Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “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 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Non-monotonic behavior of the lateral diffusivity in an adsorbate as a function of the surface coverage

Diffusion dynamics of adsorbate particles confined on a surface strongly depends on the adsorbate surface coverage. Our molecular dynamics simulation reveals that the average lateral diffusivity of the Lennard-Jones adsorbate on a flat substrate varies non-monotonically with the surface coverage. Given that the adsorbate becomes stratified into distinct layers, we propose a novel approach to analyze the lateral diffusion of the adsorbate particles in different layers, via dividing the total lateral diffusion into consecutive lateral diffusion processes, separated by the layer boundary crossing events. A new definition of the lateral diffusivity in the specific layer has been introduced, and it is revealed that the total lateral diffusivity is equal to the sum of lateral diffusivities in different layers. Furthermore, the non-monotonic behavior of the average lateral diffusivity with the surface coverage is found to result from the difference in behavior of the lateral diffusivity between the first and other layers.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Heat current fluctuations and anomalous transport in low-dimensional carbon lattices

Molecular dynamics simulations and methods of importance sampling are used to study the heat transport of low-dimensional carbon lattices. For both carbon nanotubes and graphene sheets, heat transport is found to be anomalous, violating Fourier’s law of conduction with a system size dependent thermal conductivity and concomitant nonlinear temperature profiles. For carbon nanotubes, the thermal conductivity is found to increase as the square root of the length of the nanotube, while for graphene sheets the thermal conductivity is found to increase as the logarithm of the length of the sheet over the system sizes considered. Furthermore, the particular length dependence and nonlinear temperature profiles place carbon lattices into a universality class with nonlinear lattice models, and suggest that heat transport through carbon nanostructures is better described by a Levy walk rather than simple diffusion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Uptake of N 2 O 5 by aqueous aerosol unveiled using chemically accurate many-body potentials

The reactive uptake of N 2 O 5 to aqueous aerosol is a major loss channel for nitrogen oxides in the troposphere. Despite its importance, a quantitative picture of the uptake mechanism is missing. Here we use molecular dynamics simulations with a data-driven many-body model of coupled-cluster accuracy to quantify thermodynamics and kinetics of solvation and adsorption of N 2 O 5 in water. The free energy profile highlights that N 2 O 5 is selectively adsorbed to the liquid–vapor interface and weakly solvated. Accommodation into bulk water occurs slowly, competing with evaporation upon adsorption from gas phase. Leveraging the quantitative accuracy of the model, we parameterize and solve a reaction–diffusion equation to determine hydrolysis rates consistent with experimental observations. We find a short reaction–diffusion length, indicating that the uptake is dominated by interfacial features. The parameters deduced here, including solubility, accommodation coefficient, and hydrolysis rate, afford a foundation for which to consider the reactive loss of N 2 O 5 in more complex solutions.

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

Structural and electronic characteristics of amorphous Ge 8 Sb 2 Te 11

GeTe-rich phase-change materials can be utilized in rewriteable optical memory due to the large contrast in reflectivity between amorphous and crystalline phases. Here we explored the structure and electronic properties of amorphous Ge 8 Sb 2 Te 11 using ab initio molecular dynamics simulations. The results indicate that amorphous Ge 8 Sb 2 Te 11 is dominantly composed of Ge-, Sb- and Te-centered octahedrons with distortions, while 30.4 % of Ge-centered clusters are in the form of tetrahedrons which are randomly distributed. The 5-fold rings possess a large proportion, and the Gesingle bondTe and Sbsingle bondTe bonds present larger formation energies than other bonds, leading to the ABAB bonding sequence (A: Ge and Sb, B: Te). The lone pair electrons locating at the opposite direction of bonds possess a large fraction of 14.8 %, which may enhance the distortions of local clusters. Importantly, these structural properties lead to the high stability of amorphous Ge 8 Sb 2 Te 11 and thus long data retention in the information storage.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Viscoelastic relaxation and topological fluctuations in glass-forming liquids

