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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics

Understanding the driving forces behind the nucleation of different polymorphs is of great importance for material sciences and the pharmaceutical industry. This includes understanding the reaction coordinate that governs the nucleation process and correctly calculating the relative free energies of different polymorphs. Here, we demonstrate, for the prototypical case of urea nucleation from the melt, how one can learn such a one-dimensional reaction coordinate as a function of prespecified order parameters and use it to perform efficient biased all-atom molecular dynamics simulations. The reaction coordinate is learnt as a function of the generic thermodynamic and structural order parameters using the “spectral gap optimization of order parameters (SGOOP)” approach [Tiwary, P. and Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. (2016)] and is biased using well-tempered metadynamics simulations. The reaction coordinate gives insights into the role played by different structural and thermodynamics order parameters, and the biased simulations obtain accurate relative free energies for different polymorphs. This includes an accurate prediction of the approximate pressure at which urea undergoes a phase transition and one of the metastable polymorphs becomes the most stable conformation. Here, we believe the ideas demonstrated in this work will facilitate efficient sampling of nucleation in complex, generic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Deriving reliable nucleation rates from metadynamics simulations: Application to Yukawa fluids

In order to solidify the usefulness of metadynamics in studying nucleation of crystals from supercooled liquids, this work provides a specific procedure to calculate nucleation free energy barriers. After a pedagogical review of the important elements of classical nucleation theory and how metadynamics is used to find nucleation free energy barriers, we explain the benefits of local collective variables over more common global collective variables. We show how a metadynamics free energy barrier must be carefully post-processed so that classical nucleation theory can be applied to calculate nucleation rates. We apply our procedure to a Yukawa plasma and show that a particular physically motivated fit to metadynamics data reproduces low-temperature reference data, justifying the usefulness of metadynamics to predict nucleation rates.

42 ENGINEERING↗
DOE OSTI2022

Assessing models of force-dependent unbinding rates via infrequent metadynamics

Protein–ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent “bonds” being mechanically strained, and this can be integral to proper cellular function. Broadly, two classes of force dependence have been observed—slip bonds, where the unbinding rate increases, and catch bonds, where the unbinding rate decreases. Despite much theoretical work, we cannot predict for which protein–ligand pairs, pulling coordinates, and forces a particular rate dependence will appear. Here, we assess the ability of MD simulations combined with enhanced sampling techniques to probe the force dependence of unbinding rates. We show that the infrequent metadynamics technique correctly produces both catch and slip bonding kinetics for model potentials. We then apply it to the well-studied case of a buckyball in a hydrophobic cavity, which appears to exhibit an ideal slip bond. Finally, we compute the force-dependent unbinding rate of biotin–streptavidin. Here, the complex nature of the unbinding process causes the infrequent metadynamics method to begin to break down due to the presence of unbinding intermediates, despite the use of a previously optimized sampling coordinate. Allowing for this limitation, a combination of kinetic and free energy computations predicts an overall slip bond for larger forces consistent with prior experimental results although there are substantial deviations at small forces that require further investigation. Furthermore, this work demonstrates the promise of predicting force-dependent unbinding rates using enhanced sampling MD techniques while also revealing the methodological barriers that must be overcome to tackle more complex targets in the future.

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

Metadynamics investigation of lanthanide solvation free energy landscapes and insights into separations energetics

