Two Different Template Replicators Coexisting in the Same Protocell: Stochastic Simulation of an Extended Chemoton Model
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{"title"=>"Two different template replicators coexisting in the same protocell: Stochastic simulation of an extended chemoton model", "type"=>"journal", "authors"=>[{"first_name"=>"István", "last_name"=>"Zachar", "scopus_author_id"=>"35747641700"}, {"first_name"=>"Anna", "last_name"=>"Fedor", "scopus_author_id"=>"36671092800"}, {"first_name"=>"Eörs", "last_name"=>"Szathmáry", "scopus_author_id"=>"7004300777"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"21818258", "doi"=>"10.1371/journal.pone.0021380", "pui"=>"362161330", "issn"=>"19326203", "sgr"=>"79960465032", "scopus"=>"2-s2.0-79960465032"}, "id"=>"ab0d8cd1-397c-3d33-9d14-b66145faa18f", "abstract"=>"The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system consisting of a large but fixed number of interacting molecular species, it can effectively be implemented in a process algebra-based language such as the BlenX programming language. The stochastic model behaves comparably to previous continuous deterministic models of the chemoton. Additionally to the well-known chemoton, we also implemented an extended version with two competing template cycles. The new insight from our study is that the coupling of reactions in the chemoton ensures that these templates coexist providing an alternative solution to Eigen's paradox. Our technical innovation involves the introduction of a two-state switch to control cell growth and division, thus providing an example for hybrid methods in BlenX. Further developments to the BlenX language are suggested in the Appendix.", "link"=>"http://www.mendeley.com/research/two-different-template-replicators-coexisting-same-protocell-stochastic-simulation-extended-chemoton", "reader_count"=>22, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>5, "Student > Master"=>1, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>5, "Student > Master"=>1, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Agricultural and Biological Sciences"=>11, "Medicine and Dentistry"=>1, "Philosophy"=>2, "Physics and Astronomy"=>1, "Psychology"=>1, "Computer Science"=>4, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Computer Science"=>{"Computer Science"=>4}, "Unspecified"=>{"Unspecified"=>1}, "Philosophy"=>{"Philosophy"=>2}}, "reader_count_by_country"=>{"Romania"=>1, "United States"=>1, "Japan"=>1, "Italy"=>1, "South Africa"=>1, "Germany"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/755666"], "description"=>"<p>The chemoton on the left consists of a 5-member metabolic cycle (A<sub>1</sub> to A<sub>5</sub>), while the chemoton on the right harbors a 12-strong metabolism (A<sub>1</sub> to A<sub>12</sub>). The extra metabolites feed on X and the previous metabolite, and produce the next metabolite in the cycle. The larger number of metabolic partners slightly decreases the total amount of metabolites, ∑A<i><sub>i</sub></i>. This is a phenomenon that is supported directly by the numerical results of deterministic models: the larger the number of intermediates in the metabolic cycle the less the total amount of metabolic molecules is in a splitting equilibrium. It is a consequence of the relative position where T<sub>m</sub> is produced in the cycle: the earlier it is generated (i.e. the more metabolites are in the cycle after T<sub>m</sub> is generated), the less the total amount of metabolites will be, as T<sub>m</sub> defines the critical value for splitting.</p>", "links"=>[], "tags"=>["metabolic"], "article_id"=>426045, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["István Zachar", "Anna Fedor", "Eörs Szathmáry"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021380.g005", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_different_metabolic_subsystems_/426045", "title"=>"Comparison of different metabolic subsystems.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:39:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/755547"], "description"=>"<p><i>k</i><sub>V6</sub> = <i>k</i><sub>V7</sub> = <i>k</i><sub>W6</sub> = 1, critical T<sub>m</sub> = 1000. Top row: the polymerization rate of V (<i>k</i><sub>V7</sub>) and W (<i>k</i><sub>W7</sub>) are identical. Middle row: k<sub>W7</sub> = 10. Bottom row: <i>k</i><sub>W7</sub> = 100. In the last two cases, <i>k<sub>V7</sub></i> = 1. Volume and surface variables are omitted from the figure. Initial amounts: 100 A<sub>1</sub>, 100 X, 100 <i>p</i>V(0), 100 <i>p</i>W(0), 100 T<sub>m</sub> and 1 Growth. Influx rate of X is 10; Z<sub>1</sub> and Z<sub>2</sub> are still constant.