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At least 505 records · Page 28

Performant implementation of the atomic cluster expansion

The atomic cluster expansion is a general polynomial expansion of the atomic energy in multi-atom basis functions. Here we implement the atomic cluster expansion in the performant C++ code PACE that is suitable for use in large scale atomistic simulations. We briefly review the atomic cluster expansion and give detailed expressions for energies and forces as well as efficient algorithms for their evaluation. We demonstrate that the atomic cluster expansion as implemented in PACE shifts a previously established Pareto front for machine learning interatomic potentials towards faster and more accurate calculations. Moreover, general purpose parameterizations are presented for copper and silicon and evaluated in detail. We show that the new Cu and Si potentials significantly improve on the best available potentials for highly accurate large-scale atomistic simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗

Multiphysics FISPACT-II and TENDL-2019 simulation: neutron-induced damage metrics

Nuclear interactions can be the source of atomic displacement, irradiation-induced defects and transmutation in structural materials. Such quantities are derived from, or can be correlated to, nuclear kinematic simulations of primary atomic energy distributions spectra and the quantification of the numbers of secondary defects produced per primary as a function of the available recoils, residual and emitted, energies. Recoil kinematics of neutral, residual, gas, proton, alpha particle emissions are now more rigorously treated based on recent, complete and enhanced nuclear data parsed in state-of-the-art processing tools. Defect production metrics are the starting point in the complex problem of correlating and simulating the behaviour of materials under irradiation, as experimental information is rare or scattered. Detailed, segregated primary knock-on-atom metrics are now becoming available as the starting point of further simulation processes of isolated and clustered defects in material lattices. This allows more materials, lattices, neutron incident energy ranges, and irradiation conditions to be explored with sufficient data to adequately cover both standard and novel applications and materials: the broader reactor applications landscape. The damage metrics of of materials are systematically explored under typical but different reactor's type environment. The inventory code FISPACT-II combined with the enhanced nuclear data forms of the TENDL-2019 libraries allow one to not only calculate dpa from mostly scattering events but to also properly predict gas production, nuclear heating and transmutation under the same conditions.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Uncovering the role of nanoscale precipitates on martensitic transformation and superelasticity

Here we characterize the role of coherent nanoscale B2 Ni 50 Al 50 precipitates on the temperature- and stress-induced martensitic phase transformation in nanocrystalline Ni 63 Al 37 shape memory alloys using multi-million-atoms molecular dynamics (MD) simulations. We studied two types of precipitates: one with single crystal precipitates (SXP) and a second where grain boundaries cut through precipitates (PXP). Simulations reveal that the presence of B2 precipitates stabilizes the cyclic flag-shaped stress-strain response, characteristic of superelasticity, and reduces remnant strain. In contrast, single-phase nanocrystalline Ni 63 Al 37 exhibits degradation of the reverse transformation during cyclic loading and, eventually, incomplete reversible transformation within a few cycles. This is consistent with previous experimental findings of ultra-low fatigue in Ni-Ti-Cu alloys with Ti 2 Cu precipitates. The simulations reveal that the presence of precipitates significantly improves the reversibility of the transformation by acting as elastic zones that partially shield the martensitic transformation and drive the reverse transformation. A detailed analysis of the MD trajectories reveals that the martensitic transformation of the matrix induces ultra-large elastic deformation in some of the B2 precipitates (approximately 12%) to the point of resulting in a martensite-like atomic structure.

36 MATERIALS SCIENCE↗

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↗

Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis

Reverse transcription, an essential event in the HIV-1 life cycle, requires deoxynucleotide triphosphates (dNTPs) to fuel DNA synthesis, thus requiring penetration of dNTPs into the viral capsid. The central cavity of the capsid protein (CA) hexamer reveals itself as a plausible channel that allows the passage of dNTPs into assembled capsids. Nevertheless, the molecular mechanism of nucleotide import into the capsid remains unknown. Employing all-atom molecular dynamics (MD) simulations, we established that cooperative binding between nucleotides inside a CA hexamer cavity results in energetically favorable conditions for passive translocation of dNTPs into the HIV-1 capsid. Furthermore, binding of the host cell metabolite inositol hexakisphosphate (IP 6 ) enhances dNTP import, while binding of synthesized molecules like benzenehexacarboxylic acid (BHC) inhibits it. The enhancing effect on reverse transcription by IP 6 and the consequences of interactions between CA and nucleotides were corroborated using atomic force microscopy, transmission electron microscopy, and virological assays. Collectively, our results provide an atomistic description of the permeability of the HIV-1 capsid to small molecules and reveal a novel mechanism for the involvement of metabolites in HIV-1 capsid stabilization, nucleotide import, and reverse transcription.

