Coarse-grained Particles Research Articles

Modeling complex polycrystalline alloys using a Generative Adversarial Network enabled computational platform

Creating statistically equivalent virtual microstructures (SEVM) for polycrystalline materials with complex microstructures that encompass multi-modal morphological and crystallographic distributions is a challenging enterprise. Cold spray-formed (CSF) AA7050 alloy containing coarse-grained prior particles and ultra-fine grains (UFG) and additively manufactured (AM) Ti64 alloys with alpha laths in beta substrates. The paper introduces an approach strategically integrating a Generative Adversarial Network (GAN) for multi-modal microstructures with a synthetic microstructure builder DREAM.3D for packing grains conforming to statistics in electron backscatter diffraction (EBSD) maps for generating SEVMs of CSF and AM alloy microstructures. A robust multiscale model is subsequently developed for self-consistent coupling of crystal plasticity finite element model (CPFEM) for coarse-grained crystals with an upscaled constitutive model for UFGs. Sub-volume elements are simulated for efficient computations and their responses are averaged for overall stress-strain response. The methods developed are important for image-based micromechanical modeling that is necessary for microstructure-property relations.

Radial gradient characteristics formed by the interstitial space of MWCNT yarn owing to twisting

The interstitial space of a multiwalled carbon nanotube (MWCNT) yarn is key to creating electric double-layer capacitance for harvesting energy. Despite various fabrication methods for MWCNT yarns, the formation mechanism of the interstitial space inside the yarns is poorly understood. Herein, the twisting process of a cylindrical MWCNT bundle into a yarn was simulated using the mesoscale coarse-grained particle dynamics model. A larger fraction of interstitial space was observed in the sheath region of the yarn, where large-diameter MWCNTs were mainly distributed. Small-diameter MWCNTs first swirled toward the inner core during the twisting process, causing the large-diameter MWCNTs to be sparsely distributed throughout the sheath region. The proposed methodology and its results can be applied to the geometric design of twisted MWCNT bundles to maximize the fraction of the interstitial space therein.

Organic carbon cycling in the sediments of Prydz Bay, Eastern Antarctica: Implications for a high carbon sequestration potential

Understanding the dynamics of sedimentary organic carbon (SOC) in the productive continental marginal sea surrounding Antarctica is crucial for elucidating the effect of this sea on the global carbon cycle. We analyzed 31 surface sediment samples and eight sediment cores collected from Prydz Bay (PB) and the adjacent basin area. The element and stable isotope compositions, grain size compositions, and biogenic silica and lithogenic minerals of these samples were used to evaluate the spatial variations in the sources, transport mechanisms, and preservation patterns of SOC, with a particular focus on the efficiency of the biological carbon pump (BCP). Our findings reveal that the SOC originated from mixed marine/terrestrial sources. The δ13C values were higher in the Prydz Bay Gyre (PBG) region than in the open sea area. Biogenic matter-rich debris, associated with fine-grained particles (silt and clay), was concentrated in the PBG, while abiotic ice-rafted debris and coarse-grained particles were preferentially deposited in the bank and ice shelf front regions. Lithogenic matter predominated in the basin sediments. The annual accumulation rate of SOC in PB ranged from 1.6 to 6.2 g·m−2·yr−1 (mean 4.2 ± 1.9 g·m−2·yr−1), and the rates were higher in the PBG than in the ice shelf front region. Estimates based on our tentative box model suggest that the efficiency of the BCP, which refers to the proportion of surface-produced organic carbon successfully transferred to deep waters, is approximately 5.7 % in PB, surpassing the global average (∼0.8 %) and the efficiencies reported for other polar environments. Furthermore, our calculations indicate that the SOC preservation efficiency (the ratio of preserved to initially deposited organic carbon in sediments) in PB is approximately 79 % ± 20 %, underscoring the significant carbon sequestration potential within PB. The results of this study have important implications for the effects of sediment dynamics on the carbon cycle in the sea surrounding Antarctica.

