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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Molecular dynamics studies of helium bubble effects on grain boundary fracture vulnerabilities in an Fe 70 Ni 11 Cr 19 –1%H austenitic stainless steel

Comprehensive molecular dynamics tensile test simulations have been performed to study the delamination processes of seven different grain boundaries / cleavage planes (Σ1{111}, Σ3{111}, Σ5{100}, Σ7{111}, Σ9{411}, Σ11{311}, and R{100}/{411}) containing a helium bubble. Combinations of a variety of conditions are explored including different strain rates, system dimensions, bubble density, bubble radius, bubble pressure, and temperature. We found that in general, grain boundaries absorb less energies with decreasing strain rate but increasing bubble areal density, bubble pressure, bubble radius, and temperature. The propensity of grain boundary delamination is sensitive to grain boundary type: The random grain boundary R{100}/{411} is one of the most brittle boundaries whereas the Σ1{111} cleavage plane and the Σ3{111} twin boundary are two of the toughest boundaries. The sorted list of grain boundary fracture vulnerability obtained from our dynamic tensile test simulations differs from the one obtained from our decohesion energy calculations, confirming the important role of plastic deformation during fracture. Finally, detailed mechanistic analyses are performed to interpret the simulated results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2017

Modeling Chemical Reactions in Classical Molecular Dynamics Simulations

An algorithm capable of incorporating multi-step reaction mechanisms into atomistic molecular dynamics (MD) simulations using traditional fixed valence force fields is proposed and implemented within the framework of LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator). This extension, referred to as fix bond/react, enables bonding topology modifications during a running MD simulation using pre- and post-reaction bonding templates to carry out a pre-specified reaction. Candidate reactants are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. This is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations. Two case studies, the condensation polymerization of nylon 6,6 and the formation of a highly-crosslinked epoxy, are simulated to demonstrate the robustness, stability, and speed of the algorithm. Improvements which could increase its utility are discussed.

Jacob R Gissinger↗
DOE OSTI2023

Evaluation of 6-OxP-CD, an Oxime-based cyclodextrin as a viable medical countermeasure against nerve agent poisoning: Experimental and molecular dynamic simulation studies on its inclusion complexes with cyclosarin, soman and VX

The ability of the cyclodextrin-oxime construct 6-OxP-CD to bind and degrade the nerve agents Cyclosarin (GF), Soman (GD) and S -[2-[Di(propan-2-yl)amino]ethyl] O -ethyl methylphosphonothioate (VX) has been studied using 31 P-nuclear magnetic resonance (NMR) under physiological conditions. While 6-OxP-CD was found to degrade GF instantaneously under these conditions, it was found to form an inclusion complex with GD and significantly improve its degradation (t 1/2 ~ 2 hrs) relative over background (t 1/2 ~ 22 hrs). Consequently, effective formation of the 6-OxP-CD:GD inclusion complex results in the immediate neutralization of GD and thus preventing it from inhibiting its biological target. In contrast, NMR experiments did not find evidence for an inclusion complex between 6-OxP-CD and VX, and the agent’s degradation profile was identical to that of background degradation (t 1/2 ~ 24 hrs). As a complement to this experimental work, molecular dynamics (MD) simulations coupled with Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) calculations have been applied to the study of inclusion complexes between 6-OxP-CD and the three nerve agents. These studies provide data that informs the understanding of the different degradative interactions exhibited by 6-OxP-CD with each nerve agent as it is introduced in the CD cavity in two different orientations (up and down). For its complex with GF, it was found that the oxime in 6-OxP-CD lies in very close proximity (P GF …O Oxime ~ 4–5 Å) to the phosphorus center of GF in the ‘down GF ’ orientation for most of the simulation accurately describing the ability of 6-OxP-CD to degrade this nerve agent rapidly and efficiently. Further computational studies involving the center of masses (COMs) for both components (GF and 6-OxP-CD) also provided some insight on the nature of this inclusion complex. Distances between the COMs (ΔCOM) lie closer in space in the ‘down GF ’ orientation than in the ‘up GF ’ orientation; a correlation that seems to hold true not only for GF but also for its congener, GD. In the case of GD, calculations for the ‘down GD ’ orientation showed that the oxime functional group in 6-OxP-CD although lying in close proximity (P GD …O Oxime ~ 4–5 Å) to the phosphorus center of the nerve agent for most of the simulation, adopts another stable conformation that increase this distance to ~ 12–14 Å, thus explaining the ability of 6-OxP-CD to bind and degrade GD but with less efficiency as observed experimentally (t 1/2 ~ 4 hr. vs. immediate). Lastly, studies on the VX:6-OxP-CD system demonstrated that VX does not form a stable inclusion complex with the oxime-bearing cyclodextrin and as such does not interact in a way that is conducive to an accelerated degradation scenario. Collectively, these studies serve as a basic platform from which the development of new cyclodextrin scaffolds based on 6-OxP-CD can be designed in the development of medical countermeasures against these highly toxic chemical warfare agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Stability of Calcium Ion Battery Electrolytes: Predictions from Ab Initio Molecular Dynamics Simulations

