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At least 199 records · Page 11

Dynamics and lipid membrane coupling of the RAS-RAF complex revealed via multiscale simulations

To gain molecular and mechanistic insights into initiation of the RAS-RAF signaling cascade, we developed and used a combination of multiscale simulation and experimental approaches. The influence and impact of the membrane on RAS and RAF proteins is a factor we are just beginning to understand and appreciate in more detail. Molecular simulation is an ideal methodology to further study this complicated relationship between the membrane and associated proteins. Our previous work using Multiscale Machine-learned Modeling Infrastructure investigated different lipid compositions solely around the KRAS4b protein and the interplay between protein behavior and these membrane environments. Multiscale Machine-learned Modeling Infrastructure uses machine learning to couple adjacent simulation scales and has been efficiently scaled across some of the world’s largest high-performance computers. Recently, we have expanded this multiresolution framework to include the all-atom simulation scale and to incorporate the RAF RBDCRD domains. Here, we present the overall analysis results from this new simulation campaign comprising a mixture of RAS and RAF RBDCRD proteins. Approximately 35,000 coarse-grained and 10,000 all-atom molecular dynamics simulations were completed, sampled from a variety of protein/lipid composition configurations that were generated from a micron-scale continuum simulation containing hundreds of copies of the proteins. Our studies suggest that orientations of the RAS-RBDCRD complex on the membrane occupy distinct configurational states, and the spatial patterns of lipid arrangements around these different protein states are unique to each state. The extent and size of lipid “fingerprints” imposed on the membrane by the RAS-RBDCRD protein complex are significantly larger than observed for just the RAS protein on its own. These protein complexes strongly associate, but we do not observe statistically significant preferred protein-protein orientations. These observations indicate that spatial colocalization of RAS-RBDCRD proteins in the same vicinity may be assisted by specific membrane environments, acting to increase the probability of signaling complex formation.

Carpenter, Timothy S. [Lawrence Livermore National↗

A gradient-based deep neural network model for simulating multiphase flow in porous media

We report simulation of multiphase flow in porous media is crucial for the effective management of subsurface energy and environment-related activities. The numerical simulators used for modeling such processes rely on spatial and temporal discretization of the governing mass and energy balance partial-differential equations (PDEs) into algebraic systems via finite-difference/volume/element methods. These simulators usually require dedicated software development and maintenance, and suffer low efficiency from a runtime and memory standpoint for problems with multi-scale heterogeneity, coupled-physics processes or fluids with complex phase behavior. Therefore, developing cost-effective, data-driven models can become a practical choice, and in this work, we choose deep learning approaches as they can handle high dimensional data and accurately predict state variables with strong nonlinearity. In this paper, we describe a gradient-based deep neural network (GDNN) constrained by the physics related to multiphase flow in porous media. We tackle the nonlinearity of flow in porous media induced by rock heterogeneity, fluid properties, and fluid-rock interactions by decomposing the nonlinear PDEs into a dictionary of elementary differential operators. We use a combination of operators to handle rock spatial heterogeneity and fluid flow by advection. Since the augmented differential operators are inherently related to the physics of fluid flow, we treat them as first principles prior knowledge to regularize the GDNN training. We use the example of pressure management at geologic CO 2 storage sites, where CO 2 is injected in saline aquifers and brine is produced, and apply GDNN to construct a predictive model that is trained with physics-based simulation data and emulates the physics process. We demonstrate that GDNN can effectively predict the nonlinear patterns of subsurface responses, including the temporal and spatial evolution of the pressure and saturation plumes. We also successfully extend the GDNN to convolutional neural network (CNN), namely gradient-based CNN (GCNN), and validate its capability to improve the prediction accuracy. GDNN has great potential to tackle challenging problems that are governed by highly nonlinear physics and enable the development of data-driven models with higher fidelity.

