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At least 91 records · Page 5

Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.

59 BASIC BIOLOGICAL SCIENCES↗

A Transferable Force Field for Predicting Adsorption and Diffusion of Water in Cationic Zeolites with Coupled Cluster Accuracy

We present a transferable force field for water in proton-exchanged, alkali (Li, Na, K, Rb, and Cs) metal-exchanged, and alkaline-earth (Mg, Ca, Sr, and Ba) metal-exchanged zeolites. The fitting methodology is based on adsorbate–adsorbent interaction energies obtained from periodic density functional theory calculations and corrected using the coupled-cluster method applied to small model clusters. To ensure an accurate prediction of both adsorption and diffusion properties of water, sets of configurations that sample both adsorption sites and intracrystalline hopping transition states were used in the fitting. The quality of the force field is assessed for a wide range of zeolites with different topologies and chemical compositions, demonstrating good agreement between theoretical predictions and experimental measurements of water adsorption and diffusion.

Adsorption↗

Diffuse X-ray emission from Abell clusters

Abell clusters of galaxies, specifically Abell 401 and Abell 399 regions, are discussed. Two sets of satellite observations were made. One was a lunar occultation pointed observation where there were two orbits in which to look at the regions while the moon scanned over it. The other was a scanning observation through the area. Two diffuse models of the X-ray emission were developed. Also, during the investigation three binary cluster systems were found where at least one member was an X-ray source. They were Abell 508, 509, 2177, 2178, 2204, and 2210.

Ulmer, M.↗

Search for decaying dark matter in the Virgo cluster of galaxies with HAWC

The decay or annihilation of dark matter particles may produce a steady flux of very-high-energy gamma rays detectable above the diffuse background. Nearby clusters of galaxies provide excellent targets to search for the signatures of particle dark matter interactions. In particular, the Virgo cluster spans several degrees across the sky and can be efficiently probed with a wide field-of-view instrument. The High Altitude Water Cherenkov (HAWC) observatory, due to its wide field of view and sensitivity to gamma rays at an energy scale of 300 GeV–100 TeV is well-suited for this search. Using 2141 days of data, we search for γ -ray emission from the Virgo cluster, assuming well-motivated dark matter substructure models. Our results provide some of the strongest constraints on the decay lifetime of dark matter for masses above 10 TeV. Published by the American Physical Society 2024

Albert, A.↗

Stable Rate of Slip Along the Karakax Section of the Altyn Tagh Fault from Observation of Interglacial and Postglacial Offset Morphology and Surface Dating

Digital elevation maps obtained using TanDEM-X and Pleiades data combined with newly obtained surface age estimates using cosmogenic radionuclide (CRN) and optically simulated luminescence (OSL) methods are used to quantify the slip rate along the western section of the Altyn Tagh Fault in southern Xinjiang. The reconstruction of the conical shape of massive alluvial fans inferred to be from the Eemian (115±7 ka) from CRN dating shows consistent left-lateral offsets of 300±20 m, yielding a slip rate of 2.6±0.3 mm/year. Successive episodes of incision have left cut terraces inset in wide canyons, 10–25 m below the fans' surface. The incision was followed by the deposition of a broad terrace of early Holocene age, which is reincised by modern stream channels. Near the village of Shanxili, a 200 m wide valley is partially dammed by a shutter ridge displaced by the fault. A fill terrace deposited upstream from the ridge has an OSL age of 8.8±0.6 ka. The 23±2 m offset of the riser incising the terrace indicates a minimum postdepositional movement on the fault, yielding a Holocene rate of 2.6±0.5 mm/year, consistent with the 115-ka average slip rate. Furthermore, scarp degradation analysis using mass diffusion reveals a nonlinear relationship between fault displacement and degradation coefficient along the progressively exposed fault scarp, a pattern suggesting either seismic clustering or variable diffusion rate since the Eemian. Together with the Gozha Co-Longmu Co fault to the south, the Karakax section of the Altyn Tagh Fault contributes to the eastward movement of the western corner of Tibet.

