Phase separation dynamics in a symmetric binary mixture of ultrasoft particles.

Phase separation plays a key role in determining the self-assembly of biological and soft-matter systems. In biological systems, liquid-liquid phase separation inside a cell leads to the formation of various macromolecular aggregates. The interaction among these aggregates is soft, i.e., they can significantly overlap at a small energy cost. From a computer simulation point of view, these complex macromolecular aggregates are generally modeled by soft particles. The effective interaction between two particles is defined via the generalized exponential model of index n, with n = 4. Here, using molecular dynamics simulations, we study the phase separation dynamics of a size-symmetric binary mixture of ultrasoft particles. We find that when the mixture is quenched to a temperature below the critical temperature, the two components spontaneously start to separate. Domains of the two components form, and the equal-time order parameter reveals that the domain sizes grow with time in a power-law manner with an exponent of 1/3, which is consistent with the Lifshitz-Slyozov law for conserved systems. Furthermore, the static structure factor shows a power-law decay with an exponent of 4, consistent with the Porod law.

Microswimmers learning chemotaxis with genetic algorithms.

Various microorganisms and some mammalian cells are able to swim in viscous fluids by performing nonreciprocal body deformations, such as rotating attached flagella or by distorting their entire body. In order to perform chemotaxis (i.e., to move toward and to stay at high concentrations of nutrients), they adapt their swimming gaits in a nontrivial manner. Here, we propose a computational model, which features autonomous shape adaptation of microswimmers moving in one dimension toward high field concentrations. As an internal decision-making machinery, we use artificial neural networks, which control the motion of the microswimmer. We present two methods to measure chemical gradients, spatial and temporal sensing, as known for swimming mammalian cells and bacteria, respectively. Using the genetic algorithm NeuroEvolution of Augmenting Topologies, surprisingly simple neural networks evolve. These networks control the shape deformations of the microswimmers and allow them to navigate in static and complex time-dependent chemical environments. By introducing noisy signal transmission in the neural network, the well-known biased run-and-tumble motion emerges. Our work demonstrates that the evolution of a simple and interpretable internal decision-making machinery coupled to the environment allows navigation in diverse chemical landscapes. These findings are of relevance for intracellular biochemical sensing mechanisms of single cells or for the simple nervous system of small multicellular organisms such as Caenorhabditis elegans.

Ordered ground state configurations of the asymmetric Wigner bilayer system-Revisited with unsupervised learning.

We have reanalyzed the rich plethora of ground state configurations of the asymmetric Wigner bilayer system that we had recently published in a related diagram of states [Antlanger et al., Phys. Rev. Lett. 117, 118002 (2016)], comprising roughly 60 000 state points in the phase space spanned by the distance between the plates and the charge asymmetry parameter of the system. In contrast to this preceding contribution where the classification of the emerging structures was carried out "by hand," we have used for the present contribution machine learning concepts, notably based on a principal component analysis and a k-means clustering approach: using a 30-dimensional feature vector for each emerging structure (containing relevant information, such as the composition of the configuration as well as the most relevant order parameters), we were able to reanalyze these ground state configurations in a considerably more systematic and comprehensive manner than we could possibly do in the previously published classification scheme. Indeed, we were now able to identify new structures in previously unclassified regions of the parameter space and could considerably refine the previous classification scheme, thereby identifying a rich wealth of new emerging ground state configurations. Thorough consistency checks confirm the validity of the newly defined diagram of states.

Elasticity in crystals with a high density of local defects: Insights from ultra-soft colloids.

In complex crystals close to melting or at finite temperatures, different types of defects are ubiquitous and their role becomes relevant in the mechanical response of these solids. Conventional elasticity theory fails to provide a microscopic basis to include and account for the motion of point defects in an otherwise ordered crystalline structure. We study the elastic properties of a point-defect rich crystal within a first principles theoretical framework derived from the microscopic equations of motion. This framework allows us to make specific predictions pertaining to the mechanical properties that we can validate through deformation experiments performed in molecular dynamics simulations.

On the yielding of a point-defect-rich model crystal under shear: insights from molecular dynamics simulations.

