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DOE OSTI2024

Prediction of photodynamics of 200 nm excited cyclobutanone with linear response electronic structure and ab initio multiple spawning

Simulations of photochemical reaction dynamics have been a challenge to the theoretical chemistry community for some time. In an effort to determine the predictive character of current approaches, we predict the results of an upcoming ultrafast diffraction experiment on the photodynamics of cyclobutanone after excitation to the lowest lying Rydberg state (S 2 ). A picosecond of nonadiabatic dynamics is described with ab initio multiple spawning. Herein we use both time dependent density functional theory (TDDFT) and equation-of-motion coupled cluster singles and doubles (EOM-CCSD) theory for the underlying electronic structure theory. We find that the lifetime of the S 2 state is more than a picosecond (with both TDDFT and EOM-CCSD). The predicted ultrafast electron diffraction spectrum exhibits numerous structural features, but weak time dependence over the course of the simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Computational characterization of the secondary droplets formed during the impingement of a train of ethanol drops

This paper uniquely characterizes the secondary droplets formed during the impingement of a train of ethanol drops, using three-dimensional direct numerical simulations performed under conditions studied experimentally by Yarin and Weiss. Our numerical results have been previously validated against experimental data demonstrating the ability to accurately capture the splashing dynamics. In this work, the predictive ability of the model is leveraged to gain further insight into secondary droplet formation. We present a robust post-processing algorithm, which scrutinizes the liquid volume fraction field in the volume-of-fluid method and quantifies the number, volume and velocity of secondary droplets. The high-resolution computational simulations enable secondary droplet characterization within close proximity of the impingement point at small length and time scales, which is extremely challenging to achieve experimentally. By studying the temporal evolution of secondary droplet formation, direct connections are made between liquid structures seen in the simulation and the instantaneous distribution of secondary droplets, leading to detailed insight into the instability-driven breakup process of lamellae. Time-averaged secondary droplet characteristics are also studied to describe the global distribution of secondary droplets. Such analysis is vital to understanding fuel drop impingement in direct injection engines, facilitating the development of highly accurate spray–wall interaction models for use in Lagrangian solvers.

42 ENGINEERING↗

DOE OSTI2021

Density Functional Tight-Binding Simulations Reveal the Presence of Surface Defects on the Quartz (101)–Water Interface

Understanding the structure and reactivity of quartz–water interfaces is critical for numerous applications in the geological, environmental, and biological sciences. However, disagreements on the atomic-level structure of the interfaces between experiments and simulations are hampering our ability to predict the surface reactivity. Here, we used density functional tight-binding (DFTB)-based molecular dynamics to simulate a series of quartz (101) surfaces having different types and densities of surface defects in water and compared them with the structures determined by X-ray reflectivity measurements. The DFTB simulations are able to reproduce previous classical and quantum mechanical predictions of the pristine quartz (101)–water interface that disagree with experimental observations. To remedy this situation, a set of defective quartz surfaces having various surface silicon (Si) vacancies were built as indicated by recent experimental studies. We found that the rotation of surface [SiO 4 ] tetrahedra near Si vacancies can lead to outward displacements of Si atoms similar to those observed in the experiments. The presence of additional surface Si vacancies caused inward relaxations of terminal oxygens through the formation of hydrogen bonds. Finally, the overall results indicate that the quartz (101)–water interface may include a mixture of geminal (≡Si–(OH) 2 )- and vicinal (≡Si–OH)-type silanol groups together with the presence of surface Si vacancies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Structural Loads Analysis for Wave Energy Converters: Preprint

