Methane adsorption of nanocomposite shale in the presence of water: Insights from molecular simulations

S Babaei, H Ghasemzadeh, S Tesson - Chemical Engineering Journal, 2023 - Elsevier
Accurately predicting gas adsorption in shale gas is essential for estimating production
capacity and optimizing extraction processes. However, the complex nature of shale …

Mesoscale simulations: an indispensable approach to understand biomembranes

AL Duncan, W Pezeshkian - Biophysical Journal, 2023 - cell.com
Computer simulation techniques form a versatile tool, a computational microscope, for
exploring biological processes. This tool has been particularly effective in exploring different …

Multiscale simulation of fluids: coupling molecular and continuum

ER Smith, PE Theodorakis - Physical Chemistry Chemical Physics, 2024 - pubs.rsc.org
Computer simulation is an important tool for scientific progress, especially when lab
experiments are either extremely costly and difficult or lack the required resolution. However …

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles

A Conev, MM Rigo, D Devaurs… - Briefings in …, 2023 - academic.oup.com
Proteins are dynamic macromolecules that perform vital functions in cells. A protein structure
determines its function, but this structure is not static, as proteins change their conformation …

Impact of loading-dependent intrinsic framework flexibility on adsorption in UiO-66

PB Shukla, JK Johnson - The Journal of Physical Chemistry C, 2022 - ACS Publications
The vast majority of molecular simulations of adsorption in porous materials make use of the
assumption that the framework of the porous material may be held rigid without significantly …

Elucidating the inhibitory mechanism of Zika virus NS2B-NS3 protease with dipeptide inhibitors: Insights from molecular docking and molecular dynamics simulations

S Ullah, F Ullah, W Rahman, A Ullah, S Haider… - Plos one, 2024 - journals.plos.org
Microcephaly, Guillain-Barré syndrome, and potential sexual transmission stand as
prominent complications associated with Zika virus (ZIKV) infection. The absence of FDA …

Efficient determination of free energies of non-ideal solid solutions via hybrid Monte Carlo simulations

Z Li, S Scandolo - Computer Physics Communications, 2024 - Elsevier
Predicting the phase diagram of solid solutions is crucial for understanding their physical
behavior under various conditions and at different compositions. However, conventional …

[HTML][HTML] Helium expansion Revisited: Effects of accessible volume on excess adsorption in kerogen matrices

B Liu, S Babaei, M Kanduč, S Tian, L Bai, Y Xu… - Chemical Engineering …, 2024 - Elsevier
Enhancing our understanding of the excess adsorption capacity in shale gas reservoirs is
paramount for accurately predicting production capabilities and refining extraction …

MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC

B Crawford, U Timalsina, CD Quach… - Journal of Chemical …, 2023 - ACS Publications
MoSDeF-GOMC is a python interface for the Monte Carlo software GOMC to the Molecular
Simulation Design Framework (MoSDeF) ecosystem. MoSDeF-GOMC automates the …

GRACE: Generative Redesign in Artificial Computational Enzymology

RE Hu, CH Yu, IS Ng - ACS Synthetic Biology, 2024 - ACS Publications
Designing de novo enzymes is complex and challenging, especially to maintain the activity.
This research focused on motif design to identify the crucial domain in the enzyme and …