메뉴 건너뛰기




Volumn 91, Issue 3, 2008, Pages 458-472

Stochastic P systems and the simulation of biochemical processes with dynamic compartments

Author keywords

Biochemical processes; Dynamic compartments; P systems; SP systems; Stochastic simulation algorithm (SSA)

Indexed keywords

BIOCHEMISTRY; CATALYSIS; GENETIC ALGORITHM; LIFE CYCLE; STOCHASTICITY; VIRUS;

EID: 38949179852     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2006.12.009     Document Type: Article
Times cited : (36)

References (58)
  • 1
    • 85194558331 scopus 로고    scopus 로고
    • Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., Watson, J., 1994. Molecular Biology of the Cell, 3rd ed. Garland, New York.
    • Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., Watson, J., 1994. Molecular Biology of the Cell, 3rd ed. Garland, New York.
  • 2
    • 4344680283 scopus 로고    scopus 로고
    • Modelling biological processes by using a probabilistic P system software
    • Ardelean I., and Cavaliere M. Modelling biological processes by using a probabilistic P system software. Nat. Comput. 2 2 (2003) 173-197
    • (2003) Nat. Comput. , vol.2 , Issue.2 , pp. 173-197
    • Ardelean, I.1    Cavaliere, M.2
  • 3
    • 33748279268 scopus 로고    scopus 로고
    • R-leaping: accelerating the stochastic simulation algorithm by reaction leaps.
    • 084103-1-084103-13
    • Auger A., Chatelain P., and Koumoutsakosa P. R-leaping: accelerating the stochastic simulation algorithm by reaction leaps. J. Chem. Phys. 125 (2006) 084103-1-084103-13
    • (2006) J. Chem. Phys. , vol.125
    • Auger, A.1    Chatelain, P.2    Koumoutsakosa, P.3
  • 4
    • 85194571288 scopus 로고    scopus 로고
    • Banâtre, J.P., Le Métayer, D., 1986. A new computational model and its discipline of programming. Technical Report RR-0566, INRIA.
    • Banâtre, J.P., Le Métayer, D., 1986. A new computational model and its discipline of programming. Technical Report RR-0566, INRIA.
  • 5
    • 85194541457 scopus 로고    scopus 로고
    • Bernardini, F., 2005. Membrane systems for molecular computing and biological modelling. Ph.D. thesis, University of Sheffield, Sheffield, UK.
    • Bernardini, F., 2005. Membrane systems for molecular computing and biological modelling. Ph.D. thesis, University of Sheffield, Sheffield, UK.
  • 6
    • 85194532980 scopus 로고    scopus 로고
    • Bernardini, F., Gheorghe, M., Krasnogor, N., Muniyandi, R.C., Pérez-Jiménez, M.J., Romero-Campero, F.J., 2005. On P systems as a modelling tool for biological systems. In: Freund, R., Pǎun, Gh., Rozenberg, G., Salomaa, A. (Eds.), Workshop on Membrane Computing, vol. 3850. Lecture Notes in Computer Science. Springer, pp. 114-133.
    • Bernardini, F., Gheorghe, M., Krasnogor, N., Muniyandi, R.C., Pérez-Jiménez, M.J., Romero-Campero, F.J., 2005. On P systems as a modelling tool for biological systems. In: Freund, R., Pǎun, Gh., Rozenberg, G., Salomaa, A. (Eds.), Workshop on Membrane Computing, vol. 3850. Lecture Notes in Computer Science. Springer, pp. 114-133.
  • 12
    • 85194549313 scopus 로고    scopus 로고
    • Cieslak, M., 2006. Stochastic simulation of pattern formation: an application of L-systems. Master's thesis, University of Calgary.
    • Cieslak, M., 2006. Stochastic simulation of pattern formation: an application of L-systems. Master's thesis, University of Calgary.
  • 13
    • 85194552796 scopus 로고    scopus 로고