60 APPLIED LIFE SCIENCES↗

Quantifying Membrane Structure and Dynamics during Bioproduct Production in Zymomonas mobilis by Molecular Simulation

The conversion of lignocellulosic biomass into biofuels and bioproducts by microbial biorefineries is central to a sustainable chemical industry. Zymomonas mobilis is one such biorefinery chassis and is resistant to ethanol stress, leading to its use in biomass conversion to biofuels and bioproducts. However, Z. mobilis growth is often inhibited by organic acids, aldehydes, alcohols, ketones, and amides found in biomass hydrolysate. The resulting slow growth inhibits production and as a result drives up the price for the resulting products. One hypothesis is that these molecules interact with or disrupt the bacterial membrane, triggering stress responses and hindering growth. To test this hypothesis at the molecular level, we employ all-atom molecular dynamics (MD) simulations to investigate lignocellulose-derived small molecules and their impact on a biologically relevant Z. mobilis membrane model. Simulations were conducted across a range of inhibitor concentrations from 0 to 2.5 mol %, analyzing key membrane properties such as area per lipid (APL), membrane thickness, lipid-order parameter (−S CH ), lateral diffusion coefficient (D xy ), and permeability coefficient (Pm). From simulation, we observed altered membrane structure and dynamics at these modest small molecule concentrations commonly found in hydrolysates. Generally, the membranes become thinner, with a higher area per lipid and lower-order parameter as the small molecule concentration increases. These trends are stronger for more hydrophobic molecules with greater hydrophobic bulk, as isobutanol, propanol, and propanoic acid showed greater membrane perturbations as the concentration increased compared to other small molecules. Tracking small molecule distributions directly in our equilibrium simulations allows us to determine concentration-dependent free energy profiles for these molecules. While the trends are noisy, generally the barriers to crossing the membrane decrease as the concentration increases, indicating that the membranes become leakier as small molecule concentrations rise. Comparing between native Z. mobilis membranes with hopanoids and membranes sharing the same phospholipid composition but without hopanoids, hopanoids stabilize and order the membrane for smaller molecules to maintain membrane structure but appear insufficient for larger hydrophobic molecules like isobutanol. These findings provide a mechanistic understanding of how small molecules found in biomass degradation streams interact with the Z. mobilis membrane, offering valuable insights for future strain engineering efforts to optimize biofuel and bioproduct synthesis from biomass feedstocks by highlighting limits to small molecule tolerance. This knowledge can guide the modification of membrane composition to develop more robust microbes, thereby improving microbial survival and yields in industrial contexts.

Singh, Nitin Kumar [Michigan State Univ., East Lan↗

Sequential Infiltration Synthesis of Cadmium Sulfide Discrete Atom Clusters

Exposure of soft material templates to alternating volatile chemical precursors can produce inorganic deposition within the permeable template (e.g. a polymer thin film) in a process akin to atomic layer deposition (ALD). While such sequential infiltration synthesis (SIS) processes have now been demonstrated for many metal oxides, we report an SIS process for a transition metal sulfide – CdS. Gas phase dimethyl cadmium and hydrogen sulfide precursors infiltrated into poly(4-vinylpyridine) thin films result in the 3D-nucleation of clusters consistent with a cubane-type Cd 4 S 4 core that are variably terminated with methyl, thiol and hydroxy capping ligands. First principles models and simulation of few-atom Cd-based clusters are consistent with electronic and vibrational spectroscopy and grazing-incidence total X-ray scattering measurements of 3D-cluster-arrays synthesized at 80 °C. The direct synthesis of few-atom transition metal sulfide clusters within polymer thin films will provide a versatile new route to precision architectures for light-absorbing materials including solar energy harvesting and conversion applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulation-Based Inference for Neutrino Interaction Model Parameter Tuning

High-energy physics experiments studying neutrinos rely heavily on simulations of their interactions with atomic nuclei. Limitations in the theoretical understanding of these interactions typically necessitate ad hoc tuning of simulation model parameters to data. Traditional tuning methods for neutrino experiments have largely relied on simple algorithms for numerical optimization. While adequate for the modest goals of initial efforts, the complexity of future neutrino tuning campaigns is expected to increase substantially, and new approaches will be needed to make progress. In this paper, we examine the application of simulation-based inference (SBI) to the neutrino interaction model tuning for the first time. Using a previous tuning study performed by the MicroBooNE experiment as a test case, we find that our SBI algorithm can correctly infer the tuned parameter values when confronted with a mock data set generated according to the MicroBooNE procedure. This initial proof-of-principle illustrates a promising new technique for next-generation simulation tuning campaigns for the neutrino experimental community.

