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Results for “atomistic simulation”
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Atomistic computer simulations of dissolution of inorganic glasses.
Abstract not provided.
Active sampling for neural network potentials: Accelerated simulations of shear-induced deformation in Cu–Ni multilayers
Neural network potentials (NNPs) can greatly accelerate atomistic simulations relative to ab initio methods, allowing one to sample a broader range of structural outcomes and transformation pathways. In this work, we demonstrate an active sampling algorithm that trains an NNP that is able to produce microstructural evolutions with accuracy comparable to those obtained by density functional theory, exemplified during structure optimizations for a model Cu–Ni multilayer system. We then use the NNP, in conjunction with a perturbation scheme, to stochastically sample structural and energetic changes caused by shear-induced deformation, demonstrating the range of possible intermixing and vacancy migration pathways that can be obtained as a result of the speedups provided by the NNP. The code to implement our active learning strategy and NNP-driven stochastic shear simulations is openly available at https://github.com/pnnl/Active-Sampling-for-Atomistic-Potentials .
Molecular latent space simulators
Latent space simulators learn kinetic models for atomistic simulations and generate novel trajectories at six orders of magnitude lower cost.
Salts in Hot Water: Developing a Scientific Basis for Supercritical Desalination and Strategic Metal Recovery
The w21_superdesal project is part of an LDRD-DR on supercritical desalination (20190057DR). The goal of the simulation work is to use atomistic simulations to understand at a molecular level the changes in hydrogen bonding and ion solvation that occur as we increase the temperature and/or pressure and change the density and ion concentration. Our simulation results will also aid in the interpretation of experimental data and guide the development of applied thermodynamic models for engineering design calculations.
Scalable Simulation of Pressure Gradient-Driven Transport of Rarefied Gases in Complex Permeable Media Using Lattice Boltzmann Method
Accurate representations of slip and transitional flow regimes present a challenge in the simulation of rarefied gas flow in confined systems with complex geometries. In these regimes, continuum-based formulations may not capture the physics correctly. This work considers a regularized multi-relaxation time lattice Boltzmann (LB) method with mixed Maxwellian diffusive and halfway bounce-back wall boundary treatments to capture flow at high Kn. The simulation results are validated against atomistic simulation results from the literature. We examine the convergence behavior of LB for confined systems as a function of inlet and outlet treatments, complexity of the geometry, and magnitude of pressure gradient and show that convergence is sensitive to all three. The inlet and outlet boundary treatments considered in this work include periodic, pressure, and a generalized periodic boundary condition. Compared to periodic and pressure treatments, simulations of complex domains using a generalized boundary treatment conserve mass but require more iterations to converge. Convergence behavior in complex domains improves at higher magnitudes of pressure gradient across the computational domain, and lowering the porosity deteriorates the convergence behavior for complex domains.
Patchy particle model of hydrated amorphous silica
Glasses corroded in static aqueous conditions typically reach a slow, residual rate of dissolution as a result of the complex interplay between multiple processes. While intrinsically suited to address this problem, Monte Carlo (MC) models developed to date have relied on lattices to describe the amorphous structure of glass and are thus unable to reproduce the residual rate of glass corrosion. A recently developed MC approach based on amorphous structures derived from molecular dynamics simulations offers a solution [Kerisit and Du J. Non-Cryst. Solids 522 (2019) 119601], but it requires a simple model that can rapidly relax the glass-water interface upon each dissolution/condensation event to retain the ability of MC simulations to reach large spatial and temporal scales. To this end, a patchy particle model of hydrated amorphous silica was developed and evaluated against atomistic simulations in this work. Models of water and amorphous silica were first developed separately, and cross terms were then defined to enable simulations of hydrated amorphous silica structures with varying water content. While the nature of its interaction potential prevents the patchy particle model from reproducing simultaneously the structure and dynamics of the systems of interest with a single set of parameters, it described well the connectivity of hydrated amorphous silica structures and the local coordination geometry of individual species. Therefore, this model opens the door to MC simulations of the residual rate of glass corrosion and offers an alternative to atomistic models to investigate the evolution of silica gels over large spatial and temporal scales.