42 ENGINEERING↗

Micro-beam bending of FCC bicrystals: A comparison between defect dynamics simulations and experiments

To understand the role of the grain boundary (GB) in plasticity at small scale, a concurrently coupled mesoscale plasticity model was developed to simulate micro-bending of bicrystalline micron-sized beams. By coupling dislocation dynamics (DD) with a finite element model (FEM), a novel defect dynamics model provides the means to investigate intricate interactions between dislocations and GBs under various loading conditions. Our simulations of micro-bending agree well with corresponding micro-bending experiments, and they show that mechanical response of bicrystals could have not only hardening but also softening depending on the characters of the GB. In addition, changing the location of the GB in the microbeams results in different mechanical responses; GBs located at the neutral plane show softening compared to single crystals, while inclined GBs located halfway along the length of the beam show little effect. In conclusion, simulation results could provide a clear picture on detailed dislocation-GB interactions, and quantitative resolved shear stress analysis supplemented by dislocation density distribution is used to analyze the mechanical response of bicrystalline samples.

36 MATERIALS SCIENCE↗

Morphology and Transport of Multivalent Cation-Exchanged Ionomer Membranes Using Perfluorosulfonic Acid–Ce Z+ as a Model System

Perfluorosulfonic acids (PFSAs) are commonly used as solid polymer electrolyte membranes (PEMs) in electrochemical energy devices, where they are vulnerable to attack by radical species during operation. A popular strategy to combat this problem is to introduce radical scavengers like cerium (Ce) ions that neutralize these species before they attack the PFSA. Such cation doping creates a multi-ion system, in which understanding the mechanisms of cation solvation and transport becomes important for the effective design and utilization of PFSA–cation systems. Ce ions also provide a representative model system for multication-exchanged ionomers in electrochemical systems. In this study, hydration and conductivity measurements, along with X-ray fluorescence and scattering, are employed to elucidate how Ce ion exchange alters PFSA’s ionic solvation, as well as nano- and mesoscale morphologies, which ultimately control its ion transport properties. A molecular transport model is used to deconvolute the impact of Ce ions on the local solvation structure of water in the membrane from mesoscale changes of the transport pathways. The combined experimental and theoretical analysis reveals a nonlinear decrease in conductivity driven by cation solvation at the molecular level and morphological changes at longer length scales. Migration–diffusion coupling, its nonlinear dependence on ion exchange and hydration, and its overall implications for ionomer performance are also discussed. Finally, these findings have the potential to be translated into other mixed cation–ionomer systems for a wide range of energy and environmental devices.

36 MATERIALS SCIENCE↗

Pathways to High-Performance Salt Hydrate Thermochemical Energy Storage Materials and Systems

Thermochemical materials (TCMs) based on salt hydrates are promising for thermal energy storage as they combine high energy densities with low reaction temperatures. However, their adoption is hindered by poor structural integrity and degradation under hygrothermal cycling. Storage performance is governed not only by the chemical reaction, but also by the coupled thermo-chemo-mechanical behavior that evolves with cycling. Understanding and controlling this coupling across length scales (material-to-reactor) is necessary to improve TCM stability and lifetime. In this perspective, we discuss the shortcomings of current characterization approaches and emphasize the need for measuring transport properties and structural transformations using in situ techniques that capture the dynamic evolution of these materials. We also outline opportunities for multiscale modeling frameworks that link thermodynamics and mechanics, enabling predictive evaluation of composite architectures designed for cycling stability. We conclude by identifying research questions that must be addressed to transform TCMs into viable energy storage technologies.

Composites↗

Corrosive Influence of Carbon Dioxide on Crack Initiation in Quartz: Comparison With Liquid Water and Vacuum Environments

The stimulation of crack growth in quartz and siliceous materials by injecting carbon dioxide (CO 2 ) represents a key technology in long-term carbon storage and in the development of natural gas wells. While this technology is widely used, the molecular impact of CO 2 interactions on the solid matrix is only incompletely understood. In this work, we employ reactive molecular dynamics simulations to study how the CO 2 fluid environment affects the mechanical properties of pre-cracked single-crystal quartz. The thermodynamic conditions of interest are those relevant to subsurface reservoirs. We report how structural properties of quartz—bond length distribution and crack tip shape—evolve upon introduction of a fluid. These properties are directly related to macroscopic quantities of the global stress-strain curves, thus reaffirming the inherent coupling across multiple scales for fluid-solid interactions in the subsurface. Here, we find that CO 2 reduces the fracture toughness of quartz by 12.1% compared to that of quartz in vacuum, thereby promoting crack growth and enhancing fluid transport in the subsurface.

