# From Coal and Steam to ChatGPT: Chapters in the History of Technology

Mark Twain once famously wrote in a letter from London to a New York newspaper editor:

“I have … heard on good authority that I was dead [but] the report of my death was an exaggeration.”

The same may be true of recent reports on the grave illness and possible impending death of human culture at the hands of ChatGPT and other so-called Large Language Models (LLM).  It is argued that these algorithms have such sophisticated access to the bulk of human knowledge, and can write with apparent authority on virtually any topic, that no-one needs to learn or create anything new. It can all be recycled—the end of human culture!

While there may be a kernel of truth to these reports, they are premature.  ChatGPT is just the latest in a continuing string of advances that have disrupted human life and human culture ever since the invention of the steam engine.  We—humans, that is—weathered the steam engine in the short term and are just as likely to weather the LLM’s.

## ChatGPT: What is it?

For all the hype, ChatGPT is mainly just a very sophisticated statistical language model (SLM).

To start with a very simple example of SLM, imagine you are playing a word scramble game and have the letter “Q”. You can be pretty certain that the “Q“ will be followed by a “U” to make “QU”.  Or if you have the initial pair “TH” there is a very high probability that it will be followed by a vowel as “THA…”, “THE…”, ”THI…”, “THO..” or “THU…” and possibly with an “R” as “THR…”.  This almost exhausts the probabilities.  This is all determined by the statistical properties of English.

Statistical language models build probability distributions for the likelihood that some sequence of letters will be followed by another sequence of letters, or a sequence of words (and punctuations) will be followed by another sequence of words.  The bigger the chains of letters and words, the number of possible permutations grows exponentially.  This is why SLMs usually stop at some moderate order of statistics.  If you build sentences from such a model, it sounds OK for a sentence or two, but then it just drifts around like it’s dreaming or hallucinating in a stream of consciousness without any coherence.

ChatGPT works in much the same way.  It just extends the length of the sequences where it sounds coherent up to a paragraph or two.  In this sense, it is no more “intelligent” than the SLM that follows “Q” with “U”.  ChatGPT simply sustains the charade longer.

Now the details of how ChatGPT accomplishes this charade is nothing less than revolutionary.  The acronym GPT means Generative Pre-Trained Transformer.  Transformers were a new type of neural net architecture invented in 2017 by the Google Brain team.  Transformers removed the need to feed sentences word-by-word into a neural net, instead allowing whole sentences and even whole paragraphs to be input in parallel.  Then, by feeding the transformers on more than a Terabyte of textual data from the web, they absorbed the vast output of virtually all the crowd-sourced information from the past 20 years.  (This what transformed the model from an SLM to an LLM.)  Finally, using humans to provide scores on what good answers looked like versus bad answers, ChatGPT was supervised to provide human-like responses.  The result is a chatbot that in any practical sense passes the Turing Test—if you query it for an extended period of time, you would be hard pressed to decide if it was a computer program or a human giving you the answers.  But Turing Tests are boring and not very useful.

The true value of ChatGPT is the access it has to that vast wealth of information (note it is information and not knowledge).  Give it almost any moderately technical query, and it will provide a coherent summary for you—on amazingly esoteric topics—because almost every esoteric topic has found its way onto the net by now, and ChatGPT can find it.

As a form of search engine, this is tremendous!  Think how frustrating it has always been searching the web for something specific.  Furthermore, the lengthened coherence made possible by the transformer neural net means that a first query that leads to an unsatisfactory answer from the chatbot can be refined, and ChatGPT will find a “better” response, conditioned by the statistics of its first response that was not optimal.  In a feedback cycle, with the user in the loop, very specific information can be isolated.

Or, imagine that you are not a strong writer, or don’t know the English language as well as you would like.  But entering your own text, you can ask ChatGPT to do a copy-edit, even rephrasing your writing where necessary, because ChatGPT above all else has an unequaled command of the structure of English.

Or, for customer service, instead of the frustratingly discrete menu of 5 or 10 potted topics, ChatGPT with a voice synthesizer could respond to continuously finely graded nuances of the customer’s problem—not with any understanding or intelligence, but with probabilistic likelihoods of what the solutions are for a broad range of possible customer problems.

In the midst of all the hype surrounding ChatGPT, it is important to keep in mind two things:  First, we are witnessing the beginning of a revolution and a disruptive technology that will change how we live.  Second, it is still very early days, just like the early days of the first steam engines running on coal.

## Disruptive Technology

Disruptive technologies are the coin of the high-tech realm of Silicon Valley.  But this is nothing new.  There have always been disruptive technologies—all the way back to Thomas Newcomen and James Watt and the steam engines they developed between 1712 and 1776 in England.  At first, steam engines were so crude they were used only to drain water from mines, increasing the number jobs in and around the copper and tin mines of Cornwall (viz. the popular BBC series Poldark) and the coal mines of northern England.  But over the next 50 years, steam engines improved, and they became the power source for textile factories that displaced the cottage industry of spinning and weaving that had sustained marginal farms for centuries before.

There is a pattern to a disruptive technology.  It not only disrupts an existing economic model, but it displaces human workers.  Once-plentiful jobs in an economic sector can vanish quickly after the introduction of the new technology.  The change can happen so fast, that there is not enough time for the workforce to adapt, followed by human misery in some sectors.  Yet other, newer, sectors always flourish, with new jobs, new opportunities, and new wealth.  The displaced workers often never see these benefits because they lack skills for the new jobs.

The same is likely true for the LLMs and the new market models they will launch. There will be a wealth of new jobs curating and editing LLM outputs. There will also be new jobs in the generation of annotated data and in the technical fields surrounding the support of LLMs. LLMs are incredibly hungry for high-quality annotated data in a form best provided by humans. Jobs unlikely to be at risk, despite prophesies of doom, include teachers who can use ChatGPT as an aide by providing appropriate context to its answers. Conversely, jobs that require a human to assemble information will likely disappear, such as news aggregators. The same will be true of jobs in which effort is repeated, or which follow a set of patterns, such as some computer coding jobs or data analysts. Customer service positions will continue to erode, as will library services. Media jobs are at risk, as well as technical writing. The writing of legal briefs may be taken over by LLMs, along with market and financial analysts. By some estimates, there are 300 million jobs around the world that will be impacted one way or another by the coming spectrum of LLMs.

This pattern of disruption is so set and so clear and so consistent, that forward-looking politicians or city and state planners could plan ahead, because we have been on a path of continuing waves disruption for over two hundred years.

## Waves of Disruption

In the history of technology, it is common to describe a series of revolutions as if they were distinct.  The list looks something like this:

First:          Power (The Industrial Revolution: 1760 – 1840)

Second:     Electricity and Connectivity (Technological Revolution: 1860 – 1920)

Third:        Automation, Information, Cybernetics (Digital Revolution: 1950 – )

Fourth:      Intelligence, cyber-physical (Imagination Revolution: 2010 – )

The first revolution revolved around steam power fueled by coal, radically increasing output of goods.  The second revolution shifted to electrical technologies, including communication networks through telegraph and the telephones.  The third revolution focused on automation and digital information.

Yet this discrete list belies an underlying fact:  There is, and has been, only one continuous Industrial Revolution punctuated by waves.

The Age of Industrial Revolutions began around 1760 with the invention of the spinning jenny by James Hargreaves—and that Age has continued, almost without pause, up to today and will go beyond.  Each disruptive technology has displaced the last.  Each newly trained workforce has been displaced by the last.  The waves keep coming.

Note that the fourth wave is happening now, as artificial intelligence matures. This is ironic, because this latest wave of the Industrial Revolution is referred to as the “Imagination Revolution” by the optimists who believe that we are moving into a period where human creativity is unleashed by the unlimited resources of human connectivity across the web. Yet this moment of human ascension to the heights of creativity is happening at just the moment when LLM’s are threatening to remove the need to create anything new.

So is it the end of human culture? Will all knowledge now just be recycled with nothing new added?

## A Post-Human Future?

The limitations of the generative aspects of ChatGPT might be best visualized by using an image-based generative algorithm that has also gotten a lot of attention lately. This is the ability to input a photograph, and input a Van Gogh painting, and create a new painting of the photograph in the style of Van Gogh.

In this example, the output on the right looks like a Van Gogh painting. It is even recognizable as a Van Gogh. But in fact it is a parody. Van Gogh consciously created something never before seen by humans.

Even if an algorithm can create “new” art, it is a type of “found” art, like a picturesque stone formation or a sunset. The beauty becomes real only in the response it elicits in the human viewer. Art and beauty do not exist by themselves; they only exist in relationship to the internal state of the conscious observer, like a text or symbol signifying to an interpreter. The interpreter is human, even if the artist is not.

ChatGPT, or any LLM like Google’s Bard, can generate original text, but its value only resides in the human response to it. The human interpreter can actually add value to the LLM text by “finding” sections that are interesting or new, or that inspire new thoughts in the interpreter. The interpreter can also “edit” the text, to bring it in line with their aesthetic values. This way, the LLM becomes a tool for discovery. It cannot “discover” anything on its own, but it can present information to a human interpreter who can mold it into something that they recognize as new. From a semiotic perspective, the LLM can create the signifier, but the signified is only made real by the Human interpreter—emphasize Human.

Therefore, ChatGPT and the LLMs become part of the Fourth Wave of the human Industrial Revolution rather than replacing it.

We are moving into an exciting time in the history of technology, giving us a rare opportunity to watch as the newest wave of revolution takes shape before our very eyes. That said … just as the long-term consequences of the steam engine are only now coming home to roost two hundred years later in the form of threats to our global climate, the effect of ChatGPT in the long run may be hard to divine until far in the future—and then, maybe after it’s too late, so a little caution now would be prudent.

## Resources

OpenAI ChatGPT: https://openai.com/blog/chatgpt/

Training GPT with human input: https://arxiv.org/pdf/2203.02155.pdf

Generative art: https://github.com/Adi-iitd/AI-Art

Status of Large Language Models: https://www.tasq.ai/blog/large-language-models/

The start of the Transformer: https://arxiv.org/abs/1706.03762

# Frontiers of Physics: The Year in Review (2022)

Physics forged ahead in 2022, making a wide range of advances. From a telescope far out in space to a telescope that spans the size of the Earth, from solid state physics and quantum computing at ultra-low temperatures to particle and nuclear physics at ultra-high energies, the year saw a number of firsts. Here’s a list of eight discoveries of 2022 that define the frontiers of physics.

## James Webb Space Telescope

“First Light” has two meanings: the “First Light” that originated at the beginning of the universe, and the “First Light” that is collected by a new telescope. In the beginning of this year, the the James Webb Space Telescope (JWST) saw both types of first light, and with it came first surprises.

The JWST has found that galaxies are too well formed too early in the universe relative to current models of galaxy formation. Almost as soon as the JWST began forming images, it acquired evidence of massive galaxies from only a few hundred million years old. Existing theories of galaxy formation did not predict such large galaxies so soon after the Big Bang.

Another surprise came from images of the Southern Ring Nebula. While the Hubble did not find anything unusual about this planetary nebula, the JWST found cold dust surrounding the white dwarf that remained after the explosion of the supernova. This dust was not supposed to be there, but it may be coming from a third member of the intra-nebular environment. In addition, the ring-shaped nebula contained masses of swirling streams and ripples that are challenging astrophysicists who study supernova and nebula formation to refine their current models.

## Quantum Machine Learning

Machine learning—the training of computers to identify and manipulate complicated patterns within massive data—has been on a roll in recent years, ever since efficient training algorithms were developed in the early 2000’s for large multilayer neural networks. Classical machine learning can take billions of bits of data and condense it down to understandable information in a matter of minutes. However, there are types of problems that even conventional machine learning might take the age of the universe to calculate, for instance calculating the properties of quantum systems based on a set of quantum measurements of the system.

In June of 2022, researchers at Caltech and Google announced that a quantum computer—Google’s Sycamore quantum computer—could calculate properties of quantum systems using exponentially fewer measurements than would be required to perform the same task using conventional computers. Quantum machine learning uses the resource of quantum entanglement that is not available to conventional machine learning, enabling new types of algorithms that can exponentially speed up calculations of quantum systems. It may come as no surprise that quantum computers are ideally suited to making calculations of quantum systems.

## A Possible Heavy W Boson

High-energy particle physics has been in a crisis ever since 2012 when they reached the pinnacle of a dogged half-century search for the fundamental constituents of the universe. The Higgs boson was the crowning achievement, and was supposed to be the vanguard of a new frontier of physics uncovered by CERN. But little new physics has emerged, even though fundamental physics is in dire need of new results. For instance, dark matter and dark energy remain unsolved mysteries despite making up the vast majority of all there is. Therefore, when physicists at Fermilab announced that the W boson, a particle that carries the nuclear weak interaction, was heavier than predicted by the Standard Model, some physicists heaved sighs of relief. The excess mass could signal higher-energy contributions that might lead to new particles or interactions … if the excess weight holds up under continued scrutiny.

## Imaging the Black Hole at the Center of the Milky Way

Imagine building a telescope the size of the Earth. What could it see?