In this study, a method for characterizing the topological fluctuations in liquids is proposed. This approach exploits the concept of the weighted gyration tensor of a collection of particles and permits the definition of a local configurational unit (LCU). The first principal axis of the gyration tensor serves as the director of the LCU, which can be tracked and analyzed by molecular dynamics simulations. Analysis of moderately supercooled Kob–Andersen mixtures suggests that orientational relaxation of the LCU closely follows viscoelastic relaxation and exhibits a two-stage behavior. The slow relaxing component of the LCU corresponds to the structural, Maxwellian mechanical relaxation. Additionally, it is found that the mean curvature of the LCUs is approximately zero at the Maxwell relaxation time with the Gaussian curvature being negative. This observation implies that structural relaxation occurs when the configurationally stable and destabilized regions interpenetrate each other in a bicontinuous manner. Finally, the mean and Gaussian curvatures of the LCUs can serve as reduced variables for the shear stress correlation, providing a compelling proof of the close connection between viscoelastic relaxation and topological fluctuations in glass-forming liquids.

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

Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

Residing in the 5' untranslated region of the mRNA, the 2'-deoxyguanosine (2'-dG) riboswitch mRNA element adopts an alternative structure upon binding of the 2'-dG molecule, which terminates transcription. RNA conformations are generally strongly affected by positively charged metal ions (especially Mg 2+ ). We have quantitatively explored the combined effect of ligand (2'-dG) and Mg 2+ binding on the energy landscape of the aptamer domain of the 2'-dG riboswitch with both explicit solvent all-atom molecular dynamics simulations (99 μsec aggregate sampling for the study) and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments. We show that both ligand and Mg 2+ are required for the stabilization of the aptamer domain; however, the two factors act with different modalities. The addition of Mg 2+ remodels the energy landscape and reduces its frustration by the formation of additional contacts. In contrast, the binding of 2'-dG eliminates the metastable states by nucleating a compact core for the aptamer domain. Mg 2+ ions and ligand binding are required to stabilize the least stable helix, P1 (which needs to unfold to activate the transcription platform), and the riboswitch core formed by the backbone of the P2 and P3 helices. Mg 2+ and ligand also facilitate a more compact structure in the three-way junction region.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Protonation Dynamics of Confined Ethanol–Water Mixtures in H-ZSM-5 from Machine Learning-Driven Metadynamics

Zeolites are indispensable heterogeneous catalysts in industrial chemical processes, valued for their strong Brønsted acidity, well-defined microporous frameworks, and tunable pore structures. Their catalytic activity arises primarily from Brønsted acid sites (BAS), typically present as bridging hydroxyl groups (Si–OH–Al). Under aqueous reaction conditions, these protons interact dynamically with water and alcohol molecules, leading to complex solvation and protonation behavior within confined pores. In this study, we investigate the protonation equilibrium occurring between ethanol and water at the BAS of acidic zeolites under varying hydration levels, i.e., C2H5OH–(H2O)n, n=1–4. Local structure was analyzed through an adaptive-learning global optimization algorithm, while enhanced sampling molecular dynamics simulations with Well-Tempered Metadynamics (WMetaD) and machine learning interatomic potentials (MLPs) provide free-energy surfaces (FES) at variable hydration levels. The results reveal a strong dependence of proton localization on the degree of hydration. At low hydration (1 water molecule), the proton resides predominantly on ethanol; with 2 water molecules, it shifts toward water, and at higher hydration (3 or more water molecules), it becomes extensively delocalized over the water cluster. These findings underscore the critical role of solvation in modulating acid site behavior and suggest that a minimum of three water molecules is necessary to fully stabilize the proton on water within the zeolite framework. This solvation threshold has significant implications for catalytic processes, particularly in biomass conversion reactions where alcohol protonation is a key step in dehydration mechanisms.

machine learning↗
DOE OSTI2025

Intrinsic bulk viscosity of the one-component plasma

The intrinsic bulk viscosity of the one-component plasma (OCP) is computed and analyzed using equilibrium molecular dynamics simulations and the Green-Kubo formalism. It is found that bulk viscosity exhibits a maximum at Γ ≈ 1, corresponding to the condition that the average kinetic energy of particles equals the potential energy at the average interparticle spacing. The weakly coupled and strongly coupled limits are analyzed and used to construct a model that captures the full range of coupling strengths simulated: Γ ≈ 10 –2 –10 2 . Simulations are also run of the Yukawa one-component plasma (YOCP) in order to understand the impact of electron screening. It is found that electron screening leads to a smaller bulk viscosity due to a reduction in the excess heat capacity of the system. Bulk viscosity is shown to be at least an order of magnitude smaller than shear viscosity in both the OCP and YOCP. The generalized frequency-dependent bulk viscosity coefficient is also analyzed. This is found to exhibit a peak near twice the plasma frequency in strongly coupled conditions, which is associated with the oscillatory decay observed in the bulk viscosity autocorrelation function. As a result, the generalized shear and bulk viscosity coefficients are found to have a similar magnitude for ω ≳ 2⁢ω p at strongly coupled conditions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

