanical behavior. The versatility and efficacy of the approach have the potential to address longstanding interphase challenges in the composite industry.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Characterizing the Geometry and Quantifying the Impact of Nanoscopic Electrocatalyst/Semiconductor Interfaces under Solar Water Splitting Conditions

The materials that are receiving the most attention in photoelectrochemical water splitting are metallic nanoparticle electrocatalysts (np-EC) attached to the surface of a semiconductor (SC) light absorber. In these multicomponent systems, the interface between the semiconductor and electrocatalysts critically affects performance. However, the np-EC/SC interface remains poorly understood as it is complex on atomic scales, dynamic under reaction conditions, and inaccessible to direct experimental probes. This contribution sheds light on how the electrocatalyst/semiconductor interface evolves under reaction conditions by investigating the behavior of nickel electrocatalysts (as nanoparticles and films) deposited on silicon semiconductors. Rigorous electrochemical experiments, interfacial atomistic characterization, and computational modeling are combined to demonstrate critical links between the atomistic features of the interface and the overall performance. It is shown that electrolyte-induced atomistic changes to the interface lead to (1) modulation of the charge carrier fluxes and a dramatic decrease in the electron/hole recombination rates and (2) a change in the barrier height of the interface. Additionally, the critical roles of nonidealities and electrocatalyst coverage due to interfacial geometry are explored. Each of these factors must be considered to optimize the design of metal/semiconductor interfaces which are broadly applicable to photoelectrocatalysis and photovoltaic research.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Molecular basis for higher affinity of SARS-CoV-2 spike RBD for human ACE2 receptor

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused substantially more infections, deaths, and economic disruptions than the 2002-2003 SARSCoV. The key to understanding SARS-CoV-2's higher infectivity lies partly in its host receptor recognition mechanism. Experiments show that the human angiotensin converting enzyme 2 (ACE2) protein, which serves as the primary receptor for both CoVs, binds to the receptor binding domain (RBD) of CoV-2's spike protein stronger than SARS-CoV's spike RBD. The molecular basis for this difference in binding affinity, however, remains unexplained from X-ray structures. To go beyond insights gained from X-ray structures and investigate the role of thermal fluctuations in structure, we employ all-atom molecular dynamics simulations. Microseconds-long simulations reveal that while CoV and CoV-2 spike-ACE2 interfaces have similar conformational binding modes, CoV-2 spike interacts with ACE2 via a larger combinatorics of polar contacts, and on average, makes 45% more polar contacts. Correlation analysis and thermodynamic calculations indicate that these differences in the density and dynamics of polar contacts arise from differences in spatial arrangements of interfacial residues, and dynamical coupling between interfacial and non-interfacial residues. Furthermore, these results recommend that ongoing efforts to design spike-ACE2 peptide blockers will benefit from incorporating dynamical information as well as allosteric coupling effects.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods

Three-dimensional structure determination and prediction of proteins with intrinsically disordered regions, unstructured regions, conformational flexibility, and lacking homologous structures are challenging. We previously predicted and refined an in silico structure of a plant cellulose synthase from cotton (GhCESA1), and more recently, cryo-electron microscopy (cryo-EM) has resolved a majority of the lengths of two CESA structures from poplar (PttCESA8) and cotton (GhCESA7). However, 26–30% of these cryo-EM structures remain unresolved, including the N-terminal domain, half of the class-specific region, the gating loop region, and the C-terminal domain. Here, we describe the generation and evaluation of a full-length hybrid GhCESA1 model based on this cryo-EM PttCESA8 structure, with unresolved regions completed using this in silico refined GhCESA1 model. All-atom molecular dynamics simulations and subsequent energy minimizations were performed for the in silico and hybrid GhCESA1 models in a lipid bilayer-water-ion environment, and structural stability, dynamics, energetics, contacts, and quality were evaluated. The unresolved regions were found to be the most dynamic, in agreement with their poor electron density with cryo-EM. The hybrid model exhibited a higher total secondary structure content, more favorable intra-protein and protein-lipid interaction energies, and improved quality metrics. Moreover, hydrogen bonding was revealed to be a primary mechanism for intra-protein and protein-lipid contacts. These results demonstrate that in silico structure prediction and refinement may be useful to augment experimental structure determination, especially for disordered and unstructured regions. Furthermore, this hybrid model can serve as a steppingstone to derive full-length homology models of other CESAs found in more experimentally tractable organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The relation between lignin sequence and its 3D structure