If it detected in the optical regime, it could see a baseball on the surface of the Moon. If it detected at microwave frequencies, then it could see the material swirling around distant black holes. This is what the Event Horizon Telescope (EHT) can do. In 2019, it revealed the first image of a black hole: the super-massive black hole at the core of the M87 galaxy 53 million light years away. They did this Herculean feat by combining the signals of microwave telescopes from across the globe, combining their signals interferometrically to create an effective telescope aperture that was the size of the Earth.

The next obvious candidate was the black hole at the center of our own galaxy, the Milky Way. Even though our own black hole is much smaller than the one in M87, ours is much closer, and both subtend about the same solid angle. The challenge was observing it through the swirling stars and dust at the core of our galaxy. In May of this year, the EHT unveiled the first image of our own black hole, showing the radiation emitted by the in-falling material.

## Tetraneutrons

Nuclear physics is a venerable part of modern physics that harkens back to the days of Bohr and Rutherford and the beginning of quantum physics, but in recent years it has yielded few new surprises (except at the RHIC collider which smashes heavy nuclei against each other to create quark-gluon plasma). That changed in June of 2022, when researchers in Germany announced the successful measurement of a tetraneutron–a cluster of four neutrons bound transiently together by the strong nuclear force.

Neutrons are the super-glue that holds together the nucleons in standard nuclei. The force is immense, strong enough to counteract the Coulomb repulsion of protons in a nucleus. For instance, Uranium 238 has 92 protons crammed within a volume of about 10 femtometer radius. It takes 146 neutrons to bind these together without flying apart. But neutrons don’t tend to bind to themselves, except in “resonance” states that decay rapidly. In 2012, a dineutron (two neutrons bound in a transient resonance state) was observed, but four neutrons were expected to produce an even more transient resonance (a three-neutron state is not allowed). When the German group created the tetraneutron, it had a lifetime of only about 1×10-21 seconds, so it is extremely ephemeral. Nonetheless, studying the properties of the tetraneutron may give insights into both the strong and weak nuclear forces.

## Hi-Tc superconductivity

When Bednorz and Müller discovered Hi-Tc superconductivity in 1986, it set off both a boom and a crisis. The boom was the opportunity to raise the critical temperature of superconductivity from 23 K that had been the world record held by Nb3Ge for 13 years since it was set in 1973. The crisis was that the new Hi-Tc materials violated the established theory of superconductivity explained by Bardeen-Cooper-Schrieffer (BCS). There was almost nothing in the theory of solid state physics that could explain how such high critical temperatures could be attained. At the March Meeting of the APS the following year in 1987, the session on the new Hi-Tc materials and possible new theories became known as the Woodstock of Physics, where physicists camped out in the hallway straining their ears to hear the latest ideas on the subject.

One of the ideas put forward at the session was the idea of superexchange by Phil Anderson. The superexchange of two electrons is related to their ability to hop from one lattice site to another. If the hops are coordinated, then there can be an overall reduction in their energy, creating a ground state of long-range coordinated electron hopping that could support superconductivity. Anderson was perhaps the physicist best situated to suggest this theory because of his close familiarity with what was, even then, known as the Anderson Hamiltonian that explicitly describes the role of hopping in solid-state many-body phenomena.

Ever since, the idea of superexchange has been floating around the field of Hi-Tc superconductivity, but no one had been able to pin it down conclusively, until now. In a paper published in the PNAS in September of 2022, an experimental group at Oxford presented direct observations of the spatial density of Cooper pairs in relation to the spatial hopping rates—where hopping was easiest then the Cooper pair density was highest, and vice versa. This experiment provides almost indisputable evidence in favor of Anderson’s superexchange mechanism for Cooper pair formation in the Hi-Tc materials, laying to rest the crisis launched 36 years ago.

## Holographic Wormhole

The holographic principle of cosmology proposes that our three-dimensional physical reality—stars, galaxies, expanding universe—is like the projection of information encoded on a two-dimensional boundary—just as a two-dimensional optical hologram can be illuminated to recreate a three-dimensional visual representation. This 2D to 3D projection was first proposed by Gerald t’Hooft, inspired by the black hole information paradox in which the entropy of a black hole scales as surface area of the black hole instead of its volume. The holographic principle was expanded by Leonard Susskind in 1995 based on string theory and is one path to reconciling quantum physics with the physics of gravitation in a theory of quantum gravity—one of the Holy Grails of physics.

While it is an elegant cosmic idea, the holographic principle could not be viewed as anything down to Earth, until now. In November 2022 a research group at Caltech published a paper in Nature describing how they used Google’s Sycamore quantum computer (housed at UC Santa Barbara) to manipulate a set of qubits into creating a laboratory-based analog of a Einstein-Rosen bridge, also known as a “wormhole”, through spacetime. The ability to use quantum information states to simulate a highly-warped spacetime analog provides the first experimental evidence for the validity of the cosmological holographic principle. Although the simulation did not produce a physical wormhole in our spacetime, it showed how quantum information and differential geometry (the mathematics of general relativity) can be connected.

One of the most important consequences of this work is the proposal that ER = EPR (Einstein-Rosen = Einstein-Podolsky-Rosen). The EPR paradox of quantum entanglement has long been viewed as a fundamental paradox of physics that requires instantaneous non-local correlations among quantum particles that can be arbitrarily far apart. Although EPR violates local realism, it is a valuable real-world resource for quantum teleportation. By demonstrating the holographic wormhole, the recent Caltech results show how quantum teleportation and gravitational wormholes may arise from the same physics.

## Net-Positive-Energy from Nuclear Fusion

Ever since nuclear fission was harnessed to generate energy, the idea of tapping the even greater potential of nuclear fusion to power the world has been a dream of nuclear physicists. Nuclear fusion energy would be clean and green and could help us avoid the long-run disaster of global warming. However, achieving that dream has been surprisingly frustrating. While nuclear fission was harnessed for energy (and weapons) within only a few years of discovery, and a fusion “boost” was added to nuclear destructive power in the so-called hydrogen bomb, sustained energy production from fusion has remained elusive.

In December of 2022, the National Ignition Facility (NIF) focussed the power of 192 pulsed lasers onto a deuterium-tritium pellet, causing it to implode, and the nuclei to fuse, releasing about 50% more energy that it absorbed. This was the first time that controlled fusion released net positive energy—about 3 million Joules out from 2 million Joules in—enough energy to boil about 3 liters of water. This accomplishment represents a major milestone in the history of physics and could one day provide useful energy. The annual budget of the NIF is about 300 million dollars, so there is a long road ahead (probably several more decades) before this energy source can be scaled down to an economical level.

By David D. Nolte Jan. 16, 2023

# Climate Change Physics 101

When our son was ten years old, he came home from a town fair in Battleground, Indiana, with an unwanted pet—a goldfish in a plastic bag.  The family rushed out to buy a fish bowl and food and plopped the golden-red animal into it.  In three days, it was dead!

It turns out that you can’t just put a gold fish in a fish bowl.  When it metabolizes its food and expels its waste, it builds up toxic levels of ammonia unless you add filters or plants or treat the water with chemicals.  In the end, the goldfish died because it was asphyxiated by its own pee.

It’s a basic rule—don’t pee in your own fish bowl.

The same can be said for humans living on the surface of our planet.  Polluting the atmosphere with our wastes cannot be a good idea.  In the end it will kill us.  The atmosphere may look vast—the fish bowl was a big one—but it is shocking how thin it is.

Turn on your Apple TV, click on the screen saver, and you are skimming over our planet on the dark side of the Earth. Then you see a thin blue line extending over the limb of the dark disc.  Hold!  That thin blue line!  That is our atmosphere! Is it really so thin?

When you look upwards on a clear sunny day, the atmosphere seems like it goes on forever.  It doesn’t.  It is a thin veneer on the surface of the Earth barely one percent of the Earth’s radius.  The Earth’s atmosphere is frighteningly thin.

Consider Mars.  It’s half the size of Earth, yet it cannot hold on to an atmosphere even 1/100th the thickness of ours.  When Mars first formed, it had an atmosphere not unlike our own, but through the eons its atmosphere has wafted away irretrievably into space.

An atmosphere is a precious fragile thing for a planet.  It gives life and it gives protection.  It separates us from the deathly cold of space, holding heat like a blanket.  That heat has served us well over the eons, allowing water to stay liquid and allowing life to arise on Earth.  But too much of a good thing is not a good thing.

## Common Sense

If the fluid you are bathed in gives you life, then don’t mess with it.  Don’t run your car in the garage while you are working in it.  Don’t use a charcoal stove in an enclosed space.  Don’t dump carbon dioxide into the atmosphere because it also is an enclosed space.

At the end of winter, as the warm spring days get warmer, you take the winter blanket off your bed because blankets hold in heat.  The thicker the blanket, the more heat it holds in.  Common sense tells you to reduce the thickness of the blanket if you don’t want to get too warm.  Carbon dioxide in the atmosphere acts like a blanket.  If we don’t want the Earth to get too warm, then we need to limit the thickness of the blanket.

Without getting into the details of any climate change model, common sense already tells us what we should do.  Keep the atmosphere clean and stable (Don’t’ pee in our fishbowl) and limit the amount of carbon dioxide we put into it (Don’t let the blanket get too thick).

## Some Atmospheric Facts

Here are some facts about the atmosphere, about the effect humans have on it, and about the climate:

Fact 1.  Humans have increased the amount of carbon dioxide in the atmosphere by 45% since 1850 (the beginning of the industrial age) and by 30% since just 1960.

Fact 2.  Carbon dioxide in the atmosphere prevents some of the heat absorbed from the Sun to re-radiate out to space.  More carbon dioxide stores more heat.

Fact 3.  Heat added to the Earth’s atmosphere increases its temperature.  This is a law of physics.

Fact 4.  The Earth’s average temperature has risen by 1.2 degrees Celsius since 1850 and 0.8 degrees of that has been just since 1960, so the effect is accelerating.

These facts are indisputable.  They hold true regardless of whether there is a Republican or a Democrat in the White House or in control of Congress.

There is another interesting observation which is not so direct, but may hold a harbinger for the distant future: The last time the Earth was 3 degrees Celsius warmer than it is today was during the Pliocene when the sea level was tens of meters higher.  If that sea level were to occur today, all of Delaware, most of Florida, half of Louisiana and the entire east coast of the US would be under water, including Houston, Miami, New Orleans, Philadelphia and New York City.  There are many reasons why this may not be an immediate worry. The distribution of water and ice now is different than in the Pliocene, and the effect of warming on the ice sheets and water levels could take centuries. Within this century, the amount of sea level rise is likely to be only about 1 meter, but accelerating after that.

## Balance and Feedback

It is relatively easy to create a “rule-of-thumb” model for the Earth’s climate (see Ref. [2]).  This model is not accurate, but it qualitatively captures the basic effects of climate change and is a good way to get an intuitive feeling for how the Earth responds to changes, like changes in CO2 or to the amount of ice cover.  It can also provide semi-quantitative results, so that relative importance of various processes or perturbations can be understood.

The model is a simple energy balance statement:  In equilibrium, as much energy flows into the Earth system as out.

This statement is both simple and immediately understandable.  But then the work starts as we need to pin down how much energy is flowing in and how much is flowing out.  The energy flowing in comes from the sun, and the energy flowing out comes from thermal radiation into space.

We also need to separate the Earth system into two components: the surface and the atmosphere.  These are two very different things that have two different average temperatures.  In addition, the atmosphere transmits sunlight to the surface, unless clouds reflect it back into space.  And the Earth radiates thermally into space, unless clouds or carbon dioxide layers reflect it back to the surface.

The energy fluxes are shown in the diagram in Fig. 3 for the 4-component system: Sun, Surface, Atmosphere, and Space. The light from the sun, mostly in the visible range of the spectrum, is partially absorbed by the atmosphere and partially transmitted and reflected. The transmitted portion is partially absorbed and partially reflected by the surface. The heat of the Earth is radiated at long wavelengths to the atmosphere, where it is partially transmitted out into space, but also partially reflected by the fraction a’a which is the blanket effect. In addition, the atmosphere itself radiates in equal parts to the surface and into outer space. On top of all of these radiative processes, there is also non-radiative convective interaction between the atmosphere and the surface.

These processes are captured by two energy flux equations, one for the atmosphere and one for the surface, in Fig. 4. The individual contributions from Fig. 3 are annotated in each case. In equilibrium, each flux equals zero, which can then be used to solve for the two unknowns: Ts0 and Ta0: the surface and atmosphere temperatures.

After the equilibrium temperatures Ts0 and Ta0 are found, they go into a set of dynamic response equations that governs how deviations in the temperatures relax back to the equilibrium values. These relaxation equations are

where ks and ka are the relaxation rates for the surface and atmosphere. These can be quite slow, in the range of a century. For illustration, we can take ks = 1/75 years and ka = 1/25 years. The equilibrium temperatures for the surface and atmosphere differ by about 50 degrees Celsius, with Ts = 289 K and Ta = 248 K. These are rough averages over the entire planet. The solar constant is S = 1.36×103 W/m2, the Stefan-Boltzman constant is σ = 5.67×10-8 W/m2/K4, and the convective interaction constant is c = 2.5 W m-2 K-1. Other parameters are given in Table I.

