Particle-based Model Research Articles

Gecko Adhesion on Flat and Rough Surfaces: Simulations with a Multi‐Scale Molecular Model

A multiscale modeling approach is used to develop a particle-based mesoscale gecko spatula model that is able to link atomistic simulations and mesoscale (0.44 µm) simulations. It is used to study the detachment of spatulae from flat as well as nanostructured surfaces. The spatula model is based on microscopical information about spatulae structure and on atomistic molecular simulation results. Target properties for the coarse-graining result from a united-atom model of gecko keratin in periodic boundary conditions (PBC), previously developed by the authors. Pull-off forces necessary to detach gecko keratin under 2D PBC parallel to the surface are previously overestimated when only a small region of a spatula is examined. It is shown here that this is due to the restricted geometry (i.e., missing peel-off mode) and not model parameters. The spatula model peels off when pulled away from a surface, both in the molecular picture of the pull-off process and in the force-extension curve of non-equilibrium simulations mimicking single-spatula detachment studied with atomic force microscopy equipment. The force field and spatula model can reproduce experimental pull-off forces. Inspired by experimental results, the underlying mechanism that causes pull-off forces to be at a minimum on surfaces of varying roughnesses is also investigated. A clear sigmoidal increase in the pull-off force of spatulae with surface roughness shows that adhesion is determined by the ratio between spatula pad area and the area between surface peaks. Experiments showed a correlation with root-mean-square roughness of the surface, but the results of this work indicate that this is not a causality but depends on the areaaccessible.

Estimating microscale DE parameters of brittle adhesive joints using genetic expression programming

Particle-based model has strength and flexibility in modelling the microstructures of adhesives and interface in adhesive joints. In this work, a procedure with genetic expression programming (GEP) technique to calibrate the microscale parameters of discrete element (DE) model was proposed for brittle adhesives. Two categories of adhesive properties, the bulk property of thick adhesive and interlaminar-like property of thin adhesive, were discussed. For the bulk property, three target properties of adhesives, i.e. tensile strength, peak strain, secant modulus, were set as the reproduced features. 300 sets of adjustable microscale parameters were produced to run the numerical tests and generate datasets. GEP was then employed to find regression formulas for predicting the target properties as a function of the microscale parameters. For the interlaminar-like property, fracture energies of the cohesive failure of thin adhesives were approximated. A similar procedure of combined DE modelling and GEP was performed to find the regression models to estimate the fracture energy. The developed regression formulas can cover a general range of brittle adhesives. Loctite EA 9497 adhesive was selected to perform a series of lab tests, of which the results were subsequently used to examine the applicability of the DE model with calibrated parameters. The numerical results exhibit good agreements with testing data and observation.

A Tunable, Particle-Based Model for the Diverse Conformations Exhibited by Chiral Homopolymers

Chiral block copolymers capable of hierarchical self-assembly can also exhibit chirality transfer─the transfer of chirality at the monomer or conformational scale to the self-assembly. Prior studies focused on experimental and theoretical methods that are unable to fully decouple the thermodynamic origins of chirality transfer and necessitate the development of particle-based models that can be used to quantify intrachain, interchain, and entropic contributions. With this goal in mind, in this work, we developed a parametrized coarse-grained model of a chiral homopolymer and extensively characterized the resulting conformations. Specifically, the energetic parameter in the angular and dihedral potentials, the angular set point, and the dihedral set point are systematically varied to produce a wide range of conformations from a random coil to a nearly ideal helix. The average helicity, pitch, persistence length, and end-to-end distance are measured, and correlations between the model parameters and resulting conformations are obtained. Using available experimental data on model polypeptoid-based chiral polymers, we back out the required parameters that produce similar pitch and persistence length ratios reported in the experiments. The conformations for the experimentally matched chains appear to be somewhat flexible, exhibiting some helical turns. Our model is versatile and can be used to perform molecular dynamics simulations of chiral block copolymers and even sequence-specific polypeptides to study their self-assembly and to gain thermodynamic insights.