Multivalent batteries, such as magnesium-ion, calcium-ion, and zinc-ion batteries, have attracted significant attention as next-generation electrochemical energy storage devices to complement conventional lithium-ion batteries (LIBs). Among them, calcium-ion batteries (CIBs) are the least explored due to the difficult reversible Ca deposition-dissolution. In this work, we examined the stability of four different Ca salts with weakly coordinating anions and three different solvents commonly employed in existing battery technologies to identify suitable candidates for CIBs. By employing Born-Oppenheimer molecular dynamics (BOMD) simulations on salt-Ca and solvent-Ca interfaces, we find that the tetraglyme solvent and carborane salt are promising candidates for CIBs. Due to the strong reducing nature of the calcium surface, the other salts and solvents readily decompose. Further, we explain the microscopic mechanisms of salt/solvent decomposition on the Ca surface using time-dependent projected density of states, time-dependent charge-transfer plots, and climbing-image nudged elastic band calculations. Collectively, this work presents the first mechanistic assessment of the dynamical stability of candidate salts and solvents on a Ca surface using BOMD simulations, and provides a predictive path toward designing stable electrolytes for CIBs.

Born-Oppenheimer molecular dynamics↗
DOE OSTI2021

Molecular dynamics simulations of a dicationic ionic liquid for CO 2 capture

A dicationic ionic liquid ([DBU-PEG][Tf 2 N] 2 ) was studied using classical molecular dynamics simulations to examine its structural and gas separation properties. The dication was designed in an attempt to improve CO 2 solubility by means of tuning the cation-anion interactions of the ionic liquid (IL). The computational model was compared to experimentally obtained density, viscosity, and powder X-ray diffraction spectra. The structure of the IL was further investigated with radial distribution functions and free volume analysis through cavity distributions. It was found that the shape and charge distribution of the dication enhances CO 2 interaction: the CO 2 molecule is hugged by the dication along the PEG linker and close to one of the cationic ends. Here, the geminal design of the dication allows for strong interaction with CO 2 , showing promise as a means of carbon capture.

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

ReaxFF molecular dynamics simulations of electrolyte–water systems at supercritical temperature

We have performed ReaxFF molecular dynamics simulations of alkali metal–chlorine pairs in different water densities at supercritical temperature (700 K) to elucidate the structural and dynamical properties of the system. The radial distribution function and the angular distribution function explain the inter-ionic structural and orientational arrangements of atoms during the simulation. The coordination number of water molecules in the solvation shell of ions increases with an increase in the radius of ions. We find that the self-diffusion coefficient of metal ions increases with a decrease in density under supercritical conditions due to the formation of voids within the system. The hydrogen bond dynamics has been interpreted by the residence time distribution of various ions, which shows Li+ having the highest water retaining capability. The void distribution within the system has been analyzed by using the Voronoi polyhedra algorithm providing an estimation of void formation within the system at high temperatures. We observe the formation of salt clusters of Na+ and K+ at low densities due to the loss of dielectric constants of ions. The diffusion of ions gets altered dramatically due to the formation of voids and nucleation of ions in the system.

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

Molecular dynamics simulations of inelastic x-ray scattering from shocked copper

By taking the spatial and temporal Fourier transforms of the coordinates of the atoms in molecular dynamics simulations conducted using an embedded-atom-method potential, we calculate the inelastic scattering of x rays from copper single crystals shocked along [001] to pressures of up to 70 GPa. Above the Hugoniot elastic limit, we find that the copious stacking faults generated at the shock front introduce strong quasi-elastic scattering (QES) that competes with the inelastic scattering signal, which remains discernible within the first Brillouin zone; for specific directions in reciprocal space outside the first zone, the QES dominates the inelastic signal overwhelmingly. The synthetic scattering spectra we generate from our Fourier transforms suggest that energy resolutions of order 10 meV would be required to distinguish inelastic from quasi-elastic scattering within the first Brillouin zone of shock-loaded copper. We further note that high-resolution inelastic scattering also affords the possibility of directly measuring particle velocities via the Doppler shift. These simulations are of relevance to future planned inelastic scattering experiments at x-ray Free Electron Laser facilities.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Understanding Hydrogenation Chemistry at MgB 2 Reactive Edges from Ab Initio Molecular Dynamics

