African Physics Newsletter

What use is physics for a pandemic?

SARS-CoV-2(2019-nCoV)coronavirusmainprotease,withinhibitorinturquoise.

Physicists are at the forefront of the fight against coronavirus.

Tonight in Africa, we are washing our hands as we face curfews, closed borders, and lockdowns.

It is, however, worth remembering how strongly these decisions are based on science. As physicists, we readily understand the simpler models of epidemiology.

The Susceptible-Infected-Recovered model

A glance at the article on compartmental models in epidemiology on Wikipedia reminds me of my first encounters with modelling in Applied Mathematics classes. The Susceptible-Infected-Recovered model, described in this article, is strongly dependent on the reproduction number: the expected number of people directly infected by one case, in a population where everyone is susceptible.

The model is a set of ordinary differential equations, and the nature of the solution depends strongly on the basic reproduction number. In our terms as physical scientists, reducing the basic reproduction number is the reason why we practice social distancing and quarantine.

Sirsys p9

An epidemiological graph for the SIR model (Blue=Susceptible, Green=Infected, and Red=Recovered)

 A spatial distribution model

The same article shows the simplest of spatial distribution models: students of algorithmic models will recognise this as a cellular automaton model. Each cell can infect the 8 cells around it at a rate determinedby the probability of infection, and the simulation proceeds in time steps.

Control of borders and ports of entry are the boundary conditions that we are setting for the spatial development of this disease.

SIR model simulated using python

SIR model simulated in python. The 100x100 matrix is first randomly seeded. A value of 1 indicates a person is recovered, a value that is larger than 0.5 indicates a person is infected, and a value that is less than 1 indicates a person is susceptible. In this case, an infected person can spread the disease to the eight people around him/her, with people on the border as an exception. The outermost ring of points are not included as the simulation, and should be considered as irrelevant. (Andrew Luo, CC BY-SA 3.0)

Molecular modelling

Many physicists collaborate in molecular modelling or electronic structure method groups. It is an eye-opener that this community shares its results fast and generously through the Protein DataBase (PDB): these are results from X-ray crystallography.

Not surprisingly, the Molecule of the Month is part of theSARS-CoV-2 coronavirus. The single long strand of RNA, RiboNucleic Acid, in the virus uses the amino acids in the infected cell to build just two long strings of proteins joined together. They are cut into functional parts by the protease to make the machinery to construct new virions.

Need for more science in Africa

If the protease can be jammed, the virus replication can be inhibited. ​Unfortunately, a lot of these inhibitors are harmful to the host - that's the main problem in sorting out the potential treatments from the weed-killers.

What could be a more compelling illustration of the impact of physics this month? Our global community of scientists has provided the tools with which we can understand the most practical and simple steps to take – saving lives by social distancing – and the most sophisticated ways forward, through rational drug design to find lead molecules for treatment. These are the reasons why we ask our governments to foster science, to research the diseases of Africa ​in Africa​, and to set scientific advisors in place.

This month and in the months ahead, we wish you good health and safety for you and your community.

Igle Gledhill, South Africa

This article has first been published by the African Physics Newsletter. © American Physical Society, 2020

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