메뉴 건너뛰기




Volumn 4, Issue 4, 2014, Pages 837-864

Growth and division in a dynamic protocell model

Author keywords

Artificial chemistries; Collectively replicating chemical systems; Dynamical models; Emergence of novelties; Evolvability; Protocell; Synchronization

Indexed keywords


EID: 84922041594     PISSN: None     EISSN: 20751729     Source Type: Journal    
DOI: 10.3390/life4040837     Document Type: Article
Times cited : (24)

References (67)
  • 4
    • 52149100341 scopus 로고    scopus 로고
    • Sufficient conditions for emergent synchronization in protocell models
    • Carletti, T.; Serra, R.; Villani, M.; Poli, I.; Filisetti, A. Sufficient conditions for emergent synchronization in protocell models. J. Theor. Biol. 2008, 254, 741-751.
    • (2008) J. Theor. Biol. , vol.254 , pp. 741-751
    • Carletti, T.1    Serra, R.2    Villani, M.3    Poli, I.4    Filisetti, A.5
  • 6
    • 33646010071 scopus 로고    scopus 로고
    • 3rd ed.; Kluwer Academic: New York, NY, USA
    • Ganti, T. Chemoton Theory, 3rd ed.; Kluwer Academic: New York, NY, USA, 2003.
    • (2003) Chemoton Theory
    • Ganti, T.1
  • 7
    • 31344455122 scopus 로고    scopus 로고
    • Approaches to semi-synthetic minimal cells: A review
    • Luisi, P.L.; Ferri, F.; Stano, P. Approaches to semi-synthetic minimal cells: A review. Naturwissenschaften 2006, 93, 1-13
    • (2006) Naturwissenschaften , vol.93 , pp. 1-13
    • Luisi, P.L.1    Ferri, F.2    Stano, P.3
  • 10
    • 33646235398 scopus 로고    scopus 로고
    • Phenotypic diversity and chaos in a minimal cell model
    • Munteanu, A.; Solé, R.V. Phenotypic diversity and chaos in a minimal cell model. J. Theor. Biol. 2006, 240, 434-442.
    • (2006) J. Theor. Biol. , vol.240 , pp. 434-442
    • Munteanu, A.1    Solé, R.V.2
  • 13
    • 0034280783 scopus 로고    scopus 로고
    • Composing life
    • Segrè, D.; Lancet, D. Composing life. EMBO Rep. 2000, 1, 217-222, doi:10.1093/embo-reports/ kvd063.
    • (2000) EMBO Rep. , vol.1 , pp. 217-222
    • Segrè, D.1    Lancet, D.2
  • 14
    • 77952364826 scopus 로고    scopus 로고
    • Achievements and open questions in the self-reproduction of vesicles and synthetic minimal cells
    • Stano, P.; Luisi, L.P. Achievements and open questions in the self-reproduction of vesicles and synthetic minimal cells. Chem. Commun. 2010, 46, 3639-3653.
    • (2010) Chem. Commun. , vol.46 , pp. 3639-3653
    • Stano, P.1    Luisi, L.P.2
  • 16
    • 8844249335 scopus 로고    scopus 로고
    • Replicating vesicles as models of primitive cell growth and division
    • Hanczyc, M.M.; Szostak, J.W. Replicating vesicles as models of primitive cell growth and division. Curr. Opin. Chem. Biol. 2004, 8, 660-664.
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 660-664
    • Hanczyc, M.M.1    Szostak, J.W.2
  • 18
    • 84949729272 scopus 로고    scopus 로고
    • Models of Protocell Replication
    • Rasmussen, S., Bedau, M.A., Chen, L., Deamer, D., Krakauer, D.C., Packard, N.H., Stadler, P.F., Eds.; The MIT Press: Cambridge, MA, USA; London, UK
    • Solé, R.V.; Macía, J.; Fellermann, H.; Munteanu, A.; Sardanyés, J.; Valverde, S. Models of Protocell Replication; In Protocells: Bridging Nonliving and Living Matter; Rasmussen, S., Bedau, M.A., Chen, L., Deamer, D., Krakauer, D.C., Packard, N.H., Stadler, P.F., Eds.; The MIT Press: Cambridge, MA, USA; London, UK, 2008.
