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At least 271 records · Page 15

Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics

In this work, we evaluate the biomolecular dynamics behaviors when conventionally iterating between all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations over multiple cycles. We implemented the workflow to iterate between AA and CG in OpenMM, namely the iterative multiscale MD (iMMD) simulation workflow. In particular, we aim to identify practical applications for iterating between AA and CG simulations in a conventional manner without any constraints or model modifications. We evaluate the iMMD workflow on four representative systems, spanning folding of two soluble proteins and protein-protein as well as protein-lipid interactions of two membrane proteins. We observe that iteration between AA and CG representations could help the soluble proteins exit undesirable metastable states to fold, resulting from random protein structural distortions due to cycling. Consequently, the most reliable use of iterative AA and CG simulations appears to be to accelerating complex lipid mixing for membrane-bound protein systems rather than sampling protein conformational space. Our work explores the practical usages and limitations for iterative AA and CG simulations using readily available AA and CG force fields. The evaluated iMMD workflow in OpenMM is made available at https://github.com/lanl/iMMD.

59 BASIC BIOLOGICAL SCIENCES↗

SciDAC ISEP: Integrated Simulation of Energetic Particles in Burning Plasmas

The objective of the SciDAC Center for Integrated Simulation of Energetic Particles in Burning Plasmas (ISEP) is to improve physics understanding of energetic particle (EP) confinement and EP interactions with burning thermal plasmas through large-scale simulations. The ISEP center will develop a multiscale and multiphysics ISEP framework for a predictive capability of EP physics and deliver an EP module incorporating both first-principles simulations and high fidelity reduced transport models to the fusion whole device modeling (WDM) project. The ISEP framework will enable us to perform long time, global kinetic simulations of EP physics in burning plasmas, by utilizing the full power of the next generation supercomputers. Our research and development activities will build on fruitful collaborations with computer scientists and applied mathematicians to offer enabling technologies for performance scalability, portability, solvers, coupling for integration with the fusion WDM project, and long-term preservation of data.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Time-domain all-frequency stable formulation for low-frequency electromagnetic simulation with Newmark-β time integration

An implicitly Coulomb-gauged A-ϕ formulation has previously been proposed and validated for finite ele- ment simulations of low-frequency and multiscale electromag- netic problems in the frequency domain. This formulation has demonstrated numerical stability across all frequencies, with its accuracy, efficiency, and iterative convergence established in various frequency-domain scenarios. However, direct time- domain computation is often preferable for wideband electro- magnetic problems and is typically indispensable in nonlinear and multiphysics simulations. In this work, the A-ϕ formulation is extended to the time domain. By incorporating the well-known Newmark-β time integration scheme, the proposed formulation is validated through capacitive and inductive test cases. The results confirm the solution’s accuracy and demonstrate the formulation’s stability in the time domain.

Mekonnen, Minyechil↗

Data-driven equation-free dynamics applied to many-protein complexes: The microtubule tip relaxation

Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5'-triphosphate) to GDP (guanosine-5'-diphosphate) within the β-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems. This study employs the “equation-free” multiscale computational method to accelerate the relaxation of all-atom simulations of MT tips toward their putative equilibrium conformation. Using large MT lattice systems (14 protofilaments × 8 heterodimers) comprising ~21-38 million atoms, we applied this multiscale approach to leapfrog through time and nearly double the computational efficiency in realizing relaxed all-atom conformations of GDP- and GTP-complexed MT tips. Commencing from an initial 4 μs unbiased all-atom simulation, we interleave coarse projective “equation-free” jumps with short bursts of all-atom molecular dynamics simulation to realize an additional effective simulation time of 1.875 μs. Our 5.875 μs of effective simulation trajectories for each system expose the subtle yet essential differences in the structures of MT tips as a function of whether β-tubulin monomer is complexed with GDP or GTP, as well as the lateral interactions within the MT tip, offering a refined understanding of features underlying MT dynamic instability. Furthermore, the approach presents a robust and generalizable framework for future explorations of large biomolecular systems at atomic resolution.

