Cellular automata models of biochemical phenomena

Future Generation Computer Systems

Volumn 16, Issue 2, 1999, Pages 273-289

  Kier, Lemont B ^a   Cheng, Chao Kun ^a   Testa, Bernard ^b  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL ENGINEERING; COMPUTER SIMULATION; DISSOLUTION; SOLUBILITY;

CELLULAR AUTOMATA (CA);

AUTOMATA THEORY;

EID: 0033324108     PISSN: 0167739X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-739X(99)00052-7     Document Type: Article

References (49)

1. Kier L.B., Testa B. Complexity and emergence in drug research. Advances in Drug Research. 26:1995;1-43.
2. Geiger A., Stillinger F.H., Rahman A. Aspects of the percolation process for hydrogen bonded networks in water. J. Chem. Phys. 70:1979;4186-4192.
3. W.L. Jorgensen, J. Gao, C. Ravimohan, Monte Carlo simulations of alkanes in water: hydration numbers and the hydrophobic effect, J. Phys. Chem. 89 (1985) 3470-3477.
4. Mezei M., Beveridge D.L. Theoretical studies of hydrogen bonding in liquid water and aqueous solutions. J. Chem. Phys. 74:1981;622-632.
5. Plummer P.L.M. Molecular dynamics simulations and quantum mechanical studies of the hydrogen bond in water cluster systems. J. Mol. Struct. 237:1991;47-61.
6. Rossky P.J., Karplus M. Solvation - a molecular dynamics study of a dipeptide in water. J. Am. Chem. Soc. 101:1979;1913-1921.
7. J. von Neumann, in: A.W. Burks (Ed.), Theory of Self-Reproducing Automata, University of Illinois Press, Champaign. IL, 1966.
8. Ermentrout F.B., Edelstein-Keshet L. Cellular automata approaches to biological modeling. J. Theor. Biol. 160:1993;97-133.
9. Blumberg R.L., Shlifer G., Stanley H.E. Monte Carlo tests of universality in a correlated-site percolation problem. J. Phys. A: Math. Gen. 13:1980;147-150.
10. Brodsky M.H., Leary P.H. The temperature dependence of the refractive index of hydrogenated amorphous silicon and implications for electroreflectance. Bull. Am. Phys. Soc. 25:1980;260-265.
11. Rice S.A., Skeats M.G. A random network model for water. J. Phys. Chem. 85:1981;1108-1119.
12. Kier L.B., Cheng C.-K. A cellular automata model of water. J. Chem. Inf. Comput. Sci. 34:1994;647-652.
13. Haggis G.H., Hasted J.B., Buchanan T.J. The dielectric properties of water in solutions. J. Phys. Chem. 54:1952;1452-1464.
14. G.E. Walrafen, in: A.K. Covington, P. Jones (Eds.), Structure of Water, Hydrogen-Bonded Systems, Taylor and Francis Publ., London, 1968, pp. 9-29.
15. Luck W.A.P. Role of hydrogen bonding in the structure of liquids. Acta Chim. Hung. Acad. Sci. Hung. 121:1986;119-145.
16. Kier L.B., Cheng C.-K. A cellular automata model of an aqueous solution. J. Chem. Inf. Comput.Sci. 34:1994;1334-1337.
17. Kier L.B., Cheng C.-K. A cellular automata model of the soluble state. J. Math Chem. 21:1997;71-81.
18. Kier L.B., Cheng C.-K., Testa B., Carrupt P.-A. A cellular automata model of the hydrophobic effect. Pharm. Res. 12:1995;615-620.
19. Blokzijl W., Engberts J.B.F.N. Hydrophobic effects, opinions and facts. Angew. Chem. Int. Ed. Engl. 32:1993;1545-1579.
20. Hummer G., Garde S., Garcia A.E., Pohorille A., Pratt L.R. An information theory model of hydrophobic interactions. Proc. Nat. Acad. Sci. 93:1996;8951-8955.
21. Ohmine I., Tanaka H. Fluctuation, relaxations and hydration in liquid water, hydrogen bond rearrangement dynamics. Chem. Rev. 93:1993;2545-2566.
22. Kier L.B., Cheng C.-K., Testa B., Carrupt P.-A. A cellular automata model of dissolution. Pharm. Res. 12:1995;1521-1525.
23. Kier L.B., Cheng C.-K., Testa B., Carrupt P.-A. A cellular automata model of diffusion in aqueous systems. J. Pharm. Sci. 86:1997;774-778.
