Search NASA⌕ Search

SEARCH · Search NASA

Results for “Implicit modeling”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

QM Investigation of Rare Earth Ion Interactions with First Hydration Shell Waters and Protein-Based Coordination Models

Here, conventional methods for extracting rare earth metals (REMs) from mined mineral ores are inefficient, expensive, and environmentally damaging. Recent discovery of lanmodulin (LanM), a protein that coordinates REMs with high-affinity and selectivity over competing ions, provides inspiration for new REM refinement methods. Here, we used quantum mechanical (QM) methods to investigate trivalent lanthanide cation (Ln 3+ ) interactions with coordination systems representing bulk solvent water and protein binding sites. Energy decomposition analysis (EDA) showed differences in the energetic components of Ln 3+ interaction with representatives of solvent (water, H 2 O) and protein binding sites (acetate, CH 3 COO – ), highlighting the importance of accurate description of electrostatics and polarization in computational modeling of REM interactions with biological and bioinspired molecules. Relative binding free energies were obtained for Ln 3+ with coordination complexes originating from binding sites in PDB structures of a lanthanum binding peptide (PDB entry 7CCO) and LanM, with explicit consideration of the first hydration shell waters, according to quasi-chemical theory (QCT). Beyond the first shell, the bulk solvent environment was represented with an implicit continuum model. Ln 3+ interactions with (H 2 O) 9 and both binding site models became more favorable, moving down the periodic series. This trend was more pronounced with the protein binding site models than with water, resulting in affinity increasing with periodic number, except for the last REM, Lu 3+ , which bound less favorably than the preceding element, Yb 3+ . Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln 3+ relative binding free energies for the whole 7CCO peptide were reproduced. Conversely, the previously reported experimental data for LanM show a preference for the earlier lanthanides; this is likely due to longer-range interactions and cooperative effects, which are not represented by the reduced models. Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln 3+ relative binding free energies for the whole 7CCO peptide were reproduced. In contrast to the previously reported experimental data for LanM, the peptide preferentially binds the earlier lanthanides. This difference likely arises due to longer-range interactions and cooperative effects not represented by the peptide. Further investigation of Ln 3+ interactions with whole proteins using polarizable molecular mechanics models with explicit solvent is warranted to understand the influence of longer-ranged interactions, cooperativity, and bulk solvent. Nevertheless, the present work provides new insights into Ln 3+ interactions with biomolecules and presents an effective computational platform for designing specific single-site REM binding peptides more efficiently.

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

Modeling supercritical CO 2 flow and mineralization in reactive host rocks with PFLOTRAN v7.0

Understanding the flow and reactivity of CO 2 injected into geological reservoirs is important for many subsurface applications including secure geologic carbon storage (GCS), critical mineral extraction, enhanced geothermal systems (EGS), and enhanced oil recovery (EOR). Traditionally, subsurface CO 2 injection for GCS applications has focused on geologic formations with favorable subsurface configurations for CO 2 migration and trapping through non-reactive mechanisms such as structural, solubility, and petrophysical trapping. Recently, CO 2 -reactive rocks such as mafic and ultramafic basalts have been investigated for their potential to react with injected CO 2 in situ to simultaneously dissolve host rock minerals and mineralize CO 2 as carbonates. Engineering rapid CO 2 mineralization in the subsurface is attractive because of the increased density of stored CO 2 , the additional safety factors associated with solidification, and the potential to extract valuable critical minerals. Here we present recent developments in the parallel flow and reactive transport simulator PFLOTRAN to model coupled CO 2 -brine flow and reactive transport for a wide range of injection and production applications involving reactive CO 2 -brine systems. These developments are based on the well established and trusted CO 2 flow capabilities in the STOMP-CO 2 simulator. New capabilities added to PFLOTRAN include new CO 2 -brine equations of state with optional thermal coupling, several new constitutive relationships like capillary pressure smoothing and scanning path hysteresis, a fully implicit well model, and native linkage with PFLOTRAN's well-established reactive transport libraries. A series of benchmarks between PFLOTRAN and STOMP-CO 2 verify the newly developed CO 2 -brine flow capabilities. Demonstrations of coupled CO 2 -brine flow modeling and reactive transport show how CO 2 mineralization can be engineered in reactive host rocks. Finally, an example use case involving copper leaching by CO 2 and critical mineral extraction is presented to showcase the strengths of this new implementation. Several limitations still remain, including limited availability of field data to parameterize models. Future work should constrain the evolution of mineral surface area during mineralization and the temperature and/or pH dependence of geochemical reactions for specific systems of interest.