A sub-grid gas–solid interaction model for coarse-grained CFD–DEM simulations

Computational fluid dynamics has been coupled with coarse-grained discrete element method (CFD–CGDEM) to study industrial-scale gas–solid fluidized beds. However, solving the fluid flow at a grid size of several coarse-grained particles (CGPs) cannot accurately predict the gas–solid interaction, and thus reasonable correction model is required. This study develops a sub-grid model to correct the gas–solid interaction and thereby improve the accuracy of coarse-grid CFD–CGDEM simulation. First, the fluid grids with the size of several CGPs are divided into the auxiliary three-dimensional sub-grids. Then, the CGPs are mapped onto the sub-grids by the weight function to reconstruct the local solid velocities and solid fractions of the sub-grids. After that, the simplified mass and momentum conservation equations are solved to resolve the local gas velocities of sub-grids. Finally, the drag on each CGP is corrected based on the local gas-phase hydrodynamics of sub-grids. Results show that the sub-grid model resolving the local gas velocity in all the three directions works better than that just in the main stream direction. The coarse-grid CFD–CGDEM simulations with this sub-grid model agree well with the experiment for the bubbling, turbulent and rapid fluidized beds. Besides, by solving the simplified conservation equations with graphics processing units, the coarse-grid CFD–CGDEM coupled with the sub-grid model achieves 674 times speedup compared to the fine-grid simulation, demonstrating a much more efficient method to study industrial-scale gas–solid fluidized beds.

Expanding density-correlation machine learning representations for anisotropic coarse-grained particles.

Physics-based, atom-centered machine learning (ML) representations have been instrumental to the effective integration of ML within the atomistic simulation community. Many of these representations build off the idea of atoms as having spherical, or isotropic, interactions. In many communities, there is often a need to represent groups of atoms, either to increase the computational efficiency of simulation via coarse-graining or to understand molecular influences on system behavior. In such cases, atom-centered representations will have limited utility, as groups of atoms may not be well-approximated as spheres. In this work, we extend the popular Smooth Overlap of Atomic Positions (SOAP) ML representation for systems consisting of non-spherical anisotropic particles or clusters of atoms. We show the power of this anisotropic extension of SOAP, which we deem AniSOAP, in accurately characterizing liquid crystal systems and predicting the energetics of Gay-Berne ellipsoids and coarse-grained benzene crystals. With our study of these prototypical anisotropic systems, we derive fundamental insights on how molecular shape influences mesoscale behavior and explain how to reincorporate important atom-atom interactions typically not captured by coarse-grained models. Moving forward, we propose AniSOAP as a flexible, unified framework for coarse-graining in complex, multiscale simulation.

GCMe: Efficient Implementation of the Gaussian Core Model with Smeared Electrostatic Interactions for Molecular Dynamics Simulations of Soft Matter Systems.

In recent years, molecular dynamics (MD) simulations have emerged as an essential tool for understanding the structure, dynamics, and phase behavior of charged soft matter systems. To explore phenomena across greater length and time scales in MD simulations, molecules are often coarse-grained for better computational performance. However, commonly used force fields represent particles as hard-core interaction centers with point charges, which often overemphasizes the packing effect and short-range electrostatics, especially in systems with bulky deformable organic molecules and systems with strong coarse-graining. This underscores the need for an efficient soft-core model to physically capture the effective interactions between coarse-grained particles. To this end, we implement a soft-core model uniting the Gaussian core model with smeared electrostatic interactions that is phenomenologically equivalent to recent theoretical models. We first parametrize it generically using water as the model solvent. Then, we benchmark its performance in the OpenMM toolkit for different boundary conditions to highlight a computational speedup of up to 34 × compared to commonly used force fields and existing implementations. Finally, we demonstrate its utility by investigating how boundary polarizability affects the adsorption behavior of a polyelectrolyte solution on perfectly conducting and nonmetal boundaries.

Effect of Median Soil–Particle Size Ratio on Water Storage Capacity of Capillary Barrier

Capillary barriers are widely used as a cover system to enhance the upper-soil-layer water storage capacity and reduce water infiltrate into the lower soil layer. In this paper, the effects of the median soil–particle size ratio on the water storage capacity of capillary barriers were studied using a series of indoor one-dimensional soil column infiltration tests. The results show that the water storage capacity rises with an increase in the median soil–particle size ratio until it exceeds 10. The variation in the total water storage capacity is related to not only the median soil–particle size ratio but also the particle size of coarse-grained soil or fine-grained soil. When the fine-grained soil-layer particle size is constant, the total water storage first increases, then decreases, and finally remains constant after increasing the median soil–particle size ratio. In contrast, when the coarse-grained soil layer particle size is constant, the relationship between the capillary barrier’s total water storage and median soil–particle size ratio can be defined as a power function. Using the capillary barrier can increase coarse-grained sand by 90% in water storage capacity and can only increase fine-grained sand by 7% in water storage capacity. The breakthrough time increases with the increase in the median soil–particle size ratio. The presence of the coarse and fine-grained soil layer interface in the capillary barrier can affect the fine-grained soil layer infiltration rate.