    • (2008) Protocells: Bridging Nonliving and Living Matter
    • Solé, R.V.1    Macía, J.2    Fellermann, H.3    Munteanu, A.4    Sardanyés, J.5    Valverde, S.6
  • 19
    • 84922027113 scopus 로고    scopus 로고
    • note
    • This is of course an approximate description of the actual process of vesicle fission: the daughter cells may be of different size and, perhaps more important, the breakup is a complex process and it does not always take place at a fixed size. However, for modeling purposes, we will first consider the simplest version, and we will postpone to further works the consideration of fluctuations in the size of the daughter cells and in the value of the threshold on the parent cell volume that leads to fission.
  • 20
    • 33947240912 scopus 로고    scopus 로고
    • Synchronization phenomena in surface-reaction models of protocells
    • Serra, R.; Carletti, T.; Poli, I. Synchronization phenomena in surface-reaction models of protocells. Artif. Life 2007, 123, 123-138.
    • (2007) Artif. Life , vol.123 , pp. 123-138
    • Serra, R.1    Carletti, T.2    Poli, I.3
  • 21
    • 65149102393 scopus 로고    scopus 로고
    • Symmetry and order in systems chemistry
    • Wagner, N.; Ashkenasy, G. Symmetry and order in systems chemistry. J. Chem. Phys. 2009, 130, 164907.
    • (2009) J. Chem. Phys , vol.130
    • Wagner, N.1    Ashkenasy, G.2
  • 22
    • 0028306647 scopus 로고
    • Self-replication of complementary nucleotide-based oligomers
    • Sievers, D.; von Kiedrowski, G. Self-replication of complementary nucleotide-based oligomers. Nature 1994, 369, 221-224.
    • (1994) Nature , vol.369 , pp. 221-224
    • Sievers, D.1    von Kiedrowski, G.2
  • 23
    • 63449115566 scopus 로고    scopus 로고
    • Model protocells from single-chain lipids
    • Mansy, S.S. Model protocells from single-chain lipids. Int. J. Mol. Sci. 2009, 10, 835-843.
    • (2009) Int. J. Mol. Sci. , vol.10 , pp. 835-843
    • Mansy, S.S.1
  • 24
    • 0032173377 scopus 로고
    • Graded autocatalysis replication domain (GARD): Kinetic analysis of self-replication in mutually catalytic sets
    • Segre, D.; Lancet, D.; Kedem, O.; Pilpel, Y. Graded autocatalysis replication domain (GARD): Kinetic analysis of self-replication in mutually catalytic sets. Orig. Life Evol. Biosph. 1988, 28, 501-514.
    • (1988) Orig. Life Evol. Biosph. , vol.28 , pp. 501-514
    • Segre, D.1    Lancet, D.2    Kedem, O.3    Pilpel, Y.4
  • 25
    • 0022619420 scopus 로고
    • Autocatalytic sets of proteins
    • Kauffman, S.A. Autocatalytic sets of proteins. J. Theor. Biol. 1986, 119, 1-24.
    • (1986) J. Theor. Biol. , vol.119 , pp. 1-24
    • Kauffman, S.A.1
  • 27
    • 84859741820 scopus 로고    scopus 로고
    • The stochastic evolution of a protocell: The Gillespie algorithm in a dynamically varying volume
    • Carletti, T.; Filisetti, A. The stochastic evolution of a protocell: The Gillespie algorithm in a dynamically varying volume. Comput. Math. Methods Med. 2012, 2012, Article ID 423627.
    • (2012) Comput. Math. Methods Med. , vol.2012
    • Carletti, T.1    Filisetti, A.2
  • 28
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie, D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 1977, 81, 2340-2361.
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 29
    • 85052408161 scopus 로고    scopus 로고
    • The Role of Backward Reactions in a Stochastic Model of Catalytic Reaction Networks
    • Taormina, Italy, 2-6 September 2013; Liò, P., Miglino, O., Nicosia, G., Nolfi, S., Pavone, M., Eds.; The MIT Press: Cambridge, MA, USA
    • Filisetti, A.; Graudenzi, A.; Damiani, C.; Villani, M.; Roberto, S. The Role of Backward Reactions in a Stochastic Model of Catalytic Reaction Networks. In Proceedings of the 12th European Conference on Artificial Life (ECAL2013), Taormina, Italy, 2-6 September 2013; Liò, P., Miglino, O., Nicosia, G., Nolfi, S., Pavone, M., Eds.; The MIT Press: Cambridge, MA, USA, 2013.
