APL_voro

APL_voro analyzes and visualizes molecular dynamics (MD) simulations of cell membranes generated with GROMACS to quantify membrane structure, lipid distribution, leaflet assignment, and macromolecule–membrane interactions.

Key Features:

• Visualization: Generates visualization renderings of MD membrane simulation data to support analysis of membrane structure and dynamics.
• Lipid Leaflet Assignment: Assigns lipids to upper or lower bilayer leaflets for analysis of membrane asymmetry and lipid distribution.
• Comparative Analysis: Compares related simulations to assess the effects of varying conditions or compositions on membrane properties.
• Algorithmic Updates: Incorporates new algorithms and methodological updates to improve accuracy and efficiency of membrane analysis.

Scientific Applications:

• Membrane Dynamics: Quantitative analysis of temporal changes in membrane structure from MD simulations.
• Lipid Rafts: Analysis of lipid raft formation and behavior within simulated bilayers.
• Macromolecule Interaction: Characterization of protein and other macromolecule incorporation, interaction, and translocation across membranes in MD simulations.

Methodology:

Processes MD trajectories generated with GROMACS, applies visualization techniques, assigns lipids to bilayer leaflets, performs comparative analyses of simulations, and integrates algorithmic/methodological updates.