Simulation of pandemics in real cities: enhanced and accurate digital laboratories

A. Alexiadis; A. Albano; A. Rahmat; M. Yildiz; A. Kefal; M. Ozbulut; N. Bakirci; D. A. Garzón-Alvarado; C. A. Duque-Daza; J. H. Eslava-Schmalbach

doi:10.1098/rspa.2020.0653

Simulation of pandemics in real cities: enhanced and accurate digital laboratories

A. Alexiadis, A. Albano, A. Rahmat, M. Yildiz, A. Kefal, M. Ozbulut, N. Bakirci, D. A. Garzón-Alvarado, C. A. Duque-Daza, J. H. Eslava-Schmalbach

Research output: Contribution to journal › Article › peer-review

142 Downloads (Pure)

Abstract

This study develops a modelling framework for simulating the spread of infectious diseases within real cities. Digital copies of Birmingham (UK) and Bogotá (Colombia) are generated, reproducing their urban environment, infrastructure and population. The digital inhabitants have the same statistical features of the real population. Their motion is a combination of predictable trips (commute to work, school, etc.) and random walks (shopping, leisure, etc.). Millions of individuals, their encounters and the spread of the disease are simulated by means of high-performance computing and massively parallel algorithms for several months and a time resolution of 1 minute. Simulations accurately reproduce the COVID-19 data for Birmingham and Bogotá both before and during the lockdown. The model has only one adjustable parameter calculable in the early stages of the pandemic. Policymakers can use our digital cities as virtual laboratories for testing, predicting and comparing the effects of policies aimed at containing epidemics. [Abstract copyright: © 2021 The Authors.]

Original language	English
Article number	20200653
Number of pages	28
Journal	Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
Volume	477
Issue number	2245
DOIs	https://doi.org/10.1098/rspa.2020.0653
Publication status	Published - 27 Jan 2021

Bibliographical note

Funding Information:
Data accessibility. The code used for the simulations is freely available under the GNU General Public License v3 and can be downloaded from the University of Birmingham repository http://edata.bham.ac.uk/545/. Competing interests. We declare we have no competing interests. Funding. This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) grant no. EP/S019227/1. The computations described in this paper were performed using (i) University of Birmingham’s BlueBEAR HPC service and (ii) Athena at HPC Midlands+ (funded by the EPSRC with grant no. EP/P020232/1). Acknowledgements. The authors would like to thank Prof. Mikhail Prokopenko (Centre for Complex Systems, University of Sydney), Prof. Philip Kuchel (School of Life and Environmental Sciences, University of Sydney) and Dr Lucy Gabriela Delgado (Public Health Laboratories Subdirectorate, Bogota’s District Health Secretary) for their advice and comments. The authors would also like to acknowledge the support with Athena of Dr Simon Branford at Birmingham’s IT Research Group. Simulation for the sensitivity and statistical analysis of the Bogotá model was carried out on the ARCHER UK National Supercomputing Service (http://www. archer.ac.uk).

Publisher Copyright:
© 2021 The Authors.

Keywords

COVID-19
discrete epidemiology
epidemiology
numerical modelling
particle-based methods

ASJC Scopus subject areas

General Mathematics
General Engineering
General Physics and Astronomy

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1098/rspa.2020.0653Licence: Creative Commons: Attribution (CC BY)

AlexiadisA2021SimulationFinal published version, 6.26 MBLicence: Creative Commons: Attribution (CC BY)

A Computing Framework for Disclosure for Discrete Multiphysics
Alexiadis, A. (Principal Investigator)
Engineering & Physical Science Research Council
1/01/19 → 30/06/21
Project: Research Councils

LAMMPS code for "Simulation of Pandemics in Real-cities: Enhanced and Accurate Digital-labs"
Alexiadis, A. (Creator), University of Birmingham, 11 Sept 2020
DOI: 10.25500/edata.bham.00000545
Dataset