Critical Minerals↗
DOE OSTI2020

Stoichiometrically coupled carbon and nitrogen cycling in the MIcrobial-MIneral Carbon Stabilization model version 1.0 (MIMICS-CN v1.0)

Explicit consideration of microbial physiology in soil biogeochemical models that represent coupled carbon–nitrogen dynamics presents opportunities to deepen understanding of ecosystem responses to environmental change. The MIcrobial-MIneral Carbon Stabilization (MIMICS) model explicitly represents microbial physiology and physicochemical stabilization of soil carbon (C) on regional and global scales. Here we present a new version of MIMICS with coupled C and nitrogen (N) cycling through litter, microbial, and soil organic matter (SOM) pools. The model was parameterized and validated against C and N data from the Long-Term Inter-site Decomposition Experiment Team (LIDET; six litter types, 10 years of observations, and 13 sites across North America). The model simulates C and N losses from litterbags in the LIDET study with reasonable accuracy (C: R 2 =0.63; N: R 2 =0.29), which is comparable with simulations from the DAYCENT model that implicitly represents microbial activity (C: R 2 =0.67; N: R 2 =0.30). Subsequently, we evaluated equilibrium values of stocks (total soil C and N, microbial biomass C and N, inorganic N) and microbial process rates (soil heterotrophic respiration, N mineralization) simulated by MIMICS-CN across the 13 simulated LIDET sites against published observations from other continent-wide datasets. We found that MIMICS-CN produces equilibrium values in line with measured values, showing that the model generates plausible estimates of ecosystem soil biogeochemical dynamics across continental-scale gradients. MIMICS-CN provides a platform for coupling C and N projections in a microbially explicit model, but experiments still need to identify the physiological and stoichiometric characteristics of soil microbes, especially under environmental change scenarios.

58 GEOSCIENCES↗
DOE OSTI2025

Liquid Phase Modeling in Porous Media: Adsorption of Methanol and Ethanol in H-MFI in Condensed Water

Zeolites are used in the chemical and separation industries for their exceptional selectivity, adsorption capacity, regenerability, and stability in gas and liquid phase processing. Here, we developed an explicit solvation method for predicting solvent/condensed phase effects on adsorption free energies in microporous media such as zeolites based on the hybrid quantum mechanical/molecular mechanical free energy perturbation (QM/MM-FEP) technique. Our explicit solvation method for zeolite systems, called eSZS, aims to capture site-specific interactions during the adsorption process at the Brønsted acid sites of H-MFI zeolite while still considering the diverse configuration space of the solvent molecules. This strategy is ideal for chemical reactions or adsorbates that interact with the microporous medium in few distinct adsorbate/transition state configurations, i.e., the harmonic or similar approximations are acceptable for the adsorbate/transition state while such approximations break down for the solvent molecules that require extensive configuration space sampling. In this way, our approach effectively overcomes the limitations of implicit solvation models and classical force field methods for describing solvation effects on chemical reactions within porous materials such as zeolites. Specifically, in this study, we investigated various aspects of our hybrid QM/MM approach, including QM cluster size dependencies in a periodic electrostatically embedded cluster model (PEECM), rules for link atoms at the QM/MM boundary, and functional and basis set considerations for converged and reasonably accurate gas and aqueous phase methanol and ethanol adsorption free energy predictions in H-MFI. For gas phase adsorption of methanol and ethanol in H-MFI at a Brønsted acid site in T12 position, we compute adsorption free energies at 298 K of −0.61 and −0.75 eV, respectively, using a PEECM containing 50 Si and 1 Al atom with ωB97x-D/def2-TZVP level of theory. For solvent effect calculations, we sample the aqueous phase using grand canonical Monte Carlo (GCMC) simulations to (1) obtain a mean field of electrostatic interactions in the reaction system and (2) perform a rigorous free energy perturbation calculation. Similar to the experimentally and computationally observed endergonic solvation effects observed for hydrocarbon adsorption on metal surfaces, we also observe that a condensed aqueous environment destabilizes methanol and ethanol at these acid sites in H-MFI at 298 K. Specifically, the computed solvation free energies of adsorption (ΔΔG solv ) for methanol and ethanol are +0.44 and +0.54 eV, respectively. From this study, it is evident that adsorbates (methanol and ethanol) are competing with water for adsorption space inside the H-MFI zeolite, leading to an endergonic solvation effect. Here, we expect that the endergonic, aqueous solvent effect during adsorption in microporous zeolites is highly tunable by changing the pore size and hydrophobicity of the microporous material as this will affect the water density inside the pore structure.