In real crystals and at finite temperatures point defects are inevitable. Under shear their dynamics severely influence the mechanical properties of these crystals, giving rise to non-linear effects, such as ductility. In an effort to elucidate the complex behavior of crystals under plastic deformation it is crucial to explore and to understand the interplay between the timescale related to the equilibrium point-defect diffusion and the shear-induced timescale. Based on extensive non-equilibrium molecular dynamics simulations we present a detailed investigation on the yielding behavior of cluster crystals, an archetypical model for a defect-rich crystal: in such a system clusters of overlapping particles occupy the lattice sites of a regular (FCC) structure. In equilibrium particles diffuse via site-to-site hopping while maintaining the crystalline structure intact. We investigate these cluster crystals at a fixed density and at different temperatures where the system remains in the FCC structure: temperature allows us to vary the diffusion timescale appropriately. We then expose the crystal to shear, thereby choosing shear rates which cover timescales that are both higher and lower than the equilibrium diffusion timescales. We investigate the macroscopic and microscopic response of our cluster crystal to shear and find that the yielding scenario of such a system does not rely on the diffusion of the particles - it is rather related to the plastic deformation of the underlying crystalline structure. The local bond order parameters and the measurement of local angles between neighboring clusters confirm the cooperative movement of the clusters close to the yield point. Performing complementary, related simulations for an FCC crystal formed by harshly repulsive particles reveals similarities in the yielding behavior between both systems. Still we find that the diffusion of particles does influence characteristic features in the cluster crystal, such as a less prominent increase of order parameters close to the yield point. Our simulations provide for the first time an insight into the role of the diffusion of defects in the yielding behavior of a defect-rich crystal under shear. These observations will thus be helpful in the development of theories for the plastic deformation of defect-rich crystals.

Deformable hard particles confined in a disordered porous matrix.

With suitably designed Monte Carlo simulations, we have investigated the properties of mobile, impenetrable, yet deformable particles that are immersed into a porous matrix, the latter one realized by a frozen configuration of spherical particles. By virtue of a model put forward by Batista and Miller [Phys. Rev. Lett. 105, 088305 (2010)], the fluid particles can change in their surroundings, formed by other fluid particles or the matrix particles, their shape within the class of ellipsoids of revolution; such a change in shape is related to a change in energy, which is fed into suitably defined selection rules in the deformation "moves" of the Monte Carlo simulations. This concept represents a simple yet powerful model of realistic, deformable molecules with complex internal structures (such as dendrimers or polymers). For the evaluation of the properties of the system, we have used the well-known quenched-annealed protocol (with its characteristic double average prescription) and have analyzed the simulation data in terms of static properties (the radial distribution function and aspect ratio distribution of the ellipsoids) and dynamic features (notably the mean squared displacement). Our data provide evidence that the degree of deformability of the fluid particles has a distinct impact on the aforementioned properties of the system.

On the degeneracy of ordered ground state configurations of the aspherical Gaussian core model.

We provide rigorous evidence that the ordered ground state configurations of a system of parallel oriented, ellipsoidal particles, interacting via a Gaussian potential (termed in the literature as Gaussian core nematics), must be infinitely degenerate; we have demonstrated that these configurations originate from the related ground state configuration of the corresponding symmetric Gaussian core system via a suitable stretching operation of this lattice in combination with an arbitrary rotation. These findings explain related observations in former investigations, which then remained unexplained. Our conclusions have far reaching consequences for the search of ground state configurations of other nematic particles.

Hydrodynamic correlations of viscoelastic fluids by multiparticle collision dynamics simulations.

The emergent fluctuating hydrodynamics of a viscoelastic fluid modeled by the multiparticle collision dynamics (MPC) approach is studied. The fluid is composed of flexible, Gaussian phantom polymers that interact by local momentum-conserving stochastic MPCs. For comparison, the analytical solution of the linearized Navier-Stokes equation is calculated, where viscoelasticity is taken into account by a time-dependent shear relaxation modulus. The fluid properties are characterized by the transverse velocity autocorrelation function in Fourier space as well as in real space. Various polymer lengths are considered-from dumbbells to (near-)continuous polymers. Viscoelasticity affects the fluid properties and leads to strong correlations, which overall decay exponentially in Fourier space. In real space, the center-of-mass velocity autocorrelation function of individual polymers exhibits a long-time tail, independent of the polymer length, which decays as t-3/2, similar to a Newtonian fluid, in the asymptotic limit t → ∞. Moreover, for long polymers, an additional power-law decay appears at time scales shorter than the longest polymer relaxation time with the same time dependence, but negative correlations, and the polymer length dependence L-1/2. Good agreement is found between the analytical and simulation results.

Molecular dynamics simulations of inverse patchy colloids.

Inverse patchy colloids are patchy particles with differently charged surface regions. In this paper we focus on inverse patchy colloids with two different polar patches and an oppositely charged equatorial belt, and we describe a model and a reliable and efficient numerical algorithm that can be applied to investigate the properties of these particles in molecular dynamics simulations.

The asymmetric Wigner bilayer.

