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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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

CO{sub 2} isolated line shapes by classical molecular dynamics simulations: Influence of the intermolecular potential and comparison with new measurements

Room temperature absorption spectra of various transitions of pure CO{sub 2} have been measured in a broad pressure range using a tunable diode-laser and a cavity ring-down spectrometer, respectively, in the 1.6 μm and 0.8 μm regions. Their spectral shapes have been calculated by requantized classical molecular dynamics simulations. From the time-dependent auto-correlation function of the molecular dipole, including Doppler and collisional effects, spectral shapes are directly computed without the use of any adjusted parameter. Analysis of the spectra calculated using three different anisotropic intermolecular potentials shows that the shapes of pure CO{sub 2} lines, in terms of both the Lorentz widths and non-Voigt effects, slightly depend on the used potential. Comparisons between these ab initio calculations and the measured spectra show satisfactory agreement for all considered transitions (from J = 6 to J = 46). They also show that non-Voigt effects on the shape of CO{sub 2} transitions are almost independent of the rotational quantum number of the considered lines.

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

Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis

Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholine catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Effect of Strain Field on Threshold Displacement Energy of Tungsten Studied by Molecular Dynamics Simulation

The influence of strain field on defect formation energy and threshold displacement energy (Ed) in body-centered cubic (BCC) tungsten (W) has been studied with molecular dynamics simulations. Two different W potentials (Fikar and Juslin) were compared and the results indicate that the connection distance and selected function linking the short-range and long-range portions of the potentials affects the threshold displacement energy and its direction-specific values. The minimum Ed direction calculated with the Fikar-potential is <100> and with the Juslin-potential is <111>. Nevertheless, the most stable self-interstitial configuration is found to be a <111>-crowdion for both potentials. This stable configuration does not change with applied strain. Varying the strain from compression to tension increases the vacancy formation energy but decreases the self-interstitial formation energy. The formation energy of a self-interstitial changes more significantly than a vacancy such that Ed decreases with applied hydrostatic strain from compression to tension.

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

Modeling of Grid-Forming and Grid-Following Inverters for Dynamic Simulation of Large-Scale Distribution Systems

Historically, distribution system planning studies mainly focused on steady state and quasi-steady state analysis, with limited attention paid to dynamic analysis. This paper develops three-phase, electromechanical models for both grid-forming and grid-following inverters, and integrates them into an open source, three-phase distribution network solver, thereby enabling dynamic simulation of large-scale, three-phase unbalanced distribution systems with high penetration of inverter-based DERs. The proposed inverter models are validated against electromagnetic simulation and field test data from the CERTS/AEP microgrid testbed, and simulated in an islanded 5252 node distribution system in the GridLAB-D simulation environment. Simulation verifies the effectiveness of the proposed inverter models for large-scale distribution system analysis. Finally, study results show that compared to traditional grid-following inverters, the high penetration of grid-forming inverters can improve the voltage and frequency stability of islanded distribution systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2012

Deformation Twins in Nanocrystalline Body-Centered Cubic Mo as Predicted by Molecular Dynamics Simulations

This work studies deformation twins in nanocrystalline body-centered cubic Mo, including the nucleation and growth mechanisms as well as their effects on ductility, through molecular dynamics simulations. The deformation processes of nanocrystalline Mo are simulated using a columnar grain model with three different orientations. The deformation mechanisms identified, including dislocation slip, grain-boundary-mediated plasticity, deformation twins and martensitic transformation, are in agreement with previous studies. In (1 1 0) columnar grains, the deformation is dominated by twinning, which nucleates primarily from the grain boundaries by successive emission of twinning partials and thickens by jog nucleation in the grain interiors. Upon arrest by a grain boundary, the twin may either produce continuous plastic strain across the grain boundary by activating compatible twinning/slip systems or result in intergranular failure in the absence of compatible twinning/slip systems in the neighboring grain. Multiple twinning systems can be activated in the same grain, and the competition between them favors those capable of producing continuous deformation across the grain boundary.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Electronic stopping in molecular dynamics simulations of cascades in 3C–SiC

Here, we investigate the effect of the electronic stopping power on defect production due to ion irradiation of cubic silicon carbide using molecular dynamics simulations. We simulate 20 keV and 30 keV Si and C ions, with and without the electronic energy loss. The results show that the electronic stopping effects are more profound in the case of C irradiation, where the ratio of the electronic energy loss S e to the nuclear energy loss S n is much larger compared to the ratio for Si ions. These findings indicate that this ratio plays a role in the effect of the electronic stopping on ion irradiation.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2017

Different dynamics and pathway of disulfide bonds reduction of two human defensins, a molecular dynamics simulation study

