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At least 703 records · Page 39

Active Learning A Neural Network Model For Gold Clusters & Bulk From Sparse First Principles Training Data

Small metal clusters are of fundamental scientific interest and of tremendous significance in catalysis. These nanoscale clusters display diverse geometries and structural motifs depending on the cluster size; a knowledge of this size-dependent structural motifs and their dynamical evolution has been of longstanding interest. Given the high computational cost of first-principles calculations, molecular modeling and atomistic simulations such as molecular dynamics (MD) has proven to be an important complementary tool to aid this understanding. Classical MD typically employ predefined functional forms which limits their ability to capture such complex size-dependent structural and dynamical transformation. Neural Network (NN) based potentials represent flexible alternatives and in principle, well-trained NN potentials can provide high level of flexibility, transferability and accuracy on-par with the reference model used for training. A major challenge, however, is that NN models are interpolative and requires large quantities (similar to 10 4 or greater) of training data to ensure that the model adequately samples the energy landscape both near and far-from-equilibrium. A highly desirable goal is minimize the number of training data, especially if the underlying reference model is first-principles based and hence expensive. In this work, we introduce an active learning (AL) scheme that trains a NN model on-the-fly with minimal amount of first-principles based training data. Our AL workflow is initiated with a sparse training dataset (similar to 1 to 5 data points) and is updated on-the-fly via a Nested Ensemble Monte Carlo scheme that iteratively queries the energy landscape in regions of failure and updates the training pool to improve the network performance. Using a representative system of gold clusters, we demonstrate that our AL workflow can train a NN with similar to 500 total reference calculations. Using an extensive DFT test set of similar to 1100 configurations, we show that our AL-NN is able to accurately predict both the DFT energies and the forces for clusters of a myriad of different sizes. Our NN predictions are within 30 meV/atom and 40 meV/angstrom of the reference DFT calculations. Moreover, our AL-NN model also adequately captures the various size-dependent structural and dynamical properties of gold clusters in excellent agreement with DFT calculations and available experiments. We finally show that our AL-NN model also captures bulk properties reasonably well, even though they were not included in the training data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phase evolution in two-phase alloys during severe plastic deformation

Herein, phase evolution in FCC metals with strongly interacting alloy components during severe plastic deformation is investigated using molecular dynamics simulations. Specifically, we study the alloy microstructure in steady state, nucleation and growth of precipitates in supersaturated alloys, and the decomposition of precipitates in undersaturated alloys. The results are compared to a modified effective temperature model, providing a physical understanding for the atomic processes underlying the model and a perspective on its strengths and weaknesses. Key observations in this work are nucleation and growth of precipitates during SPD at a temperature of 100 K; Gibbs-Thomson-like behavior relating solubility to precipitate size under steady-state shearing; a direct relationship between the effective temperature and the shear modulus; and the importance of cluster agglomeration during precipitate growth. The study also reveals that the mechanisms of forced chemical mixing depends on precipitate size, adding complications for effective temperature models describing inhomogeneous systems. The simulations are shown to provide good semiquantitative agreement with experimental findings reported in the literature.

36 MATERIALS SCIENCE↗

Experimental and theoretical investigation of the crystalline surface, film, and interface properties of antiperovskite Mn 3 GaN grown by molecular beam epitaxy on MgO(001)

Here, we present a study of the epitaxial growth, characterization, and theoretical modeling of thin film antiperovskite Mn 3 GaN, an antiferromagnetic material with kagome structure which is grown on MgO (001) substrates using N-plasma-assisted molecular beam epitaxy. Reflection high energy electron diffraction is used to assess the in-plane evolution of the film structure during growth, and the surface is investigated in-situ using scanning tunneling microscopy and Auger electron spectroscopy. These results are combined with precision measurements done ex-situ determining the film lattice constants using a combination of x-ray diffraction with reciprocal space mapping and scanning transmission electron microscopy. Overall, a uniform, homogeneous film with an atomically smooth vacuum surface and atomically sharp substrate interface is found having very small in-plane tensile strain and mild out-of-plane compressive strain. First-principles theoretical calculations are applied in order to ascertain the lowest energy models for both the Mn 3 GaN surface and the Mn 3 GaN/MgO film/substrate interface. Models including MnGa versus MnN surface layers and MnGa versus MnN interfacial layers are considered as functions of both the Mn and Ga chemical potentials. The predictions are discussed in comparison to the experimental results. The overall findings suggest that Mn 3 GaN on MgO(001) is a viable epitaxial film which can be further explored in connection with antiferromagnetic spintronics.

