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At least 1,225 records · Page 68
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Rotational memory function of SPC/E water

Memory effects are essential for the dynamics of condensed materials and are responsible for non-exponential relaxation of correlation functions of dynamic variables through the memory function. Memory functions of dipole rotations for water have never been calculated directly from molecular dynamics simulations. We present here calculations of memory functions for single-dipole rotations and for the overall dipole moment of the sample for SPC/E water. The normalized memory functions for single-particle and collective dipole dynamics turn out to be nearly identical. This result validates theories of dielectric spectroscopy in terms of single-particle time correlation functions and the connection between the collective and single-particle relaxation times through the Kirkwood factor. The dielectric function in this formalism contains no new dynamic information that does not exist in the single-dipole correlation function. A short memory time, ≲1 fs, justifies the use of the mathematics of rotational diffusion to describe the dynamics of a single molecular dipole moment in bulk water. Here, an analytical equation for the rotational memory time is derived.

Asthagiri, Dilipkumar N. [Oak Ridge National Labor↗
DOE OSTI2021

Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

When more data hurts: Optimizing data coverage while mitigating diversity-induced underfitting in an ultrafast machine-learned potential

Machine-learned interatomic potentials (MLIPs) are becoming an essential tool in materials modeling. However, optimizing the generation of training data used to parametrize the MLIPs remains a significant challenge. This is because MLIPs can fail when encountering local environments too different from those present in the training data. The difficulty of determining a priori the environments that will be encountered during molecular dynamics simulation necessitates diverse, high-quality training data. Here, this study investigates how training data diversity affects the performance of MLIPs using the Ultra-Fast force field (UF 3 ) to model amorphous silicon nitride. We employ expert and autonomously generated data to create the training data and fit four force field variants to subsets of the data. Our findings reveal a critical balance in training data diversity: insufficient diversity hinders generalization, while excessive diversity can exceed the MLIP's learning capacity, reducing simulation accuracy. Specifically, we found that the UF 3 variant trained on a subset of the training data, in which nitrogen-rich structures were removed, offered vastly better prediction and simulation accuracy than any other variant. By comparing these UF 3 variants, we highlight the nuanced requirements for creating accurate MLIPs, emphasizing the importance of application-specific training data to achieve optimal performance in modeling complex material behaviors.

ab initio molecular dynamics↗
DOE OSTI2022

Uptake of N 2 O 5 by aqueous aerosol unveiled using chemically accurate many-body potentials

The reactive uptake of N 2 O 5 to aqueous aerosol is a major loss channel for nitrogen oxides in the troposphere. Despite its importance, a quantitative picture of the uptake mechanism is missing. Here we use molecular dynamics simulations with a data-driven many-body model of coupled-cluster accuracy to quantify thermodynamics and kinetics of solvation and adsorption of N 2 O 5 in water. The free energy profile highlights that N 2 O 5 is selectively adsorbed to the liquid–vapor interface and weakly solvated. Accommodation into bulk water occurs slowly, competing with evaporation upon adsorption from gas phase. Leveraging the quantitative accuracy of the model, we parameterize and solve a reaction–diffusion equation to determine hydrolysis rates consistent with experimental observations. We find a short reaction–diffusion length, indicating that the uptake is dominated by interfacial features. The parameters deduced here, including solubility, accommodation coefficient, and hydrolysis rate, afford a foundation for which to consider the reactive loss of N 2 O 5 in more complex solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

UV-Induced Reaction Pathways in Bromoform Probed with Ultrafast Electron Diffraction

