Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “dynamic simulations”

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 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Molecular Dynamics Simulations of Supercritical Carbon Dioxide and Water using TraPPE and SWM4-NDP Force Fields

The increased levels of carbon dioxide (CO 2 ) emissions due to the combustion of fossil fuels and the consequential impact on global climate change have made CO 2 capture, storage, and utilization a significant area of focus for current research. In most electrochemical CO 2 applications, water is used as a proton donor due to its high availability and mobility and use as a polar solvent. Additionally, supercritical CO 2 is a promising avenue for electrochemical applications due to its unique chemical and physical properties. Consequently, understanding the interactions between water and supercritical CO 2 is of great importance for future electrochemical applications. Molecular dynamics (MD) simulation is a powerful tool that enables atomistic-resolution dynamics of molecular systems, which can complement and guide future experimental investigations. This study employed atomistic MD to study the cosolubilities, codiffusivities, and structure of supercritical CO 2 and water systems, with a polarizable water model (SWM4-NDP) and a nonpolarizable CO 2 model (TraPPE). Additionally, ab initio MD simulations were used to better understand how atomistic polarizable/nonpolarizable models compare to explicit modeling of electron densities. The polarizable water model exhibited substantial improvement in water-associated properties. In conclusion, we anticipate the development of a compatible polarizable CO 2 model to yield similar improvement, providing a pathway for realizing novel high-pressure electrochemical systems.

25 ENERGY STORAGE↗
DOE OSTI2023

Direct comparison between experiments and dislocation dynamics simulations of high rate deformation of single crystal copper

A long standing challenge in computational materials science is to establish a quantitative connection between the macroscopic properties of plastic deformation with the microscopic mechanisms of dislocations in crystalline materials. Although the discrete dislocation dynamics (DDD) simulation method has been developed for several decades with the goal of addressing this challenge, a one-to-one comparison between the DDD predictions on single crystal stress–strain curves and experimental measurements under identical conditions has not been possible to date. Such a comparison is an essential step towards establishing a dislocation-physics based theory of plasticity and a multiscale framework of the plastic behaviors of crystalline materials. Here we provide direct comparisons between the stress–strain curves of Cu single crystals under high strain rate loading in the [0 0 1] and [0 1 1] directions obtained from miniaturized desktop Kolsky bar experiments and those from DDD simulations under identical loading conditions. With an appropriate set of parameters, DDD simulations can produce stress–strain curves that are in reasonable agreement with the experimental results. However, the dislocation mobility values needed to achieve this agreement are an order of magnitude lower than expected based on previous measurements and atomistic simulations. We hypothesize that this discrepancy could be caused by drag forces from jogs and point defects produced during the plastic deformation. Cross-slip of screw dislocations is also found to be necessary to capture the experimental stress–strain behavior, especially for the [0 1 1] loading direction. Finally, this work provides an example of how direct comparisons between DDD simulations and experimental measurements can provide new insight into the fundamental mechanisms of plastic deformation.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Molecular Dynamics Simulation Study of the Protonation State Dependence of Glutamic Acid Transport through a Cyclic Peptide Nanotube

The effect of the protonation state of glutamic acid on its translocation through cyclic peptide nanotubes (CPNs) was assessed by using molecular dynamics (MD) simulations. Anionic (GLU–), neutral zwitterionic (GLU0), and cationic (GLU+) forms of glutamic acid were selected as three different protonation states for an analysis of energetics and diffusivity for acid transport across a cyclic decapeptide nanotube. Based on the solubility-diffusion model, permeability coefficients for the three protonation states of the acid were calculated and compared with experimental results for CPN-mediated glutamate transport through CPNs. Potential of mean force (PMF) calculations reveal that, due to the cation-selective nature of the lumen of CPNs, GLU–, so-called glutamate, shows significantly high free energy barriers, while GLU+ displays deep energy wells and GLU0 has mild free energy barriers and wells inside the CPN. The considerable energy barriers for GLU– inside CPNs are mainly attributed to unfavorable interactions with DMPC bilayers and CPNs and are reduced by favorable interactions with channel water molecules through attractive electrostatic interactions and hydrogen bonding. Unlike the distinct PMF curves, position-dependent diffusion coefficient profiles exhibit comparable frictional behaviors regardless of the charge status of three protonation states due to similar confined environments imposed by the lumen of the CPN. The calculated permeability coefficients for the three protonation states clearly demonstrate that glutamic acid has a strong protonation state dependence for its transport through CPNs, as determined by the energetics rather than the diffusivity of the protonation state. In addition, the permeability coefficients also imply that GLU– is unlikely to pass through a CPN due to the high energy barriers inside the CPN, which is in disagreement with experimental measurements, where a considerable amount of glutamate permeating through the CPN was detected. To resolve the discrepancy between this work and the experimental observations, several possibilities are proposed, including a large concentration gradient of glutamate between the inside and outside of lipid vesicles and bilayers in the experiments, the glutamate activity difference between our MD simulations and experiments, an overestimation of energy barriers due to the artifacts imposed in MD simulations, and/or finally a transformation of the protonation state from GLU– to GLU0 to reduce the energy barriers. Altogether, our study demonstrates that the protonation state of glutamic acid has a strong effect on the transport of the acid and suggests a possible protonation state change for glutamate permeating through CPNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Functional uncertainty quantification for isobaric molecular dynamics simulations and defect formation energies

