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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 1,513 records · Page 84
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Binding orientation and interaction of bile salt in its ternary complex with pancreatic lipase-colipase system

Highlights: • Molecular dynamic simulation of porcine lipase-colipase with bile salt is performed. • Interactions between lipase-colipase and bile salt are analyzed. • Ternary complex is stabilized by van der Waals interactions. • Binding orientation of bile salt micelle on lipase-colipase is modelled. The interfacial activity of pancreatic lipases (PL) depends on the presence of colipase and bile salt. The activity of PL is inhibited by micellar concentrations of bile salt which can be restored by the addition of colipase. Though the formation of 1:1:1 tertiary complex by lipase-colipase-bile salt micelle is well accepted, the residue-level interactions between lipase-colipase and bile salt are yet to be clearly understood. Molecular dynamic simulations of lipase-colipase complex, lipase and colipase were performed in the presence of a model bile salt, sodium taurocholate (NaTC), at its near-CMC and supra-micellar concentrations. From the interactions obtained from the molecular dynamic simulations, the ternary complex was modelled and compared with earlier reports. The analysis suggested that a micelle of NaTC consisting of nine monomers was formed at the concave groove between lipase and colipase chain and it mainly interacted with the fourth finger of colipase. This complex was mainly stabilized by van der Waals interactions. Interestingly, the C-terminal domain of lipase which holds the colipase did not show any significant role in formation or stabilization of NaTC micelle.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Local vibrational dynamics of hematite (α-Fe{sub 2}O{sub 3}) studied by extended x-ray absorption fine structure and molecular dynamics

The local vibrational dynamics of hematite (α-Fe{sub 2}O{sub 3}) has been investigated by temperature-dependent extended x-ray absorption fine structure spectroscopy and molecular dynamics simulations. The local dynamics of both the short and long nearest-neighbor Fe–O distances has been singled out, i.e., their local thermal expansion and the parallel and perpendicular mean-square relative atomic displacements have been determined, obtaining a partial agreement with molecular dynamics. No evidence of the Morin transition has been observed. More importantly, the strong anisotropy of relative thermal vibrations found for the short Fe–O distance has been related to its negative thermal expansion. The differences between the local dynamics of short and long Fe–O distances are discussed in terms of projection and correlation of atomic motion. As a result, we can conclude that the short Fe–O bond is stiffer to stretching and softer to bending than the long Fe–O bond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Fouling behavior of zwitterionic membranes compared to polyamide membranes

Membrane fouling remains a critical bottleneck for reverse osmosis (RO) desalination, driving energy consumption and reducing membrane lifetime. Here, we employ all-atom molecular dynamics simulations to investigate the antifouling behavior of random zwitterionic amphiphilic copolymer (r-ZAC) membranes composed of sulfobetaine methacrylate (SBMA) and allyl methacrylate (AMA), benchmarked against conventional polyamide (PA) RO membranes. Structural and dynamical analyses—including radial distribution functions, coordination numbers, tetrahedral order parameters, vector orientation, and residence-time correlation functions—reveal that r-ZAC surfaces sustain tightly bound, long-lived hydration layers with preserved tetrahedrality and anisotropic water orientation, in sharp contrast to the weak and disordered hydration of PA. Steered molecular dynamics simulations demonstrate that r-ZAC membranes impose substantial free-energy barriers to foulant approach (alginate ≈ 90 kcal/mol, sucrose ≈ 35 kcal/mol, humic acid ≈ 15 kcal/mol), whereas PA membranes exhibit negligible barriers (< 1 kcal/mol) and thermodynamically favorable adsorption. Detailed foulant–surface interaction analyses show that zwitterionic hydration and electrostatic heterogeneity in r-ZAC suppress adhesion, except in the case of amphiphilic humic acid, which exploits multiple binding modes. Together, these results establish molecular-level design principles for antifouling membranes: the combination of zwitterionic hydration, structured interfacial water, and controlled amphiphilic balance in r-ZAC membranes provides superior resistance to organic fouling relative to PA.

