Competition between shape anisotropy and deformation in the ordering and close packing properties of quasi-one-dimensional hard superellipse fluids.

We investigate the orientational ordering and close-packing behavior of a quasi-one-dimensional (q1D) system of hard superellipses, where the centers of the particles are confined to a line, but they can rotate freely within a two-dimensional plane. The particle shape is tuned between an ellipse and a rectangle by varying the deformation parameter (n). The elongation of the particle is changed using the aspect ratio (k).

Neural density functional theory in higher dimensions with convolutional layers.

Based on recent advancements in using machine learning for classical density functional theory for systems with one-dimensional, planar inhomogeneities, we propose a machine learning model for application in two dimensions (2D) akin to density functionals in weighted density forms, as, e.g., in fundamental measure theory.

Island formation in heteroepitaxial growth.

Island formation in strain-free heteroepitaxial deposition of thin films is analyzed using kinetic Monte Carlo simulations of two minimal lattice models and scaling approaches. The transition from layer-by-layer (LBL) to island (ISL) growth is driven by a weaker binding strength of the substrate, which, in the kinetic model, is equivalent to an increased diffusivity of particles on the substrate compared to particles on the film. The LBL-ISL transition region is characterized by particle fluxes between layers 1 and 2 significantly exceeding the net flux between them, which sets a quasiequilibrium condition.

The orientational structure of a model patchy particle fluid: Simulations, integral equations, density functional theory, and machine learning.

We investigate the orientational properties of a homogeneous and inhomogeneous tetrahedral four-patch fluid (Bol-Kern-Frenkel model). Using integral equations, either (i) HNC or (ii) a modified HNC scheme with a simulation input, the full orientational dependence of pair and direct correlation functions is determined. Density functionals for the inhomogeneous problem are constructed via two different methods.

Machine Learning of a Density Functional for Anisotropic Patchy Particles.

Anisotropic patchy particles have become an archetypical statistical model system for associating fluids. Here, we formulate an approach to the Kern-Frenkel model via the classical density functional theory to describe the positionally and orientationally resolved equilibrium density distributions in flat wall geometries. The density functional is split into a reference part for the orientationally averaged density and an orientational part in mean-field approximation.

Approaching the hard sphere limit in colloids suitable for confocal microscopy - the end of a decade lasting quest.

PMMA-PHSA particles serve as the hard sphere model system since the 1980s. We investigate the fluid structure of fluorescent ones in three different solvents by laser scanning confocal microscopy: a decalin-tetrachloroethylene (TCE)-mixture and a decalin-cyclohexylbromide (CHB)-mixture with and without tetrabutylammoniumbromide (TBAB). The experimental 3D radial distribution functions are modeled by analytical theory and computer simulations taking polydispersity and the experimental position uncertainty into account.

Effects of flexibility in coarse-grained models for bovine serum albumin and immunoglobulin G.

We construct a coarse-grained, structure-based, low-resolution, 6-bead flexible model of bovine serum albumin (BSA, PDB: 4F5S), which is a popular example of a globular protein in biophysical research. The model is obtained via direct Boltzmann inversion using all-atom simulations of a single molecule, and its particular form is selected from a large pool of 6-bead coarse-grained models using two suitable metrics that quantify the agreement in the distribution of collective coordinates between all-atom and coarse-grained Brownian dynamics simulations of solutions in the dilute limit. For immunoglobulin G (IgG), a similar structure-based 12-bead model has been introduced in the literature [Chaudhri et al.

Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture.

The crowded environment of biological systems such as the interior of living cells is occupied by macromolecules with a broad size distribution. This situation of polydispersity might influence the dependence of the diffusive dynamics of a given tracer macromolecule in a monodisperse solution on its hydrodynamic size and on the volume fraction. The resulting size dependence of diffusive transport crucially influences the function of a living cell.

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.

Reconsidering power functional theory.

The original derivation of power functional theory [M. Schmidt and J. M.

Protein Short-Time Diffusion in a Naturally Crowded Environment.

The interior of living cells is a dense and polydisperse suspension of macromolecules. Such a complex system challenges an understanding in terms of colloidal suspensions. As a fundamental test we employ neutron spectroscopy to measure the diffusion of tracer proteins (immunoglobulins) in a cell-like environment (cell lysate) with explicit control over crowding conditions.

Bulk structural information from density functionals for patchy particles.