Density functional theory↗

Protocol for engineering poly(ethylene terephthalate) hydrolases via directed evolution using a high-throughput screening assay

Poly(ethylene terephthalate) (PET) hydrolases, which depolymerize PET to its monomers, have gained attention for their potential to facilitate bio-industrial recycling of this waste plastic. Here, we present a protocol for screening large, random mutagenesis enzyme libraries simultaneously for enhanced activity, solubility, and stability. We outline steps for library construction, screening using plate-based split GFP and model substrate assays, and determination of enzyme thermostability. We then detail procedures for validation assays on PET substrates and characterization of final variants.

59 BASIC BIOLOGICAL SCIENCES↗

Miscibility of rock and ice in the interiors of water worlds

Abstract Super-Earths and sub-Neptunes are the most common planet types in our galaxy. A subset of these planets is predicted to be water worlds, bodies that are rich in water and poor in hydrogen gas. The interior structures of water worlds have been assumed to consist of water surrounding a rocky mantle and iron core. In small planets, water and rock form distinct layers with limited incorporation of water into silicate phases, but these materials may interact differently during the growth and evolution of water worlds due to greater interior pressures and temperatures. Here, we use density functional molecular dynamics (DFT-MD) simulations to study the miscibility and interactions of enstatite (MgSiO 3 ), a major end-member silicate phase, and water (H 2 O) at extreme conditions in water world interiors. We explore pressures ranging from 30 to 120 GPa and temperatures from 500 to 8000 K. Our results demonstrate that enstatite and water are miscible in all proportions if the temperature exceeds the melting point of MgSiO 3 . Furthermore, we performed smoothed particle hydrodynamics simulations to demonstrate that the conditions necessary for rock-water miscibility are reached during giant impacts between water-rich bodies of 0.7–4.7 Earth masses. Our simulations lead to water worlds that include a mixed layer of rock and water.

79 ASTRONOMY AND ASTROPHYSICS↗

Investigating shock-induced chemical reactions in Ni+Al multilayers: A continuum-based mesoscale approach with Arrhenius kinetics and artificial thermal conduction

A new continuum-based mesoscale modeling approach for shock-induced chemical reactions (SICRs) in Ni+Al multilayers is demonstrated in Sandia’s shock physics hydrocode, CTH. The approach utilizes Arrhenius-type kinetics and artificial thermal conduction. Our work builds upon previous efforts to parameterize equations of state for Ni x Al y [J. Appl. Phys. 137, 075102 (2025)], as well as simulations of inert shocks in realistic 2D microstructures [J. Appl. Phys. 137, 225301 (2025)]. To calibrate the reaction kinetics, pairs of the reaction coordinate, R′, vs time are extracted from the molecular dynamics (MD) literature. Here, the MD-informed kinetics are used to simulate the dynamic evolution of pressure and temperature in 2D mesoscale simulations. Overall, the MD-informed kinetics obtained for planar interfaces are too slow, as initial reaction is not observed on a nanosecond time scale. Even with quasi-periodic shock focusing leading to the formation of so-called “hot-spots,” the hot spots are unable to grow and coalesce using the fitted Arrhenius rate constants. However, by increasing the rate constants by two orders of magnitude, SICRs are observed at a shock pressure near 30 GPa, which is supported by experiments. Consequently, these mesoscale simulations suggest that unresolved shear-based mechanical mixing might possibly account for the discrepancies in kinetic rates, with shock-generated intense perturbations, interfacial vortical flows, and elevated temperatures serving as favorable reaction conditions. Future work will calibrate a shear-dependent reaction rate from the MD simulations with realistic interfaces that are wavy, diffuse, and disordered.