    • (2013) Proceedings of the 12th European Conference on Artificial Life (ECAL2013)
    • Filisetti, A.1    Graudenzi, A.2    Damiani, C.3    Villani, M.4    Roberto, S.5
  • 30
    • 84865247934 scopus 로고    scopus 로고
    • The Role of Energy in a Stochastic Model of the Emergence of Autocatalytic Sets
    • Paris, France, 8-12 August 2011; Lenaerts, T., Giacobini, M., Bersini, H., Bourgine, P., Dorigo, M., Doursat, R., Eds.; The MIT Press: Cambridge, MA, USA
    • Filisetti, A.; Graudenzi, A.; Roberto, S.; Villani, M.; de Lucrezia, D.; Poli, I. The Role of Energy in a Stochastic Model of the Emergence of Autocatalytic Sets. In Proceedings of the 11th European Conference on Artificial Life (ECAL2011), Paris, France, 8-12 August 2011; Lenaerts, T., Giacobini, M., Bersini, H., Bourgine, P., Dorigo, M., Doursat, R., Eds.; The MIT Press: Cambridge, MA, USA, 2011; pp. 227-234.
    • (2011) Proceedings of the 11th European Conference on Artificial Life (ECAL2011) , pp. 227-234
    • Filisetti, A.1    Graudenzi, A.2    Roberto, S.3    Villani, M.4    de Lucrezia, D.5    Poli, I.6
  • 32
    • 84922027111 scopus 로고    scopus 로고
    • note
    • In that paper we assumed that a semipermeable membrane exists, and that some chemical species can cross the membrane (leading to an instantaneous equilibrium between the internal and external chemical potential of those species) ,while for others crossing is prohibited.
  • 33
    • 84922027110 scopus 로고    scopus 로고
    • note
    • If R is the set of all possible reactions, a RAF set is defined as a subset R' ⊆ R of reactions in which: (i) each reaction r ∈ R' is catalyzed by at least one molecule type involved in R' and (ii) all reactants and catalysts in R' can be created from the species whose presence is guaranteed (the so-called food set F) by using reactions only from R' itself. See Section 3 for more details.
  • 34
    • 1642298923 scopus 로고    scopus 로고
    • Detecting autocatalytic, self-sustaining sets in chemical reaction systems
    • Hordijk, W.; Steel, M. Detecting autocatalytic, self-sustaining sets in chemical reaction systems. J. Theor. Biol. 2004, 227, 451-461.
    • (2004) J. Theor. Biol. , vol.227 , pp. 451-461
    • Hordijk, W.1    Steel, M.2
  • 35
    • 84922027109 scopus 로고    scopus 로고
    • note
    • The presence of a RAF set in this type of model of chemical reactions plays a role analogous to that of the presence of an eigenvalue with a positive real part in the case of linear kinetic equations discussed in [4].
  • 36
    • 84901460760 scopus 로고    scopus 로고
    • Multispecies population dynamics of prebiotic compositional assemblies
    • Markovitch, O.; Lancet, D. Multispecies population dynamics of prebiotic compositional assemblies. J. Theor. Biol. 2014, 357, 26-34.
    • (2014) J. Theor. Biol. , vol.357 , pp. 26-34
    • Markovitch, O.1    Lancet, D.2
  • 37
    • 84922027108 scopus 로고    scopus 로고
    • note
    • If not differently indicated in this article, all the kinetic constants of the same kind are set to the same value (see Appendix A for the details); note, however, that the structure of the relationships among RAFs, membranes and protocell growth does not depend on the particular values of these parameters (whereas, of course, these parameters determine the rates of the phenomena).
  • 38
    • 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. 1976, 22, 403-434.
    • (1976) J. Comput. Phys. , vol.22 , pp. 403-434
    • Gillespie, D.T.1
  • 39
    • 0003165572 scopus 로고
    • Spontaneous Emergence of a Metabolism
    • Langton, H.G., Taylor, C., Farmer, J.D., Rasmussen, S., Eds.; Addison-Wesley: Cambridge, MA, USA
    • Bagley, R.J.; Farmer, J.D. Spontaneous Emergence of a Metabolism. In Artificial Life II; Series Santa Fe Institute Studies in the Sciences of Complexity; Langton, H.G., Taylor, C., Farmer, J.D., Rasmussen, S., Eds.; Addison-Wesley: Cambridge, MA, USA, 1991; pp. 227-234.
