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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Determining the Overpotential of Electrochemical Fuel Synthesis Mediated by Molecular Catalysts: Recommended Practices, Standard Reduction Potentials, and Challenges

Molecular catalysts capable of performing electrochemical transformations are frequently utilized in the synthesis of fuels. A common benchmark for evaluating catalysts for electrochemical reactions is overpotential (η) and minimizing η remains an active goal in catalysis. This Review details approaches for the determination of thermodynamic potentials for common fuel-forming reactions and for the determination of electrochemical overpotential, and underscores the need to employ methods that enable meaningful comparisons between molecular catalysts. Strategies for minimizing overpotential while maintaining high activity are highlighted.

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

Kinetic Monte Carlo Framework for Coupled Degradation and Dehydration of Anion Exchange Membranes

Kinetic Monte Carlo (kMC) simulations, augmented with temporal-acceleration schemes, can efficiently handle stiff reaction-transport networks when fast processes rapidly relax to quasi-equilibrium on a fixed lattice. However, in glassy anion-exchange membranes (AEM), rare and irreversible chemical degradation events continuously reshape the nanoscale morphology, and the associated hydration and transport degrees of freedom remain far from a well-defined local equilibrium. This combination of evolving state space and nonequilibrated fast dynamics lies outside the scope of existing kMC acceleration frameworks. Here, to address this challenge, we introduce an auxiliary-particle kinetic Monte Carlo (AP-kMC) scheme. In AP-kMC, short-lived mobile particles spawned at degradation sites execute hop, water-elimination, and decay moves, enforcing rapid local relaxation of the hydration structure while preserving the stochastic rules of kMC. Parameterized with molecular-dynamics morphologies and experimental solution degradation kinetics, AP-kMC reproduces the evolution of ion-exchange capacity, water uptake, and conductivity, and reveals a feedback loop in which poorly hydrated sites degrade first and each degradation event induces further local dehydration. The resulting thinning and fragmentation of water channels cause loss of hydrophilic percolation and abrupt conductivity collapse well before complete charge loss. AP-kMC thus reframes AEM durability as a coupled degradation–drying–percolation problem and provides a transferable strategy to simulate reactive, out-of-equilibrium polymer electrolytes where local solvation controls reactivity.

organic↗
DOE OSTI2024

Thermal Shape Stability of fcc Metal Nanocrystals Synthesized with Faceted Nonequilibrium Shapes

Highly refined capabilities of the shape-controlled solution-phase synthesis of metal nanocrystals (NCs) allow the generation of NCs with faceted nonequilibrium shapes, which optimize properties for target applications such as catalysis and plasmonics. Often, for such applications and also for TEM analysis, the NCs are removed from the solution-phase environment. We explore the postsynthesis evolution of these metastable NCs in a high-vacuum TEM environment. Specifically, here we analyze their reshaping toward the equilibrium Wulff shapes mediated by surface diffusion, where such reshaping degrades the above-mentioned optimized properties. Typical sizes for these NCs range from 5 to 30 nm or 10 3 –10 6 atoms, and reshaping often occurs on the time scale of minutes for temperatures around, say, 400 °C. We discuss the development of predictive stochastic atomistic-level models for NC evolution with a realistic description of surface diffusion. These models, in contrast to Molecular Dynamics, can naturally address the relevant time and length scales for these systems. KMC simulation results for the stochastic models are described, focusing on the reshaping of slightly elongated nanorods and of mildly truncated octahedra and nanocubes. In addition, we review appropriate theoretical formulations for reshaping, which involves the nucleation and growth on 2D islands or layers on outer facets of the NC. We note the limitations of classical nucleation theory in some scenarios and demonstrate the successes of a more fundamental and general master equation-based analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Nontrivial nanostructure, stress relaxation mechanisms, and crystallography for pressure-induced Si-I → Si-II phase transformation

