abp_sirs_contagion_dynamics
MATLAB and HOOMD scripts to simulate contagion dynamics in a collection of active Brownian particles
Science Score: 44.0%
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Repository
MATLAB and HOOMD scripts to simulate contagion dynamics in a collection of active Brownian particles
Basic Info
- Host: GitHub
- Owner: khair-group
- License: mit
- Language: Python
- Default Branch: main
- Size: 53.7 KB
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- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
abpsirscontagion_dynamics
MATLAB and HOOMD scripts to simulate contagion dynamics in a collection of active Brownian particles
In the description that follows, S=Susceptible, I=Infected, and R=Recovered. See https://en.wikipedia.org/wiki/Compartmentalmodelsin_epidemiology for a detailed discussion on compartmental models in epidemiology.
(1) The folder "macroscopic_model" consists of MATLAB scripts that solve a system of coupled ordinary differential equations governing the time evolution of {S,I,R} populations. Within this folder:
(i) "transient_evolution_contagion_dynamics.mlx" plots the transient population as a function of time.
(ii) "sir_model_engine.m" is a function with the same computational function as (i), except that it returns the
time series of {S,I,R} and does not plot anything.
(iii) "steady_state_results_contagion_dynamics.m" is a driver routine that calls (ii) and stores the steady-state
values of {S,I,R} for a range of epidemiological constants {\beta,\gamma,\alpha}.
The macroscopic model codes are slightly modified versions of the material uploaded by Giovanni Valentini on Mathworks File Exchange [https://www.mathworks.com/matlabcentral/fileexchange/75100-sir-epidemic-spread-model].
The microscopic model for contagion dynamics considers each member of the various populations as a self-propelled agent, i.e., an active Brownian particle.
(2) The file "microscopicmodelprotocol_A.py" is a HOOMD script that implements the one-to-one protocol (Protocol A) in the microscopic model for contagion dynamics, in which each infected agent can potentially transmit the disease to only one susceptible agent within a contagion radius.
(3) The file "microscopicmodelprotocol_B.py" is a HOOMD script that implements the one-to-many protocol (Protocol B) in the microscopic model for contagion dynamics, in which each infected agent can potentially transmit the disease to many susceptible agents within a contagion radius.
Owner
- Name: khair-group
- Login: khair-group
- Kind: organization
- Location: United States of America
- Repositories: 1
- Profile: https://github.com/khair-group
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Kailasham" given-names: "R." - family-names: "Khair" given-names: "Aditya S." title: "Contagion dynamics in active Brownian particle systems" date-released: 2023-05-24 url: "https://github.com/khair-group/abp_sirs_contagion_dynamics"