    • Debian, 2006. The Debian project web site. http://www.debian.org.
    • Debian, 2006. The Debian project web site. http://www.debian.org.
  • 14
    • 0035381291 scopus 로고    scopus 로고
    • Artificial chemistries-a review
    • Dittrich P., Ziegler J., and Banzhaf W. Artificial chemistries-a review. Artif. Life 7 3 (2001) 225-275
    • (2001) Artif. Life , vol.7 , Issue.3 , pp. 225-275
    • Dittrich, P.1    Ziegler, J.2    Banzhaf, W.3
  • 16
    • 0000476780 scopus 로고
    • Growth functions of stochastic Lindenmayer systems
    • Eichhorst P., and Savitch W.J. Growth functions of stochastic Lindenmayer systems. Inform. Control 45 3 (1980) 217-228
    • (1980) Inform. Control , vol.45 , Issue.3 , pp. 217-228
    • Eichhorst, P.1    Savitch, W.J.2
  • 17
    • 85194538278 scopus 로고    scopus 로고
    • Giavitto, J.-L., Godin, C., Michel, O., Prusinkiewicz, P., 2003. Modeling and simulation of biological processes in the context of genomics. In: Hermes, Dieppe, Ch. (Eds.), Computational Models for Integrative and Developmental Biology.
    • Giavitto, J.-L., Godin, C., Michel, O., Prusinkiewicz, P., 2003. Modeling and simulation of biological processes in the context of genomics. In: Hermes, Dieppe, Ch. (Eds.), Computational Models for Integrative and Developmental Biology.
  • 18
    • 19144364511 scopus 로고    scopus 로고
    • M G S: a rule-based programming language for complex objects and collections
    • Giavitto J.-L., and Michel O. M G S: a rule-based programming language for complex objects and collections. Electr. Notes Theor. Comput. Sci. 4 (2001) 59
    • (2001) Electr. Notes Theor. Comput. Sci. , vol.4 , pp. 59
    • Giavitto, J.-L.1    Michel, O.2
  • 19
    • 0036190735 scopus 로고    scopus 로고
    • The topological structures of membrane computing
    • Giavitto J.-L., and Michel O. The topological structures of membrane computing. Fund. Inform. 49 1-3 (2002) 107-129
    • (2002) Fund. Inform. , vol.49 , Issue.1-3 , pp. 107-129
    • Giavitto, J.-L.1    Michel, O.2
  • 20
    • 0001144902 scopus 로고    scopus 로고
    • Efficient exact stochastic simulation of chemical systems with many species and many channels
    • Gibson M.A., and Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Chem. Phys. 104 (2000) 1876-1889
    • (2000) J. Chem. Phys. , vol.104 , pp. 1876-1889
    • Gibson, M.A.1    Bruck, J.2
  • 21
    • 0017030517 scopus 로고
    • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    • Gillespie D.T. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22 (1976) 403-434
    • (1976) J. Comput. Phys. , vol.22 , pp. 403-434
    • Gillespie, D.T.1
  • 22
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 25 (1977) 2340-2361
    • (1977) J. Phys. Chem. , vol.81 , Issue.25 , pp. 2340-2361
    • Gillespie, D.T.1
  • 23
    • 0034225547 scopus 로고    scopus 로고
    • Chemical Langevin equation
    • Gillespie D.T. Chemical Langevin equation. J. Chem. Phys. 113 (2000) 297-306
    • (2000) J. Chem. Phys. , vol.113 , pp. 297-306
    • Gillespie, D.T.1
  • 24
    • 0035933994 scopus 로고    scopus 로고
    • Approximate ¡!-¡query¿Please check the deletion of reference Gillespie (2001b) which was the repetition of reference Gillespie (2001a).¡/query¿-¿accelerated stochastic simulation of chemically reacting systems
