biological-computation / crn-engine Goto Github PK

I think the simulation of ClassicDSD has rounding / precision issues.

When does the issue arise?
When simulation CRN in ClassicDSD where the rate constants are numbers with very different magnitudes.

How can one produce the problem?
Simulate the following CRN

directive simulation { final=20; points=1000}
directive simulator stochastic

| On + A->{1} On + A + A
| On + A + A+ A->{1E-15} 

| 200 A
| 1 On

What happens?
The A population grows and the second reaction never occurs. The grows continues way beyond 10^6 x A.

What should happen?
Once the A populiton is large enough, the second reaction should be
come very likely. This should disable the system. Other tools predict that this happens around 10^5 x A. But basically always before 10^6 x A.

They produce the same interface (at least for ClassicDSD). So what's the difference?

If I just run the .exe that was build, the server only listens to ports from the local machine (127.0.0.1:8084).
How can I run the server so that it listens to external requests (0.0.0.0:8084)?

For that matter: What if I want to deploy the HTML5 version? Is that easier?

I am not sure if VisualDSD can simulate strand displacement when an internal toehold is used to initiate the reaction. The invading strand did not pair with the toehold in this case. This is shown below, where no reaction takes place.

The second picture below shows what I would expect to happen, the only difference being that it is external now. Am I missing a possible directive or is this a bug?

I also have Nupack simulations which show that the structure of the complex to the left of the toehold shouldn't affect how the toehold is attached. Below is the code I used in VisualDSD to generate the reactions, where the commented line is the external toehold.

directive simulation {
  final=600; 
  plots=[Backbone();Access()];
}
directive simulator deterministic
directive parameters [k=0.003;u=0.1]
directive compilation detailed
directive polymers

directive rendering {mode = nucleotides}
directive unproductive

dom tag = {bind=k;unbind=u;colour="red"}
dom val0 = {bind=k;unbind=u;colour="green"}
dom val1 = {bind=k;unbind=u;colour="blue"}
//def Backbone() = {cap}<tag^>[reg1]
def Backbone() = [reg0]:<tag^>[reg1]
def Access() = {tag^* reg1*}
( 1 Backbone()
| 1 Access()
)

In classical DSD programming, the following reactions occur normally, but in the new programming language they do not.


The reaction can occur by adding ^ to the foothold s1 and s2, but the reaction is irreversible.