For many chemical reactions, it remains notoriously difficult to predict and experimentally determine the rates and branching ratios between different reaction channels. This is particularly the case for reactions involving short-lived intermediates, whose observation requires ultrafast methods. The UV photochemistry of bromoform (CHBr 3 ) is among the most intensely studied photoreactions. Yet, a detailed understanding of the chemical pathways leading to the production of atomic Br and molecular Br 2 fragments has proven challenging. In particular, the role of isomerization and/or roaming and their competition with direct C–Br bond scission has been a matter of continued debate. Here, in this work, gas-phase ultrafast megaelectronvolt electron diffraction (MeV-UED) is used to directly study structural dynamics in bromoform after single 267 nm photon excitation with femtosecond temporal resolution. The results show unambiguously that isomerization contributes significantly to the early stages of the UV photochemistry of bromoform. In addition to direct C–Br bond breaking within <200 fs, formation of iso-CHBr 3 (Br-CH-Br-Br) is observed on the same time scale and with an isomer lifetime of >1.1 ps. The branching ratio between direct dissociation and isomerization is determined to be 0.4 ± 0.2:0.6 ± 0.2, i.e., approximately 60% of molecules undergo isomerization within the first few hundred femtoseconds after UV excitation. The structure and time of formation of iso-CHBr 3 compare favorably with the results of an ab initio molecular dynamics simulation. The lifetime and interatomic distances of the isomer are consistent with the involvement of a roaming reaction mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structural and electronic characteristics of amorphous Ge 8 Sb 2 Te 11

GeTe-rich phase-change materials can be utilized in rewriteable optical memory due to the large contrast in reflectivity between amorphous and crystalline phases. Here we explored the structure and electronic properties of amorphous Ge 8 Sb 2 Te 11 using ab initio molecular dynamics simulations. The results indicate that amorphous Ge 8 Sb 2 Te 11 is dominantly composed of Ge-, Sb- and Te-centered octahedrons with distortions, while 30.4 % of Ge-centered clusters are in the form of tetrahedrons which are randomly distributed. The 5-fold rings possess a large proportion, and the Gesingle bondTe and Sbsingle bondTe bonds present larger formation energies than other bonds, leading to the ABAB bonding sequence (A: Ge and Sb, B: Te). The lone pair electrons locating at the opposite direction of bonds possess a large fraction of 14.8 %, which may enhance the distortions of local clusters. Importantly, these structural properties lead to the high stability of amorphous Ge 8 Sb 2 Te 11 and thus long data retention in the information storage.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Effect of Mixed-Solvent Environments on the Selectivity of Acid-Catalyzed Dehydration Reactions

The composition of the liquid phase can alter the rates of individual reaction steps and thus alter the selectivity of acid-catalyzed reactions, but these solvent effects are difficult to anticipate for design purposes. Herein, we report the kinetics and selectivity of Brønsted acid-catalyzed 1,2-propanediol dehydration in pure water and in aqueous mixtures of the polar aprotic cosolvents γ-valerolactone, 1,4-dioxane, tetrahydrofuran, N-methyl-2-pyrrolidone, tetramethylene sulfoxide, and dimethyl sulfoxide at 433 K. We find that the major product of 1,2-propanediol dehydration is propanal in most mixed-solvent environments with selectivities between 1 and 68 mol %. In contrast, 1,2-propanediol dehydration in aqueous mixtures of dimethyl sulfoxide affords acetone as the major product with up to 48% selectivity with minimal propanal formation. We use classical molecular dynamics simulations to probe these solvent effects by computing the difference between the solvation free energies of 1,2-propanediol and propanal in aqueous mixtures of polar aprotic cosolvents and in pure water. We find that the difference in the solvation free energies is correlated with the rates of propanal formation in all mixed-solvent environments, indicating that the solvent-mediated stabilization of the product state relative to the reactant state translates to increased selectivity toward the same product. Similar agreement between simulated solvation free energies and experimental reaction rates/selectivities is established for the acid-catalyzed dehydration of cis- and trans-1,2-cyclohexanediol and 1,3-cyclohexanediol. Finally, analysis of the solvation environment around 1,2-propanediol shows that dimethyl sulfoxide uniquely competes against water to solvate reactive hydroxyl groups, which causes a change in reaction mechanism in this solvent system that leads to the formation of acetone rather than propanal. Here, these results represent a step toward the computationally efficient screening of solvent systems for acid-catalyzed, liquid-phase processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Viscoelastic relaxation and topological fluctuations in glass-forming liquids

