Journal de Physique I

Competition between deformation and free volume quantified by 3D image analysis of red blood cell

Mehrnaz Babaki, Dmitry A. Fedosov, Amirreza Gholivand, Joeri Opdam, Remco Tuinier and Minne Paul Lettinga
Biophysical Journal 122 (9) 1646 (2023)
DOI: 10.1016/j.bpj.2023.03.030
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Stability of Branched Tubular Membrane Structures

Maike Jung, Gerhard Jung and Friederike Schmid
Physical Review Letters 130 (14) (2023)
DOI: 10.1103/PhysRevLett.130.148401
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Dynamics of fluid bilayer vesicles: Soft meshes and robust curvature energy discretization

Ali Farnudi, Mohammad Reza Ejtehadi and Ralf Everaers
Physical Review E 108 (1) (2023)
DOI: 10.1103/PhysRevE.108.015301
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Flow-network-controlled shape transformation of a thin membrane through differential fluid storage and surface expansion

Yongtian Luo, Che-Ling Ho, Brent R. Helliker and Eleni Katifori
Physical Review E 107 (2) (2023)
DOI: 10.1103/PhysRevE.107.024419
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Mitja Drab, Raj Kumar Sadhu, Yoav Ravid, Aleš Iglič, Veronika Kralj-Iglič and Nir S. Gov
415 (2023)
DOI: 10.1016/B978-0-323-89911-6.00002-9
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Dynamic shapes of floppy vesicles enclosing active Brownian particles with membrane adhesion

Priyanka Iyer, Gerhard Gompper and Dmitry A. Fedosov
Soft Matter 19 (19) 3436 (2023)
DOI: 10.1039/D3SM00004D
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Oscillating non-progressing flows induce directed cell motion

Winfried Schmidt, Andre Förtsch, Matthias Laumann and Walter Zimmermann
Physical Review Fluids 7 (3) (2022)
DOI: 10.1103/PhysRevFluids.7.L032201
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Mem3DG: Modeling membrane mechanochemical dynamics in 3D using discrete differential geometry

Cuncheng Zhu, Christopher T. Lee and Padmini Rangamani
Biophysical Reports 2 (3) 100062 (2022)
DOI: 10.1016/j.bpr.2022.100062
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Statistical Mechanics of Thermal Fluctuations of Nearly Spherical Membranes: the Influence of Bending and Stretching Elasticities

N. S. Tonchev
Physics of Particles and Nuclei 52 (2) 290 (2021)
DOI: 10.1134/S1063779621020064
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Vesicle shape transformations driven by confined active filaments

Matthew S. E. Peterson, Aparna Baskaran and Michael F. Hagan
Nature Communications 12 (1) (2021)
DOI: 10.1038/s41467-021-27310-8
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Raj Kumar Sadhu, Samo Penič, Aleš Iglič and Nir S. Gov
(2021)
DOI: 10.1101/2021.01.02.425086
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Creasing of flexible membranes at vanishing tension

Weria Pezeshkian and John H. Ipsen
Physical Review E 103 (4) (2021)
DOI: 10.1103/PhysRevE.103.L041001
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Effect of malaria parasite shape on its alignment at erythrocyte membrane

Anil K Dasanna, Sebastian Hillringhaus, Gerhard Gompper and Dmitry A Fedosov
eLife 10 (2021)
DOI: 10.7554/eLife.68818
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Effect of Poiseuille flow on the dynamics of active vesicle

Prabha Chuphal, Soudamini Sahoo and Snigdha Thakur
Soft Materials 19 (3) 359 (2021)
DOI: 10.1080/1539445X.2021.1937222
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Importance of Viscosity Contrast for the Motion of Erythrocytes in Microcapillaries

Anil K. Dasanna, Johannes Mauer, Gerhard Gompper and Dmitry A. Fedosov
Frontiers in Physics 9 (2021)
DOI: 10.3389/fphy.2021.666913
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Optimal Elasticity of Biological Networks

Henrik Ronellenfitsch
Physical Review Letters 126 (3) (2021)
DOI: 10.1103/PhysRevLett.126.038101
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Modelling cellular spreading and emergence of motility in the presence of curved membrane proteins and active cytoskeleton forces