    • (1991) Artificial Life II; Series Santa Fe Institute Studies in the Sciences of Complexity , pp. 227-234
    • Bagley, R.J.1    Farmer, J.D.2
  • 40
    • 0025156542 scopus 로고
    • Dynamics of small autocatalytic reaction networks-I. Bifurcations, permanence and exclusion
    • Stadler, P.F.; Schuster, P. Dynamics of small autocatalytic reaction networks-I. Bifurcations, permanence and exclusion. Bull. Math. Biol. 1990, 52, 485-508.
    • (1990) Bull. Math. Biol. , vol.52 , pp. 485-508
    • Stadler, P.F.1    Schuster, P.2
  • 41
    • 0025997144 scopus 로고
    • Dynamics of autocatalytic reaction networks. IV: Inhomogeneous replicator networks
    • Stadler, P.F. Dynamics of autocatalytic reaction networks. IV: Inhomogeneous replicator networks. Biosystems 1991, 26, 1-19.
    • (1991) Biosystems , vol.26 , pp. 1-19
    • Stadler, P.F.1
  • 42
    • 0002843699 scopus 로고
    • Dynamics of small autocatalytic reaction networks II replication, mutation and catalysis
    • Stadler, P.F.; Schnabl, W.; Forst, C.; Schuster, P. Dynamics of small autocatalytic reaction networks II replication, mutation and catalysis. Bull. Math. Biol. 1995, 57, 21-61.
    • (1995) Bull. Math. Biol. , vol.57 , pp. 21-61
    • Stadler, P.F.1    Schnabl, W.2    Forst, C.3    Schuster, P.4
  • 43
    • 0035895246 scopus 로고    scopus 로고
    • A model for the emergence of cooperation, interdependence, and structure in evolving networks
    • Jain, S.; Krishna, S. A model for the emergence of cooperation, interdependence, and structure in evolving networks. Proc. Natl. Acad. Sci. USA 2001, 98, 543-547.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 543-547
    • Jain, S.1    Krishna, S.2
  • 46
    • 84879086656 scopus 로고    scopus 로고
    • Competition between model protocells driven by an encapsulated catalyst
    • Adamala, K.; Szostak, J.W. Competition between model protocells driven by an encapsulated catalyst. Nat. Chem. 2013, 5, 495-501.
    • (2013) Nat. Chem. , vol.5 , pp. 495-501
    • Adamala, K.1    Szostak, J.W.2
  • 47
    • 84922027107 scopus 로고    scopus 로고
    • note
    • The hypothesis that the two daughters have identical volumes is a non-essential assumption, because of the supposition that the division phenomenon happens at a given threshold independent from the initial size: conversely, it allows a more compact result presentation. In any case, we checked if the hypothesis can be released without effecting the presented results (simulations not shown).
  • 48
    • 0002065228 scopus 로고
    • Autocatalytic replication of polymers
    • Farmer, J.D.; Kauffman, S.A. Autocatalytic replication of polymers. Physica D 1986, 220, 50-67.
    • (1986) Physica D , vol.220 , pp. 50-67
    • Farmer, J.D.1    Kauffman, S.A.2
  • 49
    • 77956401687 scopus 로고    scopus 로고
    • Autocatalytic sets and the origin of life
    • Hordijk, W.; Hein, J.; Steel, M. Autocatalytic sets and the origin of life. Entropy 2010, 12, 1733-1742.
    • (2010) Entropy , vol.12 , pp. 1733-1742
    • Hordijk, W.1    Hein, J.2    Steel, M.3
  • 50
    • 0004190112 scopus 로고
    • Cambridge University Press: Cambridge, UK
    • Dyson, F.J. Origins of Life; Cambridge University Press: Cambridge, UK, 1985.
    • (1985) Origins of Life
    • Dyson, F.J.1
  • 51
    • 0017667182 scopus 로고
    • A principle of natural self-organization
    • Eigen, M.; Schuster, P. A principle of natural self-organization. Naturwissenschaften 1977, 64, 541-565.
    • (1977) Naturwissenschaften , vol.64 , pp. 541-565
    • Eigen, M.1    Schuster, P.2
  • 52
    • 0001524340 scopus 로고
    • Autocatalytic set and the growth of complexity in an evolutionary model
    • Jain, S.; Krishna, S. Autocatalytic set and the growth of complexity in an evolutionary model. Phys. Rev. Lett. 1988, 81, 5684-5687.
