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At least 199 records · Page 11

KRAS4a and KRAS4b show distinct lipid-dependent regulation of RAS-RAF membrane dynamics

KRAS4a and KRAS4b are important regulators of signaling, and their interactions with the plasma membrane are dynamic and influenced by lipid composition. KRAS 4a and 4b have nearly identical globular domains but differ in their membrane-associated hyper variable region (HVR). The functional distinctions between these isoforms remain unclear, particularly with regards to their dependence on specific lipids and the membrane environment. Previous work showed that the membrane orientation of KRAS4b affects its ability to bind to RAF kinase RBDCRD and that the KRAS–RBDCRD complex adopts different poses on the membrane as well as influences the size and composition of the lipid environment. To model differences between KRAS 4a and 4b protein–lipid interactions, we extended the Multiscale Machine-Learned Modeling Infrastructure (MuMMI) to incorporate continuum simulations in the grand canonical ensemble, enabling sampling across macroscopic, coarse-grained, and all-atom resolutions. Using this framework, we systematically altered PIP2 concentrations, KRAS 4a versus 4b, and RAF RBDCRD complexation to assess impacts on membrane–protein interactions and dynamics. Our results reveal that reducing PIP2 shifts and broadens the membrane orientational preference of both KRAS 4b and 4a, with stronger effects on 4b HVR localization versus 4a. We demonstrate that with depletion of the strong negatively charged PIP2 lipid, the less charged phosphatidylserine replaces PIP2. Our findings highlight similarities and distinctions in the dynamics and lipid dependency of KRAS isoforms and suggest that ordering of the local lipid composition by HVRs is a shared property and key modulator of RAS-mediated signaling at the plasma membrane.

Biological and medical sciences↗

Paper or Plastic? Multiscale Material Handling Properties of Two Model Municipal Solid Waste Streams

Purpose: Municipal Solid Waste (MSW) is a potentially valuable sustainable feedstock for fuel and chemical production due to its carbon-rich content and low cost. This study aims to assess the material handling properties of paperand plastic-rich MSW feedstocks to mitigate equipment failure and processing downtime. Methods: The material handling properties of crumbled MSW feedstocks were measured using apowder rheometer with mass flow hopper calculations to assess handling performance. Inverse gas chromatography was use to measure the surface energy differences between feedstocks. Electron microscopy and Raman spectroscopy was used to evaluate microscale features that may contribute to material handling differences. Results: Plastic and paper rich feedstocks crumbled to a nominal 2 mm particle size were observed to have similar flow and handling characteristics with reasonable hopper outlets. 2 mm plastic rich crumbles, with their higher bulk density, exhibited superior flow performance. By contrast, 4 mm material required significantly larger hopper outlets, indicating poor flowability. Paper rich and 4 mm plastic rich samples displayed broad particle size distributions, which contributed to particle interlocking, jamming, and other flow issues. Electron microscopy revealed that plastic rich samples were significantly smoother, enhancing their flowability compared to the rougher, paper rich materials. Conclusions: This study establishes critical material handling baselines for processing MSW as a viable feedstock for fuel and chemical production. The findings highlight the importance of optimizing particle size and feedstock composition to improve flowability and handling performance.

09 BIOMASS FUELS↗

Neural network representations of multiphase Equations of State

Abstract Equations of State model relations between thermodynamic variables and are ubiquitous in scientific modelling, appearing in modern day applications ranging from Astrophysics to Climate Science. The three desired properties of a general Equation of State model are adherence to the Laws of Thermodynamics, incorporation of phase transitions, and multiscale accuracy. Analytic models that adhere to all three are hard to develop and cumbersome to work with, often resulting in sacrificing one of these elements for the sake of efficiency. In this work, two deep-learning methods are proposed that provably satisfy the first and second conditions on a large-enough region of thermodynamic variable space. The first is based on learning the generating function (thermodynamic potential) while the second is based on structure-preserving, symplectic neural networks, respectively allowing modifications near or on phase transition regions. They can be used either “from scratch” to learn a full Equation of State, or in conjunction with a pre-existing consistent model, functioning as a modification that better adheres to experimental data. We formulate the theory and provide several computational examples to justify both approaches, highlighting their advantages and shortcomings.