Solid-state hydrogen storage materials often operate via transient, multistep chemical reactions at complex interfaces that are difficult to capture. Here, we use direct ab initio molecular dynamics simulations at accelerated temperatures and hydrogen pressures to probe the hydrogenation chemistry of the candidate material MgB 2 without a priori assumption of reaction pathways. Focusing on highly reactive ($10\overline{1}0$) edge planes where initial hydrogen attack is likely to occur, we track mechanistic steps toward the formation of hydrogen-saturated BH 4 – units and key chemical intermediates, involving H 2 dissociation, generation of functionalities and molecular complexes containing BH 2 and BH 3 motifs, and B–B bond breaking. Further, the genesis of higher-order boron clustering is also observed. Different charge states and chemical environments at the B-rich and Mg-rich edge planes are found to produce different chemical pathways and preferred speciation, with implications for overall hydrogenation kinetics. The reaction processes rely on B–H bond polarization and fluctuations between ionic and covalent character, which are critically enabled by the presence of Mg 2+ cations in the nearby interphase region. Our results provide guidance for devising kinetic improvement strategies for MgB 2 -based hydrogen storage materials, while also providing a template for exploring chemical pathways in other solid-state energy storage reactions.

08 HYDROGEN↗
DOE OSTI2020

Cavity molecular dynamics simulations of liquid water under vibrational ultrastrong coupling

We simulate vibrational strong coupling (VSC) and vibrational ultrastrong coupling (V-USC) for liquid water with classical molecular dynamics simulations. When the cavity modes are resonantly coupled to the O–H stretch mode of liquid water, the infrared spectrum shows asymmetric Rabi splitting. The lower polariton (LP) may be suppressed or enhanced relative to the upper polariton (UP) depending on the frequency of the cavity mode. Furthermore, although the static properties and the translational diffusion of water are not changed under VSC or V-USC, we do find the modification of the orientational autocorrelation function of H 2 O molecules especially under V-USC, which could play a role in ground-state chemistry.

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

The role of the Heisenberg principle in constrained molecular dynamics model

In this study, we implement the Heisenberg principle into the Constrained Molecular Dynamics model with a similar approach to the Pauli principle using the one-body occupation probability $\bar{f}_i$. Results of the modified and the original model with comparisons to data are given. The binding energies and the radii of light nuclei obtained with the modified model are more consistent with the experimental data than the original one. The collision term and the density distribution are tested through a comparison to p+ 12 C elastic scattering data. Some simulations for fragmentation and superheavy nuclei production are also discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1991

Molecular dynamics of phenol at the liquid-vapor interface of water

Results of molecular dynamics calculations on phenol at the water liquid-vapor interface are presented. The density profile of the center of mass of phenol exhibits a maximum 1 A from the Gibbs surface toward the vapor phase, indicating that the molecule is surface-active. Changes in the profile caused by the interface extend 6 A from the Gibbs surface into the liquid, significantly more than change in the density profile of water. The most probable orientation of the solute at the surface is such that its symmetry axis is perpendicular to the interface with the OH substituent pointing toward the liquid. An additional simulation with benzene shows that this molecule at the surface most often adopts orientations parallel to the interface. Deeper in the liquid all the solutes are preferentially ordered perpendicular to the surface. In the interfacial region the orientational preferences of the solute are primarily determined by cavity formation needed to accommodate the hydrophobic portion of the dissolved molecule.

Pohorille, Andrew↗
DOE OSTI2020

Na ion dynamics in P2-Na x [Ni 1/3 Ti 2/3 ]O 2 : a combination of quasi-elastic neutron scattering and first-principles molecular dynamics study

