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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Reversible motions and disordered structure of soft particles in amorphous solids

In amorphous solids, soft vibrational modes derived from normal mode analysis can be utilized to identify the soft particles that are prone to irreversible rearrangements. However, the normal mode analysis approach cannot explain why the spatial distributions of clustered soft particles do not change over time. We define a softness parameter based on the vibrational density of states calculated directly from molecular dynamics simulations with both the harmonic vibrations and anharmonic relaxations being properly captured at finite temperatures. This parameter spontaneously correlates with the real space atomic motions and the dynamics heterogeneity. Using the softness parameter, we show that the softest particles are confined within rigid cages. These particles keep rearranging reversibly without long-range diffusion. The moderately soft particles rearrange irreversibly, and the hard particles mainly participate in vibrations without rearrangement. Here, we also show that the soft particles form locally disordered structures, while the hard particles present strong ordering. These findings confirm the defective nature of soft particles, and provide insights on the nature of softness as the ability to rearrange, but not necessarily irreversibly.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Studying performance portability of LAMMPS across diverse GPU-based platforms

The molecular dynamics simulation software, LAMMPS, utilizes the Kokkos acceleration library to port computation to a diverse set of architectures including those based on GPU accelerators. In addition to Kokkos, LAMMPS contains a vast code base that leverages the CUDA application programming interface using library functions such as cuFFT, CUDA's fast-fourier transform (FFT) library, and, more recently, also support for AMD's Heterogeneous Interface for Portability (HIP) that is rapidly growing. While preparing LAMMPS tests for the AMD GPU-based test system precursors to Frontier, we investigated several strategies for accelerating LAMMPS on AMD GPUs, using the AMD Instinct MI100 and MI250X. In this work, we integrated the HIP FFT library, hipFFT, into the particle-particle particle-mesh (PPPM) long-range solver, which allowed the porting of PPPM calculations to the GPUs. Kokkos behavior on the MI100 and MI250X was also investigated through the package kokkos command of LAMMPS, targeting communication, memory usage, and particle grid decomposition. The Tersoff, Reax, Lennard-Jones (LJ), EAM, Granular, and PPPM potentials were investigated in this effort, and results from these experiments are provided. In conclusion, the selected potentials were run on Spock (AMD Instinct MI100), Crusher (AMD Instinct MI250X), AFW HPC11 (NVIDIA A100) and Summit (NVIDIA V100), for comparison. Operational roofline models were constructed and analyzed for the Tersoff, Reax, and Lennard–Jones potentials on Crusher and Summit.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Dynamic aspects of graphene deformation and fracture from approximate density functional theory

Graphene is one of the most intriguing two-dimensional carbon materials. Its mechanical strength and failure are key concerns for materials engineering and applications. Despite the success of fracture mechanics, the mechanism of how pristine materials fail remains an elusive problem. While many theoretical studies based on molecular dynamics using empirical forcefields have tried to address this question, atomic-scale mechanics are not clearly understood. Especially, a widely employed bond-breaking approach based on the critical bond length has not been rigorously tested. Here, utilizing molecular dynamics simulations with density functional based tight binding, we investigate how the failure of the pristine material initiates. The Wiberg bond order (W BO ) to estimate the change of chemical bonds shows a transition from sp 2 (W BO ~ 1.33) to sp 3 (WBO < 1.0) during the deformation. However, it reveals that a single threshold value for either the WBO or bond length is insufficient to decide failure of pristine material without free edges or defects. Instead, collective behaviors of the local atomic group govern the fracture initiation of pristine graphene. Overall, our study provides dynamic mechanical responses based on quantum mechanics, which have not been captured by empirical forcefields, opening opportunities to design properties by precisely coupling the mechanics and quantum mechanics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

The Influence of Alkyl Spacers and Molecular Weight on the Charge Transport and Storage Properties of Oxy‐Bithiophene‐Based Conjugated Polymers

