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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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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Molecular Dynamics Simulation of the Structures, Dynamics, and Aggregation of Dissolved Organic Matter

Dissolved organic matter (DOM) plays a significant role in the transport and transformation of pollutants in the aquatic environment. However, the experimental characterization of DOM has been limited mainly to bulk properties, and the molecular-level interactions among various components of DOM remain to be fully characterized. In this study, we use molecular dynamics (MD) simulations to probe the structural properties of model DOM systems at atomic detail. The 200 ns simulations, validated by available experimental data, reveal processes and mechanisms by which chemical species (cations, peptides, lipids, lignin, carbohydrates, and some low-molecular-weight aliphatic and aromatic compounds) aggregate to form complex DOM. The DOM aggregates are dynamic, consisting of a hydrophobic core and amphiphilic exterior. The lipid tails and other hydrophobic fragments form the core, with hydrophilic and amphiphilic groups exposed to water, making DOM accessible to both polar and nonpolar species. Thus, the lipid component acts as a nucleator, whereas cations (especially Ca 2+ ) connect the molecular fragments on the surface by coordinating with the O-containing functional groups of DOM. The structural details revealed here provide new insights including surface accessible atoms, overall assemblage, and interactions among the molecules of DOM for understanding the kinetics and mechanisms through which DOM interacts with metal and other contaminants.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Enabling Predictive Scale-Bridging Simulations through Active Learning (Institutional Computing Annual Report (Project w20_alscalebridging)) [Slides]

The goal of this project was to develop, demonstrate, and provide a new capability to achieve greater physical fidelity in large-scale simulations, rather than the usual brute-force increases in the number of mesh elements or particles. This was done by using machine learning (ML) techniques to develop emulators for subscale physics that can be used in coarse-scale continuum simulations, trained on fine-scale molecular dynamics (MD) simulations that are launched on-the-fly via active learning. raditional inertial confinement fusion (ICF) simulations rely on numerical diffusion to simulate molecular effects such as non-local transport and mixing without truly accounting for molecular interactions; our approach directly accounts for this physics.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

MISPR : an open-source package for high-throughput multiscale molecular simulations

Computational tools provide a unique opportunity to study and design optimal materials by enhancing our ability to comprehend the connections between their atomistic structure and functional properties. However, designing materials with tailored functionalities is complicated due to the necessity to integrate various computational-chemistry software (not necessarily compatible with one another), the heterogeneous nature of the generated data, and the need to explore vast chemical and parameter spaces. The latter is especially important to avoid bias in scattered data points-based models and derive statistical trends only accessible by systematic datasets. Here, we introduce a robust high-throughput multi-scale computational infrastructure coined MISPR (Materials Informatics for Structure–Property Relationships) that seamlessly integrates classical molecular dynamics (MD) simulations with density functional theory (DFT). By enabling high-performance data analytics and coupling between different methods and scales, MISPR addresses critical challenges arising from the needs of automated workflow management and data provenance recording. The major features of MISPR include automated DFT and MD simulations, error handling, derivation of molecular and ensemble properties, and creation of output databases that organize results from individual calculations to enable reproducibility and transparency. In this work, we describe fully automated DFT workflows implemented in MISPR to compute various properties such as nuclear magnetic resonance chemical shift, binding energy, bond dissociation energy, and redox potential with support for multiple methods such as electron transfer and proton-coupled electron transfer reactions. The infrastructure also enables the characterization of large-scale ensemble properties by providing MD workflows that calculate a wide range of structural and dynamical properties in liquid solutions. MISPR employs the methodologies of materials informatics to facilitate understanding and prediction of phenomenological structure–property relationships, which are crucial to designing novel optimal materials for numerous scientific applications and engineering technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Revealing EDL-driven reduction mechanisms in binary, ternary, and quaternary fluorinated electrolytes via an integrated MD–DFT–ML framework

