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Pathak, Shivesh

Publications and source records attributed to Pathak, Shivesh.

8 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Building an ab initio solvated DNA model using Euclidean neural networks

Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine-learned electron density model based on a Euclidean neural network framework that includes a built-in understanding of equivariance to model explicitly solvated double-stranded DNA. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Accurate tight-binding model for twisted bilayer graphene describes topological flat bands without geometric relaxation

A major hurdle in understanding the phase diagram of twisted bilayer graphene is the roles of lattice relaxation and electronic structure on isolated band flattening near magic twist angles. Here in this work, the authors develop an accurate local environment tight-binding model fit to tight-binding parameters computed from ab initio density-functional theory calculations across many atomic configurations. With the accurate parametrization, it is found that the magic angle shifts to slightly lower angles than often quoted, from around 1.05° to around 0.99°, and that isolated flat bands appear for rigidly rotated graphene layers, with enhancement of the flat bands when the layers are allowed to distort. Study of the orbital localization supports the emergence of fragile topology in the isolated flat bands without the need for lattice relaxation.

36 MATERIALS SCIENCE↗