Raj Kumar Sadhu, Samo Penič, Aleš Iglič and Nir S. Gov
The European Physical Journal Plus 136 (5) (2021)
DOI: 10.1140/epjp/s13360-021-01433-9
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Bending models of lipid bilayer membranes: Spontaneous curvature and area-difference elasticity

Xin Bian, Sergey Litvinov and Petros Koumoutsakos
Computer Methods in Applied Mechanics and Engineering 359 112758 (2020)
DOI: 10.1016/j.cma.2019.112758
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Efficient viscosity contrast calculation for blood flow simulations using the lattice Boltzmann method

Moritz Lehmann, Sebastian Johannes Müller and Stephan Gekle
International Journal for Numerical Methods in Fluids 92 (11) 1463 (2020)
DOI: 10.1002/fld.4835
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On the Optimal Prediction of the Stress Field Associated with Discrete Element Models

Ada Amendola
Journal of Optimization Theory and Applications 187 (3) 613 (2020)
DOI: 10.1007/s10957-019-01572-1
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Sebastian Hillringhaus, Anil K. Dasanna, Gerhard Gompper and Dmitry A. Fedosov
(2020)
DOI: 10.1101/2020.03.01.971986
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Stochastic bond dynamics facilitates alignment of malaria parasite at erythrocyte membrane upon invasion

Sebastian Hillringhaus, Anil K Dasanna, Gerhard Gompper and Dmitry A Fedosov
eLife 9 (2020)
DOI: 10.7554/eLife.56500
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Effects of size and elasticity on the relation between flow velocity and wall shear stress in side-wall aneurysms: A lattice Boltzmann-based computer simulation study

Haifeng Wang, Timm Krüger, Fathollah Varnik and Fang-Bao Tian
PLOS ONE 15 (1) e0227770 (2020)
DOI: 10.1371/journal.pone.0227770
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Role of combined cell membrane and wall mechanical properties regulated by polarity signals in cell budding

Kevin Tsai, Samuel Britton, Ali Nematbakhsh, et al.
Physical Biology 17 (6) 065011 (2020)
DOI: 10.1088/1478-3975/abb208
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Effect of particles with repulsive interactions enclosed in both rigid spherical shells and flexible fluid vesicles studied by Monte Carlo simulation

Hibiki Itoga, Ryota Morikawa, Tsuyoshi Ueta, et al.
Physical Review E 99 (4) (2019)
DOI: 10.1103/PhysRevE.99.042418
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Haifeng Wang, Timm Krüger and Fathollah Varnik
(2019)
DOI: 10.1101/711564
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Dynamics of diffusiophoretic vesicle under external shear flow

Prabha Chuphal, Varun P and Snigdha Thakur
The Journal of Chemical Physics 151 (6) (2019)
DOI: 10.1063/1.5112808
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Engineering passive swimmers by shaking liquids

M Laumann, A Förtsch, E Kanso and W Zimmermann
New Journal of Physics 21 (7) 073012 (2019)
DOI: 10.1088/1367-2630/ab240c
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Importance of Erythrocyte Deformability for the Alignment of Malaria Parasite upon Invasion

Sebastian Hillringhaus, Anil K. Dasanna, Gerhard Gompper and Dmitry A. Fedosov
Biophysical Journal 117 (7) 1202 (2019)
DOI: 10.1016/j.bpj.2019.08.027
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Sharp-edged geometric obstacles in microfluidics promote deformability-based sorting of cells

Zunmin Zhang, Wei Chien, Ewan Henry, Dmitry A. Fedosov and Gerhard Gompper
Physical Review Fluids 4 (2) (2019)
DOI: 10.1103/PhysRevFluids.4.024201
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Emerging Attractor in Wavy Poiseuille Flows Triggers Sorting of Biological Cells

Matthias Laumann, Winfried Schmidt, Alexander Farutin, et al.
Physical Review Letters 122 (12) (2019)
DOI: 10.1103/PhysRevLett.122.128002
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Crystalline membrane morphology beyond polyhedra

Hang Yuan and Monica Olvera de la Cruz
Physical Review E 100 (1) (2019)
DOI: 10.1103/PhysRevE.100.012610
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Coarse-grained area-difference-elasticity membrane model coupled with IB–LB method for simulation of red blood cell morphology

Zi-Xiang Tong, Xi Chen, Ya-Ling He and Xiang-Biao Liao
Physica A: Statistical Mechanics and its Applications 509 1183 (2018)
DOI: 10.1016/j.physa.2018.06.050
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A method to compute elastic and entropic interactions of membrane inclusions