Kittell, David E. [Sandia National Laboratories (S↗

The structure of fly Teneurin-m reveals an asymmetric self-assembly that allows expansion into zippers

Teneurins are conserved cell adhesion molecules essential for embryogenesis and neural development in animals. Key to teneurin function is the ability of its extracellular region to form homophilic interactions in cis and/or in trans. However, our molecular understanding of teneurin homophilic interaction remains largely incomplete. Here, we showed that an extracellular fragment of Teneurin-m, the major teneurin homolog in flies, behaves as a homodimer in solution. The structure of Teneurin-m revealed that the transthyretin-related domain from one protomer and the β-propeller domain from the other mediates Teneurin-m self-association, which is abolished by point mutation of conserved residues. Strikingly, this architecture generates an asymmetric oligomerization interface that enables expansion of Teneurin-m into long zipper arrays reminiscent of protocadherins. An alternatively spliced site that exists only in vertebrates and regulates homophilic interaction in mammalian teneurins overlaps with the fly Teneurin-m self-association interface. Our work provides a molecular understanding of teneurin homophilic interaction and sheds light on its role in teneurin function throughout evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Detecting and measuring metabolic byproducts by electrochemical sensing

Method of detecting certain groups of bacteria is based on sensing buildup in molecular hydrogen. Apparatus is easy to assemble and use, and it has added advantage that hydrogen evolution by test micro-organisms can be measured automatically and accurately. System has been used to detect and enumerate variety of gram-negative bacteria of enterobacteriaceae group.

Wilkins, J. R.↗

The study of comets, part 1

Papers are presented dealing with observations of comets. Topic discussed include: photometry, polarimetry, and astrometry of comets; detection of water and molecular transitions in comets; ion motions in comet tails; determination of comet brightness and luminosity; and evolution of cometary orbits. Emphasis is placed on analysis of observations of comet Kohoutek.

Donn, B.↗

Organic chemical evolution

The course of organic chemical evolution preceding the emergence of life on earth is discussed based on evidence of processes occurring in interstellar space, the solar system and the primitive earth. Following a brief review of the equilibrium condensation model for the origin and evolution of the solar system, consideration is given to the nature and organic chemistry of interstellar clouds, comets, Jupiter, meteorites, Venus and Mars, and the prebiotic earth. Major issues to be resolved in the study of organic chemical evolution on earth are identified regarding condensation and accretion in the solar nebula, early geological evolution, the origin and evolution of the atmosphere, organic production rates, organic-inorganic interactions, environmental fluctuations, phase separation and molecular selectivity.

Chang, S.↗

Starbursts triggered by central overpressure in interacting galaxies

A triggering mechanism for the origin of enhanced, massive-star formation in the central regions of interacting spiral galaxy pairs is proposed. Our mechanism is based on the detailed evolution of a realistic interstellar medium in a galaxy following an encounter. As a disk giant molecular cloud (GMC) tumbles into the central region following a galaxy encounter, it undergoes a radiative shock compression via the pre-existing high pressure of the central intercloud medium. The shocked outer shell of a GMC becomes gravitationally unstable and begins to fragment thus resulting in a burst of star formation, when the growth time for the gravitational instabilities in the shell becomes smaller than the crossing time of the shock. The resulting values of typical infrared luminosity agree with observations.

Jog, Chanda J.↗

Equally parsimonious pathways through an RNA sequence space are not equally likely

An experimental system for determining the potential ability of sequences resembling 5S ribosomal RNA (rRNA) to perform as functional 5S rRNAs in vivo in the Escherichia coli cellular environment was devised previously. Presumably, the only 5S rRNA sequences that would have been fixed by ancestral populations are ones that were functionally valid, and hence the actual historical paths taken through RNA sequence space during 5S rRNA evolution would have most likely utilized valid sequences. Herein, we examine the potential validity of all sequence intermediates along alternative equally parsimonious trajectories through RNA sequence space which connect two pairs of sequences that had previously been shown to behave as valid 5S rRNAs in E. coli. The first trajectory requires a total of four changes. The 14 sequence intermediates provide 24 apparently equally parsimonious paths by which the transition could occur. The second trajectory involves three changes, six intermediate sequences, and six potentially equally parsimonious paths. In total, only eight of the 20 sequence intermediates were found to be clearly invalid. As a consequence of the position of these invalid intermediates in the sequence space, seven of the 30 possible paths consisted of exclusively valid sequences. In several cases, the apparent validity/invalidity of the intermediate sequences could not be anticipated on the basis of current knowledge of the 5S rRNA structure. This suggests that the interdependencies in RNA sequence space may be more complex than currently appreciated. If ancestral sequences predicted by parsimony are to be regarded as actual historical sequences, then the present results would suggest that they should also satisfy a validity requirement and that, in at least limited cases, this conjecture can be tested experimentally.