Thermal behavior (in cooling) of soil mass with varying fine and water contents: Experimental and numerical investigation

This paper presents a preliminary study on the thermal behavior and response of soil samples with varying water content to assess their significance in addressing the nighttime urban heat island (UHI) effect. For this reason, the experimental program and the analysis focus on the cooling phase of the heated soil samples. To ensure a representative analysis of field conditions, the soil samples were prepared in the laboratory with varying coarse-grained (sand) and fine-grained (kaolin) soil particles. The thermal properties of the soil samples, including thermal conductivity and transmissivity, decrease with increasing fine content and particle packing. In contrast, the thermal conductivity and transmissivity values increase with water content. The thermal diffusivity followed a similar behavior but was relatively less prominent. On the other hand, the specific heat capacity is higher in samples with higher moisture and clay contents but lower with dry unit weight. However, having a higher specific heat capacity also resulted in samples retaining the heat relatively longer and releasing it slowly, which could contribute to delayed nighttime UHI. The numerical models considering natural convective conditions and their analysis further confirm that the water content of the soil samples has a relatively more prominent effect on the soil’s specific heat capacity than the increasing clay contents. To this end, it is noted that the measurement, analysis, and estimation of heat transfer and cooling mechanisms in the soil requires careful consideration of the soil type, water content, and the surrounding environmental conditions.

Transferable local density-dependent friction in tert-butanol/water mixtures.

Coarse-grained (CG) models informed from molecular dynamics simulations provide a way to represent the structure of an underlying all-atom (AA) model by deriving an effective interaction potential. However, this leads to a speed-up in dynamics due to the lost friction, which is especially pronounced in CG implicit solvent models. Applying a thermostat based on the Langevin equation (LE) provides a way to represent the long-time dynamics of CG particles by reintroducing friction to the system. To improve the representability CG models of heterogeneous molecular mixtures and their transferability over the mixture compositions, we parameterize an LE thermostat in which the friction coefficient depends on the local particle density (LD). The thermostat friction was iteratively optimized with a Markovian variant of the recently introduced Iterative Optimization of Memory Kernels (IOMK) method. We simulated tert-butanol/water mixtures over a range of compositions, which show a distinct clustering behavior. Our model with LD-dependent friction reproduces the AA diffusion coefficients well over the full range of mixtures and is, therefore, transferable with respect to dynamics.

Formations of force network and softening of amorphous elastic materials from a coarsen-grained particle model

Amorphous materials, such as granular substances, glasses, emulsions, foams, and cells, play significant roles in various aspects of daily life, serving as building materials, plastics, food products, and agricultural items. Understanding the mechanical response of these materials to external forces is crucial for comprehending their deformation, toughness, and stiffness. Despite the recognition of the formation of force networks within amorphous materials, the mechanisms behind their formation and their impact on macroscopic physical properties remain elusive. In this study, we employ a coarse-grained particle model to investigate the mechanical response, wherein local physical properties are integrated into the softness of the particles. Our findings reveal the emergence of a chain-like force distribution, which correlates with the planar distribution of softness and heterogeneous density variations. Additionally, we observe that the amorphous material undergoes softening due to the heterogeneous distribution of softness, a phenomenon explicable through a simple theoretical framework. Moreover, we demonstrate that the ambiguity regarding the size ratio of the blob to the force network can be adjusted by the amplitude of planar fluctuations in softness, underscoring the robustness of the coarse-grained particle model.

A Structure Independent Molecular Fragment Interfuse Model for Mesoscale Dissipative Particle Dynamics Simulation of Peptides.

