FreeDTS

FreeDTS performs mesoscale simulations of biomembranes, enabling research on membrane shape, protein organization, and the effects of membrane proteins.

Key Features:

• Dynamically triangulated surface representation: The software represents a membrane by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins.
• Vertex-based inclusions: The software integrates vertex-based inclusions to represent membrane proteins and their effects on membrane behavior.
• Multiple membrane condition algorithms: Several algorithms simulate complex membranes at different conditions including framed membranes with constant tension, vesicles, and high-genus membranes with various fixed volumes or constant pressure differences.
• External force application: The software supports applying external forces to membrane regions.
• Static shape mode for protein organization: The software allows turning off the shape evolution of the membrane to focus solely on the organization of proteins.
• Cryo-electron tomography backmapping: Realistic membrane shapes obtained from cryo-electron tomography can be backmapped into a finer simulation model.

Scientific Applications:

• Membrane shape research: FreeDTS enables computational research on biomembrane shape and morphology at the mesoscale.
• Protein organization studies: The software supports investigation of the organization of integral and peripheral membrane proteins on biomembranes.
• Membrane protein effects: FreeDTS enables study of the effects of membrane proteins on membrane properties and behavior.
• Realistic membrane simulation with molecular resolution: The software advances simulation of realistic biomembranes with molecular resolution.

Methodology:

FreeDTS represents a membrane by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins, and includes several algorithms to simulate complex membranes at different conditions.