Lanthanide ion solvation chemistry in nonaqueous phases is key to understanding and developing effective separation processes for these critical materials. Due to the complexity and inherent disorder of the solution phase, a comprehensive picture of the solvated metal ion is often difficult to generate solely from conventional spectroscopic approaches and electronic structure calculations, particularly in the extractant phase. In this work, we use classical molecular dynamics (MD) simulation with an advanced sampling technique, metadynamics, supplemented by experimental spectroscopy and speciation analysis, to measure lanthanide solvation free energy landscapes. We define coordination-based collective variables to probe the entire range of solvation configurations in the organic phase of lanthanum (La), europium (Eu), and lutetium (Lu) nitrate salts bound with a commonly used extractant, N,N′-dimethyl, N,N′-dioctylhexylethoxymalonamide (DMDOHEMA). The known lanthanide extraction trend of La ≈ Eu > Lu is readily explained by the measured free energy surfaces, which show consistent DMDOHEMA coordination from La to Eu, followed by loss of DMDOHEMA coordination from Eu to Lu. These simulations suggest how ligand crowding at the metal center can control selectivity, in this case resulting in the opposite extraction trend as observed with other conventional extractants, where the enthalpic contribution from increasing lanthanide charge density across the series dominates the extraction energetics. We also find that the presence of inner-sphere water, verified by time-resolved fluorescence, diversifies the accessible solvation structures. As a result, understanding solvation requires consideration of an entire thermodynamic ensemble, rather than the single dominant lowest-energy structure, as is often considered out of necessity in interpretation of spectroscopic data or in electronic structure-based ligand design approaches. In general, we demonstrate how metadynamics uniquely enables investigation of complex, multidimensional solvation energetic landscapes, and how it can explain selectivity trends where extraction is controlled by more complex mechanisms than simple charge density-based selectivity.

Wang, Xiaoyu↗
DOE OSTI2025

Assessment of metadynamic recrystallization in single copper particle impacts by focused ion beam tomography

We study single Cu-on-Cu impacts relevant to cold spray deposition and quantitatively analyze the metadynamic recrystallization (mDRX) that takes place after the impact by virtue of lingering impact adiabatic heat. Unlike prior studies, the current full 3D tomographic analysis of the mDRX volume shows that mDRX is extremely common in such impacts, although it is often missed when examining 2D sections. We also report an unexpected trend: there is a “sour spot” for mDRX at velocities about 20–40 % above the velocity for particle adhesion. This non-monotonic trend is contrary to the expectations based on increasing adiabatic heating with velocity. With a schematic model, we show that the trend can be explained on the basis of heat transfer: cooling of the heat-affected region is limited by transport through the bonded regions at the particle-substrate interface. Thus, bonding has a prominent role in the heat dissipation process and the best bonded particles most rapidly bulk quench, avoiding mDRX. Here, the developed semi-empirical model aligns with the experimental findings and may help inform microstructural evolution during cold spray and post-spray processing.

FIB-SEM tomography↗
DOE OSTI2023

Identification of inhibitors against SARS-CoV-2 variants of concern using virtual screening and metadynamics-based enhanced sampling

Among the variants of SARS-CoV-2, some are more infectious than the Wild-type. Interestingly, these mutations enable the virus to evade the therapeutic efforts. Hence, there is a need for candidate drug molecules that can potently bind with all the variants. Here we have adopted a strategy combining virtual screening, molecular docking followed by rigorous sampling by metadynamics simulations to find candidate molecules. From our results we found four highly potent drug candidates that can bind to the Spike-RBD of all the variants of the virus. Additionally, we also found that certain signature residues on the RBM region commonly bind to each of these inhibitors. Thus, our study not only gives information on the chemical compounds, but also residues on the proteins which could be targeted for future drug and vaccine development studies.

60 APPLIED LIFE SCIENCES↗
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↗
DOE OSTI2024

Cryptate binding energies towards high throughput chelator design: metadynamics ensembles with cluster–continuum solvation

A tiered forcefield/semiempirical/meta-GGA pipeline together with a thermodynamic scheme designed with error cancellation in mind was developed to calculate binding energies of [2.2.2] cryptate complexes of mono- and divalent cations. Stable complexes of Na, K, Rb, Ca, Zn and Pb were generated, revealing consistent cation–N lengths but highly variable cation–O lengths and an amine stacking mechanism potentially augmenting the cation size selectivity. Metadynamics, used for searching the high-dimensional potential energy surface, together with a cluster–continuum model for affordable – yet accurate – solvation modeling, enabled the discovery of more stable geometries than those previously reported. Similar solvation energy curve shapes for lone vs. coordinated ions enabled rapid solvation convergence via the cancellation of errors stemming from finite cluster sizes. In conclusion, an R 2 of 0.850 vs. experimental aqueous binding energies was obtained, validating this scheme as the backbone of a high-throughput workflow for chelator design.