Tame-Narvaez, Karla Maria [Fermilab]↗

Simulation-based inference for neutrino interaction model parameter tuning

High-energy physics experiments studying neutrinos rely heavily on simulations of their interactions with atomic nuclei. Limitations in the theoretical understanding of these interactions typically necessitate ad hoc tuning of simulation model parameters to data. Traditional tuning methods for neutrino experiments have largely relied on simple algorithms for numerical optimization. While adequate for the modest goals of initial efforts, the complexity of future neutrino tuning campaigns is expected to increase substantially, and new approaches will be needed to make progress. In this paper, we examine the application of simulation-based inference (SBI) to the neutrino interaction model tuning for the first time. Using a previous tuning study performed by the MicroBooNE experiment as a test case, we find that our SBI algorithm can correctly infer the tuned parameter values when confronted with a mock data set generated according to the MicroBooNE procedure. This initial proof-of-principle illustrates a promising new technique for next-generation simulation tuning campaigns for the neutrino experimental community.

Tame-Narvaez, Karla [Fermilab] (ORCID:000000022249↗

NNL.Fe.qSNAP-ZBL.2024.1: A Fe Spectral Neighbor Analysis Potential for Radiation Damage Simulations

The NNL.Fe.qSNAP-ZBL.2024.1 machine-learned potential (MLP) has been generated to support the development of an elemental body-centered cubic (BCC) Fe athermal recombination corrected neutron damage model and simulations of primary recoil atom (PRA) cascades in BCC Fe. This MLP is a quadratic spectral neighbor analysis potential (qSNAP) hybridized with the universal Ziegler-Beirsack-Littmark (ZBL) potential at short-range and is named according to Naval Nuclear Laboratory MLP naming conventions (NNL.material-system.MLP-type.year.version). Training set calculations for Fe are presented along with the subsequent MLP fitting procedure. A key criterion of the fitting procedure is that ZBL describes the short-range interaction with minimal impact on the MLP. The MLP is compared to density functional theory (DFT) predicted properties relevant to radiation damage simulation, including threshold displacement energies, for validation. The NNL.Fe.qSNAP-ZBL.2024.1 potential is considered suitable for molecular dynamics (MD) simulations of radiation defects up to 800 K and PRA cascades in BCC Fe up to around 10 keV. The potential can additionally be used on a limited basis for recoils of 10–20 keV, within which range the emergence of structures outside the training set in cascade simulations may cause system instabilities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Coarse-grained simulation of colloidal self-assembly, cation exchange, and rheology in Na/Ca smectite clay gels

Knowledge Gap: The aggregation of clay minerals—layered silicate nanoparticles—strongly impacts fluid flow, solute migration, and solid mechanics in soils, sediments, and sedimentary rocks. Experimental and computational characterization of clay aggregation is inhibited by the delicate water-mediated nature of clay colloidal interactions and by the range of spatial scales involved, from 1 nm thick platelets to flocs with dimensions up to micrometers or more. Simulations: Using a new coarse-grained molecular dynamics (CGMD) approach, we predicted the microstructure, dynamics, and rheology of hydrated smectite (more precisely, montmorillonite) clay gels containing up to 2,000 clay platelets on length scales up to 0.1 μm. Further, simulations investigated the impact of simulation time, platelet diameters (6 to 25nm), and the ratio of Na to Ca exchangeable cations on the assembly of tactoids (i.e., stacks of parallel clay platelets) and larger aggregates (i.e., assemblages of tactoids). We analyzed structural features including tactoid size and size distribution, basal spacing, counterion distribution in the electrical double layer, clay association modes, and the rheological properties of smectite gels. Findings: Our results demonstrate new potential to characterize and understand clay aggregation in dilute suspensions and gels on a scale of thousands of particles with explicit representation of counterion clouds and with accuracy approaching that of all-atom molecular dynamics (MD) simulations. For example, our simulations predict the strong impact of Na/Ca ratio on clay tactoid formation and the shear-thinning rheology of clay gels.

