On the Path to Optimal Alchemistry.

Alchemical free energy calculations have become a standard and widely used tool, in particular for calculating and comparing binding affinities of drugs. Although methods to compute such free energies have improved significantly over the last decades, the choice of path between the end states of interest is usually still the same as two decades ago. We will show that there is a fundamentally arbitrary, implicit choice of parametrization of this path.

Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates.

A molecular-level understanding of skin permeation may rationalize and streamline product development, and improve quality and control, of transdermal and topical drug delivery systems. It may also facilitate toxicity and safety assessment of cosmetics and skin care products. Here, we present new molecular dynamics simulation approaches that make it possible to efficiently sample the free energy and local diffusion coefficient across the skin's barrier structure to predict skin permeability and the effects of chemical penetration enhancers.

The accelerated weight histogram method for alchemical free energy calculations.

The accelerated weight histogram method is an enhanced sampling technique used to explore free energy landscapes by applying an adaptive bias. The method is general and easy to extend. Herein, we show how it can be used to efficiently sample alchemical transformations, commonly used for, e.

Melting of a two-dimensional monodisperse cluster crystal to a cluster liquid.

Monodisperse ensembles of particles that have cluster crystalline phases at low temperatures can model a number of physical systems, such as vortices in type-1.5 superconductors, colloidal suspensions, and cold atoms. In this work, we study a two-dimensional cluster-forming particle system interacting via an ultrasoft potential.

Phase-change switching in 2D via soft interactions.

We present a new type of phase-change behavior relevant for information storage applications, that can be observed in 2D systems with cluster-forming ability. The temperature-based control of the ordering in 2D particle systems depends on the existence of a crystal-to-glass transition. We perform molecular dynamics simulations of models with soft interactions, demonstrating that the crystalline and amorphous structures can be easily tuned by heat pulses.