Science & Technology - Other Topics↗

An adaptive, data-driven multiscale approach for dense granular flows

The accuracy of coarse-grained continuum models of dense granular flows is limited by the lack of high-fidelity closure models for granular rheology. One approach to addressing this issue, referred to as the hierarchical multiscale method, is to use a high-fidelity fine-grained model to compute the closure terms needed by the coarse-grained model. The difficulty with this approach is that the overall model can become computationally intractable due to the high computational cost of the high-fidelity model. In this work, we describe a multiscale modeling approach for dense granular flows that utilizes neural networks trained using high-fidelity discrete element method (DEM) simulations to approximate the constitutive granular rheology for a continuum incompressible flow model. Our approach leverages an ensemble of neural networks to estimate predictive uncertainty that allows us to determine whether the rheology at a given point is accurately represented by the neural network model. Additional DEM simulations are only performed when needed, minimizing the number of additional DEM simulations required when updating the rheology. This adaptive coupling significantly reduces the overall computational cost of the approach while controlling the error. In addition, the neural networks are customized to learn regularized rheological behavior to ensure well-posedness of the continuum solution. We first validate the approach using two-dimensional steady-state and decelerating inclined flows. We then demonstrate the efficiency of our approach by modeling three-dimensional sub-aerial granular column collapse for varying initial column aspect ratios, where our multiscale method compares well with the computationally expensive computational fluid dynamics (CFD)-DEM simulation.

Dense granular flows↗

Fluid modeling of low-temperature plasmas

Fluid models are essential for understanding and predicting low-temperature plasma (LTP) behavior in various scientific and industrial settings. This paper provides an introductory tutorial on fluid modeling of LTPs, covering model formulation, implementation, and computational simulations. The tutorial focuses on five main components of the formulation of LTP fluid models: fluid flow, energy, chemistry, electromagnetism, and material properties, as well as in essential aspects of model implementations, including multiscale phenomena, multiphysics coupling, and numerical convergence. Designed for students and early-career researchers, this work offers a practical foundation for developing and using fluid models, from in-house computational codes to commercial software, bridging fundamental theory with real-world applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Advancing material modeling in hydrocodes using a concurrent finite-element and molecular dynamics multiscale framework

We present a multiscale simulation framework that couples the finite-element method with molecular dynamics. Bypassing traditional equations of state (EOS) by using in-line atomistic simulations, the method offers the advantage of incorporating detailed microscale physics not easily represented with coarse-grained models. Coupling consistency with the continuum code is ensured through the use of lifting and restriction operators, in line with heterogeneous multiscale methods. The concurrent continuum-atomistic framework is validated through comparison with experimental results and conventional EOS models, and demonstrated in a shock-driven hydrodynamic flow simulation under extreme conditions. We further evaluate the framework's usability by comparing it to state-of-the-art EOS models of deuterium. A computational performance study reveals that the atomistic EOS evaluation is a feasible alternative to conventional approaches, and demonstrates a weak scaling of 99% efficiency. These results highlight the framework's potential for large-scale multiscale modeling across a broad range of materials and conditions.

Computer science↗

Micrometer: Micromechanics transformer for predicting full field mechanical responses of heterogeneous materials

Predicting mechanical responses of heterogeneous materials across scales remains a significant challenge. Traditional computational methods often struggle with complex and multiscale nature of these materials, limiting their effectiveness in real-world applications. Here, in this paper, we introduce Micrometer, a vision transformer based deep learning model designed to predict full field mechanical responses of heterogeneous materials, bridging the gap between computer vision and solid mechanics problems. We show that Micrometer, trained on a large-scale high-resolution dataset of 2D fiber-reinforced composites, can achieve state-of-the-art performance in predicting microscale strain fields across a wide range of material properties and loading conditions. Our model demonstrates accuracy and computational efficiency in applications such as computational homogenization and multiscale modeling, reducing computational time by up to two orders of magnitude compared to conventional numerical solvers while maintaining less than 1 % errors in predicting macroscale stress fields. Furthermore, we showcase Micrometer’s adaptability through transfer learning experiments on new materials with limited data, highlighting its potential to tackle diverse scenarios in computational solid mechanics. These results represent a significant step towards AI-driven innovation in materials science, addressing the limitations of traditional numerical methods and paving the way for more efficient simulations of heterogeneous materials across various industrial applications.