Microscale Discrete Element Model for Simulating Bridging Behavior of Fractured Glass Laminates

The bridging behavior between fragments is one vital factor in the post-fracture stage of glass laminates. A particle-based discrete element model was developed in this work to simulate the bridging behavior of fractured glass laminates. The model was based on the calibration of hyperelastic PVB material properties using soft-bond model and further validated with the experimental data as well as the observations from through-crack-tensile tests. In order to investigate the bridging performance of fractured glass laminates with multiple fragments under uniaxial tension, three factors encompassing the crack aligning, fragment number and adhesion conditions were considered to perform a parametric study. The results give an exploratory application of the developed discrete element models in the estimation of the post-fracture behaviors. It is found that the smaller fragment size can diminish the tension-stiffening effect in the non-aligned case which might generate an enhancing ratio of initial modulus up to nearly 3.6. The non-aligned cracks can also lead to a very high strength if the adhesion ability can be guaranteed. However, the delamination of fragments is expected to control the post-fracture strength of fractured glass laminates with PVB interlayer.

Soliton motion in skyrmion chains: Stabilization and guidance by nanoengineered pinning

Using a particle-based model we examine the depinning motion of solitons in skyrmion chains in quasi-one-dimensional (1D) and two-dimensional (2D) systems containing embedded 1D interfaces. The solitons take the form of a particle or hole in a commensurate chain of skyrmions. Under an applied drive, just above a critical depinning threshold, the soliton moves with a skyrmion Hall angle of zero. For higher drives, the entire chain depins, and in a 2D system we observe that both the solitons and chain move at zero skyrmion Hall angle and then transition to a finite skyrmion Hall angle as the drive increases. In a 2D system with a 1D interface that is at an angle to the driving direction, there can be a reversal of the sign of the skyrmion Hall angle from positive to negative. Our results suggest that solitons in skyrmion systems could be used as information carriers in racetrack geometries that would avoid the drawbacks of finite skyrmion Hall angles. The soliton states become mobile at significantly lower drives than the depinning transition of the skyrmion chains themselves.

Modified Poisson-Boltzmann theory for polyelectrolytes in monovalent salt solutions with finite-size ions.

We present a soft-potential-enhanced Poisson-Boltzmann (SPB) theory to efficiently capture ion distributions and electrostatic potential around rodlike charged macromolecules. The SPB model is calibrated with a coarse-grained particle-based model for polyelectrolytes (PEs) in monovalent salt solutions as well as compared to a full atomistic molecular dynamics simulation with the explicit solvent. We demonstrate that our modification enables the SPB theory to accurately predict monovalent ion distributions around a rodlike PE in a wide range of ion and charge distribution conditions in the weak-coupling regime. These include excess salt concentrations up to 1M and ion sizes ranging from small ions, such as Na+ or Cl-, to softer and larger ions with a size comparable to the PE diameter. The work provides a simple way to implement an enhancement that effectively captures the influence of ion size and species into the PB theory in the context of PEs in aqueous salt solutions.

Critical behavior of active Brownian particles: Connection to field theories.

We explore the relation between active Brownian particles, a minimal particle-based model for active matter, and scalar field theories. Both show a liquid-gas-like phase transition toward stable coexistence of a dense liquid with a dilute active gas that terminates in a critical point. However, a comprehensive mapping between the particle-based model parameters and the effective coefficients governing the field theories has not been established yet. We discuss conflicting recent numerical results for the critical exponents of active Brownian particles in two dimensions. Starting from the intermediate effective hydrodynamic equations, we then present a construction for a scalar order parameter for active Brownian particles that yields the active model B+. We argue that a crucial ingredient is the coupling between density and polarization in the particle current. The renormalization flow close to two dimensions exhibits a pair of perturbative fixed points that limit the attractive basin of the Wilson-Fisher fixed point, with the perspective that the critical behavior of active Brownian particles in two dimensions is governed by a strong-coupling fixed point different from Wilson-Fisher and not necessarily corresponding to Ising universality.