Cite this

Alexiadis, A., Albano, A., Rahmat, A., Yildiz, M., Kefal, A., Ozbulut, M., Bakirci, N., Garzón-Alvarado, D. A., Duque-Daza, C. A., & Eslava-Schmalbach, J. H. (2021). Simulation of pandemics in real cities: enhanced and accurate digital laboratories. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 477(2245), Article 20200653. https://doi.org/10.1098/rspa.2020.0653

@article{e56dd16ad01b48e7bfc3a4b7e1fc943e,

title = "Simulation of pandemics in real cities: enhanced and accurate digital laboratories",

abstract = "This study develops a modelling framework for simulating the spread of infectious diseases within real cities. Digital copies of Birmingham (UK) and Bogot{\'a} (Colombia) are generated, reproducing their urban environment, infrastructure and population. The digital inhabitants have the same statistical features of the real population. Their motion is a combination of predictable trips (commute to work, school, etc.) and random walks (shopping, leisure, etc.). Millions of individuals, their encounters and the spread of the disease are simulated by means of high-performance computing and massively parallel algorithms for several months and a time resolution of 1 minute. Simulations accurately reproduce the COVID-19 data for Birmingham and Bogot{\'a} both before and during the lockdown. The model has only one adjustable parameter calculable in the early stages of the pandemic. Policymakers can use our digital cities as virtual laboratories for testing, predicting and comparing the effects of policies aimed at containing epidemics. [Abstract copyright: {\textcopyright} 2021 The Authors.]",

keywords = "COVID-19, discrete epidemiology, epidemiology, numerical modelling, particle-based methods",

author = "A. Alexiadis and A. Albano and A. Rahmat and M. Yildiz and A. Kefal and M. Ozbulut and N. Bakirci and Garz{\'o}n-Alvarado, {D. A.} and Duque-Daza, {C. A.} and Eslava-Schmalbach, {J. H.}",

note = "Funding Information: Data accessibility. The code used for the simulations is freely available under the GNU General Public License v3 and can be downloaded from the University of Birmingham repository http://edata.bham.ac.uk/545/. Competing interests. We declare we have no competing interests. Funding. This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) grant no. EP/S019227/1. The computations described in this paper were performed using (i) University of Birmingham{\textquoteright}s BlueBEAR HPC service and (ii) Athena at HPC Midlands+ (funded by the EPSRC with grant no. EP/P020232/1). Acknowledgements. The authors would like to thank Prof. Mikhail Prokopenko (Centre for Complex Systems, University of Sydney), Prof. Philip Kuchel (School of Life and Environmental Sciences, University of Sydney) and Dr Lucy Gabriela Delgado (Public Health Laboratories Subdirectorate, Bogota{\textquoteright}s District Health Secretary) for their advice and comments. The authors would also like to acknowledge the support with Athena of Dr Simon Branford at Birmingham{\textquoteright}s IT Research Group. Simulation for the sensitivity and statistical analysis of the Bogot{\'a} model was carried out on the ARCHER UK National Supercomputing Service (http://www. archer.ac.uk). Publisher Copyright: {\textcopyright} 2021 The Authors.",

year = "2021",

month = jan,

day = "27",

doi = "10.1098/rspa.2020.0653",

language = "English",

volume = "477",

journal = "Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences",

issn = "0080-4630",

publisher = "The Royal Society",

number = "2245",

}

Alexiadis, A, Albano, A, Rahmat, A, Yildiz, M, Kefal, A, Ozbulut, M, Bakirci, N, Garzón-Alvarado, DA, Duque-Daza, CA & Eslava-Schmalbach, JH 2021, 'Simulation of pandemics in real cities: enhanced and accurate digital laboratories', Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 477, no. 2245, 20200653. https://doi.org/10.1098/rspa.2020.0653

TY - JOUR

T1 - Simulation of pandemics in real cities

T2 - enhanced and accurate digital laboratories

AU - Alexiadis, A.

AU - Albano, A.

AU - Rahmat, A.

AU - Yildiz, M.

