Literature DB >> 26366141

Seeing the Forest in Lieu of the Trees: Continuum Simulations of Cell Membranes at Large Length Scales.

Kayla Sapp1, Roie Shlomovitz2, Lutz Maibaum1.   

Abstract

Biological membranes exhibit long-range spatial structure in both chemical composition and geometric shape, which gives rise to remarkable physical phenomena and important biological functions. Continuum models that describe these effects play an important role in our understanding of membrane biophysics at large length scales. We review the mathematical framework used to describe both composition and shape degrees of freedom, and present best practices to implement such models in a computer simulation. We discuss in detail two applications of continuum models of cell membranes: the formation of microemulsion and modulated phases, and the effect of membrane-mediated interactions on the assembly of membrane proteins.

Entities:  

Year:  2014        PMID: 26366141      PMCID: PMC4567254          DOI: 10.1016/B978-0-444-63378-1.00003-3

Source DB:  PubMed          Journal:  Annu Rep Comput Chem        ISSN: 1574-1400


  49 in total

1.  Large-scale simulations of fluctuating biological membranes.

Authors:  Andrea Pasqua; Lutz Maibaum; George Oster; Daniel A Fletcher; Phillip L Geissler
Journal:  J Chem Phys       Date:  2010-04-21       Impact factor: 3.488

2.  Dynamics of vesicle self-assembly and dissolution.

Authors:  Hiroshi Noguchi; Gerhard Gompper
Journal:  J Chem Phys       Date:  2006-10-28       Impact factor: 3.488

3.  Curvature coupling dependence of membrane protein diffusion coefficients.

Authors:  Stefan M Leitenberger; Ellen Reister-Gottfried; Udo Seifert
Journal:  Langmuir       Date:  2007-12-12       Impact factor: 3.882

Review 4.  Perspective on the Martini model.

Authors:  Siewert J Marrink; D Peter Tieleman
Journal:  Chem Soc Rev       Date:  2013-08-21       Impact factor: 54.564

5.  Effective free energy for pinned membranes.

Authors:  Thomas Speck
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2011-05-04

6.  A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations.

Authors:  Zun-Jing Wang; Markus Deserno
Journal:  J Phys Chem B       Date:  2010-09-02       Impact factor: 2.991

7.  A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models.

Authors:  Anand Srivastava; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2013-01-08       Impact factor: 6.006

8.  Membrane-induced bundling of actin filaments.

Authors:  Allen P Liu; David L Richmond; Lutz Maibaum; Sander Pronk; Phillip L Geissler; Daniel A Fletcher
Journal:  Nat Phys       Date:  2008-08-31       Impact factor: 20.034

9.  Separation of liquid phases in giant vesicles of ternary mixtures of phospholipids and cholesterol.

Authors:  Sarah L Veatch; Sarah L Keller
Journal:  Biophys J       Date:  2003-11       Impact factor: 4.033

10.  Direct imaging reveals stable, micrometer-scale lipid domains that segregate proteins in live cells.

Authors:  Alexandre Toulmay; William A Prinz
Journal:  J Cell Biol       Date:  2013-07-08       Impact factor: 10.539

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  5 in total

1.  Simple differences in the protein-membrane attachment mechanism have functional consequences for surface mechanics.

Authors:  K Sapp; L Maibaum; A J Sodt
Journal:  J Chem Phys       Date:  2019-10-28       Impact factor: 3.488

2.  Simulation Best Practices for Lipid Membranes [Article v1.0].

Authors:  David J Smith; Jeffery B Klauda; Alexander J Sodt
Journal:  Living J Comput Mol Sci       Date:  2019-01-09

3.  Suppressing membrane height fluctuations leads to a membrane-mediated interaction among proteins.

Authors:  Kayla Sapp; Lutz Maibaum
Journal:  Phys Rev E       Date:  2016-11-29       Impact factor: 2.529

4.  Tuning Length Scales of Small Domains in Cell-Derived Membranes and Synthetic Model Membranes.

Authors:  Caitlin E Cornell; Allison D Skinkle; Shushan He; Ilya Levental; Kandice R Levental; Sarah L Keller
Journal:  Biophys J       Date:  2018-07-11       Impact factor: 4.033

5.  Spatial extent of a single lipid's influence on bilayer mechanics.

Authors:  Kayla C Sapp; Andrew H Beaven; Alexander J Sodt
Journal:  Phys Rev E       Date:  2021-04       Impact factor: 2.529

  5 in total

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