Functional uncertainty quantification (FunUQ) was recently proposed to quantify uncertainties in models and simulations that originate from input functions, as opposed to parameters. This paper extends here FunUQ to quantify uncertainties originating from interatomic potentials in isothermal-isobaric molecular dynamics (MD) simulations and to the calculation of defect formation energies. We derive and verify a computationally inexpensive expression to compute functional derivatives in MD based on perturbation theory. We show that this functional derivative of the quantities of interest (average internal energy, volume, and defect energies in our case) with respect to the interatomic potential can be used to predict those quantities for a different interatomic potential, without re-running the simulation. The codes and scripts to perform FunUQ in MD are freely available for download. In addition, to facilitate reproducibility and to enable use of best practices for the approach, we created Jupyter notebooks to perform FunUQ analysis on MD simulations and made them available for online simulation in nanoHUB. The tool uses cloud computing resources and users can view, edit, and run end-to-end workflows from a standard web-browser without the need to download or install any software.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Direct comparisons of X-ray scattering and atomistic molecular dynamics simulations for precise acid copolymers and ionomers

Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. In these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the average distance between branches of type 2 or 3 aggregates. Furthermore, this direct comparison of X-ray scattering data to the atomistic MD simulations is a substantive step toward providing a comprehensive, predictive model for ionomer morphology, gives substantial support for this atomistic MD model, and provides new credibility to the presence of stringy, branched, and percolated ionic aggregates in precise ionomer melts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Structural phase transitions in a MoWSe 2 monolayer: Molecular dynamics simulations and variational autoencoder analysis

Electrical and optoelectronic properties of two-dimensional (2D) transition metal dichalcogenides (TMDCs) can be tuned by exploiting their structural phase transitions. Here semiconducting (2H) to metallic (1T) phase transition is investigated in a strained MoWSe 2 monolayer using molecular dynamics (MD) simulations. Novel intermediate structures called α and β are found between the 2H and 1T phases. These intermediate structures are similar to those observed in a 2D MoS 2 by scanning transmission electron microscopy. Here, a deep generative model, namely the variational autoencoder (VAE) trained by MD data, is used to generate novel heterostructures with α and β interfaces. Quantum simulations based on density functional theory show that these heterostructures are stable and suitable for novel nanoelectronics applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Orientation and Conformation of Proteins at the Air–Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy

Understanding the assembly of proteins at the air-water interface (AWI) informs the formation of protein films, emulsion properties, and protein aggregation. Determination of protein conformation and orientation at an interface is difficult to resolve with a single experimental or simulation technique alone. To date, the interfacial structure of even one of the most widely studied proteins, lysozyme, at the AWI remains unresolved. Here in this study, molecular dynamics (MD) simulations are used to determine if the protein adopts a side-on, head-on, or axial orientation at the AWI with two different forcefields, GROMOS-53a6 + SPC/E and a99SB-disp + TIP4P-D. Vibrational sum frequency generation (SFG) spectroscopy experiments and spectral SFG calculations validate consistency between the structure determined from MD and experiments. Overall, we show with strong agreement that lysozyme adopts an axial conformation at pH 7. Further, we provide molecular-level insight as to how pH influences the binding domains of lysozyme resulting in side-on adsorption near the isoelectric point of the lysozyme.

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

Evaluation of adsorption and mechanical strength of 13X zeolite mixtures with phyllosilicate binders using molecular dynamics simulation and positron annihilation spectroscopy