This study explores and verifies the generalized body-modes method for evaluating the structural loads on a wave energy converter (WEC). Historically, WEC design methodologies have focused primarily on accurately evaluating hydrodynamic loads, while methodologies for evaluating structural loads have yet to be fully considered and incorporated into the WEC design process. As wave energy technologies continue to advance, however, it has become increasingly evident that an accurate evaluation of the structural loads will enable an optimized structural design, as well as the potential utilization of composites and flexible materials, and hence reduce WEC costs. Although there are many computational fluid dynamics, structural analyses and fluid-structure-interaction (FSI) codes available, the application of these codes is typically too computationally intensive to be practical in the early stages of the WEC design process. The generalized body-modes method, however, is a reduced order, linearized, frequency-domain FSI approach, performed in conjunction with the linear hydrodynamic analysis, with computation times that could realistically be incorporated into the WEC design process. The objective of this study is to verify the generalized body-modes approach in comparison to high-fidelity FSI simulations to accurately predict structural deflections and stress loads in a WEC. Two verification cases are considered, a free-floating barge and a fixed-bottom column. Details for both the generalized body-modes models and FSI models are first provided. Results for each of the models are then compared and discussed. Finally, based on the verification results obtained, future plans for incorporating the generalized body-modes method into the WEC simulation tool, WEC-Sim, and the overall WEC design process are discussed.

17 WIND ENERGY↗

DOE OSTI2016

Zoomed high-resolution simulations of Multi-coupled Dark Energy: cored galaxy density profiles at high redshift

We perform for the first time high-resolution zoom-in re-simulations of individual halos in the context of the Multi-coupled Dark Energy (McDE) scenario, which is characterised by the existence of two distinct Dark Matter particle species with opposite couplings to a Dark Energy scalar field. We compare the structural properties of the simulated halos to the standard ΛCDM results. The zoomed-in initial conditions are set up using a specifically designed code called ZInCo that we publicly release along with the present paper. Our numerical results allow to investigate in detail and with unprecedented resolution the halo segregation process that characterises McDE cosmologies from its very early stages. In particular, we find that in contrast to what could be inferred from previous numerical analysis at lower resolution, the segregation process is already in place at redshifts as high as z ∼ 7. Most remarkably, we find that the subsequent evolution of the segregation leads to the formation of cored total matter density profiles with a core size that progressively increases in time. The shape of the cored profiles can be accurately predicted as the superposition of two NFW profiles with an increasing offset, thereby confirming the interpretation of the simulations results in terms of the segregation of the two dark matter components of the halo as a consequence of their different coupling to the Dark Energy field.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Crystal structure of dihydrofolate reductase from the filarial nematode W. bancrofti in complex with NADPH and folate

Lymphatic filariasis is a debilitating illness with an estimated 50 million cases as of 2018. The majority of cases are caused by the parasitic worm W. bancrofti and additional cases by the worms B. malayi and B. timori. Dihydrofolate reductase (DHFR) is an established target in the treatment of cancer, bacterial, and protozoal infections and may be a potential target for drugs targeting parasitic worm infections, including filariasis. Recent studies have shown that known antifolate compounds, including methotrexate, inhibit the activity of W. bancrofti DHFR (WbDHFR). However, the absence of structural information for filarial DHFRs has limited the study of more in-depth structure-function relationships. We report the structure of WbDHFR complexed with NADPH and folate using X-ray diffraction data measured to 2.47 Å resolution. The structure of WbDHFR reveals the usual DHFR fold and is currently only the second nematode DHFR structure in the Protein Data Bank. The equilibrium dissociation constants for NADPH (90 ± 29 nM) and folate (23 ± 4 nM) were determined by equilibrium titrations. The interactions of known antifolates with WbDHFR were analyzed using molecular docking programs and molecular dynamics simulations. Antifolates with a hydrophobic core and extended linker formed favorable interactions with WbDHFR. These combined data should now facilitate the rational design of filarial DHFR inhibitors, which in turn can be used to determine whether DHFR is a viable drug target for filariasis and whether existing antifolates may be repurposed for its treatment.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Liquid Structure and Transport Properties of the Deep Eutectic Solvent Ethaline

A range of techniques including physical property measurements, neutron scattering experiments, ab initio molecular dynamics, and classical molecular dynamics simulations are used to probe the structural, thermodynamic, and transport properties of a deep eutectic solvent comprised of a 1:2 molar ratio of choline chloride and ethylene glycol. This mixture, known as Ethaline, has many desirable properties for use in a range of applications, and therefore, understanding its liquid structure and transport properties is of interest. Simulation results are able to capture experimental densities, diffusivities, viscosities, and structure factors extremely well. Here, the solvation environment is dynamic and dominated by different hydrogen bonding interactions. Dynamic heterogeneities resulting from hydrogen bonding interactions are quantified. Rotational dynamics of molecular dipole moments of choline and ethylene glycol are computed and found to exhibit a fast and slow mode.