Background: Lignin, the second most abundant biopolymer on earth, plays a major structural role in plants, conferring mechanical strength and regulating water conduction. Understanding the three-dimensional structure of lignin is important for fundamental reasons as well as engineering plants towards lignin valorization. Lignin lacks a specific primary sequence, making its average chemical composition the focus of most recent studies. However, it remains unclear whether the 3D structure of lignin molecules depends on their sequence. Methods: In this work, we performed all-atom molecular dynamics simulation of three S/G-lignin molecules with the same average composition but different sequence. Results: A detailed statistical analysis of the radius of gyration and relative shape anisotropy reveals that the lignin sequence has no statistically significant effect on the global three-dimensional structure. We found however, that homopolymers of C-lignin with the same molecular weight have smaller radii of gyration than S/G-lignin. We attribute this to lower hydroxyl content of C-lignin, which makes it more compact and rigid. Conclusions: The 3D structure of lignin is influenced by the overall content of monomeric units and interunit linkages and not by its precise primary sequence. General Significance: Lignin is assumed to not have a well-defined primary structure. The results presented here demonstrate there are no significant differences in the global 3D structure of lignin molecules with the same average composition but different primary sequence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Scanning the RBD-ACE2 molecular interactions in Omicron variant

The emergence of new SARS-CoV-2 variants poses a threat to the human population where it is difficult to assess the severity of a particular variant of the virus. Spike protein and specifically its receptor binding domain (RBD) which makes direct interaction with the ACE2 receptor of the human has shown prominent amino acid substitutions in most of the Variants of Concern. Here, in this work, by using all-atom molecular dynamics simulations we compare the interaction of Wild-type RBD/ACE2 receptor complex with that of the latest Omicron variant of the virus. We observed a very interesting diversification of the charge, dynamics and energetics of the protein complex formed upon mutations. These results would help us in understanding the molecular basis of binding of the Omicron variant with that of SARS-CoV-2 Wild-type.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Molecular-Level Behavior of Imidazolium-Based Ionic Liquid Mixtures

Understanding the molecular-level organization of anions and cations in a mixture of different ionic liquids (ILs) is challenging, but it can be very important for designing solvents and IL-based membrane materials. In this work, we perform all-atom molecular dynamics (MD) simulations to understand the intermolecular interactions and structuring of both neat and mixed IL compositions containing 1-benzyl-3-methylimidazolium [ZMIM + ], 1-butyl-3-methylimidazolium [BMIM + ], bistriflimide [Tf 2 N – ], and tetrafluoroborate [BF 4 – ]. We observe very strong underlying molecular-level migrations in these mixtures, and this tends to mainly involve the anion species. As compared to the systems with a single anion, the mixed anions lead to large increases/decreases in the radial distribution function peak heights, whereas the cation mixing is relatively benign. The [BF 4 – ] anions have a strong tendency to displace the [Tf 2 N – ] anions in the mixtures, and this is seen with respect to both [BMIM + ] and [ZMIM + ].

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Molecular simulation of the structural and thermodynamic properties of n-alkane/brine interfacial systems with nonionic surfactants

All-atom molecular dynamics (MD) simulations are used to study the structural and thermodynamic properties of water + n-heptane interfacial systems in the presence of salinity (NaCl, NaI, KCl, and KI) and two different nonionic surfactants. Excellent qualitative and quantitative agreement with interfacial tension experimental data is obtained, but this requires applying a charge scaling factor to the ionic species, suggesting the likely role of polarizability effects. Tensoactive behavior is observed for the NaI and KI systems, coinciding with layering of the iodide species near the interface. Further, there are significant interaction differences between the surfactants and the different ionic species, but the structural and thermodynamic behavior of the surfactant molecules is relatively unaffected by the specific salt species. Our analysis suggest that the surfactant-surfactant interactions play a critical role in determining the interfacial behavior, with a much smaller impact associated with the composition of the brine phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Machine learning for domain transfer between simulated and experimental 2D X-ray diffraction patterns using generative adversarial networks

X-ray diffraction (XRD) is a well-established technique for analyzing materials at an atomic level. Dynamic compression experiments (DCE), in which materials are subject to extreme pressures, can provide fundamental understanding to pressure-induced phase transitions and compression of the crystal lattice. The analysis of XRD patterns from highly compressed samples is non-trivial given the sparsity of data, high experimental costs, and the fact that the data is often marred with X-ray background and other artifacts. While accurate computational frameworks exist, they solve the forward problem—from structures and orientations to XRD patterns. Solving the inverse problem for 2D experimental diffraction patterns is currently a complex manual process of matching and comparing experimentally observed patterns to computationally generated ones. Machine learning is a promising tool for automating the matching process but often requires data-intensive architectures. Here, in this study, we use a CycleGAN to translate the domain of limited experimental data to a domain in which there is readily available simulated data. This domain shift allows data-intensive machine learning models that have only been trained on simulated XRD patterns to be used in the analysis of experiments.