The relaxation equations are in the standard form of a mathematical “flow” (see Ref. [1]) and the solutions are plotted as a phase-space portrait in Fig. 5 as a video of the flow as the parameters in Table I shift because of the addition of greenhouse gases to the atmosphere. The video runs from the year 1850 (the dawn of the industrial age) through to the year 2060 about 40 years from now.

The scariest part of the video is how fast it accelerates. From 1850 to 1950 there is almost no change, but then it accelerates, faster and faster, reflecting the time-lag in temperature rise in response to increased greenhouse gases.

## What if the Models are Wrong?  Russian Roulette

Now come the caveats.

This model is just for teaching purposes, not for any realistic modeling of climate change. It captures the basic physics, and it provides a semi-quantitative set of parameters that leads to roughly accurate current temperatures. But of course, the biggest elephant in the room is that it averages over the entire planet, which is a very crude approximation.

It does get the basic facts correct, though, showing an alarming trend in the rise in average temperatures with the temperature rising by 3 degrees by 2060.

The professionals in this business have computer models that are orders of magnitude more more accurate than this one. To understand the details of the real climate models, one needs to go to appropriate resources, like this NOAA link, this NASA link, this national climate assessment link, and this government portal link, among many others.

One of the frequent questions that is asked is: What if these models are wrong? What if global warming isn’t as bad as these models say? The answer is simple: If they are wrong, then the worst case is that life goes on. If they are right, then in the worst case life on this planet may end.

It’s like playing Russian Roulette. If just one of the cylinders on the revolver has a live bullet, do you want to pull the trigger?

## Matlab Code

```function flowatmos.m

mov_flag = 1;
if mov_flag == 1
moviename = 'atmostmp';
aviobj = VideoWriter(moviename,'MPEG-4');
aviobj.FrameRate = 12;
open(aviobj);
end

Solar = 1.36e3;		% Solar constant outside atmosphere [J/sec/m2]
sig = 5.67e-8;		% Stefan-Boltzman constant [W/m2/K4]

% 1st-order model of Earth + Atmosphere

ta = 0.53;			% (0.53)transmissivity of air
tpa0 = 0.06;			% (0.06)primes are for thermal radiation
as0 = 0.11;			% (0.11)
aa0 = 0.30;			% (0.30)
apa0 = 0.31;        % (0.31)
c = 2.5;               % W/m2/K

xrange = [287 293];
yrange = [247 251];

rngx = xrange(2) - xrange(1);
rngy = yrange(2) - yrange(1);

[X,Y] = meshgrid(xrange(1):0.05:xrange(2), yrange(1):0.05:yrange(2));

smallarrow = 1;
Delta0 = 0.0000009;
for tloop =1:80

Delta = Delta0*(exp((tloop-1)/8)-1);   % This Delta is exponential, but should become more linear over time
date = floor(1850 + (tloop-1)*(2060-1850)/79);

[x,y] = f5(X,Y);

clf
hold off
eps = 0.002;
for xloop = 1:11
xs = xrange(1) +(xloop-1)*rngx/10 + eps;
for yloop = 1:11
ys = yrange(1) +(yloop-1)*rngy/10 + eps;

streamline(X,Y,x,y,xs,ys)

end
end
hold on
[XQ,YQ] = meshgrid(xrange(1):1:xrange(2),yrange(1):1:yrange(2));
smallarrow = 1;
[xq,yq] = f5(XQ,YQ);
quiver(XQ,YQ,xq,yq,.2,'r','filled')
hold off

axis([xrange(1) xrange(2) yrange(1) yrange(2)])
set(gcf,'Color','White')

fun = @root2d;
x0 = [0 -40];
x = fsolve(fun,x0);

Ts = x(1) + 288
Ta = x(2) + 288

hold on
rectangle('Position',[Ts-0.05 Ta-0.05 0.1 0.1],'Curvature',[1 1],'FaceColor',[1 0 0],'EdgeColor','k','LineWidth',2)

posTs(tloop) = Ts;
posTa(tloop) = Ta;

plot(posTs,posTa,'k','LineWidth',2);
hold off

text(287.5,250.5,strcat('Date = ',num2str(date)),'FontSize',24)
box on
xlabel('Surface Temperature (oC)','FontSize',24)
ylabel('Atmosphere Temperature (oC)','FontSize',24)

hh = figure(1);
pause(0.01)
if mov_flag == 1
frame = getframe(hh);
writeVideo(aviobj,frame);
end

end     % end tloop

if mov_flag == 1
close(aviobj);
end

function F = root2d(xp)   % Energy fluxes

x = xp + 288;
feedfac = 0.001;      % feedback parameter

apa = apa0 + feedfac*(x(2)-248) + Delta;  % Changes in the atmospheric blanket
tpa = tpa0 - feedfac*(x(2)-248) - Delta;
as = as0 - feedfac*(x(1)-289);

F(1) = c*(x(1)-x(2)) + sig*(1-apa)*x(1).^4 - sig*x(2).^4 - ta*(1-as)*Solar/4;
F(2) = c*(x(1)-x(2)) + sig*(1-tpa - apa)*x(1).^4 - 2*sig*x(2).^4 + (1-aa0-ta+as*ta)*Solar/4;

end

function [x,y] = f5(X,Y)   % Dynamical flow equations

k1 = 1/75;   % 75 year time constant for the Earth
k2 = 1/25;   % 25 year time constant for the Atmosphere

fun = @root2d;
x0 = [0 0];
x = fsolve(fun,x0);   % Solve for the temperatures that set the energy fluxes to zero

Ts0 = x(1) + 288;   % Surface temperature in Kelvin
Ta0 = x(2) + 288;   % Atmosphere temperature in Kelvin

xtmp = -k1*(X - Ts0);   % Dynamical equations
ytmp = -k2*(Y - Ta0);

nrm = sqrt(xtmp.^2 + ytmp.^2);

if smallarrow == 1
x = xtmp./nrm;
y = ytmp./nrm;
else
x = xtmp;
y = ytmp;
end

end     % end f5

end       % end flowatmos

```

This model has a lot of parameters that can be tweaked. In addition to the parameters in the Table, the time dependence on the blanket properties of the atmosphere are governed by Delta0 and by feedfac for feedback of temperature on the atmosphere, such as increasing cloud cover and decrease ice cover. As an exercise, and using only small changes in the given parameters, find the following cases: 1) An increasing surface temperature is moderated by a falling atmosphere temperature; 2) The Earth goes into thermal run-away and ends like Venus; 3) The Earth initially warms then plummets into an ice age.

By David D. Nolte Oct. 16, 2022

## References

[1] D. D. Nolte, Introduction to Modern Dynamics: Chaos, Networks, Space and Time, 2nd Ed. (Oxford University Press, 2019)

[2] E. Boeker and R. van Grondelle, Environmental Physics (Wiley, 1995)

[3] Recent lecture at the National Academy of Engineering by John Holdren.

# The Physics of Starflight: Proxima Centauri b or Bust!

The ability to travel to the stars has been one of mankind’s deepest desires. Ever since we learned that we are just one world in a vast universe of limitless worlds, we have yearned to visit some of those others. Yet nature has thrown up an almost insurmountable barrier to that desire–the speed of light. Only by traveling at or near the speed of light may we venture to far-off worlds, and even then, decades or centuries will pass during the voyage. The vast distances of space keep all the worlds isolated–possibly for the better.

Yet the closest worlds are not so far away that they will always remain out of reach. The very limit of the speed of light provides ways of getting there within human lifetimes. The non-intuitive effects of special relativity come to our rescue, and we may yet travel to the closest exoplanet we know of.

## Proxima Centauri b

The closest habitable Earth-like exoplanet is Proxima Centauri b, orbiting the red dwarf star Proxima Centauri that is about 4.2 lightyears away from Earth. The planet has a short orbital period of only about 11 Earth days, but the dimness of the red dwarf puts the planet in what may be a habitable zone where water is in liquid form. Its official discovery date was August 24, 2016 by the European Southern Observatory in the Atacama Desert of Chile using the Doppler method. The Alpha Centauri system is a three-star system, and even before the discovery of the planet, this nearest star system to Earth was the inspiration for the Hugo-Award winning sci-fi trilogy The Three Body Problem by Chinese author Liu Cixin, originally published in 2008.

It may seem like a coincidence that the closest Earth-like planet to Earth is in the closest star system to Earth, but it says something about how common such exoplanets may be in our galaxy.

## Breakthrough Starshot

There are already plans to send centimeter-sized spacecraft to Alpha Centauri. One such project that has received a lot of press is Breakthrough Starshot, a project of the Breakthrough Initiatives. Breakthrough Starshot would send around 1000 centimeter-sized camera-carrying laser-fitted spacecraft with 5-meter-diameter solar sails propelled by a large array of high-power lasers. The reason there are so many of these tine spacecraft is because of the collisions that are expected to take place with interstellar dust during the voyage. It is possible that only a few dozen of the craft will finally make it to Alpha Centauri intact.

As these spacecraft fly by the Alpha Centauri system, possibly within one hundred million miles of Proxima Centauri b, their tiny HR digital cameras will take pictures of the planet’s surface with enough resolution to see surface features. The on-board lasers will then transmit the pictures back to Earth. The travel time to the planet is expected to be 20 or 30 years, plus the four years for the laser information to make it back to Earth. Therefore, it would take a quarter century after launch to find out if Proxima Centauri b is habitable or not. The biggest question is whether it has an atmosphere. The red dwarf it orbits sends out catastrophic electromagnetic bursts that could strip the planet of its atmosphere thus preventing any chance for life to evolve or even to be sustained there if introduced.

There are multiple projects under consideration for travel to the Alpha Centauri systems. Even NASA has a tentative mission plan called the 2069 Mission (100 year anniversary of the Moon landing). This would entail a single spacecraft with a much larger solar sail than the small starshot units. Some of the mission plans proposed star-drive technology, such as nuclear propulsion systems, rather than light sails. Some of these designs could sustain a 1-g acceleration throughout the entire mission. It is intriguing to do the math on what such a mission could look like, in terms of travel time. Could we get an unmanned probe to Alpha Centauri in a matter of years? Let’s find out.

## Special Relativity of Acceleration

The most surprising aspect of deriving the properties of relativistic acceleration using special relativity is that it works at all. We were all taught as young physicists that special relativity deals with inertial frames in constant motion. So the idea of frames that are accelerating might first seem to be outside the scope of special relativity. But one of Einstein’s key insights, as he sought to extend special relativity towards a more general theory, was that one can define a series of instantaneously inertial co-moving frames relative to an accelerating body. In other words, at any instant in time, the accelerating frame has an inertial co-moving frame. Once this is defined, one can construct invariants, just as in usual special relativity. And these invariants unlock the full mathematical structure of accelerating objects within the scope of special relativity.

For instance, the four-velocity and the four-acceleration in a co-moving frame for an object accelerating at g are given by

The object is momentarily stationary in the co-moving frame, which is why the four-velocity has only the zeroth component, and the four-acceleration has simply g for its first component.

Armed with these four-vectors, one constructs the invariants

and

This last equation is solved for the specific co-moving frame as

But the invariant is more general, allowing the expression

which yields

From these, putting them all together, one obtains the general differential equations for the change in velocity as a set of coupled equations

The solution to these equations is

where the unprimed frame is the lab frame (or Earth frame), and the primed frame is the frame of the accelerating object, for instance a starship heading towards Alpha Centauri. These equations allow one to calculate distances, times and speeds as seen in the Earth frame as well as the distances, times and speeds as seen in the starship frame. If the starship is accelerating at some acceleration g’ other than g, then the results are obtained simply by replacing g by g’ in the equations.

## Relativistic Flight

It turns out that the acceleration due to gravity on our home planet provides a very convenient (but purely coincidental) correspondence

With a similarly convenient expression

These considerably simplify the math for a starship accelerating at g.

Let’s now consider a starship accelerating by g for the first half of the flight to Alpha Centauri, turning around and decelerating at g for the second half of the flight, so that the starship comes to a stop at its destination. The equations for the times to the half-way point are

This means at the midpoint that 1.83 years have elapsed on the starship, and about 3 years have elapsed on Earth. The total time to get to Alpha Centauri (and come to a stop) is then simply

It is interesting to look at the speed at the midpoint. This is obtained by

which is solved to give

This amazing result shows that the starship is traveling at 95% of the speed of light at the midpoint when accelerating at the modest value of g for about 3 years. Of course, the engineering challenges for providing such an acceleration for such a long time are currently prohibitive … but who knows? There is a lot of time ahead of us for technology to advance to such a point in the next century or so.