First-principles molten salt phase diagrams through thermodynamic integration

Precise prediction of phase diagrams in molecular dynamics simulations is challenging due to the simultaneous need for long time and large length scales and accurate interatomic potentials. Here, we show that thermodynamic integration from low-cost force fields to neural network potentials trained using density-functional theory (DFT) enables rapid first-principles prediction of the solid–liquid phase boundary in the model salt NaCl. We use this technique to compare the accuracy of several DFT exchange–correlation functionals for predicting the NaCl phase boundary and find that the inclusion of dispersion interactions is critical to obtain good agreement with experiment. Importantly, our approach introduces a method to predict solid–liquid phase boundaries for any material at an ab initio level of accuracy, with the majority of the computational cost at the level of classical potentials.

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

Atomistic insights into the synergistic effects of tensile strain and hydroxyl group on increasing the thermal conductivity of monohydric alcohols as latent heat storage materials

The low thermal conductivity of linear monohydric alcohols significantly limits their performance when used as latent heat storage materials. It was found that imposing certain mechanical strains on nanomaterials with highly ordered structures can lead to appreciable thermal conductivity enhancement. To explore the potential of enhancing the intrinsic thermal conductivity of monohydric alcohols, a simplified ideal crystal model was employed for molecular arrangement in this work. The variation of atomistic heat transfer as a function of tensile strains was exploited by non-equilibrium molecular dynamics simulations. Furthermore, the influence of stretching on the vibration density of states and the corresponding molecular morphology were revealed. The results suggested that the thermal conductivity of monohydric alcohols with such simplified ideal crystalline structures can increase by about 170 % at the strain of 0.1. The distance between neighboring interfaces was found to determine the energy of inter-molecular interactions at the crystal grain boundaries. The hydrogen bonds energy has not reached the critical value when increasing tensile strains from 0 to 0.1. In contrast, the strongest van der Walls interactions for alkanes were obtained at the strain of 0.06 where the interfacial distances of alkanes have achieved their equilibrium distances. In addition, the interfacial heat transfer coefficient of ideal crystal monohydric alcohols at hydroxyl interfaces was found to be threefold than that between methyl interfaces, in consistent with the strength of inter-molecular interactions between functional groups at the interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Tuning martensitic transformations via coherent second phases in nanolaminates using free energy landscape engineering

In this work we explore the possibilities and limitations of using a coherent second phase to engineer the thermo-mechanical properties of a martensitic alloy by modifying the underlying free energy landscape that controls the transformation. We use molecular dynamics simulations of a model atomistic system where the properties of a coherent, nanoscale second phase can be varied systematically. With a base martensitic material that undergoes a temperature-induced transformation from a cubic austenite to a monoclinic martensite, simulations show significant ability to engineer the transformation temperatures, from a ~50% reduction to a ~200% increase, with 50 at.% of the cubic second phase. We establish correlations between the properties of the second phase, the transformation characteristics, and the microstructure via the free energy landscape of the twophase systems. Coherency stresses have a strong influence on the martensitic variants observed and can even cause the non-martensitic second phase to undergo a transformation. Reducing the stiffness of the second phase increases the transformation strain and modifies the martensitic microstructure, increasing the volume fraction of the transformed material. This increase in transformation strain is accompanied by a significant increase in Af and thermal hysteresis, while Ms remains unaltered. Our findings on the tunability of martensitic transformations can be used for informed searches of second phases to achieve desired material properties, such as achieving room temperature, lightweight shape memory alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Irradiation-enhanced torsional buckling capacity of carbon nanotube bundles

