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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Probing Molecular Interactions at MXene-Organic Heterointerfaces
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Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance
By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semilocal density functional theory (DFT) and thereby furnish a more accurate and reliable description of the underlying electronic structure in systems throughout biology, chemistry, physics, and materials science. However, the high computational cost associated with the evaluation of all required EXX quantities has limited the applicability of hybrid DFT in the treatment of large molecules and complex condensed-phase materials. To overcome this limitation, we describe a linear-scaling approach that utilizes a local representation of the occupied orbitals (e.g., maximally localized Wannier functions (MLWFs)) to exploit the sparsity in the real-space evaluation of the quantum mechanical exchange interaction in finite-gap systems. In this work, we present a detailed description of the theoretical and algorithmic advances required to perform MLWF-based ab initio molecular dynamics (AIMD) simulations of large-scale condensed-phase systems of interest at the hybrid DFT level. We focus our theoretical discussion on the integration of this approach into the framework of Car–Parrinello AIMD, and highlight the central role played by the MLWF-product potential (i.e., the solution of Poisson’s equation for each corresponding MLWF-product density) in the evaluation of the EXX energy and wave function forces. We then provide a comprehensive description of the exx algorithm implemented in the open-source Quantum ESPRESSO program, which employs a hybrid MPI/OpenMP parallelization scheme to efficiently utilize the high-performance computing (HPC) resources available on current- and next-generation supercomputer architectures. Furthermore, this is followed by a critical assessment of the accuracy and parallel performance (e.g., strong and weak scaling) of this approach when AIMD simulations of liquid water are performed in the canonical (NVT) ensemble. With access to HPC resources, we demonstrate that exx enables hybrid DFT-based AIMD simulations of condensed-phase systems containing 500–1000 atoms (e.g., (H₂O)₂₅₆) with a wall time cost that is comparable to that of semilocal DFT. In doing so, exx takes us one step closer to routinely performing AIMD simulations of complex and large-scale condensed-phase systems for sufficiently long time scales at the hybrid DFT level of theory.
Understanding Strain and Failure of a Knot in Polyethylene Using Molecular Dynamics with Machine-Learned Potentials
A neural network potential (NNP) has been developed by fitting to ab initio electronic structure data on hydrocarbons and is used to study failure of linear and knotted polyethylene (PE) chains. A linear PE chain must be highly strained before breaking as the stress is equally distributed across the chain. In contrast, the stress in a PE chain with a 31 or overhand knot, accumulates at the knot’s entrance/exit. We find the strain energy is greatest when the bond length and angle are strained simultaneously, and that the knot weakens the chain by increasing the variance of the C–C–C angle, thereby allowing rupture at lower bond strains. Here, we extend our analysis to both 51 and 52 knots and find that both break at the entrance/exit of a loop. Notably, molecular scale PE knots exhibit many of the same characteristics as knots in a macroscopic rope, with stick–slip phenomena upon tightening and similar points of failure.
Formation of Fe(iii)-As(v) complexes: effect on the solubility of ferric hydroxide precipitates and molecular structural identification
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Molecular dynamics simulations of a hydrophilic MIL-160-based membrane demonstrate pressure-dependent selective uptake of industrially relevant greenhouse
Oral presentation for ACS Spring Meeting
Molecular simulation data for 'Data-guided Multi-Map variables for ensemble refinement of molecular movies'
These trajectories, scripts, and analysis performed on Summit underly the work published as 'Data-guided Multi-Map variables for ensemble refinement of molecular movies'. The trajectories include equilibrium and non-equilibrium sampling of ADK, CODH, and FLPP3, the scripts used to build the systems, and the scripts used to analyze the output. The directory structure is explained further in an internal README file.
High;#8208;Sensitivity Acoustic Molecular Sensors Based on Large;#8208;Area, Spray;#8208;Coated 2D C
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Crystals of Benzamide, the First Polymorphous Molecular Compound, Are Helicoidal
Abstract not provided
Isomer-Tailored Carbon Molecular Sieve Membranes with High Gas Separation Performance
Not provided.
