In-Silico Investigation of Geological and Biological Materials by Molecular Dynamics Simulations

Abstract

Molecular dynamics (MD) simulation is a computational technique that predicts the time-dependent behavior of a molecular system utilizing molecular mechanics. MD simulations are extensively employed in the scientific arena to investigate a wide range of material systems at the nanoscale (atoms and molecules), including organics, inorganics, polymer, composites, biomacromolecules, etc. This work investigates the properties of a range of geological (Green River oil shale and swelling clays) and biological materials (coronaviral proteins) at the molecular level using MD simulations. Oil shale, a sedimentary rock containing organic crude oil precursor named kerogen trapped in an inorganic mineral matrix, has long been considered an alternative source of petroleum. Molecular dynamics simulation of Green River oil shale Type I kerogen has been performed in the proximity of predominantly present calcite and quartz minerals to identify their binding interactions with trapped kerogen from the mineral matrix for efficient crude oil production. Sodium-montmorillonite (Na-MMT), a member of the smectite group, is one of the swelling clay minerals components that find various geo-environmental and industrial applications due to its high swelling capacity. Steered molecular dynamics (SMD) simulations have been performed to determine the nanomechanical properties of both dry and hydrated Na-MMT clay tactoid. Besides the geological materials, MD and SMD simulations have also been used to computationally inspect the coronaviral protein-ACE2 protein interactions to elucidate the potential reasons why COVID-19 results in significantly more infections and deaths compared to other coronaviruses. The coronaviral attachment to host cell through spike-ACE2 interactions and coronaviral replication mechanism through tri non-structural protein (nsp12-nsp7-nsp8) interactions have been simulated to understand the differences between SARS-CoV and SARSCoV-2 (COVID-19). The major findings obtained from coronaviral protein interactions may point towards the underlying reasons behind the severity of COVID-19. Moreover, the potency of different phytochemicals has been examined for breast cancer treatment. Compounds commonly found in Rhodiola, and Oregano plants extracts have been targeted against a series of breast cancer proteins utilizing molecular docking to determine the most potent phytochemical for breast cancer treatment.