Proton radiation effects in indium oxide using cascade molecular dynamics simulations
Metal oxide (MO) semiconductors, characterized by their wide band gaps and notable charge transport properties, are promising candidates for electronic applications in extreme environments, including near-Earth space. However, atomistic simulations of radiation–matter interactions in MOs remain challenging due to the limitations of existing interatomic potentials, which often fail to capture both the short-range repulsive forces essential for radiation damage modeling and the long-range electrostatic effects governing defect evolution. In this work, we develop a customized interatomic potential tailored for radiation damage simulations in indium oxide (In 2 O 3 ) as a model system, a representative MO material. Our potential integrates the Ziegler-Biersack-Littmark potential to accurately describe short-range interactions with Buckingham and Coulombic potentials to account for long-range forces. We perform molecular dynamics simulations of low-energy proton irradiation using this custom potential. We employ the primary knock-on atom (PKA) cascade method to study atomic displacements and primary defect formation. Simulations were conducted for 1 keV proton irradiation in four randomly chosen directions, and PKA-driven defect analyses at 5, 10, and 15 keV to examine the effects of direction and energy level on damage generation. Our results provide insight into the impact of irradiation direction and energy level on the cascade evolution and defect formation mechanisms.
Scale and rate in CdS pressure-induced phase transition
Here, we describe recent efforts to improve our predictive modeling of rate-dependent behavior at, or near, a phase transition using molecular dynamics simulations. Cadmium sulfide (CdS) is a well-studied material that undergoes a solid-solid phase transition from wurtzite to rock salt structures between 3 and 9 GPa. Atomistic simulations are used to investigate the dominant transition mechanisms as a function of orientation, size and rate. We found that the final rock salt orientations were determined relative to the initial wurtzite orientation, and that these orientations were different for the two orientations and two pressure regimes studied. The CdS solid-solid phase transition is studied, for both a bulk single crystal and for polymer-encapsulated spherical nanoparticles of various sizes.
Minimal implicit-solvent coarse-grained simulation of Pluronic block copolymers with ionic liquids
Pluronic block copolymers, composed of poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO) in a triblock structure (PEO–PPO–PEO), are well known for their amphiphilic character and ability to self‐assemble into micelles in aqueous solution. The addition of ionic liquids (ILs) can further modulate the core–shell structures of these copolymers, influencing their stability, critical micellization temperature, and size. However, fully atomistic simulations often become prohibitively expensive due to the size and complexity of these systems. In this work, coarse‐grained simulations using a minimal implicit‐solvent model were performed to examine how two classes of ILs, namely, 1‐alkyl‐3‐methylimidazolium ([C n C 1 im]) and 1‐alkyl‐3‐methylpyrrolidinium ([C n C 1 pyrr]), change the micellization of Pluronic block copolymers in aqueous solution. The effects of IL concentration and alkyl group length were investigated, and the model greatly improved the efficiency of simulating large‐scale micelle systems. Furthermore, the numerical simulations are qualitatively compared with experimental investigations. Our results show that adding ILs expands the micelle core by embedding IL tails among the PPO blocks, thereby increasing overall micelle size. Less polar ILs generally induce more pronounced micellar growth. However, the effect of IL tail length on conformation and micellar packing is non‐monotonic. Up to moderate chain lengths (around C8–C10), the IL tails can extend sufficiently to increase local separation within the micelle; at longer tail lengths, enhanced hydrophobic clustering and steric hindrance cause the tails to bend or fold, capping further expansion. In addition, although block copolymer chains tend to pack more closely in the presence of longer‐tailed ILs, the random coil size of an individual polymer chain does not necessarily shrink. Meanwhile, these insights provide a deeper understanding of how Pluronic/IL systems interact, informing applications in drug delivery, cosmetics, food, and environmental engineering. Finally, our minimal implicit‐solvent model can be applied to larger systems and longer timescales, substantially reducing computational cost while reproducing key structural trends observed experimentally.
