From aromaticity to self-organized criticality in graphene

The unique properties of graphene are rooted in its peculiar electronic structure where effects of electron delocalization are pivotal. We show that the traditional view of delocalization as formation of a local or global aromatic bonding framework has to be expanded in this case. A modification of the π-electron system of a finite-size graphene substrate results in a scale-invariant response in the relaxation of interatomic distances and reveals self-organized criticality as a mode of delocalized bonding. Graphene is shown to belong to a diverse class of finite-size extended systems with simple local interactions where complexity emerges spontaneously under very general conditions that can be a critical factor controlling observable properties such as chemical activity, electron transport, and spin-polarization.     

Molecular dynamics simulations of self-organized polyicosahedral Si nanowire

A novel polyicosahedral nanowire is spontaneously formed in a series of annealing molecular dynamics simulations of liquid Si inside a nanopore of 1.36 nm in diameter. The polyicosahedral Si nanowire is stable even in a vacuum up to about 77% of the melting temperature of bulk Si. Our structural energy calculations reveal that the polyicosahedral nanowire is energetically advantageous over the pentagonal one for a wire whose diameter is less than 6.02 nm, though the latter has been recently proposed as the lowest energy wire. These results suggest the possibility of the formation of a new stable polyicosahedral Si nanowire.     

Efficient particle labeling in atomistic simulations

The authors develop an efficient particle labeling procedure based on a linked cell algorithm which is shown to reduce the computing time for a molecular dynamics simulation by a factor of 3. They prove that the improvement of performance is due to the efficient fulfillment of both spatial and temporal locality principles, as implemented by the contiguity of labels corresponding to interacting atoms. Finally, they show that the present label reordering procedure can be used to devise an efficient parallel one-dimensional domain decomposition molecular dynamics scheme.     

Dissipative particle dynamics simulations of polymersomes

A DPD model of PEO-based block copolymer vesicles in water is developed by introducing a new density based coarse graining and by using experimental data for interfacial tension. Simulated as a membrane patch, the DPD model is in excellent agreement with experimental data for both the area expansion modulus and the scaling of hydrophobic core thickness with molecular weight. Rupture simulations of polymer vesicles, or "polymersomes", are presented to illustrate the system sizes feasible with DPD. The results should provide guidance for theoretical derivations of scaling laws and also illustrate how spherical polymer vesicles might be studied in simulation.     

Finite-size effects in dissipative particle dynamics simulations

We have performed dissipative particle dynamics (DPD) simulations to evaluate the effect that finite size of transversal area has on stress anisotropy and interfacial tension. The simulations were carried out in one phase and two phases in parallelepiped cells. In one-phase simulations there is no finite-size effect on stress anisotropy when the simulation is performed using repulsive forces. However, an oscillatory function of stress anisotropy is found for attractive-repulsive interactions. In the case of liquid-liquid interfaces with repulsive interaction between molecules, there is only a small effect of surface area on interfacial tension when the simulations are performed using the Monte Carlo method at constant temperature and normal pressure. An important but artificial finite-size effect of interfacial area on surface tension is found in simulations in the canonical ensemble. Reliable results of interfacial tension from DPD simulations can be obtained using small systems, less than 2000 particles, when they interact exclusively with repulsive forces.     

Constant-pressure and constant-surface tension simulations in dissipative particle dynamics

We present a method for constant-pressure and constant-surface tension simulations in dissipative particle dynamics using a Langevin piston approach. We demonstrate that the corresponding equations of motion lead to the relevant ensembles and propose an appropriate scheme of integration. After having identified a suitable set of parameters for the approach, we demonstrate the feasibility of the approach by applying it to two different systems, a simple isotropic fluid and an anisotropic fluid lipid-bilayer membrane in water. Results are presented for, respectively, isothermal bulk compressibility, tracer diffusion coefficient, lipid head-group area, and isothermal area compressibility. We find that our Langevin piston approach leads to improvements over other approaches in terms of faster equilibration and shorter correlation times of various system variables.     