    • (1988) Phys. Rev. Lett. , vol.81 , pp. 5684-5687
    • Jain, S.1    Krishna, S.2
  • 54
    • 84870250526 scopus 로고    scopus 로고
    • The structure of autocatalytic sets: Evolvability, enablement, and emergence
    • Hordijk, W.; Steel, M.; Kauffman, S.A. The structure of autocatalytic sets: Evolvability, enablement, and emergence. Acta Biotheor. 2012, 60, 379-392.
    • (2012) Acta Biotheor. , vol.60 , pp. 379-392
    • Hordijk, W.1    Steel, M.2    Kauffman, S.A.3
  • 55
    • 84922027106 scopus 로고    scopus 로고
    • note
    • If R is the set of all possible reaction, a RAF set is defined as the subset R'⊆ R of reactions in which: (i) each reaction r ∈ R' is catalyzed by at least one molecule type involved in R' and (ii) all reactants and catalysts in R' can be created from the molecules whose presence is guaranteed (the so-called food set F) by using reactions only from R' itself. See [34] for a more detailed explanation.
  • 56
    • 84922027105 scopus 로고    scopus 로고
    • note
    • It should be observed that also periodic variations in the growth and duplication rates are compatible with a viable protocell population, provided that the variations are also synchronized (a phenomenon that was called supersynchronization in [5].
  • 57
    • 84873289358 scopus 로고    scopus 로고
    • Theoretical conditions for the stationary reproduction of model protocells
    • Mavelli, F.; Ruiz-Mirazo, K. Theoretical conditions for the stationary reproduction of model protocells. Integr. Biol. 2013, 5, 324-341.
    • (2013) Integr. Biol. , vol.5 , pp. 324-341
    • Mavelli, F.1    Ruiz-Mirazo, K.2
  • 60
    • 84922027104 scopus 로고    scopus 로고
    • note
    • Further novelties might be due to the interactions between different protocells, whose contents may differ (see Section 6 for a discussion on the role of heterogeneity in protocell populations). However, these novelties would be less radical than those discussed here; it has been argued that a system can be deemed truly evolvable only if it can accept some "true novelties" of the kind discussed in the text [17,27].
  • 61
    • 84922027103 scopus 로고    scopus 로고
    • note
    • Or if it is capable to directly catalyze its own formation at a rate higher than those of the already existing ones; in this case the new irrRAF will replace the already existing ones.
  • 64
    • 84879835496 scopus 로고    scopus 로고
    • Mechanism for the formation of density gradients through semipermeable membranes
    • Serra, R.; Villani, M. Mechanism for the formation of density gradients through semipermeable membranes. Phys. Rev. E 2013, 87, 062814.
    • (2013) Phys. Rev. E , vol.87
    • Serra, R.1    Villani, M.2
  • 65
    • 77957197223 scopus 로고    scopus 로고
    • Spontaneous protein crowding in liposomes: A new vista for the origin of cellular metabolism
    • Luisi, P.L.; Allegretti, M.; Souza, T.; Steineger, F.; Fahr, A.; Stano, P. Spontaneous protein crowding in liposomes: A new vista for the origin of cellular metabolism. ChemBioChem 2010, 11, 1989-1992.
    • (2010) ChemBioChem , vol.11 , pp. 1989-1992
    • Luisi, P.L.1    Allegretti, M.2    Souza, T.3    Steineger, F.4    Fahr, A.5    Stano, P.6
  • 66
    • 84882295217 scopus 로고    scopus 로고
    • Primitive Membrane Formation, Characteristics and Roles in the Emergent Properties of a Protocell
    • Maurer, S.E.; Monnard, P.A. Primitive Membrane Formation, Characteristics and Roles in the Emergent Properties of a Protocell. Entropy 2011, 13, 466-484.
    • (2011) Entropy , vol.13 , pp. 466-484
    • Maurer, S.E.1    Monnard, P.A.2
  • 67
    • 79051470446 scopus 로고    scopus 로고
    • From chemical reactions to evolution: Emergence of species
    • Carletti, T.; Fanelli, D. From chemical reactions to evolution: Emergence of species. Eur. Phys. Lett. 2007, 77, doi:10.1209/0295-5075/77/18005.
    • (2007) Eur. Phys. Lett. , vol.77
    • Carletti, T.1    Fanelli, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.