Stochastic vs. deterministic modeling of intracellular viral kinetics

Journal of Theoretical Biology

Volumn 218, Issue 3, 2002, Pages 309-321

  Srivastava, R ^a,b   You, L ^a   Summers, J ^c   Yin, J ^b  

^a 3633 Engineering Hall ^*  (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS PROTEIN;

KINETICS; VIRUS;

ARTICLE; CELL SUBPOPULATION; HOST CELL; KINETICS; MATHEMATICAL MODEL; MOLECULE; PRIORITY JOURNAL; SIMULATION; STEADY STATE; STOCHASTIC MODEL; SYNTHESIS; VIRUS INFECTION; VIRUS PARTICLE;

EID: 0036400749     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.2002.3078     Document Type: Article

References (22)

1. Arkin, A., Ross, J. & McAdams, H. H. (1998). Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 149, 1633-1648.
2. Chin, T. M. & Willsky, A. S. (1989). Stochastic Petri net modeling of wave sequences in cardiac arrhythmias. Comput. Biomed. Res. 22, 136-159.
3. Endy, D. & Yin, J. (2000). Toward antiviral strategies that resist viral escape. Antimicrob. Agents Chemother. 44, 1097-1099.
4. Endy, D., Kong, D. & Yin, J. (1997). Intracellular kinetics of a growing virus: a genetically structured simulation for bacteriophage T7. Biotechnol. Bioeng. 55, 375-389.
5. Endy, D., You, L., Yin, J. & Molineux, I. J. (2000). Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. Proc. Natl Acad. Sci. U.S.A. 97, 5375-5380.
6. Érdi, P. & Tóth, J. (1988). Mathematical Models of Chemical Reactions: Theory and Applications of Deterministic and Stochastic Models. Princeton, NJ: Princeton University Press.
7. Gillespie, D. T. (1976). A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22, 403-434.
8. Goss, P. J. & Peccoud, J. (1998). Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc. Natl Acad. Sci. U.S.A. 95, 6750-6755.
9. Goss, P. J. & Peccoud, J. (1999). Analysis of the stabilizing effect of Rom on the genetic network controlling ColE1 plasmid replication. In: Pacific Symposium on Biocomputing, Mauna Lani, Hawaii, pp. 65-76.
10. Jilbert, A. R., Miller, D. S., Scougall, C. A., Turnbull, H. & Burrell, C. J. (1996). Kinetics of duck hepatitis B virus infection following low dose virus inoculation: one virus DNA genome is infectious in neonatal ducks. Virology 226, 338-345.
11. Knipe, D. M. & Howley, P. M. (eds). (2001). Fields Virology. Baltimore, MD: Lippincott Williams & Wilkins Publishers.
12. Kurtz, T. G. (1972). The relationship between stochastic and deterministic models for chemical reactions. J. Chem. Phys. 57, 2976-2978.
13. Marsan, M. A., Balbo, G., Conte, G., Donatelli, S. & Franceschinis, G. (1995). Modelling with Generalized Stochastic Petri Nets. Chichester: John Wiley & Sons.
14. McAdams, H. H. & Arkin, A. (1997). Stochastic mechanisms in gene expression. Proc. Natl Acad. Sci. U.S.A. 94, 814-819.
15. McAdams, H. H. & Arkin, A. (1999). It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 15, 65-69.
16. Reddy, B. & Yin, J. (1999). Quantitative intracellular kinetics of HIV Type 1. AIDS Res. Human Retroviruses 15, 273-283.
17. Srivastava, R., Peterson, M. S. & Bentley, W. E. (2001). Stochastic kinetic analysis of the Escherichia coli stress circuit using sigma(32)-targeted antisense. Biotechnol. Bioeng. 75, 120-129.
18. Walpole, R. E. & Myers, R. H. (1989). Probability and Statistics for Engineers and Scientists. New York: Macmillan Publishing Company.
19. You, L. & Yin, J. (2000). Patterns of regulation from mRNA and protein time-series. Metab. Eng. 2, 210-217.
20. You, L. & Yin, J. (2001). Simulating the growth of viruses. In: Pacific Symposium on Biocomputing (Altman, R. B., Dunker, A. K., Hunter, L., Lauderdale, K. & Klein, T. E. (eds)), Singapore: World Scientific.
21. You, L., Suthers, P. & Yin, J. (2002). Effects of Escherichia coli physiology on the growth of phage T7 in vivo and in silico. J. Bacteriol. 184, 1888-1894.
22. Zheng, Q. & Ross, J. (1991). Comparison of deterministic and stochastic kinetics for nonlinear systems. J. Chem. Phys. 94, 3644-3648.