42 ENGINEERING↗

Performant implementation of the atomic cluster expansion (PACE) and application to copper and silicon

The atomic cluster expansion is a general polynomial expansion of the atomic energy in multi-atom basis functions. Here we implement the atomic cluster expansion in the performant C++ code that is suitable for use in large-scale atomistic simulations. We briefly review the atomic cluster expansion and give detailed expressions for energies and forces as well as efficient algorithms for their evaluation. We demonstrate that the atomic cluster expansion as implemented in shifts a previously established Pareto front for machine learning interatomic potentials toward faster and more accurate calculations. Moreover, general purpose parameterizations are presented for copper and silicon and evaluated in detail. We show that the Cu and Si potentials significantly improve on the best available potentials for highly accurate large-scale atomistic simulations.

36 MATERIALS SCIENCE↗

Elucidation of puzzling questions regarding the CrO x /Al 2 O 3 catalyst I. X-ray absorption spectroscopy aided identification of the nature of the chromium oxide species in the CrO x /Al 2 O 3 dehydrogenation catalyst system

The CATOFIN© process produces propylene from propane using a CrO x /Al 2 O 3 catalyst. Despite its use, there are still uncertainties surrounding the nature of Cr species formed during synthesis, regeneration, and aging. It has been observed that ppm levels of Cr 2 O 3 can be oxidized to Cr(VI) in air; however, when Cr 2 O 3 is in direct contact with Al 2 O 3 , Cr(VI) formation increased more than 100-fold. Here, to confirm physical contact between Cr 2 O 3 and Al 2 O 3 results in increased Cr(VI) formation, Cr 2 O 3 and Cr 2 O 3 /Al 2 O 3 samples were synthesized, calcined, and characterized. Catalytic activity measurements confirm propylene selectivity inversely tracks with Cr(VI). Wet chemical titration and X-ray absorption spectroscopy (XAS) quantified and determined the structure of the Cr(VI) species. FEFF X-ray absorption near edge structure simulations determined the potential sensitivity of the XAS to the presence of Al 3+ /Cr 3+ neighboring atoms. XAS correlated to FEFF simulations suggested that Al 3+ x Cr 3+ 2–x Cr 6+ 3 O 12 comprises a significant fraction of the Cr(VI) species formed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin

Serum albumin is the most abundant protein in blood plasma, and it is involved in multiple biological processes. Serum albumin has recently been adapted for improving biomaterial integration with bone tissue, and studies have shown the importance of this protein in bone repair and regeneration. However, the mechanism of action is not yet clear. In stark contrast, other studies have demonstrated that albumin blocks cell adhesion to surfaces, which is seen as a limitation to its bone healing role. These apparent contradictions suggest that the conformation of albumin facilitates its bioactivity, leading to enhanced bone repair. Serum albumin is known to play a major role in maintaining the calcium ion concentration in blood plasma. Due to the prevalence of calcium at bone repair and regeneration sites, it has been hypothesized that calcium binding to serum albumin triggers a conformational change, leading to bioactivity. In the current study, molecular modeling approaches including molecular docking, atomic molecular dynamics (MD) simulation, and coarse-grained MD simulation were used to test this hypothesis by investigating the conformational changes induced in bovine serum albumin by interaction with calcium ions. The computational results were qualitatively validated with experimental Fourier-transform infrared spectroscopy analysis. We find that free calcium ions in solution transiently bind with the three major loops in albumin, triggering a conformational change where N-terminal and C-terminal domains separate from each other in a partial unfolding process. The separation distance between these domains was found to correlate with the calcium ion concentration. The experimental data support the simulation results showing that albumin has enhanced conformational heterogeneity upon exposure to intermediate levels of calcium, without any significant secondary structure changes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Elucidating the Atomic Structures of the Gel Layer Formed during Aluminoborosilicate Glass Dissolution: An Integrated Experimental and Simulation Study