In this study, a method for characterizing the topological fluctuations in liquids is proposed. This approach exploits the concept of the weighted gyration tensor of a collection of particles and permits the definition of a local configurational unit (LCU). The first principal axis of the gyration tensor serves as the director of the LCU, which can be tracked and analyzed by molecular dynamics simulations. Analysis of moderately supercooled Kob–Andersen mixtures suggests that orientational relaxation of the LCU closely follows viscoelastic relaxation and exhibits a two-stage behavior. The slow relaxing component of the LCU corresponds to the structural, Maxwellian mechanical relaxation. Additionally, it is found that the mean curvature of the LCUs is approximately zero at the Maxwell relaxation time with the Gaussian curvature being negative. This observation implies that structural relaxation occurs when the configurationally stable and destabilized regions interpenetrate each other in a bicontinuous manner. Finally, the mean and Gaussian curvatures of the LCUs can serve as reduced variables for the shear stress correlation, providing a compelling proof of the close connection between viscoelastic relaxation and topological fluctuations in glass-forming liquids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

Residing in the 5' untranslated region of the mRNA, the 2'-deoxyguanosine (2'-dG) riboswitch mRNA element adopts an alternative structure upon binding of the 2'-dG molecule, which terminates transcription. RNA conformations are generally strongly affected by positively charged metal ions (especially Mg 2+ ). We have quantitatively explored the combined effect of ligand (2'-dG) and Mg 2+ binding on the energy landscape of the aptamer domain of the 2'-dG riboswitch with both explicit solvent all-atom molecular dynamics simulations (99 μsec aggregate sampling for the study) and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments. We show that both ligand and Mg 2+ are required for the stabilization of the aptamer domain; however, the two factors act with different modalities. The addition of Mg 2+ remodels the energy landscape and reduces its frustration by the formation of additional contacts. In contrast, the binding of 2'-dG eliminates the metastable states by nucleating a compact core for the aptamer domain. Mg 2+ ions and ligand binding are required to stabilize the least stable helix, P1 (which needs to unfold to activate the transcription platform), and the riboswitch core formed by the backbone of the P2 and P3 helices. Mg 2+ and ligand also facilitate a more compact structure in the three-way junction region.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Perspective—Lithium Metal Nucleation and Growth on Conductive Substrates: A Multi-Scale Understanding from Atomistic, Nano-, Meso-, to Micro-Scales

Reversible lithium (Li) deposition and stripping on conductive substrates like copper is vital for long-life high-energy rechargeable Li batteries. The reversibility is believed hindered by solid electrolyte interphase (SEI) formation and Li dendritic growth. Via in situ, operando cryo-microscopy and molecular dynamics simulation, we discovered amorphous Li before a disorder-order phase transition to bcc phase. The kinetics plays a significant role in Li nucleation and morphology evolution. This perspective on Li nucleation and growth from atomistic to nano- (<20 nm), meso- (20–100 nm), and micro-scales (>100 nm) provides a practical guidance on regulating dense Li deposits reversibly for long life performance.

25 ENERGY STORAGE↗
DOE OSTI2026

Protonation Dynamics of Confined Ethanol–Water Mixtures in H-ZSM-5 from Machine Learning-Driven Metadynamics

Zeolites are indispensable heterogeneous catalysts in industrial chemical processes, valued for their strong Brønsted acidity, well-defined microporous frameworks, and tunable pore structures. Their catalytic activity arises primarily from Brønsted acid sites (BAS), typically present as bridging hydroxyl groups (Si–OH–Al). Under aqueous reaction conditions, these protons interact dynamically with water and alcohol molecules, leading to complex solvation and protonation behavior within confined pores. In this study, we investigate the protonation equilibrium occurring between ethanol and water at the BAS of acidic zeolites under varying hydration levels, i.e., C2H5OH–(H2O)n, n=1–4. Local structure was analyzed through an adaptive-learning global optimization algorithm, while enhanced sampling molecular dynamics simulations with Well-Tempered Metadynamics (WMetaD) and machine learning interatomic potentials (MLPs) provide free-energy surfaces (FES) at variable hydration levels. The results reveal a strong dependence of proton localization on the degree of hydration. At low hydration (1 water molecule), the proton resides predominantly on ethanol; with 2 water molecules, it shifts toward water, and at higher hydration (3 or more water molecules), it becomes extensively delocalized over the water cluster. These findings underscore the critical role of solvation in modulating acid site behavior and suggest that a minimum of three water molecules is necessary to fully stabilize the proton on water within the zeolite framework. This solvation threshold has significant implications for catalytic processes, particularly in biomass conversion reactions where alcohol protonation is a key step in dehydration mechanisms.