Wu, Jiangbo [University of Chicago, IL (United Sta↗

Understanding and Strategies for Controlled Interfacial Phenomena in Lithium-Ion Batteries and Beyond

Electrolyte chemistry and properties and electrode structure and chemical properties particularly at the interfaces are crucial for the development of advanced battery components. This project focused on elucidating the roles of the electrolyte and electrode on the formation and evolution of the SEI layer and cell electrochemical performance on silicon and on Li metal anodes. For Si nano/microstructures we evaluated lithiation, volume changes, reactivity, and chemo-mechanical transformations as functions of nanoparticle size, shape, presence of coatings, electrolyte composition, electron leakage to the electrolyte, and cycling. For Li metal anodes we provided detailed analyses of the electrode and electrolyte effects on interfacial reactivity and as a function of microstructural evolution and underlying stochasticity as dendrites nucleate and grow. We thoroughly investigated and simulated how the chemistry of the various components of the electrolyte and the electrode architecture may affect the electrochemical reactions as well as cell degradation. A multiscale modeling approach was utilized, where atomistic simulations informed about the microscopic behavior of the system, and intermediate time and length scales were investigated with mesoscopic models. Results were also tested against selected experiments from our collaborators. The combined theoretical-experimental strategy saves costs by utilizing predictions from computational analyses to guide experimentation.

25 ENERGY STORAGE↗

Woven ceramic matrix composite surrogate model based on physics-informed recurrent neural network

A recurrent neural network (RNN) based surrogate model is developed to emulate the nonlinear constitutive behavior of woven ceramic matrix composites (CMCs) driven by matrix damage at multiple length scales. Physics-informed constraints are introduced into the surrogate model through regularization to ground the prediction in physics and improve its predictive capabilities. Training data is generated using the multiscale generalized method of cells (MSGMC) approach coupled with a matrix damage model. This coupling permits simulating the nonlinear behavior of woven CMCs based on constituent response at the micro-, meso-, and macroscales. The multiscale repeating unit cell is loaded under non-monotonic conditions including multiple load / unload cycles and tension / compression. The fiber volume fraction as well as the intra- and intertow void volume fractions are also varied in the generation of training data. Therefore, the RNN-based surrogate model is tasked with predicting, as a function of variable input strain sequence and fiber and void volume fractions, the resulting stress versus strain response while satisfying physical constraints such as positive semi-definiteness of the tangent stiffness matrix and linear elastic unloading. Further, the trained surrogate model effectively matches the stress versus strain response and successfully predicts the tangent modulus throughout the loading regime. Neural network based surrogate models can offer efficient alternatives to running computationally intensive multiscale material models to simulate the nonlinear response of large structural models. Therefore the presented work provides evidence towards the feasibility of developing, training, and running such models for CMCs with complex architectures, nonlinear multiaxial material response, and under non-monotonic loading conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Flow-shear destabilization of multiscale electron turbulence

The impact of sheared ${\mathbf{E} \hskip -1pt \times \hskip -1pt \mathbf{B}}$ flow on multiscale turbulence is studied with nonlinear gyrokinetic simulations. Simulations are based on DIII-D-like, high-confinement mode (H-mode) pedestal parameters in the regime of low ion temperature gradient drive, where there is a broad spectrum of electron temperature gradient (ETG)-driven turbulence. It is found that ${\mathbf{E} \hskip -1pt \times \hskip -1pt \mathbf{B}}$ shear can have a significant effect on ETG-driven electron transport, with an unexpected transition from a turbulence stabilization regime at moderate to large shearing rates $γ_E$ to a novel turbulence destabilization regime at low levels of $γ_E$. In the turbulence stabilization regime, the electron energy flux decreases monotonically with $γ_E$, even when $γ_E$ is small compared to electron mode growth rates. The stabilizing effect comes dominantly from the electron, not ion, gyrokinetic equation. In the novel destabilization regime, reduction of zonal energy results from the interaction of $γ_E$-modulated nonlinear drive in the zonal ion gyrokinetic equation, increasing the electron transport over a broad range of shearing rates. Finally, neither of these effects has been observed in previous electron-scale simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A simplified all-frequency stable formulation with an implicit Coulomb gauge

A potential-based finite element formulation has been developed in the past to circumvent the low-frequency breakdown issues commonly encountered in electromagnetic (EM) simulations of low-frequency and multiscale problems. In this formulation, the magnetic vector and electric scalar potentials have been employed to express the electric field and magnetic flux, leading to a set of two equations that represents all four Maxwell’s equations and the current continuity equation. To enforce the Coulomb gauge, an auxiliary potential has been introduced, which results in a total of three equations to be solved simultaneously. To reduce the number of equations and unknowns needed in a simulation, a simplified formulation is proposed in this paper to enforce the Coulomb gauge implicitly without the need for the auxiliary potential. A numerical example is given to demonstrate the accuracy of the proposed formulation.