The altered glasses produced during aqueous dissolution of silicate and borosilicate glasses are among the most complex structures to understand at the atomic level due to their amorphous nature, random porosity and various levels of hydration. In this study, we gained insights of the complex atomic structures of altered aluminoborosilicate glasses by combining a range of experimental and computational approaches. The altered glasses were prepared by dissolution of three glasses with varying level of alumina in acid for 7 days. A comprehensive set of experimental [elemental analysis, high-energy X-ray diffraction, 29 Si and 27 Al solid-state nuclear magnetic resonance (NMR), and O 1s X-ray photoelectron spectroscopy (XPS)] and modeling (molecular dynamics (MD) simulations using non-reactive and reactive force fields) were used to study the atomic structures of these altered glasses. Elemental analysis showed that most of the B in the pristine glasses was leached into the solution and was not contained in the altered glass. The 29 Si and 27 Al solid-state NMR spectra revealed that the altered glasses have more polymerized silicate network as compared to those in the pristine glasses due to the reformation of linkages among Si and Al oxygen polyhedral in the altered glasses. The bridging and non-bridging (or hydroxyl O) atoms in the altered glasses were also quantified from their O 1s XPS spectra. Atomic structure models of the altered glasses were constructed by using MD simulations using the reactive force field based on the compositional information obtained from experiments. Various pore structures were generated using the charge-scaling (CS) method by using different initial densities and CS temperatures; the best CS parameters of each alternated glass were then determined by comparing with the experimental structure factors obtained from high energy X-ray diffraction. Pore and the atomic structures and vibrational properties around these pore surfaces were analyzed. Furthermore, these results from this comprehensive study thus provides a realistic insight into the pore morphology, atomic structure, and vibrational properties of altered glasses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials

Silicon carbide (SiC) divacancies are attractive candidates for spin-defect qubits possessing long coherence times and optical addressability. The high activation barriers associated with SiC defect formation and motion pose challenges for their study by first-principles molecular dynamics. In this work, we develop and deploy machine learning interatomic potentials (MLIPs) to accelerate defect dynamics simulations while retaining ab initio accuracy. We employ an active learning strategy comprising symmetry-adapted collective variable discovery and enhanced sampling to compile configurationally diverse training data, calculation of energies and forces using density functional theory (DFT), and training of an E(3)-equivariant MLIP based on the Allegro model. Here, the trained MLIP reproduces DFT-level accuracy in defect transition activation free energy barriers, enables the efficient and stable simulation of multidefect 216-atom supercells, and permits an analysis of the temperature dependence of defect thermodynamic stability and formation/annihilation kinetics to propose an optimal annealing temperature to maximally stabilize VV divacancies.

Computer simulations↗

Structure–Thermodynamic Relationship of a Polysaccharide Gel (Alginate) as a Function of Water Content and Counterion Type (Na vs Ca)

Biofilms are the predominant mode of microbial life on Earth, and so a deep understanding of microbial communities-and their impacts on environmental processes-requires a firm understanding of biofilm properties. Because of the importance of biofilms to their microbial inhabitants, microbes have evolved different ways of engineering and reconfiguring the matrix of extracellular polymeric substances (EPS) that constitute the main non-living component of biofilms. This ability makes it difficult to distinguish between the biotic and abiotic origins of biofilm properties. An important route toward establishing this distinction has been the study of simplified models of the EPS matrix. This study builds on such efforts by using atomistic simulations to predict the nanoscale (≤10 nm scale) structure of a model EPS matrix and the sensitivity of this structure to interpolymer interactions and water content. To accomplish this, we use replica exchange molecular dynamics (REMD) simulations to generate all-atom configurations of ten 3.4 kDa alginate polymers at a range of water contents and Ca–Na ratios. Simulated systems are solvated with explicitly modeled water molecules, which allows us to capture the discrete structure of the hydrating water and to examine the thermodynamic stability of water in the gels as they are progressively dehydrated. Our primary findings are that (i) the structure of the hydrogels is highly sensitive to the identity of the charge-compensating cations, (ii) the thermodynamics of water within the gels (specific enthalpy and free energy) are, surprisingly, only weakly sensitive to cation identity, and (iii) predictions of the differential enthalpy and free energy of hydration include a short-ranged enthalpic term that promotes hydration and a longer-ranged (presumably entropic) term that promotes dehydration, where short and long ranges refer to distances shorter or longer than ~0.6 nm between alginate strands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Shake-up and shake-off spectra in the electron capture decay of atomic $^7$Be

The most stringent laboratory-based experimental limits on the existence of sub-MeV sterile neutrinos are currently set by decay spectroscopy of radioactive $^7$Be embedded into superconducting sensors. The systematic uncertainties are dominated by the modeling of the electron shake-up and shake-off spectra that are not based on state-of-the-art atomic theory and do not include electron correlations or relativistic effects. We have used the multiconfiguration Dirac-Fock formalism to obtain correlated wavefunctions ab initio and compute all single and double shake processes in the electron capture decay of atomic $^7$Be. The simulations can explain some but not all of the observed spectral features, likely because the wave functions are modified by the Ta sensor material that the $^7$Be is embedded into. The new models also show that the L/K electron capture ratio of $^7$Be in Ta has previously been slightly underestimated revising the previous value of 0.070(7) to a new value of 0.0756(20).

Atomic Physics (physics.atom-ph)↗