Human defensins are a class of antimicrobial peptides that are crucial components of the innate immune system. Both human α defensin type 5 (HD5) and human β defensin type 3 (hBD-3) have 6 cysteine residues which form 3 pairs of disulfide bonds in oxidizing condition. Disulfide bond linking is important to the protein structure stabilization, and the disulfide bond linking and breaking order have been shown to influence protein function. In this project, microsecond long molecular dynamics simulations were performed to study the structure and dynamics of HD5 and hBD-3 wildtype and analogs which have all 3 disulfide bonds released in reducing condition. The structure of hBD-3 was found to be more dynamic and flexible than HD5, based on RMSD, RMSF, and radius of gyration calculations. The disulfide bridge breaking order of HD5 and hBD-3 in reducing condition was predicted by two kinds of methods, which gave consistent results. It was found that the disulfide bonds breaking pathways for HD5 and hBD-3 are very different. The breaking of disulfide bonds can influence the dimer interface by making the dimer structure less stable for both kinds of defensin. In order to understand the difference in dynamics and disulfide bond breaking pathway, hydrophilic and hydrophobic accessible surface areas (ASA), buried surface area between cysteine pairs, entropy of cysteine pairs, and internal energy were calculated. Comparing to the wildtype, hBD-3 analog is more hydrophobic, while HD5 is more hydrophilic. For hBD-3, the disulfide breaking is mainly entropy driven, while other factors such as the solvation effects may take the major role in controlling HD5 disulfide breaking pathway. Proteins 2017; 85:665–681. © 2016 Wiley Periodicals, Inc.

Biochemistry & Molecular Biology↗
DOE OSTI2016

Molecular Dynamics Simulation Study of Solvent and State of Charge Effects on Solid-Phase Structure and Counterion Binding in a Nitroxide Radical Containing Polymer Energy Storage Material

Here we performed molecular dynamics simulations to understand the effects of solvent swelling and state of charge (SOC) on the redox active, organic radical cathode material poly(2,2,6,6-tetramethylpiperidinyloxy methacrylate) (PTMA). We show that the polar solvent acetonitrile primarily solvates the nitroxide radical without disrupting the packing of the (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) pendant groups of PTMA. We also simulated bulk PTMA in different SOC, 25%, 50%, 75%, and 100%, by converting the appropriate number of TEMPO groups to the cation charge state and adding BF 4 - counterions to the simulation. At each SOC the packing of PTMA, the solvent, and the counterions were examined. The binding of the anion to the nitroxide cation site was examined using the potential of mean force and found to be on the order of tens of meV, with a binding energy that decreased with increasing SOC. Additionally, we found that the cation state is stabilized by the presence of a nearby anion by more than 1 eV, and the implications of this stabilization on charge transport are discussed. Finally, we describe the implications of our results for how the SOC of an organic electrode affects electron and anion charge transport during the charging and discharging processes.

36 MATERIALS SCIENCE↗
DOE OSTI2014

All-atom molecular dynamics simulation of a photosystem I/detergent complex

All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n -dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Moreover, we find that the docking of soluble electron mediators such as cytochrome c 6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2019

Ab initio molecular dynamics simulation of supercritical aqueous ionic solutions: Spectral diffusion of water in the vicinity of Br¯ and I¯ ions

Supercritical aqueous ionic solutions containing bromide (Br¯) and iodide (I¯) ions have been studied using Car-Parrinello molecular dynamics simulation at two different concentrations and at two different densities. The time dependent trajectory has been used for calculating vibrational spectral diffusion, structural properties and, for other dynamical properties such as hydrogen bond dynamics, orientational relaxation and residence dynamics. The vibrational spectral diffusion of fluctuating OD stretch mode inside the solvation shell of the ions and in the bulk has been studied using frequency-frequency time correlation function. Hydrogen bond dynamics, orientational relaxation and residence dynamics of Sc-water have been investigated using population correlation function approach. The water molecules inside the solvation shell of Br¯ and I¯ ions are found to show complex molecular dynamics in comparison to the water-water dynamics. The concentration dependent spectral diffusion has been observed and it occurs in multiple time scales in the solvation shell of Br¯ and I¯ ions. Here, at supercritical condition, the ion-water hydrogen bond shows faster dynamics with respect to the same at ambient condition and slower dynamics with respect to the water-water hydrogen bond dynamics at supercritical condition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease

The rapid increase in computing power, especially with the integration of graphics processing units, has dramatically increased the capabilities of molecular dynamics simulations. To date, these capabilities extend from running very long simulations (tens to hundreds of microseconds) to thousands of short simulations. However, the expansive data generated in these simulations must be made interpretable not only by the investigator who performs them but also by others as well. Here, we demonstrate how integrating learning techniques, such as artificial intelligence, machine learning, and neural networks, into analysis pipelines can reveal the kinetics of Alzheimer's disease (AD) protein aggregation. Finally, we review select AD targets, describe current simulation methods, and introduce learning concepts and their application in AD, highlighting limitations and potential solutions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1996

Electromechanical Dynamics Simulations of Superconducting LSM Rocket Launcher System in Attractive-Mode

Further feasibility study on a superconducting linear synchronous motor (LSM) rocket launcher system is presented on the basis of dynamic simulations of electric power, efficiency and power factor as well as the ascending motions of the launcher and rocket. The advantages of attractive-mode operation are found from comparison with repulsive-mode operation. It is made clear that the LSM rocket launcher system, of which the long-stator is divided optimally into 60 sections according to launcher speeds, can obtain high efficiency and power factor.

