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The COVID-19 pandemic has led to unprecedented efforts to identify drugs that can reduce its associated morbidity/mortality rate. Computational chemistry approaches hold the potential for triaging potential candidates far more quickly than…
The development of quantum computing for molecular simulations is constrained by the limited number of qubits available on current Noisy Intermediate-Scale Quantum (NISQ) devices. The present work introduces the Virtual Orbital…
OpenFMO framework, an open-source software (OSS) platform for Fragment Molecular Orbital (FMO) method, is extended to multi-physics simulations (MPS). After reviewing the several FMO implementations on distributed computer environments, the…
We present our perspective and goals on highperformance computing for nanoscience in accordance with the global trend toward "peta-scale computing." After reviewing our results obtained through the grid-enabled version of the fragment…
Despite the recent progress in quantum computational algorithms for chemistry, there is a dearth of quantum computational simulations focused on material science applications, especially for the energy sector, where next generation sorbing…
The fragment molecular orbital (FMO) scheme is one of the popular fragmentation-based methods and has the potential advantage of making the circuit flat in quantum chemical calculations on quantum computers. In this study, we used a…
Quantum computers are special purpose machines that are expected to be particularly useful in simulating strongly correlated chemical systems. The quantum computer excels at treating a moderate number of orbitals within an active space in a…
We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including…
There remains an urgent need to identify existing drugs that might be suitable for treating patients suffering from COVID-19 infection. Drugs rarely act at a single molecular target, with off target effects often being responsible for…
The main source of reduced nitrogen for living things comes from nitrogenase, which converts N2 to NH3 at the FeMo-cofactor (FeMo-co). Because of its role in supporting life, the uncertainty surrounding the catalytic cycle, and its…
Structure-based Deep Fusion models were recently shown to outperform several physics- and machine learning-based protein-ligand binding affinity prediction methods. As part of a multi-institutional COVID-19 pandemic response, over 500…
To shorten the time required to find effective new drugs, like antivirals, a key parameter to consider is membrane permeability, as a compound intended for an intracellular target with poor permeability will have low efficacy. Here, we…
The world has witnessed unprecedented human and economic loss from the COVID-19 disease, caused by the novel coronavirus SARS-CoV-2. Extensive research is being conducted across the globe to identify therapeutic agents against the…
The COVID-19 crisis called for rapid reaction from all the fields of biomedical research. Traditional drug development involves time consuming pipelines that conflict with the urgence of identifying effective therapies during a health and…
The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome -- millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of…
Molecular orbital (MO) is one of the most fundamental concepts for molecules, relating to all branches of chemistry, while scanning tunneling microscopy (STM) has been widely recognized for its potential to measure the spatial distribution…
A new, very fast, implementation of the exact (Fock) exchange operator for electronic structure calculations within the plane-wave pseudopotential method is described in detail for both molecular and periodic systems, and carefully…
Metal Organic Frameworks (MOFs) are promising materials to help mitigate the effects of global warming by selectively absorbing $\text{CO}_{2}$ for direct capture. Accurate quantum chemistry simulations are a useful tool to help select and…
The non-orthogonal local submatrix method applied to electronic-structure based molecular dynamics simulations is shown to exceed 1.1 EFLOP/s in FP16/FP32 mixed floating-point arithmetic when using 4,400 NVIDIA A100 GPUs of the Perlmutter…
The method of increments and frozen natural orbital (MI-FNO) framework is introduced to help expedite the application of noisy, intermediate-scale quantum~(NISQ) devices for quantum chemistry simulations. The MI-FNO framework provides a…