CSCI 4446/5446 Course materials:
 TA Help Hours! mondays from 9:3010:30am
in ECCE 1B16 and 56pm in ECCR
1B11 (this is in the basement of the classroom wing, along the south
corridor).

General information and administrivia
 A version of CSCI 4446 is available through
the Complexity Explorer
MOOC platform housed by the
Santa Fe Institute. We'll be supplementing the course
with some of these materials during CSCI 4446/5446 this spring. These
MOOC materials may be useful to you in other ways as well, especially
if you have to miss a lecture. Please go to that website, register
for the course, and look around a bit (including through the
``supplementary materials'' page).
 Problem Set 1: logistic map. You
can
use
the logistic map app on the Complexity Explorer MOOC to check that
your solutions are correct (look in the "supplementary materials"
tab). Also, you may wish to take some time this week to review
section 1 of the ODE notes listed below if your knowledge of
differential equations is at all rusty.
 Problem Set 2: bifurcation diagrams
and Feigenbaum's constant. Again, you can use the Complexity Explorer
logistic map app mentioned above to check your solutions. Here's
a tutorial on
the unix plotting tool gnuplot.
 Problem Set 3: fractals. For some
examples of fractals in the wild,
click
here or
here. If you missed the classes in which I talked about fractals,
this video
is a good makeup.
 Problem Set 4 : RungeKutta and the
driven pendulum equations.

Final Project Guidelines . You can
find tech reports that compile projects from some previous semesters
(2010, 2011, 2012, and 2015) here. Search for the
title "Projects in Chaotic Dynamics..."

Problem Set 5 : adaptive RungeKutta and
the Lorenz and Rossler systems.
The following materials may be useful to you as
you do this problem set:
 Problem Set 6 : Poincare sections.
The netnews posts about numerical dynamics that are listed above (PS5)
may be useful here as well.
 Final Project Details
 Problem Set 7 : variational equation.
See the notes listed below.

Problem Set 8 : embedding.
The following materials may be useful to you as
you do this problem set:
 A detailed list of the assigned
reading for PS810 ("Reading assignments for timeseries
analysis")
 Instructions on getting the data for
this problem set and an example of
how to embed a data set .
 The
TISEAN timeseries analysis toolkit is available on the official
CS department virtual machine ("VM"). Instructions for downloading
and installing your virtual machine
are here. After
that, run 'sudo aptget install tisean' to install the TISEAN tools.
If you have path problems (can't run it from where you want to), here
is a set of commands that 'user' would use to run the 'mutual' command
on the file 'data2.first250sec' in the 'Downloads' directory and put
the 'answer' in that directory. Modify as appropriate:
user@cucsvm:~$ export PATH=$PATH:/usr/lib/tisean
user@cucsvm:~$ mutual ~/Downloads/ps8data/data2.first250sec o ~/Downloads/ps8data/answer
 If you want to install TISEAN on your own machine,
these helpful hints regarding installing
and using it and this link to
the pytisean wrapper
on github may be useful. 'brew tap brewsci/science' followed by
'brew install tisean' works on Macs if you're a brew user, but leaves
the commands prefaced by a '' ... i.e., 'tiseanmutual'. If you're
running the latest version of Mac OS X, though, brew doesn't do the
right thing (as of 1/7/2019), but you can find binaries
here, courtesy of Joshua
Garland. I also have binaries
for Mac OSX 10.5 from long ago.

Here are some examples
of
how to run TISEAN from MATLAB.
 Jay Kominek's mpeg movie of
what happens as you change tau in embeddings of data from the Lorenz
system.
 There are lots of other references and resources for this problem
set in the "interesting links" section below.
 Problem Set 9 : Lyapunov exponents.
The following materials may be useful to you as
you do this problem set:
 Problem Set 10 : fractal dimension.
Click here for a detailed list of
the assigned reading for this topic
and here for a scan of
some of that reading (pp166191 of Parker & Chua).
 Problem Set 11 : playing with bike
wheels, writing Lagrangians, and starting to explore the twobody
problem for a binary star. This material is covered in the first few
sections of the classical mechanics notes listed below. Click here for a picture defining true
anomaly,
here for an interactive simulator that you can use to explore
orbits, and
here for a wonderful lecture on dynamical toys like tops and
rattlebacks.
 Some hints about
presentations.
 Problem Set 12 : integrating the
twobody equations. See section 4 of the classical mechanics notes
listed below. Here's an interesting
link that Kristine Washburn found about a variant of this problem.
You may also wish to check out the nbody section of Colonna's webpage
(listed below). Here is the "Chaos
Hits Wall Street" article that's on the reading assignment.
 Problem Set 13 : integrating the
threebody equations for a binaryfield star collision. See section
4.2 of the classical mechanics notes listed below. The "visualization
of dynamical systems" page in the "interesting links" list below has
source code for a lovely visualization of this problem.
 The endofsemester
evaluation.
Liz's videos and written materials:
Some useful and/or interesting links: (caveat emptor!)
 xkcd's takes on chaos (and
curvefitting)
 A nice
youtube lecture
about fractals (21 min)
 An amazing
animated bifurcation diagram