Crystallographic theory based on energy minimization suggests austenite-twinned martensite interfaces with specific orientation, which are confirmed experimentally for various materials. Pressure-induced phase transformation (PT) from semiconducting Si-I to metallic Si-II, due to very large and anisotropic transformation strain, may challenge this theory. Here, unexpected nanostructure evolution during Si-I → Si-II PT is revealed by combining molecular dynamics (MD), crystallographic theory, generalized for strained crystals, and in situ real-time Laue X-ray diffraction (XRD). Twinned Si-II, consisting of two martensitic variants, and unexpected nanobands, consisting of alternating strongly deformed and rotated residual Si-I and third variant of Si-II, form {111} interface with Si-I and produce almost self-accommodated nanostructure despite the large transformation volumetric strain of -0.237. The interfacial bands arrest the {111} interfaces, leading to repeating nucleation-growth-arrest process and to growth by propagating {110} interface, which (as well as {111} interface) do not appear in traditional crystallographic theory.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Sub-100-fs energy transfer in coenzyme NADH is a coherent process assisted by a charge-transfer state

Excitation energy transfer (EET) is a key photoinduced process in biological chromophoric assemblies. Here we investigate the factors which can drive EET into efficient ultrafast sub-ps regimes. We demonstrate how a coherent transport of electronic population could facilitate this in water solvated NADH coenzyme and uncover the role of an intermediate dark charge-transfer state. High temporal resolution ultrafast optical spectroscopy gives a 54 ± 11 fs time constant for the EET process. Nonadiabatic quantum dynamical simulations computed through the time-evolution of multidimensional wavepackets suggest that the population transfer is mediated by photoexcited molecular vibrations due to strong coupling between the electronic states. The polar aqueous solvent environment leads to the active participation of a dark charge transfer state, accelerating the vibronically coherent EET process in favorably stacked conformers and solvent cavities. Our work demonstrates how the interplay of structural and environmental factors leads to diverse pathways for the EET process in flexible heterodimers and provides general insights relevant for coherent EET processes in stacked multichromophoric aggregates like DNA strands.

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

Dynamic strength of iron under pressure-temperature conditions of Earth’s inner core

Iron (Fe) is a primary constituent of terrestrial planetary cores, yet its rheological properties under extreme conditions remain uncertain. Here we present direct measurements of Fe strength at 310-430 GPa pressures and 3700-5800 K temperatures, obtained using Rayleigh-Taylor (RT) instability experiments at the National Ignition Facility. Single-crystal α-Fe samples with [001] and [111] orientations are shock-ramp compressed past the α-ε transition along paths approaching Earth’s inner core conditions. We find that ε-Fe derived from [001] α-Fe is consistently stronger (11-20 GPa) than that from [111] α-Fe (8-18 GPa), contrary to the trend at ambient conditions. Large-scale molecular dynamics simulations reproduce this atypical strength anisotropy and attribute it to microstructural evolution during the phase transition and subsequent ε-phase plasticity. Ripple growth analysis further constrains viscosities of 100-170 Pa·s under the driven conditions. Our results provide experimental benchmarks for Fe rheology at inner-core conditions, with implications for seismic anisotropy and the geodynamo.

Condensed-matter physics↗
DOE OSTI2024

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study

There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994–2018) and four hyperendemic Lake Victoria fishing communities (2011–2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index, and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population subgroups, including by migration status. 9931 HIV sequences were available from 4999 PLHIV, including 3060 and 1939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (P < .001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (P < .001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population subgroups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Discovery of multimechanisms of screw dislocation interaction in bcc iron from open-ended saddle point searches