24. Gary-Bobo C.M., Weber H.W. Diffusion of alcohols and amides in water from 4 to. 37° J. Phys. Chem. 73:1969;1155-1156.
25. Horowitz S.B., Fenichel I.R. Solute diffusional specificity in hydrogen bonding systems. J. Phys. Chem. 68:1964;3378-3385.
26. Cheng C.-K, Kier L.B. A cellular automata model of oil-water partitioning. J. Chem. Inf. Comput. Sci. 35:1995;1054-1059.
27. L.B. Kier, C.-K. Cheng, Cellular Automata Model of Partitioning Between Liquid Phases, in: V. Pliska, B. Testa, H. van de Waterbeemd (Eds.), Lipophilicity in Drug Action and Toxicology VCH Publ. Weinheim, Germany 1995, pp. 181-194.
28. Benjamin I. Theoretical study of the water/1,2-dichloroethane interface: structure, dynamics and conformational equilibria at the liquid-liquid interface. J. Chem. Phys. 97:1992;1432-1445.
29. Carpenter I.L., Hebre W.J. A molecular dynamics study of the hexane/water interface. J. Phys. Chem. 94:1990;531-536.
30. Gao J., Jorgensen W.L. Theoretical examination of hexanol-water interfaces. J. Phys. Chem. 92:1988;5813-5822.
31. Luise P. Monte Carlo simulation of liquid-liquid benzene-water interface. J. Chem. Phys. 86:1987;4177-4187.
32. Meyer M., Mareschal M., Hayoun M. Computer modeling of a liquid-liquid interface. J. Chem. Phys. 89:1988;1067-1073.
33. Smit B., Hilbers P.A.J., Esselink K., Rubert L.A.M., Os N.M. va, Schlijper A.G. Structure of a water/oil interface in the presence of micelles: a computer simulation study. J. Phys. Chem. 95:1991;6361-6368.
34. M.N. Jones, D. Chapman, Micelles, Monolayers, Biomembranes, Wiley, New York, 1994.
35. C. Tanford, The Hydrophobic Effect: The Formation of Micelles and Biological Membranes, John Wiley, New York, 1980.
36. Kier L.B., Cheng C.-K., Testa B., Carrupt P.-A. A cellular automata model of micelle formation. Pharm. Res. 13:1996;1419-1422.
37. Espada L., Jones M.N., Pilcher G. Enthalpy of micellization d-dodecyltrimethyl ammonium bromide. J. Chem. Thermo. 12:1970;1-8.
38. P. Mukergee, K.J. Mysels, Critical Micelle Concentration Aqueous Surfactant Systems, National Bureau of Standards, Washington, DC, 1971.
39. Kier L.B., Cheng C.-K. A cellular automata model of membrane permeability. J. theor. Biol. 86:1997;75-80.
40. S. Cornell, M. Droz, B. Chopard, Role of fluctuations for inhomogeneous reaction-diffusion phenomena, Phys. Rev. A, 44.
41. Cornell S., Droz M., Chopard B. Some properties of the diffusion-limited reaction. nA+mB→C with homogeneous and inhomogeneous initial conditions Physica A. 188:1992;322-336.
42. Kier L.B., Cheng C.-K., Testa B., Carrupt P.-A. A cellular automata model of enzyme kinetics. J. Molec. Graphics. 14:1996;226-231.
43. L.B. Kier, C.-K. Cheng, M. Tute, P. Seybold, A cellular automata model of acid dissociation, J. Chem. Inf. Comput. Sci. 38 (1998) 271-275.
44. Calder G.V., Barton T.J. Actual effects controlling the acidity of carboxylic acids. J. Chem. Ed. 48:1971;338-340.
45. Barlin G.B., Perrin D.D. Prediction of the strength of organic acids. Quart. Rev. Chem. Soc. 20:1966;75-101.
46. Seybold P.G., Kier L.B., Cheng C.-K. Simulation of first-order kinetics using cellular automata. J. Chem. Inf. Comput.Sci. 37:1997;386-391.
47. Seybold P.G., Kier L.B., Cheng C.-K. Stochastic cellular automata models of molecular excited-state dynamics. J. Phys. Chem. 102:1998;886-891.
48. Okazaki S., Nakanishi K., Touhara N., Watanabi N., Adashi Y. A Monte Carlo study on the size dependence in hydrophobic hydration. J. Chem. Phys. 74:1981;5863-5868.
49. Walter A., Gutknect J. The movement of molecules across lipid membranes: a molecular theory. J. Membr. Biol. 90:1986;207-217.