Cross-linked polyamide↗
DOE OSTI2015

Numerical experiment of thermal conductivity in two-dimensional Yukawa liquids

A newly improved homogenous nonequilibrium molecular dynamics simulation (HNEMDS) method, proposed by the Evans, has been used to compute the thermal conductivity of two-dimensional (2D) strongly coupled complex (dusty) plasma liquids (SCCDPLs), for the first time. The effects of equilibrium external field strength along with different system sizes and plasma states (Γ, κ) on the thermal conductivity of SCCDPLs have been calculated using an enhanced HNEMDS method. A simple analytical temperature representation of Yukawa 2D thermal conductivity with appropriate normalized frequencies (plasma and Einstein) has also been calculated. The new HNEMDS algorithm shows that the present method provides more accurate results with fast convergence and small size effects over a wide range of plasma states. The presented thermal conductivity obtained from HNEMDS method is found to be in very good agreement with that obtained through the previously known numerical simulations and experimental results for 2D Yukawa liquids (SCCDPLs) and with the three-dimensional nonequilibrium molecular dynamics simulation (MDS) and equilibrium MDS calculations. It is shown that the HNEMDS algorithm is a powerful tool, making the calculations very efficient and can be used to predict the thermal conductivity in 2D Yukawa liquid systems.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Towards Highly Scalable Ab Initio Molecular Dynamics (AIMD) Simulations on the Intel Knights Landing Manycore Processor

The Ab Initio Molecular Dynamics (AIMD) method allows scientists to treat the dynamics of molecular and condensed phase systems while retaining a first-principles-based description of their interactions. This extremely important method has tremendous computational requirements, because the electronic Schr¨odinger equation, approximated using Kohn-Sham Density Functional Theory (DFT), is solved at every time step. With the advent of manycore architectures, application developers have a significant amount of processing power within each compute node that can only be exploited through massive parallelism. A compute intensive application such as AIMD forms a good candidate to leverage this processing power. In this paper, we focus on adding thread level parallelism to the plane wave DFT methodology implemented in NWChem. Through a careful optimization of tall-skinny matrix products, which are at the heart of the Lagrange multiplier and nonlocal pseudopotential kernels, as well as 3D FFTs, our OpenMP implementation delivers excellent strong scaling on the latest Intel Knights Landing (KNL) processor. We assess the efficiency of our Lagrange multiplier kernels by building a Roofline model of the platform, and verify that our implementation is close to the roofline for various problem sizes. Finally, we present strong scaling results on the complete AIMD simulation for a 64 water molecules test case, that scales up to all 68 cores of the Knights Landing processor.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2025

Fast methods for multisite charge transfer processes. I. Constrained, state averaged CASSCF(1,n) and CASSCF(2n − 1,n) simulations

We design a dynamically weighted state-averaged constrained complete active space self-consistent field (DW-SA-cCASSCF) algorithm to treat electrons or holes moving between n molecular fragments (where n can be larger than 2). Within such a so-called eDSCn/hDSCn approach, we consider configurations that are mutually single excitations of each other, and we apply a generalized set of constraints to tailor the method for studying charge transfer problems. The constrained optimization problem is efficiently solved using a DIIS-SQP algorithm, thus maintaining computational efficiency. We demonstrate the method for a finite Su–Schrieffer–Heeger chain, successfully reproducing the expected exponential decay of diabatic couplings with distance. When combined with a gradient, the current extension immediately enables efficient nonadiabatic dynamics simulations of complex multi-state charge transfer processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Application of bi-Helmholtz nonlocal elasticity and molecular simulations to the dynamical response of carbon nanotubes