Adsorption↗
DOE OSTI2022

Time-discretization of a plasma-neutral MHD model with a semi-implicit leapfrog algorithm

The semi-implicit leapfrog time-discretization is a workhorse algorithm for initial-value MHD codes to bridge between vastly separated time scales. Inclusion of atomic interactions with neutrals breaks the functional structure of the MHD equations that exploited by the leapfrog. In this work, we address how to best integrate atomic physics into the semi-implicit leapfrog. Following the Crank-Nicolson method, one approach is to time-center the atomic interactions in the linear solver and use a Newton method to include the nonlinear contributions. Alternatively, another family of methods are based on operator-splitting the terms associated with the atomic interactions using a Strang-splitting technique. These methods naturally break equations into constituent ODE and PDE parts and preserve the structure exploited by the semi-implicit leapfrog. We study the accuracy and efficiency of these methods through a battery of 0D and 1D cases and show that a second-order-in-time Douglas-Rachford inspired coupling between the ODE and PDE advances is effective in reducing the time-discretization error to be comparable to that of Crank-Nicolson with Newton iteration of the nonlinear terms. Splitting ODE and PDE parts results in independent matrix solves for each field which reduces the computational cost considerably and provides parallelization over species relative to Crank-Nicolson.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Optimal experimental design: Formulations and computations

Questions of ‘how best to acquire data’ are essential to modelling and prediction in the natural and social sciences, engineering applications, and beyond. Optimal experimental design (OED) formalizes these questions and creates computational methods to answer them. This article presents a systematic survey of modern OED, from its foundations in classical design theory to current research involving OED for complex models. We begin by reviewing criteria used to formulate an OED problem and thus to encode the goal of performing an experiment. We emphasize the flexibility of the Bayesian and decision-theoretic approach, which encompasses information-based criteria that are well-suited to nonlinear and non-Gaussian statistical models. We then discuss methods for estimating or bounding the values of these design criteria; this endeavour can be quite challenging due to strong nonlinearities, high parameter dimension, large per-sample costs, or settings where the model is implicit. A complementary set of computational issues involves optimization methods used to find a design; we discuss such methods in the discrete (combinatorial) setting of observation selection and in settings where an exact design can be continuously parametrized. Finally we present emerging methods for sequential OED that build non-myopic design policies, rather than explicit designs; these methods naturally adapt to the outcomes of past experiments in proposing new experiments, while seeking coordination among all experiments to be performed. Throughout, we highlight important open questions and challenges.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Elucidating the Impact of Cis – Trans Organic Structure Directing Agent Isomer Ratios on the Aluminum Distribution Within SSZ-39

Despite their widespread use, the mechanisms governing the synthesis of zeolite catalysts are still poorly understood. A notable example of this problem is the uncertainty surrounding the influence of synthesis conditions on the placement of Al atoms in the zeolite framework which determines the active sites available for catalytic species. In this work, the role of the cis to trans isomer ratio of the OSDA N,N-dimethyl-3-5-dimethylpiperidinium on the energetics of 26 distinct Al pair distributions in SSZ-39 is examined both in the presence and absence of Na using density functional theory calculations. The initial orientation of the OSDA was found to have a significant impact on the final energies present, necessitating the screening of a large number of initial orientations with force field calculations and single point DFT calculations. Ground state energies were found to vary significantly with the ratio of cis to trans OSDAs with a Boltzmann distribution revealing the most likely Al pair distributions shift from sharing the same 8 membered rings to sharing the same double six membered rings to having no shared subunits as one increases the amount of cis OSDA present within the framework. The presence of Na was found to favor Al pair distributions where both Als occupied the same 6-membered ring. When an implicit solvent model was used to evaluate ground state energies the ideal Na sites shifted from 6-membered rings to empty SSZ-39 cages while OSDA positions and orientations remained largely the same. To provide insight on how kinetic factors may influence Al distributions, formation energies we calculated for connected double six membered rings. Further, these formation energies revealed a preference for Al pairs to occupy the same 4-membered ring which indicates kinetic and thermodynamic control may lead to different Al distributions in SSZ-39.