Constant-pressure simulations with dissipative particle dynamics

Dissipative particle dynamics (DPD) is a mesoscopic simulation method for studying hydrodynamic behavior of complex fluids. Ideally, a mesoscopic model should correctly represent the thermodynamic and hydrodynamic properties of a real system beyond certain length and time scales. Traditionally defined DPD quite successfully mimics hydrodynamics but is not flexible enough to accurately describe the thermodynamics of a real system. The so-called multibody DPD (MDPD) is a pragmatic extension of the classical DPD that allows one to prescribe the thermodynamic behavior of a system with only a small performance impact. In an earlier paper [S. Y. Trofimov, E. L. F. Nies, and M. A. J. Michels, J. Chem. Phys. 117, 9383 (2002)] we much improved the accuracy of the MDPD model for strongly nonideal systems, which are of most practical interest. The ability to correctly reproduce the equation of state of realistic systems in turn makes simulations at constant pressure sensible and useful. This situation of constant-pressure conditions is very common in experimental studies of (soft) condensed matter but has so far remained unexplored with the traditional DPD. Here, as a proof of concept, we integrate a modified version of the Andersen barostat into our improved MDPD model and make an evaluation of the performance of the new model on a set of single- and multicomponent systems. The modification of the barostat suppresses the "unphysical" volume oscillations after a sudden pressure change and simplifies the equilibration of the system.     

Dissipative particle dynamics simulations of polymer-protected nanoparticle self-assembly

Dissipative particle dynamics simulations were used to study the effects of mixing time, solute solubility, solute and diblock copolymer concentrations, and copolymer block length on the rapid coprecipitation of polymer-protected nanoparticles. The simulations were aimed at modeling Flash NanoPrecipitation, a process in which hydrophobic solutes and amphiphilic block copolymers are dissolved in a water-miscible organic solvent and then rapidly mixed with water to produce composite nanoparticles. A previously developed model by Spaeth et al. [J. Chem. Phys. 134, 164902 (2011)] was used. The model was parameterized to reproduce equilibrium and transport properties of the solvent, hydrophobic solute, and diblock copolymer. Anti-solvent mixing was modeled using time-dependent solvent-solute and solvent-copolymer interactions. We find that particle size increases with mixing time, due to the difference in solute and polymer solubilities. Increasing the solubility of the solute leads to larger nanoparticles for unfavorable solute-polymer interactions and to smaller nanoparticles for favorable solute-polymer interactions. A decrease in overall solute and polymer concentration produces smaller nanoparticles, because the difference in the diffusion coefficients of a single polymer and of larger clusters becomes more important to their relative rates of collisions under more dilute conditions. An increase in the solute-polymer ratio produces larger nanoparticles, since a collection of large particles has less surface area than a collection of small particles with the same total volume. An increase in the hydrophilic block length of the polymer leads to smaller nanoparticles, due to an enhanced ability of each polymer to shield the nanoparticle core. For unfavorable solute-polymer interactions, the nanoparticle size increases with hydrophobic block length. However, for favorable solute-polymer interactions, nanoparticle size exhibits a local minimum with respect to the hydrophobic block length. Our results provide insights on ways in which experimentally controllable parameters of the Flash NanoPrecipitation process can be used to influence aggregate size and composition during self-assembly.     

Improved dissipative particle dynamics simulations of lipid bilayers

The authors introduce a new parameterization for the dissipative particle dynamics simulations of lipid bilayers. In this parameterization, the conservative pairwise forces between beads of the same type in two different hydrophobic chains are chosen to be less repulsive than the water-water interaction, but the intrachain bead interactions are the same as the water-water interaction. For a certain range of parameters, the new bilayer can only be stretched up to 30% before it ruptures. Membrane tension, density profiles, and the in-plane lipid diffusion coefficient of the new bilayer are discussed in detail. They find two kinds of finite size effects that influence the membrane tension: lateral finite size effects, for which larger membranes rupture at a smaller stretch, and transverse finite size effects, for which tensionless bilayers are more compact in larger systems. These finite size effects become rather small when the simulation box is sufficiently large.     

