GGAM Newsletter for GGAM members

Fall 2009

Today's Editor: Naoki Saito

Today's Topics:

1. A message from GGAM chair
2. GGAM Mini-Conference is scheduled on January 9 (Sat), 2010

3. GGAM related seminars

4. Winter & Spring courses by GGAM faculty

5. Apply nationally competitive graduate fellowships

6. Free SIAM student membership and the UC Davis SIAM Club

7. A list of good books for publications and career planning for students

8. Conference participation

9. Summer schools at NSF Mathematical Sciences Institutes

1. A message from GGAM chair

Dear GGAM members,
GGAM welcomed 10 new graduate students this year. These are a distinguished group of students, including a recipient of the UCD Graduate Scholar Fellowship (Charles Brummitt). GGAM now consists of 66 students and 86 faculty members. Since September 2008, GGAM has welcomed 6 new faculty members:
Ian Davidson (CS); Francois Gygi (Applied Science); Alessandro Pizzo (Math); Michael Savageau (Biomedical Engineering); Burkhard Schipper (Economics); and Albert Schwarz (Math).

As for the continuing students, Jia-Ming "Frank" Liou received the Henry Alder Award. We also granted 4 Ph.D. and 5 MS degrees in the last academic year.

I would like to thank Joseph Biello, Michael Zhang (CEE), Tami Joy Schlichter (student representative) for their service as a member of the GGAM Executive committee. Joseph, Michael, and Tami were replaced by Jim Bremer (Math), Alan Hastings (Env. Sci. & Policy), and Julie Blackwood, respectively.
The continuing GGAM Executive Committee members are: Tim Lewis (Math); Naoki Saito (Math); and Sebastian Schreiber (Evolution & Ecology). I thank the committee members for their willingness to serve!

I am very interested in hearing what ideas you have for GGAM!
Please contact me or the GGAM Executive Committee at .

Naoki Saito

2. GGAM Mini-Conference

The fifth Annual GGAM Mini-Conference is scheduled on Saturday, January 9, 2010. Please mark your calendar. The conference manifests what GGAM is all about: a coming together of our students with faculty from across campus in order to facilitate fruitful collaborations. Tim Lewis will be the lead organizer this
time. Thanks, Tim, for doing this!
Although attendance is mandatory for all 1st-year Applied students, all students are welcome to attend. In particular, any students who do not have official Ph.D. advisers yet are strongly encouraged to attend this.
CRN to register for one unit (attendance will be taken): 50224 (Winter 2010)

The fourth Annual GGAM Mini-Conference was held on January 10, 2009. In an informal day-long forum, 9 faculty members described their research interests, giving our students an opportunity to experience the broad directions available to them in applied mathematics. The departments and units represented at the conference included: Applied Science; Bodega Marine Laboratory; Center for Neuroscience; Evolution and Ecology; Land, Air, Water Resources; Mathematics; and Neurobiology, Physiology and Behavior.
Similarly to the previous year, a large number of guests (about 60) attended the dinner afterward held in our large colloquium room, which was another opportunity for faculty and students to get to know each other.

Let's get together again for the GGAM Mini-Conference and dinner after that!
More details will be announced later.

3. GGAM-related Seminars

Applied Mathematics at UC Davis is nationally and internationally recognized. I would like to keep our vigorous activities and help you achieve your goals. Your active participation in one or more of the projects listed below is what will keep GGAM strong.

Fall (4pm, Tue): Joseph Biello <>
Winter (4pm, Tue?): John Hunter <>
Spring (4pm, Tue?): Gerry Puckett <>

I would like to note that Joseph Biello implemented the following nice idea for the Applied Math/PDE seminar this Fall. There will be an extra 1/2 hour scheduled that will allow opportunities for the speakers to interact with our graduate students on a more personal, less formal manner.

Student Organizers: David Cherney <>
Overseeing Faculty:
Thomas Strohmer <>
Winter & Spring:
Naoki Saito <>

Of course, there are many other relevant seminars. Please check the seminar page: .
Also, there is a list of seminars offered by the other departments and nearby schools. Please take a look at: .
Thanks to Thomas Harter's suggestion, we have now links to some useful video lectures.
Please take a look at:
If you have any suggestions, please send an email to .

4. Winter and Spring Courses by GGAM faculty

There are many relevant graduate courses that will be taught by GGAM faculty in Winter and Spring 2010. I asked the entire GGAM faculty about such courses, and here are their replies, listed in the order in which I received them.

1. ECI 212A (Winter 2010): Finite Element Procedures in Applied Mechanics
Introduces students to the strong, weak and variational forms of elliptic boundary-value problems and their numerical solution using the finite element method (programming in Matlab). Syllabus at:

2. ECI 289F (Spring 2010): Meshfree Methods and Partition of Unity Finite Element Methods
Course focuses on meshfree approximations and partition-of-unity enriched finite element solution for PDEs that admit singularities, boundary layers and/or localized solutions: applications in solid/bio mechanics, fluids, quantum mechanics, and graphics have been explored so far. Web page:

The Spring class is contingent on enough students being interested (I had 2
math students who registered when I taught it last time around).

