Visualizing Molecular Dynamics: a scientific expedition into the world of atoms

16/03/24 20:46 Filed in: Paper

Recently, I had the opportunity to contribute to two review articles on the visualization of molecular dynamics simulations. The first one deals with this topic in depth, while the second article takes a more targeted approach and focuses on membrane systems in a concise perspective. The first review article addresses challenges and opportunities in visualizing complex MD simulations. It emphasizes the need for novel visual representations tailored to the dynamics and intricacies of large biomolecular systems. In our work, we present a classification scheme based on a visual abstraction formalism that serves as a guiding framework and identifies potential areas for future progress. In the second manuscript, we address the current challenge of visualizing the complex dynamics of membrane systems. We provide a historical overview of the development of visualization techniques and trace their evolution from simple line representations in the 1980s to sophisticated graphics and virtual reality applications today.

More detailed summaries are below. If you want to directly access the manuscripts, they are here:

Hayet Belghit, Mariano Spivak, Manuel Dauchez, Marc Baaden, Jessica Jonquet. From complex data to clear insights: visualizing molecular dynamics trajectories. Front. Bioinform., Sec. Data Visualization, Volume 4 - 2024 | doi: 10.3389/fbinf.2024.1356659 (links to be completed – temporary link)
Robin A Corey, Marc Baaden, Matthieu Chavent. A brief history of visualizing membrane systems in molecular dynamics simulations. Frontiers in Bioinformatics, 2023, 3, pp.1149744.

From complex data to clear insights: visualizing molecular dynamics trajectories

This article briefly reviews the history of molecular visualization and simulation and outlines the advances in computational power and techniques that have enabled the study of increasingly complex biomolecular systems. We then introduce the formalism of visual abstraction, which we have adapted to the context of MD simulations by proposing four axes of abstraction: Scale, Time, Molecule and Image.

We discuss different approaches and techniques along these axes, including multiscale visualization, temporal aggregation, molecule class-dependent visualization, and representations specifically developed for MD visualization. They highlight the strengths and limitations of existing methods and emphasize the need for new visual metaphors that can effectively capture the dynamics and complexity of modern MD simulations.

The article highlights several challenges and future perspectives, such as the increasing complexity of data, the need to expand the repertoire of representations, the lack of standards for visualization, the visualization of ensembles of MD trajectories, technical challenges for efficient graphical representation, the gap between computer graphics and bioinformatics, and the limitations of virtual reality (VR), augmented reality (AR), and mixed reality (MR) tools for MD visualization.

Overall, this article attempts to provide a comprehensive overview of the current state of MD visualization and calls for further research and development to address the emerging challenges posed by the rapid growth of MD simulations in terms of scale, complexity and data volume.

A brief history of visualizing membrane systems in molecular dynamics simulations

Here we explore the remarkable journey to visualize the intricate world of membrane dynamics through molecular simulations. From humble beginnings with simple line representations in the 1980s, the field has seen a remarkable evolution driven by advances in computing power and innovative visualization techniques. The article takes us through the decades, starting with the early days when analyzes focused on internal lipid movements due to limited simulation times. With the expansion of computational resources, a flourishing era of molecular viewers began in the 1990s, enabling more complex visualizations of membrane proteins, pores, and global biophysical changes. With the advent of coarse-grained force fields in the 2000s, the complexity of membrane systems skyrocketed, requiring new visualization methods. Tools emerged to analyze global membrane properties such as curvature, volume and surface area, while others focused on molecular details such as lipid flip-flop rates and lipid-lipid interactions.

As ambitions grew, so did the scale of simulations, creating a need for elegant visualization techniques that balanced visual clarity with biological accuracy. Automation and simplification became a critical factor, with tools such as ProLint and PyLipID identifying and visualizing protein-lipid interactions in large membrane systems. In the face of ever-increasing complexity, the article highlights the importance of advanced computer graphics, virtual reality and augmented reality to shed new light on these crowded environments. It suggests working with computer scientists, designers and other experts to find innovative ways to visualize and abstract these complicated systems. Finally, we point out the need to combine the visualization of simulated membrane models with experimental data to blur the lines between theory and experiment.

Tags: membrane, MD

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Visualizing Molecular Dynamics: a scientific expedition into the world of atoms

From complex data to clear insights: visualizing molecular dynamics trajectories

A brief history of visualizing membrane systems in molecular dynamics simulations