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

Data-Driven Recommendation of Optimal Tuning Scheme for Range-Separated Hybrid Functionals in Solution-Phase UV/Vis Absorption Energy Prediction

Time-dependent density functional theory (TDDFT) combined with range-separated hybrid (RSH) functionals and a tuned range-separation parameter γ offers a computationally economical approach for high-throughput excited- state property predictions. The γ-tuning procedure in the gas phase is well established. However, no agreement on the best γ- tuning procedure has been made when considering the solvent effect with implicit solvent models like the polarizable continuum model (PCM). To answer that question, this study created a diverse dataset with 937 molecules with experimental solutionphase UV/vis absorption spectra. Three γ-tuning methods, the gasphase γ-tuning (GPγT), the partial vertical γ-tuning (PVγT), and the strict vertical γ-tuning (SVγT), were evaluated for the ωPBEh functional over the entire dataset. Additional benchmarks are done for the optimally tuned screened range-separated hybrid combined with the PCM approach (SRSH-PCM) and the solvation-mediated tuning procedure (sol-med-OT). Our findings revealed that the optimal γ-values obtained by the PVγT and the SVγT are significantly smaller than the GPγT. This trend holds consistently across all molecules in our dataset, and we explained the origin of this phenomenon. TDDFT calculations with PVγTand SVγT-tuned γ-values and default global Fock exchange fraction achieve superior performance compared to those using GPγTtuned or default γ and slightly outperform SRSH-PCM and sol-med-OT with similar or lesser computational cost. Furthermore, we found that the smaller γ-values from SVγT captured the expected 1/(εR) asymptotic behavior in the solution phase, resulting in accurate prediction of solution-phase CT excitations, consistent with the screened asymptote behavior encoded in SRSH-PCM. These results show that SVγT is the best scheme for high-throughput UV/vis absorption spectrum calculations using the ωPBEh functional from a data-driven perspective.

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

Assessing Implicit and Explicit Polarizable Solvation Models for Nuclear–Electronic Orbital Systems: Quantum Proton Polarization and Solvation Energetics

Accurate simulations of many chemical processes require the inclusion of both nuclear quantum effects and a solvent environment. The nuclear–electronic orbital (NEO) approach, which treats electrons and select nuclei quantum mechanically on the same level, combined with a polarizable continuum model (PCM) for the solvent environment, addresses this challenge in a computationally practical manner. In this work, the NEO-PCM approach is extended beyond the IEF-PCM (integral equation formalism PCM) and C-PCM (conductor PCM) approaches to the SS(V)PE (surface and simulation of volume polarization for electrostatics) and ddCOSMO (domain decomposed conductor-like screening model) approaches. IEF-PCM, SS(V)PE, C-PCM, and ddCOSMO all exhibit similar solvation energies as well as comparable nuclear polarization within the NEO framework. The calculations show that the nuclear density does not leak out of the molecular cavity because it is much more localized than the electronic density. Finally, the polarization of quantized protons is analyzed in both continuum solvent and explicit solvent environments described by the polarizable MB-pol model, illustrating the impact of specific hydrogen-bonding interactions captured only by explicit solvation. Furthermore, these calculations highlight the relationship among solvation formalism, nuclear polarization, and energetics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Prediction of Redox Potentials for U, Np, Pu, and Am in Aqueous Solution

The redox properties of the actinides in aqueous solution are important for fuel production/reprocessing and understanding the environmental impact of nuclear waste. The redox potentials for U, Np, Pu, and Am in oxidation states from 0 up to VII (as appropriate) in aqueous solutions have been predicted at the density functional theory level with the B3LYP functional, Stuttgart small core pseudopotential basis sets for the actinides, and explicit (30H 2 O molecules)/implicit treatment of the aqueous solvent using the self-consistent reaction field COSMO and SMD approaches for the implicit solvation. The predictions of the structural parameters of clusters incorporating first and second solvation shells are consistent with the available experimental data., Our results are typically within 0.2 V of the available experimental data using two explicit solvation shells with an implicit solvent model. The use of the PW91 functional substantially improved the prediction of the Pu(VI/V) redox couple. The redox couples for An(VI/IV) and An(V/IV) which involve the addition of protons and removal of the actinyl oxygens led to slightly larger differences from experiment. Here, the An(IV/0) and An(III/0) couples were reliably predicted with our approach. Predictions of the unknown An(II/I) redox potentials were negative, consistent with expectations, and predictions for unknown An(VII/VI), An(III/II), and An(II/0) redox couples improve prior estimates.