There is a need to develop robust computational models for mesoscale simulation of the structure of peptides over large length scales toward the discovery of novel peptides for medical applications to address the issues of peptide aggregation, enzymatic degradation, and short half-life. The primary objective was to predict the structure and conformation of peptides whose native structures are not known. This work presents a new model for computation of interaction parameters between the beads in coarse-grained dissipative particle dynamics (DPD) simulation that is properly calibrated for amino acids, supports compressibility requirement of water molecules, and accounts for subtle differences in the structure of amino acids and the charge in the side chain of charged amino acids. This new model is referred to as Structure Independent Molecular Fragment Interfuse Model, abbreviated as SIMFIM, because it accounts for specific interactions between different beads, which represent molecular fragments of the amino acids, in calculating nonbonded interaction parameters in the absence of knowing the actual peptide structure. The electrostatic interactions are incorporated in this model by using a normal distribution of charges around the center of the beads to prevent the collapse of oppositely charged soft beads. The uniquely parameterized DPD force field in the SIMFIM model is optimized for a given peptide with respect to the degree of coarse-grained graining for simulating the peptide over long times and length scales. The SIMFIM model was tested in this work using four peptides, namely, TrpZip2, Rubrivinodin, Lihuanodin, and IC3-CB1/Gai peptides, whose structures were sourced from the Protein Data Bank. The SIMFIM model predicted radius of gyration (Rg) values for the peptides closer to the actual structures as compared to the conventional model, and there was less deviation between the predicted and actual structures of the peptides.

Validation study on a coarse-grained DEM-CFD simulation in a bead mill

A bead mill is often employed in powder processes. In the bead mill, the bead-particles move rapidly under high shear rate due to the moving structures. The discrete element method (DEM) coupled with the computational fluid dynamics (CFD) has been applied to simulate the bead-particle behavior for the optimization of the bead mill design and operating conditions. However, the existing DEM-CFD method faces essential problems regarding the substantial limit of the number of computational particles, stable calculations, and modeling of rapidly moving structures. To solve these problems, we newly investigate a numerical model combining the coarse-grained DEM-CFD, an implicit algorithm for the drag force term, and a scalar field-based wall boundary in the calculation of a bead mill commonly employed in industrial powder processes. In this study, our proposed model is shown to successfully simulate the macroscopic behavior of the bead-particles through the validation test of the coarse-grained DEM-CFD simulation in the bead mill system. Specifically, the macroscopic characteristics such as the particle location, the particle velocity, and total kinetic energy, are shown to agree well between the original particle system and coarse-grained particle systems. Consequently, this study illustrates the combination of the coarse-grained DEM-CFD, an implicit algorithm for the drag force term, and the scalar field-based wall boundary is essential for simulating the typically industrial bead mill, where an enormous number of bead-particles should be calculated in liquid under high shear rate.

Microscopic characteristics and sources of atmospheric dustfall in open-pit mining coal resource-based city in the arid desert area of Northwest China

Atmospheric dustfall is solid air pollutant, has a major impact on the environment and human health. The objective of this study was to investigate the microscopic characteristics and sources of atmospheric dustfall in open-pit mining coal resource-based city in the arid desert area of Northwest China. The characteristics of size and shape factors, variation of shape factors with size distribution, types of individual particles, and sources of atmospheric dustfall, which were collected in the open-pit mining area and surrounding areas, were analyzed by X-ray diffraction (XRD) and scanning electron microscopy coupled with an energy dispersive spectrometer (SEM–EDS) combined with graphical method and shape factors. The results showed that the atmospheric dustfall in all functional areas was dominated by coarse-grained particles. The shape of the atmospheric dustfall deviated from spherical shape, and with decreasing particle size, the difference in shape factors increased in each functional area. The EDS and XRD analyses indicated the presence of 13 types of particles. The sources were mainly local and included soil dust from each functional area; industrial dust, construction dust, biogenic impurities, fossil fuel combustion, wear products of motor vehicle parts, motor vehicle exhaust emissions, and emission and excreta from biological activities in each functional area except the desert area; emissions from a steel plant in the industrial area; coal-associated ore, coal dust, coal gangue emissions, and emissions from the spontaneous combustion of coal gangue in the open-pit mining area; secondary chemical crystallization products in the industrial area and the open-pit mining area; dust generated by vehicles abrading the surface of the off-mine coal road and in the open-pit mining area.