machine learning↗
NASA NTRSDate not supplied

Multiscale Modeling of Thermoplastics Using Atomistic-informed Micromechanics

A multiscale model was developed for predicting the thermoelastic behavior of semi-crystalline thermoplastic materials for composite aerospace applications. At the highest scale containing the semi-crystalline spherulite in an amorphous matrix, the generalized method of cells, or high fidelity method of cells, was used to perform the homogenization calculations to obtain the effective properties. Models were developed assuming a cubic, or spherical shape, for the spherulite to understand if the morphology of the spherulite affects the effective thermoelastic properties. The generalized method of cells was used to model at the repeating unit cells at the subscales of the microstructure including the lamellae stacks and granular crystal blocks. The scales are integrated using the multiscale micromechanics method in the NASA Multiscale Analysis Tool. Data from molecular dynamics simulations were used as inputs for the amorphous and crystalline constituents. Convergence studies were performed to determine the best level of discretization for the repeating unit cell at the highest scale. Effective Young’s modulus, shear modulus, Poisson’s ratio, coefficient of thermal expansion, and thermal conductivity were predicted for polyether ether ketone and polyether ketone ketone, and very good agreement between the model utilizing the cubic spherulite and the experimental data, where available, was observed for polyether ketone ketone. Normalization of the data for the bulk polyether ketone ketone, against amorphous data, improved the predictions as compared to experimental data. Overall, the high fidelity method of cells predicted a stiffer response then the generalized method of cells as the crystallinity was increased. The shape of the spherulite had a minimal effect on the predicted bulk properties of the polymers.

thermoplastics↗
DOE OSTI2026

Image Distinguishability Analysis Testing Through Principal Components and Its Application to Hot Spot Scale Invariance

Hot spots are spatial regions of intense energy localization that govern initiation of secondary high explosives. Studies that characterize or compare simulated hot spots are frequently either qualitatively descriptive or resort to quantitative distribution functions that neglect stochastic variations and spatial correlations—effects that are also neglected in common comparison tests like the Kolmogorov–Smirnov test. To this end, we develop an image distinguishability analysis (IDA) test based on principal component (PC) analysis that makes pixel-by-pixel comparisons between small, for example, O(<10), image data sets. The IDA test makes comparisons through a generalized distance metric in the PC space and a test statistic that is derived to calculate mathematical equation-values. Here, we derive a statistical distribution and criticality criterion to determine whether images are distinguishable from established baselines. We apply the IDA test on images generated from molecular dynamics simulations of hot spots from pore collapse in TATB to assess scale invariance in the complex patterns of hot spots that form in a representative high explosive crystal. The IDA test shows that TATB hot spot spatial temperature fields and their derived temperature histograms exhibit scale-invariant features over specific intervals of shock orientation, strength, and initial pore diameter. However, the IDA test also shows that qualitatively different conclusions regarding invariance can be reached depending on whether the hot spot is treated as a spatially correlated field as opposed to a distribution function that lacks spatial information.

organic↗
DOE OSTI2023

First-principles molten salt phase diagrams through thermodynamic integration

Precise prediction of phase diagrams in molecular dynamics simulations is challenging due to the simultaneous need for long time and large length scales and accurate interatomic potentials. Here, we show that thermodynamic integration from low-cost force fields to neural network potentials trained using density-functional theory (DFT) enables rapid first-principles prediction of the solid–liquid phase boundary in the model salt NaCl. We use this technique to compare the accuracy of several DFT exchange–correlation functionals for predicting the NaCl phase boundary and find that the inclusion of dispersion interactions is critical to obtain good agreement with experiment. Importantly, our approach introduces a method to predict solid–liquid phase boundaries for any material at an ab initio level of accuracy, with the majority of the computational cost at the level of classical potentials.