Mekonnen, Minyechil↗

Multiscale Nuclear-Electronic Orbital Quantum Dynamics in Complex Environments

Many renewable energy conversion processes rely on the movement of protons as well as electrons through either electrocatalysis or photoexcitation. The simulation of such processes requires a quantum mechanical description of coupled nuclear-electronic dynamics in a solvent or heterogeneous chemical environment. The overall objective of this project is the development of theoretical and computational capabilities for simulating nuclear-electronic quantum dynamics in complex environments and the creation of high-performance, open-source software. This multiscale framework will enable simulations of the real-time dynamics of nonequilibrium excited state proton-coupled electron transfer, quantum decoherence, vibronic energy transfer, and ultrafast radiolysis, as well as their associated time-resolved multidimensional spectroscopies. An important outcome of this project will be a sustainable, reusable, and interoperable open-source software ecosystem. This software will be designed for emerging exascale and future national leadership computers. Another key outcome will be a multiscale quantum dynamics method and software enabling simulations of nonequilibrium nuclear-electronic quantum dynamics in complex environments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Simulation Models for Exploring Magnetic Reconnection

Simulations have played a critical role in the advancement of our knowledge of magnetic reconnection. However, due to the inherently multiscale nature of reconnection, it is impossible to simulate all physics at all scales. For this reason, a wide range of simulation methods have been crafted to study particular aspects and consequences of magnetic reconnection. This article reviews many of these methods, laying out critical assumptions, numerical techniques, and giving examples of scientific results. Plasma models described include magnetohydrodynamics (MHD), Hall MHD, Hybrid, kinetic particle-in-cell (PIC), kinetic Vlasov, Fluid models with embedded PIC, Fluid models with direct feedback from energetic populations, and the Rice Convection Model (RCM).

79 ASTRONOMY AND ASTROPHYSICS↗

Calibration of RAFM Micromechanical Model for Creep Using Bayesian Optimization for Functional Output

A Bayesian optimization procedure is presented for calibrating a multimechanism micromechanical model for creep to experimental data of F82H steel. Reduced activation ferritic martensitic (RAFM) steels based on Fe(8–9)%Cr are the most promising candidates for some fusion reactor structures. Although there are indications that RAFM steel could be viable for fusion applications at temperatures up to 600°C, the maximum operating temperature will be determined by the creep properties of the structural material and the breeder material compatibility with the structural material. Due to the relative paucity of available creep data on F82H steel compared to other alloys such as Grade 91 steel, micromechanical models are sought for simulating creep based on relevant deformation mechanisms. As a point of departure, this work recalibrates a model form that was previously proposed for Grade 91 steel to match creep curves for F82H steel. Due to the large number of parameters (9) and cost of the nonlinear simulations, an automated approach for tuning the parameters is pursued using a recently developed Bayesian optimization for functional output (BOFO) framework (Huang et al., 2021, “Bayesian optimization of functional output in inverse problems,” Optim. Eng., 22, pp. 2553–2574). Incorporating extensions such as batch sequencing and weighted experimental load cases into BOFO, a reasonably small error between experimental and simulated creep curves at two load levels is achieved in a reasonable number of iterations. In conclusion, validation with an additional creep curve provides confidence in the fitted parameters obtained from the automated calibration procedure to describe the creep behavior of F82H steel.

