Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model
| Autor: | Umesh V. Waghmare, Chiranjib Bhattacharyya, Abhishek Aggarwal, Saientan Bag, Vinayak Vinayak, Prabal K. Maiti |
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| Rok vydání: | 2020 |
| Předmět: |
Coupling
Physics Quantitative Biology::Biomolecules 010304 chemical physics Artificial neural network Base pair General Chemical Engineering Matrix representation Intermolecular force Molecular electronics Charge (physics) General Chemistry DNA Library and Information Sciences 01 natural sciences 0104 chemical sciences Computer Science Applications Machine Learning 010404 medicinal & biomolecular chemistry 0103 physical sciences Feedforward neural network Neural Networks Computer Electronics Biological system Base Pairing |
| Zdroj: | Journal of chemical information and modeling. 61(1) |
| ISSN: | 1549-960X |
| Popis: | Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic couplings strongly depend on the intermolecular geometry and orientation. Estimating these electronic couplings for all the possible relative geometries of molecules using the computationally demanding first-principles calculations requires a lot of time and computational resources. In this article, we present a machine learning (ML)-based model to calculate the electronic coupling between any two bases of dsDNA/dsRNA and bypass the computationally expensive first-principles calculations. Using the Coulomb matrix representation which encodes the atomic identities and coordinates of the DNA base pairs to prepare the input dataset, we train a feedforward neural network model. Our neural network (NN) model can predict the electronic couplings between dsDNA base pairs with any structural orientation with a mean absolute error (MAE) of less than 0.014 eV. We further use the NN-predicted electronic coupling values to compute the dsDNA/dsRNA conductance. |
| Databáze: | OpenAIRE |
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