58 GEOSCIENCES↗

Rotation and flattening of globular clusters

Methods for measuring globular cluster ellipticities and the results of such measurements are reviewed, and the processes that determine the shapes of globular clusters and the ways in which they change with time are discussed. The use of the virial tensor theorem to study the connection between the global rotation, velocity anisotropy, and the shape of a self-gravitating system is addressed, and the employment of N-body models to simulate the evolution of globular clusters with initially anisotropic velocity distributions is examined. The application of a simple evaporation model and Fokker-Planck integrations to study the two-body diffusion in globular clusters is reviewed.

Fall, S. M.↗

A model of the evaporation of binary-fuel clusters of drops

A formulation has been developed to describe the evaporation of dense or dilute clusters of binary-fuel drops. The binary fuel is assumed to be made of a solute and a solvent whose volatility is much lower than that of the solute. Convective flow effects, inducing a circulatory motion inside the drops, are taken into account, as well as turbulence external to the cluster volume. Results obtained with this model show that, similar to the conclusions for single isolated drops, the evaporation of the volatile is controlled by liquid mass diffusion when the cluster is dilute. In contrast, when the cluster is dense, the evaporation of the volatile is controlled by surface layer stripping, that is, by the regression rate of the drop, which is in fact controlled by the evaporation rate of the solvent. These conclusions are in agreement with existing experimental observations. Parametric studies show that these conclusions remain valid with changes in ambient temperature, initial slip velocity between drops and gas, initial drop size, initial cluster size, initial liquid mass fraction of the solute, and various combinations of solvent and solute. The implications of these results for computationally intensive combustor calculations are discussed.

Harstad, K.↗

Spatial distribution of Compton-produced X-ray flux from rich and regular clusters of galaxies

The spatial distribution of radio and X-ray fluxes from rich and regular clusters of galaxies is discussed. A diffusion model is investigated in which high-energy electrons are ejected from a point source at the center of the cluster. While diffusing out, the electrons lose energy by Compton scattering with the universal blackbody photons, thus producing the X-ray emission. Traversing intracluster magnetic fields, the electrons emit synchrotron radio emission. For the Coma cluster of galaxies good agreement is found between the observed and predicted X-ray counting-rate distribution for the Compton model. From the observed radio data a value of about 3 by 10 to the -8th power gauss is deduced for the average magnetic-field strength in the central region of Coma.

Rephaeli, Y.↗

Atomically Precise Single Metal Oxide Cluster Catalyst with Oxygen–Controlled Activity

Single cluster catalysts (SCCs) consisting of atomically precise metal nanoclusters dispersed on supports represent a new frontier of heterogeneous catalysis. However, the ability to synthesize SCCs with high loading and to precisely introduce non-metal atoms to further tune their catalytic activity and reaction scope of SCCs have been longstanding challenges. In this work, a new interface confinement strategy is developed for the synthesis of a high density of atomically precise Ru oxide nanoclusters (Ru 3 O 2 ) on reduced graphene oxide (rGO), attributed to the suppression of diffusion-induced metal cluster aggregation. Ru 3 O 2 /rGO exhibits a significantly enhanced activity for oxidative dehydrogenation of 1,2,3,4-tetrahydroquinoline (THQ) to quinoline with a high yield (≈86%) and selectivity (≈99%), superior to Ru and RuO 2 nanoparticles, and homogeneous single/multiple-site Ru catalysts. In addition, Ru 3 O 2 /rGO is also capable of efficiently catalyzing more complex oxidative reactions involving three reactants. The theoretical calculations reveal that the presence of two oxygen atoms in the Ru 3 O 2 motif not only leads to a weak hydrogen bonding interaction between the THQ reactant and the active site, but also dramatically depletes the density of states near the Fermi level, which is attributed to the increased positive valence state of Ru and the enhanced oxidative activity of the Ru 3 O 2 cluster for hydrogen abstraction.