25 ENERGY STORAGE↗

DOE OSTI2023

Droplet-Gas Interactions in Nanoelectrospray Multiphase Flow

Electrospray (ES) is production of a charged droplet plume that transits from an electrically biased supply capillary to a counter electrode under the influence of an electric field. Drag interactions with the surrounding gas decelerate the droplets while transferring the momentum from droplets to accelerate the surrounding gas, resulting in an induced gas flow. This work seeks to characterize the structure of the resulting gas jet and identify the key mechanisms defining the flow structure. The phenomenon of gas jets produced by momentum transfer from nano-electrospray (nES) plumes is explored with schlieren visualization, thermal anemometry, and numerical simulations. Schlieren visualization experiments provide information on the flow structure in support of simulation predictions, and the hot thermistor anemometry measurements of gas velocities outside the spray demonstrate quantitatively validated simulation results. The study reveals the formation of a moderately high velocity coaxial gas jet within the nES plume and provides insight into the overall flow structure of the induced flow. The multiphase electrohydrodynamic simulations enable numerical experimentation to explore the fundamental physics of coupled droplet-gas transport and the resulting flow structure. The simulations, confirmed by the experiments, reveal gas jetting induced by nES with a narrow (sub hundred micrometers in diameter) core originating from the nES liquid-jet breakup region and a surrounding larger-in-extent zone (several hundred micrometers in diameter) of lower velocity gas flow within the electrospray plume. This behavior is due to nES ejecting a stream of droplets from the tip of a narrow liquid cone-jet, where the combined effect of many small droplets transferring momentum to a confined region of gas yields a narrow but high-velocity gas stream. Furthermore, the micro-jets produced by nES have practical utility for mass spectrometry, 3D printing and fabrication, and thermal management.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2017

Inclusion of Structural Flexibility in Design Load Analysis for Wave Energy Converters: Preprint

Hydroelastic interactions, caused by ocean wave loading on wave energy devices with deformable structures, are studied in the time domain. A midfidelity, hybrid modeling approach of rigid-body and flexible-body dynamics is developed and implemented in an open-source simulation tool for wave energy converters (WEC-Sim) to simulate the dynamic responses of wave energy converter component structural deformations under wave loading. A generalized coordinate system, including degrees of freedom associated with rigid bodies, structural modes, and constraints connecting multiple bodies, is utilized. A simplified method of calculating stress loads and sectional bending moments is implemented, with the purpose of sizing and designing wave energy converters. Results calculated using the method presented are verified with those of high-fidelity fluid-structure interaction simulations, as well as low-fidelity, frequency-domain, boundary element method analysis.

16 TIDAL AND WAVE POWER↗

DOE OSTI2015

Prestellar core formation, evolution, and accretion from gravitational fragmentation in turbulent converging flows

We investigate prestellar core formation and accretion based on three-dimensional hydrodynamic simulations. Our simulations represent local ∼1 pc regions within giant molecular clouds where a supersonic turbulent flow converges, triggering star formation in the post-shock layer. We include turbulence and self-gravity, applying sink particle techniques, and explore a range of inflow Mach numbers M=2−16. Two sets of cores are identified and compared: t{sub 1} cores are identified from a time snapshot in each simulation and represent dense structures in a single cloud map; t{sub coll} cores are identified at their individual time of collapse and represent the initial mass reservoir for accretion. We find that cores and filaments form and evolve at the same time. At the stage of core collapse, there is a well-defined, converged characteristic mass for isothermal fragmentation that is comparable to the critical Bonnor–Ebert mass at the post-shock pressure. The core mass functions (CMFs) of t{sub coll} cores show a deficit of high-mass cores (≳7 M{sub ⊙}) compared to the observed stellar initial mass function (IMF). However, the CMFs of t{sub 1} cores are similar to the observed CMFs and include many low-mass cores that are gravitationally stable. The difference between t{sub 1} cores and t{sub coll} cores suggests that the full sample from observed CMFs may not evolve into protostars. Individual sink particles accrete at a roughly constant rate throughout the simulations, gaining one core mass per freefall time even after the initial mass reservoir is accreted. High-mass sinks gain proportionally more mass at later times than low-mass sinks. There are outbursts in accretion rates, resulting from clumpy density structures falling into the sinks.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

