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The Ohio State University

1. Srivastava, Gopal Narayan. Neural network for the prediction of force differences between an amino acid in solution and vacuum.

Degree: MS, Chemistry, 2020, The Ohio State University

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 ┬Ás. 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. Advisors/Committee Members: Bruschweiler, Rafael (Advisor).

Subjects/Keywords: Chemistry; Molecular Dynamics Simulations; Neural Network; Force Prediction; Energy Prediction

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Srivastava, G. N. (2020). Neural network for the prediction of force differences between an amino acid in solution and vacuum. (Masters Thesis). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1587045375092676

Chicago Manual of Style (16th Edition):

Srivastava, Gopal Narayan. “Neural network for the prediction of force differences between an amino acid in solution and vacuum.” 2020. Masters Thesis, The Ohio State University. Accessed October 23, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1587045375092676.

MLA Handbook (7th Edition):

Srivastava, Gopal Narayan. “Neural network for the prediction of force differences between an amino acid in solution and vacuum.” 2020. Web. 23 Oct 2020.

Vancouver:

Srivastava GN. Neural network for the prediction of force differences between an amino acid in solution and vacuum. [Internet] [Masters thesis]. The Ohio State University; 2020. [cited 2020 Oct 23]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1587045375092676.

Council of Science Editors:

Srivastava GN. Neural network for the prediction of force differences between an amino acid in solution and vacuum. [Masters Thesis]. The Ohio State University; 2020. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1587045375092676

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