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Neural network for the prediction of force differences between an amino acid in solution and vacuum

Srivastava, Gopal Narayan
http://rave.ohiolink.edu/etdc/view?acc_num=osu1587045375092676

Abstract Details

2020, Master of Science, Ohio State University, Chemistry.
Molecular dynamics simulations are widely used to study dynamics of molecular structure. The impact of molecular dynamics simulation in the field of chemistry and biology has expanded drastically in past decade. The simulations capture properties and behavior of biological macromolecules at atomistic level with a fine temporal resolution. Molecular dynamics simulations use implicit and explicit solvents. Explicit solvents are more accurate but add to the size of the simulation box, limiting the duration of simulations to hundreds of µs. To be able to study MD systems at larger time scale we introduce a neural network-based method that uses solute coordinates to output solvation energy and in turn giving the forces exerted by solvents. Using the amino acids and their dipeptide coordinates, interatomic distances were calculated and used in the neural network to get energies. Out of twenty amino acid dipeptides, six amino acid dipeptides, ALA, TYR, ASP, GLN, LYS and GLY gave an energy difference average of ~100 kJmol-1.
Rafael Bruschweiler, Prof (Advisor)
Marcos Sotomayor, Dr (Committee Member)
147 p.
Chemistry
Molecular Dynamics Simulations; Neural Network; Force Prediction; Energy Prediction

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Citations

  • Srivastava, G. N. (2020). Neural network for the prediction of force differences between an amino acid in solution and vacuum [Master's thesis, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1587045375092676

    APA Style (7th edition)

  • Srivastava, Gopal. Neural network for the prediction of force differences between an amino acid in solution and vacuum. 2020. Ohio State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1587045375092676.

    MLA Style (8th edition)

  • Srivastava, Gopal. "Neural network for the prediction of force differences between an amino acid in solution and vacuum." Master's thesis, Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1587045375092676

    Chicago Manual of Style (17th edition)

osu1587045375092676
130
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