Accurately predicting solid electrolyte interphase (SEI) formation requires explicitly resolving the electric double layer (EDL) structure, which deviates significantly from that of the bulk electrolyte. Although an established molecular dynamics (MD) and Density Functional Theory (DFT) framework can model SEI formation by evaluating reduction reactions of local clusters in the EDL, it suffers from a combinatorial computational bottleneck. To overcome this limitation, we introduce a machine-learning-accelerated simulation workflow (MD–DFT–ML), integrating a gradient-boosted regression model trained on EDL composition data to efficiently predict reduction potentials. We apply this framework to seven fluorinated electrolytes comprising fluorinated anions, a fluorinated ester solvent, two types of diluent (ion-solvating ester vs. non-solvating ether), and an FEC additive. The analysis shows that the EDL selectively accumulates cation-binding species; consequently, the non–cation-binding ether diluent rarely enters the EDL and makes minimal contributions to SEI formation. DFT calculations on statistically representative EDL clusters provide reduction potentials and fluorine-release pathways, while the ML model, which substantially reduces the DFT workload, predicts cluster reduction energies with a mean absolute error of 0.1 eV. The combined MD–DFT–ML approach also quantifies contributions from different sources to LiF formation in the SEI. This methodology establishes a generalizable route for multiscale modeling electrolyte and interphase design for next-generation electrochemical energy-storage systems.

DFT-MD-ML workflow↗
DOE OSTI2022

Investigation of fracture in porous materials: a phase-field fracture study informed by ReaxFF

Microscopic features (e.g, pore shapes, sizes, and distribution) in porous material substantially affect the overall mechanical properties such as stiffness and strength. In turn, these material properties determine the macroscopic behaviors of fracture in the porous material. In certain cases, macroscopic properties can be derived from the porous skeleton and void ratio (i.e., porosity), but in many other cases, such derivation is a challenging task. This paper presents a numerical investigation of microporosity and micropore shapes effect on the macrofracture behavior in porous amorphous silica. For this study, we extend the recently-proposed combined molecular dynamic (MD) and phase-field (PF) fracture modeling approach by including different pore shapes in the atomistic domain. In the MD simulations, we adopt ReaxFF to evaluate the material properties, where four different micropore cases are considered. Based on the material properties derived from MD simulations, the macrofracture propagation of porous media is studied using hybrid PF simulation. In the characterization of the pore structure, the concept of pore ligament is proposed to relate the pore shape and the critical energy release rate. Two classical fracture problems were used to evaluate the effect of pore shape on the macrofracture behavior. The results of the case study show that although the micropore shapes change the macrofracture behaviors, these effects vary with the geometry and loading conditions of macroscopic boundary value problems. Furthermore, the case study also shows that the influence of micropore structure can be captured at the macroscopic level through the material properties derived from the MD simulations.

42 ENGINEERING↗
DOE OSTI2026

Investigating Lignin Aggregation and Interactions with Solvents during γ-Valerolactone (GVL) Pretreatment: A Combined Small Angle Neutron Scattering and Molecular Simulations Study

The strong tendency of lignin to aggregate in solution, coupled with limited understanding of how its molecular structure governs this behavior, hinders its effective utilization in biorefineries. Here, in this study, we investigated the solution behavior of lignin extracted from poplar using γ-valerolactone/water (GVL/H2O, 9:1 wt/wt) through combined small-angle neutron scattering (SANS) and molecular dynamics (MD) simulations. Lignin samples obtained at 100 °C (L100) and 120 °C (L120) differed in β–O–4 content, hydroxyl distribution, and S/G ratio, enabling direct assessment of how molecular composition governs solvation and aggregation. SANS showed that L120 formed rigid and elongated cylindrical aggregates at 25 °C that transitioned to more flexible spheroidal structures by 50 °C and remained stable up to 80 °C, whereas L100 adopted globular aggregates that progressively collapsed with increasing temperature. MD simulations reinforced these observations by showing that S-rich (L120-like) oligomers had larger radii of gyration, stronger solvent coordination driven by methoxy groups, and fewer lignin–lignin contacts. In contrast, G-rich (L100-like) oligomers displayed persistent aggregation and lower solubility. Collectively, these results reveal that increased aromatic methoxylation enhances lignin–solvent interactions and suppresses self-association, whereas reduced methoxylation and higher β–O–4 content promote persistent aggregation into colloid-like structures with restricted solvent penetration into the aggregate interior.