The midpoint method for parallelization of particle simulations

The evaluation of interactions between nearby particles constitutes the majority of the computational workload involved in classical molecular dynamics (MD) simulations. In this paper, we introduce a new method for the parallelization of range-limited particle interactions that proves particularly suitable to MD applications. Because it applies not only to pairwise interactions but also to interactions involving three or more particles, the method can be used for evaluation of both nonbonded and bonded forces in a MD simulation. It requires less interprocessor data transfer than traditional spatial decomposition methods at all but the lowest levels of parallelism. It gains an additional practical advantage in certain commonly used interprocessor communication networks by distributing the communication burden more evenly across network links and by decreasing the associated latency. When used to parallelize MD, it further reduces communication requirements by allowing the computations associated with short-range nonbonded interactions, long-range electrostatics, bonded interactions, and particle migration to use much of the same communicated data. We also introduce certain variants of this method that can significantly improve the balance of computational load across processors.     

Configurational temperature in membrane simulations using dissipative particle dynamics

The use of excessively long time steps in dissipative particle dynamics simulations may produce simulation artifacts due to the generation of configurations which are not representative of the desired canonical ensemble. The configurational temperature, among other quantities, may be used to assess the extent of the deviation from equilibrium. This paper presents results for simulations of models of water and lipid bilayer membranes to illustrate the nature of the problems.     

Incremental update of electrostatic interactions in adaptively restrained particle simulations

The computation of long‐range potentials is one of the demanding tasks in Molecular Dynamics. During the last decades, an inventive panoply of methods was developed to reduce the CPU time of this task. In this work, we propose a fast method dedicated to the computation of the electrostatic potential in adaptively restrained systems. We exploit the fact that, in such systems, only some particles are allowed to move at each timestep. We developed an incremental algorithm derived from a multigrid‐based alternative to traditional Fourier‐based methods. Our algorithm was implemented inside LAMMPS, a popular molecular dynamics simulation package. We evaluated the method on different systems. We showed that the new algorithm's computational complexity scales with the number of active particles in the simulated system, and is able to outperform the well‐established Particle Particle Particle Mesh (P3M) for adaptively restrained simulations. © 2018 Wiley Periodicals, Inc.     

Micellar polymerization: Computer simulations by dissipative particle dynamics

Nowadays, micellar polymerization is widely used in different fields of industry and research, including modern living polymerization technique. However, this process has many variables and there is no comprehensive model to describe all features. This research presents simulation methodology which describes key properties of such reactions to take a guide through a variety of their modifications. Dissipative particle dynamics is used in addition to Monte Carlo scheme to simulate initiation, propagation, and termination events. Influence of initiation probability and different termination processes on final conversion and molecular‐weight distribution are presented. We demonstrate that prolonged initiation leads to increasing in polymer average molecular weight, and surface termination events play major role in conversion limitation, in comparison with recombination. © 2018 Wiley Periodicals, Inc.     

Molecular dynamics simulations of polyelectrolyte multilayering on a charged particle

Molecular dynamics simulations of polyelectrolyte multilayering on a charged spherical particle revealed that the sequential adsorption of oppositely charged flexible polyelectrolytes proceeds with surface charge reversal and highlighted electrostatic interactions as the major driving force of layer deposition. Far from being completely immobilized, multilayers feature a constant surge of chain intermixing during the deposition process, consistent with experimental observations of extensive interlayer mixing in these films. The formation of multilayers as well as the extent of layer intermixing depends on the degree of polymerization of the polyelectrolyte chains and the fraction of charge on its backbone. The presence of ionic pairs between oppositely charged macromolecules forming layers seems to play an important role in stabilizing the multilayer film.     

Computer simulations of particle-bubble interactions and particle sliding using Discrete Element Method

