COS 598E
Advanced Topics in Computer Science: Cool Systems Ideas: Inspirations from Theory
Professor(s): Kai Li

Description/Objectives:
Study of the crossover research results between computer systems and theory. Read about recent systems based on their results and some recent theory papers that potentially influence future systems designs. Initial papers include various storage systems and networking protocols as well as the theory results in competitive algorithms, fingerprinting techniques, sketch data structures, similarity searches, and eraser codes. Guest speakers from both theory and systems communities will be invited.

Students who take this course can consider it as a "crossover" seminar between systems and theory. We will be reading and discussing some selected papers in systems whose designs are heavily influenced by theory results and some in theory whose ideas are promising for designing future systems. The topics being considered include storage systems, similarity searches and data explorations. When reading theory papers, we will take a systems approach: focusing on data structures, algorithms and properties, not on how to prove the properties. We plan to explore several kinds of data including images, audio data, microarray genomic data, time series data, and network data.

Schedule/Classroom Assignment:
Class Number: 42615 - Seminar S01 : 1:30 pm - 4:20 pm F
Computer Science Building (COMPU) 301 Location Photo

CEE 525
Applied Numerical Methods
Professor(s): Yin L. Young

Description/Objectives:
The goal of this course is to introduce students to a broad spectrum of numerical methods for the analysis of typical mathematics, physics, or engineering problems. Topics covered include: error analysis, interpolation and polynomial approximation, numerical differentiation and integration, ordinary differential equations, and partial differential equations.

Sample Reading List:
Chopra & Canale , Numerical Methods for Engineers

Requirements/Grading:
Midterm Exam: 30%
Design Project(s): 40%
Problem Set(s): 30%

Schedule/Classroom Assignment:
Class Number: 40556 - Lecture L01 : 1:30 pm - 2:50 pm M W

CHE 527
Nonlinear and Mixed-Integer Optimization: Fundamentals and Applications
Professor(s): Christodoulos A. Floudas

Description/Objectives:
This course provides an introduction to the fundamentals of convex analysis, nonlinear programming, duality theory, mixed integer linear and nonlinear optimization. The theory is complemented by a variety of application in process synthesis design, and operations. An introduction to deterministic global optimization and its applications will be provided.

Sample Reading List:
C.A. Floudas , Nonlinear and Mixed-Integer Optimization, Oxford Univ. Press
C.A. Floudas , Deterministic Global Optimization, Kluwer Acad. Pub., 2000

Examination Type: Final

Other Requirements:
Course Not Open to Freshmen

Schedule/Classroom Assignment:
Class Number: 40431 - Lecture L01 : 2:00 pm - 4:30 pm F

ORF 523
Nonlinear Optimization
Professor(s): John M. Mulvey

Description/Objectives:
An introduction to the central concepts needed for studying the theory, algorithms, and applications of nonlinear optimization problems. Topics covered include first- and second-order optimality conditions; unconstrained methods, including steepest descent, conjugate gradient, and quasi-Newtonian methods; constrained active-set methods; and duality theory and Lagrangian methods. Prerequisite: linear optimization.

Sample Reading List:
D. Luenberger , Linear and Nonlinear Programming
A. Sofer and S. Nash , Nonlinear Programming
R. Fouver, D. Gay, B. Kernighan , AMPL: A Modeling Language In Mathematical Programing

Other Requirements:
Course Not Open to Freshmen

Other Information: The course is open to graduate students and seniors.

Reserved Seats:
Seniors 7

Schedule/Classroom Assignment:
Class Number: 41798 - Lecture L01 : 9:00 am - 10:20 am T Th
Precept P01 : TBA

MAE 503/APC 507
Basic Numerical Methods for Ordinary and Partial Differential Equations
Professor(s): Weinan E

Description/Objectives:
Methods for moelcular and continuium simulatins of solids and fluids. Molecular dynamics, kinetic montecarlo methods

Other Requirements:
Course Not Open to Freshmen

Schedule/Classroom Assignment:
Class Number: 41072 - Lecture L01 : 2:00 pm - 4:50 pm W

MAT 594/APC 584
Wavelets: Applications of Wavelets in Mathematics and Other Fields
*/AUD/NC
Professor(s): Radu V. Balan

Description/Objectives:
This course will cover topics of wavelet and time-frequency analysis, with special emphasis on wavelet basis construction and filterbanks. It aims at building a bridge between the mathematics of harmonic analysis and its applications in engineering sciences. Two-thirds of the time will be spent on theory, with remaining one-third to be devoted to applications.

