Up-Down-Up
Down-Up-Down
Output
D33
Input M1
Output D44
Input M1
Input M1
10
-3
10
-2
10
-3
10
3
1
10
-1
1
Concentration
Response
of D33
Concentration
10
-3
10
-2
10
-1
1
Input M1
10
-3
10
3
1
Response
of D44
Output
D13
Output
D33
Output
D33
Output
D13
Ratio: M1 / M2
Input
M2
Input
M1
M3
M1 = M2
Input
M2
Input
M1
M1 NOT M2
(3 monomers)
Input
M2
Input
M1
M1 NOR M2
Input
M2
Input
M1
Input M1
Input M2
Input M1
Input M1
Input M1
Concentration
10
-3
10
3
1
10
-3
10
-3
10
3
Dimer D13
10
-3
10
3
1
10
-3
10
-3
10
3
Dimer D33
10
-3
10
3
1
Dimer D33
10
-3
10
3
1
10
-1
10
-3
10
1
10
-1
10
1
10
-1
10
1
1
10
-3
10
3
1
10
-3
10
3
1
1
1
10
-3
10
3
Dimer D13
Output
D22
Switch Off
Input M1
Input M1
10
-3
10
-1
10
-3
10
3
1
10
1
Concentration
Response
of D22
M2
Inverted Bump Function
Input M1
Output
D44
Input M1
10
-3
10
-3
10
3
1
1
10
-2
10
-1
Response
of D44
M2
M3
M4
Bump Function
Input M1
Output
D33
Input M1
10
-3
10
-3
10
3
1
1
10
-2
10
-1
Response
of D33
M2
M3
Switch On
Input M1
Output
D33
10
-1
Input M1
10
-3
10
-3
10
3
1
10
1
Response
of D33
M2
M3
M2
M3
M4
M2
M3
M4
M5
M3
M3
M3
M1 NOT M2
(4 monomers)
M1 NAND M2
M1 ≠ M2
Output
D44
Input
M2
Input
M1
M1 XNOR M2
Output
D55
Input
M2
Input
M1
M5
M3
M4
Two-input Bump Function
M1 AND M2
Out-
put
D12
M3
M4
M1 OR M2
Input
M2
Input
M1
Output D44
Input
M2
Input
M1
XOR Gate
Input M1
Input M2
Input M1
Input M1
Input M1
Concentration
10
-3
10
3
1
10
-1
10
-1
10
-3
10
1
10
1
10
-3
10
3
Dimer D12
10
-3
10
3
1
10
-3
10
-3
10
3
Dimer D34
10
-3
10
3
1
10
-1
10
-3
10
1
10
-3
10
3
Dimer D44
10
-3
10
3
1
10
-1
10
-3
10
1
10
-3
10
3
Dimer D13
Input M1
Input M2
Input M1
Input M1
Input M1
Concentration
10
-3
10
3
1
10
-2
10
-3
10
-1
10
-3
10
3
Dimer D66
10
-3
10
3
1
10
-3
10
-2
10
-1
1
10
-3
10
3
Dimer D55
10
-3
10
3
1
10
-3
10
-3
10
3
Dimer D55
10
-3
10
3
1
10
-3
10
2
10
-3
10
3
Dimer D44
1
1
1
1
1
1
1
1
1
10
-1
10
1
Output
D13
Input
M2
Input
M1
M3
M4
Input
M2
Input
M1
Output
D34
M3
M4
M3
M5
M6
M4
Output
D66
Input
M2
Input
M1
Output
D55
Input
M2
Input
M1
M3
M4
M5
M3
M4
M3
M4
A
B
H
G
2
3
4
5
6
7
8
9
10
11
12
Network Size
0.0
0.5
1.0
Fraction
Fraction Dimers Perturbed
and Non-zero (1 input)
Local Extrema:
0
1
2
3
4
10
-7
10
-5
10
-3
1
2
3
4
5
6
7
8
9
10
11
12
Network Size
Fraction of
Responses
Local Extrema
Network Size
3
4
5
6
7
8
9
10
11
12
2
C
F
E
D
10
2
10
4
10
2
10
5
10
4
10
3
10
6
10
2
10
3
10
4
10
3
10
2
Networks Sampled
Networks Sampled
Unique Functions
Discovered
Bootstrap Sampling of
1-input Networks
Bootstrap Sampling of
2-input Networks
10
-5
10
-3
10
-7
1
Local Extrema:
0
1
2
3
4
Original K Range
Limited K Range
Fraction of Responses
Local Extrema
Observed
10
-4
10
-2
1
0
1
2
3
4
Dimer Distance
from Input
Fraction
Perturbed Dimers
Propagation of
Perturbations
Unique Functions: Measured
Unique Functions: Random Combinations
I
2
4
6
8
10
12
Network Size
0
50,000
100,000
150,000
200,000
250,000
Unique 2-input, 2-output
Functions by Network Size
2
4
6
8
10
12
Network Size
0
20,000
40,000
60,000
80,000
Unique Discretized
Functions
Unique 1-input, 2-output
Functions by Network Size
Input 1
Input 2
Output 1
Output 2
Compare to Random
Combinations: