MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes

Harsh Bhatia, Helgi I. Ingólfsson, Timothy S. Carpenter, Felice C. Lightstone, Peer Timo Bremer

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Advances in simulation methodologies, code efficiency, and computing power have enabled larger, longer, and more-complicated biological membrane simulations. The resulting membranes can be highly complex and have curved geometries that greatly deviate from a simple planar state. Studying these membranes requires appropriate characterization of geometric and topological properties of the membrane surface before any local lipid properties, such as areas and curvatures, can be computed. We present MemSurfer, an efficient and versatile tool to robustly compute membrane surfaces for a wide variety of large-scale molecular simulations. MemSurfer works independent of the type of simulation, and directly on 3D point coordinates. As a result, MemSurfer can handle a variety of membranes. Using Delaunay triangulations and surface parameterizations, MemSurfer not only computes common lipid properties of interest, but also provides direct access to the membrane surface itself, allowing the user to potentially conceive and compute a variety of nonstandard properties. The software provides a simple-to-use Python API and is released open-source under a GPL3 license.

Original languageEnglish (US)
JournalJournal of Chemical Theory and Computation
DOIs
StateAccepted/In press - Jan 1 2019
Externally publishedYes

Fingerprint

membranes
Membranes
Lipids
lipids
Biological membranes
simulation
application programming interface
Triangulation
Parameterization
Application programming interfaces (API)
triangulation
parameterization
curvature
methodology
Geometry
computer programs
geometry

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Cite this

MemSurfer : A Tool for Robust Computation and Characterization of Curved Membranes. / Bhatia, Harsh; Ingólfsson, Helgi I.; Carpenter, Timothy S.; Lightstone, Felice C.; Bremer, Peer Timo.

In: Journal of Chemical Theory and Computation, 01.01.2019.

Research output: Contribution to journalArticle

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