Sample Reading List:
I. Daubechies , Ten Lectures on Wavelets
G. Strang and T. Nguyen , Wavelets and Filter Banks

Other Requirements:
Course Not Open to Freshmen

Schedule/Classroom Assignment:
Class Number: 42246 - Class C01 : 2:00 pm - 3:20 pm T Th

AST 560
Computational Methods in Plasma Physics
Professor(s): Stephen C. Jardin

Description/Objectives:
Analysis of methods for the numerical solution of the partial differential equations of plasma physics, including those of elliptic, parabolic, hyperbolic, and eigenvalue type. Topics include finite difference, finite element, spectral, particle-in-cell, Monte Carlo, moving grid, and multiple-time-scale techniques, applied to the problems of plasma equilibrium, transport and stability. Basic parallel programming concepts are discussed.

Sample Reading List:
R.J. LeVeque , Finite Volume Methods for Hyperbolic Problems
Richtmyer & Morton , Difference Methods for Initial Value Problems
Tajima , Computational Plasma Physics: Appls. to Fusion & Astrophys.
Briggs , A Multigrid Tutorial
C. Hirsch , Numerical Computation of Internal and External Flows

Other Requirements:
Course Not Open to Freshmen

Prerequisites and Restrictions: Graduate students and seniors only.

Schedule/Classroom Assignment:
Class Number: 42163 - Class C01 : 10:30 am - 11:50 am T Th

MAE 557
Simulation and Modeling of Fluid Flows
Professor(s): Maria P. Martin

Description/Objectives:
Numerical methods are applied to solve the equations that govern fluid motion. Fluid flow problems involve convection, diffusion, and source terms. The governing equations are non-linear and coupled. Finite-difference and finite volume methods are considered, together with concepts of accuracy, consistency, stability, convergence, conservation, and shock capturing. A range of current methods is reviewed with emphasis on multidimensional steady and unsteady compressible flows. Homework topics include writing codes to solve the conservation equation for a scalar, boundary layer flow, shock tube flow, application to curvilinear coordinates.

Examination Type: Final

Schedule/Classroom Assignment:
Class Number: 41093 - Lecture L01 : 10:30 am - 11:50 am T Th

CHM 510/MSE 520
Topics in Physical Chemistry: Quantum Simulations in Chemistry and Physics
Professor(s): Roberto Car

Description/Objectives:
This course will discuss computational methodologies to simulate quantum many body systems in molecular and condensed phases. The following topics will be treated: ab-initio molecular dynamics, quantum Monte Carlo (variational and diffusion), path integrals, fermions and bosons, auxillary field quantum Monte Carlo, dynamics and open quantum systems.

Sample Reading List:
Review articles and books - as per lecture discussion

Other Requirements:
Course Open to Graduate Students Only.

Prerequisites and Restrictions: Requires a background in intermediate level quantum mechanics and quantum statistical mechanics

Schedule/Classroom Assignment:
Class Number: 41142 - Lecture L01 : 10:00 am - 10:50 am M W F

CHE 432
Dynamics of Cellular Processes
Professor(s): Stanislav Y. Shvartsman

Description/Objectives:
The goal of this class is to present a framework for the analysis of cellular responses, such as proliferation, migration, and differentiation. The emphasis is on mechanistic models of biotransformation, signal transduction, and cell-cell communication in tissues. The first section of the class will focus on unit operations of cell physiology transcription, translation, and signal transduction. Models of these processes will rely on tools of reaction engineering and transport. Then, we will use process dynamics and control to analyze the regulatory structure of networks of interacting genes and proteins.

Sample Reading List:
J.P. Keener , Mathematical Physiology, Springer 1998
Lauffenburger and Linderman , Receptors: models for binding, trafficking and signaling '93

Requirements/Grading:
Midterm Exam: 15%
Final Exam: 25%
Design Project(s): 20%
Problem Set(s): 20%
Other (See Instructor): 20%

Prerequisites and Restrictions: Mathematics level MAT 303 or APC 350/CEE 350 or MAE 305/MAT 301. Chemical Reaction Engineering. One undergraduate course in introductory biology (e.g. MOLBIO 214).

Schedule/Classroom Assignment:
Class Number: 40265 - Lecture L01 : 7:30 pm - 10:20 pm T

COS 557
Analysis & Visualization of Large-Scale Genomic Data Sets
Maximum Enrollment: 30
Professor(s): Olga G. Troyanskaya

Description/Objectives:
Introduces students to computational issues involved in analysis and display of large-scale biological data sets. Algorithms covered will include clustering and machine learning techniques for gene expression and proteomics data analysis, biological networks, joint learning from multiple data sources, and visualization issues for large-scale biological data sets. No prior knowledge of biology or bioinformatics is required; an introduction to bioinformatics and the nature of biological data will be provided. In depth knowledge of computer science is not required, but students should have some understanding of programming and computation.