Composite materials↗

Spatial Optimization of Multiscale Biorefinery Deployment for a Diversified Bioeconomy in the United States

Strategic biorefinery siting is critical for a diversified bioeconomy, yet industry, policy, and research often focus on either large-scale biofuel plants or smaller-scale specialty bioproduct facilities, with limited coordination across scales. We address this gap by modeling biorefinery deployment spanning a 28-fold difference in capacity. We developed an open-source, spatially explicit framework integrating techno-economic analysis with logistics and refinery cost surrogate models to evaluate multiscale miscanthus-derived biorefineries across the rainfed U.S. for the production of ethanol, succinic acid, lactic acid, potassium sorbate, and acrylic acid. Overall costs change little as feedstock density increases, while transport distances decrease by ∼30 to 67% (∼100 km) and siting flexibility improves. Specifically, a 5-fold feedstock density increase (2% to 10% of suitable land) reduces minimum selling prices by <10% (e.g., 0.27 USD·gal –1 for ethanol). This limited economic sensitivity suggests dense planting is not required for competitive deployment, particularly for smaller-scale facilities. Representing collection areas as irregular rather than circular expands the feasible space under low-density scenarios. While large-scale refineries anchor regional supply chains, smaller facilities retain spatial flexibility even when large refineries are established. These findings highlight the importance of spatial representation and multiscale coordination for robust, regionally tailored biomanufacturing networks to advance renewable carbon integration without extensive land conversion.

biorefinery siting↗

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↗

COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Correction to “COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins”

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Molecular interactions↗

Generalized fractional approach to solving partial differential equations with arbitrary dispersion relations

The dynamics of physical systems are typically modeled by partial differential equations (PDEs). Because of the complexity in physical systems, PDE models rely on approximations or limiting cases. To model the full complexity of physical systems, it is necessary to use multiscale approaches where appropriate models are used at each level. Alternatively, complexity can be directly tackled by fractional integrodifferential equations that must be derived for each system. Here, we argue that complexity can be restored in PDEs by describing them from a fractional calculus perspective. Rather than deriving a fractional integrodifferential equation, we reinterpret the dispersion relation of the system by use of the Riesz definition, which contains the required information relating the energy and momentum space of the system and thus fully describes their dynamics. The approach is demonstrated by two examples: the Landau–Lifshitz equation in a 1D ferromagnetic chain and a modified KdV equation supporting surface gravity waves or Euler dispersion. The presented approach is applicable to fluids, soft matter, and solid-state matter and can be readily generalized to higher dimensions and more complex systems. While numerical calculations are needed to determine the fractional operator, the approach is analytical and can be utilized to determine analytical solutions and investigate nonlinear problems.

97 MATHEMATICS AND COMPUTING↗

Mortality attributable to PM 2.5 from wildland fires in California from 2008 to 2018

In California, wildfire risk and severity have grown substantially in the last several decades. Research has characterized extensive adverse health impacts from exposure to wildfire-attributable fine particulate matter (PM 2.5 ), but few studies have quantified long-term outcomes, and none have used a wildfire-specific chronic dose-response mortality coefficient. Here, we quantified the mortality burden for PM 2.5 exposure from California fires from 2008 to 2018 using Community Multiscale Air Quality modeling system wildland fire PM 2.5 estimates. We used a concentration-response function for PM 2.5 , applying ZIP code–level mortality data and an estimated wildfire-specific dose-response coefficient accounting for the likely toxicity of wildfire smoke. We estimate a total of 52,480 to 55,710 premature deaths are attributable to wildland fire PM 2.5 over the 11-year period with respect to two exposure scenarios, equating to an economic impact of $\$432$ to $\$456$ billion. These findings extend evidence on climate-related health impacts, suggesting that wildfires account for a greater mortality and economic burden than indicated by earlier studies.

60 APPLIED LIFE SCIENCES↗

Learning Physically Interpretable Atmospheric Models From Data With WSINDy

The multiscale and turbulent nature of Earth's atmosphere has historically rendered accurate weather modeling a hard problem. Recently, there has been an explosion of interest surrounding data-driven approaches to weather modeling, which in many cases show improved forecasting accuracy and computational efficiency when compared to traditional methods. However, many of the current data-driven approaches employ highly parameterized neural networks, often resulting in uninterpretable models and limited gains in scientific understanding. In this work, we address the interpretability problem by explicitly discovering partial differential equations governing atmospheric phenomena, identifying symbolic mathematical models with direct physical interpretations. The purpose of this paper is to demonstrate that, in particular, the weak-form sparse identification of nonlinear dynamics (WSINDy) algorithm can learn effective atmospheric models from both simulated and assimilated data. Our approach adapts the standard WSINDy algorithm to work with high-dimensional fluid data of arbitrary spatial dimension.