Molecular level insight into non-bilayer structure formation in thylakoid membranes: a molecular dynamics study
In oxygenic photosynthetic organisms, the light reactions are performed by protein complexes embedded in the lipid bilayer of thylakoid membranes (TMs). The organization of the bulk lipid molecules into bilayer structures provide optimal conditions for the build-up of the proton motive force (pmf) and its utilization for ATP synthesis. However, the lipid composition of TMs is dominated by the non-bilayer lipid species monogalactosyl diacylglycerol (MGDG), and functional plant TMs, besides the bilayer, contain large amounts of non-bilayer lipid phases. Bulk lipids have been shown to be associated with lumenal, stromal-side and marginal-region proteins and proposed to play roles in the self-assembly and photoprotection of the photosynthetic machinery. Furthermore, it has recently been pointed out that the generation and utilization of pmf for ATP synthesis according to the ‘protet’ or protonic charge transfer model Kell (Biochim Biophys Acta Bioenerg 1865(4):149504, 2024), requires high MGDG content Garab (Physiol Plant 177(2):e70230, 2025). In this study, to gain better insight into the structural and functional roles of MGDG, we employed all atom and coarse-grained molecular dynamics simulations to explore how temperature, hydration levels and varying MGDG concentrations affect the structural and dynamic properties of bilayer membranes constituted of plant thylakoid lipids. Our findings reveal that MGDG promotes increased membrane fluidity and dynamic fluctuations in membrane thickness. MGDG-rich stacked bilayers spontaneously formed inverted hexagonal phases; these transitions were enhanced at low hydration levels and at elevated but physiologically relevant temperatures. It can thus be inferred that MGDG plays important roles in heat and drought stress mechanisms.
Ab initio molecular dynamics simulation of Nd3+ incorporation in calcite
Trivalent rare-earth elements (REEs) readily incorporate in Ca-bearing minerals such as calcite (CaCO3), a phenomenon with important implications for the use of REEs as biogeochemical tracers as well as for environmental remediation. Despite substantial efforts, determining the incorporation modes of trivalent REEs in calcite has remained challenging due to their presence in multiple coordination environments. This is particularly problematic for the interpretation of extended X-ray absorption fine structure (EXAFS) spectroscopy. In this work, ab initio molecular dynamics (AIMD) simulations of Nd3+ incorporated in calcite were performed to resolve its incorporation modes. Nd3+ and Ca2+ have very similar ionic radii but the additional positive charge requires a charge compensation scheme (CCS). Five CCSs were considered in AIMD simulations, and the resulting atomic trajectories were then used to compute EXAFS spectra for direct fitting to a published experimental spectrum. The results of the fits indicated that Nd3+ incorporates at the Ca2+ site in calcite in a mixture of six- and seven-fold coordination environments and through three main incorporation modes: associated with a protonated nearest-neighbor Ca2+ vacancy, incorporated as NdOH2+, and charge compensated by a remote species (on the spatial scale probed by EXAFS). The incorporation of Nd3+ in calcite via multiple modes was consistent with previous work, but the AIMD-EXAFS approach allowed for resolving the nature, proportion, and structure of the different coordination environments.
Data-driven molecular modeling with the generalized Langevin equation
Not Available
Impact of Cr and Co on 99Tc retention in magnetite: A combined study of ab initio molecular dynamics and experiments
This work explores the effect of co-mingled dopants, Co(II) and Cr(III), on Tc(IV) incorporation and retention in magnetite when heat treated to 625 or 700 °C. Key trends in Tc retention in the high temperature regime were identified using a combination of density-functional-theory based ab initio molecular dynamics (AIMD) simulations, and batch experiments including solid phase characterization techniques, e.g. X-ray absorption spectroscopy. A stabilizing effect on Tc(IV) was observed when the number of Tc and Cr atoms are equal or when the magnetite surface is oversaturated with Tc and Cr inclusions. Here, oversaturation is hypothesized to force Cr from the magnetite surface to form a Cr2O3 phase, which may act as a protective layer that prevents Tc release. With the addition of Co, Tc(IV) is stabilized via redox processes. The presence of Cr in low concentrations interferes with this redox stabilization and Cr is preferentially stabilized as opposed to Tc. As a result, using Co as a stabilizing dopant for Tc may be compromised in the presence of Cr. When the relative concentration of Tc, Cr and Co is the same, or more Co atoms are added to high Cr incorporated systems, the formation of the Cr2O3 phase may be suppressed. Although waste streams with co-mingled Tc and Cr potentially may benefit from a Co dopant, since the formation of a Cr2O3 passivation layer may protect incorporated Tc from being released, the relative concentration of the three elements will be a critical parameter for maximizing effectiveness of this strategy.
An atomistic picture is worth a thousand words: New details on supported molecular catalysts
Here, homogeneous and heterogeneous catalysts have advantages and disadvantages. Molecular catalysts supported on heterogeneous materials have the potential to combine the advantages of both fields. Jabbour et al. report a detailed study of the 3D structure of an Ir-catalyst on silica.