Catalytic Network Evolution Model - Reference Material

Chapter 4
Population Dynamics
4.1
The population dynamics equation
Chapter 4. Population Dynamics
4.2
Attractors of the population dynamics equation
4.2. Attractors of the population dynamics equation
4.3
Attractor shape theorem
4.4
The attractor for a graph with no ACS
4.5
The dominant ACS of a graph
4.6. Examples of the attractor for specic graphs
1
2
4
3
5
6
7
4.6
Examples of the attractor for specic graphs
a)
b)
c)
d)
e)
f)
g)
a)
e1 = ( 1 0 0 0 0 0 0 )
e2 = ( 0 0 0 1 0 0 0 ) T
T
e3 = ( 0 0 0 0 0 0 1 )
b)
1
e1 = ( 1 1 0 0 0 0 0 0 0 0 0 0 ) / 2
T
e2 = ( 0 0 0 0 1 1 0 0 0 0 0 0 ) / 2
7
10
11
12
e3 = ( 0 0 0 0 0 0 0 0 0 0 1 1 ) / 2
4.7
Timescale for reaching the attractor
4.8
Core and periphery of a graph
4.9. Keystone nodes
a)
b)
c)
5
1
1=1.00
Keystone nodes
1
4
4
2
4
2
4.9
d)
2
3
1=1.19
4
2
1=1.36
1=1.52
a)
b)
1
1
3
2
Chapter 5
Graph Dynamics
5.1
Graph dynamics rules
Chapter 5. Graph Dynamics
Node with least Xi
Population
Dynamics
(step 1)
Selection
(step 2)
New node
Novelty
(step 3)
5.2. Features of the graph dynamics
5.2
Features of the graph dynamics
5.2.1 Evolution in a prebiotic pool
5.2.2 Coupling of population and graph dynamics: two timescales
5.2.3 Absence of self-replicators
200
180
p=0.005
160
number of links
140
120
p=0.001
100
p=0.0025
80
60
40
no selection
20
1000
2000
3000
5.2.4 Selection and novelty
4000
5000
n
6000
7000
8000
9000
10000
5.3. Implementation
5.3
Implementation
5.4
Results of graph evolution
110
100
100
90
80
70
60
50
40
30
s1
20
10
0
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5000
n
6000
7000
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9000
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n
6000
7000
8000
9000
10000
5000
n
6000
7000
8000
9000
10000
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100 1
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120
100
80
60
40
s1
20
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2000
3000
4000
250
100
200
150
100
s
50
1000
2000
3000
4000
5.4. Results of graph evolution
60
50
interdependency
40
30
20
10
0
0
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4000
6000
8000
10000
100
90
80
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60
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37
95
35
96
34
97
75
Chapter 6
Formation and Growth of

Autocatalytic Sets
6.1
The random phase
Chapter 6. Formation and Growth of Autocatalytic Sets
95
96
97
51
67
36
38
3
21
81 56
39 10
66
84
54
52
85
61
41
93
47
74
87
32
62
77
43
31
27
37
17
35
34
26
63
19
13
70
42
15
24
65
72
75
78
92
99
69
80
40
18
16
53
23
68
22
48
94
83
98
79
20
82
49
50
76
33
46
30
91
45
55
25
86
100
28
64
11
90
71
12
73
29
58
57
59
88
89
44
60
14
6.1. The random phase
0.1
0.01
Pin (k)
0.001
0.0001
1e-05
1e-06
1e-07
-1
0.1
0.01
Pout (k)
0.001
0.0001
1e-05
1e-06
1e-07
-1
2
k
0.1
0.01
0.001
D(d)
0.0001
1e-05
1e-06
1e-07
1e-08
1e-09
0
8
d
6.2
The growth phase
10
12
14
6.2. The growth phase
6.2.1 Timescale for growth of the dominant ACS
12
11
ln( g )
10
5
-11
-10
-9
-8
ln(p)
6.3
Fully autocatalytic graphs
-7
-6
-5
6.3. Fully autocatalytic graphs
84
35
21
12
61
88
30
53
65
64
81
33
52
18
36
14
96
34
78
28
80
66
37
58
41 50
63
89
42
62
60
45
24 29
56
54
4
20
49
9
48
55
73 8
59
19
32
72
39
77
69
44
70
47
91
43
57
92
99
74
94
98
26
79
17
85
90
25
68
16
71
13
46 51
95
82
15
22
38
100
10
23
86
87
40
76
83
27
11 75
67
31
97
93

Catalytic Network Evolution Model - Reference Material

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Chapter 4

The population dynamics equation

Chapter 4. Population Dynamics

Attractors of the population dynamics equation

4.2. Attractors of the population dynamics equation

Chapter 4. Population Dynamics

Attractor shape theorem

The attractor for a graph with no ACS

The dominant ACS of a graph

4.6. Examples of the attractor for specic graphs

Examples of the attractor for specic graphs

Chapter 4. Population Dynamics

4.6. Examples of the attractor for specic graphs

Chapter 4. Population Dynamics

4.6. Examples of the attractor for specic graphs

Chapter 4. Population Dynamics

Timescale for reaching the attractor

Core and periphery of a graph

4.9. Keystone nodes

Chapter 4. Population Dynamics

Graph dynamics rules

Chapter 5. Graph Dynamics

Node with least Xi

5.2. Features of the graph dynamics

Features of the graph dynamics

5.2.1 Evolution in a prebiotic pool

5.2.2 Coupling of population and graph dynamics: two timescales

5.2.3 Absence of self-replicators

Chapter 5. Graph Dynamics

5.2.4 Selection and novelty

Results of graph evolution

Chapter 5. Graph Dynamics

5.4. Results of graph evolution

Chapter 5. Graph Dynamics

5.4. Results of graph evolution

Chapter 5. Graph Dynamics

5.4. Results of graph evolution

Chapter 5. Graph Dynamics

5.4. Results of graph evolution

Chapter 5. Graph Dynamics

Formation and Growth of

The random phase

Chapter 6. Formation and Growth of Autocatalytic Sets

6.1. The random phase

Chapter 6. Formation and Growth of Autocatalytic Sets

The growth phase

6.2. The growth phase

6.2.1 Timescale for growth of the dominant ACS

Chapter 6. Formation and Growth of Autocatalytic Sets

Fully autocatalytic graphs

6.3. Fully autocatalytic graphs

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