Molecular dynamics simulations are used to understand the torsional buckling of pristine and irradiated carbon nanotube (CNT) bundles. Irradiation-induced inter-tube defects are shown to significantly increase the critical buckling torque and critical buckling angle, while slightly increasing the torsional stiffness. In contrast, intra-tube defects are found to degrade the torsional properties. Such competing interactions cause irradiation enhancement to occur in large bundles where significant inter-tube bonding can occur. However, the irradiation enhancement effect becomes weak for very large bundles in which enhanced inter-tube interactions already exist in unirradiated bundles. In pristine CNT bundles of all sizes under torsional loading, CNTs can slip via the weakly interacting van der Waals force, whereas in the irradiated bundles, the inter-tube defects prevent slipping. The study further shows that the formation of one-dimensional carbon chain defects contributes to enhanced friction under slipping.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus

The highly and slightly condensed forms of chromatin, heterochromatin and euchromatin, respectively, segregate in the cell nucleus. Heterochromatin is more abundant in the nucleus periphery. Here, in this work, we study the mechanism of heterochromatin segregation by modeling interphase chromosomes as diblock ring copolymers confined in a rigid spherical shell using molecular dynamics simulations. In our model, heterochromatin and euchromatin are distinguished by their bending stiffnesses only, while an interaction potential between the spherical shell and chromatin is used to model lamin-associated proteins. Our simulations indicate that in the absence of attractive interactions between the nuclear shell and the chromatin, most heterochromatin segregates towards the nuclear interior due to the depletion of less flexible heterochromatin segments from the nuclear periphery. This inverted chromatin distribution, which is opposite to the conventional case with heterochromatin dominating at the periphery, is in accord with experimental observations in rod cells. This “inversion” is also found to be independent of the heterochromatin concentration and chromosome number. The chromatin distribution at the periphery found in vivo can be recovered by further increasing the bending stiffness of heterochromatin segments or by turning on attractive interactions between the nuclear shell and heterochromatin. Our results indicate that the bending stiffness of chromatin could be a contributor to chromosome organization along with differential effects of HP ⁢1⁢𝛼-driven phase segregation and of loop extruders and interactions with the nuclear envelope and topological constraints.

biomolecular & subcellular processes↗
DOE OSTI2023

Hybrid interatomic potential for Sn

To design materials for extreme applications, it is important to understand and predict phase transitions and their influence on material properties under high pressures and temperatures. Atomistic modeling can be a useful tool to assess these behaviors. However, this can be difficult due to the lack of fidelity of the interatomic potentials in reproducing this high pressure and temperature extreme behavior. Here, in this work, a hybrid EAM-R—which is the combination of embedded atom method (EAM) and rapid artificial neural network potential—for Tin (Sn) is described which is capable of accurately modeling the complex sequence of phase transitions between different metallic polymorphs as a function of pressure. This hybrid approach ensures that a basic empirical potential like EAM is used as a lower energy bound. By using the final activation function, the neural network contribution to energy must be positive, assuring stability over the whole configuration space. This implementation has the capacity to reproduce density functional theory results at 6 orders of magnitude slower than a pair potential for molecular dynamics simulation, including elastic and plastic characteristics and relative energies of each phase. Using calculations of the Gibbs free energy, it is demonstrated that the potential precisely predicts the experimentally observed phase changes at temperatures and pressures across the whole phase diagram. At 10.2 GPa, the present potential predicts a first-order phase transition between body-centered tetragonal (BCT) β-Sn and another polymorph of BCT-Sn. This structure transforms into body-centered cubic near the experimentally reported value at 33 GPa. Thus, the Sn potential developed in this paper can be used to study complex deformation mechanisms under extreme conditions of high pressure and strain rates unlike existing potentials. Moreover, the framework developed in this paper can be extended for different material systems with complex phase diagrams.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Alloying effects on low-energy recoil events in concentrated solid-solution alloys