Xiaojun Liang and Prashant K. Purohit
Extreme Mechanics Letters 18 29 (2018)
DOI: 10.1016/j.eml.2017.10.003
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An Enhanced Spring-Particle Model for Red Blood Cell Structural Mechanics: Application to the Stomatocyte–Discocyte–Echinocyte Transformation

Mingzhu Chen and Fergal J. Boyle
Journal of Biomechanical Engineering 139 (12) (2017)
DOI: 10.1115/1.4037590
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Cellular Level In-silico Modeling of Blood Rheology with An Improved Material Model for Red Blood Cells

Gábor Závodszky, Britt van Rooij, Victor Azizi and Alfons Hoekstra
Frontiers in Physiology 8 (2017)
DOI: 10.3389/fphys.2017.00563
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Scaffolding the cup-shaped double membrane in autophagy

Amir Houshang Bahrami, Mary G. Lin, Xuefeng Ren, et al.
PLOS Computational Biology 13 (10) e1005817 (2017)
DOI: 10.1371/journal.pcbi.1005817
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Theory and algorithms to compute Helfrich bending forces: a review

Achim Guckenberger and Stephan Gekle
Journal of Physics: Condensed Matter 29 (20) 203001 (2017)
DOI: 10.1088/1361-648X/aa6313
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Static and dynamic light scattering by red blood cells: A numerical study

Johannes Mauer, Matti Peltomäki, Simón Poblete, et al.
PLOS ONE 12 (5) e0176799 (2017)
DOI: 10.1371/journal.pone.0176799
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Early stages of clathrin aggregation at a membrane in coarse-grained simulations

M. Giani, W. K. den Otter and W. J. Briels
The Journal of Chemical Physics 146 (15) (2017)
DOI: 10.1063/1.4979985
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Atomistic–continuum model for probing the biomechanical properties of human erythrocyte membrane under extreme conditions

A.S. Ademiloye, L.W. Zhang and K.M. Liew
Computer Methods in Applied Mechanics and Engineering (2017)
DOI: 10.1016/j.cma.2017.06.033
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A fluctuating elastic plate and a cell model for lipid membranes

Xiaojun Liang and Prashant K. Purohit
Journal of the Mechanics and Physics of Solids (2016)
DOI: 10.1016/j.jmps.2016.02.019
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A Fluctuating Elastic Plate Model Applied to Graphene

Xiaojun Liang and Prashant K. Purohit
Journal of Applied Mechanics 83 (8) (2016)
DOI: 10.1115/1.4033681
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On the bending algorithms for soft objects in flows

Achim Guckenberger, Marcel P. Schraml, Paul G. Chen, Marc Leonetti and Stephan Gekle
Computer Physics Communications (2016)
DOI: 10.1016/j.cpc.2016.04.018
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Smoothed dissipative particle dynamics with angular momentum conservation

Kathrin Müller, Dmitry A. Fedosov and Gerhard Gompper
Journal of Computational Physics 281 301 (2015)
DOI: 10.1016/j.jcp.2014.10.017
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Hibiki Itoga, Ryota Morikawa, Takeshi Miyakawa, Hironao Yamada, Yuno Natsume, Tsuyoshi Ueta and Masako Takasu
(2015)
DOI: 10.7566/JPSCP.5.011002
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A discrete-to-continuum approach to the curvatures of membrane networks and parametric surfaces

F. Fraternali, I. Farina and G. Carpentieri
Mechanics Research Communications 56 18 (2014)
DOI: 10.1016/j.mechrescom.2013.10.015
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Modeling of closed membrane shapes

S Penič, L Mesarec, M Fošnarič, et al.
Journal of Physics: Conference Series 558 012010 (2014)
DOI: 10.1088/1742-6596/558/1/012010
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Numerical Study of Membrane Configurations

Luka Mesarec, Miha Fošnarič, Samo Penič, et al.
Advances in Condensed Matter Physics 2014 1 (2014)
DOI: 10.1155/2014/373674
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Multiscale modeling of blood flow: from single cells to blood rheology

Dmitry A. Fedosov, Hiroshi Noguchi and Gerhard Gompper
Biomechanics and Modeling in Mechanobiology 13 (2) 239 (2014)
DOI: 10.1007/s10237-013-0497-9
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Buckling pathways in spherical shells with soft spots