Grain boundary structure search by using an evolutionary algorithm with effective mutation methods
Grain boundaries (GBs) accommodate the misorientation between adjacent grains in a polycrystalline material. GBs are geometrically described by the macroscopic and microscopic degrees of freedom. Besides, at the atomistic level, GBs exhibit complicated behaviors under varying thermodynamic conditions. The complexity of atomistic GB structures demands stochastic searching for possible states. The effectiveness of stochastic search methods relies on techniques to recreate and select atomistic structures. In this work, we developed a new mutation operator that can induce direct and collective atomistic structure changes to boost the search efficiency of exploring GB structures with evolutionary algorithms (EA). We implemented the mutation methods along with innovative selection, crossover, boundary condition preprocessing methods to form an EA-based package to explore GB structures in grand canonical ensembles with atomistic simulations. We used this package to study the [001] symmetric tilt grain boundaries (STGBs) in FCC copper (Cu), the [110] STGBs in BCC tungsten (W), and the $[1\bar{2}10]$ STGBs in HCP magnesium (Mg). The results show that our design and implementation based on new mutation procedures, selection, and boundary conditions provide a high-quality search of atomistic GB structures in the grand canonical ensemble for different crystal lattices.
Predicting the Mechanical Response of Polyhydroxyalkanoate Biopolymers Using Molecular Dynamics Simulations
Polyhydroxyalkanoates (PHAs) have emerged as a promising class of biosynthesizable, biocompatible, and biodegradable polymers to replace petroleum-based plastics for addressing the global plastic pollution problem. Although PHAs offer a wide range of chemical diversity, the structure–property relationships in this class of polymers remain poorly established. In particular, the available experimental data on the mechanical properties is scarce. In this contribution, we have used molecular dynamics simulations employing a recently developed forcefield to predict chemical trends in mechanical properties of PHAs. Specifically, we make predictions for Young’s modulus, and yield stress for a wide range of PHAs that exhibit varying lengths of backbone and side chains as well as different side chain functional groups. Deformation simulations were performed at six different strain rates and six different temperatures to elucidate their influence on the mechanical properties. Our results indicate that Young’s modulus and yield stress decrease systematically with increase in the number of carbon atoms in the side chain as well as in the polymer backbone. In addition, we find that the mechanical properties were strongly correlated with the chemical nature of the functional group. The functional groups that enhance the interchain interactions lead to an enhancement in both the Young’s modulus and yield stress. Finally, we applied the developed methodology to study composition-dependence of the mechanical properties for a selected set of binary and ternary copolymers. Overall, our work not only provides insights into rational design rules for tailoring mechanical properties in PHAs, but also opens up avenues for future high throughput atomistic simulation studies geared towards identifying functional PHA polymer candidates for targeted applications.
Kernel fusion in atomistic spin dynamics simulations on Nvidia GPUs using tensor core
In atomistic spin dynamics simulations, the time cost of constructing the space- and time-displaced pair correlation function in real space increases quadratically as the number of spins N, leading to significant computational effort. The GEMM subroutine can be adopted to accelerate the calculation of the dynamical spin-spin correlation function, but the computational cost of simulating large spin systems (>40000 spins) on CPUs remains expensive. In this work, we perform the simulation on the graphics processing unit (GPU), a hardware solution widely used as an accelerator for scientific computing and deep learning. Here we show that GPUs can accelerate the simulation up to 25-fold compared to multi-core CPUs when using the GEMM subroutine on both. To hide memory latency, we fuse the element-wise operation into the GEMM kernel using CUTLASS that can improve the performance by 26% ~ 33% compared to implementation based on cuBLAS. Furthermore, we perform the on-the-fly calculation in the epilogue of the GEMM subroutine to avoid saving intermediate results on global memory, which makes the large-scale atomistic spin dynamics simulation feasible and affordable.