We investigate bulk structural properties of tetravalent associating particles within the framework of classical density functional theory, building upon Wertheim's thermodynamic perturbation theory. To this end, we calculate density profiles within an effective test-particle geometry and compare to radial distribution functions obtained from computer simulations. We demonstrate that a modified version of the functional proposed by Yu and Wu [J.

Phase diagrams and crystal-fluid surface tensions in additive and nonadditive two-dimensional binary hard-disk mixtures.

Using density functionals from fundamental measure theory, phase diagrams and crystal-fluid surface tensions in additive and nonadditive (Asakura-Oosawa model) two-dimensional binary hard-disk mixtures are determined for the whole range of size ratios q=smalldiameter/largediameter, assuming random disorder (lattice points or interstitial occupied by large or small disks at random) in the crystal phase. The fluid-crystal transitions are first order due to the assumption of a periodic unit cell in the density-functional calculations. Qualitatively, the shape of the phase diagrams is similar to the case of three-dimensional hard-sphere mixtures.

A fundamental measure density functional for fluid and crystal phases of the Asakura-Oosawa model.

We investigate a density functional for the Asakura-Oosawa model of colloid-polymer mixtures, describing both fluid and crystal phases. It is derived by linearizing the two-component fundamental-measure hard sphere tensor functional in the second (polymer) component. We discuss the formulation of an effective density functional for colloids only.

A dynamic DFT approach to generalized diffusion equations in a system with long-ranged and hydrodynamic interactions.

We build on an existing approximation scheme to the Smoluchowski equation in order to derive a dynamic density functional theory (DDFT) including two-body hydrodynamic interactions. A generalized diffusion equation and a wavenumber-dependent diffusion coefficient D(k) are derived by linearization in the density fluctuations. The result is applied to a colloidal monolayer at a fluid interface, having bulk-like hydrodynamic interactions and/or interacting via long-ranged capillary forces.

Fundamental measure theory for the inhomogeneous hard-sphere system based on Santos' consistent free energy.

Based on Santos' general solution for the scaled-particle differential equation [Phys. Rev. E 86, 040102(R) (2012)], we construct a free-energy functional for the hard-sphere system.

3D hydrodynamic interactions lead to divergences in 2D diffusion.

We investigate the influence of 3D hydrodynamic interactions on confined colloidal suspensions, where only the colloids are restricted to one or two dimensions. In the absence of static interactions among the colloids, i.e.

Solid-liquid surface tensions of critical nuclei and nucleation barriers from a phase-field-crystal study of a model binary alloy using finite system sizes.

Phase-field-crystal (PFC) modeling has emerged as a computationally efficient tool to address crystal growth phenomena on atomistic length and diffusive time scales. We use a two-dimensional phase-field-crystal model for a binary system based on Elder et al. [Phys.

Strong effect of weak charging in suspensions of anisotropic colloids.

Suspensions of hard colloidal particles frequently serve as model systems in studies on fundamental aspects of phase transitions. But often colloidal particles that are considered as "hard" are in fact weakly charged. If the colloids are spherical, weak charging has only a weak effect on the structural properties of the suspension, which can be easily corrected for.

Protein cluster formation in aqueous solution in the presence of multivalent metal ions--a light scattering study.

The formation of protein clusters as precursors for crystallization and phase separation is of fundamental and practical interest in protein science. Using multivalent ions, the strengths of both long-range Coulomb repulsion and short-range attraction can be tuned in protein solutions, representing a well-controlled model system to study static and dynamic properties of clustering during the transition from a charge-stabilized to an aggregate regime. Here, we study compressibility, diffusion, and size of solutes by means of static (SLS) and dynamic light scattering (DLS) in solutions of bovine serum albumin (BSA) and YCl3.

Connectivity percolation in suspensions of hard platelets.

We present a study on connectivity percolation in suspensions of hard platelets by means of Monte Carlo simulation. We interpret our results using a contact-volume argument based on an effective single-particle cell model. It is commonly assumed that the percolation threshold of anisotropic objects scales as their inverse aspect ratio.

Communication: Fundamental measure theory for hard disks: fluid and solid.

Two-dimensional hard-particle systems are rather easy to simulate but surprisingly difficult to treat by theory. Despite their importance from both theoretical and experimental points of view, theoretical approaches are usually qualitative or at best semi-quantitative. Here, we present a density functional theory based on the ideas of fundamental measure theory for two-dimensional hard-disk mixtures, which allows for the first time an accurate description of the structure of the dense fluid and the equation of state for the solid phase within the framework of density functional theory.