In this work, the P2-type layered material Na 2/3 [Ni 1/3 Ti 2/3 ]O 2 was studied as a promising bi-functional electrode material for sodium-ion batteries. To assess the electrochemical performance of this material, we investigated the diffusion mechanism as well as ionic and electronic conductivity with a combination of experimental and computational techniques. The quasi-elastic neutron scattering (QENS) experiments and first-principles molecular dynamics (FPMD) simulations were performed to identify the diffusion mechanism. The QENS data showed that Na ion diffusion can be well described by the Singwi–Sjölander jump diffusion model, where the obtained mean jump length matched the distances between the neighboring edge-share and face-share Na sites. FPMD predicted diffusivity values similar to those from QENS. The computed composition dependence of ionic and electronic conductivity of Na x [Ni 1/3 Ti 2/3 ]O 2 suggested that electronic conductivity changes significantly when x deviates from 2/3 as the redox couple of Ni and Ti is activated, while the change of ionic conductivity with x is relatively small.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Molecular Dynamics Simulations of a Catalytic Multivalent Peptide–Nanoparticle Complex

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

High-order cumulants and correlation functions near the critical point from molecular dynamics

We present a systematic investigation of particle-number fluctuations in the crossover region near the critical end point of a first-order phase transition using molecular dynamics simulations of the classical Lennard-Jones fluid. We extend our prior studies to third- and fourth-order cumulants in both coordinate- and momentum-space acceptances and integrated correlation functions (factorial cumulants). We find that, even near the critical point, non-Gaussian cumulants equilibrate on timescales comparable to those of the second-order cumulants, but show stronger finite-size effects. The presence of interactions and of the critical point leads to strong deviations of the cumulants from the ideal-gas baseline in coordinate space; these deviations are expected to persist in momentum space in the presence of collective expansion. In particular, the kurtosis becomes strongly negative, κσ 2 ≪ − 1 , on the crossover side of the critical point. However, this signal is significantly diluted once an efficiency cut used to distinguish protons from baryons is applied, leading to |κσ 2 | ≲ 1 even in the presence of the critical point. We discuss our results in the context of ongoing measurements of proton-number cumulants in heavy-ion collisions in RHIC-BES-II.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

The “good,” the “bad,” and the “hidden” in neutron scattering and molecular dynamics of ionic aqueous solutions

We characterize a concentrated 7.3 m CaCl 2 solution, combining neutron diffraction with chloride isotopic substitution (Cl-NDIS) in null water and molecular dynamics (MD) simulations. We elucidate the solution structure, thermodynamic properties, and extent of ion pairing previously suggested as concentration-dependent and often not observed at lower concentrations. Our Cl-NDIS measurements designate the solvent-shared ion pairing as dominant and the contact ion pairing (CIP) as insignificant even under conditions close to the solubility limit. The MD models parameterized against neutron diffraction with calcium isotopic substitution (Ca-NDIS) overestimate CIP despite successfully reproducing most of the Cl-NDIS signal. This drawback originates from the fact that Ca 2+ –Cl - interactions were primarily “hidden” in the Ca-NDIS signal due to overlapping with Ca 2+ –O w and Ca 2+ –H w contributions to the total scattering. Contrary, MD models with moderate CIP and possessing generally good performance at high concentrations fail to reproduce the NDIS measurements accurately. Therefore, the electronic polarization, introduced in most of the recent MD models via scaling ionic charges, resolves some but not all parameterization drawbacks. We conclude that despite improving the quality of MD models “on average,” the question “which model is the best” has not been answered but replaced by the question “which model is better for a given research.” An overall “good” model can still be inappropriate or, in some instances, “bad” and, unfortunately, produce erroneous results. Additionally, the accurate interpretation of several NDIS datasets, complemented by MD simulations, can prevent such mistakes and help identify the strengths, weaknesses, and convenient applications for corresponding computational models.

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

Ab Initio Molecular Dynamics Spectra for Characterization of Hydrated Al 2 O 3 Supported MoO x

The structure of supported MoO x /Al 2 O 3 catalysts is investigated using ab initio molecular dynamics (AIMD) and density-functional theory (DFT). Phase diagrams were computed to understand the hydroxylation coverage as a function of the temperature, H 2 O partial pressure, and MoO x loading. We relate the shifts in experimental Raman vibrational frequencies under hydrated conditions to hydrogen bonding interactions and the MoO x anchoring location. We showcase that the use of AIMD as a benchmark for DFT can provide insight into how, under certain hydrated conditions, DFT excels as an inexpensive method for computing vibrational frequencies, while, under dehydrated conditions, it is susceptible to the largest errors. Additionally, to facilitate the analysis of the hydroxyl region of experimental infrared spectra, we compute the power spectra of individual hydroxyls and see a strong relationship between OH stretching frequencies and the surrounding coordination environment, which are also impacted by anchored MoO x . Here, we compare computational and experimental IR and Raman spectra of catalysts synthesized herein under the same conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