We present a comprehensive discussion of the so-called asymmetric Wigner bilayer system, where mobile point charges, all of the same sign, are immersed into the space left between two parallel, homogeneously charged plates (with possibly different charge densities). At vanishing temperatures, the particles are expelled from the slab interior; they necessarily stick to one of the two plates and form there ordered sublattices. Using complementary tools (analytic and numerical), we study systematically the self-assembly of the point charges into ordered ground state configurations as the inter-layer separation and the asymmetry in the charge densities are varied. The overwhelming plethora of emerging Wigner bilayer ground states can be understood in terms of the competition of two strategies of the system: net charge neutrality on each of the plates on the one hand and particles' self-organization into commensurate sublattices on the other hand. The emerging structures range from simple, highly commensurate (and thus very stable) lattices (such as staggered structures, built up by simple motives) to structures with a complicated internal structure. The combined application of our two approaches (whose results agree within remarkable accuracy) allows us to study on a quantitative level phenomena such as over- and underpopulation of the plates by the mobile particles, the nature of phase transitions between the emerging phases (which pertain to two different universality classes), and the physical laws that govern the long-range behaviour of the forces acting between the plates. Extensive, complementary Monte Carlo simulations in the canonical ensemble, which have been carried out at small, but finite temperatures along selected, well-defined pathways in parameter space confirm the analytical and numerical predictions within high accuracy. The simple setup of the Wigner bilayer system offers an attractive possibility to study and to control complex scenarios and strategies of colloidal self-assembly, via the variation of two system parameters.

On the applicability of density dependent effective interactions in cluster-forming systems.

We systematically studied the validity and transferability of the force-matching algorithm for computing effective pair potentials in a system of dendritic polymers, i.e., a particular class of ultrasoft colloids. We focused on amphiphilic dendrimers, macromolecules which can aggregate into clusters of overlapping particles to minimize the contact area with the surrounding implicit solvent. Simulations were performed for both the monomeric and coarse-grained models in the liquid phase at densities ranging from infinite dilution up to values close to the freezing point. The effective pair potentials for the coarse-grained simulations were computed from the monomeric simulations both in the zero-density limit (Φeff0) and at each investigated finite density (Φeff). Conducting the coarse-grained simulations with Φeff0 at higher densities is not appropriate as they failed at reproducing the structural properties of the monomeric simulations. In contrast, we found excellent agreement between the spatial dendrimer distributions obtained from the coarse-grained simulations with Φeff and the microscopically detailed simulations at low densities, where the macromolecules were distributed homogeneously in the system. However, the reliability of the coarse-grained simulations deteriorated significantly as the density was increased further and the cluster occupation became more polydisperse. Under these conditions, the effective pair potential of the coarse-grained model can no longer be computed by averaging over the whole system, but the local density needs to be taken into account instead.

Rich Polymorphic Behavior of Wigner Bilayers.

Self-assembly into target structures is an efficient material design strategy. Combining analytical calculations and computational techniques of evolutionary and Monte Carlo types, we report about a remarkable structural variability of Wigner bilayer ground states, when charges are confined between parallel charged plates. Changing the interlayer separation, or the plate charge asymmetry, a cascade of ordered patterns emerges. At variance with the symmetric case phenomenology, the competition between commensurability features and charge neutralization leads to long range attraction, appearance of macroscopic charges, exotic phases, and nonconventional phase transitions with distinct critical indices, offering the possibility of a subtle, but precise and convenient control over patterns.

Equilibrium structures of anisometric, quadrupolar particles confined to a monolayer.

We investigate the structural properties of a two-dimensional system of ellipsoidal particles carrying a linear quadrupole moment in their center. These particles represent a simple model for a variety of uncharged, non-polar conjugated organic molecules. Using optimization tools based on ideas of evolutionary algorithms, we first examine the ground state structures as we vary the aspect ratio of the particles and the pressure. Interestingly, we find, besides the intuitively expected T-like configurations, a variety of complex structures, characterized with up to three different particle orientations. In an effort to explore the impact of thermal fluctuations, we perform constant-pressure molecular dynamics simulations within a range of rather low temperatures. We observe that ground state structures formed by particles with a large aspect ratio are in particular suited to withstand fluctuations up to rather high temperatures. Our comprehensive investigations allow for a deeper understanding of molecular or colloidal monolayer arrangements under the influence of a typical electrostatic interaction on a coarse-grained level.

Generalized inverse patchy colloid model.

We generalize the inverse patchy colloid model that was originally developed for heterogeneously charged particles with two identical polar patches and an oppositely charged equator to a model that can have a considerably richer surface pattern. Based on a Debye-Hückel framework, we propose a coarse-grained description of the effective pair interactions that is applicable to particles with an arbitrary patch decoration. We demonstrate the versatility of this approach by applying it to models with (i) two differently charged and/or sized patches, and (ii) three, possibly different patches.

Theoretical and numerical investigations of inverse patchy colloids in the fluid phase.