58 GEOSCIENCES↗

Coupling to octahedral tilts in halide perovskite nanocrystals induces phonon-mediated attractive interactions between excitons

Understanding the origin of electron–phonon coupling in lead halide perovskites is key to interpreting and leveraging their optical and electronic properties. Here we show that photoexcitation drives a reduction of the lead–halide–lead bond angles, a result of deformation potential coupling to low-energy optical phonons. We accomplish this by performing femtosecond-resolved, optical-pump–electron-diffraction-probe measurements to quantify the lattice reorganization occurring as a result of photoexcitation in nanocrystals of FAPbBr 3 . Our results indicate a stronger coupling in FAPbBr 3 than CsPbBr 3 . We attribute the enhanced coupling in FAPbBr 3 to its disordered crystal structure, which persists down to cryogenic temperatures. We find the reorganizations induced by each exciton in a multi-excitonic state constructively interfere, giving rise to a coupling strength that scales quadratically with the exciton number. This superlinear scaling induces phonon-mediated attractive interactions between excitations in lead halide perovskites.

36 MATERIALS SCIENCE↗

Investigation of warm dense matter by combining static and dynamic compression

Shock-compressing material samples that are precompressed with diamond-anvil cells (DACs) enables benchmarking equation of state measurements over a wide range of high-pressure conditions, in particular, warm dense matter relevant to planetary science, astrophysics, and inertial confinement fusion. These targets provide optical access to the shocked sample, so optical velocity interferometry and pyrometry are typical diagnostics. We present a scaling for the coupling of the laser drive to the shock pressure in DACs based on over 150 prior experiments that can be used to design future experiments. For initial static pressures ≤ 5 GPa, using a sapphire window mitigates the effect of photoionization compared to diamond windows and allows the measurement of shock pressures up to 1 TPa with optical diagnostics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Experimental test of a predicted dynamics–structure–thermodynamics connection in molecularly complex glass-forming liquids

Significance The physical origin of cooperative activated relaxation in glass-forming liquids, which underlies the huge growth of viscosity and suppression of diffusion with cooling, remains elusive. Understanding this problem is of fundamental scientific interest and can assist in the design of new materials. We combine experimental relaxation time and equation-of-state data of molecular liquids to provide strong evidence for the recent theoretical prediction that activated relaxation, though causally driven by dynamically coupled cage-scale hopping and nonlocal collective elasticity quantified by local structural correlations, is well captured based on a thermodynamic description with dimensionless compressibility as the key variable. A mechanistic deduction is the crossover from fragile to strong (e.g., inorganic networks) relaxation behavior arises from the irrelevance of long-range elasticity effects.

36 MATERIALS SCIENCE↗

Instant folded strings, dark energy and a cyclic bouncing universe

We present a wholly self-consistent, complete cyclic bouncing cosmology based on components drawn from string theory and constructed in a way that is under perturbative control throughout (e.g., with temperature much less than the string scale and string coupling g s ≪ 1 at all times). The cyclic evolution is governed by standard dilaton-gravity in (3+1)-dimensions with a perturbatively generated potential and a coupling between the dilaton and a second field that becomes massless at ϕ = ϕ ESP , resulting in an enhanced symmetry point (ESP) that prevents the dilaton from running all the way to zero coupling. A central role is played by instant folded strings (IFSs) — fundamental strings with the unusual property of being much lighter than the string mass while extending far beyond the string length, and violating the Null Energy Condition (NEC). IFSs are produced classically when the string coupling grows with time, which occurs at two critical points in each cycle. In turn, they fulfill a dual function: Enabling cosmological bounces and initiating transient epochs of dark-energy domination that naturally transition into slow contraction. The resulting cosmology eliminates the cosmic singularity and multiverse problems of big bang inflationary models and robustly predicts time-varying IFS-induced dark energy and the absence of primordial B-mode polarization in the cosmic microwave background.