Hydrology 298 [Group Study] (Spring 2010): Practice of Groundwater Flow & Transport Modeling
Units: 2 (S/U)
Time: 6 Lecture-Laboratory Sessions of 4 hours each, April-May.
Course Topics:

  • overview of groundwater modeling software
  • data collection and preparation
  • model grid design
  • boundary conditions
  • transient flow modeling
  • sensitivity analysis, model calibration and verification
  • capture zone analysis
  • contaminant transport modeling
  • geostatistical modeling
For more info, visit

MAE 254 (Spring 2010): Engineering Software Design (4)
Principle and design of engineering software. Advanced topics in engineering software design, applications of object-oriented programming, very high-level languages, real-time multi-thread computing and sensor fusion, Web-based network computing, graphics, and GUI in engineering.

MAE 263 (Winter 2010): Introduction to Computational Aerodynamics and Fluid Dynamics
The course deals with the numerical solution of PDEs of hyperbolic, parabolic and elliptic type. The course also covers the case of a non-linear PDE of mixed-type (Transonic Small Disturbance equation and the Murmann-Cole method) and systems of conservation laws such as the equations of gas dynamics, including the associated jump conditions.

1. Physics 256 (Winter 2010): Natural Computation and Self-Organization---
The Physics of Information Processing in Complex Systems

2. Physics 250 (Spring 2010): Special Topics in Physics of Computation
Physics 256 is a prerequisite. This new course will analyze computational structures embedded in nonlinear systems.

3. Physics 250 (Spring 2010): Nonlinear Physics---Modeling Chaos and Complexity
Learn scientific programming by building software tools to explore nonlinear dynamics and pattern formation. Website:

MAT 280 (Spring 2010): Sparse Representations and Compressed Sensing
Sparsity has become a very important concept in recent years in applied mathematics. The key idea is that many types of functions and signals arising naturally in applications can be described by only a small number of significant degrees of freedom. Compressed sensing is a ingenious means to exploit sparsity. Compressed sensing is not only one of the hottest topics in mathematics in recent years, but it also has the potential to revolutionize the technology of data acquisition in a broad sense. This course will discuss the theoretical, numerical and practical foundations of sparse representations and compressed sensing. We will investigate the many fascinating connections between these topics and other areas such as harmonic analysis, random matrix theory, optimization, statistics, information theory and signal processing.

ECS 229 (Winter 2010): Advanced Computational Structural Bioinformatics
This class covers: - algorithmic problems in structural biology, - protein structure classification, - protein structure prediction (including comparative modeling and ab initio protein structure prediction) - molecular simulations (molecular dynamics and Monte Carlo simulations).

I often had GGAM students taking this calls, it seems always with success!

BIM 271 (Winter 2010): Gene Circuit Theory: Analysis of Function and Design
Objectives: This course will cover modeling, analysis, design and construction of gene circuitry. It will first review several elements of design, develop mathematical methods to study variations in design, and present case studies that illustrate the discovered of design principles for elementary gene circuits in prokaryotes. This approach will then be extended to more complexgene circuits and to synthetic gene circuits that have been designed and constructed with a specific engineering objective in mind.
Prerequisites: Math through calculus and introductory biology, or permission of instructor.

BIM 285 (Spring 2010): Computational Modeling in Biology and Immunology
Theory and applications of computer simulation techniques to biomedical and immunological problems. We will mainly discuss Monte Carlo simulation techniques. Students will be introduced to Monte Carlo simulations in C or/and MATLAB.

MAT 266 (Winter 2010): Statistical Mechanics and Quantum Field Theory
I will primarily focus on Statistical Mechanics. The course will cover the foundations of statistical mechanics (classical and quantum) with an emphasis on lattice systems.

EAD 229 (Spring 2010): Computational Molecular Modeling
This course is taught jointly by Profs Jensen, Canning and Gygi of the Department of Applied Science. It provides an introduction to the computational methods and algorithms used in molecular modeling and includes classical molecular dynamics, elements of electronic structure theory and quantum molecular dynamics. The course also includes hands-on exercises usingmolecular simulation software.

This course may be relevant for students interested in understanding the applied mathematics aspects of molecular simulations.