First-principles study on the bulk and (1 1 1) surface half-metallicity of KS and RbS in CsCl structure

Graphical abstract: Spin-polarized total and atomic DOS at S-(1 1 1) terminated slab and bulk in CsCl-type RbS. - Highlights: • The half metallic properties of CsCl-type RbS and KS have been studied. • The RbS's and KS's (1 1 1) slabs have been investigated. • Surface energy of RbS's and KS's (1 1 1) slabs are calculated. - Abstract: The electronic and magnetic properties of RbS and KS in CsCl structure have been investigated by using the full-potential local-orbital minimum-basis method. Calculating the relation between the total energies and lattice parameters for RbS and KS, we find out that the equilibrium lattice parameters are 4.02 Å and 3.84 Å for RbS and KS, respectively. According to our calculations in generalized gradient approximation approximation, both RbS and KS are half-metallic ferromagnets with the magnetic moments of 1 μ{sub B} per formula unit, and band gap of 4.287 eV for RbS and 4.395 eV for KS. We also have studied the electronic and magnetic properties of (1 1 1) surfaces of RbS and KS, and have found out that the half-metallicity of their bulk is preserved in all of those surfaces. Finally, through the calculations of formation energy of RbS and KS, it is found that their thin films are stable in the equilibrium conditions, and the Rb-terminated (1 1 1) slab of RbS and the K-terminated (1 1 1) slab of KS are more stable than their S-terminated (1 1 1) slabs. All of the above properties lead the compounds of RbS and KS in CsCl structure to be promising candidates for spintronic applications.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Molecular-scale origins of solution nanostructure and excess thermodynamic properties in a water/amphiphile mixture

The molecular and nanoscale origins of nonideality in excess thermodynamic properties are essential to understanding cosolvent mixtures, yet they remain challenging to determine. Here, we consider a binary mixture of water and an amphiphile, N,N,N',N'-tetramethylmalonamide (TMMA), which is characterized by strong hydrogen bonding between the two components and no hydrogen bonding between amphiphiles. Using molecular dynamics simulation, validated with excess volume measurements and X-ray scattering, we identify three distinct solution regimes across the composition range of the binary mixture and find that the transition between two of these regimes, marked by the water percolation threshold, is closely correlated with minima in the excess volume and excess enthalpy. Structural analysis of the simulations reveals an interplay between local interactions and solution nanostructure, determined by the relative strength of the water–water and water–amphiphile hydrogen bonding interactions. By comparison with other amphiphiles, such as linear alcohols, the relative strength of like and unlike interactions between water and amphiphile affects the relationship between thermodynamics and structural regimes. This provides insight into how molecular forces of mutual solvation interact across length scales and how they manifest in excess thermodynamic properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Coexistence of multiple metastable polytypes in rhombohedral bismuth

Derivative structural polytypes coexisting with the rhombohedral A7 structure of elemental bismuth (Bi) have been discovered at ambient condition, based on microstructure analyses of pure Bi samples treated under high pressure and high temperature conditions. Three structures with atomic positions close to those of the A7 structure have been identified through first-principles calculations, showing these polytypes energetically comparable to the A7 structure under ambient condition. Simulated diffraction data are in excellent agreement with the experimental observations. We argue that previously reported some variations of physical properties (e.g., density, electrical conductivity and magnetism) in bismuth could be due to the formation of these polytypes. The coexistence of metastable derivative structural polytypes may be a widely occurring phenomenon in other elemental materials.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Simulations of the surfaces of soda lime aluminoborosilicate glasses exposed to water

