Computer Science COMP 199 (Winter term)
Excursions in Computing Science
(or
We Know a Lot More than *Bleep*)

Instructor: T. H. Merrett

"Excursions in Computing Science" explores the role of computing in understanding the universe. So we link up theoretical science, mathematics and computing. Specifically, we look at some of the big ideas in science, such as quantum theory, special relativity, and gene expression; at the supporting mathematical concepts in linear algebra, mathematical logic, and nonlinear attractors; and at computing techniques including data structures, procedural abstraction, and object-orientation.

This course is a dance of science, mathematics and computing, with each of these subjects treated in novel ways, without prerequisites beyond high school.
(A CEGEP graduate may have seen some of the material before, but from a quite different approach.)

The science motivates the mathematics and the computing. The mathematics provides the concepts for the science and the formalisms for the computing. The computing gives experience with the mathematics and predictions for the science; later in the course, advanced computing applications are based on the mathematics. We can understand the science through mathematical analogies, which are better for abstract science than conventional analogies such as waves and particles. The mathematics captures the subtleties; the computing captures the complexities. The mathematics explains the science; the computing explains the mathematics.

The intention of the course is to to be a head start, by experiencing the abstractions by which we do science. We do this by progressing from the science from which the abstractions emerge, to the mathematics which explores the abstractions, to the computing which extracts the predictions and brings the abstractions back to science. Playing the three against each other gives a better grasp than looking at any one of them on its own. We do real science, real math and real computing. The novel way of looking at them will complement the detailed coverage of later, more advanced courses. You will encounter again the abstractions experienced here, and you will be ahead of the game by having experienced them.

                 For Grade Scholars and the Young at Heart

Week i Rules and Calculations                                                                     Notes PDF 308K
 Math: some neat numbers and rules for finding them; calculating with letters.
 Computing: programming your calculator or MATLAB makes it faster; graphics
       turns it into pictures.

Week ii Powers and Trees                                                         MATLABpak        Notes PDF 737K
 Math: numbers can get very big very fast or very small very fast.
 Science: from us to the universe in 9 steps; from us to smaller than the atom
       in 5 steps.
 Computing: searching by using trees upside-down.

Week iii Bases and Polynomials                                                   MATLABpak        Notes PDF 918K
 Math: counting on our fingers; decimals that go on forever; arithmetic on
       polynomials and why multiplication etc. work the way they do.
 Computing: counting on the computer's "fingers"
 Science: the genetic code.

Week iv Space Math                                                                                 Notes PDF 298K
 Math: arithmetic on matrices.
 Science: rotating and transforming space.
 Computing: matrices on the calculator and in MATLAB.

Week v Milli-micro-nano-..math I                                                                   Notes PDF 260K
  Math: functions and their zeros, slopes, square roots,
  slope equations, De Moivre's theorem.
  Computing: Newton's method, summing (convergent) infinite
  series.

Week v Milli-micro-nano-..math II                                                                  Notes PDF 140K
  Math: slopes and antislopes.
  Computing: Newton's method for solving equations.


COMP 199                                         Excursions in Computing Science

                            COURSE SUMMARY

Part I Time and Spaces
The science discussed is quantum physics and special relativity, with
motivation from and applications to polarized light, quantum electrodynamics
and nuclear physics.
The mathematics covered is the linear algebra of (mainly) two-dimensional
vectors, matrices and tensors, and excursions into higher dimensions, especially
three-dimensional Clifford algebra.
The computing aspect introduces array data structures and operations, functions
as procedural abstraction, some numerical linear algebra in the form of equation
solution, discussion of algorithm complexity and divide-and-conquer, and
applications to graphics, multimedia and Internet search engines. A guest
lecture introduces quantum computing.
A discussion of symmetry introduces the mathematics, and many applications from
molecular vibrations, crystals and wallpaper to the electron structure of the
atom, quarks and the conservation laws of physics.
A discussion of heat introduces the mathematics of distributions and timeseries
and a computer simulation of gas dynamics, leading to the thermostatic
abstractions of entropy, temperature and pressure and to many ramifications
of transport thermodynamics, including Brownian motion, electricity and
thermoelectricity, rheology and chemical reactions. Phase transitions are
introduced with computer simulations rather than mathematically, leading to the
many-scale (fractal) nature of criticality.

Week 1 Polarized Light                                                                             Notes PDF 365K
 Science: building a scientific theory to predict by calculating;
        light through one, two and three polarizing filters.
 Math: trigonometry in a nutshell.
 Computing: programming with MATLAB.