Actinides↗
DOE OSTI2024

Prediction of Redox Potentials for Ac, Th, and Pa in Aqueous Solution

Density functional theory in conjunction with small core pseudopotentials and the associated basis sets was used to calculate potentials for multiple redox couples, covering a range of oxidation states for Ac (0 to III), Th (0 to IV), and Pa (0 to V) in aqueous solution. Solvation effects were incorporated using a supermolecule-continuum approach, with 30 water molecules representing two solvation shells, and the COSMO and SMD implicit solvation models. The calculated geometries for Ac(III), Th(IV), and Pa(V) were in reasonable agreement with the available experimental data. Using the COSMO model with the B3LYP functional, the calculated redox potentials were within ± 0.2 V from experiment for most redox couples. Several pathways were explored for the Pa(V/IV) redox couple for different forms of Pa(V) and Pa(IV). Most Pa(V/IV) redox couples have very similar potentials, ranging from 0 to -0.4 V up to a pH of 1.4. At pH = 1.4, the potentials shift to values that are more negative than -0.7 V, reflecting the growing unfavorable nature of the redox process at higher pH levels. The calculated values for An(III/II) potentials were consistent with prior estimates and the available experimental data. The predicted redox potentials for An(II/I) were highly negative, as expected. For An(I/0) potentials, Th and Pa exhibited positive values, contrasting with the negative values calculated for Ac. Furthermore, the An +m /An(0) potentials agreed better with the experimental data when using the COSMO solvation model as compared to the SMD model.

Chemical calculations↗
DOE OSTI2025

Prediction of Redox Potentials for the Late Actinides Cm to Lr Using Electronic Structure Methods

Our previously developed computational method for calculating the aqueous redox potentials of the early actinides has been extended to the later elements in the actinide series: Cm, Bk, Cf, Es, Fm, Md, No, and Lr in multiple oxidation states. These calculations were performed using density functional theory with small-core pseudopotentials and their associated basis sets. Solvation effects were considered via a supermolecule-continuum approach, with 30 water molecules representing two solvation shells. Both the COSMO and SMD implicit solvation models were utilized. The structural parameters and hydration numbers for Cm(III), Bk(III), Bk(IV), and Cf(III) are in reasonable agreement with the available experimental data. For redox processes involving atomic cations in solution, the B3LYP/COSMO approach predicted redox potentials to within ±0.2 V of experiment for most redox couples, consistent with our prior work. Inclusion of spin-orbit corrections in specific redox pairs, especially those with the later actinides in high oxidation states, yields improved results relative to calculations including only scalar-relativistic corrections. The An +m /An(0) redox potentials were calculated using a Born-Haber cycle incorporating sublimation, ionization, and hydration energies. Due to a lack of experimental data, three sets of ionization energies were used for the Born-Haber cycle. The calculated An(III/0) potentials showed better agreement with experimental data when using the COSMO solvation model and the test set comprising the NIST recommended ionization energies. Furthermore, the Md(II/0) potential was better described with the SMD model, whereas No(II/0) was not well described by all methods. Finally, the computational approach was able to predict redox potentials that for most cases agreed with the current available experimental or estimated data.