There is growing interest in developing zeolites with novel internal structures that have optimal adsorptive capacity and high mechanical strength, while offering advantages, such as being light weight. We integrate computational and experimental methods to explore the effect of binder/zeolite types, and weight percentages on the mechanical strength of 13X zeolite and adsorption capacities of N 2 , H 2 O, and CO 2 for additive manufacturing (AM) applications with the goal of maximizing both adsorption and strength. Zeolite 13X mixtures and phyllosilicate binders (either bentonite or kaolin) are combined using molecular dynamics (MD) simulations to create structures with various binder/zeolite weight percentages. Further, adsorption capabilities and mechanical strength are assessed using the grand canonical Monte Carlo (GCMC) and ReaxFF modules, respectively. Our modeling shows that an optimized zeolite/binder ratio for N 2 adsorption is around 15 wt% for kaolin and roughly 10 wt% for bentonite. The resulting parameters can be applied to facilitate macro-scale computational fluid dynamics (CFD) and finite element method (FEM) simulations of an AM zeolite structure. We also performed Positron Annihilation Lifetime Spectroscopy (PALS) measurements on zeolite samples to explore the effect of changes in the internal volume. The results show an inverse relationship between the free volume and the solid loading and adding a binder changes the morphology of the zeolite-binder compound and decreases open-volume area significantly.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

Computational Fluid Dynamics Simulation of Methane Slosh and Drain Experiments

NASA possesses a wealth of historical cryogenic experiments that provide valuable insights into the design, troubleshooting, and understanding involved in the complex fluid and thermodynamics of managing cryogenic propellants. One approach to leveraging these historical datasets is by simulating these experiments to validate the accuracy of simulation environments and constituent models. This study focused on simulating a selection of the K site test series for both static and sloshing pressurized liquid methane draining experiments conducted at NASA in the 1970’s, utilizing computational fluid dynamics. The simulations were performed in the ANSYS FLUENT environment using the Volume of Fluid (VOF) numerical approach. A k-omega turbulence model was used with interfacial turbulence damping, and accurately predicted the amount of pressurant needed to maintain the required tank pressure throughout the static drain. The static simulation predicted the temperature stratification in the ullage observed at the end of the drain. During the methane expulsion with sloshing test, many features were successfully captured using the k-omega turbulence model with interfacial turbulence damping included. The rate of phase change and liquid temperature was overpredicted compared to the experimental measurements. The overprediction may be attributed to uncertainties in the vessel geometry, methane pressurant temperature and composition, and methodological differences in how the sloshing frequency was adjusted during the expulsion.

Cryogenic Propellants↗
DOE OSTI2016

Structure of rigid polymers confined to nanoparticles: Molecular dynamics simulations insight

Nanoparticles (NPs) grafted with organic layers form hybrids able to retain their unique properties through integration into the mesoscopic scale. The organic layer structure and response often determine the functionality of the hybrids on the mesoscopic length scale. Using molecular dynamics (MD) simulations, we probe the conformation of luminescent rigid polymers, dialkyl poly(p-phenylene ethynylene)s (PPE), end-grafted onto a silica nanoparticle in different solvents as the molecular weights and polymer coverages are varied. We find that, in contrast to NP-grafted flexible polymers, the chains are fully extended independent of the solvent. In toluene and decane, which are good solvents, the grafted PPEs chains assume a similar conformation to that observed in dilute solutions. In water, which is a poor solvent for the PPEs, the polymer chains form one large cluster but remain extended. The radial distribution of the chains around the core of the nanoparticle is homogeneous in good solvents, whereas in poor solvents clusters are formed independent of molecular weights and coverages. As a result, the clustering is distinctively different from the response of grafted flexible and semiflexible polymers.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Probing High-Pressure Structural Evolution in Polyurea with In Situ Energy-Dispersive X-ray Diffraction and Molecular Dynamics Simulations

Polyurea, an elastomer with a phase-segregated microstructure, has been proven as an effective coating in defense applications. To gain a more complete understanding of the high-pressure atomic-level morphology of these phases and to validate molecular dynamics (MD) simulations, multi-angle energy-dispersive X-ray diffraction experiments were performed in situ up to pressures of ~6 GPa at room temperature. Structure factors were obtained and compared to MD simulations with an average error of less than 5% between major peak positions. The first sharp diffraction peak shifted from 4.56 Å to lower d-spacing with pressure, indicating compression between hard segments. This was further supported by the behavior of a peak at ~3.86 Å from the pair distribution function (PDF), suspected to represent π-stacking and separation between soft segments. Compression within the hard segments themselves is minimal as low-r peaks in the PDF are not greatly affected by pressure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Mott Transition in a Metallic Liquid: Gutzwiller Molecular Dynamics Simulations

We present here a formulation of quantum molecular dynamics that includes electron correlation effects via the Gutzwiller method. Our new scheme enables the study of the dynamical behavior of atoms and molecules with strong electron interactions. The Gutzwiller approach goes beyond the conventional mean-field treatment of the intra-atomic electron repulsion and captures crucial correlation effects such as band narrowing and electron localization. Finally, we use Gutzwiller quantum molecular dynamics to investigate the Mott transition in the liquid phase of a single-band metal and uncover intriguing structural and transport properties of the atoms.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2019

Integrating CryoEM and Molecular dynamic simulations [Slide]