Week 2 Operators                                                                MATLABpak          Notes PDF 174K
 Science: physical measurements and observations as operators;
        polarizing filter as projection.
 Math: vector and matrix products; projection and rotation operators;
       Pythagoras; linear operators.
 Computing: experiencing abstractions through programming; cost and
        complexity of algorithms.

Week 3 Speed of Light                                                           MATLABpak          Notes PDF 173K
 Science: there is a maximum speed for anything; laws of nature are not
        affected by uniform speed; lightspeed is a law of nature;
        the twin paradox.
 Math: fixed-point vectors of transformations; shear transformations;
        determinants; anti-Pythagoras.
 Computing: visualizing transformations by calculating them; procedural
        abstraction.

Week 4 Two-dimensional Numbers and Turtles                                                         Notes PDF 186K
 Science: adding and multiplying arrows; is an imaginary dimension science?
 Math: rotations off the real line - right angle, any angle; the field axioms;
        multiplying rotations is adding angles - exponentials.
 Computing: turtle graphics.

Week 5 Particles with Periods                                                                      Notes PDF 126K
 Science: QED, the strange theory of light and matter; amplitudes and
        probabilities; amplitudes under particle exchange - fermions and bosons.
 Math: 2-numbers give particles frequencies, wavelengths and periods;
        approximate calculation.
 Computing: playing with consequences through programming; errors and artefacts
        of the computation itself.

Week 6 Spin                                                                                        Notes PDF 126K
 Science: polarization states of electrons; half-angles and walking dogs; two
        spin-1/2s make two qbits; two spin-1/2s make one spin-1; fermions and
        bosons;
 Math: matrices of complex numbers; anticommutativity.
 Computing: a preparation for quantum computing.

Week 7 Bonus lectures

 a) E=mc^2                                                                                         Notes PDF 137K
 Science: frequency and wavenumber transform like time and space; energy and
        momentum are frequency and wavenumber; units and dimensional analysis;
        classical limits - E = mc^2; conservation, anti-Pythagoras and nuclear
        fusion and fission; scattering light from electrons - the Compton
        effect; Doppler effect; equations of quantum mechanics.
 Math: practice
 Computing: (small) databases.

 b) invited lecture on quantum computing: Patrick Hayden                                           Notes PDF 77K

 c) Coordinates, angles and reality                                                                Notes PDF 200K
 Science: vectors are real - something is invariant as coordinate systems
        transform; some arrays do not transform like vectors; some real things
        do not transform like vectors; angles, reflections and rotations in 2D
        and 3D.
 Math: tensor products; Clifford algebra [PDF 103K].
 Computing: practice

Week 8  Higher dimensions: Sketchpad and Web page rank                          MATLABpak          Notes PDF 321K
 Science: constraint-based graphics for drawing and design; how important is a
        web page? Measuring personality. Surveying and GPS.
 Math: underdetermined and overdetermined linear equations - Lagrange
        multipliers and least-squares; linear approximations to nonlinear
        functions; optimization; eigenvectors and eigenvalues.
 Computing: iterative methods to find an eigenvector, gaussian elimination for
        solving linear systems; parallelization; Sketchpad [Postscript file on constraints in Sketchpad, 110K].

Book 8c Symmetry: Simplifying Matrices
(This is an extensive treatment of symmetry, a study rich in implications for
science and requiring challenging computations. It will require a couple of
months of dedicated effort, if you are starting from scratch, but this
treatment is self-contained and accessible to anyone prepared to do the work.
Prerequisites from other Weeks in this course are given explicitly when they
are needed.
 This "week" on symmetry was added in 2009 and is not intended, which earlier
Weeks are, to be covered in one week.)

     8c Part I Discrete symmetries and molecules                                MATLABpak          Notes PDF 1025K
 Math: the mathematics of symmetry - group theory; abstracting groups from
       matrices and then representing them back as matrices again.
 Science: vibrations of molecules.

     8c Part II Infinite symmetries and crystals                                MATLABpak          Notes PDF 1511K
 Math: infinite commutative groups in 1D and 2D; wallpaper - point groups and
       space groups.
 Science: waves; measuring CD track spacings and crystal atomic spacings.

     8c Part III Continuous symmetries and the atom                             MATLABpak          Notes PDF 1172K
 Math: rotational symmetry in 2D and 3D; commutators; spherical harmonics.
 Science: the electronic structure and fine structure of atoms.