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

Molecular Insight into the Effects of Clustering on the Dynamics of Ionomers in Solutions

Ionizable groups tethered to polymers enable their many current and potential applications. However, these functionalities drive the formation of physical networks through clustering of the ionic groups, resulting in constrained dynamics of the macromolecules. Understanding the molecular origin of this hindrance remains a critical fundamental question, whose solution will directly impact the processing of ionizable polymers from molecules to viable materials. Here, in this work, using quasielastic neutron scattering accompanied by molecular dynamics simulations, segmental dynamics of slightly sulfonated polystyrene is studied in solutions as the cohesion of the ionic assemblies is tuned. We find that in cyclohexane the ionic assemblies act as centers of confinement, affecting dynamics both on macroscopic lengths and in the vicinity of the ionic assemblies. Addition of a small amount of ethanol affects the packing of the ionizable groups within the assemblies, which in turn enhances the chain dynamics.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Revealing the structure and electronic characteristics of Te-rich threshold switching materials for high-density integration

Ovonic threshold switching (OTS) selectors play an important role in the integration of advanced three-dimensional memory. Selectors based on tellurium (Te)-containing materials exhibit significant promise due to their low threshold voltages and superior consistency. Here we have theoretically studied the structure and electronic properties of a typical OTS material, amorphous GeTe 6 , to explore the switching mechanisms using ab initio molecular dynamics simulations. The results indicate that Ge atoms tend to bond with Te atoms, forming stable chemical bonds. The Te-centered clusters are predominantly in the form of distorted octahedrons, while the Ge-centered clusters are in the form of both octahedrons and tetrahedrons. Notably, the proportion of tetrahedrons within the 4-coordinated Ge-centered clusters reaches an impressive 66.9%. These tetrahedrons are randomly dispersed throughout the simulated cell, leading to a stable amorphous configuration. The mid-gap state observed in the mobility bandgap originates from the atomic chain composed of both over-coordinated Ge and Te atoms. It is the inherent stability of the chemical environment within amorphous GeTe 6 that enables it to maintain its amorphous phase under a repeated threshold voltage, a characteristic that distinguishes it from non-OTS materials, such as amorphous tellurium. Furthermore, our findings provide an in-depth understanding of the structure and electronic characteristics of amorphous GeTe 6 , which can promote the design and application of the Te-rich threshold switching materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Charge transfer rate constants for the carotenoid-porphyrin-C 60 molecular triad dissolved in tetrahydrofuran: The spin-boson model vs the linearized semiclassical approximation

Charge transfer rate constants were calculated for the carotenoid-porphyrin-C 60 (CPC 60 ) molecular triad dissolved in explicit tetrahydrofuran. The calculation was based on mapping the all-atom anharmonic Hamiltonian of this system onto the spin-boson Hamiltonian. The mapping was based on discretizing the spectral density from the time correlation function of the donor–acceptor potential energy gap, as obtained from all-atom molecular dynamics simulations. Different spin-boson Hamiltonians were constructed for each of the possible transitions between the three excited electronic states in two different triad conformations. The rate constants of three possible transitions were calculated via the quantum-mechanically exact Fermi’s golden rule (FGR), as well as a progression of more approximate expressions that lead to the classical Marcus expression. The advantage of the spin-boson approach is that once the mapping is established, the quantum-mechanically exact FGR and the hierarchy of approximations are known in closed form. The classical Marcus charge transfer rate constants obtained with the spin-boson Hamiltonians were found to reproduce those obtained from all-atom simulations with the linearized semiclassical approximation, thereby confirming the equivalence of the two approaches for this system. Furthermore, within the spin-boson Hamiltonian, we also found that the quantum-mechanically exact FGR rate constants were significantly enhanced compared to the classical Marcus theory rate constants for two out of three transitions in one of the two conformations under consideration. The results confirm that mapping to the spin-boson model can yield accurate predictions for charge transfer rate constants in a system as complex as CPC 60 dissolved in tetrahydrofuran.

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

Irradiation-enhanced torsional buckling capacity of carbon nanotube bundles

Molecular dynamics simulations are used to understand the torsional buckling of pristine and irradiated carbon nanotube (CNT) bundles. Irradiation-induced inter-tube defects are shown to significantly increase the critical buckling torque and critical buckling angle, while slightly increasing the torsional stiffness. In contrast, intra-tube defects are found to degrade the torsional properties. Such competing interactions cause irradiation enhancement to occur in large bundles where significant inter-tube bonding can occur. However, the irradiation enhancement effect becomes weak for very large bundles in which enhanced inter-tube interactions already exist in unirradiated bundles. In pristine CNT bundles of all sizes under torsional loading, CNTs can slip via the weakly interacting van der Waals force, whereas in the irradiated bundles, the inter-tube defects prevent slipping. The study further shows that the formation of one-dimensional carbon chain defects contributes to enhanced friction under slipping.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