36 MATERIALS SCIENCE↗

Probing Supercritical Phase Transition using Ultrafast X-ray Diagnostics (Final Technical Report)

Over recent years, several hypotheses have been put forward to elucidate supercritical transition states. Despite significant progress on the fundamental understanding of fluids at these supercritical conditions, important questions concerning the microstructure and dynamical processes remain. A particular research issue is hereby the fundamental understanding of the morphology of the molecular microstructure and its effect on the macroscopic behaviour and thermodynamic response functions. It is widely believed that the supercritical state is homogeneous without structural and dynamic observables to distinguish between a liquid and a vapor. However, recent investigations have identified regions of distinct liquid-like or vapor-like properties even under supercritical conditions. Specifically, it was shown that the transition between liquid-like and vapor-like states occurs across an extension to the coexistence line, marked by almost discontinuous changes in fluid properties. This transition was first identified experimentally by Nishikawa and Tanaka and stands in contrast to the classical presentation of the supercritical state space as a featureless, homogeneous domain. Structurally, the most important properties of supercritical fluids are the dynamic heterogeneities and local density fluctuations that are present within the fluid state at the microscopic level. These inhomogeneities are associated with the formation of molecular clusters of various sizes with liquid-like properties separated by voids of unbound gas-phase molecules which continuously restructure itself at picosecond timescales. By utilizing ultrafast X-ray Photon Correlation Spectroscopy (XPCS) at the Linac Coherent Light Source (LCLS) and X-ray synchrotron measurements as an experimental probe of these structural changes at the molecular level we seek to elucidate the higher-order phase transition from a liquid-like to a vapor-like state in the region extending the critical point. Open questions we seek to address particularly with XPCS are: (i) the underlying mechanisms responsible for the density fluctuations at supercritical conditions and how these dynamical processes at the molecular level affect the thermodynamic response functions and (ii) on what timescales do dynamical processes evolve that are associated with thermalization, molecular diffusion, and intermolecular cluster transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experimental Evaluation of Rocket Exhaust Diffusers for Altitude Simulation

An experimental investigation of exhaust diffusers has been conducted to evaluate various methods of minimizing the overall pressure ratio (from chamber to ambient pressure) required to establish and maintain full expansion of the nozzle flow (altitude simulation). Exhaust-diffuser configurations investigated were (1) cylindrical diffusers, (2) diffusers with contraction, and (3) diffusers including a right-angle turn. Cylindrical diffusers were evaluated with primary nozzles of various area ratios and types, as well as two clustered configurations; the other diffusers were evaluated with individual nozzles of constant area ratio and varied type. Air was the working fluid, except for two check points obtained with JP-4 fuel and liquid-oxygen rocket engines and cylindrical diffusers. The minimum length-diameter ratio of cylindrical diffusers was about 6 for minimum pressure-ratio requirements. With cylindrical diffusers of adequate length, the pressure-ratio requirements were primarily a function of the ratio of diffuser to nozzle-throat areas and were essentially independent of primary-nozzle type (including two clustered configurations) or area ratio. The two check points obtained with rocket engines indicated the pressure-ratio requirements at given ratios of diffuser to nozzle-throat areas were lowered, as compared with the requirements with air, as a result of the reduced ratio of specific heats. The minimum length-diameter ratio of the contraction throat of convergent-divergent diffusers was also about 6 for minimum pressure-ratio requirements. With adequate contraction-throat length, the pressure-ratio requirements of such diffusers were appreciably below those of comparable cylindrical diffusers when used with conical and cutoff-isentropic nozzles, but not when used with a bell nozzle. Minimum pressure-ratio requirements of a diffuser including a simple long-radius right-angle turn at maximum diffuser area, obtained with the center of radius of the turn a minimum of 2 diffuser diameters downstream of the nozzle exit, were not appreciably above those of a comparable optimum cylindrical diffuser. A diffuser including a long-radius right-angle turn at a contraction minimum area had somewhat lower pressure-ratio requirements than the aforementioned simple turn.

