Brownian Dynamics Simulation of Macromolecule Diffusion In a Protocell

Quantum Bio-informatics IV: From Quantum Information to Bio-informatics

Volumn , Issue , 2011, Pages 413-426

  Ando, Tadashi ^a   Skolnick, Jeffrey ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85044109290     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9789814343763_0032     Document Type: Chapter

References (25)

1. Elowitz MB, Surette MG, Wolf PE, Stock JB, & Leibler S (1999) Protein mobility in the cytoplasm of Escherichia coli. J Bacterial 181(1): 197-203.
2. Konopka MC, Shkel lA, Cayley S, Record MT, & Weisshaar JC (2006) Crowding and confinement effects on protein diffusion in vivo. J Bacterial 188(17):6115-6123.
3. Carrasco B & Garcia de la Torre J (1999) Hydrodynamic properties of rigid particles: comparison of different modeling and computational procedures. Biophys J 76(6):3044-3057.
4. Garcia De La Torre J, Huertas ML, & Carrasco B (2000) Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys J 78(2):719-730.
5. Garcia De La Torre J, Jimenez A, & Freire JJ (1982) Monte-Carlo Calculation of Hydrodynamic Properties of Freely Jointed, Freely Rotating, and Real Polymethylene Chains. Macromolecules 15(1): 148-154.
6. Rotne J & Prager S (1969) Variational Treatment of Hydrodynamic Interaction in Polymers. J Chern Phys 50(11):4831-4837.
7. Yamakawa H (1970) Transport Properties of Polymer Chains in Dilute Solution-Hydrodynamic Interaction. J Chern Phys 53(1):436-443.
8. Allen MP & Tildesley DJ (1987) Computer simulation of liquids (Oxford University Press, Oxford New York).
9. Ermak DL & Mccammon JA (1978) Brownian Dynamics with Hydrodynamic Interactions. J Chern Phys 69(4):1352-1360.
10. Hiyama M, Kinjo T, & Hyodo S (2008) Angular momentum form of Verlet algorithm for rigid molecules. J Phys Soc Jpn 77(6):064001.
11. Swaminathan R, Hoang CP, & Verkman AS (1997) Photobleaching recovery and anisotropy decay of green fluorescent protein GFP-S65T in solution and cells: Cytoplasmic viscosity probed by green fluorescent protein translational and rotational diffusion. Biophysical Journal 72(4): 1900-1907.
12. Terry BR, Matthews EK, & Haseloff J (1995) Molecular Characterization of Recombinant Green Fluorescent Protein by Fluorescence Correlation Microscopy. Biochem Bioph Res Co 217(1):21-27.
13. Potts R, Fournier MJ, & Ford NC (1977) Effect of Aminoacy1ation on Conformation of Yeast Phenylalanine Transfer-Rna. Nature 268(5620):563-564.
14. Sundararaj S, et al. (2004) The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res 32:D293-D295.
15. Zimmerman SB & Trach SO (1991) Estimation of Macromolecule Concentrations and Excluded Volume Effects for the Cytoplasm of Escherichia-Coli. J Mol Bioi 222(3):599-620.
16. Ishihama Y, et al. (2008) Protein abundance profiling of the Escherichia coli cytosol. Bmc Genomics 9: 102.
17. Humphrey W, Dalke A, & Schulten K (1996) VMD: Visual molecular dynamics. J Mol Graphics 14(1):33-38.
18. McGuffee SR & Elcock AH (2010) Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Com put Biol 6(3):e1000694.
19. Ridgway D, et al. (2008) Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Biophysical Journal 94(10):3748-3759.
20. Roberts E, Stone JE, Sepulveda L, Hwu W-MW, & Luthey-Schulten Z (2009) Long time-scale simulations of in vivo diffusion using GPU hardware. in Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing (IEEE Computer Society), pp 1-8.
21. Luby-Phelps K (2000) Cytoarchitecture and physical properties of cytoplasm: Volume, viscosity. diffusion, intracellular surface area. Int Rev Cytol 192:189-221.
22. Brady JF & Bossis G (1988) Stokesian Dynamics. Annu Rev Fluid Mech 20:111-157.
23. Phillips RJ, Brady JF, & Bossis G (1988) Hydrodynamic Transport-Properties of Hard-Sphere Dispersions. 1. Suspensions of Freely Mobile Particles. Phys Fluids 31(12):3462-3472.
24. Lu H, Lu L, & Skolnick J (2003) Development of unified statistical potentials describing protein-protein interactions. Biophys J 84(3): 1895-1901.
25. Yang F, Moss LG, & Phillips GN (1996) The molecular structure of green fluorescent protein. Nat Biotechnol 14(10): 1246-1251.