We investigate the structural and thermodynamic properties of a new class of patchy colloids, referred to as inverse patchy colloids (IPCs) in their fluid phase via both theoretical methods and simulations. IPCs are nano- or micro- meter sized particles with differently charged surface regions. We extend conventional integral equation schemes to this particular class of systems: our approach is based on the so-called multi-density Ornstein-Zernike equation, supplemented with the associative Percus-Yevick approximation (APY). To validate the accuracy of our framework, we compare the obtained results with data extracted from NpT and NVT Monte Carlo simulations. In addition, other theoretical approaches are used to calculate the properties of the system: the reference hypernetted-chain (RHNC) method and the Barker-Henderson thermodynamic perturbation theory. Both APY and RHNC frameworks provide accurate predictions for the pair distribution functions: APY results are in slightly better agreement with MC data, in particular at lower temperatures where the RHNC solution does not converge.

Tunable assembly of heterogeneously charged colloids.

The self-assembly of colloidal particles is a route to designed materials production that combines high flexibility, cost effectiveness, and the opportunity to create ordered structures at length scales ranging from nano- to micrometers. For many practical applications in electronics, photovoltaics, and biomimetic material synthesis, ordered mono- and bilayers are often needed. Here we present a novel and simple way to tune via external parameters the ordering of heterogeneously charged colloids into quasi two-dimensional structures. Depending on the charges of the underlying substrate and of the particles, a rich and versatile assembly scenario takes place, resulting from the complex interplay between directional attractive and repulsive particle-particle and particle-substrate interactions. Upon subtle variations of the relative charge of the system components, emerging via pH modification, reversible changes either from extended aggregates to a monomeric phase or from triangular to square domains are observed.

Phase diagram of inverse patchy colloids assembling into an equilibrium laminar phase.

We numerically study the phase behavior of colloidal particles with two charged patches at the poles and an oppositely charged equatorial belt. Interactions between particles are described using the inverse patchy colloid model, where the term inverse emphasizes the difference with respect to conventional patchy particles: as a consequence of the heterogeneous charge distribution, the patches on the particle surface repel each other, whereas the patches and non-patch regions mutually attract. For the model parameters considered in this work, the system exhibits an unusual equilibrium phase diagram characterized by a broad region where a novel structure composed of parallel colloidal monolayers is stable.

Explicit spatial description of fluid inclusions in porous matrices in terms of an inhomogeneous integral equation.

We study the fluid inclusion of both Lennard-Jones (LJ) particles and particles with competing interaction ranges--short range attractive and long range repulsive (SALR)--in a disordered porous medium constructed as a controlled pore glass in two dimensions. With the aid of a full two-dimensional Ornstein-Zernike approach, complemented by a Replica Ornstein-Zernike integral equation, we explicitly obtain the spatial density distribution of the fluid adsorbed in the porous matrix and a good approximation for the average fluid-matrix correlations. The results illustrate the remarkable differences between the adsorbed LJ and SALR systems. In the latter instance, particles tend to aggregate in clusters which occupy pockets and bays in the porous structure, whereas the LJ fluid uniformly wets the porous walls. A comparison with Molecular Dynamics simulations shows that the two-dimensional Ornstein-Zernike approach with a Hypernetted Chain closure together with a sensible approximation for the fluid-fluid correlations can provide an accurate picture of the spatial distribution of adsorbed fluids for a given configuration of porous material.

Merging and hopping processes in systems of ultrasoft, cluster forming particles under compression.

We have exposed a two-dimensional nanodrop of particles interacting via an ultrasoft (i.e., bounded), purely repulsive potential to a combined thermo- and barostat. While increasing the pressure steadily via a suitable pressure increment the temperature of the system is kept at a fixed target temperature. Once the hexagonal crystal composed of clusters of overlapping particles has formed, we investigate the system's reaction on the non-equilibrium conditions. Recording the trajectories of the particles in molecular dynamics simulations, we can identify how particle hopping and cluster merging events are realized. We find that the number of particles involved in these processes is of comparable size and that under-populated clusters (with ∼70% of the average cluster size) are prone for merging processes. Theoretical predictions about the density-dependence of the average cluster size and of the nearest cluster-distance are confirmed within good accuracy.

Crystal phases of soft spheres systems in a slab geometry.

We have identified the ground state configurations of soft particles (interacting via inverse power potentials) confined between two hard, impenetrable walls. To this end we have used a highly reliable optimization scheme at vanishing temperature while varying the wall separation over a representative range. Apart from the expected layered triangular and square structures (which are compatible with the three-dimensional bulk fcc lattice), we have identified a cascade of highly complex intermediate structures. Taking benefit of the general scaling properties of inverse power potentials, we could identify - for a given softness value - one single master curve which relates the energy to the wall separation, irrespective of the density of the system. Via extensive Monte Carlo simulations, we have performed closer investigations of these intermediate structures at finite temperature: we could provide evidence to which extent these particle arrangements remain stable over a relatively large temperature range.