Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular dynamic simulation”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Evaluating Cryo–TEM Reconstruction Accuracy of Self–Assembled Polymer Nanostructures

Cryogenic transmission electron microscopy (cryo–TEM) combined with single particle analysis (SPA) is an emerging imaging approach for soft materials. However, the accuracy of SPA–reconstructed nanostructures, particularly those formed by synthetic polymers, remains uncertain due to potential packing heterogeneity of the nanostructures. In this study, the combination of molecular dynamics (MD) simulations and image simulations is utilized to validate the accuracy of cryo–TEM 3D reconstructions of self–assembled polypeptoid fibril nanostructures. Using CryoSPARC software, image simulations, 2D classifications, ab initio reconstructions, and homogenous refinements are performed. By comparing the results with atomic models, the recovery of molecular details is assessed, heterogeneous structures are identified, and the influence of extraction location on the reconstructions is evaluated. In conclusion, these findings confirm the fidelity of single particle analysis in accurately resolving complex structural characteristics and heterogeneous structures, exhibiting its potential as a valuable tool for detailed structural analysis of synthetic polymers and soft materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Atomistic simulations to reveal HIP-bonding mechanisms of Al6061/Al6061

Molecular dynamics simulations were employed to understand the diffusion bonding process during hot isostatic pressing (HIP) of Al6061/Al6061 alloy. Simulations of the HIP process reveal atomistic phenomena that are difficult or unlikely to be observed experimentally and provide useful insights into the mechanism of diffusion and bonding. Here, the results reveal that at the start of the HIP process, a massive incursion of oxygen atoms occurs from the pre-existing γ-Al 2 O 3 to the 6061 region across the interphase interface. These oxygen atoms interact with the enriched Mg atom layer present at the existing γ-Al 2 O 3 and 6061 matrix to form a secondary complex Mg 2 Al 2 O 5 phase. Diffusion calculations also show that transport of atoms due to the applied pressure is 4–5 orders of magnitude higher than would occur in the absence of HIP conditions. The Mg 2 Al 2 O 5 phase also provides efficient pathways for the rapid transport of Mg atoms. Because of the higher diffusion coefficients observed for Mg within the phase, Mg atoms can move more swiftly compared to their diffusion within other phases such as γ-Al 2 O 3 . This accelerated mobility facilitates the rapid movement of Mg atoms across the interface, leading to changes in the local composition and the potential growth of the Mg 2 Al 2 O 5 phase.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Large scale polymer toughening of two-dimensional materials revealed by in situ TEM fracture tests and multiscale simulations

Two-dimensional (2D) materials offer significant potential for applications in energy-harvesting devices, batteries, sensors, and transistors. However, their intrinsic brittleness makes them prone to mechanical failure, limiting their practical use. In this work, we perform in situ transmission electron microscopy (TEM) fracture tests on monolayer MoSe2 and uncover an extrinsic toughening effect induced by an ultrathin adsorbed polystyrene adlayer. This adlayer substantially enhances the fracture resistance of the 2D flakes. Through a combination of molecular dynamics simulations and finite element analysis, we elucidate the molecular mechanism behind this toughening effect. Further, it arises from the active crack-bridging behavior of entangled polymer chains and the formation of a fracture process zone that stabilizes crack propagation and increases the energy required for crack extension. The proposed toughening mechanism offers a pathway to improving the mechanical reliability of 2D material-based devices by mitigating the risk of sudden failure.

2D materials↗
DOE OSTI2025

High Energy Density Physics of Inertial Confinement Fusion Ablator Materials

The historic December 5, 2022 experiment at Lawrence Livermore National Lab’s (LLNL) National Ignition Facility (NIF) reached fusion energy ignition for the first time. This is the most important scientific breakthrough of the 21st century paves the way to future clean inertial fusion energy (IFE). The diamond (high density carbon (HDC)) ablator material used in this experiment displays detrimental effects due to the development of hydrodynamic instabilities at the diamond/fuel interface under shock compression. New alternatives to diamond ablators are required to step up the energy yield in ICF experiments. The unique combination of mechanical strength (approaching that of diamond), the ability to accommodate high-Z dopants (in contrast to diamond), and the tunability of the properties (through synthesis material with varying sp 3 content) make amorphous carbon (a-C) a promising material for next-generation IFE ablative capsules. However, despite its critical importance to the IFE program, the behavior of a-C carbon at extreme temperatures and pressures remains largely unexplored. The primary goals of this project were to perform groundbreaking dynamic compression experiments and predictive simulations to uncover the fundamental high-energy-density physics of amorphous carbon. Our goals were (1) to uncover the metastability range of amorphous carbon and probe phase transitions to diamond or metastable supercooled liquid carbon; (2) to acquire high-quality equation of state (EOS) data and develop an experimentally validated EOS from machine-learning MD simulations of the complex states of carbon; and (3) to uncover the complex behavior of carbon liquid in both thermodynamically stable and metastable supercooled states by accessing large areas of carbon phase diagram with amorphous samples with variable sp 3 content. Our proposed experimental program included measurements of equation of state and diffraction measurements using the Omega EP laser at the Laboratory of Laser Energetics at the University of Rochester. The theoretical/simulation program involved the development of machine-learning models of the complex response of amorphous carbon under dynamic compression by performing molecular dynamics simulations at experimental time and length scales using leadership class DOE supercomputers. Simulations guided experiments to observe predicted phenomena and acquire critical experimental data in specific pressure-temperature domains to validate theoretical models. This research delivered fundamental properties of novel amorphous carbon IFE ablator material, including phase diagram and EOS. These results will aid in IFE target design and implosion experiments. A unique combination of predictive simulations and dynamic and static experiments provided a highly inspirational intellectual environment for graduate students and postdocs involved in this project.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Excess Density as a Descriptor for Electrolyte Solvent Design

