table of contents
introduction
overview
I. infectious diseases
a brief history of infectious diseases
classical infectious diseases smallpox, polio, measles, rubella, influenza
corona virus type diseases SARS, MERS, COVID-19
statistic vs. mechanistic modeling
data science vs. data-driven modeling
examples: the measles
reading: bar-on et al., SARS-CoV-2 (COVID-19) by the numbers, elife 9 (2020) e57309.
II. mathematical epidemiology
II.1. introduction to compartment modeling
concept of compartment modeling
the kermack-mc kendrick theory
the classical S, I, R model
SIR model with and without vital dynamics
examples: the plaque
reading: bauer f, compartment models in epidemiology, mathematical epidemiology (2008) 19-79.
II.2. compartment modeling of epidemiology
overview of compartment models
the M, S, E, I, R, D compartments SIR, SIS, SIRD, MSIR, SEIR, MSEIR, MSEIRS models
latent, contact, and infectious periods
examples: the measles
reading: hethcode hw, the mathematics of infectious disease, siam review 42 (2020) 599-653.
II.3. concepts of endemic disease modeling
concept of basic reproduction number
endemic equilibrium herd immunity
eradicating disease through vaccination
examples: measles
reading: dietz k, the estimation of the basic reproduction number for infectious diseases, stat meth med res 2 (1993) 23-41.
III. data-driven modeling in epidemiology
III.1. compartment modeling of COVID19
characteristic timeline of COVID-19
SIR and SEIR models for COVID-19
susceptible, exposed, infectious, and recovered populations
latent, contact, and infectious periods of COVID-19
examples: sensitivity analysis for COVID-19
reading: peirlinck m, et al. outbreak dynamics of COVID-19 in china and the united states. biomech model mechanobio 19 (2020) 2179-2193.
III.2. early outbreak dynamics of COVID-19
basic reproduction number of COVID-19
SEIR model and parameter identification of Ro
comparison with other infectious diseases and with directly measured Ro
implications for exponential growth and herd immunity
examples: parameter identification for china and the united states
reading: park et al., reconciling early-outbreak estimates of the basic reproduction number and its uncertainty. j royal soc interface 17 (2020) 20200144.
III.3. asymptomatic transmission of COVID-19
concept of asymptomatic transmission
SEIIR model
antibody seroprevalence studies
undercount and its implications on herd immunity
examples: santa clara county, new york city, heinsberg
reading: ioannis j, the invection fatality rate of COVID-19 inferred from seroprevalence data, medRxiv, doi:10.1101/2020.05.13.20101253
III.4. inferring outbreak dynamics of COVID-19
concept of data-driven modeling
bayesian SEIIR model
machine learning and bayesian methods
uncertainty quantification
inferring the beginning of the outbreak
examples: santa clara county
reading: peirlinck m et al., visualizing the invisible: the effect of asymptomatic transmission. comp meth appl mech eng. 372 (2020) 113410.
IV. modeling outbreak control
IV.1. managing infectious diseases
overview of commu
About the Author:
Ellen Kuhl is the Walter B. Reinhold Professor in the School of Engineering and Robert Bosch Chair of Mechanical Engineering at Stanford University. She is a Professor of Mechanical Engineering and, by courtesy, Bioengineering. She received her PhD from the University of Stuttgart in 2000 and her Habilitation from the University of Kaiserslautern in 2004. Her area of expertise is Living Matter Physics, the design of theoretical and computational models to simulate and predict the behavior of living systems. Ellen has published more than 200 peer-reviewed journal articles and edited two books; she is an active reviewer for more than 20 journals at the interface of engineering and medicine and an editorial board member of seven international journals in her field. She is a founding member of the Living Heart Project, a translational research initiative to revolutionize cardiovascular science through realistic simulation with 400 participants from research, industry, and medicine from 24 countries. Ellen is the current Chair of the US National Committee on Biomechanics and a Member-Elect of the World Council of Biomechanics. She is a Fellow of the American Society of Mechanical Engineers and of the American Institute for Mechanical and Biological Engineering. She received the National Science Foundation Career Award in 2010, was selected as Midwest Mechanics Seminar Speaker in 2014,
and received the Humboldt Research Award in 2016 and the ASME Ted Belytschko Applied Mechanics Award in 2021. Ellen is an All American triathlete on the Wattie Ink. Elite Team, a multiple Boston, Chicago, and New York marathon runner, and a Kona Ironman World Championship finisher.