Bridging adsorption behavior of confined CH 4 -CO 2 binary mixtures across scales
An accurate understanding of the competitive adsorption of CH 4 -CO 2 binary mixtures in nano-confined systems is critical for engineering CO 2 storage in shale gas reservoirs. Due to difficulties in making reliable experimental observations in nano-scale, atomistic simulations (ASs), such as the Grand Canonical Monte Carlo (GCMC) method, provide a viable approach to studying the adsorption behavior of confined fluids. ASs are, however, limited in the size of the compositional domain due to the high computational cost. This work proposes a framework that combines AS and the lattice Boltzmann (LB) method to bridge the physics of confined fluids across scales. The Peng–Robinson equation of state (PR-EoS) produces fugacity coefficients, which serve as input for conducting multi-component GCMC simulations. These GCMC simulations explore the competitive adsorption behavior of CH 4 -CO 2 in nano-slits at various composition, pressure, and channel-width conditions. Both components generate adsorption layers with high densities near the walls with CO 2 preferentially adsorbing compared to CH 4 on the organic walls of carbon sheets. At the mesoscale, a pseudopotential model represents the intermolecular forces in multi-component, multiple-relaxation-time LB simulations. The LB simulations are in good agreement with the GCMC results, allowing us to obtain values for tunable LB parameters. We then extend the use of LB to simulate adsorption behavior in complex networks with nano-sized channels. The phase behavior and fluid properties in the complex geometries of nano-channels differ from nano-slits and bulk systems. Furthermore, the bridging of physics from GCMC (microscale) to LB (mesoscale) via the macroscale PR-EoS connects the adsorption behavior of binary systems across scales.
Statistical perspective on embrittling potency for intergranular fracture
Embrittling potency is a thermodynamic metric that assesses the influence of solute segregation to a grain boundary (GB) on intergranular fracture. Historically, authors of studies have reported embrittling potency as a single scalar value, assuming a single segregation site of importance at a GB and a particular cleavage plane. However, the topography of intergranular fracture surfaces is not generally known a priori. Accordingly, we, in this study, present a statistical ensemble approach to compute embrittling potency, where many free surface (FS) permutations are systematically considered to model fracture of a GB. The result is a statistical description of the thermodynamics of GB embrittlement. As a specific example, embrittling potency distributions are presented for Cr segregation to sites at two Ni $\langle 111 \rangle$ symmetric tilt GBs using atomistic simulations. We show that the average embrittling potency for a particular GB site, considering an ensemble of FS permutations, is not equal to the embrittling potency computed using the lowest energy pair of FSs. A mean GB embrittlement is proposed, considering both the likelihood of formation of a particular FS and the probability of solute occupancy at each GB site, to compare the relative embrittling behavior of two distinct GBs.
Shadow molecular dynamics for flexible multipole models
Shadow molecular dynamics provide an efficient and stable atomistic simulation framework for flexible charge models with long-range electrostatic interactions. Shadow molecular dynamics simulations are driven by approximate “shadow” Born–Oppenheimer potentials for which the exact charges and forces are directly accessible without relying on costly (and approximate) iterative solvers. While previous implementations have been limited to atomic monopole charge distributions, we extend this approach to flexible multipole models. We derive detailed expressions for the shadow energy functions, potentials, and force terms, explicitly incorporating monopole–monopole, dipole–monopole, and dipole–dipole interactions. In our formulation, both atomic monopoles and atomic dipoles are treated as extended dynamical variables alongside the propagation of the nuclear degrees of freedom. We demonstrate that introducing the additional dipole degrees of freedom preserves the stability and accuracy previously seen in monopole-only shadow molecular dynamics simulations. In addition, we present a shadow molecular dynamics scheme where the monopole charges are held fixed while the dipoles remain flexible. Our extended shadow dynamics provide a framework for stable, computationally efficient, and versatile molecular dynamics simulations involving long-range interactions between flexible multipoles. This is of particular current interest in combination with machine-learned interatomic potentials, including long-range electrostatic interactions.
Age hardening response of Cu-30Ni alloys: The role of Si microalloying additions
Cu-30Ni alloys offer high strength and excellent corrosion resistance for maritime applications. While primarily a solid solution system, industrial alloys typically include microalloying additions of Fe, Mn, Nb and/or Si to enable age hardening. However, an understanding of the microstructural evolution during age hardening remains incomplete. Here, we conduct systematic ageing treatments and report the resulting hardness and microstructures. The Cu-30Ni alloy with Si aged at 650 °C for 6 h demonstrates significantly enhanced Vickers hardness, reaching ∼201 HV 1 compared to 103 HV 1 for the as-homogenised sample. Si-rich clusters and γ′ precipitates are identified, with their composition, size, and volume fraction quantified to determine their strengthening contributions. First-principles atomistic simulations elucidate the underlying formation mechanisms of these clusters and precipitates, highlighting the critical role of Si in driving their nucleation and growth. This study advances the design of high-strength, Cu alloys with the potential for corrosion resistance in demanding maritime environments.