Molecular dynamics simulations of 7 compositionally different sodium calcium alumino–borosilicate glasses showed formation of 4 B and 5 Al more consistent with experimental data without compromising the other structural features that match experimental results observed in recent simulations of these glasses. Analysis of the dry surfaces of these glasses show a lack of 4 B in the top 5–6 Å of the surface in comparison to the bulk concentration for all glasses and no 5 Al. Upon exposure to water, the simulations show that the 3 B in the top 5–6 Å of the glasses are preferentially attacked, decreasing the number of B bonds to O originally from the glass, indicating a change in the glass network. Inclusion of all B–O bonds in the top 5–6 Å (i.e., including O from water) shows a decrease in 3 B but an increase in 4 B that is consistent with NEXAFS analysis, which the simulations show are hydroxylated. Furthermore, there is an increase in the concentration of 3 Al in the dry surface in comparison to the bulk, but exposure to water converts almost all of these 3 Al to 4 Al. Hydroxyl concentrations vary from 2.6/nm 2 to 4.1/nm 2 , with SiOH and BOH dominating these surface hydroxyls. Upon exposure to water, network linkages to B are preferentially ruptured. This, and the preferential loss of the nonbridging oxygen sites attached to Na, provide atomistic evidence of the initial stages of removal of B and Na from glass surfaces exposed to water.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Simulations of graphite boronization: A molecular dynamics study of amorphization resulting from bombardment

The molecular dynamics code LAMMPS was used to simulate the bombardment of a graphite structure by atomic boron with impact energies ranging from 50–250 eV. The transient structural evolution, penetration depth, and amorphous layer thickness were analyzed. Simulations show that larger impact energies lead to a greater volume of amorphization and penetration of boron, but that the growth rate of the amorphous layer decreases with increasing fluence. Furthermore, the change in surface chemistry of the amorphized structures was studied using the ReaxFF formalism, which found that the amorphization process introduces dangling bonds thus increasing reactivity in the amorphous region.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Investigations of water/oxide interfaces by molecular dynamics simulations

Water/oxide interfaces are ubiquitous on earth and show significant influence on many chemical processes. For example, understanding water and solute adsorption as well as catalytic water splitting can help build better fuel cells and solar cells to overcome our looming energy crisis; the interaction between biomolecules and water/oxide interfaces is one hypothesis to explain the origin of life. However, knowledge in this area is still limited due to the difficulty of studying water/solid interfaces. As a result, research using increasingly sophisticated experimental techniques and computational simulations has been carried out in recent years. Although it is difficult for experimental techniques to provide detailed microscopic structural information, molecular dynamics (MD) simulations have satisfactory performance. In this report, we discuss classical and ab initio MD simulations of water/oxide interfaces. Generally, we are interested in the following questions: How do solid surfaces perturb interfacial water structure? How do interfacial water molecules and adsorbed solutes affect solid surfaces and how do interfacial environments affect solvent and solute behavior? Finally, we discuss progress in the application of neural network potential based MD simulations, which offer a promising future because this approach has already enabled ab initio level accuracy for very large systems and long trajectories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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 OSTI2026

Quantum fluctuations in dense plasma simulations

Molecular dynamics (MD) simulations are a powerful tool for modeling warm and hot dense matter. Density functional theory (DFT) MD simulations are often preferred in dense plasmas in order to accurately model quantum electronic structure. However, DFT-MD simulations neglect interaction effects due to fluctuations in excited states. In this work, we present an MD approach that uses excited state method pseudoatoms to run dense plasma simulations with many different core-electron configurations at classical MD speeds. We also allow for transitions between different configurations in our simulations and find that these fluctuations are especially important for highly excited states. Our results suggest that finite configuration lifetimes that are comparable to the inverse ion plasma frequency need to be accounted for in order to accurately model ion distributions in dense plasma simulations. We also demonstrate that excited state fluctuations have a direct impact on ion plasma microfields, generate different plasma microfields for different excitation levels, and thereby induce absorption–emission line shape asymmetries even in steady-state plasmas.

36 MATERIALS SCIENCE↗