Schedule/Classroom Assignment:
Class Number: 22690 - Lecture L01 : 1:30 pm - 2:50 pm M W
    Computer Science Building (COMPU) 401   Location  Photo

ELE 573/ CHE 573
Cellular and Biochemical Computing Systems
Professor(s): Ron Weiss

Description/Objectives:
A discussion of computational issues in modeling cellular systems and the engineering of synthetic biochemical computing systems. Topics include modeling of genetic regulatory networks using continuous and stochastic methods, construction of synthetic gene networks, metabolic networks, signal transduction pathways, cell-to-cell signaling, molecular and DNA computing, molecular self-assembly, directed molecular evolution, transcriptional and translational regulation, oscillation and circadian clocks, cell differentiation and pattern formation, chemotaxis, molecular switches and molecular electronics, theory of chemical computation.

Schedule/Classroom Assignment:
Class Number: 23001 - Lecture L01 : 3:00 pm - 4:20 pm M W
    Friend Center (FRIEN) 306   Location  Photo

COS 551/ MOL 551
Introduction to Genomics and Computational Molecular Biology
No P/D/F
Maximum Enrollment: 50
Professor(s): Mona Singh, Saeed Tavazoie

Description/Objectives:
Introduction to basic computational methods used for problems arising in molecular biology. Topics include computational approaches to: sequence similarity and alignment, phylogenic inference, gene recognition, gene expression analysis, structure prediction, and whole- and cross-genome analysis.

Other Requirements:
Course Not Open to Freshmen

Schedule/Classroom Assignment:
Class Number: 22676 - Seminar S01 : 3:00 pm - 4:20 pm T Th
    Carl Icahn Laboratory (ICAHN) 101   Location  Photo

APC 514/ MOL 514/EEB 514
Biological Dynamics
Maximum Enrollment: 20
Professor(s): Edward C. Cox, David W. Tank, William Bialek

Description/Objectives:
Introduction to the mathematical desciption of quantitative phenomena in living systems; Hodgkin Huxley equations of nerve membranes; the generation of spatial patterns in development, single cells, and colonies of cells; chemotaxis; the population dynamics of disease; dynamics activity of networks of neurons; intracellular chemical and gene-networks. Emphasis on formulation and experimental basis for the equations, and their relationship to significant biological issues.

Other Information: No background in the relevant biology is required. However, a solid preparation in mathematics including differential equations, integral calculus, and linear algebra is essential, as is some experience in using mathematics to model the real world. Graduate students with undergraduate degrees in mathematics, physics, electrical engineering, mathematical biology, and biophysics will have such backgrounds, as should Princeton seniors with these majors.

Related Web Site

Schedule/Classroom Assignment:
Class Number: 21413 - Lecture L01 : 1:30 pm - 2:50 pm T Th
    Carl Icahn Laboratory (ICAHN) 200   Location  Photo

COS 402
Artificial Intelligence
Maximum Enrollment: 25
Professor(s): Robert E. Schapire

Description/Objectives:
The fundamental principles, algorithms and techniques of modern artificial intelligence research and practice. Likely topics include: problem solving using search, game playing, logical inference, probabilistic reasoning in the presence of uncertainty, hidden Markov models, speech recognition, Markov decision processes, machine learning.Two 90-minute lectures. Prerequisites: 217 and 226.

Related Web Site

Schedule/Classroom Assignment:
Class Number: 22919 - Lecture L01 : 11:00 am - 12:20 pm T Th
    Computer Science Building (COMPU) 102   Location  Photo

COS 425
Database Systems
Maximum Enrollment: 50
Professor(s): Andrea S. LaPaugh

Description/Objectives:
The objective of this course is to study both the theoretical and practical aspects of database systems. We will also study the application of database concepts to web and digital library activities. Some of the topics covered are: levels of abstraction and views of data; file organizations; data models; examples of query languages; query evaluation; transactions; concurrency; unstructured data retrieval.

Related Web Site

Schedule/Classroom Assignment:
Class Number: 22908 - Lecture L01 : 1:30 pm - 2:50 pm M W
    Computer Science Building (COMPU) 105   Location  Photo

MAE 501/ APC 501
Mathematical Methods of Engineering Analysis I
No P/D/F
Maximum Enrollment: 40
Professor(s): Philip J. Holmes

Description/Objectives:
Methods of mathematical analysis for the solution of problems in physics and engineering. Topics include an introduction to functional analysis, linear analysis & eigenvalue problems for matrices & operators, Sturm-Liouville theory, Green's functions for the solution of linear ordinary differential equations and Poisson's equation, and the calculus of variations.