58 GEOSCIENCES↗

Universal Electronic‐Structure Relationship Governing Intrinsic Magnetic Properties in Permanent Magnets

An electronic-structure-centered perspective is presented on permanent-magnet (PM) design, highlighting two key levers, that is, saturation magnetization (M s ), governed by 3d-band filling and exchange physics, and magnetocrystalline anisotropy energy (MAE), arising from spin-orbit coupling (SOC) on anisotropic orbital populations. Reviewing current practices, including DFT-based MAE/J ij extraction, atomistic-spin and micromagnetic modeling, and high-throughput machine learning (ML) pipelines, three bottlenecks limiting predictive discovery is identified that is i) electronic-structure accuracy for small MAE (sensitive to functional choice, Hubbard U, and many-body effects), ii) finite-temperature and kinetic realism (phonon/magnon renormalization, ordering kinetics), and iii) descriptor and multiscale decoupling (lack of SOC-weighted and orbital-resolved fingerprints). Deep dives into the electronic-structure of Nd─Fe─B and Fe─N show how these fingerprints govern magnetic performance, motivating DFT- and quantum-mechanics-based descriptors for discovery. Unbiased, structure-driven exploration, coupled with high-throughput simulations, ML, generative AI, and reasoning models, accelerates candidate identification and propagates insights across scales. Addressing supply-chain risks, on future needs of designing “critical-element-free” magnets with tailored microstructure and high energy products is emphasized. By integrating electronic fingerprints, AI reasoning, and multiscale modeling, a practical roadmap is provided for rare-earth-lean or rare-earth free, high-performance, sustainable PMs.

Singh, Prashant [Ames Laboratory, and Iowa State U↗

Mechanistic Multiscale Uncertainty Propagation in Support of Accelerated Fuel Qualification

Taking a nuclear fuel concept through the research, development, and qualification stages has historically taken on the order of 20 to 25 years because of extensive irradiation tests required for a variety of conditions. The concept of accelerated fuel qualification (AFQ) has been proposed to increase the innovation pace for nuclear fuels. The goal of AFQ is not to replace the traditional qualification approach but rather to reduce the total number of experiments required to ensure approval from the regulatory authority. Of the many AFQ approaches being explored, advanced modeling—and, in particular, mechanistic modeling—is in a uniquely cross-cutting position to reduce the number of required integral tests through the inclusion of separate-effects testing, while helping to extrapolate reactor performance during rare events. We make the case that propagation of uncertainty through various computational length scales helps contextualize mechanistic modeling. We will utilize UO 2 fission gas diffusion predictions from the atomistically informed cluster dynamics code Centipede to inform fuel performance rodlet simulations using the BISON finite element code as the metric for showing how multiscale mechanistic uncertainty quantification can help reduce uncertainty in fuel performance. In conclusion, by quantifying uncertainty and its reduction through multiscale modeling, the qualification process may be accelerated through the reduction of costly irradiation experiments.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Impact of the Earthquake Rupture on Ground-Motion Variability of the 24 August 2016 M w 6.2 Amatrice, Italy, Earthquake

Here, the devastating 24 August 2016 M w 6.2 earthquake that struck Amatrice, Italy, marked the beginning of a prolonged seismic sequence dominated by three subsequent M w ≥6.0 events in the central Apennines region. The earthquake destroyed Amatrice’s historic center, claiming the lives of 299 individuals and causing widespread damage in the neighboring villages. The severity of the ground shaking, with a recorded maximum acceleration of 850 cm/s 2 on the east–west component at the Amatrice station, was far greater than the predicted acceleration based on the Italian ground-motion model (GMM). As pointed out by several investigations, the observed ground-motion amplitude and its spatial variability during the earthquake can be linked to specific rupture characteristics, including slip distribution and rupture directivity effects revealed by the observed data (Tinti et al., 2016; Pischiutta et al., 2021). In this study, we conducted physics-based 3D numerical simulations of ground motion for the Amatrice earthquake for frequencies up to 3 Hz. We employed a series of kinematic rupture models and a well-constrained local 3D velocity model incorporating surface topography. The kinematic rupture realizations were generated using multiscale hybrid and fully stochastic models, following the technique proposed by Graves and Pitarka (2016). We focused on assessing the sensitivity of near-fault ground-motion amplitudes to earthquake rupture characteristics, in particular, the spatial slip pattern. To evaluate the quality of our simulations, we employed goodness-of-fit measurements performed in comparisons of simulated and recorded ground motions. The simulated ground motions compare well with the recorded data and predictions from GMMs for Italy, ITA18 (Lanzano et al., 2019). However, we found that the simulated interevent ground-motion variability (randomness in the source process) of peak ground velocity, σ (PGV) is higher than the constant σ (PGV) predicted by conventional GMMs. Our simulations using several rupture scenarios demonstrate that the near-fault ground-motion amplification pattern is directly related to the slip distribution pattern.

3D Ground Motions Simulations↗