Toward resilient water-energy-food systems under shocks: Understanding the impact of migration, pandemics, and natural disasters

B Daher, S Hamie, K Pappas, M Nahidul Karim… - Sustainability, 2021 - mdpi.com
The historic pandemic faced by the international community today boldly demonstrates the
complexity and interconnectedness of the resource challenges we must better understand …

The impact of uncertainty on predictions of the CovidSim epidemiological code

W Edeling, H Arabnejad, R Sinclair… - Nature Computational …, 2021 - nature.com
Epidemiological modelling has assisted in identifying interventions that reduce the impact of
COVID-19. The UK government relied, in part, on the CovidSim model to guide its policy to …

Mastering the scales: a survey on the benefits of multiscale computing software

D Groen, J Knap, P Neumann… - … of the Royal …, 2019 - royalsocietypublishing.org
In the last few decades, multiscale modelling has emerged as one of the dominant
modelling paradigms in many areas of science and engineering. Its rise to dominance is …

Rapid, accurate, precise, and reliable relative free energy prediction using ensemble based thermodynamic integration

AP Bhati, S Wan, DW Wright… - Journal of chemical …, 2017 - ACS Publications
The accurate prediction of the binding affinities of ligands to proteins is a major goal in drug
discovery and personalized medicine. The time taken to make such predictions is of similar …

Large scale study of ligand–protein relative binding free energy calculations: actionable predictions from statistically robust protocols

AP Bhati, PV Coveney - Journal of Chemical Theory and …, 2022 - ACS Publications
The accurate and reliable prediction of protein–ligand binding affinities can play a central
role in the drug discovery process as well as in personalized medicine. Of considerable …

FACS: a geospatial agent-based simulator for analysing COVID-19 spread and public health measures on local regions

I Mahmood, H Arabnejad, D Suleimenova… - Journal of …, 2022 - Taylor & Francis
The recent Covid-19 outbreak has had a tremendous impact on the world, and many
countries are struggling to help incoming patients and at the same time, rapidly enact new …

Rapid and reliable binding affinity prediction of bromodomain inhibitors: a computational study

S Wan, AP Bhati, SJ Zasada, I Wall… - Journal of chemical …, 2017 - ACS Publications
Binding free energies of bromodomain inhibitors are calculated with recently formulated
approaches, namely ESMACS (enhanced sampling of molecular dynamics with …

[HTML][HTML] Multiscale computing in the exascale era

S Alowayyed, D Groen, PV Coveney… - Journal of Computational …, 2017 - Elsevier
We expect that multiscale simulations will be one of the main high performance computing
workloads in the exascale era. We propose multiscale computing patterns as a generic …

Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand–Protein Interactions and Allostery in SARS-CoV-2 Targets

AP Bhati, A Hoti, A Potterton, MK Bieniek… - Journal of Chemical …, 2023 - ACS Publications
We subject a series of five protein–ligand systems which contain important SARS-CoV-2
targets, 3-chymotrypsin-like protease (3CLPro), papain-like protease, and adenosine ribose …

Simulating refugee movements: Where would you go?

D Groen - Procedia Computer Science, 2016 - Elsevier
The challenge of understanding refugee movements is huge and affects countries
worldwide on a daily basis. Yet, in terms of simulation, the challenge appears to have been …