42 ENGINEERING↗

Interfacial solvation and slow transport of hydrated excess protons in non-ionic reverse micelles

This work employs molecular dynamics simulations to investigate the solvation and transport properties of hydrated excess protons (with a hydronium-like core structure) in non-ionic Igepal CO-520 reverse micelles of various sizes in a non-polar solvent. Multiscale Reactive Molecular Dynamics (MS-RMD) simulations were used to describe vehicular and hopping diffusion during the proton transport process. As detailed herein, an excess proton shows a marked tendency to localize in the interfacial region of micellar water pools. Slow proton transport was observed which becomes faster with increasing micellar size. Further analysis reveals that the slow diffusion of an excess proton is a combined result of slow water diffusion and the low proton hopping rate. This study also confirms that a low proton hopping rate in reverse micelles stems from the interfacial solvation of hydrated excess protons and the immobilization of interfacial water. The low water density in the interfacial region makes it difficult to form a complete hydrogen bond network near the hydrated excess proton, and therefore locks in the orientation of hydrated proton cations. The immobilization of the interfacial water also slows the relaxation of the overall hydrogen bond network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Collaborative Research: Vlasov–Maxwell Simulations to resolve electron heating and dissipation, in quasiperpendicular shocks (Final Technical Report)

The project is to study electron heating at quasi-perpendicular shocks. We have analyzed measurements from the Magnetosphere Multiscale (MMS) spacecraft and particle-in-cell simulations to address the question. One key discovery is that waves and are excited in the shock transition region, which further develop into complicated structures and thin current layers, which contribute to accelerate and heat electrons. We further investigated the excitation and evolution of these waves and structures, and their association with ion and electron dynamics. In addition, the analysis technique of Vlasov equation terms is further applied to study electron dynamics at the dayside magnetopause, to understand the effect of density, velocity and temperature variations on electron distributions and kinetics.

58 GEOSCIENCES↗

Solitary Magnetic Structures at Quasi–Parallel Collisionless Shocks: Formation

Solitary magnetic structures known as SLAMS (short large-amplitude magnetic structures) have been considered as essential elements of collisionless shocks with quasi-parallel geometries. Yet the physics underlying their formation remains an open question. In this paper, we use measurements from the magnetospheric multiscale mission combined with fully kinetic simulations to study the formation of SLAMS. We find that gyro-resonance between solar wind ions and right-hand circularly polarized electromagnetic waves results in magnetic field amplification. Gyro-trapping by the growing magnetic field builds up the plasma density that further enhances the current and field. The solitary nature of SLAMS stems from a beat-like magnetic field envelope where the maximum sets the initial location for nonlinear growth. Our results present a conceptual advance on SLAMS, and may shed new light on the open question of magnetic field amplification at astrophysical shocks.

58 GEOSCIENCES↗

Enhanced Planar Antenna Efficiency Through Magnetic Thin-Films

This work proposes to use magnetic material as the substrate of planar antennas to overcome the platform effect caused by the conducting ground plane. The upper bound of the radiation efficiency of an electric-current-driven low-profile antenna is theoretically derived, which is inversely proportional to the Gilbert damping factor of the magnetic material. Meanwhile, the improvement of radiation due to the use of magnetic material is demonstrated by a three-dimensional (3D) multiphysics and multiscale time-domain model. The simulation results match the theoretical derivation, showing 25% radiation efficiency from a planar antenna backed by a FeGaB thin film with 2.56 m thickness. Furthermore, for conductive ferromagnetic materials, it is shown that the eddy current loss can be well suppressed by laminating the thin film into multiple layers. Here, the radiation efficiency of the modeled antenna with a conductive ferromagnetic substrate is improved from 2.2% to 11.8% by dividing the substrate into 10 layers, with a ferromagnetic material fill factor of 93%.

42 ENGINEERING↗

Beyond Magic Barrels: Digital manufacturing for crystallization, process development and optimization of explosive materials: Part II Resveratrol Exemplar

This SAND report summarizes work supported by an Engineering Sciences Research Foundation (ESRF) Lab Directed Research and Development (LDRD) project entitled “Beyond Magic Barrels: Digital manufacturing for crystallization, process development and optimization of explosive materials.” This SAND report is written in two parts with Part 1 discusses recrystallization of our explosive exemplar and Part 2 summarizing our work with recrystallization of resveratrol. We have studied resveratrol recrystallization with a multiscale approach combining experiments, modeling and simulation. At the single crystal scale, microscopy experiments illuminate crystal time-dependent growth rates using advanced image analysis. Bench scale experiments were carried out to look at growth of multiple particles in a small reactor creating thousands of particles and analyzing the results with microscopy and μCT. For the modeling we combine kinetic Monte Carlo (kMC) models with subscale information from density functional theory (DFT) or molecular dynamics. This work is discussed in Part 1 and can also be found in a paper from the project discussing a coarse-grained kMC model specifically developed for resveratrol. For well-mixed systems, we have population balance equations (PBE) linked with species mass conservation forming a set of ordinary differential equations that can be solved quickly. For more complicated geometries, such as the vat crystallization used throughout the complex, a coupled computational fluid dynamic (CFD)/PBE method was developed to account for gradients in temperature and concentration and differences in crystallization rates throughout the domain. These simulations are more complex and require high performance computing. We present results for two cases: 5% seed fast cool with parameters fit to the well-mixed case and 5% seed slow cool using the same parameters. We show reasonable agreement with experiments though are particles are significantly larger than the experiments.

