Written exam Introduction Computational Science 23 October 2019, 13.00 - 16.00, OMHP D0.08 ‘This exam has 3 assignments. Each assignment has equal weight inthe inal grade, 10 2 points] | What is Uncertainty Quantification? ‘2A Whatisa continuous time model? 72 Whats an endemic sate? (3. Whatis the Critical Community Size (CCS)? A Whats a Poisson process? ‘Assignment 2 [10 points] Consider an SIR type mode! with four compartments: the Susceptible compartment with X individuals; the Recovered compartment with Z individuals; and two compartments of infoted individuals, the ‘travelling infected compartment with ¥; individuals and the non-travelling infected compartment with Yor individuals. Finally, isthe total number of individuals. As susceptible individuals become infected, assume they always first become a travelling infected individual. Suscepetble individuals canbe infected both by welling and non-ravelling infected individuals. We assume frequency dependent transmission and writ the force of infection as A = BrX E+ BypX BE, ‘The rationale of travelling versus non-traveling infected individuals is that some persons feel so sick ‘that they stay at home, while others are also infectious but sill ravel around in the community 1 tela than By vice, and explin wy. (1 pin) “Travelling infected individuals ean become non-eaelling individuals at arate @. And both travelling and non-travelling individuals can recover, with rates Yr and yr respectively, and move tothe Recovered compartment. ‘We assume no demography. 2. Write the equations for this SIR model in terms of X,Y, YrsZ (I poist) 3 Derive the fixed points for thie model (2 points) 4 Does the model have an endemic state? Explain why? (1 point) ‘We will now apply this model to childhood diseases, First, we take into account vaccination, so ‘susceptible individuals are vaceinated immediately aftr birth, before they become infected, Assume @ birth rate u, wit births only in the Susceptible compartment, and assume deaths in all compartments, ‘with equal death rates, which isthe same asthe birth rate, a. Also assume that upon birth, a fraction p is vaccinated, so they are protected from the infection and are no longer susceptible. 5 Update your model fom (2) taking into account demography and vaccination (I point) ‘Your updated model has asa special case the standard SIR model with demography as was introduced and discussed at length during the lectures. 6 What special parameter settings are needed to find the standard SIR model with demography from ‘your updated mode! from (5), and demonstrate tis indeed produces the standard SIR mode! with ‘demography. (1 point) In order to produce yearly outbreaks (of childhood diseases) one ingredient is still missing in the updated model from (5)7. Described what is missing to give yeutly outbreaks in the model, and based on your knowledge of the standard SIR with demography model, what kindof dynamics could you expect? (2 points) Finally, consider éynamic variability in childhood disease incidence in real data. The graph below is. based on Figure 5.16 from Keeling and Rohani, Case reports for measles in London 1944 to 1988. The black line demonstrates weekly reported cases, withthe gray ine depicting the per capita birth rat. ‘The dashed grey line demonstrates effective birth rate, correcting for vaccination, that started in 1968. 1950 1960 «1970 = «1980 Year 8 Describe the ypes of dynamics that you observe, and relate this back to what you know about SIR ‘models with seasonal forcing (1 point) Assignment 3 {10 points) Consider stochastic models for spreading of infectious diseases, 1 What are the five hallmarks of dynamics of such models? (1 point) 2. One of those hallmarks is stochastic extinction. What is it, and when is this most likely to happen? @ points) 13. What is a metapopulation model in infectious disease modelling? (1 point) ‘Consider two subpopulations with a one-way coupling, meaning population | is coupled to population Bubatacviceve Ako aon et poplin | gs nh ee a 4 Assuming that population 2 i also deterministic, formulate the SIR equations with demography fetes ouped populations, You may assume xual Sires nd recovery aes in oth populations (1 point) For these two coupled deterministic models, now assume that an infection is introduced in population 1 and that population 2 is fully susceptible. Also assume that this infection has a basic reproductive ratio that allows it to spread and cause an epidemic 5 Explain in words the dynamics inthis coupled model (1 point) Finally assume that population 2is too small to be considered fully deterministic. Replace the model population 2 now wih a stochastic SIR model 6 What do you observe now? Take the strength of coupling between population I and ? into account in your discussion (2 points) Finally consider @ metapopulation model with two metapopulaton, where both metapopulations are small and are modelled with a discrete event model. Within each of the subpopulations we assume the standard SIR with demography. 7) Te implement the standard SIR with demography in a discrete event model would require 6 events, What are these events? No need to also mention the rates at which these events happen. (I point) ‘The coupling between both subpopulations is via commuting. 8 What additional events are required to model commuting? Again, No need to also mention the rates at which these events happen. (1 pot) Page 20f2