    • Gillespie D.T. Approximate ¡!-¡query¿Please check the deletion of reference Gillespie (2001b) which was the repetition of reference Gillespie (2001a).¡/query¿-¿accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115 (2001) 1716-1733
    • (2001) J. Chem. Phys. , vol.115 , pp. 1716-1733
    • Gillespie, D.T.1
  • 26
    • 0002472452 scopus 로고
    • Genetic algorithms and the optimal allocation of trials
    • Holland J.H. Genetic algorithms and the optimal allocation of trials. SIAM J. Comput. 2 2 (1973) 88-105
    • (1973) SIAM J. Comput. , vol.2 , Issue.2 , pp. 88-105
    • Holland, J.H.1
  • 29
    • 38949106548 scopus 로고
    • Probabilistic L-systems
    • Lindenmayer A., and Rozenberg G. (Eds), North-Holland, Amsterdam pp. 211-225
    • Jürgensen H. Probabilistic L-systems. In: Lindenmayer A., and Rozenberg G. (Eds). Automata, Languages, Development (1976), North-Holland, Amsterdam pp. 211-225
    • (1976) Automata, Languages, Development
    • Jürgensen, H.1
  • 30
    • 85194586335 scopus 로고    scopus 로고
    • Koushik, S., Kumar, N., Meseguer, J., Agha, G., 2003. Probabilistic rewrite theories. Technical Report 2343, University of Illinois at Urbana Champaign.
    • Koushik, S., Kumar, N., Meseguer, J., Agha, G., 2003. Probabilistic rewrite theories. Technical Report 2343, University of Illinois at Urbana Champaign.
  • 32
    • 14844307095 scopus 로고    scopus 로고
    • Space as the final frontier in stochastic simulations of biological systems
    • Lemerle C., Di Ventura B., and Serrano L. Space as the final frontier in stochastic simulations of biological systems. FEBS Lett. 579 (2005) 1789-1794
    • (2005) FEBS Lett. , vol.579 , pp. 1789-1794
    • Lemerle, C.1    Di Ventura, B.2    Serrano, L.3
  • 33
    • 0014265483 scopus 로고
    • Mathematical models for cellular interaction in development. Parts I and II
    • Lindenmayer A. Mathematical models for cellular interaction in development. Parts I and II. J. Theor. Biol. 18 (1968) 280-315
    • (1968) J. Theor. Biol. , vol.18 , pp. 280-315
    • Lindenmayer, A.1
  • 35
    • 4344584888 scopus 로고    scopus 로고
    • Probabilistic rewriting P systems
    • Madhu M. Probabilistic rewriting P systems. Int. J. Found. Comput. Sci. 14 1 (2003) 157-166
    • (2003) Int. J. Found. Comput. Sci. , vol.14 , Issue.1 , pp. 157-166
    • Madhu, M.1
  • 36
    • 51249194645 scopus 로고
    • A logical calculus of ideas immanent in nervous activity
    • McCulloch W.S., and Pitts W. A logical calculus of ideas immanent in nervous activity. Bull. Math. Biophys. 5 (1943) 115-133
    • (1943) Bull. Math. Biophys. , vol.5 , pp. 115-133
    • McCulloch, W.S.1    Pitts, W.2
  • 37
    • 0002015213 scopus 로고
    • K0L-systems simulating almost but not exactly the same development-the case of Japanese cypress
    • Nishida T. K0L-systems simulating almost but not exactly the same development-the case of Japanese cypress. Memoirs Fac. Sci., Kyoto University, Ser. Biol. 8 (1980) 97-122
    • (1980) Memoirs Fac. Sci., Kyoto University, Ser. Biol. , vol.8 , pp. 97-122
    • Nishida, T.1
  • 38
    • 0034961694 scopus 로고    scopus 로고
    • STOCHSIM: modelling of stochastic biomolecular processes
    • Novère N.L., and Shimizu T.S. STOCHSIM: modelling of stochastic biomolecular processes. Bioinformatics 17 6 (2001) 575-576
    • (2001) Bioinformatics , vol.17 , Issue.6 , pp. 575-576
    • Novère, N.L.1    Shimizu, T.S.2
  • 40
    • 85194581962 scopus 로고    scopus 로고
