The idea tha taking the limit of the non-classical theories for certain parameters (relativity and quantum mechanics) should lead to the classical theory.

It appears that classical limit is only very strict for relativity. For quantum mechanics it is much more hand-wavy thing. See also: Subtle is the Lord by Abraham Pais (1982) page 55.

Basically the same as classical limit, but more for quantum mechanics.

Boooooring. Except for Navier-Stokes existence and smoothness. That's OK.

To modify the nutrients as a function of time, with To select a time series we can use something like:As mentioned in python runscripts/manual/runSim.py --help, nutrientTimeSeries is one of the choices from github.com/CovertLab/WholeCellEcoliRelease/blob/7e4cc9e57de76752df0f4e32eca95fb653ea64e4/models/ecoli/sim/variants/__init__.py#L57

25 25 means to start from index 25 and also end at 25, so running just one simulation. 25 27 would run 25 then 26 and then 27 for example.

The timeseries with index 25 is reconstruction/ecoli/flat/condition/timeseries/000025_cut_aa.tsv and containsso we understand that it starts with extra amino acids in the medium, which benefit the cell, and half way through those are removed at time 1200s = 20 minutes. We would therefore expect the cell to start expressing amino acid production genes exactly at that point.

nutrients likely means condition in that file however, see bug report with 1 1 failing: github.com/CovertLab/WholeCellEcoliRelease/issues/24

When we do this the simulation ends in:so we see that the doubling time was faster than the one with minimal conditions of 0:42:49, which makes sense, since during the first 20 minutes the cell had extra amino acid nutrients at its disposal.

The output directory now contains simulation output data under out/manual/nutrientTimeSeries_000025/. Let's run analysis and plots for that:

We can now compare the outputs of this run to the default wildtype_000000 run from Section "Install and first run".

The following plots from under out/manual/wildtype_000000/000000/{generation_000000,nutrientTimeSeries_000025}/000000/plotOut/svg_plots have been manually joined side-by-side with:

See also: existence and uniqueness of solutions of partial differential equations.

Originally it was likely created to study constrained mechanical systems where you want to use some "custom convenient" variables to parametrize things instead of global x, y, z. Classical examples that you must have in mind include:lagrangian mechanics lectures by Michel van Biezen (2017) is a good starting point.

When doing lagrangian mechanics, we just lump together all generalized coordinates into a single vector $\overrightarrow{q}(t):\mathbb{R}\to {\mathbb{R}}^n$ that maps time to the full state:where each component can be anything, either the x/y/z coordinates relative to the ground of different particles, or angles, or nay other crazy thing we want.

The Lagrangian is a function ${\mathbb{R}}^n\times {\mathbb{R}}^n\times \mathbb{R}\to \mathbb{R}$ that maps:to a real number.

Then, the stationary action principle says that the actual path taken obeys the Euler-Lagrange equation:This produces a system of partial differential equations with:

The mixture of so many derivatives is a bit mind mending, so we can clarify them a bit further. At:the $q_i$ is just identifying which argument of the Lagrangian we are differentiating by: the i-th according to the order of our definition of the Lagrangian. It is not the actual function, just a mnemonic.

Then at:

However, people later noticed that the Lagrangian had some nice properties related to Lie group continuous symmetries.

Basically it seems that the easiest way to come up with new quantum field theory models is to first find the Lagrangian, and then derive the equations of motion from them.

For every continuous symmetry in the system (modelled by a Lie group), there is a corresponding conservation law: local symmetries of the Lagrangian imply conserved currents.
Genius: Richard Feynman and Modern Physics by James Gleick (1994) chapter "The Best Path" mentions that Richard Feynman didn't like the Lagrangian mechanics approach when he started university at MIT, because he felt it was too magical. The reason is that the Lagrangian approach basically starts from the principle that "nature minimizes the action across time globally". This implies that things that will happen in the future are also taken into consideration when deciding what has to happen before them! Much like the lifeguard in the lifegard problem making global decisions about the future. However, chapter "Least Action in Quantum Mechanics" comments that Feynman later notice that this was indeed necessary while developping Wheeler-Feynman absorber theory into quantum electrodynamics, because they felt that it would make more sense to consider things that way while playing with ideas such as positrons are electrons travelling back in time. This is in contrast with Hamiltonian mechanics, where the idea of time moving foward is more directly present, e.g. as in the Schrödinger equation.

Furthermore, given the symmetry, we can calculate the derived conservation law, and vice versa.

And partly due to the above observations, it was noticed that the easiest way to describe the fundamental laws of particle physics and make calculations with them is to first formulate their Lagrangian somehow: S.

TODO advantages:

Bibliography:

Original playlist name: "PHYSICS 68 ADVANCED MECHANICS: LAGRANGIAN MECHANICS"

Author: Michel van Biezen.

High school classical mechanics material, no mention of the key continuous symmetry part.

But does have a few classic pendulum/pulley/spring worked out examples that would be really wise to get under your belt first.

As mentioned on the Wikipedia page en.wikipedia.org/w/index.php?title=Stationary_Action_Principle&oldid=1020413171, "principle of least action" is not accurate since it could not necessarily be a minima, we could just be in a saddle-point.

Calculus of variations is the field that searches for maxima and minima of Functionals, rather than the more elementary case of functions from $\mathbb{R}$ to $\mathbb{R}$.

A function that takes input function and outputs a real number.

Let's start with the one dimensional case. Let the $q:\mathbb{R}\to \mathbb{R}$ and a Functional $I$ defined by a function of three variables $F:{\mathbb{R}}^3\to \mathbb{R}$:

Then, the Euler-Lagrange equation gives the maxima and minima of the that type of functional. Note that this type of functional is just one very specific type of functional amongst all possible functionals that one might come up with. However, it turns out to be enough to do most of physics, so we are happy with with it.

Given $F$, the Euler-Lagrange equations are a system of ordinary differential equations constructed from that $F$ such that the solutions to that system are the maxima/minima.

In the one dimensional case, the system has a single ordinary differential equation:

By $\frac{\partial F}{\partial q}$ and $\frac{\partial F}{\partial \dot{q}}$ we simply mean "the partial derivative of $F$ with respect to its second and third arguments". The notation is a bit confusing at first, but that's all it means.

Therefore, that expression ends up being at most a second order ordinary differential equation where $q$ is the unknown, since:

Now let's think about the multi-dimensional case. Instead of having $q:\mathbb{R}\to \mathbb{R}$, we now have $q:\mathbb{R}\to {\mathbb{R}}^n$. Think about the Lagrangian mechanics motivation of a double pendulum where for a given time we have two angles.

Let's do the 2-dimensional case then. In that case, $F$ is going to be a function of 5 variables $F:{\mathbb{R}}^5\to \mathbb{R}$ rather than 3 as in the one dimensional case, and the functional looks like:

This time, the Euler-Lagrange equations are going to be a system of two ordinary differential equations on two unknown functions $q_1$ and $q_2$ of order up to 2 in both variables:At this point, notation is getting a bit clunky, so people will often condense the $q_i$ vectoror just omit the arguments of $F$ entirely:

These are the final equations that you derive from the Lagrangian via the Euler-Lagrange equation which specify how the system evolves with time.

The function that fully describes a physical system in Lagrangian mechanics.

Basically: S.