All Roads Lead to Rome: Diverse Etiologies of Tricuspid Regurgitation Create a Predictable Constellation of Right Ventricular Shape Changes.

Introduction: Myriad disorders cause right ventricular (RV) dilation and lead to tricuspid regurgitation (TR). Because the thin-walled, flexible RV is mechanically coupled to the pulmonary circulation and the left ventricular septum, it distorts with any disturbance in the cardiopulmonary system. TR, therefore, can result from pulmonary hypertension, left heart failure, or intrinsic RV dysfunction; but once it occurs, TR initiates a cycle of worsening RV volume overload, potentially progressing to right heart failure. Characteristic three-dimensional RV shape-changes from this process, and changes particular to individual TR causes, have not been defined in detail. Methods: Cardiac MRI was obtained in 6 healthy volunteers, 41 patients with ≥ moderate TR, and 31 control patients with cardiac disease without TR. The mean shape of each group was constructed using a three-dimensional statistical shape model via the particle-based shape modeling approach. Changes in shape were examined across pulmonary hypertension and congestive heart failure subgroups using principal component analysis (PCA). A logistic regression approach based on these PCA modes identified patients with TR using RV shape alone. Results: Mean RV shape in patients with TR exhibited free wall bulging, narrowing of the base, and blunting of the RV apex compared to controls (p 0.05). Using four primary PCA modes, a logistic regression algorithm identified patients with TR correctly with 82% recall and 87% precision. In patients with pulmonary hypertension without TR, RV shape was narrower and more streamlined than in healthy volunteers. However, in RVs with TR and pulmonary hypertension, overall RV shape continued to demonstrate the free wall bulging characteristic of TR. In the subgroup of patients with congestive heart failure without TR, this intermediate state of RV muscular hypertrophy was not present. Conclusion: The multiple causes of TR examined in this study changed RV shape in similar ways. Logistic regression classification based on these shape changes reliably identified patients with TR regardless of etiology. Furthermore, pulmonary hypertension without TR had unique shape features, described here as the “well compensated” RV. These results suggest shape modeling as a promising tool for defining severity of RV disease and risk of decompensation, particularly in patients with pulmonary hypertension.

Thermodynamic Size Control in Curvature-Frustrated Tubules: Self-Limitation with Open Boundaries.

We use computational modeling to investigate the assembly thermodynamics of a particle-based model for geometrically frustrated assembly, in which the local packing geometry of subunits is incompatible with uniform, strain-free large-scale assembly. The model considers discrete triangular subunits that drive assembly toward a closed, hexagonal-ordered tubule, but have geometries that locally favor negative Gaussian curvature. We use dynamical Monte Carlo simulations and enhanced sampling methods to compute the free energy landscape and corresponding self-assembly behavior as a function of experimentally accessible parameters that control assembly driving forces and the magnitude of frustration. The results determine the parameter range where finite-temperature self-limiting assembly occurs, in which the equilibrium assembly size distribution is sharply peaked around a well-defined finite size. The simulations also identify two mechanisms by which the system can escape frustration and assemble to unlimited size, and determine the particle-scale properties of subunits that suppress unbounded growth.

Self-propelled motors in complex fluids and as constituents of active materials

Simulation has played an important part in studies of active matter systems, and this paper considers some aspects of the use of stochastic models for the behavior of active particles in complex media and in applications to active functional materials. The scope of the work is primarily focused on small active particles whose activity is derived from chemical reactions and diffusiophoretic mechanisms that operate in the presence of fluctuations. Both Langevin and particle-based models are considered, and their relative merits are discussed.

