Density functional theory calculations of large systems: Interplay between fragments, observables, and computational complexity

Abstract

In the past decade, developments of computational technology around density functional theory (DFT) calculations have considerably increased the system sizes which can be practically simulated. The advent of robust high performance computing algorithms which scale linearly with system size has unlocked numerous opportunities for researchers. This fact enables computational physicists and chemists to investigate systems of sizes which are comparable to systems routinely considered by experimentalists, leading to collaborations with a wide range of techniques and communities. This has important consequences for the investigation paradigms which should be applied to reduce the intrinsic complexity of quantum mechanical calculations of many thousand atoms. It becomes important to consider portions of the full system in the analysis, which have to be identified, analyzed, and employed as building‐blocks from which decomposed physico‐chemical observables can be derived. After introducing the state‐of‐the‐art in the large scale DFT community, we will illustrate the emerging research practices in this rapidly expanding field, and the knowledge gaps which need to be bridged to face the stimulating challenge of the simulation of increasingly realistic systems. This article is categorized under: Electronic Structure Theory > Density Functional Theory Software > Simulation Methods Structure and Mechanism > Computational Materials Science

Anticipating future SARS-CoV-2 variants of concern through ab initio quantum mechanical modeling

“…Given an access to a modern supercomputer, hundreds of simulations can be performed in a time frame of one hour. interaction network of the SARS-CoV-2 main protease with its natural peptidic substrates, derived from traditional FF analysis, and the equivalent FBO network [21].…”

“…However, these mechanisms are independent of the QM treatment, and the investigation of such contributions can be effectively performed by coupling our model to other mechanistic treatments, such as polarizable force fields or advanced docking techniques. In addition, we here employ a common, well-established DFT approximation (PBE+D3), which already provides useful information for coarse-grained quantities and trends [21,35], and aptly fits the aim of intensive, high-throughput simulations of several structures, especially in their relaxed positions [45]. Yet, we leave out arguments about the choice of other ab initio levels of theory, which may shed light on more quantitative aspects related to processes beyond the ground-state: reaction coordinates, activation barriers, etc.…”

“…By focusing on the SARS-CoV-2 spike interaction with select substrates relevant to viral fitness, such as host cell receptor ACE2 and nAbs, we characterize elements of the spike's evolutionary trajectory and offer predictions on how it will progress. Only recently [21,34] has the progress in computing capabilities enabled QM simulations of molecular interactions which include tens of thousands of atoms, capturing biological processes involving several hundreds of amino acids. In turn, the SARS-CoV-2 pandemic has recently and rapidly made available a plethora of state-of-the-art biochemical and structural data, facilitating a full QM representation of specific molecular systems.…”

“…(see e.g. [21] for some examples). Here, we perform ab initio QM modeling of one such case: the binding of the SARS-CoV-2 spike RBD with select substrates.…”

Técnicas experimentais e teóricas aplicadas ao estudo de inibidores orgânicos de corrosão em meio ácido

“…Os cálculos TFD têm avançado nas últimas décadas devido ao avanço de tecnologias e de máquinas mais robustas sendo possível fazer cálculos que antes era inviável em termos de custos computacionais aumentando a viabilidade de sua aplicação em sistemas com um maior número de átomos (Dawson et al, 2021).…”