The nonlocal theory of elasticity is employed for the study of the free vibrations of carbon nanotubes (CNT). For the first time, a bi-Helmholtz operator has been used instead of the standard Helmholtz operator in a nonlocal beam model. Alongside the continuum formulation and its numerical solution, atomistic Molecular Dynamics (MD) simulations have been conducted in order to directly evaluate the eigenfrequencies of vibrating CNTs with a minimum of adjustable parameters. Our results show that the bi-Helmholtz operator is the most appropriate one to fit MD simulation results. However, the estimation of vibration eigenfrequencies from molecular simulations still remains an open (albeit well-posed) problem.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Nonadiabatic Molecular Dynamics by Multiconfiguration Pair-Density Functional Theory

Herein, we present the first implementation of multiconfiguration pair-density functional theory (MC-PDFT) ab initio molecular dynamics. MC-PDFT is a multireference electronic structure method that in many cases has a similar accuracy (or even better accuracy) the complete active space second-order perturbation theory (CASPT2) at a significantly lower computational cost. In this study, we introduced MC-PDFT analytical gradients into the SHARC molecular dynamics program for ab initio, nonadiabatic molecular dynamics simulations. We verify our implementation by examining the intersystem crossing dynamics of thioformaldehyde, and we observe excellent agreement with recent CASPT2 and experimental findings. Moreover, with MC-PDFT, we could perform dynamics simulations with the 12 electron in 10 orbitals active space that was computationally too expensive for direct dynamics with CASPT2.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Dynamic Fracture Simulations of Explosively Loaded Cylinders

This report documents the modeling results of high explosive experiments investigating dynamic fracture of steel (AerMet® 100 alloy) cylinders. The experiments were conducted at Lawrence Livermore National Laboratory (LLNL) during 2007 to 2008 [10]. A principal objective of this study was to gain an understanding of dynamic material failure through the analysis of hydrodynamic computer code simulations. Two-dimensional and three-dimensional computational cylinder models were analyzed using the ALE3D multi-physics computer code.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Large-scale atomistic simulations of low-energy helium implantation into tungsten single crystals

Large-scale molecular dynamics simulations of post-implantation helium behavior in plasma-facing tungsten single crystals reveal orientation-dependent depth profiles, surface evolution patterns, and other crystallographic and diffusion-related characteristics of helium behavior in tungsten during the first microsecond. Here, the flux of implanted helium atoms studied, Γ ≈ 4 × 10 25 m -2 s -1 , is about one order of magnitude larger than that expected in ITER, the experimental fusion reactor currently being constructed in France. With simulation times on the order of 1 μs, these results serve to discover the mechanisms involved in surface evolution as well as to serve as benchmarks for coarse-grained simulations such as kinetic Monte Carlo and continuum-scale drift–reaction–diffusion cluster dynamics simulations. The findings of our large-scale simulations are significant due to diminished finite-size effects and the longer times reached (corresponding to higher fluences). Specifically, our findings are drastically different from findings published previously in the literature for (001) surfaces under a helium flux of Γ ~ 10 28 m -2 s -1 , which is typical of smaller size and shorter time atomistic simulations. In particular, this study highlights the atomic-scale materials processes relevant to helium entrapment and transport in metals, which have implications not only for nuclear fusion–relevant processes, but also helium-induced embrittlement in irradiated materials such as hospital equipment and fission reactor materials.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Understanding nanofluid stability through molecular simulation

We performed molecular dynamics simulations to study solvation of a nanoparticle and nanoparticle-nanoparticle interactions in an n-hexane solution. Structural signatures are barely observed between the nanoparticle and n-hexane molecules because of weak binding and steric effects. The dynamic properties of the n-hexane molecule, on the other hand, are significantly influenced by the solvated nanoparticle. The diffusion of n-hexane molecules inside the nanoparticle is significantly decreased mainly because of the loss of dimensions of translation. Because one translational degree of freedom is lost by colliding with the wall of nanoparticle, the n-hexane molecules outside the nanoparticle diffuse 30% slower than the molecules in pure solution. The computed free energy profiles illustrate that the arrangement of the nanoparticles in bulk n-hexane solution are dependent on the orientation and functional group. We found that the n-hexane solvent exerts some effects on the interactions between the solvated nanoparticles. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences and by the Office of Energy Efficiency and Renewable Energy, Geothermal Technologies Program. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.