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

The Sluggish Diffusion of Cations in CeO 2 Probed through Molecular Dynamics and Metadynamics Simulations

Cation diffusion in fluorite‐structured CeO 2 , though far slower than anion diffusion, is an important, high‐temperature process because it governs diverse fabrication and degradation phenomena. Herein, cation diffusion is studied by means of classical molecular dynamics and metadynamics simulations. Three different mechanisms are examined: migration involving an isolated cerium vacancy, migration involving a cerium vacancy in a defect associate with an oxygen vacancy, and migration involving a cation divacancy. For each mechanism, defect diffusion coefficients are calculated as a function of temperature, from which the respective activation enthalpy of defect migration is obtained. Through comparisons with experimental cation diffusion data (specifically, of the absolute magnitude of the cation diffusivity as well as its activation enthalpy), it is concluded that cation diffusion takes place predominantly neither by isolated vacancies nor by cation vacancy–oxygen vacancy associates but by cation divacancies.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes

Understanding the impact of extractant functionalization on metal-binding energetics in liquid-liquid extraction is essential to guide the development of better separation processes. Traditionally, computational extractant design uses electronic structure calculations on metal-ligand clusters to determine the metal-binding energy of the lowest energy state. Although highly accurate, this approach does not account for all of the relevant physics encountered under experimental conditions. Such methodologies often neglect entropic contributions such as temperature effects and ligand flexibility, in addition to approximating solvent-extractant interactions with implicit solvent models. In this study, we use classical molecular dynamics simulations with an advanced sampling method, metadynamics, to map out extractant molecule conformational free energies in the condensed phase. Here we generate the complete conformational landscape in solution for a family of bidentate malonamide-based extractants with different functionalizations of the headgroup and the side chains. In particular, we show how such alkyl functionalization reshapes the free energy landscape, affecting the free energy penalty of organizing the extractant into the cis-like metal-binding conformation from the trans-like conformation of the free extractant in solution. Specifically, functionalizing alkyl tails to the center of the headgroup has a greater influence on increasing molecular rigidity and disfavoring the binding conformation than functionalizing side chains. These findings are consistent with trends in metal-binding energetics based on experimentally reported distribution ratios. We also consider a different bidentate extractant molecule, carbamoylmethylphosphine oxide, and show how the choice of solvent can further reshape the conformational energetic landscape. This study demonstrates the feasibility of using molecular dynamics simulations with advanced sampling techniques to investigate extractant conformational energetics in solution, which, more broadly, will enable extractant design that accounts for entropic effects and explicit solvation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Mechanistic insights into rubidium ion adsorption at the quartz (101) surface from quantum chemical metadynamics

Ion sorption extent and mechanism depend in part on the mineral surface termination, which can be highly complex. Variations in surface functional groups, particularly with defect density and surface roughness, influence mineral reactivity towards solutes. In this work, we investigate the adsorption of a rubidium cation (Rb + ) at pristine and defect quartz (101) surface sites using well-tempered metadynamics, based on simulations with the quantum chemical density-functional tight-binding (DFTB) method. We compare the relative energetics of Rb + adsorption across selected sites for each surface, with nanosecond-level sampling, highlighting similarities between vicinal and geminal silanol sites. We find that the positive Rb + partial atomic charge can increase by as much as 0.5e as it approaches the surface, with implications for modulation of ion adsorption strength and extent at the quartz (101) surface with surface vacancies, silanol coverage, and charge.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

From diamond to BC8 to simple cubic and back: Kinetic pathways to post-diamond carbon phases from metadynamics

Understanding the kinetic pathways connecting carbon polymorphs at multimegabar pressures remains a major unsolved problem in high-pressure physics. Here, we provide insights into the long-standing question of BC8 formation and stability by combining a state-of-the-art SNAP machine-learning interatomic potential with enhanced sampling via metadynamics, enabling direct access to transition mechanisms far beyond the reach of standard molecular dynamics. Our simulations show that carbon phase transformations are intrinsically complex, proceeding through multiple intermediate disordered and crystalline states governed by nontrivial kinetic ordering. We determine the upper pressure limit for BC8 formation and reveal that hexagonal diamond transforms to BC8 faster than cubic diamond—an unexpected and experimentally testable prediction. We also identify a 𝑃⁢222 carbon phase that becomes competitive with diamond and simple cubic above 1.8 TPa, and we demonstrate that BC8 may be quenched to ambient conditions at moderate temperatures. Altogether, these results establish a general and transferable framework for resolving kinetic pathways in solid-solid phase transitions and provide physical insights into carbon's complex high-pressure landscape.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Size-Dependent Nucleation in Crystal Phase Transition from Machine Learning Metadynamics