Testing the robustness of particle-based separation models for the magnetic separation of a complex skarn ore

Physical separation processes are best understood in terms of the behaviour of individual ore particles. Yet, while different empirical particle-based separation modelling approaches have been developed, their predictive performance has never been tested under variable process conditions. Here, we investigated the predictive performance of a state-of-the-art particle-based separation model under variable feed composition for a laboratory-scale magnetic separation of a skarn ore. Two scenarios were investigated: one in which the mass flow of the different processing streams could be measured and one in which it had to be estimated from data. In both scenarios, the predictive models were sufficiently general to predict the process outcomes of new samples of variable composition. Nevertheless, the scenario in which mass flow could be measured was ∼4% more precise in predicting mass balances. The process behaviour of minerals present at concentrations above 0.1% by weight could be accurately predicted. Our findings indicate the potential use of this method to minimize the costs of metallurgical testwork while providing in-depth understanding of the recovery behaviour of individual ore particles. Moreover, the method may be used to establish powerful tools to forecast mineral recoveries for partly new ore types at a running mining operation.

PySDM v1: particle-based cloud modeling package for warm-rain microphysics and aqueous chemistry

PySDM is an open-source Python package for simulating the dynamics of particles undergoing condensational and collisional growth, interacting with a fluid flow and subject to chemical composition changes. It is intended to serve as a building block for process-level as well as computational-fluid-dynamics simulation systems involving representation of a continuous phase (air) and a dispersed phase (aerosol), with PySDM being responsible for representation of the dispersed phase. The PySDM package core is a Pythonic high-performance implementation of the Super-Droplet Method (SDM) Monte-Carlo algorithm for representing collisional growth, hence the name. PySDM has two alternative parallel number-crunching backends available: multi-threaded CPU backend based on Numba and GPU-resident backend built on top of ThrustRTC. The usage examples are built on top of four simple atmospheric cloud modelling frameworks: box, adiabatic parcel, single-column and 2D prescribed flow kinematic models. In addition, the package ships with tutorial code depicting how PySDM can be used from Julia and Matlab.

Simulating a chemically fueled molecular motor with nonequilibrium molecular dynamics

Most computer simulations of molecular dynamics take place under equilibrium conditions—in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are introduced to those simulations to probe one type of nonequilibrium response to external forces. Catalysts and molecular motors, however, function based on the nonequilibrium dynamics induced by a chemical reaction’s thermodynamic driving force. In this scenario, simulations require chemostats capable of preserving the chemical concentrations of the nonequilibrium steady state. We develop such a dynamic scheme and use it to observe cycles of a particle-based classical model of a catenane-like molecular motor. Molecular motors are frequently modeled with detailed-balance-breaking Markov models, and we explicitly construct such a picture by coarse graining the microscopic dynamics of our simulations in order to extract rates. This work identifies inter-particle interactions that tune those rates to create a functional motor, thereby yielding a computational playground to investigate the interplay between directional bias, current generation, and coupling strength in molecular information ratchets.

Modeling ice block failure within drift ice and ice rubble.

A major challenge within material science is the proper modeling of force transmission through fragmenting materials under compression. A particularly demanding material is sea ice, which on small scales is an anisotropic material with quasibrittle characteristics under failure. Here we use the particle-based model HiDEM and laboratory-scale experiments on saline ice to develop a material model for fragmenting ice. The material behavior of the HiDEM model-ice, and the experiments are compatible on force transmission and fragmentation if: (i) the typical HiDEM glacier-scale particle size of meters is brought down to millimeters corresponding to the grain size of the laboratory ice, (ii) the often used HiDEM lattice structure is replaced by a planar random structure with an anisotropy in the direction normal to the randomized plane, and (iii) the instant tensile and bending failure criterion, used in HiDEM on glacier scale, is replaced by a cohesive softening failure potential for energy dissipation. The main outcomes of this exercise is that many of the, more or less, traditional ice modeling schemes are proven to be incomplete. In particular, local crushing of ice is not valid as a generic failure mode for fragmented ice under compression. Rather, shear failure, as described by Mohr-Coulomb theory is demonstrated to be the dominant failure mode.