NASA Discipline Exobiology↗

Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae

Representatives of the family Methanosarcinaceae were analyzed phylogenetically by comparing partial sequences of their methyl-coenzyme M reductase (mcrI) genes. A 490-bp fragment from the A subunit of the gene was selected, amplified by the PCR, cloned, and sequenced for each of 25 strains belonging to the Methanosarcinaceae. The sequences obtained were aligned with the corresponding portions of five previously published sequences, and all of the sequences were compared to determine phylogenetic distances by Fitch distance matrix methods. We prepared analogous trees based on 16S rRNA sequences; these trees corresponded closely to the mcrI trees, although the mcrI sequences of pairs of organisms had 3.01 +/- 0.541 times more changes than the respective pairs of 16S rRNA sequences, suggesting that the mcrI fragment evolved about three times more rapidly than the 16S rRNA gene. The qualitative similarity of the mcrI and 16S rRNA trees suggests that transfer of genetic information between dissimilar organisms has not significantly affected these sequences, although we found inconsistencies between some mcrI distances that we measured and and previously published DNA reassociation data. It is unlikely that multiple mcrI isogenes were present in the organisms that we examined, because we found no major discrepancies in multiple determinations of mcrI sequences from the same organism. Our primers for the PCR also match analogous sites in the previously published mcrII sequences, but all of the sequences that we obtained from members of the Methanosarcinaceae were more closely related to mcrI sequences than to mcrII sequences, suggesting that members of the Methanosarcinaceae do not have distinct mcrII genes.

NASA Discipline Number 52-30↗

Molecular Gas in Young Debris Disks

Gas-rich primordial disks and tenuous gas-poor debris disks are usually considered as two distinct evolutionary phases of the circumstellar matter. Interestingly, the debris disk around the young main-sequence star 49 Ceti possesses a substantial amount of molecular gas and possibly represents the missing link between the two phases. Motivated to understand the evolution of the gas component in circumstellar disks via finding more 49 Ceti-like systems, we carried out a CO J = 3-2 survey with the Atacama Pathfinder EXperiment, targeting 20 infrared-luminous debris disks. These systems fill the gap between primordial and old tenuous debris disks in terms of fractional luminosity. Here we report on the discovery of a second 49 Ceti-like disk around the 30 Myr old A3-type star HD21997, a member of the Columba Association. This system was also detected in the CO(2-1) transition, and the reliable age determination makes it an even clearer example of an old gas-bearing disk than 49 Ceti. While the fractional luminosities of HD21997 and 49 Ceti are not particularly high, these objects seem to harbor the most extended disks within our sample. The double-peaked profiles of HD21997 were reproduced by a Keplerian disk model combined with the LIME radiative transfer code. Based on their similarities, 49 Ceti and HD21997 may be the first representatives of a so far undefined new class of relatively old > or approx.8 Myr), gaseous dust disks. From our results, neither primordia1 origin nor steady secondary production from icy planetesima1s can unequivocally explain the presence of CO gas in the disk ofHD21997.

