arXiv subjects

Jonathan P. Mailoa

Publications and source records attributed to Jonathan P. Mailoa.

7 recordsLinked to original sources

arXiv2023

Protein-Ligand Complex Generator & Drug Screening via Tiered Tensor Transform

The generation of small molecule candidate (ligand) binding poses in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more accurate pose generation using molecular dynamics is hindered by slow protein dynamics. We develop a tiered tensor transform (3T) algorithm to rapidly generate diverse protein-ligand complex conformations for both pose and affinity estimation in drug screening, requiring neither machine learning training nor lengthy dynamics computation, while maintaining both coarse-grain-like coordinated protein dynamics and atomistic-level details of the complex pocket. The 3T conformation structures we generate achieve significantly higher accuracy in active ligand classification than traditional ensemble docking using hundreds of experimental protein conformations. Furthermore, we demonstrate that 3T can be used to explore distant protein-ligand binding poses within the protein pocket. 3T structure transformation is decoupled from the system physics, making future usage in other computational scientific domains possible.

cs.NE↗

arXiv2023

TenCirChem: An Efficient Quantum Computational Chemistry Package for the NISQ Era

TenCirChem is an open-source Python library for simulating variational quantum algorithms for quantum computational chemistry. TenCirChem shows high performance on the simulation of unitary coupled-cluster circuits, using compact representations of quantum states and excitation operators. Additionally, TenCirChem supports noisy circuit simulation and provides algorithms for variational quantum dynamics. TenCirChem's capabilities are demonstrated through various examples, such as the calculation of the potential energy curve of $\textrm{H}_2\textrm{O}$ with a 6-31G(d) basis set using a 34-qubit quantum circuit, the examination of the impact of quantum gate errors on the variational energy of the $\textrm{H}_2$ molecule, and the exploration of the Marcus inverted region for charge transfer rate based on variational quantum dynamics. Furthermore, TenCirChem is capable of running real quantum hardware experiments, making it a versatile tool for both simulation and experimentation in the field of quantum computational chemistry.

quant-ph↗

arXiv2023

Multi-Constraint Molecular Generation using Sparsely Labelled Training Data for Localized High-Concentration Electrolyte Diluent Screening

Recently, machine learning methods have been used to propose molecules with desired properties, which is especially useful for exploring large chemical spaces efficiently. However, these methods rely on fully labelled training data, and are not practical in situations where molecules with multiple property constraints are required. There is often insufficient training data for all those properties from publicly available databases, especially when ab-initio simulation or experimental property data is also desired for training the conditional molecular generative model. In this work, we show how to modify a semi-supervised variational auto-encoder (SSVAE) model which only works with fully labelled and fully unlabelled molecular property training data into the ConGen model, which also works on training data that have sparsely populated labels. We evaluate ConGen's performance in generating molecules with multiple constraints when trained on a dataset combined from multiple publicly available molecule property databases, and demonstrate an example application of building the virtual chemical space for potential Lithium-ion battery localized high-concentration electrolyte (LHCE) diluents.

physics.chem-ph↗

arXiv2021

E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials

This work presents Neural Equivariant Interatomic Potentials (NequIP), an E(3)-equivariant neural network approach for learning interatomic potentials from ab-initio calculations for molecular dynamics simulations. While most contemporary symmetry-aware models use invariant convolutions and only act on scalars, NequIP employs E(3)-equivariant convolutions for interactions of geometric tensors, resulting in a more information-rich and faithful representation of atomic environments. The method achieves state-of-the-art accuracy on a challenging and diverse set of molecules and materials while exhibiting remarkable data efficiency. NequIP outperforms existing models with up to three orders of magnitude fewer training data, challenging the widely held belief that deep neural networks require massive training sets. The high data efficiency of the method allows for the construction of accurate potentials using high-order quantum chemical level of theory as reference and enables high-fidelity molecular dynamics simulations over long time scales.

physics.comp-ph↗

arXiv2020

A community-powered search of machine learning strategy space to find NMR property prediction models

The rise of machine learning (ML) has created an explosion in the potential strategies for using data to make scientific predictions. For physical scientists wishing to apply ML strategies to a particular domain, it can be difficult to assess in advance what strategy to adopt within a vast space of possibilities. Here we outline the results of an online community-powered effort to swarm search the space of ML strategies and develop algorithms for predicting atomic-pairwise nuclear magnetic resonance (NMR) properties in molecules. Using an open-source dataset, we worked with Kaggle to design and host a 3-month competition which received 47,800 ML model predictions from 2,700 teams in 84 countries. Within 3 weeks, the Kaggle community produced models with comparable accuracy to our best previously published "in-house" efforts. A meta-ensemble model constructed as a linear combination of the top predictions has a prediction accuracy which exceeds that of any individual model, 7-19x better than our previous state-of-the-art. The results highlight the potential of transformer architectures for predicting quantum mechanical (QM) molecular properties.

physics.comp-ph↗

arXiv2020

Accurate and scalable multi-element graph neural network force field and molecular dynamics with direct force architecture

Recently, machine learning (ML) has been used to address the computational cost that has been limiting ab initio molecular dynamics (AIMD). Here, we present GNNFF, a graph neural network framework to directly predict atomic forces from automatically extracted features of the local atomic environment that are translationally-invariant, but rotationally-covariant to the coordinate of the atoms. We demonstrate that GNNFF not only achieves high performance in terms of force prediction accuracy and computational speed on various materials systems, but also accurately predicts the forces of a large MD system after being trained on forces obtained from a smaller system. Finally, we use our framework to perform an MD simulation of Li7P3S11, a superionic conductor, and show that resulting Li diffusion coefficient is within 14% of that obtained directly from AIMD. The high performance exhibited by GNNFF can be easily generalized to study atomistic level dynamics of other material systems.

physics.comp-ph↗

arXiv2019

Fast Neural Network Approach for Direct Covariant Forces Prediction in Complex Multi-Element Extended Systems

Neural network force field (NNFF) is a method for performing regression on atomic structure-force relationships, bypassing expensive quantum mechanics calculation which prevents the execution of long ab-initio quality molecular dynamics simulations. However, most NNFF methods for complex multi-element atomic systems indirectly predict atomic force vectors by exploiting just atomic structure rotation-invariant features and the network-feature spatial derivatives which are computationally expensive. We develop a staggered NNFF architecture exploiting both rotation-invariant and covariant features separately to directly predict atomic force vectors without using spatial derivatives, thereby reducing expensive structural feature calculation by ~180-480x. This acceleration enables us to develop NNFF which directly predicts atomic forces in complex ternary and quaternary-element extended systems comprised of long polymer chains, amorphous oxide, and surface chemical reactions. The staggered rotation-invariant-covariant architecture described here can also directly predict complex covariant vector outputs from local physical structures in domains beyond computational material science.

physics.comp-ph↗