biorefinery pretreatment↗
DOE OSTI2023

Near-surface damage and mixing in Si-Cl 2 -Ar atomic layer etching processes: Insights from molecular dynamics simulations

Silicon-chlorine-argon (Si-Cl 2 -Ar) atomic layer etching (ALE) is simulated using classical molecular dynamics (MD). The simulations provide a detailed view into the near-surface region during ALE processing. Bombardment of Ar + ions creates a mixed amorphous region that significantly differs from the picture of ideal ALE. There is also a significant change in the Si etch yield and the etch product distribution as a function of Ar + ion fluence. The Si etch yield is the highest at the beginning of the bombardment step but eventually decays to the physical sputtering yield. Atomic Cl and silicon chlorides are major etch products at the start of an ion bombardment step, but quickly decay. Atomic Si yields remain relatively constant as a function of Ar + ion fluence. As a result, a new schematic of Si-Cl 2 -Ar ALE is presented in order to emphasize the complex behavior observed in MD simulations.

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

The impact of physiologically relevant temperatures on physical properties of thylakoid membranes: a molecular dynamics study

Thylakoid membranes are energy-converting membranes with a unique lipid composition. Though the membranes are primarily composed of proteins, their photosynthetic function is strongly influenced by the lipid constituents. Here we characterize, with molecular dynamics (MD) simulations, lipid bilayers with compositions representative of plant thylakoid membranes. We determine, in a wide range of temperatures, the physical parameters of the model membranes which are relevant for the photosynthetic function. We found a marked impact of temperature on membrane permeability due to a combination of increased compressibility and curvature of the membrane at elevated temperatures. With increasing temperatures, we observed increasingly smeared transmembrane density profiles of the membrane forming lipid headgroups predicting increased membrane flexibility. The diffusion coefficient of the lipids increased with temperature without apparent specificity for lipid species. Instead of a comprehensive experimental dataset in the relevant temperature range, we quantitatively compared and validated our MD results with MD simulations on a dipalmitoylphosphatidylcholine model system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The Potential Energy Hotspot: Effects of Impact Velocity, Defect Geometry, and Crystallographic Orientation

In energetic materials, the localization of energy into “hotspots” is known to dictate the initiation of chemical reactions and detonation. Recent all-atom simulations have shown that more energy is localized as internal potential energy (PE) than can be inferred from the kinetic energy (KE) alone. The mechanisms associated with pore collapse and hotspot formation are known to depend on pore geometry and dynamic material response such as plasticity. Therefore, we use molecular dynamics (MD) simulations to characterize shock-induced pore collapse and the subsequent formation of hotspots in 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a highly anisotropic molecular crystal, for various defect shapes, shock strengths, and crystallographic orientations. We find that the localization of energy as PE is consistently larger than the KE in cases with significant plastic deformation. Additionally, an analysis of MD trajectories reveals the underlying molecular- and crystal-level processes that govern the effect of orientation and pore shape on PE localization. We find that the regions of highest PE relate to the areas of maximum plastic deformation, while KE is maximized at the point of impact. Comparisons against octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) reveal less energy localization in TATB, which could be a contributing factor to the latter’s insensitivity.