Polymer coatings on nano-sized remediation agents and subsurface heterogeneity will affect their transport, likely in a pH-dependent manner. The effect of pH on the aggregation of polymer-coated nanoscale zerovalent iron (nZVI) and its deposition onto sand and clay (kaolinite) surfaces was studied. nZVI coatings included a high molecular weight (90 kg/mol) strong polyanion, poly(methacrylic acid)-b-(methy methacrylate)-b-(styrenesulfonate) (PMAA-PMMA-PSS) and a low molecular weight (2.5 kg/mol) weak polyanion, polyaspartate. Aggregation and deposition increased with decreasing pH for both polyelectrolytes. The extent was greater for the low MW polyaspartate coated nZVI. Enhanced deposition at lower pH was indicated because the elutability of polyaspartate-modified hematite (which did not aggregate) also decreased at lower pH. The greater deposition onto clay minerals compared to similar sized silica fines is attributed to charge heterogeneity on clay mineral surfaces, which is sensitive to pH. Heteroaggregation between kaolinite particles and nZVI over the pH range 6-8 confirmed this assertion. Excess unadsorbed polyelectrolyte in solution (100mg/L) enhanced the transport of modified nZVI by minimizing aggregation and deposition onto sand and clay. These results indicate that site physical and chemical heterogeneity must be considered when designing an nZVI emplacement strategy.     

Numerical simulations of viscoelastic particle migration in a microchannel with triangular cross-section

The migration of a spherical particle immersed in a viscoelastic liquid flowing in a microchannel with a triangular cross-section is investigated by direct numerical simulations under inertialess conditions. The viscoelastic fluid is modeled through two constitutive equations to investigate the effect of the second normal stress difference and the resulting secondary flows on the migration phenomenon. The results are presented in terms of trajectories followed by the particles released at different initial positions over the channel cross-section in a wide range of Weissenberg numbers and confinement ratios. Particles suspended in a fluid with a negligible second normal stress difference migrate toward the channel centerline or the closest wall, depending on their initial position. A much more complex dynamics is found for particles suspended in a fluid with a relevant second normal stress difference due to the appearance of secondary flows that compete with the migration phenomenon. Depending on the Weissenberg number and confinement ratio, additional equilibrium positions (points or closed orbits) may appear. In this case, the channel centerline becomes unstable and the particles are driven to the corners or “entrapped” in recirculation regions within the channel cross-section. The inversion of the centerline stability can be exploited to design efficient size-based separation devices.     

Predicting patchy particle crystals: variable box shape simulations and evolutionary algorithms

We consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an approach based on Monte Carlo simulations in the isobaric-isothermal ensemble and (ii) an optimization technique based on ideas of evolutionary algorithms. We show that the two methods are equally successful and provide consistent results on crystalline phases of patchy particle systems.     

3D Monte Carlo simulations of a magnetic disk-like particle dispersion

We have investigated the aggregate structures of a colloidal dispersion composed of ferromagnetic disk-like particles with a magnetic moment normal to the particle axis at the particle center, by means of 3D Monte Carlo simulations. Such disk-like particles have been modeled as a circular disk-like particle with the side section shape of spherocylinder. We have attempted to clarify the influences of the magnetic field strength, magnetic interactions between particles and volumetric fraction of particles. In order to discuss quantitatively the aggregate structures of clusters, we have focused on the radial distribution and orientational pair correlation functions, etc. For no applied magnetic field cases, long column-like clusters come to be formed with increasing magnetic particle–particle interactions. The internal structures of these clusters clearly show that the particles incline in a certain direction and their magnetic moments alternate in direction between the neighboring particles in the clusters. For applied magnetic field cases, the magnetic moment of each particle inclines in the magnetic field direction and therefore the column-like clusters are not formed straightforwardly. If the magnetic field is much stronger than magnetic particle–particle interactions, the particles do not have a tendency to form the clusters. As the influence of magnetic particle–particle interactions is significantly strong, thick chain-like clusters or column-like clusters or brick-wall-like clusters come to be formed along the magnetic field direction.     

Polymerization of and within self-organized media

Self-organized surfactant solutions, such as microemulsions, vesicular solutions or dispersions, or lyotropic mesophases can serve as templates for the structure directed synthesis of organic polymers. Recent developments of templating within these equilibrium nanostructured fluids are reviewed. Depending on the template structure and the reaction conditions, the outcomes may be polyampholytes, amphiphiles, nanoparticles, hollow spheres, or mesoporous polymers. For each structure and morphology, the final product materials reflect a delicate balance between phase behavior and the reaction and mass transfer parameters that set structure. Experimental and theoretical aspects of reaction kinetics and thermodynamics such as monomer partitioning, swelling behavior and polymerization-induced phase separation are discussed.