Instability of membranes containing ionizable cationic lipids: Effects of the repulsive range of headgroups and tail structures

The stability of membranes formed by ionizable cationic lipids, which constitute the primary components in lipid nanoparticles capable of endosomal escape, is explored using coarse-grained dissipative particle dynamics. Three types of ionizable model lipids with different tail structures are considered. Endosome acidification causes the ionization of lipids, leading to an increased repulsive range between their headgroups. When electrostatic repulsion is modeled as a conservative force with a long-range cutoff distance (rc,HH), the membrane and vesicle experience a loss of structural integrity and develop holes as rc,HH is beyond a critical value, which varies with the tail structure. When Coulombic repulsion is explicitly incorporated and intensified, a fully ionized lipid membrane undergoes a loss of structural integrity, displaying a qualitative similarity to the effect observed with the increase in rc,HH on the membrane stability. Qualitatively similar results are obtained for partially ionized membranes as the fraction of charged lipids increases. The stability of a mixed lipid membrane containing both ionizable and conventional lipids is also investigated. The disruption of the bilayer structure occurs for a sufficiently high charged fraction. The membrane instability can be attributed to the decrease in the packing parameter, which significantly deviates from unity as the interaction range increases.

Representability and Dynamical Consistency in Coarse-Grained Models.

We address the challenge of representativity and dynamical consistency when unbonded fine-grained particles are collected together into coarse-grained particles. We implement a hybrid procedure for identifying and tracking the underlying fine-grained particles─e.g., atoms or molecules─by exchanging them between the coarse-grained particles periodically at a characteristic time. The exchange involves a back-mapping of the coarse-grained particles into fine-grained particles and a subsequent reassignment to coarse-grained particles conserving total mass and momentum. We find that an appropriate choice of the characteristic exchange time can lead to the correct effective diffusion rate of the fine-grained particles when simulated in hybrid coarse-grained dynamics. In the compressed (supercritical) fluid regime, without the exchange term, fine-grained particles remain associated with a given coarse-grained particle, leading to substantially lower diffusion rates than seen in all-atom molecular dynamics of the fine-grained particles. Thus, this work confirms the need for addressing the representativity of fine-grained particles within coarse-grained particles and offers a simple exchange mechanism so as to retain dynamical consistency between the fine- and coarse-grained scales.

Effect of Fine-Grained Particles and Sensitivity Analysis of Physical Indexes on Residual Strength of Granite Residual Soils

Recently, stability analyses of structures built of granite residual soils, for example, earth dams or other urban structures, particularly when under vibration, are being recognized as much more important than previously imagined. In such analyses, it is emphasized that the residual strength should be utilized considering the seismic effect. Therefore, the residual strength of granite residual soils must be evaluated accurately in order to reduce the damage to structures built on them. This paper presented a laboratory study designed to examine the effect of fine-grained particles (FGPs; particle size ≤ 0.075 mm) on residual strength by the multistage procedure of the Bromhead ring shear test and evaluate the physical indexes forecasting the residual strength of granite residual soils using soil samples composed of fifteen different percentages of FGPs artificially adjusted from a reservoir embankment soil sample. The results showed that the residual strength decreased along with the increase in FGPs and that the residual frictional angle was rarely dependent on the ratio of FGPs when the ratio was over 90%. Even in the residual state, a small amplitude of fluctuation in shear stress still existed and was affected by the coarse-grained particles (CGPs; particle size ≥ 0.075 mm), such as the quartz particles in the granite residual soils. It was also found that the amplitude of fluctuation was smaller when the FGP fraction was greater. In addition, under the same normal stress, the peak strength and residual strength decreased with an increase in the ratio of FGPs. Then, they remained almost the same when the ratios of FGPs were equal to 85% and 90%, respectively, and the post-peak attenuation tended to increase initially with an increase in the FGPs and then remained almost the same. Moreover, based on the sensitivity analysis, the order of influence of physical indexes on the residual frictional angle was also ranked for the granite residual soils.