## Matlab alphacentaur.m

```% alphacentaur.m
clear
format compact

g0 = 1;
L = 4.37;

for loop = 1:100

g = 0.1*loop*g0;

taup = (1/g)*acosh(g*L/2 + 1);
tearth = (1/g)*sinh(g*taup);

tauspacecraft(loop) = 2*taup;
tlab(loop) = 2*tearth;

acc(loop) = g;

end

figure(1)
loglog(acc,tauspacecraft,acc,tlab,'LineWidth',2)
legend('Space Craft','Earth Frame','FontSize',18)
xlabel('Acceleration (g)','FontSize',18)
ylabel('Time (years)','FontSize',18)
dum = set(gcf,'Color','White');
H = gca;
H.LineWidth = 2;
H.FontSize = 18;
```

## To Centauri and Beyond

Once we get unmanned probes to Alpha Centauri, it opens the door to star systems beyond. The next closest are Barnards star at 6 Ly away, Luhman 16 at 6.5 Ly, Wise at 7.4 Ly, and Wolf 359 at 7.9 Ly. Several of these are known to have orbiting exoplanets. Ross 128 at 11 Ly and Lyuten at 12.2 Ly have known earth-like planets. There are about 40 known earth-like planets within 40 lightyears from Earth, and likely there are more we haven’t found yet. It is almost inconceivable that none of these would have some kind of life. Finding life beyond our solar system would be a monumental milestone in the history of science. Perhaps that day will come within this century.

By David D. Nolte, March 23, 2022

## Further Reading

R. A. Mould, Basic Relativity. Springer (1994)

D. D. Nolte, Introduction to Modern Dynamics : Chaos, Networks, Space and Time, 2nd ed.: Oxford University Press (2019)

# Democracy against Authoritarians: The Physics of Public Opinion

An old joke goes that Democracy is a terrible form of government … except it’s better than all the others!

Our world today is faced with conflict between democracy and dictatorship. On the one side is the free world, where leaders are chosen by some form of representation of large numbers of citizens and sometimes even a majority. On the other side is authoritarianism where a select few are selected by a select few to govern everyone else.

[I]t has been said that democracy is the worst form of Government except all those other forms that have been tried from time to time; but there is the broad feeling in our country that the people should rule, and that public opinion expressed by all constitutional means, should shape, guide, and control the actions of Ministers who are their servants and not their masters.

Winston Churchill (1947)

An argument in favor of democracy is freedom of choice for the largest segment of the population, plus the ability to remove leaders who fail to provide for the perceived welfare of the most citizens. This makes democracy adaptive, shifting with the times. It also makes leaders accountable for their actions and crimes. An argument in favor of authoritarianism is the myth of the benevolent dictator–someone who knows what’s best for the people even if the people don’t know it themselves.

But dictators are rarely benevolent, and as they become saturated with power, they are corrupted. The criminal massacres, perpetrated by Putin, of Ukrainian civilians is one of the strongest recent arguments against authoritarianism. A single man decides, on a whim, the life and death of thousands or maybe more. The invasion of Ukraine is so egregious and unwarranted, that we wonder how the Russian people can put up with their isolated and manic leader. Yet by some measure more than 60% of the people in Russia approve of the war.

How can the free world see the invasion as the atrocity it is, while Russia’s majority sees it as a just war? The answer is a surprising result of population dynamics known as the replicator-mutator equation. The challenge for us here in the free world is to learn how to game the replicator-mutator equation to break up the monopoly of popular opinion and make Putin pay for his arrogance. This blog explains how “mass hysteria” can arise from forces within a complex environment, and how to construct a possible antidote.

## Replicator-Mutator Equation

There are several simple models of population dynamics that try to explain the rise and fall of the number of individuals that belong to varying cohorts within the population. These models incorporate aspects of relative benefit of one group over another, plus the chance to change sides–defection. The dynamics under these conditions can be highly nonlinear and highly non-intuitive. One of the simplest of these models is known as the replicator-mutator model where replication follows the fitness of the cohort, and where individuals can defect to a “more fit” cohort.

The basic dynamics of the model are

where xa is the fraction of the population that is in cohort a, Wab is a transition probability, and φ is the average fitness of the full population. The transition matrix is given by

where fb is the fitness of cohort b and Qba is a stochastic matrix that allows for defection of an individual from one cohort to another. The fitness of a cohort is given by

where pbc is the pay-off matrix for the relative benefit of one cohort at the expense of another. Finally the average fitness is

The Einstein implicit summation convention is assumed in all of these equations, and the metric space in which the dynamics are embedded is “flat” so that there is no essential difference between superscripts and subscripts. There is also a conservation law that the sum over all population fractions equals unity.

In the language of population dynamics, this model has frequency-dependent fitness, with defection and pay-off, in a zero-sum game.

One of the simplest questions to answer with this model is how so many people can come to believe one thing. This is known as “opinion uniformity”.

## Uniformity versus Diversity

This replicator-mutator model explains the property of opinion uniformity, as well as the opposite extreme of opinion diversity. The starting point for both is the pay-off matrix pbc which is assumed to be unity on the diagonal for b = c and to a constant factor a for b ~= c. This pay-off is symmetric so that all opinions are equally “believable”. The stochastic defection matrix is close to unity on the diagonal, and has random terms on the off-diagonal that are proportional to a constant ε. The defection matrix allows a person from one cohort to defect to the belief system of another cohort if they believe that the new cohort has more merit. Cohorts with greater merit (fitness) gain more members over time, while cohorts with lower merit have fewer members over time.

Note that the fitness increases with the number of members in the cohort. This is the bandwagon effect. A belief system is perceived to have more merit if there are more people who believe it. This clearly creates a positive feedback that would cause this cohort to grow. Even though all the cohorts have this same positive feedback, the zero-sum rule only allows one of the cohorts to grow to its maximum extent, taking members away from all the other cohorts. This is illustrated in Fig. 1. One belief system wins, taking almost the full population with it.

What allows the winner to take all is the positive feedback where the fitness of the cohort increases with the number of members, combined with the ability for that cohort to take members from other cohorts through the defection matrix.

However, all of the cohorts are trying the same thing, and the pay-off matrix is fully symmetric and equal for all cohorts, so no cohort is intrinsically “better” than another. This property opens the door to a strong alternative to opinion uniformity. In fact, as more members are allowed to defect, it creates a trend counter to winner-take-all, helping to equalize the cohorts. Suddenly, a bifurcation is passed when the winner-take-all converts discontinuously to a super-symmetric situation when all opinions are held by equal numbers of people. This is illustrated in Fig. 2 for a slightly higher defection rate ε = 0.03. The parameters are identical to those in Fig. 1, but the higher defection rate stabilizes the super-symmetric state of maximum diversity.

These two extreme results of the replicator-mutator equation, that switch suddenly from one to the other dependent on the defection rate, may seem to produce solutions neither of which are ideal for a healthy democracy. One the one hand, in the uniform case where the wining opinion is monolithic, everyone is a carbon-copy of everyone else, which is a form of cultural death (lack of diversity). But, on the other hand, one might argue that maximum opinion diversity is just as concerning, because no-one can agree on anything. If all opinions are equivalent, then everyone in the society believes something different and there is no common ground. But in the diversity case, at least there is no state-level control of the population. In the case of opinion uniformity, the wining opinion can be manipulated by propaganda.

## The Propaganda Machine

A government can “seed” the belief networks with propaganda that favors the fitness of what they want their citizens to hear. Because of the positive feedback, any slight advantage of one opinion over others can allow that opinion to gain large numbers through the bandwagon effect. Of course, even stronger control that stifles dissent, for instance by shutting down the free press, makes it that much more likely that the state-controlled story is believed. This may be one reason for the 60% (as of the writing of this blog) support Putin’s war, despite the obvious lies that are being told. This is illustrated in Fig. 3 by boosting the payoff between two similar lies that the government wants its people to believe. These rise to take about 60% of the population. Members of the cohort are brain-washed, not by the government alone, but by all their neighbors who are parroting the same thing.

## Breaking the Monopoly of Thought

How do we fight back? Not just against the Kremlin’s propaganda, but also against QANON and Trump’s Big Lie and the pernicious fallacy of nationalism? The answer is simple: diversity of thought! The sliver bullet in the replicator-mutator model is the defection matrix. The existence of a bifurcation means that a relatively small increase in the amount of diverse opinion, and the freedom to swap opinions, can lead to a major qualitative collapse of the monolithic thought, even when supported by government propaganda, as shown in Fig. 4. More people may still believe in the state-supported propaganda than the others, but it is no longer a majority.

The above models were all very homogeneous. It is more realistic that people are connected through small-world networks. In this case, there is much more diversity, as shown in Fig. 5, although the defection rate needs to be much higher to prevent a monolithic opinion from dominating. The state-supported propaganda is buried in the resulting mix of diverse ideas. Therefore, to counteract state control, people must feel free to hop about in their choice of beliefs and have access to other beliefs.

This is a bit paradoxical. On the one hand, the connectivity of the internet has fostered the rise of conspiracy theories and other odd-ball ideas. But sustained access to multiple sources of information is the best defense against all that crazy stuff winning out. In other words, not only do we have to put up with the lunatic fringe if we are to have full diversity of thought, but we need to encourage everyone to feel free to “shop around” for different ideas, even if some of them are crazy. Our free society shouldn’t be cancelling people who have divergent opinions, because that sets us down the path to authoritarianism. As a recent add said in the New York Times, “Cancel culture cancels culture.” Unfortunately, authoritarianism is on the rise around the world, and the US almost suffered that fate on Jan. 6, 2021. Furthermore, with Xi aligning with Putin and giving him the green light on Ukraine–cynically on the eve of the Olympic Games (of peace)–the new world order will revolve around that axis for decades to come, if the world survives that long. Diversity and freedom may be the only antidote.

By David D. Nolte, March 24, 2022

## Matlab Program: Repmut.m

```function repmut
% https://github.itap.purdue.edu/nolte/Matlab-Programs-for-Nonlinear-Dynamics

clear
format compact

N = 63;
p = 0.5;

mutype = 1;     % 0 = Hamming   1 = rand
pay = 1;        % 0 = Hamming   1 = 1/sqrt(N)
ep = 0.5;      % average mutation rate: 0.1 to 0.01 typical  (0.4835)

%%%%% Set original population
x0temp = rand(1,N);    % Initial population
sx = sum(x0temp);
y0 = x0temp/sx;
Pop0 = sum(y0);

%%%%% Set Adjacency

%node = makeglobal(N);
%node = makeER(N,0.25);       % 0.5     0.25
%node = makeSF(N,6);       % 12         6
node = makeSW(N,7,0.125);   % 15,0.5    7,0.5
[Adj,degree,Lap] = adjacency(node);

%%%%%% Set Hamming distance
for yloop = 1:N
for xloop = 1:N
H(yloop,xloop) = hamming(yloop-1,xloop-1);
end
end

%%%%%%% Set Mutation matrix
if mutype == 0
Qtemp = 1./(1+H/ep);    %Mutation matrix on Hamming
Qsum = sum(Qtemp,2);
mnQsum = mean(Qsum);

% Normalize mutation among species
for yloop = 1:N
for xloop = 1:N
Q(yloop,xloop) = Qtemp(yloop,xloop)/Qsum(xloop);
end
end

elseif mutype == 1
S = stochasticmatrix(N);
Stemp = S - diag(diag(S));
Qtemp = ep*Stemp;
sm = sum(Qtemp,2)';
Q = Qtemp + diag(ones(1,N) - sm);
end

figure(1)
imagesc(Q)
title('Mutation Matrix')
colormap(jet)

%%%%%%% Set payoff matrix
if pay == 1
payoff = zeros(N,N);
for yloop = 1:N
payoff(yloop,yloop) = 1;
for xloop = yloop + 1:N
payoff(yloop,xloop) = p;
payoff(xloop,yloop) = p;
payoff(1,N) = 1;    % Propaganda
payoff(N,1) = 1;
end
end
elseif pay == 0
payoff = zerodiag(exp(-1*H));
end

figure(2)
imagesc(payoff)
title('Payoff Matrix')
colormap(jet)

% Run time evolution
tspan = [0 4000];
[t,x] = ode45(@quasispec,tspan,y0);

Pop0
[sz,dum] = size(t);
Popend = sum(x(sz,:))

for loop = 1:N
fit(loop) = sum(payoff(:,loop)'.*x(sz,:));
end

phistar = sum(fit.*x(sz,:))       % final average fitness

xend = x(sz,:)
sortxend = sort(xend,'descend');
coher = sum(sortxend(1:2))

figure(3)
clf
h = colormap(lines);
for loop = 1:N
plot(t,x(:,loop),'Color',h(round(loop*64/N),:),'LineWidth',1.25)
hold on
end
hold off

figure(4)
clf
for loop = 1:N
semilogx(t,x(:,loop),'Color',h(round(loop*64/N),:),'LineWidth',1.25)
hold on
end
hold off

figure(5)
clf
for loop = 1:N
semilogy(t,x(:,loop),'Color',h(round(loop*64/N),:),'LineWidth',1.25)
hold on
end
hold off

figure(6)
clf
for loop = 1:N
loglog(t,x(:,loop),'Color',h(round(loop*64/N),:),'LineWidth',1.25)
hold on
end
hold off

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function yd = quasispec(~,y)

for floop = 1:N
f(floop) = sum(payoff(:,floop).*y);
end

Connect = Adj + eye(N);

% Transition matrix
for yyloop = 1:N
for xxloop = 1:N
W(yyloop,xxloop) = f(yyloop)*(Connect(yyloop,xxloop)*Q(yyloop,xxloop));
end
end

phi = sum(f'.*y);   % Average fitness of population

yd = W*y - phi*y;

end     % end quasispec
end

```

## Further Reading

M. A. Nowak, Evolutionary Dynamics: Exploring the Equations of Life. Cambridge, Mass.: Harvard University Press, 2006.

# Of Solar Flares, Cosmic Ray Physics and American Vikings

Exactly a thousand years ago this year an American Viking living in the Norse outpost on Straumfjord, on the northern tip of Newfoundland, took a metal axe and cut a tree.  The trimmed parts of the tree were cast away and, almost a thousand years later, were found by archeologists and stored for later study. What that study found was an exact date of the felling of the tree, in AD 1021.