Conjugated polymers (CPs) with polar side chains can conduct electronic and ionic charges simultaneously, making them promising for bioelectronics, electrocatalysis and energy storage. Recent work showed that adding alkyl spacers between CP backbones and polar side chains improved electronic charge carrier mobility, reduced swelling and enhanced stability, without compromising ion transport. However, how alkyl spacers impact polymer backbone conformation and, subsequently, electronic properties remain unclear. In this work, we design two oxy-bithiophene-based CP series, each featuring progressively extended alkyl spacer lengths and two distinct molecular weight (MW) distributions. Using operando characterisations, we evaluate the (spectro)electrochemical and swelling properties of the polymer thin films, and their performance in organic field-effect transistors and organic electrochemical transistors. Surprisingly, alkyl spacers negatively impact the hole mobility of our polymers, with higher MW amplifying this effect. Using molecular dynamics simulations, we show that it is thermodynamically favourable for adjacent non-polar alkyl spacers to aggregate in polar electrolytes, leading to backbone twisting. Further spectroscopic measurements corroborate this prediction. Our findings demonstrate the active interactions between side chain structure, MW and electrolyte/solvent polarity in influencing polymer performance, underscoring the importance of considering solvation environment effects on polymer conformation when designing new mixed conducting CPs for electrochemical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Base pairing, structural and functional insights into N 4 -methylcytidine (m 4 C) and N 4 ,N 4 -dimethylcytidine (m 4 2 C) modified RNA

The N 4 -methylation of cytidine (m 4 C and m 4 2 C) in RNA plays important roles in both bacterial and eukaryotic cells. In this work, we synthesized a series of m 4 C and m 4 2 C modified RNA oligonucleotides, conducted their base pairing and bioactivity studies, and solved three new crystal structures of the RNA duplexes containing these two modifications. Our thermostability and X-ray crystallography studies, together with the molecular dynamic simulation studies, demonstrated that m 4 C retains a regular C:G base pairing pattern in RNA duplex and has a relatively small effect on its base pairing stability and specificity. By contrast, the m 4 2 C modification disrupts the C:G pair and significantly decreases the duplex stability through a conformational shift of native Watson-Crick pair to a wobble-like pattern with the formation of two hydrogen bonds. This double-methylated m 4 2 C also results in the loss of base pairing discrimination between C:G and other mismatched pairs like C:A, C:T and C:C. The biochemical investigation of these two modified residues in the reverse transcription model shows that both mono- or di-methylated cytosine bases could specify the C:T pair and induce the G to T mutation using HIV-1 RT. In the presence of other reverse transcriptases with higher fidelity like AMV-RT, the methylation could either retain the normal nucleotide incorporation or completely inhibit the DNA synthesis. These results indicate the methylation at N 4 -position of cytidine is a molecular mechanism to fine tune base pairing specificity and affect the coding efficiency and fidelity during gene replication.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1988

A molecular dynamics study of chloride binding by the cryptand SC24

The capture of chloride from water by the tetraprotonated form of the spherical macrotricyclic molecule SC24 was studied using molecular dynamics simulation methods. This model ionophore represents a broad class of molecules which remove ions from water. Two binding sites for the chloride were found, one inside and one outside the ligand. These sites are separated by a potential energy barrier of approximately 20 kcal mol-1. The major contribution to this barrier comes from dehydration of the chloride. The large, unfavorable dehydration effect is compensated for by an increase in electrostatic attraction between the oppositely charged chloride and cryptand, and by energetically favorable rearrangements of water structure. Additional assistance in crossing the barrier and completing the dehydration of the ion is provided by the shift of three positively charged hydrogen atoms of the cryptand towards the chloride. This structural rigidity is partially responsible for its selectivity.

NASA Discipline Exobiology↗

DOE OSTI2021

Polarizable Water Potential Derived from a Model Electron Density

A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. This framework is used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, damped polarization, charge transfer, anisotropic Pauli repulsion, and damped dispersion interactions. Initial parameter values were fit to Symmetry Adapted Perturbation Theory (SAPT) energy components for ten water dimer configurations, as well as the radial and angular dependence of the canonical dimer. The SAPT-based parameters were then systematically refined to extend the treatment to water bulk phases. The final HIPPO water model provides a balanced representation of a wide variety of properties of gas phase clusters, liquid water, and ice polymorphs, across a range of temperatures and pressures. This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields. The HIPPO water model serves as a cornerstone around which similarly detailed physics-based models can be developed for additional molecular species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Dynamics of iodine geminate recombination in supercritical xenon solvent: Caging effect

