Construct a simulation of self-replicating RNA polymers to model their evolution over time and explore the emergence of new functions through selection and mutation processes.
The RNA world hypothesis asserts that self-replicating RNA polymers arose before DNA genome and coded proteins. Most of the literature on the origin of life focuses on chemical and biological approaches, so there is a greater need for statistical and computational models to simulate what the origin of life was like: specifically, the origins and evolution of self-replicating information polymers.
Some theoretical biologists have proposed computational origin of life models, such as Stuart Kauffman's autocatalytic sets and Manfred Eigen's quasispecies model, to describe the origin and evolution of replicating polymers. In Eigen's model, he defines a transition matrix that denotes the probability of a given k-mer mutating to another k-mer of equal length, constituting a Markov chain.
The central challenge of this project is as follows: construct a simulation of self-replicating RNA polymers and characterize its evolution over time, showing how new functions can emerge from selection acting on random mutational processes. This project has applications for mRNA design, mRNA therapeutics, and mRNA vaccines.
Provide instructions on how to install and set up the project, such as installing dependencies and preparing the environment.
# Example command to install dependencies (Python)
pip install project-dependencies
# Example command to install dependencies (R)
install.packages("project-dependencies")Provide a basic usage example or minimal code snippet that demonstrates how to use the project.
# Example usage (Python)
import my_project
demo = my_project.example_function()
print(demo)# Example usage (R)
library(my_project)
demo <- example_function()
print(demo)Add detailed information and examples on how to use the project, covering its major features and functions.
# More usage examples (Python)
import my_project
demo = my_project.advanced_function(parameter1='value1')
print(demo)# More usage examples (R)
library(demoProject)
demo <- advanced_function(parameter1 = "value1")
print(demo)Contributions are welcome! If you'd like to contribute, please open an issue or submit a pull request. See the contribution guidelines for more information.
If you have any issues or need help, please open an issue or contact the project maintainers.
This project is licensed under the MIT License.