alternatives to inflation↗

Design Principles to Govern Electrode Fabrication for the Lithium Trivanadate Cathode

A full depth of discharge mathematical model for the lithium trivanadate cathode, considering lithiation of the layered α-phase, phase change, and lithiation of the rock-salt like β-phase at lower potentials, is developed. The coupled electrode-scale and crystal-scale model is fit to electrochemical data, and additionally validated with operando EDXRD. There is good agreement between the simulated and measured spatial variation of the volume fraction of the β-phase. This mathematical model is used to guide electrode fabrication, accounting for both ionic and electronic transport effects. Values of three design parameters—electrode thickness, porosity, and volume fraction of conductor—are identified, and the sensitivity of the energy density to these design parameters is quantified. The model is also used to investigate electrode design to create electrodes that deliver the maximum achievable energy density under the constraint that the α to β-phase transition is avoided, since phase change has been demonstrated to reduce cycle life. The energy density sacrificed to avoid phase change decreases at higher discharge rates, but the target values for electrode fabrication remain the same as those when optimizing the electrode for the full depth of discharge.

25 ENERGY STORAGE↗

Autonomous MultiScale Library

AMSLib provides infrastructure to tightly couple multi-scale physics simulation code with ML surrogate model inference. It provides a wholistic runtime execution paradigm to supports uncertainty quantification, surrogate model inference, persistent data storing throughout the execution of a simulation.

Bhatia, Harsh↗

QCD factorization for hadronic quarkonium production at high $p_T$

Heavy quarkonium production at high transverse momentum ( p_T p T ) in hadronic collisions is explored in the QCD factorization approach. We find that the leading power in the 1/p_T 1 / p T expansion is responsible for high p_T p T regime, while the next-to-leading power contribution is necessary for the low p_T p T region. We present the first numerical analysis of the scale evolution of coupled twist-2 and twist-4 fragmentation functions (FFs) for heavy quarkonium production and demonstrate that the QCD factorization approach is capable of describing the p_T p T spectrum of hadronic J/\psi J / ψ production at the LHC.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Multiple Degradation Mechanisms in Reinforced Concrete Structures, Modeling and Risk Analysis

The overarching goal of this project is to complement ongoing Department of Energy (DOE) Light Water Reactor Sustainability (LWRS)-funded Grizzly concrete modeling development efforts by providing improved multi-physics models for incorporation into the Grizzly and BlackBear codes. Objectives of this work identified at the outset of this project include: 1. Coupling between mechanical damage and transport processes. The mechanical damage will be characterized by nonlinear mechanical constitutive models appropriate for concrete used in nuclear power plants (NPPs). 2. Improved representation of the coupling among the transport process, building on the current moisture and thermal transport models in Grizzly. The parameters for coupling among heat and mass transport in the multi-physics model will be experimentally determined. 3. Coupling among different scale levels of concrete constituents, fine and coarse aggregates, cement paste, hydration products, and pore structure. 4. Probabilistic analysis of the random nature of the heterogeneous concrete structure and the environmental factors (ambient temperature and humidity) and their multiple effects on concrete deterioration. 5. Benchmark verification, validation and uncertainty quantification of the thermo-hygro- chemo-mechanical (THCM) concrete formulation. The end goal of this work was to provide a comprehensive and robust simulation capability that can be applied at the engineering scale for analysis of realistic deterioration scenarios in NPP concrete structures.