Moor, A.↗

Eta Carinae & the Homunculus: Far Infrared Sub-millimeter Spectral Lines detected with the Herschel Space Observatory

The evolved massive binary star η Carinae underwent eruptive mass loss events that formed the complex bi-polar “Homunculus” nebula harboring tens of solar masses of unusually nitrogen-rich gas and dust. Despite expectations for the presence of a significant molecular component to the gas, detections have been observationally challenged by limited access to the far-infrared and the intense thermal continuum. A spectral survey of the atomic and rotational molecular transitions was carried out with theHerschel Space Observatory, revealing a rich spectrum of broad emission lines originating in the ejecta. Velocity profiles of selected PACS lines correlate well with known substructures: Hi in the central core; NH and weak [Cii] within the Homunculus; and [Nii] emissions in fast-moving structures external to the Homunculus.We have identified transitions from [Oi], Hi, and 18 separate light C- and O-bearing molecules including CO, CH, CH+, and OH, and a wide set of N-bearing molecules,NH, NH+, N2H+, NH2, NH3, HCN, HNC, CN, and N2H+. Half of these are new detections unprecedented for any early-type massive star environment. A very low ratio[12C/13C]≤4 is estimated from five molecules and their isotopologues. We demonstrate that non-LTE effects due to the strong continuum are significant. Abundance patterns are consistent with line formation in regions of carbon and oxygen depletions with nitrogen enhancements, reflecting an evolved state of the erupting star with efficient transport of CNO-processed material to the outer layers. The results offer many opportunities for further observational and theoretical investigations of the molecular chemistry under extreme physical and chemical conditions around massive stars in their final stages of evolution.

T. R. Gull↗

Off-Equilibrium Reactivity of Boron-Enriched Metal Diboride Surfaces in Electroreduction Conditions

Boron-based materials, featuring B-dependent reactivity and diverse phases, are emerging as promising catalyst systems. However, the catalytic mechanism on many borides remains poorly understood due to complex surface reconstructions under reaction conditions. Here, we investigate the MoB 2 surface in conditions of hydrogen evolution reaction in acidic media, using grand canonical global optimization, grand canonical density functional theory, ab initio molecular dynamics, free energy surface sampling, and an analytical model for electrochemical barrier evaluation. We propose a boron-enrichment strategy to tune the surface reactivity of the hexagonal face of MoB 2 . We reveal the dynamic nature of the B-enriched surface under H coverage and kinetic trapping of the system in the metastable regime with an extensive examination of the deactivation pathways. The metastable center B site on B-enriched surfaces, featuring buckled-up configuration and a usual relaxation effect, is found to be highly active toward HER via the Volmer–Heyrovsky mechanism. In conclusion, this work demonstrates how off-equilibrium behaviors can arise from the interplay between adsorbate coverage and surface reconstruction on a seemingly simple surface, and we present a theoretical framework and computational workflows to address these behaviors, along with other realistic complexities, in kinetics simulations.

Adsorption↗

Small Ion Channel Linking Molecular Simulations and Electrophysiology

Ion channels are pore-forming protein assemblies that mediate the transport of small ions across cell membranes. Otherwise, membrane bilayers would be almost impermeable to ions incapable to traverse the low dielectric constant, hydrophobic membrane core. Ion channels are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses, cardiac functions, muscle contraction and apoptosis. On the other extreme of biological complexity, viral ion channels (viroporins) influence many stages of the virus infection cycle either through regulating virus replication, such as entry, assembly and release or modulating the electrochemical balance in the subcellular compartments of host cells. Ion channels were crucial components of protocells. Their emergence facilitated adaptation of nascent life to different environmental conditions. The earliest ion channels must have been much simpler than most of their modern ancestors. Viral channels are among only a few naturally occurring models to study the structure, function and evolution of primordial channels. Experimental studies of these properties are difficult and often unreliable. In principle, computational methods, and molecular dynamics (MD) simulations in particular, can aid in providing information about both the structure and the function of ion channels. However, MD suffers from its own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. It is, therefore, essential to determine the reliability of MD simulations. We propose to do so on the basis of two criteria. One is channel stability on time scales that extend for several microseconds or longer. The other is the ability to reproduce the measured ionic conductance as a function of applied voltage. If both the stability and the calculated ionic conductance are satisfactory it will greatly increase our confidence that the structure and the function of a channel are described sufficiently accurately. To our knowledge, long time scale stability (approx.10 micro-sec) and the correct electrophysiology have been shown so far for only one channel - the synthetic LS3 hexamer). In this presentation, this approach will be discussed in application to two viral channels - Vpu, encoded by the HIV-1 genome and p7 of hepatitis C.

Pohorille, Andrzej↗