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

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Effect of Lithium Doping on MgO Hydroxylation and Carbonation

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

MgO↗
DOE OSTI2025

Investigating Morphology and Diffusion in Simulations of Precise Anion-Conducting Polymers

Using atomistic molecular dynamics simulations, we investigate the morphology and transport properties of a new class of polymers which are functionalized with quaternary ammonium groups for use as anion exchange membranes. The polymers are precision polyolefins with either a trimethylammonium (p5CNMe3) or a dimethyl-hexyl ammonium (p5CNMe2Hx) pendant group at every fifth carbon along a polyethylene backbone. Simulations are performed at hydration levels of 5, 10, 15, and 20 water molecules per ammonium group. The hydrated polymers form nanoscale, percolated hydrophilic domains (water channels) in the hydrophobic polymer matrix that become wider with increasing water content. Water and hydroxide anion diffusion coefficients also increase with increasing water content. The morphology of the water domains is similar in both polymers, while the diffusion coefficients are somewhat lower in p5CNMe2Hx at fixed water content. Furthermore, the diffusion coefficients in both polymers fall on the same curve as a function of the fractal dimension of the percolated water channels, which appears to be a useful scalar measure of the effects of the nanoscale morphology on water and hydroxide anion transport.

Anion exchange membrane↗
DOE OSTI2025

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

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

EPDM↗
DOE OSTI2025

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

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

Batteries↗
DOE OSTI2025

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

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

36 MATERIALS SCIENCE↗
DOE OSTI2026

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

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

36 MATERIALS SCIENCE↗
DOE OSTI2025

Molecular understanding of ion transport in a zwitterionic electrolyte

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

Classical molecular dynamic simulations↗
DOE OSTI2025

An atomic cluster expansion (ACE) potential for water under extreme conditions

We present a machine learning interatomic potential for water designed to capture its complex multiphase behavior, including both molecular and superionic ice phases. The potential is based on the atomic cluster expansion (ACE) formulation and has been parameterized to enable high-fidelity molecular dynamics simulations of water under extreme conditions, for pressures up to 100 GPa and for temperatures between 500 and 6000 K. A diverse range of configurations was generated through ab initio molecular dynamics (AI-MD) simulations, covering insulating and superionic ice phases, liquid water, and dissociated plasma phase. We demonstrate that the H 2 O ACE potential accurately reproduces experimental and DFT predicted isotherms and Hugoniots. Crucially, the potential is able to capture the intricate phase behavior of water, including the transition from molecular fluid to the appropriate solid ice phases, and the superionic ice phases. This work provides a robust interatomic potential that can be used for large-scale, accurate simulations of water under extreme thermodynamic conditions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

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

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

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Anisotropic interactions for continuum modeling of protein–membrane systems

In this work, a model for anisotropic interactions between proteins and cellular membranes is proposed for large-scale continuum simulations. The framework of the model is based on dynamic density functional theory, which provides a formalism to describe the lipid densities within the membrane as continuum fields while still maintaining the fidelity of the underlying molecular interactions. Within this framework, we extend recent results to include the anisotropic effects of protein–lipid interactions. As applications, we consider two membrane proteins of biological interest: a RAS–RAF complex tethered to the membrane and a membrane embedded G protein-coupled receptor. A strong qualitative and quantitative agreement is found between the numerical results and the corresponding molecular dynamics simulations. Combining the scope of continuum level simulations with the details from molecular level particle simulations enables research into protein–membrane behaviors at a more biologically relevant scale, which crucially can also be accessed via experiment.

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

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

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

Co-ion penetration↗
DOE OSTI2026

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

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

Molecular dynamics simulations↗
DOE OSTI2025

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

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

59 BASIC BIOLOGICAL SCIENCES↗