Brozak, Samantha Jean [Sandia National Laboratorie↗
DOE OSTI2025

Corrosion resistant hot melt adhesive to bind metals

Hot melt adhesives (HMAs) play an important role in many industries, and their demand is expected to grow. HMAs don't require any solvents, and their application results in the formation of strong bonds with the substrate upon cooling within seconds. These properties differentiate them from liquid glues and make them preferable for practical application. Currently, commercial HMAs are used in bonding lightweight materials such as paper, polymers, and cartons, and have limited usage in areas necessitating the bonding of heavier objects like metals. Here, in this study, we report a design and testing of versatile platform comprising an ion-coordinating polymer and ionic fillers for performance optimization and understanding of structure–property relationships, enabling the rational design of HMAs with improved adhesion to metal surfaces. All-atom Molecular dynamics (MD) simulations and various characterization methods are used to elucidate the adhesion mechanism in model composite system containing polyethylene oxide mixed with chemically diverse salt particles. The maximum adhesion strength is found in composites with Al(OH) 3 and FeCl 3 fillers. Interestingly, the presence of Al(OH) 3 also provides a multifunctional anticorrosion property as measured electrochemically using the Tafel method. The discovered path to formulations with improved adhesion to metal surfaces constitutes an important step toward advancing HMAs for use in the structural and semi-structural metal work domain.

Adhesive and cohesive forces↗
DOE OSTI2026

Interfacial Void Formation and Self-Healing in Oxide Scales on Al-containing High-Entropy Alloy

The exceptional high-temperature oxidation resistance of Al-containing high-entropy alloys (HEAs) is often attributed to the formation of a protective α-Al 2 O 3 scale. However, the dynamic, atomic-scale mechanisms governing the stability of this scale—including interfacial void formation and the often-postulated but rarely visualized “self-healing” capacity—remain poorly understood. Herein, we reveal the complex evolution of the triple-layer oxide scale on an Al 10 CoCrFeNi HEA through combined electron microscopy and diffraction study. We show that interfacial voids are an inherent consequence of the scaling process, originating from two distinct mechanisms: the Kirkendall effect at the interface between the γ-Al 2 O 3 /α-Al 2 O 3 and alloy driven by cationic diffusion imbalance and volumetric contraction due to phase transformations at the spinel/Cr 2 O 3 interface. Crucially, we provide microstructural evidence consistent with an intrinsic self-healing response. This process is driven by coupled inward diffusion of oxygen and outward diffusion of metal cations, leading to the in-situ formation of transient θ-Al 2 O 3 and spinel phases that partially fill and seal the voids. Here, these results provide atomic-scale insights into the phase evolution, defect formation, and self-repair of oxide scales in HEAs—highlighting pathways to enhance their oxidation resistance in extreme environments.

High-entropy alloy↗
DOE OSTI2023

QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations

Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose program for single-point calculations, geometry optimizations, transition-state optimizations, and molecular dynamics (MD) at the QM/MM level. It calls a QM package and an MM package to perform the required single-level calculations and combines them into a QM/MM energy by a variety of schemes. QMMM 2023 supports GAMESS-US, Gaussian, and ORCA as QM packages and Tinker as the MM package. Four types of treatments are available for embedding the QM subsystem in the MM environment: mechanical embedding with gas-phase calculations of the QM region, electronic embedding that allows polarization of the QM region by the MM environment, polarizable embedding for mutual polarization of the QM and MM regions, and flexible embedding for both mutual polarization and partial charge transfer between the QM and MM regions. Boundaries between QM and MM regions that pass through covalent bonds can be treated by several methods, including the redistributed charge (RC) scheme, redistributed charge and dipole (RCD) scheme, balanced-RC scheme, balanced-RCD scheme, screened charge scheme that takes account of charge penetration effects, and smeared charge scheme that delocalizes the MM charges near the QM–MM boundary. Geometry optimization can be done using the optimizer implemented in QMMM 2023 or the Berny optimizer in Gaussian through external calls to Gaussian. Molecular dynamics simulations can be performed at the pure-MM level, pure-QM level, fixed-partitioning QM/MM level, and adaptive-partitioning QM/MM level. As a result, the adaptive-partitioning treatments permit on-the-fly relocation of the QM–MM boundary by dynamically reclassifying atoms or groups into the QM or MM subsystems.

97 MATHEMATICS AND COMPUTING↗