Understanding the Interplay Between the Non-Valence and Valence State of the Uracil Anion Upon Mono-Hydration

Citation: Cate S. Anstöter and Spiridoula Matsika
J. Phys. Chem. A

In this work we present an ab initio investigation into the effect of mono-hydration on the interaction of uracil with low energy electrons. Electron attachment and photodetachment experimental studies have previously shown dramatic changes in uracil upon solvation with even a single water molecule, due to an inversion of the character of the ground state of the anion. Here we explore the interplay between the non-valence and valence states of the uracil anion, as a function of geometry and site of solvation. Our model provides unambiguous interpretation of previous photoelectron studies, reproducing the binding energies and photoelectron images for bare uracil and a single isomer of the U•(H2O)1 cluster. The results of this study provide insight into how electrons may attach to hydrated nucleobases. These results lay the foundations for further investigations into the effect of micro-hydration on the electronic structure and dynamics of nucleobases.

Ground state energy functional with Hartree-Fock efficiency and chemical accuracy

Yixiao Chen, Linfeng Zhang, Han Wang, Weinan E
J. Phys. Chem
arXiv: 2005.00169

We introduce the Deep Post-Hartree-Fock (DeePHF) method, a machine learning based scheme for constructing accurate and transferable models for the ground-state energy of electronic structure problems. DeePHF predicts the energy difference between results of highly accurate models such as the coupled cluster method and low accuracy models such as the the Hartree-Fock (HF) method, using the ground-state electronic orbitals as the input. It preserves all the symmetries of the original high accuracy model. The added computational cost is less than that of the reference HF or DFT and scales linearly with respect to system size. We examine the performance of DeePHF on organic molecular systems using publicly available datasets and obtain the state-of-art performance, particularly on large datasets.

Automatic machine-learning potential generation scheme and simulation protocol for the LiGePS-type superionic conductors

Jianxing Huang, Linfeng Zhang, Han Wang, Jinbao Zhao, Jun Cheng, Weinan
J. Phys. Chem. Lett.
arXiv: 2006.03320.

It has been a challenge to accurately simulate Li-ion diffusion processes in battery materials at room temperature using {\it ab initio} molecular dynamics (AIMD) due to its high computational cost. This situation has changed drastically in recent years due to the advances in machine learning-based interatomic potentials. Here we implement the Deep Potential Generator scheme to \textit{automatically} generate interatomic potentials for LiGePS-type solid-state electrolyte materials. This increases our ability to simulate such materials by several orders of magnitude without sacrificing {\it ab initio} accuracy. Important technical aspects like the statistical error and size effects are carefully investigated. We further establish a reliable protocol for accurate computation of Li-ion diffusion processes at experimental conditions, by investigating important technical aspects like the statistical error and size effects. Such a protocol and the automated workflow allow us to screen materials for their relevant properties with much-improved efficiency. By using the protocol and automated workflow developed here, we obtain the diffusivity data and activation energies of Li-ion diffusion that agree well with the experiment. Our work paves the way for future investigation of Li-ion diffusion mechanisms and optimization of Li-ion conductivity of solid-state electrolyte materials.

Pushing the limit of molecular dynamics with ab initio accuracy 100 million atoms with machine learning

W Jia, H Wang, M Chen, D Lu, J Liu, L Lin, R Car, W. E, L. Zhang
arXiv preprint arXiv:2005.00223 (2020)
Submitted to the supercomputing conference SC20
Atlanta, Nov15, 20

For 35 years, {\it ab initio} molecular dynamics (AIMD) has been the method of choice for understanding complex materials and molecules at the atomic scale from first principles. However, most applications of AIMD are limited to systems with thousands of atoms due to the high computational complexity. We report that a machine learning-based molecular simulation protocol (Deep Potential Molecular Dynamics), driven by a highly optimized code (GPU DeePMD-kit) on the Summit supercomputer, has greatly expanded the capabilities of MD simulation with {\it ab initio} accuracy, pushing its limit to simulation of over 100 million atoms for one nanosecond per day. Our code can efficiently scale up to the entire Summit supercomputer, reaching 86 PFLOPS in double precision (43% of the peak) and 137 PFLOPS in mixed precision. This success opens the door to the modeling of atomic processes in realistic materials and molecular systems with {\it ab initio} accuracy.