Sivo, Joseph N.↗

Surface diffusion activation energy determination using ion beam microtexturing

The activation energy for impurity atom (adatom) surface diffusion can be determined from the temperature dependence of the spacing of sputter cones. These cones are formed on the surface during sputtering while simultaneously adding impurities. The impurities form clusters by means of surface diffusion, and these clusters in turn initiate cone formation. Values are given for the surface diffusion activation energies for various materials on polycrystalline Cu, Al, Pb, Au, and Ni. The values for different impurity species on each of these substrates are approximately independent of impurity species within the experimental uncertainty, suggesting the absence of strong chemical bonding effects on the diffusion.

Rossnagel, S. M.↗

Relocating microseismicity from downhole monitoring of the Decatur CCS site using a modified double-difference algorithm

SUMMARY The injection of CO2 at the Decatur carbon capture and storage site has generated significant microseismic activity, which occurs in distinct spatial clusters up to approximately 2.2 km from the primary injection well. Accurate and precise event locations are vital for the characterization of the microseismicity to help understand the reservoir response to the CO2 injection, whilst enabling the identification of minor faults and fractures below the resolution of conventional active seismic imaging. However, microseismic monitoring of fluid injection sites, such as Decatur, is often performed using a network of borehole sensors often from a single well. While these downhole sensors have excellent detection capabilities, their poor azimuthal coverage limits the ability to precisely determine event locations. We have developed a modified double-difference relocation algorithm suitable for both 1-D and 3-D velocity models, and which incorporates differential back azimuth observations to allow the benefits of the original double-difference algorithm to be applicable to a downhole microseismic monitoring setting. Applying the modified double-difference algorithm to the microseismicity at Decatur, we have successfully relocated 4293 events. The relocation included over 59 million observations for 757 285 event pairs, split across seven geographic regions. Despite the majority of observations being recorded in only two boreholes, with an almost identical azimuthal coverage, the results have shown to be reliable with significantly reduced residuals and low uncertainties associated with the final locations. We have analysed the residuals in terms of their association with each geographic region, data type, station and individual events, to fully appreciate their influence in the inversion and the fit of the data to the final set of event locations. For each region, the relocated seismicity has become less diffuse with improved clustering, and with newly visible linear features often orientated in a NE–SW direction. These results show the potential improvements that can be made to microseismic event locations recorded by a borehole network with a limited and variable azimuthal distribution.

58 GEOSCIENCES↗

Temperature and salt controlled tuning of protein clusters

The formation of molecular assemblies in protein solutions is of strong interest both from a fundamental viewpoint and for biomedical applications. While ordered and desired protein assemblies are indispensable for some biological functions, undesired protein condensation can induce serious diseases. As a common cofactor, the presence of salt ions is essential for some biological processes involving proteins, and in aqueous suspensions of proteins can also give rise to complex phase diagrams including homogeneous solutions, large aggregates, and dissolution regimes. Here, we systematically study the cluster formation approaching the phase separation in aqueous solutions of the globular protein BSA as a function of temperature (T), the protein concentration (c p ) and the concentrations of the trivalent salts YCl 3 and LaCl 3 (c s ). As an important complement to structural, i.e. time-averaged, techniques we employ a dynamical technique that can detect clusters even when they are transient on the order of a few nanoseconds. By employing incoherent neutron spectroscopy, we unambiguously determine the short-time self-diffusion of the protein clusters depending on c p , c s and T. We determine the cluster size in terms of effective hydrodynamic radii as manifested by the cluster center-of-mass diffusion coefficients D. For both salts, we find a simple functional form D(c p , c s , T) in the parameter range explored. The calculated inter-particle attraction strength, determined from the microscopic and short-time diffusive properties of the samples, increases with salt concentration and temperature in the regime investigated and can be linked to the macroscopic behavior of the samples.