MAT 280 (Winter 2010): Asymptotic Methods for Nonlinear Waves
We will focus on two classes of non-linear, dispersive wave equations. The first arise in fluids with a discontinuity of vorticity and describe the dynamics of the interface of the discontinuity. The second arise in the atmosphere near the equator because in the change in the vertical component of the rotation vector at the equator. These systems were originally studied by Biello & Hunter and Majda & Biello, resepectively. The class is a continuation of this quarter's seminar on linear wave theory, the notes of which can be found online: This is associated with the VIGRE Research Focus Group on "PDEs and Nonlinear Waves". See the details at:

1. MAT 258B (Winter 2010): Discrete and Mixed-Integer Optimization
(Note that it still appears in the course catalog under the old title "Variational Analysis".) This is a completely redesigned course, which covers mathematical modeling, algorithms, software, and theory for global optimization of problems with integer variables. URL:

2. MAT 290-081 (Winter/Spring 2010): Research Focus Group seminar on Optimization

This is a combined reading and research seminar on current topics in discrete optimization and its applications. URL:

MAT 271 (Winter 2010): Applied and Computational Harmonic Analysis
Introduction to mathematical basic building blocks (wavelets, local Fourier basis, and their relatives) useful for diverse fields (signal and image processing, numerical analysis, and statistics). Emphasis on the connection between the continuum and the discrete worlds. If you are interested in taking Prof. Strohmer's MAT 280 in Spring, then you may want to take my MAT 271 first.
Here is the link to the official syllabus:
Here is the webpage of this course when I taught it last time (will be updated for this year soon):

5. Apply nationally competitive graduate fellowships

Please consider applying for national graduate fellowships. Although they are very competitive, it helps you and GGAM tremendously. Even an application process itself including writing an essay will be useful for your future career. Here is a very convenient list of such fellowships organized in terms of deadline gathered by North Carolina State Univ.:

A more extensive list with alphabetical order can be found at:

6. Free SIAM student membership and The UC Davis SIAM Club

Because UC Davis is an academic member of SIAM (Society for Industrial and Applied Mathematics as you know), all UC Davis students (not just students in the Math Department) are eligible for FREE SIAM membership. For the benefits of membership, see: .

Also, UC Davis has a local student chapter: the UC Davis SIAM Club. On May 8-9th, 2009 the UC Davis SIAM Club held the second annual Davis SIAM Student Research Conference. More than 50 conference attendees from UC Davis and CSU Sacramento saw 14 student talks and 9 student poster presentations on applied mathematics related to topics ranging from atmospheric science tomathematical biology to broadcast communications.
Keynote speakers Professor James Keener from the University of Utah and Professor Lisa Fauci from Tulane University gave great talks on mathematical biology. The conference was supported by SIAM and an NSF VIGRE mini-grant. More information including how to join the UC Davis SIAM Club can be found at SIAM Club webpage: .

7. List of good books for publications and career planning for graduate students

Although this information was disseminated in the last year's newsletter, I'm repeating this for new students with some updates.

Over the years, I found the following books very useful for my graduate students in terms of writing their theses and papers and advising their career. So, I would like to share these with you. In fact, I myself enjoyed reading these very much and highly recommend them.

On publishing papers and making presentations:

  • Robert A. Day: How to Write and Publish a Scientific Paper, 6th Edition, Greenwood Press, 2006. ISBN: 0313330409
On general advise on your career:
  • Peter J. Feibelman: A Ph.D. Is Not Enough! A Guide to Survival in Science, Basic Books, 1993. ISBN: 0201626632
  • Richard M. Reis: Tomorrow's Professor: Preparing for Careers in Science and Engineering, IEEE Press, 1997. ISBN: 0780311361
On English usage, styles, and grammar:
  • William Strunk, Jr. and E. B. White: The Elements of Style, 4th Edition, Longman, 2000. ISBN: 020530902X
  • Robert A. Day: Scientific English: A Guide for Scientists and Other Professionals, 2nd Edition, Oryx Press, 1995. ISBN: 0897749898
More about math specific career advice or writing:
  • Steven G. Krantz: A Mathematician's Survival Guide: Graduate School and Early Career Development, AMS, 2003. ISBN: 082183455X
  • Steven G. Krantz: The Survival of a Mathematician: From Tenure-Track to Emeritus, AMS, 2009. ISBN: 978-0-8218-4629-2
  • Nicholas J. Higham: Handbook of Writing for the Mathematical Sciences, 2nd Edition, SIAM, 1998. ISBN: 0898714206
  • Steven G. Krantz: A Primer of Mathematical Writing, AMS, 1997. ISBN: 0821806351
  • Ian Stewart: Letters to a Young Mathematician, Basic Books, 2007. ISBN: 0465082327

8. Conference participation

Participating in conferences may play a significant role for your future career. You must work hard to prepare your talks or posters, but it is really worth it in multiple ways. You will learn how to make your presentation materials, how to get your point across to the audience, how to interact with audience. Moreover, you can meet with all sorts of people in the conferences from preeminent scientists to your contemporaries from other universities.

We also have a small amount of student travel support if you present your talk at conferences. So, please consider to submit your paper to appropriate conferences. Also, I very much encourage you to discuss this with your adviser.

9. Summer schools at NSF Mathematical Sciences Institutes

Every summer, many of the NSF Mathematical Sciences Institute, such as MSRI, IPAM, and IMA(see more for the list of such institutes) organize graduate summer schools or special summer programs.
Examples include:
- Research in Industrial Projects for Students (RIPS) at IPAM
- Mathematical Modeling in Industry Workshop for Graduate Students at IMA
You can also find many more summer schools on special topics at these institutes.
Please consider and apply for such summer schools when those institutes start soliciting the applications (usually during the winter period).