Dislocation motion and interactions determine mechanical properties in body-centered cubic (bcc) metallic materials. However, studying mechanisms for the screw dislocation interaction is fundamentally challenging since many underlying processes involve mesotimescales and atomistic resolution, currently inaccessible by either experimental techniques or continuum theoretical methods. Here, in this paper, we develop a computational capability based on self-evolving atomistic kinetic Monte Carlo (SEAKMC) to sample the critical events and saddle point energies related to screw dislocations and their junctions. The method is first validated by calculating the stress dependence of Peierls barriers and formation energies of kink pairs and cross-slip kink pairs on a single screw dislocation in bcc iron. Then the method is applied to a binary junction of a pair of intersecting screw dislocations, the structure of which is crucial for low-temperature plastic deformation. We identify three important mechanisms: coplanar cross-slipping, jog-pinning, and a previously unknown unzipping mechanism during the evolution of the binary junction. The mechanisms are then further validated using classical molecular dynamics simulations. The computational capability developed in this paper provides an effective tool to evaluate screw dislocation related thermally activated events in complex stress conditions. The mechanisms discovered in this paper provide critical insights into temperature dependence of the anomalous slip, a breakdown of the Schmidt law, during the plastic deformation in bcc iron and can be generalized to other bcc metals.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Recent progress in atomic-scale controlled plasma processing

Atomic-scale control in plasma processing is becoming increasingly critical for fabricating of advanced semiconductor devices, particularly as the industry shifts toward three-dimensional (3D) architectures and high-aspect-ratio (HAR) structures. This review presents a comprehensive overview of recent developments in atomic-scale controlled plasma processes, organized along two key directions: the hierarchical structure of plasma–surface interactions and the generational evolution of atomic layer processing (ALP) technologies. We examined the gas phase, where molecular design enables selective generation of ions and radicals; the boundary layer, where transport phenomena govern species delivery into nanoscale features, and the surface, where temperature-dependent reactions and cyclic processing determine etching selectivity and precision. Building on this foundation, we outline five generations of ALP—from thermal atomic layer deposition to transport-aware, temporally and structurally decoupled processes—highlighting the increasing sophistication of process control. The review further explores the transition from empirical recipe development to science-based, data-driven methodologies. By integrating quantum-chemical modeling, advanced diagnostics, and machine learning, we demonstrated how predictive models can link plasma species composition to process outcomes, enabling autonomous and adaptive control strategies. Finally, this review discusses the broader societal implications of plasma process innovation through the E4 quartet: energy and resource efficiency, environmental sustainability, evolutionary advancement, and educational promotion. These principles guide the development of sustainable and intelligent atomic-scale manufacturing technologies that are not only technically advanced but also socially responsible.

Ishikawa, Kenji [Nagoya Univ. (Japan)] (ORCID:0000↗
DOE OSTI2021

Understanding the plasticity contributions during laser-shock loading and spall failure of Cu microstructures at the atomic scales

A hybrid atomic-scale and continuum modeling framework is used to study the microstructural evolution during the laser-induced shock deformation and failure (spallation) of copper microstructures. A continuum two-temperature model (TTM) is used to account for the interaction of Cu atoms with a laser in molecular dynamics (MD) simulations. The MD-TTM simulations study the effect of laser loading conditions (laser fluence) on the microstructure (defects) evolution during various stages of shock wave propagation, reflection, and interaction in single-crystal (sc) Cu systems. In addition, the role of the microstructure is investigated by comparing the defect evolution and spall response of sc-Cu and nanocrystalline (nc) Cu systems. The defect (stacking faults and twin faults) evolution behavior in the metal at various times is further characterized using virtual in situ selected area electron diffraction and x-ray diffraction during various stages of evolution of microstructure. Here, the simulations elucidate the uncertain relation between spall strength and strain-rate and the much stronger relation between the spall strength and the temperatures generated due to laser shock loading for the small Cu sample dimensions considered here.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Insight into SEI Growth in Li-Ion Batteries using Molecular Dynamics and Accelerated Chemical Reactions

