A general computational framework for the dynamics of single- and multi-phase vesicles and membranes

[1]  F. Wendler,et al.  Extracellular vesicles round off communication in the nervous system , 2016, Nature Reviews Neuroscience.

[2]  Fernando Mut,et al.  A semi-implicit finite element method for viscous lipid membranes , 2014, J. Comput. Phys..

[3]  W. Helfrich.  Elastic Properties of Lipid Bilayers: Theory and Possible Experiments , 1973, Zeitschrift fur Naturforschung. Teil C: Biochemie, Biophysik, Biologie, Virologie.

[4]  B. Engquist,et al.  Numerical approximations of singular source terms in differential equations , 2004 .

[5]  M. Deserno.  Fluid lipid membranes: from differential geometry to curvature stresses. , 2015, Chemistry and physics of lipids.

[6]  Christian Eggeling,et al.  There Is No Simple Model of the Plasma Membrane Organization , 2016, Front. Cell Dev. Biol..

[7]  T. Taniguchi,et al.  Shape deformation of ternary vesicles coupled with phase separation. , 2008, Physical review letters.

[8]  M. Imai,et al.  Three-dimensional analysis of lipid vesicle transformations , 2012 .

[9]  T. Chan,et al.  A Variational Level Set Approach to Multiphase Motion , 1996 .

[10]  Q. Du,et al.  Modelling and simulations of multi-component lipid membranes and open membranes via diffuse interface approaches , 2006, Journal of Mathematical Biology.

[11]  Primož Ziherl,et al.  Nonaxisymmetric phospholipid vesicles: Rackets, boomerangs, and starfish , 2005 .

[12]  Chunming Li,et al.  Level set evolution without re-initialization: a new variational formulation , 2005, 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05).

[13]  Mu-Ping Nieh,et al.  Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature. , 2011, Biochimica et biophysica acta.

[14]  John D. Towers.  Discretizing delta functions via finite differences and gradient normalization , 2009, J. Comput. Phys..

[15]  John D. Towers.  Two methods for discretizing a delta function supported on a level set , 2007, J. Comput. Phys..

[16]  T. Baumgart,et al.  Thermodynamics and mechanics of membrane curvature generation and sensing by proteins and lipids. , 2011, Annual review of physical chemistry.

[17]  A. Menon,et al.  Lipid somersaults: Uncovering the mechanisms of protein-mediated lipid flipping. , 2016, Progress in lipid research.

[18]  James P K Armstrong,et al.  Strategic design of extracellular vesicle drug delivery systems. , 2018, Advanced drug delivery reviews.

[19]  Qiang Du,et al.  Simulating the deformation of vesicle membranes under elastic bending energy in three dimensions , 2006, J. Comput. Phys..

[20]  Kai Simons,et al.  Lipid Rafts As a Membrane-Organizing Principle , 2010, Science.

[21]  Axel Voigt,et al.  Phase-field modeling of the dynamics of multicomponent vesicles: Spinodal decomposition, coarsening, budding, and fission. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[22]  Vahid Sandoghdar,et al.  Production of Isolated Giant Unilamellar Vesicles under High Salt Concentrations , 2017, Front. Physiol..

[23]  R. Lipowsky,et al.  Shape transformations of vesicles with intramembrane domains. , 1996, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[24]  P. Smereka.  The numerical approximation of a delta function with application to level set methods , 2006 .

[25]  John D. Towers.  A convergence rate theorem for finite difference approximations to delta functions , 2008, J. Comput. Phys..

[26]  S. Jewell.  Living systems and liquid crystals , 2011 .

[27]  Axel Voigt,et al.  Diffuse interface models of locally inextensible vesicles in a viscous fluid , 2013, J. Comput. Phys..

[28]  H. McMahon,et al.  Mechanisms of endocytosis. , 2009, Annual review of biochemistry.

[29]  Jemal Guven,et al.  Stresses in lipid membranes , 2002 .

[30]  Peter Smereka,et al.  Semi-Implicit Level Set Methods for Curvature and Surface Diffusion Motion , 2003, J. Sci. Comput..

[31]  Z C Tu,et al.  Lipid membranes with free edges. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[32]  Taniguchi,et al.  Shape deformation and phase separation dynamics of two-component vesicles. , 1996, Physical review letters.

[33]  J. Sethian,et al.  Fronts propagating with curvature-dependent speed: algorithms based on Hamilton-Jacobi formulations , 1988 .

[34]  Xianghong Jing,et al.  Influenza Virus M2 Protein Mediates ESCRT-Independent Membrane Scission , 2010, Cell.

[35]  H. Riezman,et al.  Understanding the diversity of membrane lipid composition , 2018, Nature Reviews Molecular Cell Biology.

[36]  Axel Voigt,et al.  Dynamics of multicomponent vesicles in a viscous fluid , 2010, J. Comput. Phys..

[37]  Tiankui Zhang,et al.  Sixth-Order Accurate Schemes for Reinitialization and Extrapolation in the Level Set Framework , 2020, Journal of Scientific Computing.

[38]  W. Webb,et al.  Membrane elasticity in giant vesicles with fluid phase coexistence. , 2005, Biophysical journal.

[39]  John D. Towers.  Finite difference methods for approximating Heaviside functions , 2009, J. Comput. Phys..

[40]  R Capovilla,et al.  Lipid membranes with an edge. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[41]  Stephan Gekle,et al.  On the bending algorithms for soft objects in flows , 2016, Comput. Phys. Commun..

[42]  Seifert,et al.  Budding transitions of fluid-bilayer vesicles: The effect of area-difference elasticity. , 1994, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[43]  Udo Seifert,et al.  Configurations of fluid membranes and vesicles , 1997 .

[44]  J. Mauzeroll,et al.  Ferrocene-Modified Phospholipid: An Innovative Precursor for Redox-Triggered Drug Delivery Vesicles Selective to Cancer Cells. , 2016, Langmuir : the ACS journal of surfaces and colloids.

[45]  John Lowengrub,et al.  Numerical simulation of endocytosis: Viscous flow driven by membranes with non-uniformly distributed curvature-inducing molecules , 2016, J. Comput. Phys..

[46]  Chunming Li,et al.  Distance Regularized Level Set Evolution and Its Application to Image Segmentation , 2010, IEEE Transactions on Image Processing.

[47]  W. Helfrich,et al.  Bending energy of vesicle membranes: General expressions for the first, second, and third variation of the shape energy and applications to spheres and cylinders. , 1989, Physical review. A, General physics.

[48]  Q. Du,et al.  A phase field approach in the numerical study of the elastic bending energy for vesicle membranes , 2004 .

[49]  E. N. Nolte-‘t Hoen,et al.  Extracellular vesicles and viruses: Are they close relatives? , 2016, Proceedings of the National Academy of Sciences.

[50]  B. Engquist,et al.  Discretization of Dirac delta functions in level set methods , 2005 .

[51]  H. Harashima,et al.  Learning from the Viral Journey: How to Enter Cells and How to Overcome Intracellular Barriers to Reach the Nucleus , 2009, The AAPS Journal.

[52]  Sarah L Veatch,et al.  Separation of liquid phases in giant vesicles of ternary mixtures of phospholipids and cholesterol. , 2003, Biophysical journal.