Dang, Liem X↗
DOE OSTI2014

Multiscale modeling of polyisoprene on graphite

The local dynamics and the conformational properties of polyisoprene next to a smooth graphite surface constructed by graphene layers are studied by a multiscale methodology. First, fully atomistic molecular dynamics simulations of oligomers next to the surface are performed. Subsequently, Monte Carlo simulations of a systematically derived coarse-grained model generate numerous uncorrelated structures for polymer systems. A new reverse backmapping strategy is presented that reintroduces atomistic detail. Finally, multiple extensive fully atomistic simulations with large systems of long macromolecules are employed to examine local dynamics in proximity to graphite. Polyisoprene repeat units arrange close to a parallel configuration with chains exhibiting a distribution of contact lengths. Efficient Monte Carlo algorithms with the coarse-grain model are capable of sampling these distributions for any molecular weight in quantitative agreement with predictions from atomistic models. Furthermore, molecular dynamics simulations with well-equilibrated systems at all length-scales support an increased dynamic heterogeneity that is emerging from both intermolecular interactions with the flat surface and intramolecular cooperativity. This study provides a detailed comprehensive picture of polyisoprene on a flat surface and consists of an effort to characterize such systems in atomistic detail.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Optimization of Thermal Conductance at Interfaces Using Machine Learning Algorithms

We report optimization of thermal transport across the interface of two different materials is critical to micro-/nanoscale electronic, photonic, and phononic devices. Although several examples of compositional intermixing at the interfaces having a positive effect on interfacial thermal conductance (ITC) have been reported, an optimum arrangement has not yet been determined because of the large number of potential atomic configurations and the significant computational cost of evaluation. On the other hand, computation-driven materials design efforts are rising in popularity and importance. Yet, the scalability and transferability of machine learning models remain as challenges in creating a complete pipeline for the simulation and analysis of large molecular systems. In this work we present a scalable Bayesian optimization framework, which leverages dynamic spawning of jobs through the Message Passing Interface (MPI) to run multiple parallel molecular dynamics simulations within a parent MPI job to optimize heat transfer at the silicon and aluminum (Si/Al) interface. We found a maximum of 50% increase in the ITC when introducing a two-layer intermixed region that consists of a higher percentage of Si. Because of the random nature of the intermixing, the magnitude of increase in the ITC varies. We observed that both homogeneity/heterogeneity of the intermixing and the intrinsic stochastic nature of molecular dynamics simulations account for the variance in ITC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Multi-scale modeling of inter-granular fracture in UO2

A hierarchical multi-scale approach is pursued in this work to investigate the influence of porosity, pore and grain size on the intergranular brittle fracture in UO2. In this approach, molecular dynamics simulations are performed to obtain the fracture properties for different grain boundary types. A phase-field model is then utilized to perform intergranular fracture simulations of representative microstructures with different porosities, pore and grain sizes. In these simulations the grain boundary fracture properties obtained from molecular dynamics simulations are used. The responses from the phase-field fracture simulations are then fitted with a stress-based brittle fracture model usable at the engineering scale. This approach encapsulates three different length and time scales, and allows the development of microstructurally informed engineering scale model from properties evaluated at the atomistic scale.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2017