Jayson Paulose and David R. Nelson
Soft Matter 9 (34) 8227 (2013)
DOI: 10.1039/c3sm50719j
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Crossover from tumbling to tank-treading-like motion in dense simulated suspensions of red blood cells

Timm Krüger, Markus Gross, Dierk Raabe and Fathollah Varnik
Soft Matter 9 (37) 9008 (2013)
DOI: 10.1039/c3sm51645h
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Topological defects in the buckling of elastic membranes

Chloe M. Funkhouser, Rastko Sknepnek and Monica Olvera de la Cruz
Soft Matter 9 (1) 60 (2013)
DOI: 10.1039/c2sm26607e
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Pathways to faceting of vesicles

Mark J. Bowick and Rastko Sknepnek
Soft Matter 9 (34) 8088 (2013)
DOI: 10.1039/c3sm51729b
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Dynamics of Self-assembly of Model Viral Capsids in the Presence of a Fluctuating Membrane

Richard Matthews and Christos N. Likos
The Journal of Physical Chemistry B 117 (27) 8283 (2013)
DOI: 10.1021/jp4037099
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Flexoelectricity and thermal fluctuations of lipid bilayer membranes: Renormalization of flexoelectric, dielectric, and elastic properties

L. P. Liu and P. Sharma
Physical Review E 87 (3) (2013)
DOI: 10.1103/PhysRevE.87.032715
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Mechanical model of blebbing in nuclear lamin meshworks

Chloe M. Funkhouser, Rastko Sknepnek, Takeshi Shimi, et al.
Proceedings of the National Academy of Sciences 110 (9) 3248 (2013)
DOI: 10.1073/pnas.1300215110
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Monte Carlo simulations of a polymer confined within a fluid vesicle

Miha Fošnarič, Aleš Iglič, Daniel M. Kroll and Sylvio May
Soft Matter 9 (15) 3976 (2013)
DOI: 10.1039/c3sm27938c
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Sedimentation of single red blood cells

Matti Peltomäki and Gerhard Gompper
Soft Matter 9 (34) 8346 (2013)
DOI: 10.1039/c3sm50592h
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A Tribute to Marin D. Mitov

Miha Fošnarič, Samo Penič, Aleš Iglič and Isak Bivas
Advances in Planar Lipid Bilayers and Liposomes, A Tribute to Marin D. Mitov 17 331 (2013)
DOI: 10.1016/B978-0-12-411516-3.00012-7
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Influence of Fluctuating Membranes on Self-Assembly of Patchy Colloids

Richard Matthews and Christos N. Likos
Physical Review Letters 109 (17) (2012)
DOI: 10.1103/PhysRevLett.109.178302
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Buckling of multicomponent elastic shells with line tension

Rastko Sknepnek, Graziano Vernizzi and Monica Olvera de la Cruz
Soft Matter 8 (3) 636 (2012)
DOI: 10.1039/c1sm06325a
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Scattering intensity of bicontinuous microemulsions and sponge phases

Matti Peltomäki, Gerhard Gompper and Daniel M. Kroll
The Journal of Chemical Physics 136 (13) (2012)
DOI: 10.1063/1.3701265
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A multiscale approach to the elastic moduli of biomembrane networks

F. Fraternali and G. Marcelli
Biomechanics and Modeling in Mechanobiology 11 (7) 1097 (2012)
DOI: 10.1007/s10237-012-0376-9
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On the estimation of the curvatures and bending rigidity of membrane networks via a local maximum-entropy approach

F. Fraternali, C.D. Lorenz and G. Marcelli
Journal of Computational Physics 231 (2) 528 (2012)
DOI: 10.1016/j.jcp.2011.09.017
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Shapes of pored membranes

Zhenwei Yao, Rastko Sknepnek, Creighton K. Thomas and Monica Olvera de la Cruz
Soft Matter 8 (46) 11613 (2012)
DOI: 10.1039/c2sm26608c
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Universal formulae for the limiting elastic energy of membrane networks

B. Schmidt and F. Fraternali
Journal of the Mechanics and Physics of Solids 60 (1) 172 (2012)
DOI: 10.1016/j.jmps.2011.09.003
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Compression, crumpling and collapse of spherical shells and capsules