López et al. analyze the structure and dynamics of lipid nanodiscs, both empty and in complex with pro-apoptotic BAX protein. Information from the computational derived structures prompted changes in image processing strategy, which led to quality improvements in Cryo-EM reconstructions. Together, these findings provide novel insights on the activity of BAXv.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

From Electronic Structure to Ion Transport: Photoelectron Spectroscopy and Molecular Dynamics Simulations Reveal the Role of Anions in Lithium Battery Electrolytes

Electrolyte anions are pivotal for lithium battery performance, yet their fundamental electronic structural properties are not well understood. In this work, we employ a combination of negative-ion photoelectron spectroscopy (NIPES), ab initio calculations, and molecular dynamics (MD) simulations to investigate the electronic structures of three representative electrolyte anions. This multiscale approach enables us to elucidate how their intrinsic electronic properties govern anion–solvent interactions in gas-phase clusters, as well as lithium-ion (Li + ) solvation structures and ion transport behavior in the condensed phase. NIPES reveals that difluoro(oxalato)borate (DFOB – ), bis(fluorosulfonyl)imide (FSI – ), and bis(oxalato)borate (BOB – ) all exhibit high electron binding energies, with vertical/adiabatic detachment energies increasing from DFOB – (6.09/5.70 eV) to FSI – (6.80/6.10 eV) to BOB – (6.82/6.40 eV), correlating with enhanced oxidation stability. Ab initio calculations reveal that DFOB – /FSI – –solvent complexes bind Li + ∼ 10 kcal/mol stronger than BOB – series, aligning with the strength of a Li + –anion model. DFOB – exhibits pronounced charge localization on both oxygen and fluorine atoms, enabling their involvement in Li + coordination. In contrast, fluorine atoms in FSI – are largely electron-depleted and remain excluded from direct Li + binding. MD simulations further demonstrate that LiDFOB and LiFSI systems exhibit Li + diffusion coefficients three and five times higher than those of LiBOB across four common solvents. Notably, LiFSI salt in acetonitrile (AN) exhibits the fastest Li + diffusion among 12 electrolyte systems, highlighting the synergistic effect of FSI – and AN in promoting ion mobility. In conclusion, these findings provide a molecular-level understanding of the critical roles of anion and its microsolvation in optimizing Li + diffusion dynamics, once again emphasizing the positioning of FSI – and DFOB – as prime candidates for next-generation electrolytes.

25 ENERGY STORAGE↗
NASA NTRS2023

Molecular Dynamics Simulations of Austenite-Martensite Interfaces in NiTi Shape Memory Alloys

The unique properties of shape memory alloys (SMAs) arise from a reversible martensitic transformation. The nucleation and migration of austenite-martensite interfaces are the key to understanding the SMA properties. Molecular dynamics (MD) simulations can provide important atomic-scale information about these aspects of the transformation, but their time scales prevent the interface formation under near-equilibrium conditions relevant to experiment. We present a new MD methodology which allows for the natural formation of energetically preferred austenite-martensite interfaces under near-equilibrium conditions. Our simulation demonstrates that the interfaces in NiTi are semi-coherent, composed of a series of terrace planes and structural disconnections, and they migrate rapidly through single crystals with only a small thermodynamic driving force. In bi-crystals and polycrystals, the migration of these same interfaces is significantly impeded by grain boundaries and stored elastic energy. This behavior can result in SMA hysteresis via several mechanisms associated with nucleation and non-elastic strain accommodation.

Gabriel Plummer↗
DOE OSTI2018

Dynamic simulation of powder packing structure for powder bed additive manufacturing

Here, powder packing structure is a critical parameter of powder bed-based additive manufacturing (AM). Experimental characterization of powder is typically limited to measuring bulk properties, whereas many numerical models of AM powder packing are based on geometrical consideration without accounting for particle-to-particle interactions. In the present paper, the powder packing dynamics is simulated using a discrete element method (DEM)-based model that solves the mechanical contact forces and moments between individual particles. As DEM uses explicit time integration, a main challenge in modeling dynamics of metallic powder packing is the need for extremely fine time increment size (e.g., in the order of 1 ns for a 10-μm-diameter particle). The effect of mass scaling, employed for speeding up the calculation, on the simulation results is examined in a test case of powder particles packed inside a box container. The calculated packing density for two different particle size distributions is validated against independent literature data for laser powder bed AM with AISI 316L stainless steel powder. The sensitivity of key input parameters (e.g., friction coefficient) is further evaluated in this test case. The powder packing model is then applied to a practical situation of binder jet AM involving rolling of multiple layers of IN718 powder particles onto a powder bed, for which the calculated packing density is also validated with independent literature data.

42 ENGINEERING↗