Riding around on the Lorenz
attractor
 A
transcript of Lorenz's 1972 speech to
the AAAS entitled "Predictability: Does the flap of a butterfly's
wings in Brazil set off a tornado in Texas?"
 Pendulum stuff:
 Henri Poincare didn't only play a formative role in the
foundation of the field of nonlinear dynamics. Among other things, he
came up with the theory of relativity and wrote down e=mc^2 before
Einstein did. Read a bit about
him here.
 The Fyre tool for producing
artwork based on histograms of iterated chaotic functions ,
written by an alumnus of this course.
 Michael Skirpan's
fractal tree generator (= the mother of all solutions to PS3).

CU's
site license for Matlab now covers student computers!

The
visualization of dynamical systems page from the Nonlinear
Dynamics and Time Series Analysis Group at the Max Planck Institute
for the Physics of Complex Systems.
 Video recordings of the lectures from Steve
Strogatz's introductory course on nonlinear dynamics and chaos
 Complexity, the flip side of
chaos: complex
dynamics of a flock of starlings. Here's
the Vimeo version of that
video if you prefer that channel.
 Movies of metronomes synchronizing (modernday equivalent of
Huyghens' pendulum clocks): an array of five
and an
array of 32 (!)
 The
PhET project, an interactive simulator that you can use to explore
all sorts of interesting systems. Click on "Play with sims" and go to
"Physics" for the nbody simulator (called "My Solar System").
 Analog computers for nonlinear dynamical systems: the
Antikythera
mechanism and the
digital
orrery (built by Liz's advisor)
 "Guide to
Takens' Theorem" paper (heavy going, mathematically, but very
comprehensive).
 Rigid body
dynamics in zero gravity on the international space station.
 Jim Roberge's fabulous
lectures about control theory (RIP, wonderful mentor).
 An applet that
simulates the Lorenz equations, allowing you to enter initial
conditions with a mouse click.
 A gorgeous youtube video that zooms in on the
Mandelbrot set.
 Another gorgeous video of an
evolving 3D fractal surface.
 A 'chalkmation' youtube video  complete with music  about the
Mandelbrot
set (warning: a bit of foul language at the end).
 The
TISEAN timeseries analysis toolkit. The TISEAN site has binaries
for UNIX & windows. 'brew install tisean' works on Macs if you're a
brew user. Here are some examples of
how to run all of this from MATLAB.
 Chaos in the path of a Roomba
 Chaotic music & dance stuff:
 NASA's movie of
Hyperion tumbling
 Remember that wonderful
"powers of ten" video from highschool physics?
 SIAM's dynamics
tutorials, many of which were contributed by grad students in courses
like this one.
 Wolfram's Mathworld site.
 The
FAQ for sci.nonlinear. A fabulous resource.
 The Santa Fe Institute,
which has a couple of
great educational programs for graduate students (the Complex
Systems Summer School) and undergraduates (called "Research
Experiences for Undergraduates").
 The Numerical Recipes webpage
 Some Java
demos developed by Michael Cross, who teaches the CSCI4446equivalent
course at Caltech.
 The Chaos
Hypertextbook
 Helwig Hauser's visualization
of dynamical systems page. The pages above that are interesting,
too.
 JeanFrancois Colonna's
"virtual spacetime travel" page, which includes lots of stuff
about the Lorenz system, pendula, the nbody problem, etc. Very nice
graphics.
 Some sources of economic and other time series data:
 Would you like your own double pendulum?