Yoshida, Kinjiro↗
DOE OSTI2024

Modeling bicarbonate formation in an alkaline solution with multi-level quantum mechanics/molecular dynamics simulations

Understanding carbonate speciation and how it may be modulated is essential for the advancement of carbon dioxide (CO 2 ) capture and storage technologies, which often rely on the transformation of CO 2 into carbonate, e.g. via the formation of carbonate minerals. To date, few atomic-level, quantum-mechanics-based simulations have been carried out to characterize how carbonic acid (H 2 CO 3 ) and bicarbonate ($HCO^{-}_{3}$) form in aqueous solution, and how pH affects this process. Recently, Martirez and Carter utilized rare-event sampling density functional theory molecular dynamics simulations in combination with multi-level embedded correlated wavefunction theory, thus accounting for both solvent dynamics and electron correlation accurately, to elucidate the mechanism of H 2 CO 3 formation in neutral solution (J. Am. Chem. Soc., 145, 12561, 2023). Here, we perform a complementary simulation using the same method to map out the energetics of $HCO^{-}_{3}$ formation from dissolved CO 2 in basic solution. We find that, as in H 2 CO 3 formation, including water dynamics is important to obtain an accurate prediction of the energetics for the aforementioned reaction. Furthermore, only with MD did we identify the correct pathway for the reaction, in which water – not hydroxide – acts as the initial nucleophile and only at the transition state does it lose a proton.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

The Dynamic Conformational Cycle of the Group I Chaperonin C-Termini Revealed via Molecular Dynamics Simulation

Chaperonins are large ring shaped oligomers that facilitate protein folding by encapsulation within a central cavity. All chaperonins possess flexible C-termini which protrude from the equatorial domain of each subunit into the central cavity. Biochemical evidence suggests that the termini play an important role in the allosteric regulation of the ATPase cycle, in substrate folding and in complex assembly and stability. Despite the tremendous wealth of structural data available for numerous orthologous chaperonins, little structural information is available regarding the residues within the C-terminus. Herein, molecular dynamics simulations are presented which localize the termini throughout the nucleotide cycle of the group I chaperonin, GroE, from Escherichia coli. The simulation results predict that the termini undergo a heretofore unappreciated conformational cycle which is coupled to the nucleotide state of the enzyme. As such, these results have profound implications for the mechanism by which GroE utilizes nucleotide and folds client proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Molecular dynamics simulation of zirconium tungstate amorphization and the amorphous-crystalline interface

Classical molecular dynamics (MD) simulations were performed to provide a conceptual understanding of the amorphous-crystalline interface for a candidate negative thermal expansion (NTE) material, ZrW 2 O 8 . Simulations of pressure-induced amorphization at 300 K indicate that an amorphous phase forms at pressures of 10 GPa and greater, and this phase persists when the pressure is subsequently decreased to 1 bar. However, the crystalline phase is recovered when the slightly distorted 5 GPa phase is relaxed to 1 bar. Simulations were also performed on a two-phase model consisting of the high-pressure amorphous phase in direct contact with the crystalline phase. Upon equilibration at 300 K and 1 bar, the crystalline phase remains unchanged beyond a thin layer of disrupted structure at the crystalline-amorphous interface. In conclusion, the differences in local atomic structure at the interface are quantified from the simulation trajectories.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Molecular Dynamics Simulation of the Migration of Tilt Grain Boundaries in Ni and Ni{sub 3}Al

The migration of the 〈100〉 and 〈111〉 tilt boundaries in Ni and the Ni{sub 3}Al intermetallic compound is studied by molecular dynamics simulation. The low-angle 〈100〉 boundaries in Ni and Ni{sub 3}Al are shown to migrate much more slowly (by approximately two times at a temperature of 1700 K) that the 〈111〉 boundaries, which is related to different migration mechanisms of the 〈100〉 and 〈111〉 boundaries. The migration of the 〈100〉 boundaries is found to occur by the splitting of paired grain-boundary dislocations followed by a change of partner dislocations, which proceeds via the slip of split dislocations. The 〈111〉 tilt boundaries move according to a combined action of the following two mechanisms: the mechanism described above and the mechanism consisting in joint slip of paired grain-boundary dislocations, which have common slip planes in contrast to the grain-boundary dislocations in 〈100〉 boundaries. Since the joint slip of paired dislocations has a relatively low activation energy, the mobility of the 〈111〉 tilt boundaries is higher than that of the 〈100〉 boundaries. Our molecular dynamics studies demonstrate that the migration rate of analogous boundaries in Ni{sub 3}Al is significantly lower than in Ni (by approximately three times at a temperature of 1700 K), which is partly caused by the additional energy consumed for the formation of a disordered region behind a migrating boundary in Ni{sub 3}Al. Because of a relatively low boundary mobility in Ni{sub 3}Al, the contribution of diffusion atomic displacements during boundary migration is higher as compared to Ni.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