Multi-Scale Modeling of Swelling in Accident-Tolerant U 3 Si 2 Fuel

U 3 Si 2 is a promising candidate for use as an accident-tolerant fuel for light water reactors. A multi-scale computational approach was used to calculate swelling in pellet-form U 3 Si 2 fuel. Swelling was assumed to be equal to the volume fraction of fission gas bubbles in the fuel, and the evolution of bubble volume fraction was determined from phase-field simulations. To parameterize the phase-field model, density-functional theory and molecular dynamics simulations were performed. To enable molecular dynamics simulations, a new interatomic potential for the U-Si system was developed based on the modified embedded atom method. A new phase-field model based on a grand-potential functional was also developed. The model is applicable to both intergranular and intragranular bubbles. To calculate the volume fraction of bubbles, the microstructure was decomposed into regions consisting of only intragranular or intergranular bubbles based on a truncated octahedral grain structure, and growth of the bubbles in the two regions was simulated separately. The total swelling was then calculated based on a a weighted average of bubble volume fraction in the two regions. Total swelling was of the same order of magnitude, but larger than that predicted by the existing empirical swelling model used in BISON and a rate-theory based model. Limitations of the present approach and suggestions for improvement are presented.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

High-pressure phase transition in 3-D printed nanolamellar high-entropy alloy by imaging and simulation insights

Abstract We report on the high-resolution imaging and molecular dynamics simulations of a 3D-printed eutectic high-entropy alloy (EHEA) Ni 40 Co 20 Fe 10 Cr 10 Al 18 W 2 consisting of nanolamellar BCC and FCC phases. The direct lattice imaging of 3D-printed samples shows the Kurdjumov–Sachs (K–S) orientation relation {111} FCC parallel to {110} BCC planes in the dual-phase lamellae. Unlike traditional iron and steels, this alloy shows an irreversible BCC-to-FCC phase transformation under high pressures. The nanolamellar morphology is maintained after pressure cycling to 30 GPa, and nano-diffraction studies show both layers to be in the FCC phase. The chemical compositions of the dual-phase lamellae after pressure recovery remain unchanged, suggesting a diffusion-less BCC–FCC transformation in this EHEA. The lattice imaging of the pressure-recovered sample does not show any specific orientation relation between the two resulting FCC phases, indicating that many grain orientations are produced during the BCC–FCC phase transformation. Molecular dynamics simulations on phase transformation in a nanolamellar BCC/FCC in K–S orientation show that phase transformation from BCC to FCC is completed under high pressures, and the FCC phase is retained on decompression aided by the stable interfaces. Our work elucidates the irreversible phase transformation under static compression, providing an understanding of the orientation relationships in 3-D printed EHEA under high pressures.

3-D Printing↗
DOE OSTI2017

Cry1A(b)16 toxin from Bacillus thuringiensis : Theoretical refinement of three‐dimensional structure and prediction of peptides as molecular markers for detection of genetically modified organisms

ABSTRACT Transgenic maize produced by the insertion of the Cry transgene into its genome became the second most cultivated crop worldwide. Cry gene from Bacillus thuringiensis kurstaki expresses protein derivatives of crystalline endotoxins which confer insect resistance onto the maize crop. Mandatory labeling of processed food containing or made by genetically modified organisms is in force in many countries, so, it is very urgent to develop fast and practical methods for GMO identification, for example, biosensors. In the absence of an available empirical structure of Cry1A(b)16 protein, a theoretical model was effectively generated, in this work, by homology modeling and molecular dynamics simulations based on two available homologous protein structures. Molecular dynamics simulations were carried out to refine the selected model, and an analysis of its global structure was performed. The refined models of Cry1A(b)16 showed a standard fold and structural characteristics similar to those seen in Bacillus thuringiensis Cry1A(a) insecticidal toxin and Bacillus thuringiensis serovar kurstaki Cry1A(c) toxin. After in silico analysis of Cry1A(b)16, two immunoreactive candidate peptides were selected and specific polyclonal antibodies were produced resulting in antibody–peptide interaction. Biosensing devices are expected to be developed for detection of the Cry1A(b) protein as a marker of transgenic maize in food. Proteins 2017; 85:1248–1257. © 2017 Wiley Periodicals, Inc.

Plácido, Alexandra↗