How can that date be known to such precision?  The answer comes from a confluence of modern science: solar flares, cosmic ray physics, archeology, recent advances in dendrochronology, and the historiography of Icelandic sagas. The new findings were reported in the Oct. 20, 2021 issue of Nature.

## American Vikings

Snorri Thorfinnsson was the first American Viking born in the Western Hemisphere.  He was born in Newfoundland sometime around AD 1007, the son of Thorfinn Karlsefni and his wife Gudrid Thorbjarnardottir, who were exploring the wooded coasts of Labrador and Newfoundland for timber to bring back to the Norse settlements in Greenland which had no wood for building.  Thorfinn and Gudrid traveled in a small fleet of Norse trading vessels known as knarrs.

Knarrs were not the sleek long boats of Viking raiders, but were instead the semi-trailer trucks of the Viking expansion between AD 793 and 1066.  A knarr was an open planked boat about 50 feet long and 15 feet wide with a single mast and square-rigged sail.  It had a keel and could be rigged with a sprit to run close-hauled to the wind.  Its cargo was typically walrus ivory, wood, wool, wheat and furs with enough mid-ship room for a few livestock.

By using the technique of latitude sailing, that is by sailing to a known latitude and then keeping the North Star at a fixed angle above the horizon, knarrs could traverse the North Atlantic in a matter of weeks, sailing back and forth between Norway and Iceland and Greenland.  The trip from Greenland’s eastern settlement to Norway was 3000 km and took about 4 weeks (compare that to the two months it took the Mayflower to cross the Atlantic 600 years later).  Storms and bad weather put a crimp in this type of latitude sailing when the North Star could be obscured for days or weeks, and the sailors could end up somewhere they didn’t expect.  This is what happened to the merchant Bjarni Herjólfsson circa 985 when his ships were blown west in a terrible storm and he came upon a land of white beaches and green forests stretching to the horizon.  To get home, he sailed north along the new-discovered coast to the known latitude of Greenland and then headed east until he hit land.

Bjarni never set foot on the new land, but his tale inspired Leif Eriksson, the son of Erik the Red, to explore the new world.  Leif bought Bjarni’s knarr and with a small fleet sailed up the west coast of Greenland to where Bjarni had landed, then headed due west along the latitude of what is today the Davis Straight.  Leif made landfall on Baffin Island and sailed south down the Labrador coast to Belle Island in the Gulf of St. Lawrence, that he named Straumfjord, and then across to the northern tip of Newfoundland on the edge of a shallow bay where they could run their ships onto shore.  There, sometime around AD1000 they built a small settlement of wood houses that they used as a base for wider explorations of the land they called Vinland.  Later expeditions returned to the Straumfjord settlement and expanded it, including Thorfinn and Gudrid, where their son Snorri was born.

The voyage one-way between Newfoundland and Greenland took only 3 to 4 weeks, and each successive group repaired the damage from the ravages of the Newfoundland weather.  One of these repairs happened in the year AD 1021, long after Thorfinn and Gudrid and Snorri had resettled in northern Iceland, where their descendants crafted a saga of their exploits that was passed down by oral tradition through the generations until they were written down around AD 1400 and then almost forgotten…until the archeologist Anne Stine Ingstad with her husband Helge Ingstad found the remains of wood houses in 1960 buried under the turf at a place called L’Anse aux Meadows on Newfoundland’s northern tip.

The outpost at L’Anse aux Meadows was used on and off for decades as a base for the timber and fur trade. In addition to the dwellings, vast numbers of wood chips and discarded tree parts were uncovered, pointing to an active timber operation. Some of the wood is from the butternut tree which does not grow in Newfoundland nor anywhere along the shores of the Gulf of St. Lawrence. The modern areas of the butternut tree within range of Norse excursions are from the southern coast of Maine and the coast of Connecticut on Long Island Sound. Given how freely the Norse sailed their knarrs, making routine voyages of several weeks duration, the three-week trip from L’Anse aux Meadows to Long Island Sound seems easy, and there were plenty of bays to slip into for provisions as they went. Although there is no direct evidence for the Norse presence along the northeastern coast of the US, it seems highly likely that they plied these waterways and brought back the butternut timber to L’Anse aux Meadows.

Carbon 14 dating placed the age of the outpost at L’Anse aux Meadows at around AD 1000, consistent with the chronology of the Icelandic Sagas. But with an accuracy of plus or minus several decades it was not possible to know where it fit into the story…except for a lucky accident of solar physics.

## Miyake Events and Solar Physics

In 2012, while studying tree rings from two cedar trees in Japan, Fuse Miyake of Nagoya University and his team from the Solar-Terrestrial Environment Laboratory made the unexpected discovery that a single tree ring, shared in common between the two specimens, had 20% more Carbon 14 than any of the other rings.  The ratio of Carbon 14 in nature to the usual Carbon 12 is very stable, with a variation of about 2% year to year, mostly due to measurement accuracy.  Therefore, the 20% spike in Carbon 14 was a striking anomaly.  By comparing the known ages of the cedars to the rings, using the techniques of dendrochronology, the date of the ring growth was pinpointed to the year 774-775.

Such a sudden increase in Carbon 14 over only a year’s time could only be caused by a sudden and massive influx of high-energy cosmic rays into the Earth’s upper atmosphere.  Carbon 14 is generated by the capture of 10-40 MeV neutrons by Nitrogen 14 followed by proton decay of the excited nitrogen nucleus.  The high-energy neutrons are generated as byproducts of even higher energy processes.  Miyake and his team considered high-energy gamma photons from a local super nova, but that was not consistent with the timing or amount of Carbon 14 that was generated.  They next considered a massive generation of high-energy solar protons when the sun spits out a massive surge of high-energy protons.    The exact cause of a solar proton event is still debated, but it is likely to be associated with solar flares that accelerate the protons to high energy.  The high-energy protons can penetrate the Earth’s magnetic field and cause particle cascades in the upper atmosphere.  They called it a Solar Proton Event (SPE), but it has since been renamed a Miyake Event.

Miyake Events are extremely rare.  There have been only about 3 or 4 SPE’s in the past 10,000 years.  By luck, another Miyake Event occurred in 993, about 8 years after Bjarni Herjólfsson was blown off course and about 7 years before Leif Eriksson began exploring the new world.  The excess Carbon 14 rained down on Earth and was incorporated into the fresh growth of juniper and fir trees growing near the northern Newfoundland shore.  Twenty seven years later, while repairing Leif Eriksson’s wood houses, a Viking felled the trees with a metal axe.  Chunks of the trees were discarded, with the traces of the metal axe blade as well as the outer bark of the tree intact.

The intact bark on the wood pieces was an essential part of the dating. Simply by counting the number of tree rings from the ring of 993, it was possible to know not only the year the tree was cut down, but even the season. Furthermore, the existence of the marks from the metal axe confirmed that the tree was felled by someone from the settlement because there were no metal tools among the indigenous people.

The Norse timber traders treated the indigenous people terribly from the very first expeditions, with tales of wanton murder recorded proudly in the later sagas. This was ultimately their undoing. Resistance from the local tribes could be fierce, and the Norse could spare few casualties in their small expeditions. Eventually, the Norse were driven off. The wood structures at L’Anse aux Meadows were burned before they sank beneath the turf, and human remains with arrow wounds have been uncovered from the site, hinting at how this bold tale ended.

# Cancer Holography for Personalized Medicine

Imagine if you could use the physics of coherent light to record a 3D hologram of a cancer tumor and use it to select the best therapy for the cancer patient.

This week in Scientific Reports, a Nature Research publication, we demonstrate the first step towards that goal using dynamic speckle holography on patient cancer biopsies.

In a collaboration between Purdue University and the Northwestern University School of Medicine, we performed Doppler spectroscopy of intracellular dynamics of human epithelial ovarian cancer tumor biopsies and observed how they responded to selected anti-cancer drugs. Distinctly different Doppler spectra were observed for patients who went into remission versus those who failed to achieve cancer remission. This is the first clinical pilot trial of the technology, known as Biodynamic Imaging (BDI) that uses digital holography, published in human cancer research.

BDI may, in the future, make it possible to select the most effective therapies for individual cancer patients, realizing the long-sought dream of personalized cancer care.

Read it here: This latest research on personalized medicine has just been published with @SpringerNature in @ScientificReports.

The Purdue University Office of Technology Transfer has licensed the BDI patent portfolio to Animated Dynamics, Inc., located in Indianapolis, IN, that is working to commercialize the technology to translate it to the cancer clinic. Currently less than 40% of all cancer patients respond favorably to their chemotherapy. Using BDI technology our hope is to improve rates of remission in select cancer settings.

This work was supported by the NIH under the The Office of Physical Sciences – Oncology (OPSO) and by NSF CBET.

# Physics in the Age of Contagion: Part 4. Fifty Shades of Immunity to COVID-19

This is the fourth installment in a series of blogs on the population dynamics of COVID-19. In my first blog I looked at a bifurcation physics model that held the possibility (and hope) that with sufficient preventive action the pandemic could have died out and spared millions. That hope was in vain.

What will it be like to live with COVID-19 as a constant factor of modern life for years to come?

In my second blog I looked at a two-component population dynamics model that showed the importance of locking down and not emerging too soon. It predicted that waiting only a few extra weeks before opening could have saved tens of thousands of lives. Unfortunately, because states like Texas and Florida opened too soon and refused to mandate the wearing of masks, thousands of lives were lost.

In my third blog I looked at a network physics model that showed the importance of rapid testing and contact tracing to remove infected individuals to push the infection rate low — not only to flatten the curve, but to drive it down. While most of the developed world is succeeding in achieving this, the United States is not.

In this fourth blog, I am looking at a simple mean-field model that shows what it will be like to live with COVID-19 as a constant factor of modern life for years to come. This is what will happen if the period of immunity to the disease is short and people who recover from the disease can get it again. Then the disease will never go away and the world will need to learn to deal with it. How different that world will look from the one we had just a year ago will depend on the degree of immunity that is acquired after infection, how long a vaccine will provide protection before booster shots are needed, and how many people will get the vaccine or will refus.

## SIRS for SARS

COVID-19 is a SARS corona virus known as SARS-CoV-2. SARS stands for Severe Acute Respiratory Syndrome. There is a simple and well-established mean-field model for an infectious disease like SARS that infects individuals, from which they recover, but after some lag period they become susceptible again. This is called the SIRS model, standing for Susceptible-Infected-Recovered-Susceptible. This model is similar to the SIS model of my first blog, but it now includes a mean lifetime for the acquired immunity, after an individual recovers from the infection and then becomes susceptible again. The bifurcation threshold is the same for the SIRS model as the SIS model, but with SIRS there is a constant susceptible population. The mathematical flow equations for this model are

where i is the infected fraction, r is the recovered fraction, and 1 – i – r = s is the susceptible fraction. The infection rate for an individual who has k contacts is βk. The recovery rate is μ and the mean lifetime of acquired immunity after recovery is τlife = 1/ν. This model assumes that all individuals are equivalent (no predispositions) and there is no vaccine–only natural immunity that fades in time after recovery.

The population trajectories for this model are shown in Fig. 1. The figure on the left is a 3-simplex where every point in the triangle stands for a 3-tuple (i, r, s). Our own trajectory starts at the right bottom vertex and generates the green trajectory that spirals into the fixed point. The parameters are chosen to be roughly equivalent to what is known about the virus (but with big uncertainties in the model parameters). One of the key results is that the infection will oscillate over several years, settling into a steady state after about 4 years. Thereafter, there is a steady 3% infected population with 67% of the population susceptible and 30% recovered. The decay time for the immunity is assumed to be one year in this model. Note that the first peak in the infected numbers will be about 1 year, or around March 2021. There is a second smaller peak (the graph on the right is on a vertical log scale) at about 4 years, or sometime in 2024.

Although the recovered fraction is around 30% for these parameters, it is important to understand that this is a dynamic equilibrium. If there is no vaccine, then any individual who was once infected can be infected again after about a year. So if they don’t get the disease in the first year, they still have about a 4% chance to get it every following year. In 50 years, a 20-year-old today would have almost a 90% chance of having been infected at least once and an 80% chance of having gotten it at least twice. In other words, if there is never a vaccine, and if immunity fades after each recovery, then almost everyone will eventually get the disease several times in their lifetime. Furthermore, COVID will become the third most likely cause of death in the US after heart disease (first) and cancer (second). The sad part of this story is that it all could have been avoided if the government leaders of several key nations, along with their populations, had behaved responsibly.