The performance of lithium-ion batteries (LIB) using organic electrolytes strongly depends on the formation of a stable solid electrolyte interphase (SEI) film. Elucidating the dynamic evolution and spatial composition of the SEI can be very useful to study the stability of SEI components and help optimize the formation cycles of LIB. We propose a classical molecular dynamics simulation protocol for predicting the first stages of SEI formation using a reaction method involving the decomposition of EC and LiPF 6 molecules in the electrolyte. We accelerate the formation of SEI components near the anode surface by increasing the probability of reactions, implemented through a geometry matching scheme, followed by a force-field reconfiguration. We observe the formation of gases (C 2 H 4 ), inorganic (Li 2 CO 3 and LiF) and organic (LEDC) components. Finally, this protocol shows promise to be able to evaluate the effects of varying electrolyte compositions and additives on SEI layer structure and composition.

25 ENERGY STORAGE↗
DOE OSTI2024

Methyl Termination of p-Type Silicon Enables Selective Photoelectrochemical CO 2 Reduction by a Molecular Ruthenium Catalyst

Methyl-terminated p-type silicon photoelectrodes selectively drive CO 2 reduction by a homogeneous [Ru(tpy)(Mebim-py)(NCCH 3 )] 2+ catalyst (tpy = 2,2′:6′,2″-terpyridine, Mebim-py = 1-methylbenzimidazol-2-ylidene-3-(2′-pyridine)). A 460 mV photovoltage is quantified for the photoelectrode. Under 1 sun illumination, this system achieves a Faradaic efficiency of 87% for CO at −1.7 V vs Fc +/0 , matching reports of the same catalyst at metallic electrodes operating at −2.1 V. When 5% water is introduced, the CH 3 -terminated Si photoelectrode remains stable, selectivity for CO is retained, and current density increases. Methyl termination suppresses the competitive hydrogen evolution observed for H-terminated Si photoelectrodes, which under the same conditions produce ca. 60% CO and 8% H 2 and have unstable performance. Furthermore, these results establish that a semiconductor photoelectrode can power a molecular CO 2 reduction catalyst without hydrogen evolution by the photoelectrode itself. Methyl termination of p-Si allows CO 2 reduction to kinetically outcompete proton reduction, revealing an important design principle for selective fuel formation.

Catalysts↗
DOE OSTI2023

Imaging Field–Driven Melting of a Molecular Solid at the Atomic Scale

Solid–liquid phase transitions are basic physical processes, but atomically resolved microscopy has yet to capture their full dynamics. A new technique is developed for controlling the melting and freezing of self–assembled molecular structures on a graphene field–effect transistor (FET) that allows phase–transition behavior to be imaged using atomically resolved scanning tunneling microscopy. This is achieved by applying electric fields to 2,3,5,6–tetrafluoro–7,7,8,8–tetracyanoquinodimethane–decorated FETs to induce reversible transitions between molecular solid and liquid phases at the FET surface. Nonequilibrium melting dynamics are visualized by rapidly heating the graphene substrate with an electrical current and imaging the resulting evolution toward new 2D equilibrium states. An analytical model is developed that explains observed mixed–state phases based on spectroscopic measurement of solid and liquid molecular energy levels. The observed nonequilibrium melting dynamics are consistent with Monte Carlo simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Substitution Models of Protein Evolution with Selection on Enzymatic Activity

Abstract Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme–substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.

Ferreiro, David↗
DOE OSTI2022

Cost-effective carbon fiber precursor selections of polyacrylonitrile-derived blend polymers: carbonization chemistry and structural characterizations

