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Schedule of Lectures: EE/CS 219A and EE 298-007, Fall 2009


August 2009

2009/08/26 (Wed):
  • Lecture: Class syllabus and logistics (grading/HWs/midterm/projects). Introduction.
  • Discussion: Introduction continued. Modelling basic circuit elements: linear resistor, capacitor, inductor, controlled sources, independent sources. Linearity and memorylessness.
2009/08/31 (Mon):
  • Lecture: Circuit element modelling (continued): nonlinear devices: diode, BJT, MOS (Schichman-Hodges) models. Glimpses of BSIM, Antoniadis models.
  • HW1 assigned

September 2009

2009/09/02 (Wed):
  • Lecture: Circuit element modelling (contd.).
  • Discussion: INVITED LECTURE: Sriram Venugopalan will provide insights into "industrial strength" compact models, using the BSIM MOS model as an exemplar.
2009/09/07 (Mon): NO CLASS (academic holiday).
2009/09/09 (Wed):
2009/09/14 (Mon):
  • Lecture: Circuit equation formulations (contd.). Quiescent steady state algorithms and NR.
2009/09/16 (Wed):
  • Lecture: Newton-Raphson: convergence properties.
  • Discussion: INVITED LECTURE: Matt Spencer will present his development of a NEMS switch model, focussing on challenges faced and how he solved them.
  • HW2 assigned
2009/09/21 (Mon): NO CLASS (instructor out of town). MAKE-UP LECTURE ON: Friday Sep 25, 4-5:30pm, in 540A/B Cory.
2009/09/23 (Wed):
  • Lecture: Newton-Raphson: limiting and initialization. Jacobian sparsity.
  • Discussion: Jacobian sparsity continued. Numerical solution of linear equation systems. Gaussian Elimination.
2009/09/25 (Fri): MAKE-UP LECTURE
2009/09/28 (Mon):
  • Lecture: Matrix conditioning. LU error propapation. Simple iterative techniques for linear solution.
2009/09/30 (Wed):
  • Lecture: Iterative linear methods continued. Basic data structures for sparse matrices; sparse matrix packages. Biochemical reaction pathways.
  • Discussion: Rate equations for unimolecular and bimolecular reactions. Conservation.

October 2009

2009/10/05 (Mon):
  • Lecture: Rate equations for multi-molecular reactions. Stoichiometry.
  • HW3 assigned
2009/10/07 (Wed):
  • Lecture: ))Michaelis-Menten(( approximations of enzyme-catalyzed reactions. Identifying conservation laws numerically for systems of reactions.
  • Discussion: Numerical solution of ODEs. Existence and uniqueness conditions.
2009/10/12 (Mon):
  • Lecture: FE, BE and TRAP methods. Numerical solution of ODEs: LMS methods.
2009/10/14 (Wed):
  • Lecture: MIDTERM exam.
  • Discussion: Midterm exam solution/discussion.
2009/10/19 (Mon):
  • Lecture: Application of ODE methods to DAEs. Stability of FE, BE and TRAP. Accuracy and truncation error.
2009/10/21 (Wed):
  • Lecture: Starting higher-order LMS methods. LMS exactness constraints. Best p=2 LMS method. Stability of general LMS methods.
  • Discussion: The stability polynomial. Best p=2 method unstable for any h>0. Roots of stability polynomial near h=0.
2009/10/26 (Mon):
  • Lecture: Roots of stability polynomial near h=0 (contd.). Principal and parasitic roots of the stability polynomial. Condition for simple principal root. LMS local truncation error.
2009/10/28 (Wed):
  • Lecture: LMS local truncation error (contd.). LTE formulae. Numerical estimation of higher-order derivatives. Large-sigma behaviour: Stiff systems. Relative stability. Absolute and A- stability. Dahlquist's Second Barrier.
  • Discussion: Properties for stiff stability. BDF and Gear's methods.

November 2009

2009/11/02 (Mon):
  • Lecture: NO CLASS (instructor out of town). MAKE-UP LECTURE ON: Wednesday Nov 11, 1-2:30pm, in 299 Cory.
2009/11/04 (Wed):
  • Lecture: NO CLASS (instructor out of town). MAKE-UP LECTURE ON: Friday Nov 20, 3:30-5pm, in 540 A/B Cory.
  • Discussion: NO DISCUSSION (instructor out of town). MAKE-UP DISCUSSION ON: Wednesday Nov 11, 4-5pm, in 299 Cory.
2009/11/09 (Mon):
  • Lecture: Linearization about quiescent steady states. Periodic steady state analysis of LTI systems.
  • HW4 assigned
2009/11/11 (Wed):
  • Lecture: (MAKE-UP LECTURE: 1-2:30pm in 299 Cory) LTI transfer functions from DAEs. Eigenanalysis of transfer functions. Parameter sensitivity analysis around quiescent steady state. Direct and adjoint sensitivity computation.
  • Discussion: (MAKE-UP DISCUSSION: 3-4pm in 299 Cory) Probability and random variables: primer.
2009/11/16 (Mon):
  • Lecture: RV primer (contd.). Stochastic processes primer. Stationarity.
2009/11/18 (Wed):
  • Lecture: Ergodicity. Autocorrelation Functions, Power Spectral Density ())Wiener-Khinchine(( theorem.). Propagation of stationary noise through LTI systems.
  • Discussion: White and coloured noise. Thermal, shot and flicker noise. Vector stochastic processes. Stationary noise computation for LTI systems: direct and adjoint methods.
2009/11/20 (Fri):
  • Lecture: (MAKE-UP LECTURE: 3:30-5pm in 540A/B Cory) Stochastic modelling of biochemical systems. Basic reactions and their propensities. State probabilities.
  • Discussion: (MAKE-UP DISCUSSION: 5-6pm in 540A/B Cory) The Chemical Master Equation. CME for ))Michaelis-Menten(( example.
  • video of both sessions.
2009/11/23 (Mon):
  • Lecture: Gillespie's Stochastic Simulation Algorithm.
  • HW5 assigned
2009/11/25 (Wed):
  • Lecture: NO CLASS (instructor out of town). MAKE-UP LECTURE ON: Friday Dec 4, 2-3:30pm, in 540 A/B Cory.
  • Discussion: NO DISCUSSION (instructor out of town). MAKE-UP DISCUSSION ON: Friday Nov 20, 5-6pm, in 540 A/B Cory.
2009/11/30 (Mon):
  • Lecture: Tau leaping. Continuous approximation for large populations. Chemical Langevin Equation. Reaction Rate Equations.

December 2009

2009/12/02 (Wed):
  • Lecture: Computational macromodelling. The model reduction problem.
  • Discussion: Model reduction for LTI systems. Moments. Direct computation of moments.
2009/12/04 (Fri): (last day of class)
  • Lecture: (MAKE-UP LECTURE: 2-3:30pm in 540A/B Cory) Pade approximation. Numerical conditioning issues. Companion forms. Asymptotic Waveform Evaluation. Conclusions and review.
  • HW6 assigned

2009/12/16 (Wed): FINAL EXAM (5-8pm).