A particle-based computational model to analyse remodelling of the red blood cell cytoskeleton during malaria infections.

Red blood cells can withstand the harsh mechanical conditions in the vasculature only because the bending rigidity of their plasma membrane is complemented by the shear elasticity of the underlying spectrin-actin network. During an infection by the malaria parasite Plasmodium falciparum, the parasite mines host actin from the junctional complexes and establishes a system of adhesive knobs, whose main structural component is the knob-associated histidine rich protein (KAHRP) secreted by the parasite. Here we aim at a mechanistic understanding of this dramatic transformation process. We have developed a particle-based computational model for the cytoskeleton of red blood cells and simulated it with Brownian dynamics to predict the mechanical changes resulting from actin mining and KAHRP-clustering. Our simulations include the three-dimensional conformations of the semi-flexible spectrin chains, the capping of the actin protofilaments and several established binding sites for KAHRP. For the healthy red blood cell, we find that incorporation of actin protofilaments leads to two regimes in the shear response. Actin mining decreases the shear modulus, but knob formation increases it. We show that dynamical changes in KAHRP binding affinities can explain the experimentally observed relocalization of KAHRP from ankyrin to actin complexes and demonstrate good qualitative agreement with experiments by measuring pair cross-correlations both in the computer simulations and in super-resolution imaging experiments.

Large Scale Hydrodynamically Coupled Brownian Dynamics Simulations of Polymer Solutions Flowing through Porous Media.

Large scale simulations of polymer flow through porous media provide an important tool for solving problems in enhanced oil recovery, polymer processing and biological applications. In order to include the effects of a wide range of velocity and density fluctuations, we base our work on a coarse-grain particle-based model consisting of polymers following Brownian dynamics coupled to a background fluid flow through momentum conserving interactions. The polymers are represented as Finitely Extensible Non-Linear Elastic (FENE) dumbbells with interactions including slowly decaying transient forces to properly describe dynamic effects of the eliminated degrees of freedom. Model porous media are constructed from arrays of parallel solid beams with circular or square cross-sections, arranged periodically in the plane perpendicular to their axis. No-slip boundary conditions at the solid–fluid interfaces are imposed through interactions with artificial particles embedded within the solid part of the system. We compare the results of our simulations with those of standard Smoothed Particle Hydrodynamics simulations for Newtonian flow through the same porous media. We observe that in all cases the concentration of polymers at steady state is not uniform even though we start the simulations with a uniform polymer concentration, which is indicative of shear-induced cross-flow migration. Furthermore, we see the characteristic flattening of the velocity profile experimentally observed for shear-thinning polymer solutions flowing through channels as opposed to the parabolic Poiseuille flow profile for Newtonian fluids.

Modeling the devolatilization and fragmentation of biomass pellets with the bonded particle method for fluidized bed applications

By extending the bonded particle method, the major structural changes during the devolatilization of a wood pellet in a fluidized bed and the resulting mechanical behavior have been successfully reproduced. A comparison with experiments from the literature showed that the implemented particle-based pyrolysis model enables predicting the entire pellet’s kinetics with a high agreement. The developed shrinkage model for the particles and bonds further allowed to emulate the reported formation of a large-scale pore network inside the pellet. The simulation of a radial compression test with the predicted structure showed good agreement with experimental data and could confirm the importance of the pores for the mechanical behavior. The results demonstrated that the large pores cause the fragmentation of agglomerates already at low mechanical loads which could promote attrition. In general, the results have shown that the developed extension of the bonded particle method allows studying and predicting the behavior of a single pellet during conversion inside a fluidized bed gasification reactor in more detail.