Schedule/Classroom Assignment:
Class Number: 21355 - Lecture L01 : 9:00 am - 10:20 am T Th
    Friend Center (FRIEN) 108   Location  Photo

CHE 502/ APC 502
Mathematical Methods of Engineering Analysis II
Maximum Enrollment: 30
Professor(s): Dudley A. Saville

Description/Objectives:
Solutions of ordinary differential, partial differential and finite difference equations with emphasis on second order linear partial differential equations and their applications. Topics include special functions, eigenvalues and eigenfunctions, Sturm-Liouville analysis, Green's functions, explicit and implicit finite difference methods, stability analysis, transform methods, asymptotic analysis.

Schedule/Classroom Assignment:
Class Number: 20231 - Lecture L01 : 1:30 pm - 2:20 pm M W F
    Engineering Quad A-Wing (EQUAA) A224   Location  Photo

ORF 405
Regression and Applied Time Series
Maximum Enrollment: 80
Professor(s): René A. Carmona

Description/Objectives:
Statistical Analysis of financial data: Density estimation, heavy tail distributions and dependence. Regression: linear, nonlinear, nonparametric. Time series analysis: classical models (AR, MA, ARMA, ..), state space systems and filtering, and stochastic volatility models (ARCH, GARCH, ....).

Related Web Site

Schedule/Classroom Assignment:
Class Number: 20083 - Lecture L01 : 3:00 pm - 4:20 pm M W
    Friend Center (FRIEN) 006   Location  Photo
                                  Precept P01 : 7:30 pm - 8:20 pm M
    Friend Center (FRIEN) 009   Location  Photo
                                  Precept P02 : 7:30 pm - 8:20 pm T
    Friend Center (FRIEN) 009   Location  Photo
                                  Precept P03 : 7:30 pm - 8:20 pm W
    Friend Center (FRIEN) 009   Location  Photo

ELE 488
Image Processing and Transmission
Professor(s): Peter J. Ramadge

Description/Objectives:
Introduction to the basic theory and techniques of two- and three-dimensional image processing. Topics include image perception, enhancement, restoration, compression, image transforms, tomography, and image understanding. Applications to HDTV, machine vision, medical imaging, etc.

Schedule/Classroom Assignment:
Class Number: 21526 - Laboratory B01 : TBA
Class Number: 21527 - Lecture L01 : 11:00 am - 12:20 pm T Th
    Engineering Quad B-Wing (EQUAB) B205   Location  Photo

ORF 474
Special Topics in Operations Research and Financial Engineering: Monte Carlo Simulation
Maximum Enrollment: 20
Professor(s): William A. Massey

Description/Objectives:
An introduction to the uses of simulation and direct computation in analyzing stochastic models and interpreting real phenomena. The course deals with generating discrete and continuous random variables, stochastic ordering, the statistical analysis of simulated data, variance reduction techniques, statistical validation techniques, nonstationary Markov chains and Markov chain Monte Carlo methods. Applications are drawn from problems in finance, manufacturing and communication networks.

Schedule/Classroom Assignment:
Class Number: 20091 - Class C01 : 10:00 am - 10:50 am M W F
    Engineering Quad E-Wing (EQUAE) E415   Location  Photo

MAE 541/ APC 571
Applied Dynamical Systems
Maximum Enrollment: 30
Professor(s): Clarence W. Rowley

Description/Objectives:
Phase-plane methods and single-degree-of-freedom nonlinear oscillators; invariant manifolds, local and global analysis, structural stability and bifurcation, center manifolds, and normal forms; averaging and perturbation methods, forced oscillations, homoclinic orbits, and chaos; and Melnikov's method, the Smale horseshoe, symbolic dynamics, and strange attractors.

Schedule/Classroom Assignment:
Class Number: 21363 - Lecture L01 : 11:00 am - 12:20 pm T Th
    Friend Center (FRIEN) 109   Location  Photo

EEB 533
Topics in Ecology: Modeling Epidemiology, Ecology, and Evolution
Maximum Enrollment: 20
Professor(s): Jonathan G. Dushoff

Description/Objectives:
Topics in modeling epidemiology, ecology, and evolution, including spatial modeling and stochastic modeling, with a focus on research topics of interest to students.

Schedule/Classroom Assignment:
Class Number: 20695 - Seminar S01 : 4:30 pm - 6:30 pm T