Simulation of the L-valve in the circulating fluidized bed with a coarse-grained discrete particle method

Stable and controllable solid flow is essential in circulating fluidized bed (CFB) systems. The L-valve is a typical non-mechanical valve that can provide flexible solid feeding. The investigation of the solid circulation rate and the hydrodynamic characteristics of the L-valve is crucial to its design and operation. The gas-solid flow in the L-valve of a full-loop CFB is studied with the coarse-grained discrete particle method (EMMS-DPM). Good agreements on the solid circulation rate and the pressure drop through the L-valve are achieved between the simulated and experimental data. The solid circulation rate increases linearly with the aeration velocity until the stable particle circulation of the CFB is destroyed. The flow patterns in the horizontal section of L-valve are gas-solid slug flow above the stationary solid layer and the moving solid layer, respectively. The effects of L-valve geometric parameters on the solid flow characteristics are also investigated. The results indicate that reducing the diameter and length of the horizontal section of L-valve can improve the solid transport efficiency, especially at low aeration velocity. Besides, the solid conveying capacity and flow stability are improved when the sharp bend of L-valve is modified to be a gradual bend.

From Li2NiO3 to high-performance LiNiO2 cathodes for application in Li-ion and all-solid-state batteries.

The synthesis of LiNiO2 (LNO) typically involves oxidizing Ni(II) to Ni(III), thus leading to NiLi point-defect formation. Here, materials containing Ni(IV) in the form of overlithiated Li1+xNi1-xO2 (0 ≤ x ≤ 1/3) are converted into LNO. This method produces low defect-density samples at high temperatures, offering an attractive route toward coarse-grained particles that are naturally coated by the byproduct Li2O. In thiophosphate-based solid-state batteries, this kind of self-coating effect shows a direct correlation between residual lithium content and cycling performance.

Studying on the upper limit of the coarse-grained DEM model for simulating mixing processes in a rolling drum with complex wall boundary

Compared with the original Discrete Element Method, the coarse-grained DEM significantly improves simulation efficiency. In CG DEM, the coarse-grained ratio is defined as the diameter of the coarse-grained particle divided by the diameter of the original particle. When the upper limit of coarse-grained ratio is used, the simulation is the most efficient. The upper value for simulating mixing process of spherical fuel particles was determined using a multi-level methodology. The adequacy of the upper value of the coarse-grained ratio was assessed by comparing the mixing characteristics and kinetic properties of the coarse-grained particle systems with those of the original particle systems in a rotating drum with blades. The impact of rotation speed and particle number on the upper value was examined and discussed. It was observed that the kinetic energy increases with an increase in the coarse-grained ratio, limiting the efficiency improvement. To ensure kinetic energy conservation, a scaling law for the restitution coefficient was proposed. Combined with the Reduced Particle Stiffness method, the simulation time of the coarse-grained case is only 1/3030 that of the original case (with a particle number of 2.3 million) when the upper limit of the coarse-grained ratio was used (12.0).

SEM2: Introducing mechanics in cell and tissue modeling using coarse-grained homogeneous particle dynamics.

Modeling multiscale mechanics in shape-shifting engineered tissues, such as organoids and organs-on-chip, is both important and challenging. In fact, it is difficult to model relevant tissue-level large non-linear deformations mediated by discrete cell-level behaviors, such as migration and proliferation. One approach to solve this problem is subcellular element modeling (SEM), where ensembles of coarse-grained particles interacting via empirically defined potentials are used to model individual cells while preserving cell rheology. However, an explicit treatment of multiscale mechanics in SEM was missing. Here, we incorporated analyses and visualizations of particle level stress and strain in the open-source software SEM++ to create a new framework that we call subcellular element modeling and mechanics or SEM2. To demonstrate SEM2, we provide a detailed mechanics treatment of classical SEM simulations including single-cell creep, migration, and proliferation. We also introduce an additional force to control nuclear positioning during migration and proliferation. Finally, we show how SEM2 can be used to model proliferation in engineered cell culture platforms such as organoids and organs-on-chip. For every scenario, we present the analysis of cell emergent behaviors as offered by SEM++ and examples of stress or strain distributions that are possible with SEM2. Throughout the study, we only used first-principles literature values or parametric studies, so we left to the Discussion a qualitative comparison of our insights with recently published results. The code for SEM2 is available on GitHub at https://github.com/Synthetic-Physiology-Lab/sem2.