David A. Tanzer, December 31, 2020
How complex is the English language? The question has many dimensions and nuances. What does complexity mean, and how could it be measured? This a tough nut to crack, so in this post we’ll make a retrenchment and reconsider the question in a more formal setting — computer science.
Here a language is identified with its extension — meaning … Read more
David A. Tanzer, December 29, 2020
Last time we set out the model of a leaf as a set of square cells in the plane. But there’s more structure to be defined: the veins.
All the veins taken together make up a ‘transport system’ for pumping fluid from the root to each of the cells.
Biological note: The cells need water to do … Read more
David A. Tanzer, December 25, 2020
On this Christmas day, let us take a moment to think of the tree, and wonder how it actually grows. Slowly move your attention to the leaves, and ponder how they grow. Next, forget about this type of leaf, for a conifer, with parallel veins — as our true subject is the growth of leaves with branching veins. … Read more
David A. Tanzer, August 24, 2020
The standard compartmental models for SIR, SEIR etc. use the rate equations for the dynamics, and hence assume a continuous flow model.
This works well, particularly due to the fact that population sizes in epidemics are “large”, on the order of millions of individuals, and the law of large numbers kicks in, which tells us that we … Read more
David A. Tanzer, August 24, 2020
With the advent of the rate equation, we have shifted into a model of reaction networks consisting of “pumps” that move at continuous rates, transferring “mathematical fluid” between containers. Yet, as we have indicated, the real activity proceeds by discrete steps; an individual recovers, two molecules collide to form a compound.
How are these views to be reconciled?
For concreteness, … Read more
David A. Tanzer, August 17, 2020
Recall that for dynamics, we want to get at the way that the compartments S, I, R evolve over tune,
So far, we’ve defined the rates at which the reactions fire.
So now let’s summarize the rates for the SIR model:
David A. Tanzer, August 17, 2020
The same kinetics occurs in chemical reaction networks. To illustrate, suppose there were two types of molecules, A and B, and that one A and one B molecule could collide to form a C molecule. So the reaction would be written $$A + B \rightarrow C$$.
Now imagine that a large number of A, B and C molecules are … Read more
David A. Tanzer, August 17, 2020
In the previous article, we analyzed a simple system with a simple reaction:
$$\mathrm{Unpopped} \xrightarrow{\mathrm{Cooking}} \mathrm{Popped}$$
There we saw that the rate of the reaction is proportional both to a constant associated with the reaction, and to the count in compartment Unpopped. This will hold for all reactions that take a single input connection, including recovery … Read more
David A. Tanzer, August 17, 2020
Last time, we analyzed a system with a single reaction:
And derived its rate equation:
In this article, we will see the solution to the equation, which will tell us exactly how the average popping rate evolves over time.
Note this article strikes a comparatively more quantitative tone than the others in … Read more
David A. Tanzer, August 17, 2020
Now let’s work out the equation for how the popping evolves over time.
Let Rate(t) be the average rate at which popping takes place at time $t$. Once the popping has begun, we expect Rate(t) to be high, and then dwindle down towards zero as more and more of the kernels have popped.
Suppose that Rate(20) = 5, … Read more