LiPyphilic

LiPyphilic analyzes molecular dynamics (MD) simulations of lipid membranes to quantify cholesterol flip-flop, classify local lipid environments, assess interleaflet registration, and perform trajectory transformations for membrane biophysics using MDAnalysis with NumPy and SciPy.

Key Features:

• Cholesterol Flip-Flop Events Identification: Detects and reports cholesterol flip-flop events within lipid bilayers.
• Local Lipid Environment Classification: Classifies local lipid environments to characterize spatial organization and lipid–lipid interactions.
• Interleaflet Registration Analysis: Quantifies the degree of interleaflet registration to study membrane asymmetry.
• Force Field and Resolution Agnosticism: Operates independently of specific force fields and resolution choices.
• Complex Composition Handling: Uses the MDAnalysis atom selection language to handle membranes with highly complex compositions.
• Trajectory Transformations: Performs on-the-fly trajectory transformations to fix membranes split across periodic boundaries and implements nojump coordinate unwrapping that accounts for box-volume fluctuations in the NPT ensemble.
• Implementation: Built on MDAnalysis and leverages NumPy and SciPy for computational operations.

Scientific Applications:

• Membrane Biophysics: Enables analysis of emergent phenomena in lipid membranes with complex compositions, including spatial organization and interleaflet interactions.
• Cholesterol Dynamics: Supports quantitative studies of cholesterol flip-flop and its impact on membrane dynamics.
• Pharmacology and Membrane-Targeting Studies: Facilitates investigation of membrane properties and interactions relevant to pharmacology and related fields.

Methodology:

Object-oriented Python package built on MDAnalysis and leveraging NumPy and SciPy; implements the MDAnalysis atom selection language, on-the-fly trajectory transformations to correct periodic-boundary splits, and nojump coordinate unwrapping that accounts for box-volume fluctuations under the NPT ensemble.