Understanding the dynamics of chemical reactions in solutions is vital, as their rates and kinetics are significantly affected by the solvent environment. Supercritical solvents offer extensive applications in chemical reactions by enabling the manipulation of the solution environment. Here, in this study, we investigate the geminate recombination of iodine in a supercritical xenon solvent by using ReaxFF-based molecular dynamics simulations. Our findings reveal that the highest iodine recombination rate occurs near supercritical conditions, while lower-pressure conditions lead to reduced collision rates and unstable recombination, and higher-pressure conditions hinder iodine diffusion, resulting in a lower recombination rate. Our analysis shows that the xenon local density at the time of recombination is at least 2.5 times higher than the global density, confirming the presence of xenon clusters surrounding the Iodine atoms. This observation is further supported by coordination number analysis, which confirms an elevated xenon local density during recombination. In addition, the correlation between the total energy of xenon atoms within a cluster and recombined iodine atoms underscores the kinetic energy transfer process, validating the occurrence of geminate recombination. The excess kinetic energy from the recombining iodine atoms is transferred to the surrounding xenon atoms. Our examination of geminate recombination demonstrates that iodine atoms confined within xenon clusters—whether through manual insertion of atoms or the fast dissociation of an iodine molecule within xenon clusters—are more likely to recombine as primary geminate recombination. However, extending the iodine molecule dissociation time allows iodine atoms to diffuse out of the cluster, and the recombination to shift toward secondary geminate recombination.

Cage effect↗

DOE OSTI2024

The Interplay of Solvation and Polarization Effects on Ion Pairing in Nanoconfined Electrolytes

The nature of ion–ion interactions in electrolytes confined to nanoscale pores has important implications for energy storage and separation technologies. However, the physical effects dictating the structure of nanoconfined electrolytes remain debated. Here we employ machine-learning-based molecular dynamics simulations to investigate ion–ion interactions with density functional theory level accuracy in a prototypical confined electrolyte, aqueous NaCl within graphene slit pores. We find that the free energy of ion pairing in highly confined electrolytes deviates substantially from that in bulk solutions, observing a decrease in contact ion pairing but an increase in solvent-separated ion pairing. These changes arise from an interplay of ion solvation effects and graphene’s electronic structure. Notably, the behavior observed from our first-principles-level simulations is not reproduced even qualitatively with the classical force fields conventionally used to model these systems. The insight provided in this work opens new avenues for predicting and controlling the structure of nanoconfined electrolytes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Parameterizing empirical interatomic potentials for predicting thermophysical properties via an irreducible derivative approach: the case of ThO 2 and UO 2

The accuracy of classical physical property predictions using molecular dynamics simulations is determined by the quality of the interatomic potentials. Here we introduce a training approach for empirical interatomic potentials (EIPs) which is well suited for capturing phonons and phonon-related properties. Our approach is based on direct comparisons of the second- and third-order irreducible derivatives (IDs) between an EIP and the Born–Oppenheimer potential within density functional theory (DFT) calculations. IDs fully exploit space group symmetry and allow for training without redundant information. We demonstrate the fidelity of our approach in the context of ThO 2 and UO 2 , where we optimize parameters of an embedded-atom method potential in addition to core–shell interactions. Our EIPs provide thermophysical properties in good agreement with DFT and outperform widely utilized EIPs for phonon dispersion and thermal conductivity predictions. Reasonable estimates of thermal expansion and formation energies of Frenkel pairs are also obtained.

empirical interatomic potential↗

DOE OSTI2026

Minimization of Disorder as a Key Design Principle for Natural Sizes of Light Harvesting 2 Complexes