59 BASIC BIOLOGICAL SCIENCES↗

Coupled cluster and dislocation dynamics modeling of microstructure evolution in irradiated materials

We develop here a coupled cluster and dislocation dynamics framework to study the microstructure evolution of irradiated materials. The framework not only accounts for the three dimensional diffusion of radiation-generated clusters, but also their interaction with dislocation networks and the resultant climb motion of discrete dislocations within finite crystals. The framework is solved with a superposition solution scheme, and is applied to investigate the evolution of the irradiation-induced dislocation loops in zirconium (Zr), considering the effects of various bias factors including the diffusion anisotropy difference (DAD) of interstitials and interstitial clusters, the dislocation bias of defects to discrete dislocation segments, and the production bias of defects from the radiation cascade. We find that the DAD is the most critical factor influencing the kinetics of the loop evolution in Zr, while the recombination/interaction of mobile defects can induce a strong spatial dependence of the loop evolution together with the DAD. Here, the method is also adopted to study the evolution of interstitial $\langle$a$\rangle$ and vacancy $\langle$c$\rangle$ dislocation loop ensembles consistent with the microstructure observed during irradiation-induced growth of Zr. Our findings not only reveal the spatial dependence of the size and ellipticity of the dislocation loops, but also suggest a limit on the anisotropy factor of interstitials to reproduce the co-growth of $\langle$a$\rangle$ and $\langle$c$\rangle$ loops in zirconium, in good agreement with experimental observations and other simulation results.

Bias factors↗

Comparing approaches for introducing polycyclic aromatic hydrocarbons to Ge(001) to seed graphene nanoribbon synthesis by CH 4 chemical vapor deposition

Here, we evaluate two approaches for introducing polycyclic aromatic hydrocarbons (PAHs) to a graphene catalyst substrate as part of a two-step chemical vapor deposition (CVD) process for growing graphene nanoribbons (GNRs). In this process, PAHs first form graphene-like seeds on Ge, and then GNRs are subsequently evolved from these PAH-derived seeds via substrate-mediated anisotropic growth kinetics during the CVD of CH4. The first seeding approach sublimes controlled doses of PAH thin films into the CVD chamber, while the second delivers PAHs directly from the vapor phase at set concentrations. Using these two approaches, we measure the dependence of GNR density on PAH dose and compare the experimental results with predictions from a rate model of PAH diffusion, desorption, and clustering. We find that PAHs that more strongly adsorb to the catalyst surface (generally larger PAHs) desirably remain more individualized prior to GNR evolution whereas smaller, more weakly bound PAHs aggregate into larger clusters with various sizes on Ge that are undesirable for synthesizing more monodisperse GNRs. As a result, this work is important because it offers a framework that enables the rational selection and design of seed molecules, advancing anisotropic GNR CVD synthesis.

CVD↗

A Comparison of Electronic Structure Methods for Predicting the Hydrogenation Energies of Candidate Molecules for Hydrogen Storage

The development of novel energy materials and fuels is required to expand current available energy sources. Aiming to reach this goal, there is growing interest in using molecular hydrogen as an energy carrier due to its abundance and high energy density. Liquid organic hydrogen carriers (LOHCs) are a promising route to the large-scale storage and transport of hydrogen for use in the energy economy. The search for thermodynamically viable LOHC molecules for real world use has led to a set of constraints on the dehydrogenation enthalpy and the minimum gravimetric hydrogen capacity. These constraints allow one to formulate the search for an ideal LOHC candidate molecule as an optimization problem well suited to the strengths of machine learning and artificial intelligence computational approaches. A critical barrier to a large-scale, high-throughput screening of LOHC candidate molecules is the lack of reliable training data. Computational electronic structure methods including density functional theory, coupled cluster approximations, and diffusion Monte Carlo can be used to provide training data where experimental data are either unreliable or do not exist. In this work, we use these methods to calculate the dehydrogenation energies and enthalpies of candidate LOHC molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