GGAM Newsletter for GGAM members

Fall 2011

Today's Editor: Naoki Saito

Today's Topics:

0. A message from GGAM chair

1. GGAM program review is under way

2. GGAM Mini-Conference is scheduled on January 21 (Sat), 2012

3. GGAM related seminars

4. Relevant courses by GGAM faculty

5. Apply internal and external graduate fellowships

6. Free SIAM student membership and the UC Davis SIAM Student Chapter

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

8. Conference participation

9. Summer schools at NSF Mathematical Sciences Institutes

0. A message from GGAM chair

Dear GGAM members,

This is my fifth and last newsletter as Chair of GGAM given that my term will be ending on June 30, 2012. I would like to thank all of you for your involvement on GGAM affairs over these years. As I will discuss later in this newsletter, we are going through a Graduate Program Review this year. The Ad Hoc Committee will visit us to discuss the matters on February 22 (W) and 23 (Th). So, please make every effort to participate in the activities during those two days. More details will be announced later.

GGAM welcomes 12 new graduate students to the program this year, including two UCD graduate students (Jizhou Huang and Omar Hafez) who come from different graduate programs and are now pursuing our MS degrees. These are a distinguished group of students, including two recipients of the prestigious NSF Graduate Research Fellowship (Calina Copos and Swati Patel). GGAM now consists of 58 students and 87 faculty members. During the last academic year, GGAM welcomed 3 new faculty members: John Owens (Electrical & Computer Engineering); Sam Walcott (Math); and Qing Zhao (Electrical & Computer Engineering). Also, please visit their own home pages linked from the GGAM faculty website.

Our continuing students have been doing extremely well this year. First of all, Yuji Nakatsukasa, who just graduated with his Ph.D. and left Davis for his postdoc position at Univ. Manchester, UK, won first prize in the 2011 Leslie Fox Prize in Numerical Analysis. He is the first UCD graduate student to win this award. Charlie Brummitt received the NSF GRF and the National Defense Science & Engineering Graduate (NDSEG) Fellowship, another quite prestigious award. In the end, Charlie had to make a tough choice, after serious consideration, he decided to take NDSEG. Jeff Irion also received the NDSEG. In addition, the UCD Graduate Research Mentorship Award went to Ricky Kwok; Alice Leung Scholarship went to David Renfrew; and Yueh-Jin Lin Scholarship went to Yuji Nakatsukasa. We have never seen such a number of major fellowship/award recipients simultaneously in our program, and we should be very proud of their achievements!

By the end of Summer 2011, we granted 9 Ph.D. degrees (Thomas Hunt, Blake Hunter, Eunghyun Lee, Jia-Ming "Frank" Liou, Yuji Nakatsukasa, Anastasia Raymer, Moritz Reintjes, Tami Schlichter, Martha Shott) and 1 MS degree (Jacob Porter) in Applied Mathematics.

I would like to thank Jim Bremer (Math) and Alan Hastings (Env. Sci. & Policy
) for their service as a member of the GGAM Executive Committee. Jim and Alan were replaced by Alex Mogilner (Math/NPB), Louise Kellogg (Geology). The continuing GGAM Executive Committee members are Albert Fannjiang (Math), Raissa D'Souza (MAE and CS), and Naoki Saito (Math) with Greg Shinault serving as our student representative. I thank the committee members for their willingness to serve.

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

Naoki Saito

1. GGAM Program Review is under way

Every eighth year or so, every graduate program must go through the so-called program review, whose purpose is to promote excellence in graduate programs at UC Davis and provide an opportunity for programs to evaluate past achievements, current status, and future directions related to graduate education. The last one for GGAM was conducted in Year 2001-2, and we got positive review: "... the considerable stature of GGAM, which appears to be an excellent graduate program with very strong faculty." On the other hand, it also included the following points to be improved: Space problems; Insufficient block grant; Interaction with LLNL. We now see that these have been improved since then.