G A Vliegenthart and G Gompper
New Journal of Physics 13 (4) 045020 (2011)
DOI: 10.1088/1367-2630/13/4/045020
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Deformation and clustering of red blood cells in microcapillary flows

J. Liam McWhirter, Hiroshi Noguchi and Gerhard Gompper
Soft Matter 7 (22) 10967 (2011)
DOI: 10.1039/c1sm05794d
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From the Cover: Platonic and Archimedean geometries in multicomponent elastic membranes

G. Vernizzi, R. Sknepnek and M. Olvera de la Cruz
Proceedings of the National Academy of Sciences 108 (11) 4292 (2011)
DOI: 10.1073/pnas.1012872108
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Active rheology of phospholipid vesicles

Aidan T. Brown, Jurij Kotar and Pietro Cicuta
Physical Review E 84 (2) (2011)
DOI: 10.1103/PhysRevE.84.021930
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3D vesicle dynamics simulations with a linearly triangulated surface

G. Boedec, M. Leonetti and M. Jaeger
Journal of Computational Physics 230 (4) 1020 (2011)
DOI: 10.1016/j.jcp.2010.10.021
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Blood Flow and Cell-Free Layer in Microvessels

DMITRY A. FEDOSOV, BRUCE CASWELL, ALEKSANDER S. POPEL and GEORGE EM KARNIADAKIS
Microcirculation 17 (8) 615 (2010)
DOI: 10.1111/j.1549-8719.2010.00056.x
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Large-scale simulations of fluctuating biological membranes

Andrea Pasqua, Lutz Maibaum, George Oster, Daniel A. Fletcher and Phillip L. Geissler
The Journal of Chemical Physics 132 (15) (2010)
DOI: 10.1063/1.3382349
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Advanced Computer Simulation Approaches for Soft Matter Sciences III

G. Gompper, T. Ihle, D. M. Kroll and R. G. Winkler
Advanced Computer Simulation Approaches for Soft Matter Sciences III 1 (2009)
DOI: 10.1007/978-3-540-87706-6_1
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Red blood cell thermal fluctuations: comparison between experiment and molecular dynamics simulations

John P. Hale, Gianluca Marcelli, Kim H. Parker, C. Peter Winlove and Peter G. Petrov
Soft Matter 5 (19) 3603 (2009)
DOI: 10.1039/b910422d
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Monte Carlo simulations of complex formation between a mixed fluid vesicle and a charged colloid

Miha Fošnarič, Aleš Iglič, Daniel M. Kroll and Sylvio May
The Journal of Chemical Physics 131 (10) (2009)
DOI: 10.1063/1.3191782
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Elastic properties and mechanical stability of chiral and filled viral capsids

Mathias Buenemann and Peter Lenz
Physical Review E 78 (5) 051924 (2008)
DOI: 10.1103/PhysRevE.78.051924
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Limits of Filopodium Stability

Sander Pronk, Phillip L. Geissler and Daniel A. Fletcher
Physical Review Letters 100 (25) 258102 (2008)
DOI: 10.1103/PhysRevLett.100.258102
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Small-angle-neutron-scattering from giant water-in-oil microemulsion droplets. II. Polymer-decorated droplets in a quaternary system

Tobias Foster, Thomas Sottmann, Ralf Schweins and Reinhard Strey
The Journal of Chemical Physics 128 (6) (2008)
DOI: 10.1063/1.2812564
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High resolution neutron spectroscopy—a tool for the investigation of dynamics of polymers and soft matter

Michael Monkenbusch and Dieter Richter
Comptes Rendus Physique 8 (7-8) 845 (2007)
DOI: 10.1016/j.crhy.2007.10.001
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Bending Elasticity of Anti-Parallel β-Sheets

Seungho Choe and Sean X. Sun
Biophysical Journal 92 (4) 1204 (2007)
DOI: 10.1529/biophysj.106.095786
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Thermal Fluctuations of Red Blood Cell Membrane via a Constant-Area Particle-Dynamics Model

Gianluca Marcelli, Kim H. Parker and C. Peter Winlove
Biophysical Journal 89 (4) 2473 (2005)
DOI: 10.1529/biophysj.104.056168
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Free fluid vesicles are not exactly spherical