36 MATERIALS SCIENCE↗
NASA NTRS1998

Nanoscale Etching and Indentation of Silicon Surfaces with Carbon Nanotubes

The possibility of nanolithography of silicon and germanium surfaces with bare carbon nanotube tips of scanning probe microscopy devices is considered with large scale classical molecular dynamics (MD) simulations employing Tersoff's reactive many-body potential for heteroatomic C/Si/Ge system. Lithography plays a key role in semiconductor manufacturing, and it is expected that future molecular and quantum electronic devices will be fabricated with nanolithographic and nanodeposition techniques. Carbon nanotubes, rolled up sheets of graphene made of carbon, are excellent candidates for use in nanolithography because they are extremely strong along axial direction and yet extremely elastic along radial direction. In the simulations, the interaction of a carbon nanotube tip with silicon surfaces is explored in two regimes. In the first scenario, the nanotubes barely touch the surface, while in the second they are pushed into the surface to make "nano holes". The first - gentle scenario mimics the nanotube-surface chemical reaction induced by the vertical mechanical manipulation of the nanotube. The second -digging - scenario intends to study the indentation profiles. The following results are reported in the two cases. In the first regime, depending on the surface impact site, two major outcomes outcomes are the selective removal of either a single surface atom or a surface dimer off the silicon surface. In the second regime, the indentation of a silicon substrate by the nanotube is observed. Upon the nanotube withdrawal, several surface silicon atoms are adsorbed at the tip of the nanotube causing significant rearrangements of atoms comprising the surface layer of the silicon substrate. The results are explained in terms of relative strength of C-C, C-Si, and Si-Si bonds. The proposed method is very robust and does not require applied voltage between the nanotube tips and the surface. The implications of the reported controllable etching and hole-creating for nanolithography on silicon are discussed in detail.

Dzegilenko, Fedor N.↗
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 OSTI2022

Characterization of Heparin’s Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy

Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin’s solution conformational dynamics and structure–function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule’s underlying conformational ensemble, which then provides important information necessary for understanding structure–function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin’s conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. In this work, the anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Molecular dynamics study on interface formation and bond strength of impact-welded Mg-steel joints

It was recently demonstrated that the vaporizing foil actuator welding (VFAW) method can directly join immiscible magnesium and steel alloys without coating or a third chemical element based intermetallic compound layer. The VFAW Mg/steel joint exhibits a mixed interface layer of up to 200μm thickness consisting of Mg matrix and Fe particles. Computer simulations have suggested the formation of the interlayer is from the high-velocity frictional shearing between the Mg/steel substrates during the oblique impact in the VFAW process. This paper investigates the formation of Mg-Fe interlayer under VFAW condition with different shearing velocities using molecular dynamics (MD) model, and studies the bonding strength under different scenarios. Finally, the results elucidate the critical role of shearing velocity and surface roughness in achieving Mg/Fe joint.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Applying molecular dynamics simulations to the study of micro cold spray of yttria

Micro cold spray (MCS) is a novel manufacturing process with proven success depositing dense, thick films of technical ceramics without the need for elevated processing temperatures or chemical precursors. The process transforms a loose sub-micrometer powder into an adherent film with mechanical properties approaching that of the bulk material through a phenomenon known as room temperature impact consolidation. While this phenomenon has been demonstrated for a wide variety of ceramic materials and film substrates, yttria stands out as a material that is both well-characterized in experiments and of significant interest for industrial applications due to its excellent refractory properties. This dissertation seeks to investigate the fundamental mechanisms that enable room temperature impact consolidation by using molecular dynamics (MD) simulations of yttria particle impacts and characterizing the deformation behavior of the system.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Effective Fragment Potential-Based Molecular Dynamics Studies of Diffusion in Acetone and Hexane

To facilitate more reliable descriptions of transport properties in liquids, molecular dynamics (MD) simulations are performed based on the effective fragment potential (EFP) method derived from first-principles quantum mechanics (in contrast to MD based upon empirically fitted potentials). The EFP method describes molecular interactions in terms of Coulomb, polarization/induction, dispersion, exchange-repulsion, and charge-transfer interactions. The EFP MD simulations described in this paper, performed on hexane and acetone, are able to track the mean-square displacement of molecules for sufficient time to reliably extract translational diffusion coefficients. Finally, the results reported here are in reasonable agreement with experiment.