36 MATERIALS SCIENCE↗

Micropolar deep material network

This study extends the Deep Material Network (DMN), a physics-informed machine learning framework, to predict the homogenized mechanical response of composite materials with micropolar (Cosserat-type) constitutive behavior. This extension incorporates microstructure-dependent size effects, enabling accurate, efficient, and size-aware predictions for composites with complex internal architectures. While traditional, direct numerical simulation micropolar models effectively capture size effects by introducing extra local degrees of freedom, they bring significant computational challenges, particularly for multiscale analyses relevant to engineering applications. The micropolar DMN developed in this paper achieves high accuracy while significantly reducing computation time compared to micropolar direct numerical simulations. This advancement enables multiscale analyses and parameter studies that were previously impractical, such as high-cycle fatigue simulations and comprehensive investigations of internal length scale effects notably in size-dependent plastic response and the optimization of lattice structures. By uniting microstructure-sensitive modeling, physics-driven learning, and scalable surrogate modeling, the micropolar DMN paves the way for accelerated material design, large-scale parametric studies, and the reliable incorporation of size-dependent effects across a wide range of engineering applications, including optimization and next-generation composite design.

36 MATERIALS SCIENCE↗

Develop a new integrated macro→micro←nano (MMN) multiscale modeling framework to optimize high strength aluminum alloys and processes for vehicle light-weighting​

Bending tests provide a means to study plane strain fracture performance of 6000 series aluminum alloys. Metrics from bending tests have been correlated with self-pierce riveting (SPR) performance of a high strength AA6111 automotive aluminum alloy in previous works. Using the ORNL HPC resources, this project developed an innovative macro→micro←nano (MMN) multiscale microstructure-based finite element (FE) code to further understanding of the relationship between microstructure and fracture properties of high-strength 6000-series alloys. This work started with microstructural characterization in both mesoscale and nanoscale and bending performance characterization of AA6111 HS2-T6 alloy at Ford, the MMN framework was applied to this alloy to simulate 3-point VDA bending. From the results of the macro-modeling of 3-point VDA bending, the critical region of fracture was identified, and the region geometry was used to construct the micro-model. The fracture criterion of micron-scale precipitates and aluminum matrix which contains submicron and nano particles (AL-SMP-NP) in the micro-model was calibrated and validated by comparing simulated and measured bending results. With the AL-SMP-NP fracture strain obtained, the fracture strain of Al-matrix containing nano particles (ALNP) will similarly be determined by a submicron scale-model using an edge-constrained FE modeling approach developed by Hu et al. With the ALNP fracture strain obtained, the fracture strain of Al-matrix containing no particles will similarly be determined by a nano scale-model using an edge-constrained FE modeling approach. After the MMN framework is built and fracture criterion calibrated, nano-model FE simulations with virtual microstructures was performed to obtain a reduced order model (ROM) of the fracture criterion of the ALNP as a function of volume fraction, size, and distribution of the nanoparticle. This nano→submicron→micro modeling part allows exploration of the influence of different material nanostructures from different process conditions on the bending properties within the multiscale bending simulation framework and the ROM of material bendability as a function of nanoparticle size and shape was established. This obtained reduced order model (ROM) could help guide the design and selection of materials to improve existing SPR process models that could replace trial-and-error rivet/die selection and help to design new rivet/die combinations capable of robustly joining new higher strength 6000 5 series alloys in automotive body structures. This would enable lightweighting of Ford vehicles leading to greater fuel efficiency and reduce manufacturing time and energy.

36 MATERIALS SCIENCE↗