    • Pǎun, Gh., 2000. The P system web page: http://psystems.disco.unimib.it/.
    • Pǎun, Gh., 2000. The P system web page: http://psystems.disco.unimib.it/.
  • 41
    • 0035053070 scopus 로고    scopus 로고
    • From cells to computers: computing with membranes (P systems)
    • Pǎun Gh. From cells to computers: computing with membranes (P systems). Biosystems 59 3 (2001) 139-158
    • (2001) Biosystems , vol.59 , Issue.3 , pp. 139-158
    • Pǎun, Gh.1
  • 44
    • 0033047164 scopus 로고    scopus 로고
    • A look at the visual modeling of plants using L-systems
    • Prusinkiewicz P. A look at the visual modeling of plants using L-systems. Agronomie 29 (1999) 211-224
    • (1999) Agronomie , vol.29 , pp. 211-224
    • Prusinkiewicz, P.1
  • 47
    • 0008361824 scopus 로고
    • Synthesis of space-filling curves on the square grid
    • Peitgen H.-O., Henriques J.M., and Penedo L.F. (Eds), North-Holland, Amsterdam pp. 341-366
    • Prusinkiewicz P., Lindenmayer A., and Fracchia F.D. Synthesis of space-filling curves on the square grid. In: Peitgen H.-O., Henriques J.M., and Penedo L.F. (Eds). Fractals in the Fundamental and Applied Sciences (1991), North-Holland, Amsterdam pp. 341-366
    • (1991) Fractals in the Fundamental and Applied Sciences
    • Prusinkiewicz, P.1    Lindenmayer, A.2    Fracchia, F.D.3
  • 52
    • 85194536319 scopus 로고    scopus 로고
    • Stratgie d'application stochastique de rgles de rcritures dans le langage MGS
    • Michel O. (Ed), INRIA, Rocquencourt
    • Spicher A., and Michel O. Stratgie d'application stochastique de rgles de rcritures dans le langage MGS. In: Michel O. (Ed). Journes Francophones des Langages Applicatifs (2006), INRIA, Rocquencourt
    • (2006) Journes Francophones des Langages Applicatifs
    • Spicher, A.1    Michel, O.2
  • 53
    • 85194531131 scopus 로고    scopus 로고
    • Spicher, A., Michel, O., Giavitto, J.-L., 2006. Rewriting and Simulation-Application to the Modeling of the Lambda Phage Switch. No. 5 in Modlisation de systmes biologiques complexes dans le contexte de la gnomique. Genopole, Evry.
    • Spicher, A., Michel, O., Giavitto, J.-L., 2006. Rewriting and Simulation-Application to the Modeling of the Lambda Phage Switch. No. 5 in Modlisation de systmes biologiques complexes dans le contexte de la gnomique. Genopole, Evry.
  • 54
    • 14844321288 scopus 로고    scopus 로고
    • Space in systems biology of signaling pathways-towards intracellular molecular crowding in silico
    • Takahashi K., Arjunan S.N.V., and Tomita M. Space in systems biology of signaling pathways-towards intracellular molecular crowding in silico. FEBS Lett. 579 (2005) 1783-1788
    • (2005) FEBS Lett. , vol.579 , pp. 1783-1788
    • Takahashi, K.1    Arjunan, S.N.V.2    Tomita, M.3
  • 56
    • 0008507891 scopus 로고
    • On some mathematical problems connected with patterns of growth of figures
    • Ulam S.M. On some mathematical problems connected with patterns of growth of figures. Proc. Symp. Appl. Math. 14 (1962) 215-224
    • (1962) Proc. Symp. Appl. Math. , vol.14 , pp. 215-224
    • Ulam, S.M.1
  • 58
    • 0019004184 scopus 로고
    • Stochastic characterizations of EOL languages
    • Yokomori T. Stochastic characterizations of EOL languages. Inform. Control 45 1 (1980) 26-33
    • (1980) Inform. Control , vol.45 , Issue.1 , pp. 26-33
    • Yokomori, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.