</p>", "links"=>[], "tags"=>["chemoton", "influx"], "article_id"=>425923, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["István Zachar", "Anna Fedor", "Eörs Szathmáry"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021380.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dynamics_of_the_chemoton_with_two_different_templates_p_V_and_p_W_when_the_main_food_molecule_X_has_a_low_influx_rate_/425923", "title"=>"Dynamics of the chemoton with two different templates, <i>p</i>V and <i>p</i>W, when the main food molecule (X) has a low influx rate.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:39:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/755171"], "description"=>"<p>T<sub>m</sub>…T<sub>m+k</sub> represent the boundary subsystem, A<sub>1</sub>…A<sub>5</sub> represent the metabolic subsystem and pV(0)…pV(n−1) and pW(0)…pW(n−1) represent two different template polymerization cycles (informational subsystems), T<sub>1</sub> and T<sub>2</sub>. Z<sub>1</sub>, Z<sub>2</sub> and X are food molecules. See text for further details.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary biology"], "article_id"=>425540, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["István Zachar", "Anna Fedor", "Eörs Szathmáry"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021380.g001", "stats"=>{"downloads"=>3, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chemoton_with_two_templates_/425540", "title"=>"Chemoton with two templates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:36:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/755409"], "description"=>"<p><i>k</i><sub>V6</sub> = <i>k</i><sub>V7</sub> = <i>k</i><sub>W6</sub> = 1, critical T<sub>m</sub> = 1000. Top row: the polymerization rate of V (<i>k</i><sub>V7</sub>) and W (<i>k</i><sub>W7</sub>) are identical (1). Middle row: <i>k</i><sub>W7</sub> = 10. Bottom row: <i>k</i><sub>W7</sub> = 100. In the last two cases, <i>k</i><sub>V7</sub> = 1. Volume and surface variables are omitted from the figure. Initial amounts: 100 A<sub>1</sub>, 100 <i>p</i>V(0), 100 <i>p</i>W(0), 100 T<sub>m</sub> and 1 Growth. X has constant amount at 20, Z<sub>1</sub> and Z<sub>2</sub> at 10. Note that since division is set to a 100 times slower than in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021380#pone-0021380-g002\" target=\"_blank\">Figures 2</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021380#pone-0021380-g004\" target=\"_blank\">4</a>, removal of molecules is actually slower than growth. This has no effect on the outcome of the simulation, as the removal process is deterministic. ∑A<i><sub>i</sub></i> stands for the total amount of all metabolites, ∑<i>p</i>V<i><sub>i</sub></i> and ∑<i>p</i>W<i><sub>j</sub></i> for the total amount of all <i>p</i>V and <i>p</i>W polymer stages, respectively.</p>", "links"=>[], "tags"=>["chemoton", "molecules"], "article_id"=>425785, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["István Zachar", "Anna Fedor", "Eörs Szathmáry"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021380.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dynamics_of_the_chemoton_with_two_different_templates_p_V_and_p_W_when_the_concentration_of_food_molecules_is_constant_/425785", "title"=>"Dynamics of the chemoton with two different templates, <i>p</i>V and <i>p</i>W, when the concentration of food molecules is constant.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:38:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/755289"], "description"=>"<p>A: The food molecule X has an initial amount of 200 and is constantly added to the system with a low rate (10). B: The influx rate of X is increased (200). C: X has a constant amount (10), representing a stable outside world. Runs were initialized with 200 A<sub>1</sub>, 20 <i>p</i>V(0), 10 T<sub>m</sub> and 1 Growth. Critical T<sub>m</sub> is at 200. ∑A<sub>i</sub> stands for the total amount of all metabolites, ∑<i>p</i>V<sub>i</sub> for the total amount of all <i>p</i>V polymer stages.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary biology"], "article_id"=>425671, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["István Zachar", "Anna Fedor", "Eörs Szathmáry"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021380.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Stochastic_behavior_of_the_chemoton_/425671", "title"=>"Stochastic behavior of the chemoton.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:37:44"}

PMC Usage Stats | Further Information

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Relative Metric

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