The light harvesting 2 (LH2) complex of purple bacteria has excellent energy conversion efficiency. Clarifying the design principle behind such efficiency at the atomistic level is crucial for understanding its structure–function relationship and can be utilized for the design of artificial light harvesting systems. To this end, we conducted comprehensive computational investigation of the dynamical and statistical nature of electronic excited states of pigment molecules in a natural LH2 complex with 9-fold symmetry and its two non-natural in silico analogues with 6- and 12-fold symmetries. To ensure reliable and efficient all-atomistic molecular dynamics simulations, we combined a well established interpolation approach for the construction of the potential energy surface with a neural network machine learning approach. Outcomes of these calculations clarify that non-natural forms of LH2-type complexes have significantly larger quasistatic disorder than those for the natural one. In addition, non-natural systems have more disruptions of the hydrogen bonding, underscoring its crucial role for reducing the disorder. On the other hand, local environmental dynamics are relatively insensitive to the structural changes although there is moderate enhancement in the anharmonic or interatomic components for the synthetic ones. These findings based on all-atomistic simulations provide direct computational evidence that the structure and sizes of natural LH2 complexes are designed to minimize the energetic disorder. We analyze quantitative implications of these for the energy transferring capability of the LH2 complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2014

Investigation of Structure and Transport in Li-Doped Ionic Liquid Electrolytes: [pyr14][TFSI], [pyr13][FSI], [EMIM][BF4]

Ionic liquid electrolytes have been proposed as a means of improving the safety and cycling behavior of advanced lithium batteries; however, the properties of these electrolytes under high lithium doping are poorly understood. Here, we employ both polarizable molecular dynamics simulation and experiment to investigate the structure, thermodynamics and transport of three potential electrolytes, N-methyl-N-butylpyrrolidinium bis(trifluoromethylsufonyl)imide ([pyr14][TFSI]), N- methyl-N-propylpyrrolidinium bis(fluorosufonyl)imide ([pyr13][FSI]), and 1-ethyl-3-- methylimidazolium boron tetrafluoride ([EMIM][BF4]), as a function of Li (-) salt concentration and temperature. Structurally, Li(+) is shown to be solvated by three anion neighbors in [pyr14][TFSI] and four anion neighbors in both [pyr13][FSI] and [EMIM][BF4], and at all levels of xLi we find the presence of lithium aggregates. Furthermore, the computed density, diffusion, viscosity, and ionic conductivity show excellent agreement with experimental data. While the diffusion and viscosity exhibit a systematic decrease and increase, respectively, with increasing xLi, the contribution of Li(+) to ionic conductivity increases until reaching a saturation doping level of xLi 0.10. Comparatively, the Li(+) conductivity of [pyr14][TFSI] is an order of magnitude lower than that of the other liquids, which range between 0.1-0.3 mScm. The differences in Li(+) transport are reflected in the residence times of Li(+) with the anions, which are revealed to be much larger for [pyr14][TFSI] (up to 100 ns at the highest doping levels) than in either [EMIM][BF4] or [pyr13][FSI]. Finally, we comment on the relative kinetics of Li(+) transport in each liquid and we present strong evidence for transport through anion exchange (hopping) as opposed to the net motion of Li(+) with its solvation shell (vehicular).

molecular dynamics↗

DOE OSTI2020

Field-Dependent Ionic Conductivities from Generalized Fluctuation-Dissipation Relations

We derive a relationship for the electric field dependent ionic conductivity in terms of fluctuations of time integrated microscopic variables. We demonstrate this formalism with molecular dynamics simulations of solutions of differing ionic strength with implicit solvent conditions and molten salts. These calculations are aided by a novel nonequilibrium statistical reweighting scheme that allows for the conductivity to be computed as a continuous function of the applied field. In strong electrolytes, we find the fluctuations of the ionic current are Gaussian, and subsequently, the conductivity is constant with applied field. In weaker electrolytes and molten salts, we find the fluctuations of the ionic current are strongly non-Gaussian, and the conductivity increases with applied field. Furthermore, this nonlinear behavior, known phenomenologically for dilute electrolytes as the Onsager-Wien effect, is general and results from the suppression of ionic correlations at large applied fields, as we elucidate through both dynamic and static correlations within nonequilibrium steady states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS2014