Alloying elements at low-concentrations into pure metals is usually adopted to improve their mechanical properties and irradiation performance. Recently developed single-phase concentrated solid-solution alloys (CSAs) comprised of two or more elements, all at high concentrations, have demonstrated good radiation resistance. CSAs are characterized by their extreme disordered states that arise from the random arrangement of different elements and accompanied random local lattice distortions. In this work, we investigate low-energy recoil events in Ni 0.5 X 0.5 (X = Fe and Co) CSAs and Ni 0.8 X 0.2 (X = Fe, Co, Cr, and Pd) CSAs using ab initio molecular dynamics simulations to understand the effects of different disorder on defect production in CSAs. The threshold displacement energies are determined along three high-symmetric directions by randomly choosing independent primary knock-on atoms in each direction. As expected, the threshold energies in Ni and its CSAs are anisotropic, with the highest values found in the [111] direction. The calculated threshold energies of Fe in NiFe are smaller than those in NiCo and Ni, especially along the [111] direction. An inspection of the atomic trajectories inside the collision cascade reveals that the effect of chemical disorder outweighs the site-to-site lattice distortions in determining the threshold energies. Especially, different interaction properties between elements due to their different electronic structures are responsible for the observed different threshold energies. Finally, the local environment dependence of threshold energies suggests that local elemental arrangement can be used to understand and predict threshold energies in disordered alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Low-temperature carbonization of polyacrylonitrile/graphene carbon fibers: A combined ReaxFF molecular dynamics and experimental study

Graphene inclusion in a polymer matrix is a promising route to significantly enhance the mechanical properties of low-grade carbon fibers (CFs). Using ReaxFF molecular dynamics simulation, the atomistic mechanism leading to this enhancement is investigated. We demonstrate that the graphene edges along with the nitrogen and oxygen functional groups play a catalytic role and act as seeds to expedite alignment of the all-carbon rings, which are starting sites for the growth of graphitic structures. To examine the role of this proposed mechanism that enhances the graphitic structure of PAN/graphene CFs, we discuss the experimental results wherein the PAN/graphene CFs carbonized at 1250 C demonstrate 91% (from 632 to 1207 MPa) increase in strength and 101% (from 88 to 177 GPa) enhancement in Young’s modulus compared to PAN-based CFs carbonized at 1500 C. In conclusion, these enhanced mechanical properties of low-grade carbon fibers achieved via graphene inclusion at decreased carbonization temperature provide a means to realize both energy savings and cost reduction.

42 ENGINEERING↗
DOE OSTI2025

Crystal nucleation rates in one-component Yukawa systems

Nucleation in the supercooled Yukawa system is relevant for addressing current challenges in understanding a range of crystallizing systems including white dwarf (WD) stars. We use both brute force and seeded molecular dynamics simulations to study homogeneous nucleation of crystals from supercooled Yukawa liquids. With our improved approach to seeded simulations, we obtain quantitative predictions of the crystal nucleation rate and cluster size distributions as a function of temperature and screening length. These quantitative results show trends towards fast nucleation with short-ranged potentials. They also indicate that for temperatures T > 0.9⁢T m , where T m is the melt temperature, classical homogeneous nucleation is too slow to initiate crystallization but transient clusters of ~100 particles should be common. As a result, we apply these general results to a typical WD model and obtain a delay of ~0.6 Gyr in the onset of crystallization that may be observable.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Designing sequence-defined peptoids for fibrillar self-assembly and silicification

In the biological environment, mineral crystals exquisitely controlled by biomacromolecules often show intricate hierarchical structures and superior mechanical properties. Among these biominerals, spicules, hybrid silica/protein superstructures serving as skeletal elements in demosponges, represent an excellent example for motivating the synthesis of silica materials. Herein, by designing sequence-defined peptoids containing side chains with a strong binding to silica, we demonstrated that self-assembly of these peptoids into fiber structures enables the mimicking of both biocatalytic and templating functions of silicatein filaments for the formation of silica fibers at near-neutral pH and ambient temperature. We further showed that the presence of amino groups is significant for the nucleation of silica on self-assembled peptoid nanofibers. Molecular dynamics simulation further confirmed that having silica-binding of amino side chains is critical for self-assembled peptoid fibers in triggering silica formation. Here, we demonstrated that tuning inter-peptoid interactions by varying carboxyl and amino side chains significantly influences the assembly kinetics and final morphologies of peptoid assemblies as scaffolds for directing silica mineralization to form silica spheres, fibers, and sheets. The formation of silica shell on peptoid fibers increased the mechanical property of peptoid hydrogel materials by nearly 1000-fold, highlighting the great potential of using silicification to enhance the mechanical property of hydrogel materials for applications including tissue engineering. Since peptoids are highly robust and programmable, we expect that self-assembly of peptoids containing solid-binding side chains into hierarchical materials opens new opportunities in the design and synthesis of highly tunable scaffolds that direct the formation of composite nanomaterials.

59 BASIC BIOLOGICAL SCIENCES↗