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

Rapid activation of non-oriented mechanophores via shock loading and spallation

Mechanophores (MPs), stimuli-responsive molecules that respond chromatically to mechanochemical reactions, are important for understanding the coupling between mechanics and chemistry as well as in engineering applications. However, the atomic-level understanding of their activation originates from gas phase studies or under simple linear elongation forces directly on molecules or polymer chains containing MPs. The effect of many-body distortions, pervasive in condensed-phase applications, is not understood. Therefore, we performed large-scale molecular dynamics (MD) simulations of a poly(methyl methacrylate)-spiropyran copolymer under dynamic mechanical loading and studied the activation of the MP under various conditions from dynamical compression to tension during unloading. Detailed analysis of the all-atom MD trajectories shows that the MP blocks experience significant many-body intramolecular distortion that can significantly decrease the activation barrier as compared with when deformation rates are slow relative to molecular relaxation time scales. Here we find that the reactivity of MPs under material compression states is governed by many-body effects of intramolecular torsions, whereas under tension, the reactions are governed by tensile stresses.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Thermal and concentration effects on 1 H NMR relaxation of Gd 3+ -aqua using MD simulations and measurements

We report gadolinium-based contrast agents are key in clinical MRI for enhancing the longitudinal NMR relativity (r 1 ) of hydrogen nuclei ( 1 H) in water and improving the contrast among different tissues. The importance of MRI in clinical practice cannot be gainsaid, yet the interpretation of MRI relies on models with severe assumptions, reflecting a poor understanding of the molecular-scale relaxation processes. In a step towards building a clearer understanding of the relaxation processes, here we investigate thermal and concentration effects on r 1 of the Gd 3+ -aqua complex using both semi-classical molecular dynamics (MD) simulations and measurements. We follow the MD simulation approach recently introduced by [Singer et al., Phys. Chem. Chem. Phys., 2021, 23, 20974], in which no NMR relaxation model or free-parameter is assumed to predict r 1 , thereby bringing new insights into the physics of r 1 on a molecular scale. We expand the autocorrelation function G(t) in terms of molecular modes and determine the thermal activation energies of the two largest modes, both of which are consistent with the range of literature values for rotational diffusion. We also determine the activation energies for translational diffusion and low-field electron-spin relaxation, both of which are consistent with the literature. Furthermore, we validate the MD simulations at human body temperature and concentrations of the paramagnetic ion used in clinical MRI, and we quantify the uncertainties in both simulations and measurements.

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

Atomistic insight into the effects of electrostatic fields on hydrocarbon reaction kinetics

Reactive Molecular Dynamics (MD) and Density Functional Theory (DFT) computations are performed to provide insight into the effects of external electrostatic fields on hydrocarbon reaction kinetics. By comparing the results from MD and DFT, the suitability of the MD method in modeling electrodynamics is first assessed. Results show that the electric field-induced polarization predicted by the MD charge equilibration method is in good agreement with various DFT charge partitioning schemes. Then, the effects of oriented external electric fields on the transition pathways of non-redox reactions are investigated. Results on the minimum energy path suggest that electric fields can cause catalysis or inhibition of oxidation reactions, whereas pyrolysis reactions are not affected due to the weaker electronegativity of the hydrogen and carbon atoms. MD simulations of isolated reactions show that the reaction kinetics is also affected by applied external Lorentz forces and interatomic Coulomb forces since they can increase or decrease the energy of collision depending on the molecular conformation. In addition, electric fields can affect the kinetics of polar species and force them to align in the direction of field lines. These effects are attributed to energy transfer via intermolecular collisions and stabilization under the external Lorentz force. The kinetics of apolar species is not significantly affected mainly due to the weak induced dipole moment even under strong electric fields. The dynamics and reaction rates of species are studied by means of large-scale combustion simulations of n-dodecane and oxygen mixtures. Results show that under strong electric fields, the fuel, oxidizer, and most product molecules experience translational and rotational acceleration mainly due to close charge transfer along with a reduction in their vibrational energy due to stabilization. This study will serve as a basis to improve the current methods used in MD and to develop novel methodologies for the modeling of macroscale reacting flows under external electrostatic fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