## The Asymmetry of Personal Cost under COVID

The nightly news in the US during the summer of 2020 shows endless videos of large parties, dense with people, mostly young, wearing no masks. This is actually understandable even though regrettable. It is because of the asymmetry of personal cost. Here is what that means …

On any given day, an individual who goes out and about in the US has only about a 0.01 percent chance of contracting the virus. In the entire year, there is only about a 3% chance that that individual will get the disease. And even if they get the virus, they only have a 2% chance of dying. So the actual danger per day per person is so minuscule that it is hard to understand why it is so necessary to wear a mask and socially distance. Therefore, if you go out and don’t wear a mask, almost nothing bad will happen to YOU. So why not? Why not screw the masks and just go out!

And this is why that’s such a bad idea: because if no-one wears a mask, then tens or hundreds of thousands of OTHERS will die.

This is the asymmetry of personal cost. By ignoring distancing, nothing is likely to happen to YOU, but thousands of OTHERS will die. How much of your own comfort are you willing to give up to save others? That is the existential question.

This year is the 75th anniversary of the end of WW II. During the war everyone rationed and recycled, not because they needed it for themselves, but because it was needed for the war effort. Almost no one hesitated back then. It was the right thing to do even though it cost personal comfort. There was a sense of community spirit and doing what was good for the country. Where is that spirit today? The COVID-19 pandemic is a war just as deadly as any war since WW II. There is a community need to battle it. All anyone has to do is wear a mask and behave responsibly. Is this such a high personal cost?

## The Vaccine

All of this can change if a reliable vaccine can be developed. There is no guarantee that this can be done. For instance, there has never been a reliable vaccine for the common cold. A more sobering thought is to realize is that there has never been a vaccine for the closely related virus SARS-CoV-1 that broke out in 2003 in China but was less infectious. But the need is greater now, so there is reason for optimism that a vaccine can be developed that elicits the production of antibodies with a mean lifetime at least as long as for naturally-acquired immunity.

The SIRS model has the same bifurcation threshold as the SIS model that was discussed in a previous blog. If the infection rate can be made slower than the recovery rate, then the pandemic can be eliminated entirely. The threshold is

The parameter μ, the recovery rate, is intrinsic and cannot be changed. The parameter β, the infection rate per contact, can be reduced by personal hygiene and wearing masks. The parameter <k>, the average number of contacts to a susceptible person, can be significantly reduced by vaccinating a large fraction of the population.

To simulate the effect of vaccination, the average <k> per person can be reduced at the time of vaccination. This lowers the average infection rate. The results are shown in Fig. 2 for the original dynamics, a vaccination of 20% of the populace, and a vaccination of 40% of the populace. For 20% vaccination, the epidemic is still above threshold, although the long-time infection is lower. For 40% of the population vaccinated, the disease falls below threshold and would decay away and vanish.

In this model, the vaccination is assumed to decay at the same rate as naturally acquired immunity (one year), so booster shots would be needed every year. Getting 40% of the population to get vaccinated may be achieved. Roughly that fraction get yearly flu shots in the US, so the COVID vaccine could be added to the list. But at 40% it would still be necessary for everyone to wear face masks and socially distance until the pandemic fades away. Interestingly, if the 40% got vaccinated all on the same date (across the world), then the pandemic would be gone in a few months. Unfortunately, that’s unrealistic, so with a world-wide push to get 40% of the World’s population vaccinated within five years, it would take that long to eliminate the disease, taking us to 2025 before we could go back to the way things were in November of 2019. But that would take a world-wide vaccination blitz the likes of which the world has never seen.

## Python Code: SIRS.py

```#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
SIRS.py
Created on Fri July 17 2020
D. D. Nolte, "Introduction to Modern Dynamics:
Chaos, Networks, Space and Time, 2nd Edition (Oxford University Press, 2019)
@author: nolte
"""

import numpy as np
from scipy import integrate
from matplotlib import pyplot as plt

plt.close('all')

def tripartite(x,y,z):

sm = x + y + z
xp = x/sm
yp = y/sm

f = np.sqrt(3)/2

y0 = f*xp
x0 = -0.5*xp - yp + 1;

lines = plt.plot(x0,y0)
plt.setp(lines, linewidth=0.5)
plt.plot([0, 1],[0, 0],'k',linewidth=1)
plt.plot([0, 0.5],[0, f],'k',linewidth=1)
plt.plot([1, 0.5],[0, f],'k',linewidth=1)
plt.show()

print(' ')
print('SIRS.py')

def solve_flow(param,max_time=1000.0):

def flow_deriv(x_y,tspan,mu,betap,nu):
x, y = x_y

return [-mu*x + betap*x*(1-x-y),mu*x-nu*y]

x0 = [del1, del2]

# Solve for the trajectories
t = np.linspace(0, int(tlim), int(250*tlim))
x_t = integrate.odeint(flow_deriv, x0, t, param)

return t, x_t

# rates per week
betap = 0.3;   # infection rate
mu = 0.2;      # recovery rate
nu = 0.02      # immunity decay rate

print('beta = ',betap)
print('mu = ',mu)
print('nu =',nu)
print('betap/mu = ',betap/mu)

del1 = 0.005         # initial infected
del2 = 0.005         # recovered

tlim = 600          # weeks (about 12 years)

param = (mu, betap, nu)    # flow parameters

t, y = solve_flow(param)
I = y[:,0]
R = y[:,1]
S = 1 - I - R

plt.figure(1)
lines = plt.semilogy(t,I,t,S,t,R)
plt.ylim([0.001,1])
plt.xlim([0,tlim])
plt.legend(('Infected','Susceptible','Recovered'))
plt.setp(lines, linewidth=0.5)
plt.xlabel('Days')
plt.ylabel('Fraction of Population')
plt.title('Population Dynamics for COVID-19')
plt.show()

plt.figure(2)
plt.hold(True)
for xloop in range(0,10):
del1 = xloop/10.1 + 0.001
del2 = 0.01

tlim = 300
param = (mu, betap, nu)    # flow parameters
t, y = solve_flow(param)
I = y[:,0]
R = y[:,1]
S = 1 - I - R

tripartite(I,R,S);

for yloop in range(1,6):
del1 = 0.001;
del2 = yloop/10.1
t, y = solve_flow(param)
I = y[:,0]
R = y[:,1]
S = 1 - I - R

tripartite(I,R,S);

for loop in range(2,10):
del1 = loop/10.1
del2 = 1 - del1 - 0.01
t, y = solve_flow(param)
I = y[:,0]
R = y[:,1]
S = 1 - I - R

tripartite(I,R,S);

plt.hold(False)
plt.title('Simplex Plot of COVID-19 Pop Dynamics')

vac = [1, 0.8, 0.6]
for loop in vac:

# Run the epidemic to the first peak
del1 = 0.005
del2 = 0.005
tlim = 52
param = (mu, betap, nu)
t1, y1 = solve_flow(param)

# Now vaccinate a fraction of the population
st = np.size(t1)
del1 = y1[st-1,0]
del2 = y1[st-1,1]
tlim = 400

param = (mu, loop*betap, nu)
t2, y2 = solve_flow(param)

t2 = t2 + t1[st-1]

tc = np.concatenate((t1,t2))
yc = np.concatenate((y1,y2))

I = yc[:,0]
R = yc[:,1]
S = 1 - I - R

plt.figure(3)
plt.hold(True)
lines = plt.semilogy(tc,I,tc,S,tc,R)
plt.ylim([0.001,1])
plt.xlim([0,tlim])
plt.legend(('Infected','Susceptible','Recovered'))
plt.setp(lines, linewidth=0.5)
plt.xlabel('Weeks')
plt.ylabel('Fraction of Population')
plt.title('Vaccination at 1 Year')
plt.show()

plt.hold(False)
```

## Caveats and Disclaimers

No effort was made to match parameters to the actual properties of the COVID-19 pandemic. The SIRS model is extremely simplistic and can only show general trends because it homogenizes away all the important spatial heterogeneity of the disease across the cities and states of the country. If you live in a hot spot, this model says little about what you will experience locally. The decay of immunity is also a completely open question and the decay rate is completely unknown. It is easy to modify the Python program to explore the effects of differing decay rates and vaccination fractions. The model also can be viewed as a “compartment” to model local variations in parameters.

# Physics in the Age of Contagion. Part 3: Testing and Tracing COVID-19

In the midst of this COVID crisis (and the often botched governmental responses to it), there have been several success stories: Taiwan, South Korea, Australia and New Zealand stand out. What are the secrets to their success? First, is the willingness of the population to accept the seriousness of the pandemic and to act accordingly. Second, is a rapid and coherent (and competent) governmental response. Third, is biotechnology and the physics of ultra-sensitive biomolecule detection.

## Antibody Testing

A virus consists a protein package called a capsid that surrounds polymers of coding RNA. Protein molecules on the capsid are specific to the virus and are the key to testing whether a person has been exposed to the virus. These specific molecules are called antigens, and the body produces antibodies — large biomolecules — that are rapidly evolved by the immune system and released into the blood system to recognize and bind to the antigen. The recognition and binding is highly specific (though not perfect) to the capsid proteins of the virus, so that other types of antibodies (produced to fend off other infections) tend not to bind to it. This specificity enables antibody testing.

In principle, all one needs to do is isolate the COVID-19 antigen, bind it to a surface, and run a sample of a patient’s serum (the part of the blood without the blood cells) over the same surface. If the patient has produced antibodies against the COVID-19, these antibodies will attach to the antigens stuck to the surface. After washing away the rest of the serum, what remains are anti-COVID antibodies attached to the antigens bound to the surface. The next step is to determine whether these antibodies have been bound to the surface or not.

At this stage, there are many possible alternative technologies to detecting the bound antibodies (see section below on the physics of the BioCD for one approach). A conventional detection approach is known as ELISA (Enzyme-linked immunosorbant assay). To detect the bound antibody, a secondary antibody that binds to human antibodies is added to the test well. This secondary antibody contains either a fluorescent molecular tag or an enzyme that causes the color of the well to change (kind of like how a pregnancy test causes a piece of paper to change color). If the COVID antigen binds antibodies from the patient serum, then this second antibody will bind to the first and can be detected by fluorescence or by simple color change.

The technical challenges associated with antibody assays relate to false positives and false negatives. A false positive happens when the serum is too sticky and some antibodies NOT against COVID tend to stick to the surface of the test well. This is called non-specific binding. The secondary antibodies bind to these non-specifically-bound antibodies and a color change reports a detection, when in fact no COVID-specific antibodies were there. This is a false positive — the patient had not been exposed, but the test says they were.

On the other hand, a false negative occurs when the patient serum is possibly too dilute and even though anti-COVID antibodies are present, they don’t bind sufficiently to the test well to be detectable. This is a false negative — the patient had been exposed, but the test says they weren’t. Despite how mature antibody assay technology is, false positives and false negatives are very hard to eliminate. It is fairly common for false rates to be in the range of 5% to 10% even for high-quality immunoassays. The finite accuracy of the tests must be considered when doing community planning for testing and tracking. But the bottom line is that even 90% accuracy on the test can do a lot to stop the spread of the infection. This is because of the geometry of social networks and how important it is to find and isolate the super spreaders.

## Social Networks

The web of any complex set of communities and their interconnections aren’t just random. Whether in interpersonal networks, or networks of cities and states and nations, it’s like the world-wide-web where the most popular webpages get the most links. This is the same phenomenon that makes the rich richer and the poor poorer. It produces a network with a few hubs that have a large fraction of the links. A network model that captures this network topology is known as the Barabasi-Albert model for scale-free networks [1]. A scale-free network tends to have one node that has the most links, then a couple of nodes that have a little fewer links, then several more with even fewer, and so on, until there are a vary large number of nodes with just a single link each.

When it comes to pandemics, this type of network topology is both a curse and a blessing. It is a curse, because if the popular node becomes infected it tends to infect a large fraction of the rest of the network because it is so linked in. But it is a blessing, because if that node can be identified and isolated from the rest of the network, then the chance of the pandemic sweeping across the whole network can be significantly reduced. This is where testing and contact tracing becomes so important. You have to know who is infected and who they are connected with. Only then can you isolate the central nodes of the network and make a dent in the pandemic spread.

An example of a Barabasi-Albert network is shown in Fig. 2 having 128 nodes. Some nodes have many links out (and in) the number of links connecting a node is called the node degree. There are several nodes of very high degree (a degree around 25 in this case) but also very many nodes that have only a single link. It’s the high-degree nodes that matter in a pandemic. If they get infected, then they infect almost the entire network. This scale-free network structure emphasizes the formation of central high-degree nodes. It tends to hold for many social networks, but also can stand for cities across a nation. A city like New York has links all over the country (by flights), while my little town of Lafayette IN might be modeled by a single link to Indianapolis. That same scaling structure is seen across many scales from interactions among nations to interactions among citizens in towns.

