Stmol: A component for building interactive molecular visualizations within streamlit web-applications.

Streamlit is an open-source Python coding framework for building web-applications or "web-apps" and is now being used by researchers to share large data sets from published studies and other resources. Here we present Stmol, an easy-to-use component for rendering interactive 3D molecular visualizations of protein and ligand structures within Streamlit web-apps. Stmol can render protein and ligand structures with just a few lines of Python code by utilizing popular visualization libraries, currently Py3DMol and Speck.

Design of new hole transport materials based on triphenylamine derivatives using different π-linkers for the application in perovskite solar cells. A theoretical study.

New organic molecules containing five different compounds, commonly called -linkers, located between the triphenylamine units, were theoretically designed and analyzed in order to be proposed as new hole transport materials (HTMs) in perovskite solar cells, in total ten new molecules were analyzed. The electronic, optical and hole transport properties were determined, similarly, the relationship of these properties with their molecular structure was also investigated by Density Functional Theory (DFT) and Density Functional Tight Binding (DFTB) calculations. Eight of the ten analyzed compounds exhibited the main absorption band out of the visible region; therefore these compounds did not present an overlap with the absorption spectra of the typical methylammonium lead iodide (MAPI) hybrid-perovskite.

The generalized continuous multiple step (GCMS) potential: model systems and benchmarks.

The generalized continuous multiple step (GCMS) potential is presented in this work. Its flexible form allows forand/orcontributions to be encoded through adjustable energy and length scales. The GCMS interaction provides a continuous representation of square-well, square-shoulder potentials and their variants for implementation in computer simulations.

Defect-mediated colloidal interactions in a nematic-phase discotic solvent.

Interactions between colloidal inclusions dispersed in a nematic discotic liquid-crystalline solvent were investigated for different solute-solvent coupling conditions. The solvent was treated at the level of Gay-Berne discogens. Colloidal inclusions were coupled to the solvent with a generalized sphere-ellipsoid interaction potential.

Atomic Surface Segregation and Structural Characterization of PdPt Bimetallic Nanoparticles.

Bimetallic nanoparticles are of interest since they lead to many interesting electrical, chemical, catalytic, and optical properties. They are particularly important in the field of catalysis since they show superior catalytic properties than their monometallic counterparts. The structures of bimetallic nanoparticles depend mainly on the synthesis conditions and the miscibility of the two components.

Influence of anchoring in the phase behaviour of discotic liquid crystals.

Molecular dynamics simulations were performed for a Gay-Berne discotic fluid confined in a slab geometry for two different anchorings: homeotropic (face-on) and planar (edge-on), and for two different confinement lengths. Our results show that the behaviour of the more confined system in the temperature region of the isotropic-nematic transition is critically influenced by the presence of the walls: the growth of the solid-liquid crystal interface spans over the entire width of the cell, and the character of the transition is changed from first order to continuous. For all the confined systems studied, we observe a higher nematic-columnar transition temperature and a smaller nematic phase region in the phase diagram, as compared with the behaviour of the infinite system.

Diffusion of colloidal fluids in random porous media.

The diffusive relaxation of a colloidal fluid adsorbed in a porous medium depends on many factors, including the concentration and composition of the adsorbed colloidal fluid, the average structure of the porous matrix, and the nature of the colloid-colloid and colloid-substrate interactions. A simple manner to describe these effects is to model the porous medium as a set of spherical particles fixed in space at random positions with prescribed statistical structural properties. Within this model one may describe the relaxation of concentration fluctuations of the adsorbed fluid by simply setting to zero the short-time mobility of one species (the porous matrix) in a theory of the dynamics of equilibrium colloidal mixtures, or by extending such dynamic theory to explicitly consider the porous matrix as a random external field, as recently done in the framework of mode coupling theory [V.

Simplified self-consistent theory of colloid dynamics.

One of the main elements of the self-consistent generalized Langevin equation (SCGLE) theory of colloid dynamics [Phys. Rev. E 62, 3382 (2000); 72, 031107 (2005)] is the introduction of exact short-time moment conditions in its formulation.

Dynamic arrest within the self-consistent generalized Langevin equation of colloid dynamics.

This paper presents a recently developed theory of colloid dynamics as an alternative approach to the description of phenomena of dynamic arrest in monodisperse colloidal systems. Such theory, referred to as the self-consistent generalized Langevin equation (SCGLE) theory, was devised to describe the tracer and collective diffusion properties of colloidal dispersions in the short- and intermediate-time regimes. Its self-consistent character, however, introduces a nonlinear dynamic feedback, leading to the prediction of dynamic arrest in these systems, similar to that exhibited by the well-established mode coupling theory of the ideal glass transition.

Self-consistent generalized Langevin equation for colloidal mixtures.

A self-consistent theory of collective and tracer diffusion in colloidal mixtures is presented. This theory is based on exact results for the partial intermediate scattering functions derived within the framework of the generalized Langevin equation formalism, plus a number of conceptually simple and sensible approximations. The first of these consists of a Vineyard-like approximation between collective and tracer diffusion, which writes the collective dynamics in terms of the memory function related to tracer diffusion.