dc.contributor.author
Sadeghi, Mohsen
dc.contributor.author
Weikl, Thomas R.
dc.contributor.author
Noe, Frank
dc.date.accessioned
2018-06-08T10:33:38Z
dc.date.available
2018-03-09T10:33:34.791Z
dc.identifier.uri
https://refubium.fu-berlin.de/handle/fub188/20658
dc.identifier.uri
http://dx.doi.org/10.17169/refubium-23958
dc.description.abstract
We present a simple and computationally efficient coarse-grained and solvent-
free model for simulating lipid bilayer membranes. In order to be used in
concert with particle-based reaction-diffusion simulations, the model is
purely based on interacting and reacting particles, each representing a coarse
patch of a lipid monolayer. Particle interactions include nearest-neighbor
bond-stretching and angle-bending and are parameterized so as to reproduce the
local membrane mechanics given by the Helfrich energy density over a range of
relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-
flipping moves. The physical accuracy of the model is verified by five tests:
(i) Power spectrum analysis of equilibrium thermal undulations is used to
verify that the particle-based representation correctly captures the dynamics
predicted by the continuum model of fluid membranes. (ii) It is verified that
the input bending stiffness, against which the potential parameters are
optimized, is accurately recovered. (iii) Isothermal area compressibility
modulus of the membrane is calculated and is shown to be tunable to reproduce
available values for different lipid bilayers, independent of the bending
rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force
is employed to measure the effective in-plane viscosity of the membrane model
and show the possibility of modeling membranes with specified viscosities. (v)
Interaction of the bilayer membrane with a spherical nanoparticle is modeled
as a test case for large membrane deformations and budding involved in
cellular processes such as endocytosis. The results are shown to coincide well
with the predicted behavior of continuum models, and the membrane model
successfully mimics the expected budding behavior. We expect our model to be
of high practical usability for ultra coarse-grained molecular dynamics or
particle-based reaction-diffusion simulations of biological systems.
en
dc.rights.uri
http://publishing.aip.org/authors/web-posting-guidelines
dc.subject.ddc
500 Naturwissenschaften und Mathematik::530 Physik
dc.title
Particle-based membrane model for mesoscopic simulation of cellular dynamics
dc.type
Wissenschaftlicher Artikel
dcterms.bibliographicCitation
Journal of Chemical Physics. - 148 (2018), 4, Artikel Nr. 044901
dcterms.bibliographicCitation.doi
10.1063/1.5009107
dcterms.bibliographicCitation.url
http://doi.org/10.1063/1.5009107
refubium.affiliation
Mathematik und Informatik
de
refubium.mycore.fudocsId
FUDOCS_document_000000029249
refubium.resourceType.isindependentpub
no
refubium.mycore.derivateId
FUDOCS_derivate_000000009512
dcterms.accessRights.openaire
open access
dcterms.isPartOf.issn
0021-9606