## Isolating the Super Spreaders

In the network of nodes in Fig. 2, each node can be considered as a “compartment” in a multi-compartment SIR model (see my previous blog for the two-compartment SIR model of COVID-19). The infection of each node depends on the SIR dynamics of that node, plus the infections coming in from links other infected nodes. The equations of the dynamics for each node are

where Aab is the adjacency matrix where self-connection is allowed (infection dynamics within a node) and the sums go over all the nodes of the network. In this model, the population of each node is set equal to the degree ka of the node. The spread of the pandemic across the network depends on the links and where the infection begins, but the overall infection is similar to the simple SIR model for a given average network degree

However, if the pandemic starts, but then the highest-degree node (the super spreader) is isolated (by testing and contact tracing), then the saturation of the disease across the network can be decreased in a much greater proportion than simply given by the population of the isolated node. For instance, in the simulation in Fig. 3, a node of degree 20 is removed at 50 days. The fraction of the population that is isolated is only 10%, yet the saturation of the disease across the whole network is decreased by more than a factor of 2.

In a more realistic model with many more nodes, and full testing to allow the infected nodes and their connections to be isolated, the disease can be virtually halted. This is what was achieved in Taiwan and South Korea. The question is why the United States, with its technologically powerful companies and all their capabilities, was so unprepared or unwilling to achieve the same thing.

## Python Code: NetSIRSF.py

```#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
NetSIRSF.py
Created on Sat May 11 08:56:41 2019
@author: nolte
D. D. Nolte, Introduction to Modern Dynamics: Chaos, Networks, Space and Time, 2nd ed. (Oxford,2019)
"""

# https://www.python-course.eu/networkx.php
# https://networkx.github.io/documentation/stable/tutorial.html
# https://networkx.github.io/documentation/stable/reference/functions.html

import numpy as np
from scipy import integrate
from matplotlib import pyplot as plt
import networkx as nx
import time
from random import random

tstart = time.time()

plt.close('all')

betap = 0.014;
mu = 0.13;

print('beta = ',betap)
print('betap/mu = ',betap/mu)

N = 128      # 50

facoef = 2
k = 1
nodecouple = nx.barabasi_albert_graph(N, k, seed=None)

indhi = 0
deg = 0
for omloop in nodecouple.node:
degtmp = nodecouple.degree(omloop)
if degtmp > deg:
deg = degtmp
indhi = omloop
print('highest degree node = ',indhi)
print('highest degree = ',deg)

plt.figure(1)
colors = [(random(), random(), random()) for _i in range(10)]
nx.draw_circular(nodecouple,node_size=75, node_color=colors)
print(nx.info(nodecouple))

# function: omegout, yout = coupleN(G)
def coupleN(G,tlim):

# function: yd = flow_deriv(x_y)
def flow_deriv(x_y,t0):

N = np.int(x_y.size/2)
yd = np.zeros(shape=(2*N,))
ind = -1
for omloop in G.node:
ind = ind + 1
temp1 = -mu*x_y[ind] + betap*x_y[ind]*x_y[N+ind]
temp2 =  -betap*x_y[ind]*x_y[N+ind]
linksz = G.node[omloop]['numlink']
for cloop in range(linksz):
cindex = G.node[omloop]['link'][cloop]
indx = G.node[cindex]['index']
g = G.node[omloop]['coupling'][cloop]

temp1 = temp1 + g*betap*x_y[indx]*x_y[N+ind]
temp2 = temp2 - g*betap*x_y[indx]*x_y[N+ind]

yd[ind] = temp1
yd[N+ind] = temp2

return yd
# end of function flow_deriv(x_y)
x0 = x_y
t = np.linspace(0,tlim,tlim)      # 600  300
y = integrate.odeint(flow_deriv, x0, t)

return t,y
# end of function: omegout, yout = coupleN(G)

lnk = np.zeros(shape = (N,), dtype=int)
ind = -1
for loop in nodecouple.node:
ind = ind + 1
nodecouple.node[loop]['index'] = ind
nodecouple.node[loop]['link'] = list(nx.neighbors(nodecouple,loop))
nodecouple.node[loop]['numlink'] = len(list(nx.neighbors(nodecouple,loop)))
lnk[ind] = len(list(nx.neighbors(nodecouple,loop)))

gfac = 0.1

ind = -1
for nodeloop in nodecouple.node:
ind = ind + 1
nodecouple.node[nodeloop]['coupling'] = np.zeros(shape=(lnk[ind],))
for linkloop in range (lnk[ind]):
nodecouple.node[nodeloop]['coupling'][linkloop] = gfac*facoef

x_y = np.zeros(shape=(2*N,))
for loop in nodecouple.node:
x_y[loop]=0
x_y[N+loop]=nodecouple.degree(loop)
#x_y[N+loop]=1
x_y[N-1 ]= 0.01
x_y[2*N-1] = x_y[2*N-1] - 0.01
N0 = np.sum(x_y[N:2*N]) - x_y[indhi] - x_y[N+indhi]
print('N0 = ',N0)

tlim0 = 600
t0,yout0 = coupleN(nodecouple,tlim0)                           # Here is the subfunction call for the flow

plt.figure(2)
plt.yscale('log')
plt.gca().set_ylim(1e-3, 1)
for loop in range(N):
lines1 = plt.plot(t0,yout0[:,loop])
lines2 = plt.plot(t0,yout0[:,N+loop])
lines3 = plt.plot(t0,N0-yout0[:,loop]-yout0[:,N+loop])

plt.setp(lines1, linewidth=0.5)
plt.setp(lines2, linewidth=0.5)
plt.setp(lines3, linewidth=0.5)

Itot = np.sum(yout0[:,0:127],axis = 1) - yout0[:,indhi]
Stot = np.sum(yout0[:,128:255],axis = 1) - yout0[:,N+indhi]
Rtot = N0 - Itot - Stot
plt.figure(3)
#plt.plot(t0,Itot,'r',t0,Stot,'g',t0,Rtot,'b')
plt.plot(t0,Itot/N0,'r',t0,Rtot/N0,'b')
#plt.legend(('Infected','Susceptible','Removed'))
plt.legend(('Infected','Removed'))
plt.hold

# Repeat but innoculate highest-degree node
x_y = np.zeros(shape=(2*N,))
for loop in nodecouple.node:
x_y[loop]=0
x_y[N+loop]=nodecouple.degree(loop)
#x_y[N+loop]=1
x_y[N-1] = 0.01
x_y[2*N-1] = x_y[2*N-1] - 0.01
N0 = np.sum(x_y[N:2*N]) - x_y[indhi] - x_y[N+indhi]

tlim0 = 50
t0,yout0 = coupleN(nodecouple,tlim0)

# remove all edges from highest-degree node
ee = list(nodecouple.edges(indhi))
nodecouple.remove_edges_from(ee)
print(nx.info(nodecouple))

#nodecouple.remove_node(indhi)
lnk = np.zeros(shape = (N,), dtype=int)
ind = -1
for loop in nodecouple.node:
ind = ind + 1
nodecouple.node[loop]['index'] = ind
nodecouple.node[loop]['link'] = list(nx.neighbors(nodecouple,loop))
nodecouple.node[loop]['numlink'] = len(list(nx.neighbors(nodecouple,loop)))
lnk[ind] = len(list(nx.neighbors(nodecouple,loop)))

ind = -1
x_y = np.zeros(shape=(2*N,))
for nodeloop in nodecouple.node:
ind = ind + 1
nodecouple.node[nodeloop]['coupling'] = np.zeros(shape=(lnk[ind],))
x_y[ind] = yout0[tlim0-1,nodeloop]
x_y[N+ind] = yout0[tlim0-1,N+nodeloop]
for linkloop in range (lnk[ind]):
nodecouple.node[nodeloop]['coupling'][linkloop] = gfac*facoef

tlim1 = 500
t1,yout1 = coupleN(nodecouple,tlim1)

t = np.zeros(shape=(tlim0+tlim1,))
yout = np.zeros(shape=(tlim0+tlim1,2*N))
t[0:tlim0] = t0
t[tlim0:tlim1+tlim0] = tlim0+t1
yout[0:tlim0,:] = yout0
yout[tlim0:tlim1+tlim0,:] = yout1

plt.figure(4)
plt.yscale('log')
plt.gca().set_ylim(1e-3, 1)
for loop in range(N):
lines1 = plt.plot(t,yout[:,loop])
lines2 = plt.plot(t,yout[:,N+loop])
lines3 = plt.plot(t,N0-yout[:,loop]-yout[:,N+loop])

plt.setp(lines1, linewidth=0.5)
plt.setp(lines2, linewidth=0.5)
plt.setp(lines3, linewidth=0.5)

Itot = np.sum(yout[:,0:127],axis = 1) - yout[:,indhi]
Stot = np.sum(yout[:,128:255],axis = 1) - yout[:,N+indhi]
Rtot = N0 - Itot - Stot
plt.figure(3)
#plt.plot(t,Itot,'r',t,Stot,'g',t,Rtot,'b',linestyle='dashed')
plt.plot(t,Itot/N0,'r',t,Rtot/N0,'b',linestyle='dashed')
#plt.legend(('Infected','Susceptible','Removed'))
plt.legend(('Infected','Removed'))
plt.xlabel('Days')
plt.ylabel('Fraction of Sub-Population')
plt.title('Network Dynamics for COVID-19')
plt.show()
plt.hold()

elapsed_time = time.time() - tstart
print('elapsed time = ',format(elapsed_time,'.2f'),'secs')

```

## Caveats and Disclaimers

No effort in the network model was made to fit actual disease statistics. In addition, the network in Figs. 2 and 3 only has 128 nodes, and each node was a “compartment” that had its own SIR dynamics. This is a coarse-graining approach that would need to be significantly improved to try to model an actual network of connections across communities and states. In addition, isolating the super spreader in this model would be like isolating a city rather than an individual, which is not realistic. The value of a heuristic model is to gain a physical intuition about scales and behaviors without being distracted by details of the model.

## Postscript: Physics of the BioCD

Because antibody testing has become such a point of public discussion, it brings to mind a chapter of my own life that was closely related to this topic. About 20 years ago my research group invented and developed an antibody assay called the BioCD [2]. The “CD” stood for “compact disc”, and it was a spinning-disk format that used laser interferometry to perform fast and sensitive measurements of antibodies in blood. We launched a start-up company called QuadraSpec in 2004 to commercialize the technology for large-scale human disease screening.

A conventional compact disc consists of about a billion individual nulling interferometers impressed as pits into plastic. When the read-out laser beam straddles one of the billion pits, it experiences a condition of perfect destructive interferences — a zero. But when it was not shining on a pit it experiences high reflection — a one. So as the laser scans across the surface of the disc as it spins, a series of high and low reflections read off bits of information. Because the disc spins very fast, the data rate is very high, and a billion bits can be read in a matter of minutes.

The idea struck me in late 1999 just before getting on a plane to spend a weekend in New York City: What if each pit were like a test tube, so that instead of reading bits of ones and zeros it could read tiny amounts of protein? Then instead of a billion ones and zeros the disc could read a billion protein concentrations. But nulling interferometers are the least sensitive way to measure something sensitively because it operates at a local minimum in the response curve. The most sensitive way to do interferometry is in the condition of phase quadrature when the signal and reference waves are ninety-degrees out of phase and where the response curve is steepest, as in Fig. 4 . Therefore, the only thing you need to turn a compact disc from reading ones and zeros to proteins is to reduce the height of the pit by half. In practice we used raised ridges of gold instead of pits, but it worked in the same way and was extremely sensitive to the attachment of small amounts of protein.

This first generation BioCD was literally a work of art. It was composed of a radial array of gold strips deposited on a silicon wafer. We were approached in 2004 by an art installation called “Massive Change” that was curated by the Vancouver Art Museum. The art installation travelled to Toronto and then to the Museum of Contemporary Art in Chicago, where we went to see it. Our gold-and-silicon BioCD was on display in a section on art in technology.

The next-gen BioCDs were much simpler, consisting simply of oxide layers on silicon wafers, but they were much more versatile and more sensitive. An optical scan of a printed antibody spot on a BioCD is shown in Fig. 5 The protein height is only about 1 nanometer (the diameter of the spot is 100 microns). Interferometry can measure a change in the height of the spot (caused by binding antibodies from patient serum) by only about 10 picometers averaged over the size of the spot. This exquisite sensitivity enabled us to detect tiny fractions of blood-born antigens and antibodies at the level of only a nanogram per milliliter.

The real estate on a 100 mm diameter disc was sufficient to do 100,000 antibody assays, which would be 256 protein targets across 512 patients on a single BioCD that would take only a few hours to finish reading!

The potential of the BioCD for massively multiplexed protein measurements made it possible to imagine testing a single patient for hundreds of diseases in a matter of hours using only a few drops of blood. Furthermore, by being simple and cheap, the test would allow people to track their health over time to look for emerging health trends.

If this sounds familiar to you, you’re right. That’s exactly what the notorious company Theranos was promising investors 10 years after we first proposed this idea. But here’s the difference: We learned that the tech did not scale. It cost us \$10M to develop a BioCD that could test for just 4 diseases. And it would cost more than an additional \$10M to get it to 8 diseases, because the antibody chemistry is not linear. Each new disease that you try to test creates a combinatorics problem of non-specific binding with all the other antibodies and antigens. To scale the test up to 100 diseases on the single platform using only a few drops of blood would have cost us more than \$1B of R&D expenses — if it was possible at all. So we stopped development at our 4-plex product and sold the technology to a veterinary testing company that uses it today to test for diseases like heart worm and Lymes disease in blood samples from pet animals.

