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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade, along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature define a high-risk disease subset, where UCHL1 expression displays prognostic value. Single-nuclei RNA sequencing of the adverse sarcomatoid and rhabdoid phenotypes uncover gene signatures and potential insights into tumor evolution. In vitro cell line studies confirm the potential of inhibiting identified phosphoproteome targets. This study molecularly stratifies aggressive histopathologic subtypes that may inform more effective treatment strategies.

CPTAC↗
DOE OSTI2024

Simulations of classical three-body thermalization in one dimension

One-dimensional systems, such as nanowires or electrons moving along strong magnetic field lines, have peculiar thermalization physics. The binary collision of pointlike particles, typically the dominant process for reaching thermal equilibrium in higher-dimensional systems, cannot thermalize a 1D system. We study how dilute classical 1D gases thermalize through three-body collisions. We consider a system of identical classical point particles with pairwise repulsive inverse power-law potential V ij ∝ 1/|x i –x j | n or the pairwise Lennard-Jones potential. Using Monte Carlo methods, we compute a collision kernel and use it in the Boltzmann equation to evolve a perturbed thermal state with temperature T toward equilibrium. We explain the shape of the kernel and its dependence on the system parameters. Additionally, we implement molecular dynamics simulations of a many-body gas and show agreement with the Boltzmann evolution in the low-density limit. For the inverse power-law potential, the rate of thermalization is proportional to ρ 2 ⁢T$\frac{1}{2}$ – $\frac{1}{n}$, where ρ is the number density. Furthermore, the corresponding proportionality constant decreases with increasing n.

1-dimensional systems↗
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↗
NASA NTRS1991

Report on carbon and nitrogen abundance studies

The aim of the proposal was to determine the nitrogen to carbon abundance ratios from transition layer lines in stars with different T(sub eff) and luminosities. The equations which give the surface emission line fluxes and the measured ratio of the NV to CIV emission line fluxes are presented and explained. The abundance results are compared with those of photospheric abundance studies for stars in common with the photospheric investigations. The results show that the analyses are at least as accurate as the photospheric determinations. These studies can be extended to F and early G stars for which photospheric abundance determinations for giants are hard to do because molecular bands become too weak. The abundance determination in the context of stellar evolution is addressed. The N/C abundance ratio increases steeply at the point of evolution for which the convection zone reaches deepest. Looking at the evolution of the rotation velocities v sin i, a steep decrease in v sin i is related to the increasing depth of the convection zone. It is concluded that the decrease in v sin i for T(sub eff) less than or approximately = 5800 K is most probably due to the rearrangement of the angular momentum in the stars due to deep convective mixing. It appears that the convection zone is rotating with nearly depth independent angular momentum. Other research results and ongoing projects are discussed.

Boehm-Vitense, Erika↗
NASA NTRS1992

Chemistry in circumstellar disks - CS toward HL Tauri

High spatial and spectral resolution dust continuum and CS line-emission maps of the material immediately surrounding HL Tauri are presented. The 3.06-thermal dust map gives an upper limit to the source size of roughly 200 AU. When combined with previous millimeter continuum measurements, a beta value of 1.2 +/-0.3 is derived along with a disk mass of 0.1 solar mass, in agreement with previous disk radiative transfer models of the IR and submillimeter flux from HL Tau. The low dust emissivity index as compared to particles in the diffuse ISM is best explained by grain growth or composition evolution. The present observations of the CS and CO emission lines forming the molecular cloud surrounding HL Tauri are consistent with the 'canonical' temperatures, densities, and abundances derived in other Taurus cloud cores. In contrast, the CS emission in aperture synthesis maps at 650-AU spatial resolution is most consistent with CS/CO ratios at least 25-50 times lower in the gas immediately surrounding HL Tauri if the CS emission is optically thin. The continuum and spectral line results obtained are strong indicators of conditions thought to be similar to those in the presolar nebula some 4.5 AE ago.

Blake, Geoffrey A.↗
NASA NTRS1991

Nature and history of the organic compounds in comets - An astrophysical view

The chemical similarities between comets, carbonaceous chondrites, and interstellar molecules and grains are reviewed first. The evolution of frosty interstellar grains is then followed during the collapse of a molecular cloud fragment and the subsequent formation of the Solar System. The paradigm clarifies the probable origin of the two populations of comets of different symmetry (the Oort Cloud and the Kuiper Belt) and implies an exogenous origin for all carbon and water on earth. This origin is explained by the orbital diffusion of planetesimals that is required by the growth of protoplanets.

Delsemme, A. H.↗
NASA NTRS1999

Ceruloplasmin ferroxidase activity stimulates cellular iron uptake by a trivalent cation-specific transport mechanism

The balance required to maintain appropriate cellular and tissue iron levels has led to the evolution of multiple mechanisms to precisely regulate iron uptake from transferrin and low molecular weight iron chelates. A role for ceruloplasmin (Cp) in vertebrate iron metabolism is suggested by its potent ferroxidase activity catalyzing conversion of Fe2+ to Fe3+, by identification of yeast copper oxidases homologous to Cp that facilitate high affinity iron uptake, and by studies of "aceruloplasminemic" patients who have extensive iron deposits in multiple tissues. We have recently shown that Cp increases iron uptake by cultured HepG2 cells. In this report, we investigated the mechanism by which Cp stimulates cellular iron uptake. Cp stimulated the rate of non-transferrin 55Fe uptake by iron-deficient K562 cells by 2-3-fold, using a transferrin receptor-independent pathway. Induction of Cp-stimulated iron uptake by iron deficiency was blocked by actinomycin D and cycloheximide, consistent with a transcriptionally induced or regulated transporter. Cp-stimulated iron uptake was completely blocked by unlabeled Fe3+ and by other trivalent cations including Al3+, Ga3+, and Cr3+, but not by divalent cations. These results indicate that Cp utilizes a trivalent cation-specific transporter. Cp ferroxidase activity was required for iron uptake as shown by the ineffectiveness of two ferroxidase-deficient Cp preparations, copper-deficient Cp and thiomolybdate-treated Cp. We propose a model in which iron reduction and subsequent re-oxidation by Cp are essential for an iron uptake pathway with high ion specificity.

NASA Discipline Regulatory Physiology↗
NASA NTRS2022

Molecular information theory meets protein folding

We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone configurational entropy, secondary structure content, residue burial layers, and mutational studies of protein stability changes. We found that the average information contained in the sequences of evolved proteins is very close to the average information needed to specify a fold ~2.2 ± 0.3 bits/(site operation). The effective alphabet size in evolved proteins equals the effective number of conformations of a residue in the compact unfolded state at around 5. We calculated an energy-to-information conversion efficiency upon folding of around 50%, lower than the theoretical limit of 70%, but much higher than human built macroscopic machines. We propose a simple mapping between molecular information theory and energy landscape theory and explore the connections between sequence evolution, configurational entropy and the energetics of protein folding.

Ignacio E. Sánchez↗
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↗