Leak-resilient enzyme-free nucleic acid dynamical systems through shadow cancellation

DNA strand displacement (DSD) emerged as a prominent reaction motif for engineering nucleic acid-based computational devices with programmable behaviors. However, strand displacement circuits are susceptible to background noise that disrupts the circuit behavior, commonly known as leaks. The side effects of leaks are particularly severe in circuits with complex dynamical elements (e.g., feedback loops), as their leaks amplify nonlinearly, disrupting the circuit function. Shadow cancellation is a dynamic leak-elimination strategy originally proposed to control the leak growth in such circuits. However, the kinetic restrictions of the proposed method introduce a significant design overhead, making it less accessible. In this work, we use domain-level DSD simulations to examine the method's capabilities, the inner workings of its components, and, most importantly, robustness to practical deviations in its design requirements. First, we show that the method could stabilize the dynamics of s..., , , # Leak-resilient enzyme-free nucleic acid dynamical systems through shadow cancellation

## Abbreviations

1. RPS: Rock-Paper-Scissors oscillator
2. UNIAMP: Unimolecular autocatalytic amplifier
3. BIAMP: Bimolecular autocatalytic amplifier

## Basic commands

To run the peppercorn command to generate the `*_enum.pil` file and the corresponding plotting data

* `$FOLDER` - The folder containing the `.pil` file
* `$NAME` - The name of the `.pil` file without the file extension
* `$INTERMEDIATE_PREFIX` - Prefix of the intermediates generated
* `$LABELS` - Space separated list of the chemical species that need to be tracked
* `$TIME`  - Time to run the simulation for 

`./sim.sh $FOLDER $TIME $NAME $LABELS $INTERMEDIATE_PREFIX` 

To run the `*_enum.pil` file in the folder `$FOLDER`

* `$NAME` - The name of the `.*_enum_pil` file without the `_enum.pil`

`./pil.sh $FOLDER $TIME $NAME $LABELS $NAME` 

## Produce-Helper Leak mechanism

`sLeakWaste = hcjr( fcr mcr scr + fcr( hckr...