Blending polyacrylonitrile (PAN) with plastic wastes and bio-based polymers provides a convenient and inexpensive method to realize cost-effective carbon fiber (CF) precursors. In this work, PAN-based blend precursors are investigated using ReaxFF reactive molecular dynamics simulations with respect to the formation of all-carbon rings, the evolutions of oxygen-containing and nitrogen-containing species, and the migration of carbon atoms to form turbostratic graphene. From these simulations, we identify that PAN/cellulose (CL) blend manifests the highest carbon yield and the most substantial all-carbon ring formation. This ReaxFF-based finding is confirmed by Raman and TEM experiments indicating high crystallinity for PAN/CL-derived blend CFs. We trace the pathway of gasification and carbonization of PAN/CL to elaborate the mechanism of the formation of all-carbon ring networks. We discover that the acetals of CL can catalyze the cyclization of the blend precursor, allowing for the search for CL derivatives or the other kinds of bio-based polymers with similar functionalities as alternative blends. In addition, we examine the structural characteristics using the carbon–carbon (C–C) radial distribution functions, C–C bond length distributions, and sp2 C atom ratios for the four representative precursors, i.e., PAN, oxidized PAN, PAN/nylon 6,6, and PAN/CL. Our simulation results show the most extensive all-carbon ring cluster and graphitic structure growths for PAN/CL. Here, we propose PAN/CL as a cost-effective alternative CF precursor, since (a) CL is naturally abundant and eco-friendly for production, (b) the blend precursor PAN/CL does not require oxidation treatment, (c) PAN/CL has a high carbon yield with substantial all-carbon ring formation, and (d) PAN/CL based CFs potentially provide a mechanical property enhancement.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Vibrational exciton nanoimaging of phases and domains in porphyrin nanocrystals

Much of the electronic transport, photophysical, or biological functions of molecular materials emerge from intermolecular interactions and associated nanoscale structure and morphology. However, competing phases, defects, and disorder give rise to confinement and many-body localization of the associated wavefunction, disturbing the performance of the material. Here, we employ vibrational excitons as a sensitive local probe of intermolecular coupling in hyperspectral infrared scattering scanning near-field optical microscopy (IR s-SNOM) with complementary small-angle X-ray scattering to map multiscale structure from molecular coupling to long-range order. In the model organic electronic material octaethyl porphyrin ruthenium(II) carbonyl (RuOEP), we observe the evolution of competing ordered and disordered phases, in nucleation, growth, and ripening of porphyrin nanocrystals. From measurement of vibrational exciton delocalization, we identify coexistence of ordered and disordered phases in RuOEP that extend down to the molecular scale. Even when reaching a high degree of macroscopic crystallinity, identify significant local disorder with correlation lengths of only a few nanometers. This minimally invasive approach of vibrational exciton nanospectroscopy and -imaging is generally applicable to provide the molecular-level insight into photoresponse and energy transport in organic photovoltaics, electronics, or proteins.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Evolution of p -coumaroylated lignin in eudicots provides new tools for cell wall engineering

Ester-linked p-coumarate (pCA) is a hallmark feature of the secondary cell walls in commelinid monocot plants. It has been shown that pCA groups arise during lignin polymerisation from the participation of monolignol conjugates assembled by p-coumaroyl-CoA:monolignol transferase (PMT) enzymes, members of the BAHD superfamily of acyltransferases. Herein we report that a eudicot species, kenaf (Hibiscus cannabinus), naturally contains p-coumaroylated lignin in the core tissues of the stems but not in the bast fibres. Moreover, we identified a novel acyltransferase, HcPMT, that shares less than 30% amino acid identity with known monocot PMT sequences. Recombinant HcPMT showed a preference in enzyme assays for p-coumaroyl-CoA and benzoyl-CoA as acyl donor substrates, and sinapyl alcohol as an acyl acceptor. Heterologous expression of HcPMT in hybrid poplar trees led to the incorporation of pCA in lignin but no improvement in the saccharification potential of the wood. This work illustrates the value in mining diverse plant taxa for new monolignol acyltransferases. Furthermore, the occurrence of pCA outside of monocot lineages may represent another example of convergent evolution in lignin structure. Furthermore, this discovery expands textbook views on cell wall biochemistry and provides a new molecular tool for engineering the lignin of biomass feedstock plants.

59 BASIC BIOLOGICAL SCIENCES↗