36 MATERIALS SCIENCE↗

Engineering scale molten salt corrosion and chemistry code development

A new engineering scale transport code Mole is described. Mole was developed using the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework for solving species transport problems in flowing liquid. It is applied to leaching of Cr from alloys into molten salts part a of a multi-physics, multi-scale approach for coupling chemistry with mechanical behavior modeling. Demonstrations of the leaching phenomenon were benchmarked to experimental data provided by the Molten Salt Reactor campaign and the results are presented.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Instant Folded Strings, Dark Energy and a Cyclic Bouncing Universe

We present a wholly self-consistent, complete cyclic bouncing cosmology based on components drawn from string theory and constructed in a way that is under perturbative control throughout (e.g., with temperature much less than the string scale and string coupling $g_s \ll 1$ at all times). The cyclic evolution is governed by standard dilaton-gravity in $(3+1)$-dimensions with a perturbatively generated potential and a coupling between the dilaton and a second field that becomes massless at $ϕ= ϕ_{ESP}$, resulting in an enhanced symmetry point (ESP) that prevents the dilaton from running all the way to zero coupling. A central role is played by instant folded strings (IFSs) - fundamental strings with the unusual property of being much lighter than the string mass while extending far beyond the string length, and violating the Null Energy Condition (NEC). IFSs are produced classically when the string coupling grows with time, which occurs at two critical points in each cycle. In turn, they fulfill a dual function: enabling cosmological bounces and initiating transient epochs of dark-energy domination that naturally transition into slow contraction. The resulting cosmology eliminates the cosmic singularity and multiverse problems of big bang inflationary models and robustly predicts time-varying IFS-induced dark energy and the absence of primordial B-mode polarization in the cosmic microwave background.

Cosmology and Nongalactic Astrophysics (astro-ph.C↗

An efficient hybrid downscaling framework to estimate high-resolution river hydrodynamics

Flow depth and velocity are the most important hydrodynamic variables that govern various river functions, including water resources, navigation, sediment transport, and biogeochemical cycling. Existing high-resolution flow depth simulations rely on either computationally expensive river hydrodynamic models (RHMs) or data-driven models with formidable training costs, whereas data-driven modeling of flow velocity has rarely been explored. Here, using the hybrid Low-fidelity, Spatial analysis, and Gaussian process learning (LSG) model, we developed a downscaling approach to construct high-resolution flow depth and velocity from a two-dimensional (2-D) RHM simulation at coarse resolution. The LSG models were trained and tested in an urban watershed in Houston using two different hurricane-driven flood events. The high-resolution (as fine as 30 m resolution) and low-resolution (mostly 1000 m resolution) meshes include 664 724 and 14 536 grid cells, respectively. The results showed that through downscaling, the simulation errors were reduced to less than one-fourth and one-third of the errors of the low-resolution 2-D RHM for flow depth and velocity, respectively. Our analysis further revealed that the dominant uncertainty sources of the downscaled hydrodynamics are different, with flow velocity dominated by the dimensionality reduction error, which we reduced by using a regionalized training procedure. The downscaling approach achieves an 84-fold acceleration in computational time compared to the high-resolution 2-D RHM, making high-fidelity ensemble flood modeling feasible. More importantly, the developed method provides an opportunity to couple large-scale hydrodynamical processes with local physical, chemical, and biological processes in river models.

Tan, Zeli [Pacific Northwest National Laboratory (↗

Topographical Controls on Hillslope-Scale Hydrology Drive Shrub Distributions on the Seward Peninsula, Alaska: Modeling Archive

The dataset is a model output used in a study that examined the role topography plays in determining shrub expansion by applying a coupled transect version of a mechanistic ecosystem model (ecosys) in a tundra hillslope site in the Seward Peninsula, Alaska. The study highlights the importance of mechanistically representing hillslope-scale coupled surface and sub-surface hydrology to accurately predict current plant distributions and future trajectories in Arctic ecosystems. The dataset contain ecosys model outputs used in a study: Article Title - Topographical Controls on Hillslope-Scale Hydrology Drive Shrub Distributions on the Seward Peninsula, Alaska. It includes the data files (ten *.csv files) used in creating figures in the publication and three *.pdf files (user guide and two Supplementary Information documents).The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