Two-stage assembly of patchy ellipses: From bent-core particles to liquid crystal analogs.

We investigate the two-dimensional behavior of colloidal patchy ellipsoids specifically designed to follow a two-step assembly process from the monomer state to mesoscopic liquid-crystal phases via the formation of the so-called bent-core units at the intermediate stage. Our model comprises a binary mixture of ellipses interacting via the Gay-Berne potential and decorated by surface patches, with the binary components being mirror-image variants of each other-referred to as left-handed and right-handed ellipses according to the position of their patches. The surface patches are designed so as in the first stage of the assembly the monomers form bent-cores units, i.

A finite-temperature study of the degeneracy of the crystal phases in systems of soft aspherical particles.

We employ classical density-functional theory to investigate the phase diagram of an assembly of mutually penetrable, parallel ellipsoids interacting via the generalized exponential model of index four (GEM-4) pair potential. We show that the crystal phases of the system are obtained from those of the spherically symmetric GEM-4 model by rescaling the lattice vectors. Performing this rescaling in combination with an arbitrary rotation of the lattice leads to infinitely many different structures with the same free energy, thereby implying their infinite degeneracy.

Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system.

We investigate the phase ordering (pattern formation) of systems of two-dimensional core-shell particles using Monte Carlo (MC) computer simulations and classical density functional theory (DFT). The particles interact via a pair potential having a hard core and a repulsive square shoulder. Our simulations show that on cooling, the liquid state structure becomes increasingly characterized by long wavelength density modulations and on further cooling forms a variety of other phases, including clustered, striped, and other patterned phases.

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.

On the lattice ground state of densely packed hard ellipses.

Among lattice configurations of densely packed hard ellipses, Monte Carlo simulations are used to identify the so-called parallel and diagonal lattices as the two favorable states. The free energies of these two states are computed for several system sizes employing the Einstein crystal method. An accurate calculation of the free energy difference between the two states reveals the parallel lattice as the state with the lowest free energy.

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.

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.

Liquid-gas critical point of a two-dimensional system of hard ellipses with attractive wells.

In an effort to illuminate the general principles governing the critical behavior of model fluids, we investigate in this study how the shape and the (attractive) interaction range of the molecule affect the gas-liquid equilibrium and the critical behavior of the system. A combination of Monte Carlo simulations and analytical theory is employed to compute critical properties, i.e.

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.

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.

Direct Correlation Function of a Crystalline Solid.

Direct correlation functions (DCFs), linked to the second functional derivative of the free energy with respect to the one-particle density, play a fundamental role in a statistical mechanics description of matter. This holds, in particular, for the ordered phases: DCFs contain information about the local structure including defects and encode the thermodynamic properties of crystalline solids; they open a route to the elastic constants beyond low temperature expansions. Via a demanding numerical approach, we have explicitly calculated for the first time the DCF of a solid: based on the fundamental measure concept, we provide results for the DCF of a hard sphere crystal.

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.

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.

Reliable Computational Prediction of the Supramolecular Ordering of Complex Molecules under Electrochemical Conditions.

We propose a computationally lean, two-stage approach that reliably predicts self-assembly behavior of complex charged molecules on metallic surfaces under electrochemical conditions. Stage one uses ab initio simulations to provide reference data for the energies (evaluated for archetypical configurations) to fit the parameters of a conceptually much simpler and computationally less expensive force field of the molecules: classical, spherical particles, representing the respective atomic entities; a flat and perfectly conducting wall represents the metallic surface. Stage two feeds the energies that emerge from this force field into highly efficient and reliable optimization techniques to identify via energy minimization the ordered ground-state configurations of the molecules.

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.

Controlled self-aggregation of polymer-based nanoparticles employing shear flow and magnetic fields.

Star polymers with magnetically functionalized end groups are presented as a novel polymeric system whose morphology, self-aggregation, and orientation can easily be tuned by exposing these macromolecules simultaneously to an external magnetic field and to shear forces. Our investigations are based on a specialized simulation technique which faithfully takes into account the hydrodynamic interactions of the surrounding, Newtonian solvent. We find that the combination of magnetic field (including both strength and direction) and shear rate controls the mean number of magnetic clusters, which in turn is largely responsible for the static and dynamic behavior.

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.

Structure and stimuli-responsiveness of all-DNA dendrimers: theory and experiment.

We present a comprehensive theoretical and experimental study of the solution phase properties of a DNA-based family of nanoparticles - dendrimer-like DNA molecules (DL-DNA). These charged DNA dendrimers are novel macromolecular aggregates, which hold high promise in targeted self-assembly of soft matter systems in the bulk and at interfaces. To describe the behaviour of this family of dendrimers (with generations ranging from G1 to G7), we use a theoretical model in which base-pairs of a single DL-DNA molecule are modeled by charged monomers, whose interactions are chosen to mimic the equilibrium properties of DNA correctly.

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.

Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination.

Background: Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected "orphan" crop that would benefit from crop improvement efforts.

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.

Spontaneous assembly of a hybrid crystal-liquid phase in inverse patchy colloid systems.

Materials with well-defined architectures are heavily sought after in view of their diverse technological applications. Among the desired target architectures, lamellar phases stand out for their exceptional mechanical and optical features. Here we show that charged colloids, decorated on their poles with two oppositely charged regions possess the unusual ability to spontaneously assemble in different morphologies of (semi-)ordered, layered particle arrangements which maintain their structural stability over a surprisingly large temperature range.

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.

Two-dimensional systems with competing interactions: dynamic properties of single particles and of clusters.

Systems with short-range attractive and long-range repulsive interactions are able to form mesophases at sufficiently low temperatures. In two dimensions, such mesophases emerge as clusters, stripes or bubbles. Using extensive Monte Carlo simulations we investigate the static and the dynamic properties of such a cluster-forming system over a broad temperature range and for different densities.