In this Letter, we present a framework that combines machine learning potential (MLP) and metadynamics to investigate solid-solid phase transition. Here, based on the spectral descriptors and neural networks regression, we develop a scalable MLP model to warrant an accurate interpolation of the energy surface where two phases coexist. Applying it to the simulation of B4–B1 phase transition of GaN under 50 GPa with different model sizes, we observe sequential change of the phase transition mechanism from collective modes to nucleation and growths. When the size is at or below 128 000 atoms, the nucleation and growth appear to follow a preferred direction. At larger sizes, the nuclei occur at multiple sites simultaneously and grow to microstructures by passing the critical size. The observed change of the atomistic mechanism manifests the importance of statistical sampling with large system size in phase transition modeling.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Metadynamics simulations reveal mechanisms of Na + and Ca 2+ transport in two open states of the channelrhodopsin chimera, C1C2

Cation conducting channelrhodopsins (ChRs) are a popular tool used in optogenetics to control the activity of excitable cells and tissues using light. ChRs with altered ion selectivity are in high demand for use in different cell types and for other specialized applications. However, a detailed mechanism of ion permeation in ChRs is not fully resolved. Here, we use complementary experimental and computational methods to uncover the mechanisms of cation transport and valence selectivity through the channelrhodopsin chimera, C1C2, in the high- and low-conducting open states. Electrophysiology measurements identified a single-residue substitution within the central gate, N297D, that increased Ca 2+ permeability vs. Na + by nearly two-fold at peak current, but less so at stationary current. We then developed molecular models of dimeric wild-type C1C2 and N297D mutant channels in both open states and calculated the PMF profiles for Na + and Ca 2+ permeation through each protein using well-tempered/multiple-walker metadynamics. Results of these studies agree well with experimental measurements and demonstrate that the pore entrance on the extracellular side differs from original predictions and is actually located in a gap between helices I and II. Cation transport occurs via a relay mechanism where cations are passed between flexible carboxylate sidechains lining the full length of the pore by sidechain swinging, like a monkey swinging on vines. In the mutant channel, residue D297 enhances Ca 2+ permeability by mediating the handoff between the central and cytosolic binding sites via direct coordination and sidechain swinging. We also found that altered cation binding affinities at both the extracellular entrance and central binding sites underly the distinct transport properties of the low-conducting open state. This work significantly advances our understanding of ion selectivity and permeation in cation channelrhodopsins and provides the insights needed for successful development of new ion-selective optogenetic tools.

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

Quantifying the Relevance of Long-Range Forces for Crystal Nucleation in Water

Understanding nucleation from aqueous solutions is of fundamental importance in a multitude of fields, ranging from materials science to biophysics. The complex solvent-mediated interactions in aqueous solutions hamper the development of a simple physical picture, elucidating the roles of different interactions in nucleation processes. In this study, we make use of three complementary techniques to disentangle the role played by short- and long-range interactions in solvent-mediated nucleation. Specifically, the first approach we utilize is the local molecular field (LMF) theory to renormalize long-range Coulomb electrostatics. Second, we use well-tempered metadynamics to speed up rare events governed by short-range interactions. Third, the deep learning-based State Predictive Information Bottleneck approach is employed in analyzing the reaction coordinate of the nucleation processes obtained from the LMF treatment coupled with well-tempered metadynamics. We find that the two-step nucleation mechanism can largely be captured by the short-range interactions, while the long-range interactions further contribute to the stability of the primary crystal state under ambient conditions. Furthermore, by analyzing the reaction coordinate obtained from the combined LMF-metadynamics treatment, we discern the fluctuations on different time scales, highlighting the need for long-range interactions when accounting for metastability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