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.

Erratum: Lattice gas study of thin-film growth scenarios and transitions between them: Role of substrate [Phys. Rev. E 103, 023302 (2021)].

This corrects the article DOI: 10.1103/PhysRevE.103.

Interplay of orientational order and roughness in simulated thin film growth of anisotropically interacting particles.

Roughness and orientational order in thin films of anisotropic particles are investigated using kinetic Monte Carlo simulations on a cubic lattice. Anisotropic next-neighbor interactions between the lattice particles were chosen to mimic the effects of shape anisotropy in the interactions of disk- or rodlike molecules with van der Waals attractions. Increasing anisotropy leads first to a preferred orientation in the film (which is close to the corresponding equilibrium transition) while the qualitative mode of roughness evolution (known from isotropic systems) does not change.

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.

Effect on ovarian activity and ovulation inhibition of different oral dosages of levonorgestrel.

Objectives: To investigate the effect of different oral dosages of levonorgestrel (LNG) on ovarian activity and to identify the lowest dosage at which no ovulation occurred. Secondary objectives were to assess return of ovulation after stopping treatment, bleeding pattern, pharmacokinetic (PK) parameters and safety and tolerability.

Study Design: A parallel-group study with adaptive design was performed in 90 healthy women with proven ovulatory cycles.

Droplet condensation in the lattice gas with density functional theory.

A density functional for the lattice gas with next-neighbor attractions (Ising model) from fundamental measure theory is applied to the problem of droplet states in three-dimensional, finite systems. The density functional is constructed via an auxiliary model with hard lattice gas particles and lattice polymers to incorporate the attractions. Similar to previous simulation studies, the sequence of droplets changing to cylinders and to planar slabs is found upon increasing the average density ρ[over ¯] in the system.

Density functional for the lattice gas from fundamental measure theory.

We construct a density functional for the lattice gas or Ising model on square and cubic lattices based on lattice fundamental measure theory. To treat the nearest-neighbor attractions between the lattice gas particles, the model is mapped to a multicomponent model of hard particles with additional lattice polymers where effective attractions between particles arise from the depletion effect. The lattice polymers are further treated via the introduction of polymer clusters (labelled by the numbers of polymer they contain) such that the model becomes a multicomponent model of particles and polymer clusters with nonadditive hard interactions.

Reconsidering power functional theory.

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

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.

Lattice gas study of thin-film growth scenarios and transitions between them: Role of substrate.

Thin-film growth is investigated in two types of lattice gas models where substrate and film particles are different, expressed by unequal interaction energy parameters. The first is of solid-on-solid type, whereas the second additionally incorporates desorption, diffusion in the gas phase above the film and readsorption at the film (appropriate for growth in colloidal systems). In both models, the difference between particle-substrate and particle-particle interactions plays a central role for the evolution of the film morphology at intermediate times.

A progestin isn't a progestin: dienogest for endometriosis as a blueprint for future research - Review as a contribution for discussion.

The different etiopathogenetic mechanisms and the diversity of clinical features of endometriosis has not yet allowed to identify a causal pharmacological monotherapy satisfying the unresolved medical needs in this important female disease. Therefore, despite the search for new therapeutic principles for the indication, the strategy of gradual optimization of established therapeutic principles should not be disregarded.In the case of progestins, the fact that each compound has its own, specific profile may allow to study the therapeutic relevance of the various signal cascades influenced by their receptors.

Analytical classical density functionals from an equation learning network.

We explore the feasibility of using machine learning methods to obtain an analytic form of the classical free energy functional for two model fluids, hard rods and Lennard-Jones, in one dimension. The equation learning network proposed by Martius and Lampert [e-print arXiv:1610.02995 (2016)] is suitably modified to construct free energy densities which are functions of a set of weighted densities and which are built from a small number of basis functions with flexible combination rules.

Nematic and gas-liquid transitions for sticky rods on square and cubic lattices.

Using grand-canonical Monte Carlo simulations, we investigate the phase diagram of hard rods of length L with additional contact (sticky) attractions on square and cubic lattices. The phase diagram shows a competition between gas-liquid and ordering transitions (which are of demixing type on the square lattice for L≥7 and of nematic type on the cubic lattice for L≥5). On the square lattice, increasing attractions initially lead to a stabilization of the isotropic phase.

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.

Two time scales for self and collective diffusion near the critical point in a simple patchy model for proteins with floating bonds.

Using dynamic Monte Carlo and Brownian dynamics, we investigate a floating bond model in which particles can bind through mobile bonds. The maximum number of bonds (here fixed to 4) can be tuned by appropriately choosing the repulsive, nonadditive interactions among bonds and particles. We compute the static and dynamic structure factor (intermediate scattering function) in the vicinity of the gas-liquid critical point.

Growth of films with anisotropic particles: Simulations and rate equations.

By means of computer simulations and kinetic rate equations, we study the formation of a film of rod-like particles which are deposited on a substrate. The rod-rod interactions are hard with a short-range attraction of variable strength and width, and the rod-substrate interactions favor lying rods with a variable strength. For a rod aspect ratio of 5 and deposition of up to an equivalent of one monolayer of standing rods, we demonstrate a rich variety of growth modes upon variation of the three interaction parameters.

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.

Comparison of dienogest effects upon 3,3'-diindolylmethane supplementation in models of endometriosis and clinical cases.

Dienogest (DNG) administration is a well-established treatment for endometriosis but bleeding irregularities remain its main disadvantage. Changes in diet, mainly to vegetable consumption, are beneficial in the treatment of estrogen-related pathologies but their use for endometriosis has been poorly studied. In this study, addition of the phytochemical 3,3'-diindolylmethane (DIM) to DNG therapy has been investigated in in vitro and ex vivo models for endometriosis and in a small cohort of women with endometriosis.

Isotropic-nematic transition for hard rods on a three-dimensional cubic lattice.

Using grand-canonical Monte Carlo (GCMC) simulations, we investigate the isotropic-nematic phase transition for hard rods of size L×1×1 on a three-dimensional cubic lattice. We observe such a transition for L≥6. For L=6, the nematic state has a negative order parameter, reflecting the co-occurrence of two dominating orientations.