AU - Kefal, A.

AU - Ozbulut, M.

AU - Bakirci, N.

AU - Garzón-Alvarado, D. A.

AU - Duque-Daza, C. A.

AU - Eslava-Schmalbach, J. H.

N1 - Funding Information: Data accessibility. The code used for the simulations is freely available under the GNU General Public License v3 and can be downloaded from the University of Birmingham repository http://edata.bham.ac.uk/545/. Competing interests. We declare we have no competing interests. Funding. This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) grant no. EP/S019227/1. The computations described in this paper were performed using (i) University of Birmingham’s BlueBEAR HPC service and (ii) Athena at HPC Midlands+ (funded by the EPSRC with grant no. EP/P020232/1). Acknowledgements. The authors would like to thank Prof. Mikhail Prokopenko (Centre for Complex Systems, University of Sydney), Prof. Philip Kuchel (School of Life and Environmental Sciences, University of Sydney) and Dr Lucy Gabriela Delgado (Public Health Laboratories Subdirectorate, Bogota’s District Health Secretary) for their advice and comments. The authors would also like to acknowledge the support with Athena of Dr Simon Branford at Birmingham’s IT Research Group. Simulation for the sensitivity and statistical analysis of the Bogotá model was carried out on the ARCHER UK National Supercomputing Service (http://www. archer.ac.uk). Publisher Copyright: © 2021 The Authors.

PY - 2021/1/27

Y1 - 2021/1/27

N2 - This study develops a modelling framework for simulating the spread of infectious diseases within real cities. Digital copies of Birmingham (UK) and Bogotá (Colombia) are generated, reproducing their urban environment, infrastructure and population. The digital inhabitants have the same statistical features of the real population. Their motion is a combination of predictable trips (commute to work, school, etc.) and random walks (shopping, leisure, etc.). Millions of individuals, their encounters and the spread of the disease are simulated by means of high-performance computing and massively parallel algorithms for several months and a time resolution of 1 minute. Simulations accurately reproduce the COVID-19 data for Birmingham and Bogotá both before and during the lockdown. The model has only one adjustable parameter calculable in the early stages of the pandemic. Policymakers can use our digital cities as virtual laboratories for testing, predicting and comparing the effects of policies aimed at containing epidemics. [Abstract copyright: © 2021 The Authors.]

AB - This study develops a modelling framework for simulating the spread of infectious diseases within real cities. Digital copies of Birmingham (UK) and Bogotá (Colombia) are generated, reproducing their urban environment, infrastructure and population. The digital inhabitants have the same statistical features of the real population. Their motion is a combination of predictable trips (commute to work, school, etc.) and random walks (shopping, leisure, etc.). Millions of individuals, their encounters and the spread of the disease are simulated by means of high-performance computing and massively parallel algorithms for several months and a time resolution of 1 minute. Simulations accurately reproduce the COVID-19 data for Birmingham and Bogotá both before and during the lockdown. The model has only one adjustable parameter calculable in the early stages of the pandemic. Policymakers can use our digital cities as virtual laboratories for testing, predicting and comparing the effects of policies aimed at containing epidemics. [Abstract copyright: © 2021 The Authors.]

KW - COVID-19

KW - discrete epidemiology

KW - epidemiology

KW - numerical modelling

KW - particle-based methods

UR - http://www.scopus.com/inward/record.url?scp=85100884983&partnerID=8YFLogxK

U2 - 10.1098/rspa.2020.0653

DO - 10.1098/rspa.2020.0653

M3 - Article

C2 - 33633493

SN - 0080-4630

VL - 477

JO - Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences

JF - Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences

IS - 2245

M1 - 20200653

ER -

Simulation of pandemics in real cities: enhanced and accurate digital laboratories

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

Fingerprint

Projects

A Computing Framework for Disclosure for Discrete Multiphysics

Datasets

LAMMPS code for "Simulation of Pandemics in Real-cities: Enhanced and Accurate Digital-labs"

Cite this