Investigation of Structure and Transport in Li-Doped Ionic Liquid Electrolytes: [pyr14][TFSI], [pyr13][FSI], [EMIM][BF4]

ionic liquids↗

DOE OSTI2021

Effect of water models on structure and dynamics of lignin in solution

Lignin, a major biomass component, can be an excellent source for different monomers in the polymer industry. However, the complex and heterogeneous structure of lignin poses a significant challenge for designing energy-efficient processes for depolymerization. As many proposed depolymerization processes are solvothermal, it is essential to understand the structure and dynamics of lignin in solution, in particular aqueous solution. Here, we utilize molecular dynamics simulations to understand the effect of water models on the structure and dynamics of different model lignin oligomers (softwood and hardwood) as a function of temperature. We have examined three different water models: TIP3P, TIP4P/Ew, and flexible SPC/Fw. We find that the diffusion constant of lignin oligomers in an aqueous solution differs significantly depending on the water model used. The diffusion constant of lignin in the TIP3P water model is almost twice as large as that in SPC/Fw and TIP4P/Ew. The softwood and hardwood oligomers adopt an extended structure in TIP3P water compared to SPC/Fw and TIP4P/Ew. Given the different levels of sensitivity of transport and structural properties of aqueous lignin on water models, it is important to take these into account when discussing results from a specific water model.

09 BIOMASS FUELS↗

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 OSTI2026

Hydration structure and energetics of iron-exchanged montmorillonite

The interaction between iron released from corroded steel canisters and bentonite is a key process influencing the long-term performance of nuclear waste repositories. In particular, the migration of Fe²⁺ into montmorillonite (Mnt) interlayers may alter its hydration, swelling, and ion-transport properties. In the present study, molecular dynamics simulations were performed to investigate the hydration behavior, structural response, and transport properties of Fe-exchanged montmorillonite (Fe-Mnt) under varying hydration states. The simulations focus on short- to intermediate-time-scale Fe 2+ and Fe 3+ interlayer exchange and hydration effects, and do not consider long-term structural substitution, Fe-bearing clay phase stabilization, or secondary iron mineral precipitation. Systems containing Na + -, Fe 2+ -, and Fe 3+ -Mnt were examined using both periodic and edge-exposed configurations to evaluate interlayer structure, ion exchange, and free energy of Fe intercalation. The results show that Fe ions influence the interlayer spacing primarily at low water contents (<1 bilayer), where Fe-Mnt exhibits a d-spacing 1–2 Å larger than Na-Mnt due to stronger hydration. The calculated hydration energies follow the order Fe 2+ $<$Fe 3+ $<$Na + . Both water and ion diffusion coefficients decrease upon Fe ion intercalation, with Fe 2+ ions diffusing an order of magnitude more slowly than those of Na + . Free energy profiles further confirm that Fe 2+ and Fe 3+ ions are thermodynamically favored in the interlayer, with Fe 3+ being the most stable. In conclusion, these findings provide molecular-scale insights into the mechanisms of Fe–Na exchange and their implications for bentonite alteration in repository environments.

clay↗

DOE OSTI2023

Molecular Rotations, Multiscale Order, Hyperuniformity, and Signatures of Metastability during the Compression/Decompression Cycles of Amorphous Ices

We model, via large-scale molecular dynamics simulations, the isothermal compression of low-density amorphous ice (LDA) to generate high-density amorphous ice (HDA) and the corresponding decompression extending to negative pressures to recover the low-density amorphous phase (LDA HDA ). Both LDA and HDA are nearly hyperuniform and are characterized by a dynamical HBN, showing that amorphous ices are nonstatic materials and implying that nearly hyperuniformity can be accommodated in dynamical networks. In correspondence with both the LDA-to-HDA and the HDA-to-LDA HDA phase transitions, the (partial) activation of rotational degrees of freedom activates a cascade effect that induces a drastic change in the connectivity and a pervasive reorganization of the HBN topology which, ultimately, break the samples’ hyperuniform character. Key to this effect is the rapid rate at which changes occur, and not their magnitude. The inspection of structural properties from the short- to the long-range shows that signatures of metastability are present at all length-scales, hence providing further solid evidence in support of the liquid–liquid critical point scenario. LDA and LDA HDA differ in terms of HBN and structural properties, implying that they are distinct low-density glasses. Our work unveils the role of molecular rotations in the phase transitions between amorphous ices and shows how the unfreezing of rotational degrees of freedom generates a cascade effect that propagates over multiple length-scales. Our findings greatly improve our basic understanding of water and amorphous ices and can potentially impact the field of molecular network-forming materials at large.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