     8c Part IV Abstract symmetries and lots of physics                         MATLABpak          Notes PDF 634K
 Math: commutator algebra; "special unitary" groups SU(2) and SU(3); Noether's
       theorem.
 Science: quarks; Lagrangian and Hamiltonian physics; symmetry and conservation
       laws.
 Computing: cubic and quintic splines.

Week 9  Many Dimensions: Data Compression and Content                           MATLABpak           Notes PDF 280K
 Science: image compression and content analysis
 Math: orthogonal vectors in higher dimensions, complex roots of unity, 
	polynomial long division and remainders
 Computing: fast Fourier transform, divide-and-conquer

Book 9c Heat: Histograms and Gases
(This is an extensive treatment of thermodynamics. All the stipulations for
Book 8c above apply here.
 This "week" on thermodynamics was added in 2012 and is also not intended to be
covered in one week.)

     9c Part I Histograms, etc.                                                                    Notes PDF 683K
 Math: histograms and combining histograms, distributions and moments, normal
 distributions (needing antislopes), surprise and ignorance, correlations and
 conditional distributions.
 Science: ecology (mutual information in trophic networks) - in the Excursions.
 Computing: Bayesian learning.

     9c Part II Heat                                                                              Notes PDF 981K
 Computing: kinetic gas and other simulations.
 Science: Boltzmann and Maxwell distributions; entropy, temperature and pressure;
 thermostatic equations of state; work and heat. A kinetic theory of conflict
 (in the Excursions).
 Math: slopes of functions of more than one variable. Topology of graphs - in
 the Excursions.

     9c Part III Linear Thermodynamics                                                           Notes PDF 1953K
 Math: correlations of timeseries and a distribution whose autocorrelation sums
 to the mean interval length, convolutions and filters
 Science: transport phenomena - intercollision times and distances, and how the
 equilibrium autocorrelation filters forces: Green, Kubo and Nyquist, and hence
 mobility and diffusion; Brownian motion and Ohm's law; potentials and
 dissipation; active transport and membrane biochemistry; Onsager relations and
 combined transport (e.g., heat and electric: Seebeck and Peltier effects). In
 the Excursions: Kirchhoff circuits, heat conduction, viscosity, elasticity of
 solids and crystals, chemical kinetics and affinity of reactions.
 Computing: everywhere.

     9c Part IV. Melt, Boil, Condense, Freeze                                                     Notes PDF 518K
 Math: random graphs, critical probabilities, and, in the Excursions, power law
 distributions.
 Science: critical temperatures, resistance networks, van der Waals gas-liquids,
 the Ising model of ferromagnetism, Bose-Einstein condensation, and, in the
 Excursions, percolation and renormalization groups.
 Computing: simulations everywhere (the systems are not hard to describe
 mathematically but solving the math is labourious where not intractable),
 double-Newton's method, Z-order for multiple dimensions, and, in the
 Excursions, standing ovations as a phase transition.


Part II Logic, Memory and Languages
The scientific aspect is the biology of gene expression. This is related to the
engineering of memory circuits in computers, which motivates this Part.
The mathematics is boolean algebra of logic and combinational circuits and the
nonlinear math of feedback loops and sequential circuits.
The computing covered is iterative techniques to find attractors and cycles in
feedback systems, automata for grammar recognition, expression evaluation, and
memory and state in high-level programming languages. A guest lecture introduces
bioinformatics.

Week 10 The laws of thought                                                                        Notes PDF 172K
Engineering: logic gates, combinational circuits such as adders for a computer,
        and circuit simplification using Karnaugh maps.
Math: axioms of boolean algebra, all possible unary and binary operators on two values,
        universal operators and reversible operators; proof by contradiction.

Week 11 Memory, feedback and automata                                           MATLABpak          Notes PDF 207K
Engineering and science: sequential circuits such as flipflops, control systems,
        gene expression and cell differentiation.
Math: (nonlinear) feedback loops of boolean circuits.
Computing: iteration, simple automata for language recognition, stacks and queues
        for expression evaluation.

Week 12 Memory and programming language: recursion and instantiation            MATLABpak          Notes PDF 279K
Science: the algorithmic beauty of plants.
Computing: grammars for operator precedence, fractal drawing, encapsulation and
        instantiation of state. (Notes on LISP HTML 3K)
Math: Mathematical induction and proving programs correct.

Week 13 invited lecture on bioinformatics: Mathieu Blanchette