References
- Allen , MP and Tildesley , DJ . 1987 . Computer Simulation of Liquids , Oxford, , UK. : Oxford Science Publications, OUP .
- Bedau , MA , Buchanan , A , Gazzola , G , Hanczyc , M , Maeke , T , McCaskill , J , Poli , I and Packard , NH . 2006 . “Evolutionary design of a DDPD model of ligation.” . In Lecture Notes in Computer Science , Edited by: Talbi , E. Vol 3871 , 201 – 212 . Berlin, Germany : Springer .
- Bhalla , U . 2004a . “Signaling in small subcellular volumes. 1. Stochastic and diffusion effects on individual pathways.” . Biophys. J. , 87 : 733 – 744 .
- Bhalla , U . 2004b . “Signaling in small subcellular volumes. 2. Stochastic and diffusion effects on synaptic network properties.” . Biophys. J. , 87 : 745 – 753 .
- Chernomordik , LV and Kozlov , MM . 2003 . “Protein‐lipid interplay in fusion and fission of biological membranes.” . Annu. Rev. Biochem. , 72 : 175 – 207 .
- Efrat , A , Chernomordik , LV and Kozlov , MM . 2007 . “Point‐like protrusion as a prestalk intermediate in membrane fusion pathway.” . Biophys. J. , 92 : L61 – 63 .
- Engelman , DM . 2005 . “Membranes are more mosaic than fluid.” . Nature (London) , 438 : 578 – 580 .
- Grafmüller , A , Shillcock , JC and Lipowsky , R . 2007 . “Pathway of membrane fusion with two tension‐dependent energy barriers.” . Phys. Rev. Lett. , 98 (1–4) : 218101
- Groot , R and Warren , PB . 1997 . “Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulation.” . J. Chem. Phys. , 107 : 4423 – 4435 .
- Illya , G , Lipowsky , R and Shillcock , JC . 2006 . “Two‐component membrane material properties and domain formation from dissipative particle dynamics.” . J. Chem. Phys. , 125 (1–9) : 114710
- Jones , RAL . 2004 . Soft Machines: Nanotechnology and Life , Oxford, , UK. : OUP .
- Kasson , PM , Kelley , NW , Singhal , N , Vrljic , M , Brunger , AT and Pande , VS . 2006 . “Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion.” . Proc. Natl. Acad. Sci. U.S.A. , 103 : 11916 – 11921 .
- Kholodenko , BN . 2006 . “Cell‐signaling dynamics in time and space.” . Nat. Rev. Mol. Cell Biol. , 7 : 165 – 176 .
- Kholodenko , BN , Brown , GC and Hoek , JB . 2000 . “Diffusion control of protein phosphorylation in signal transduction pathways.” . Biochem. J. , 350 : 901 – 907 .
- Knecht , V and Marrink , SJ . 2007 . “Molecular dynamics simulations of lipid vesicle fusion in atomic detail.” . Biophys. J. , 92 : 4254 – 4261 .
- Laradji , M and Kumar , PBS . 2005 . “Domain growth, budding, and fission in phase‐separating self‐assembled fluid bilayers.” . J. Chem. Phys. , 123 (1–10) : 224902
- Markvoort , AJ , Smeijers , AF , Pieterse , K , van Santen , RA and Hilbers , PAJ . 2007 . “Lipid‐based mechanisms for vesicle fission.” . J. Phys. Chem. B , 111 : 5719 – 5725 .
- Marrink , SJ and Mark , AE . 2003 . “The mechanism of vesicle fusion as revealed by molecular dynamics simulations.” . JACS , 125 : 11144 – 11145 .
- Martens , S , Kozlov , MM and McMahon , HT . 2007 . “How synaptotagmin promotes membrane fusion.” . Science , 316 : 1205 – 1208 .
- Müller , M , Katsov , K and Schick , M . 2003 . “A new mechanism of model membrane fusion determined from Monte Carlo simulation.” . Biophys. J. , 85 : 1611 – 1623 .
- Müller , M , Katsov , K and Schick , M . 2006 . “Biological and synthetic membranes: what can be learned from a coarse‐grained description?” . Phys. Rep. , 434 : 113 – 176 .
- Noguchi , H and Takasu , M . 2001 . “Fusion pathways of vesicles: a Brownian dynamics simulation.” . J. Chem. Phys. , 115 : 9547 – 9551 .
- Ohta‐lino , S , Pasenkiewicz‐Gierula , M , Takaoka , Y , Miyagawa , H , Kitamura , K and Kusumi , A . 2001 . “Fast lipid disorientation at the onset of membrane fusion revealed by molecular dynamics simulations.” . Biophys. J. , 81 : 217 – 224 .
- Reynwar , BJ , Illya , G , Harmandaris , VA , Müller , MM , Kremer , K and Deserno , M . 2007 . “Aggregation and vesiculation of membrane proteins by curvature‐mediated interactions.” . Nature (London , 447 : 461 – 464 .
- Ridgway , D , Broderick , G and Ellison , MJ . 2006 . “Accommodating space, time and randomness in network simulation.” . Curr. Opin. Biotechnol , 17 : 493 – 498 .
- Shillcock , JC and Lipowsky , R . 2005 . “Tension‐induced fusion of bilayer membranes and vesicles.” . Nat. Mater. , 4 : 225 – 228 .
- Shillcock , JC and Lipowsky , R . 2006 . “The computational route from bilayer membranes to vesicle fusion.” . J. Phys.: Condens. Matter , 18 : S1191 – S1219 .
- Shillcock , JC and Lipowsky , R . 2007 . “Visualizing soft matter: mesoscopic simulations of membranes, vesicles and nanoparticles.” . Biophys. Rev. Lett. , 2 : 33 – 55 .
- Sieber , JJ , Willig , KI , Kutzner , C , Gerding‐Reimers , C , Harke , B , Donnert , G , Rammner , B , Eggeling , C , Hell , SW , Grubmüller , H and Lang , T . 2007 . “Anatomy and dynamics of a supramolecular membrane protein cluster.” . Science , 317 : 1072 – 1076 .
- Singer , SJ and Nicolson , GL . 1972 . “The fluid mosaic model of the structure of cell membranes.” . Science , 175 : 720 – 731 .
- Smith , K , Jasnow , D and Balazs , AC . 2007 . “Designing synthetic vesicles that engulf nanoscopic particles.” . J. Chem. Phys. , 127 (1–10) : 084703
- Srinivas , G , Lopez , CF and Klein , ML . 2004 . “Membrane bound hydraphiles facilitate cation translocation.” . J. Phys. Chem. B , 108 : 4231 – 4235 .
- Stevens , MJ , Hoh , JH and Woolf , TB . 2003 . “Insights into the molecular mechanism of membrane fusion from simulation: evidence for the associated of splayed tails.” . Phys. Rev. Lett. , 91 (1–4) : 188102
- Takahashi , K , Arjunan , SNV and Tomita , M . 2005 . “Space in systems biology of signaling pathways—towards intracellular molecular crowding in silico.” . FEBS Lett. , 579 : 1783 – 1788 .
- Venturoli , M , Sperotto , MM , Kranenburg , M and Smit , B . 2006 . “Mesoscopic models of biological membranes.” . Phys. Rep. , 437 : 1 – 54 .
- White , SH . 2007 . “Crowds of syntaxins.” . Science , 317 : 1045 – 1046 .