Actinides↗
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 OSTI2024

Intermolecular Proton Transfer Enabled Reactive CO 2 Capture by the Malononitrile Anion

Task-specific ionic liquids (ILs) employing carbanions represent a new class of ILs for carbon capture. The deprotonated malononitrile carbanion, [CH(CN) 2 ] - , has shown close to equimolar capacity for reactive CO 2 capture. Although the formation of the [C(CN) 2 COOH] - carboxylic acid was found to be the final product, how the hydrogen atom on the [CH(CN) 2 ] - carbanion transfers to the carboxylate group as a proton has not been fully understood. In this work, we employ density functional theory calculations with an implicit solvation model to investigate the proton transfer mechanisms in forming carboxylic acid from the reaction of the [CH(CN) 2 ] - carbanion with CO 2 . We find that the intramolecular proton-transfer pathway in [CH(CN) 2 COO] - to form [C(CN) 2 COOH] - is unlikely due to the high energy barrier of 152 kJ/mol. Instead, the intermolecular proton transfer pathway between two [CH(CN) 2 COO] - anions is more feasible to form two molecules of [C(CN) 2 COOH] - , with a significantly lower activation energy of 50 kJ/mol. Moreover, the [C(CN) 2 COOH] - dimer is further stabilized by the intermolecular hydrogen bonds of the two –COOH groups in the Z-configuration of the π-conjugated planar geometry. This insight of reactive CO 2 capture enabled by intermolecular proton transfer will be useful in designing novel carbanions and ILs for carbon capture and conversion.

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

Synergic Effects of Surface Chemistry and Applied Potentials on the Kinetics of the Electrocatalytic Oxygen Evolution Reaction in IrO 2

Improving the efficacy of the oxygen evolution reaction (OER) through water oxidation is critical for advancing photoelectrochemical water splitting. Among the catalysts, IrO 2 exhibits a high OER catalytic activity and stability under acidic conditions. The OER mechanism in this system has been a topic of intense research; however, many mechanistic understandings are lacking. In this work, we carried out first-principles calculations with an implicit solvation model at a constant potential to study the OER behavior on the IrO 2 (110) surface. We find that the surface hydrogen coverage has a significant effect on OER kinetics and transition states. We then develop a microkinetics model that accounts for the continuous evolution of both OER activation energy and hydrogen coverage as a function of an applied potential. We show that this inclusion leads to significant improvement in the simulated Tafel plot compared to available experiments. In conclusion, our results point to a complex interplay between surface chemistry and the applied potential on OER kinetics.

08 HYDROGEN↗
DOE OSTI2021

The role of complementary shape in protein dimerization

Shape guides colloidal nanoparticles to form complex assemblies, but its role in defining interfaces in biomolecular complexes is less clear. In this work, we isolate the role of shape in protein complexes by studying the reversible binding processes of 46 protein dimer pairs, and investigate when entropic effects from shape complementarity alone are sufficient to predict the native protein binding interface. We employ depletants using a generic, implicit depletion model to amplify the magnitude of the entropic forces arising from lock-and-key binding and isolate the effect of shape complementarity in protein dimerization. For 13% of the complexes studied here, protein shape is sufficient to predict native complexes as equilibrium assemblies. We elucidate the results by analyzing the importance of competing binding configurations and how it affects the assembly. Furthermore, a machine learning classifier, with a precision of 89.14% and a recall of 77.11%, is able to identify the cases where shape alone predicts the native protein interface.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Membrane-mediated dimerization of spherocylindrical nanoparticles

Here we present a numerical investigation of the modes of adhesion and endocytosis of two spherocylindrical nanoparticles (SCNPs) on planar and tensionless lipid membranes, using systematic molecular dynamics simulations of an implicit-solvent model, with varying values of the SCNPs' adhesion strength and dimensions. We found that at weak values of the adhesion energy per unit of area, ξ, the SCNPs are monomeric and adhere to the membrane in the parallel mode. As ξ is slightly increased, the SCNPs dimerize into wedged dimers, with an obtuse angle between their major axes that decreases with increasing ξ. However, as ξ is further increased, we found that the final adhesion state of the two SCNPs is strongly affected by the initial distance, d 0 , between their centers of mass, upon their adhesion. Namely, the SCNPs dimerize into wedged dimers, with an acute angle between their major axes, if d 0 is relatively small. However, for relatively high d 0 , they adhere individually to the membrane in the monomeric normal mode. For even higher values of ξ and small values of d 0 , the SCNPs cluster into tubular dimers. However, they remain monomeric if d 0 is high. Finally, the SCNPs endocytose either as a tubular dimer, if d 0 is low or as monomers for large d 0 , with the onset value of ξ of dimeric endocytosis being lower than that of monomeric endocytosis. Dimeric endocytosis requires that the SCNPs adhere simultaneously at nearby locations.

36 MATERIALS SCIENCE↗