Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels

Abstract

In biology, metabolite transport across cell membranes occurs through natural channels and pores. Artificial ion-channel architectures represent potential mimics of natural ionic conduction. Many such systems were produced leading to a remarkable set of alternative artificial ion-channels. Far less advances were achieved in the area of synthetic biomimetic water channels, even though they could improve our understanding of the natural function of protein channels and may provide new strategies to generate highly selective, advanced water purification systems. Most realizations have used the selectivity components of natural protein channels embedded in artificial systems. Such biomolecules provide building blocks to constitute highly selective membrane-spanning water transport architectures. The simplification of such compounds, while preserving the high conduction activity of natural macromolecules, lead to fully synthetic artificial biomimetic channels. These simplified systems offer a particular chance to understand mechanistic and structural behaviors, providing rationales to engineer better artificial water-channels. Here we focus on computer simulations as a tool to complement experiment in understanding the properties of such systems with the aim to rationalize important concepts, design and optimize better compounds. Molecular dynamics simulations combined with advanced visual scrutiny thereof are central to such an approach. Novel technologies such as virtual reality headsets and stereoscopic large-scale display walls offer immersive collaborative insight into the complex mechanisms underlying artificial water channel function.

A brief history of visualizing membrane systems in molecular dynamics simulations

“…This scarcity may be because these approaches are often used as a tool in a research project, but are not necessarily the actual focus of the work. It is very likely that many more immersive experiments have been conducted than a literature search would reveal, as membrane objects lend themselves very well to such visualizations (Martinez et al, 2020b;Baaden, 2022). As lipid diffusion and currents can be naturally translated into field lines, it is already possible with VR to visualize such type of rendering properties (Laureanti et al, 2020).…”