Critical active dynamics is captured by a colored-noise driven field theory

Active matter may sometimes behave almost indistinguishably from equilibrium matter. This is particularly evident for some particle-based models and active field-theories close to a critical point which falls in the Ising universality class. Here we show however that, even when critical, active particles strongly violate the equilibrium fluctuation-dissipation in the high-wave-vector and high-frequency regime. Conversely, at larger spatiotemporal scales the theorem is progressively restored and the critical dynamics is in effective equilibrium. We develop a field-theoretical description of this scenario employing a space-time correlated noise field finding that the theory qualitatively captures the numerical results already at the Gaussian level. Moreover a dynamic renormalization group analysis shows that the correlated noise does not change the equilibrium critical exponents. Our results demonstrate that a correlated noise field is a fundamental ingredient to describe critical active matter at the coarse-grained level.

Numerical study of hydraulic fracture propagation in inherently laminated rocks accounting for bedding plane properties

The objective of this paper is to investigate hydraulic fracture propagation in inherently laminated rocks considering different bedding plane characteristics. To this end, a layered particle-based numerical model is first established in the framework of particle flow simulation. The mechanical behavior of rock matrix is controlled by randomly distributed bond contacts while that of bedding planes by preferentially orientated smooth joint contacts. On this basis, an improved hydromechanical coupled model is then proposed by modelling of hydraulic pipes according to contact types, which can well describe the fluid flow difference of rock matrix and bedding planes. The efficiency of improved model is assessed by comparisons with the Blanton's criterion and typical experimental evidences. Numerical predictions are in good agreement with analytical solutions. The interaction modes between induced fractures and bedding planes are also captured successfully. Hydraulic fracturing simulations of laminated rocks are then conducted and quantitatively analyzed in terms of borehole pressure and fracture propagation. Some key parameters such as the elastic, strength, permeability and thickness of bedding planes effect on hydraulic fracturing process are further investigated and discussed. • Improved coupling laws between hydraulic conductivity evolution and fracture aperture in different types of broken contact surfaces are proposed. • The differences of hydraulic fracture propagation and fluid flow in rock matrix and bedding planes are well described. • Effects of some key parameters related to bedding planes on hydraulic fracturing process are investigated.

Smoothed Particle Hydrodynamics simulations of reef surf zone processes driven by plunging irregular waves

As waves interact with the slopes of coral reefs and other steep bathymetry profiles, plunging breaking usually occurs where the free surface overturns and violent water motion is triggered. Resolving these surf zone processes pose significant challenges for conventional mesh-based hydrodynamic models, due to the rapidly-deforming nature of the free surface and associated flows. Yet the accurate prediction of these surf zone hydrodynamics is critical for predicting a wide range of nearshore processes driven by wave breaking (e.g., wave dissipation and energy transfers; mean water levels and currents; and wave runup). In this study we assess the ability of the mesh-free, Lagrangian particle-based numerical modelling approach Smoothed Particle Hydrodynamics (SPH) based on DualSPHysics, to simulate the fine-scale hydrodynamic processes driven by irregular wave transformation over a fringing reef profile, by comparing results against detailed experimental observations from a physical modelling study. To greatly improve the computational efficiency, the SPH model was coupled to the mesh-based multi-layer nonhydrostatic wave-flow model SWASH. With this coupled approach, SWASH was used to efficiently simulate the evolution of non-breaking waves from the wavemaker up to the fore reef slope, with the SPH model then used to simulate the detailed hydrodynamic processes over the reef from just offshore of the breakpoint to the shoreline. The SPH model was able to accurately reproduce the complex free surface deformations during plunging breaking, the spectral evolution of waves across the reef flat (including nonlinear wave shape), the mean water levels and currents, and wave runup at the shoreline. Using the long duration simulations (>400 wave periods), the model was able to reproduce the full range of wave motions over the reef (from sea-swell to infragravity frequencies), including the increasing dominance of low frequency waves towards the shoreline and the large cross-reef standing wave motions excited by the reef geometry.