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geneticalgorithmnetworkhamiltonian

Genetic algorithm for automated network Hamiltonian model discovery

https://github.com/ggrazioli/geneticalgorithmnetworkhamiltonian

Science Score: 54.0%

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Repository

Genetic algorithm for automated network Hamiltonian model discovery

Basic Info
  • Host: GitHub
  • Owner: ggrazioli
  • License: mit
  • Language: R
  • Default Branch: main
  • Size: 18.6 KB
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  • Watchers: 1
  • Forks: 0
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Created almost 3 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.md

geneticAlgorithmNetworkHamiltonian

DOI

Genetic algorithm for automated network Hamiltonian model parameterization

This code implements the genetic algorithm described in the article:

"A Genetic Algorithm for Automated Parameterization of Network Hamiltonian Models of Amyloid Fibril Formation"

by: Gianmarc Grazioli, Andy Tao, Inika Bhatia, and Patrick Regan

currently under review at Journal of Physical Chemistry B - American Chemical Society preprint: https://chemrxiv.org/engage/chemrxiv/article-details/64a3d048ba3e99daef7c671a

This main function carries out automated discovery of network Hamiltonian models that can self-assemble into the 2-ribbon amyloid fibril topological structure. The example used in the main function is very similar to the code used to generate the figure in the aforementioned article showing the evolution of different generations of models as the genetic algorithm converges on a region of parameter space that produces maximal fibril yield for 2-ribbon type amyloid fibril structures. To give an idea of run time, this main function runs in under 10 minutes on a 2019 MacBook Pro with a 2.4 GHz 8-Core Intel Core i9 processor and 64 GB of RAM. Users who wish to apply the genetic algorithm toward developing network Hamiltonian models for a particular graph structure of interest should use main.R script as a guide for developing their script, and also modify fibril_assay.R so that it determines membership in in the user's graph structure of interest.

Code written by Gianmarc Grazioli

Owner

  • Name: Gianmarc Grazioli
  • Login: ggrazioli
  • Kind: user
  • Company: San José State University, Department of Chemistry

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Grazioli"
  given-names: "Gianmarc"
  orcid: "https://orcid.org/0000-0003-2559-5103"
title: "Genetic Algorithm for Parameterizing Network Hamiltonians"
version: 0.1.0
doi: 10.5281/zenodo.8172363
date-released: 2023-7-21
url: "https://doi.org/10.5281/zenodo.8172363"

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