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.

<p><i>k</i>_V6 = <i>k</i>_V7 = <i>k</i>_W6 = 1, critical T_m = 1000. Top row: the polymerization rate of V (<i>k</i>_V7) and W (<i>k</i>_W7) are identical. Middle row: k_W7 = 10. Bottom row: <i>k</i>_W7 = 100. In the last two cases, <i>k_V7</i> = 1. Volume and surface variables are omitted from the figure. Initial amounts: 100 A₁, 100 X, 100 <i>p</i>V(0), 100 <i>p</i>W(0), 100 T_m and 1 Growth. Influx rate of X is 10; Z₁ and Z₂ are still constant.</p

Analysis of coexistence of two sequences of length according to method M3.

<p>Second column shows the number of scanned sequences (the whole combined sequence space for all investigated ). The third column shows the fraction of coexisting sequences, i.e. the probability of coexistence of two sequences with a given parameter set (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003193#pcbi.1003193.s009" target="_blank">Text S1</a>). (S) indicates that all cases of coexistence are locally asymptotically stable. The fourth column shows the average of the leading eigenvalues (if coexistence exists) as a measure of stability.</p

Template and copy are either different (thin) or identical (bold) for complementary (top) and homologous pairing (bottom) due to strand polarity.

<p>Reverse (top left) and direct palindromes (bottom middle) yield two identical templates with complementary and homologous pairing, respectively, just like homologous pairing with parallel polarity. Note, that in case of reverse palindromes, it is not necessary for the sequence itself to be palindromic to make the two strands identical. Cases of complementary pairing with antiparallel polarity (top left and middle) and homologous pairing with parallel polarity (bottom right) are discussed in the main text; homologous pairing with antiparallel polarity (bottom left and middle) is discussed in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003193#pcbi.1003193.s009" target="_blank">Text S1</a>. The remaining case (top right) is not discussed here.</p

Stabilizing selection increases robustness of sequences.

<p>The percentage of the random sequences having lower fraction of 1-step neutral mutants among all 1-step mutants () than the original sequence (green bars) and the best sequence after 5000 generations of stabilizing selection (orange bars). Sequences are ordered according to their length. Exact are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109987#pone.0109987.s001" target="_blank">Table S1</a>.</p

Analysis of coexistence of complementary pairs of sequences of length according to method M1.

<p>Second column shows the number of scanned sequences (and the amount as a fraction of the whole combined sequence space). The third column shows the fraction of coexisting sequences in the scanned domain, i.e. the probability of coexistence of random sequence groups of size with a given parameter set. (S) indicates that all cases of coexistence are locally asymptotically stable. The fourth column shows the average of the leading eigenvalues (if there is coexistence) as a measure of stability. For parameters, see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003193#pcbi.1003193.s009" target="_blank">Text S1</a>.</p

Analysis of coexistence of two sequences of length according to method M4.

<p>Second column shows the number of scanned sequences (and the amount as a fraction of the whole sequence space). The third column shows the fraction of coexisting sequences averaged over the scanned sequence pairs and the 1000 random parameter sets. For parameters, see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003193#pcbi.1003193.s009" target="_blank">Text S1</a>.</p

Stochastic behavior of the chemoton.

<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 A₁, 20 <i>p</i>V(0), 10 T_m and 1 Growth. Critical T_m is at 200. ∑A_i stands for the total amount of all metabolites, ∑<i>p</i>V_i for the total amount of all <i>p</i>V polymer stages.</p

Analysis of coexistence of complementary pairs of length according to method M2.

<p>Second column shows the number of scanned sequences (and the amount as a fraction of the combined sequence space). The third column shows the fraction of coexisting sequences averaged over the scanned sequence groups and over 1000 random degradation rate sets for intermediates (for parameters, see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003193#pcbi.1003193.s009" target="_blank">Text S1</a>).</p

Error thresholds of secondary structure classes (SSCs).

<p>The graphs depict the critical per digit replication accuracies (error thresholds) as a function of the frequency of sequences belonging to an SSC among all possible structures of (left) and (right). Open circles represent individual SSCs, solid circles represent super-SSCs (SSSC) that merge structures that only differ in the flanking single-stranded regions. Only SSCs are included that cover at least 0.1% of the total sequence space.</p

Probability of coexistence in case of non-uniform degradation rates and homologous pairing ().

<p>Each cell is an average of numerical results over 1000 random parameter setups. Purple indicates highly improbable coexistence, green indicates likely coexistence. Sequences are arranged along the axes first according to Hamming distance and secondly according to lexicographic ordering (increasing content towards bottom and right). For parameters, see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003193#pcbi.1003193.s009" target="_blank">Text S1</a>.</p