Five years after we walked away from massively multiplexed antibody tests, Theranos proposed the same thing and took in more than \$700M in US investment, but ultimately produced nothing that worked. The saga of Theranos and its charismatic CEO Elizabeth Holmes has been the topic of books and documentaries and movies like “The Inventor: Out for Blood in Silicon Valley” and a rumored big screen movie starring Jennifer Lawrence as Holmes.

The bottom line is that antibody testing is a difficult business, and ramping up rapidly to meet the demands of testing and tracing COVID-19 is going to be challenging. The key is not to demand too much accuracy per test. False positives are bad for the individual, because it lets them go about without immunity and they might get sick, and false negatives are bad, because it locks them in when they could be going about. But if an inexpensive test of only 90% accuracy (a level of accuracy that has already been called “unreliable” in some news reports) can be brought out in massive scale so that virtually everyone can be tested, and tested repeatedly, then the benefit to society would be great. In the scaling networks that tend to characterize human interactions, all it takes is a few high-degree nodes to be isolated to make infection rates plummet.

## References

[1] A. L. Barabasi and R. Albert, “Emergence of scaling in random networks,” Science, vol. 286, no. 5439, pp. 509-512, Oct 15 (1999)

[2] D. D. Nolte, “Review of centrifugal microfluidic and bio-optical disks,” Review Of Scientific Instruments, vol. 80, no. 10, p. 101101, Oct (2009)

[3] D. D. Nolte and F. E. Regnier, “Spinning-Disk Interferometry: The BioCD,” Optics and Photonics News, no. October 2004, pp. 48-53, (2004)

# Physics in the Age of Contagion. Part 2: The Second Wave of COVID-19

Since my last Blog on the bifurcation physics of COVID-19, most of the US has approached the crest of “the wave”, with the crest arriving sooner in hot spots like New York City and a few weeks later in rural areas like Lafayette, Indiana where I live. As of the posting of this Blog, most of the US is in lock-down with only a few hold-out states. Fortunately, this was sufficient to avoid the worst case scenarios of my last Blog, but we are still facing severe challenges.

There is good news! The second wave can be managed and minimized if we don’t come out of lock-down too soon.

One fall-out of the (absolutely necessary) lock-down is the serious damage done to the economy that is now in its greatest retraction since the Great Depression. The longer the lock-down goes, the deeper the damage and the longer to recover. The single-most important question at this point in time, as we approach the crest, is when we can emerge from lock down? This is a critical question. If we emerge too early, then the pandemic will re-kindle into a second wave that could exceed the first. But if we emerge later than necessary, then the economy may take a decade to fully recover. We need a Goldilocks solution: not too early and not too late. How do we assess that?

## The Value of Qualitative Physics

In my previous Blog I laid out a very simple model called the Susceptible-Infected-Removed (SIR) model and provided a Python program whose parameters can be tweaked to explore the qualitatitive behavior of the model, answering questions like: What is the effect of longer or shorter quarantine periods? What role does social distancing play in saving lives? What happens if only a small fraction of the population pays attention and practice social distancing?

It is necessary to wait from releasing the lock-down at least several weeks after the crest has passed to avoid the second wave.

It is important to note that none of the parameters in that SIR model are reliable and no attempt was made to fit the parameters to the actual data. To expert epidemiological modelers, this simplistic model is less than useless and potentially dangerous if wrong conclusions are arrived at and disseminated on the internet.

But here is the point: The actual numbers are less important than the functional dependences. What matters is how the solution changes as a parameter is changed. The Python programs allow non-experts to gain an intuitive understanding of the qualitative physics of the pandemic. For instance, it is valuable to gain a feeling of how sensitive the pandemic is to small changes in parameters. This is especially important because of the bifurcation physics of COVID-19 where very small changes can cause very different trajectories of the population dynamics.

In the spirit of the value of qualitative physics, I am extending here that simple SIR model to a slightly more sophisticated model that can help us understand the issues and parametric dependences of this question of when to emerge from lock-down. Again, no effort is made to fit actual data of this pandemic, but there are still important qualitative conclusions to be made.

## The Two-Compartment SIR Model of COVID-19

To approach a qualitative understanding of what happens by varying the length of time of the country-wide shelter-in-place, it helps to think of two cohorts of the public: those who are compliant and conscientious valuing the lives of others, and those who don’t care and are non-compliant.

These two cohorts can each be modeled separately by their own homogeneous SIR models, but with a coupling between them because even those who shelter in place must go out for food and medicines. The equations of this two-compartment model are

where n and q refer to the non-compliant and the compliant cohorts, respectively. I and S are the susceptible populations. The coupling parameters are knn for the coupling between non-compliants individuals, knq for the effect of the compliant individuals on the non-compliant, kqn for the effect of the non-compliant individuals on the compliant, and kqq for the effect of the compliant cohort on themselves.

There are two time frames for the model. The first time frame is the time of lock-down when the compliant cohort is sheltering in place and practicing good hygiene, but they still need to go out for food and medicines. (This model does not include the first responders. They are an important cohort, but do not make up a large fraction of the national population). The second time frame is after the lock-down is removed. Even then, good practices by the compliant group are expected to continue with the purpose to lower infections among themselves and among others.

This two-compartment model has roughly 8 adjustable parameters, all of which can be varied to study their effects on the predictions. None of them are well known, but general trends still can be explored.

## Python Code: SIRWave.py

```#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
SIRWave.py
Created on Sat March 21 2020
@author: nolte
D. D. Nolte, Introduction to Modern Dynamics: Chaos, Networks, Space and Time, 2nd ed. (Oxford,2019)
"""

import numpy as np
from scipy import integrate
from matplotlib import pyplot as plt

plt.close('all')

print(' ')
print('SIRWave.py')

def solve_flow(param,max_time=1000.0):

def flow_deriv(x_y_z_w,tspan):
In, Sn, Iq, Sq = x_y_z_w

Inp = -mu*In + beta*knn*In*Sn + beta*knq*Iq*Sn
Snp = -beta*knn*In*Sn - beta*knq*Iq*Sn

Iqp = -mu*Iq + beta*kqn*In*Sq + beta*kqq*Iq*Sq
Sqp = -beta*kqn*In*Sq - beta*kqq*Iq*Sq

return [Inp, Snp, Iqp, Sqp]

x0 = [In0, Sn0, Iq0, Sq0]

# Solve for the trajectories
t = np.linspace(tlo, thi, thi-tlo)
x_t = integrate.odeint(flow_deriv, x0, t)

return t, x_t

beta = 0.02   # infection rate
dill = 5      # mean days infectious
mu = 1/dill   # decay rate
fnq = 0.3     # fraction not quarantining
fq = 1-fnq    # fraction quarantining
P = 330       # Population of the US in millions
mr = 0.002    # Mortality rate
dq = 90       # Days of lock-down (this is the key parameter)

# During quarantine
knn = 50      # Average connections per day for non-compliant group among themselves
kqq = 0       # Connections among compliant group
knq = 0       # Effect of compliaht group on non-compliant
kqn = 5       # Effect of non-clmpliant group on compliant

initfrac = 0.0001          # Initial conditions:
In0 = initfrac*fnq         # infected non-compliant
Sn0 = (1-initfrac)*fnq     # susceptible non-compliant
Iq0 = initfrac*fq          # infected compliant
Sq0 = (1-initfrac)*fq      # susceptivle compliant

tlo = 0
thi = dq

param = (mu, beta, knn, knq, kqn, kqq)    # flow parameters

t1, y1 = solve_flow(param)

In1 = y1[:,0]
Sn1 = y1[:,1]
Rn1 = fnq - In1 - Sn1
Iq1 = y1[:,2]
Sq1 = y1[:,3]
Rq1 = fq - Iq1 - Sq1

# Lift the quarantine: Compliant group continues social distancing
knn = 50      # Adjusted coupling parameters
kqq = 5
knq = 20
kqn = 15

fin1 = len(t1)
In0 = In1[fin1-1]
Sn0 = Sn1[fin1-1]
Iq0 = Iq1[fin1-1]
Sq0 = Sq1[fin1-1]

tlo = fin1
thi = fin1 + 365-dq

param = (mu, beta, knn, knq, kqn, kqq)

t2, y2 = solve_flow(param)

In2 = y2[:,0]
Sn2 = y2[:,1]
Rn2 = fnq - In2 - Sn2
Iq2 = y2[:,2]
Sq2 = y2[:,3]
Rq2 = fq - Iq2 - Sq2

fin2 = len(t2)
t = np.zeros(shape=(fin1+fin2,))
In = np.zeros(shape=(fin1+fin2,))
Sn = np.zeros(shape=(fin1+fin2,))
Rn = np.zeros(shape=(fin1+fin2,))
Iq = np.zeros(shape=(fin1+fin2,))
Sq = np.zeros(shape=(fin1+fin2,))
Rq = np.zeros(shape=(fin1+fin2,))

t[0:fin1] = t1
In[0:fin1] = In1
Sn[0:fin1] = Sn1
Rn[0:fin1] = Rn1
Iq[0:fin1] = Iq1
Sq[0:fin1] = Sq1
Rq[0:fin1] = Rq1

t[fin1:fin1+fin2] = t2
In[fin1:fin1+fin2] = In2
Sn[fin1:fin1+fin2] = Sn2
Rn[fin1:fin1+fin2] = Rn2
Iq[fin1:fin1+fin2] = Iq2
Sq[fin1:fin1+fin2] = Sq2
Rq[fin1:fin1+fin2] = Rq2

plt.figure(1)
lines = plt.semilogy(t,In,t,Iq,t,(In+Iq))
plt.ylim([0.0001,.1])
plt.xlim([0,thi])
plt.legend(('Non-compliant','Compliant','Total'))
plt.setp(lines, linewidth=0.5)
plt.xlabel('Days')
plt.ylabel('Infected')
plt.title('Infection Dynamics for COVID-19 in US')
plt.show()

plt.figure(2)
lines = plt.semilogy(t,Rn*P*mr,t,Rq*P*mr)
plt.ylim([0.001,1])
plt.xlim([0,thi])
plt.legend(('Non-compliant','Compliant'))
plt.setp(lines, linewidth=0.5)
plt.xlabel('Days')
plt.ylabel('Deaths')
plt.title('Total Deaths for COVID-19 in US')
plt.show()

D = P*mr*(Rn[fin1+fin2-1] + Rq[fin1+fin2-1])
print('Deaths = ',D)

plt.figure(3)
lines = plt.semilogy(t,In/fnq,t,Iq/fq)
plt.ylim([0.0001,.1])
plt.xlim([0,thi])
plt.legend(('Non-compliant','Compliant'))
plt.setp(lines, linewidth=0.5)
plt.xlabel('Days')
plt.ylabel('Fraction of Sub-Population')
plt.title('Population Dynamics for COVID-19 in US')
plt.show()
```

## Trends

The obvious trend to explore is the effect of changing the quarantine period. Fig. 2 shows the results of a an early release from shelter-in-place compared to pushing the release date one month longer. The trends are:

• If the lock-down is released early, the second wave can be larger than the first wave
• If the lock-down is released early, the compliant cohort will be mostly susceptible and will have the majority of new cases
• There are 40% more deaths when the lock-down is released early

If the lock-down is ended just after the crest, this is too early. It is necessary to wait at least several weeks after the crest has passed to avoid the second wave. There are almost 40% more deaths for the 90-day period than the 120-day period. In addition, for the case when the quarantine is stopped too early, the compliant cohort, since they are the larger fraction and are mostly susceptible, will suffer a worse number of new infections than the non-compliant group who put them at risk in the first place. In addition, the second wave for the compliant group would be worse than the first wave. This would be a travesty! But by pushing the quarantine out by just 1 additional month, the compliant group will suffer fewer total deaths than the non-compliant group. Most importantly, the second wave would be substantially smaller than the first wave for both cohorts.

The lesson from this simple model is simple: push the quarantine date out as far as the economy can allow! There is good news! The second wave can be managed and minimized if we don’t come out of lock-down too soon.

## Caveats and Disclaimers

This model is purely qualitative and only has value for studying trends that depend on changing parameters. Absolute numbers are not meant to be taken too seriously. For instance, the total number of deaths in this model are about 2x larger than what we are hearing from Dr. Fauci of NIAID at this time, so this simple model overestimates fatalities. Also, it doesn’t matter whether the number of quarantine days should be 60, 90 or 120 … what matters is that an additional month makes a large difference in total number of deaths. If someone does want to model the best possible number of quarantine days — the Goldilocks solution — then they need to get their hands on a professional epidemiological model (or an actual epidemiologist). The model presented here is not appropriate for that purpose.

Note added in postscript on April 8: Since posting the original blog on April 6, Dr, Fauci announced that as many as 90% of individuals are practicing some form of social distancing. In addition, many infections are not being reported because of lack of testing, which means that the mortality rate is lower than thought. Therefore, I have changed the mortality rate and figures with numbers that better reflect the current situation (that is changing daily), but still without any attempt to fit the numerous other parameters.