Gunnar T. Linke, Reinhard Lipowsky and Thomas Gruhn
Physical Review E 71 (5) 051602 (2005)
DOI: 10.1103/PhysRevE.71.051602
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Dynamics of fluid vesicles in shear flow: Effect of membrane viscosity and thermal fluctuations

Hiroshi Noguchi and Gerhard Gompper
Physical Review E 72 (1) 011901 (2005)
DOI: 10.1103/PhysRevE.72.011901
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Shape transitions of fluid vesicles and red blood cells in capillary flows

H. Noguchi and G. Gompper
Proceedings of the National Academy of Sciences 102 (40) 14159 (2005)
DOI: 10.1073/pnas.0504243102
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Fluid Vesicles with Viscous Membranes in Shear Flow

Hiroshi Noguchi and Gerhard Gompper
Physical Review Letters 93 (25) 258102 (2004)
DOI: 10.1103/PhysRevLett.93.258102
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First-order phase transition of fixed connectivity surfaces

Hiroshi Koibuchi, Nobuyuki Kusano, Atsusi Nidaira, Komei Suzuki and Mitsuru Yamada
Physical Review E 69 (6) (2004)
DOI: 10.1103/PhysRevE.69.066139
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Budding of crystalline domains in fluid membranes

T. Kohyama, D. M. Kroll and G. Gompper
Physical Review E 68 (6) 061905 (2003)
DOI: 10.1103/PhysRevE.68.061905
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Morphology of Condensed Matter

Ulrich Schwarz and Gerhard Gompper
Lecture Notes in Physics, Morphology of Condensed Matter 600 107 (2002)
DOI: 10.1007/3-540-45782-8_5
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The freezing transition of flexible membranes

G Gompper and D. M Kroll
Europhysics Letters (EPL) 58 (1) 60 (2002)
DOI: 10.1209/epl/i2002-00606-0
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Measuring bending rigidity and spatial renormalization in bicontinuous microemulsions

G Gompper, H Endo, M Mihailescu, et al.
Europhysics Letters (EPL) 56 (5) 683 (2001)
DOI: 10.1209/epl/i2001-00574-3
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Amphiphilic block copolymers in oil-water-surfactant mixtures: efficiency boosting, structure, phase behaviour and mechanism

G Gompper, D Richter and R Strey
Journal of Physics: Condensed Matter 13 (41) 9055 (2001)
DOI: 10.1088/0953-8984/13/41/302
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Statistical mechanics of membranes: freezing, undulations, and topology fluctuations

G Gompper and D M Kroll
Journal of Physics: Condensed Matter 12 (8A) A29 (2000)
DOI: 10.1088/0953-8984/12/8A/304
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Derivative expansion of one-loop effective energy of stiff membranes with tension

M.E.S. Borelli, H. Kleinert and Adriaan M.J. Schakel
Physics Letters A 253 (3-4) 239 (1999)
DOI: 10.1016/S0375-9601(99)00035-3
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Membranes with Fluctuating Topology: Monte Carlo Simulations

G. Gompper and D. M. Kroll
Physical Review Letters 81 (11) 2284 (1998)
DOI: 10.1103/PhysRevLett.81.2284
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Entropy and fluctuations of monolayers, membranes, and microemulsions

David C Morse
Current Opinion in Colloid & Interface Science 2 (4) 365 (1997)
DOI: 10.1016/S1359-0294(97)80078-7
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Fluctuations of polymerized, fluid and hexatic membranes: Continuum models and simulations

Gerhard Gompper and Daniel M Kroll
Current Opinion in Colloid & Interface Science 2 (4) 373 (1997)
DOI: 10.1016/S1359-0294(97)80079-9
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Freezing Flexible Vesicles

G. Gompper and D. M. Kroll
Physical Review Letters 78 (14) 2859 (1997)
DOI: 10.1103/PhysRevLett.78.2859
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Small-scale lipid-membrane structure: simulation versus experiment

Ole G Mouritsen and Kent Jørgensen
Current Opinion in Structural Biology 7 (4) 518 (1997)
DOI: 10.1016/S0959-440X(97)80116-9
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Network models of fluid, hexatic and polymerized membranes

G Gompper and D M Kroll
Journal of Physics: Condensed Matter 9 (42) 8795 (1997)
DOI: 10.1088/0953-8984/9/42/001
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Random Surface Discretizations and the Renormalization of the Bending Rigidity

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