For the 2011-12 program review, all the information (e.g., your short CV, my executive summary report, etc.) was sent to the Program Review Committee (PRC), a subcommittee under the Graduate Council in July. I bugged you many times to get necessary information for this, and I truly appreciate your prompt assistance! Now, based on the inputs from the GGAM members and deans, the PRC selected both internal and external reviewers as follows:

The Ad Hoc Committee will visit us on February 22 (Wed) and 23 (Thu), 2012. So, please make every effort to participate in the review process, e.g., to meet with the review committee, etc. More details will follow as the date nears, so stay tuned!

2. GGAM Mini-Conference

The sixth Annual GGAM Mini-Conference is scheduled on Saturday, January 21, 2012. 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. Jim Bremer will be the lead organizer this time. Thanks, Jim, 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.

The fifth Annual GGAM Mini-Conference was held on January 15, 2011 organized by Sebastian Schreiber. 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: Biostatistics; Chemical Engineering & Material Science; Civil & Environmental Engineering; Computer Science; Geology; Mathematics; Mechanical & Aeronautical Engineering. More than 70 people, attended the dinner, which followed the conference and was held in our large colloquium room. This 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 on Saturday, January 21, 2012! More details will be announced later.

3. GGAM-related Seminars

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

Fall (3pm, Tue): John Hunter <>
Winter (3pm, Tue?): Blake Temple <>
Spring (3pm, Tue?): Qinglan Xia <>
Student Organizer: Greg Shinault <>

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: .

If you have any other suggestions to enhance our program, please send an email .

4. Relevant Graduate Courses by GGAM faculty

There are many relevant graduate courses that will be taught by GGAM faculty during the 2011-12 academic year. I asked the entire GGAM faculty about such courses, and here are their replies, listed in the order in which I received them.
Note that I already forwarded the fall course info to our students in September.

MAT 205AB (Winter/Spring 2012): Complex Analysis
We will cover the topics in "Complex Analysis" by Stein & Shakarchi with the additional material added if time permits.

Physics 256 (Winter/Spring 2012): Natural Computation and Self-Organization---The Physics of Information Processing in Complex Systems
Website: Offered as a two quarter sequence.
The course explores how nature's structure reflects how nature computes. It introduces intrinsic unpredictability (deterministic chaos) and the emergence of structure (self-organization) in natural complex systems. Using statistical mechanics, information theory, and computation theory, the course develops a systematic framework for analyzing processes in terms of their causal architecture. This is determined by answering three questions: (i) How much historical information does a process store? (ii) How is that information stored? And (iii) how is the stored information used to produce future behavior? The answers to these questions tell one how a system intrinsically computes.

The course develops tools to describe and quantify randomness and structure. It will show how they are necessarily complementary and how they are intimately related to concepts from the theory of computation. A number of example complex systems—taken from physics, chemistry, and biology—will be used to illustrate the phenomena and methods. The course also takes time to reflect on the intellectual history of these topics, which is quite rich and touches on many basic questions in fundamental physics and the sciences and technology generally. New topics this year include complex materials and computation in quantum systems. The course will bring students to the research frontier in nonlinear physics and complex systems.

ECS 289H (Winter 2012): Advanced Image Processing and Analysis
The course covers cutting-edge computational techniques for extracting meaningful information from data arising from photographic, 3d surface, and tomographic sensors.

ECL/PBG 231 (Fall 2012): Mathematical Methods in Population Biology
This course discusses linearity, linearization, and producing models by taking limits in the context of population biology. A way for GGAM students to see how the math gets used in a field of application.

ECL 232 (Winter 2012): Theoretical Ecology
This course provides a survey of the field of Theoretical Ecology based on both background material and a selection of recent topics which would expose GGAM students to a wide variety of interesting biological questions that can be approached using quantitative ideas. The course is based on a project and reading in the original literature.

ECS 277 (Spring 2012): Advanced Visualization
This course is concerned with advanced methods needed for scientific data analysis and visualization, Examples of mathematical and geometrical topics covered in this course include:data approximation and interpolation methods; spline curves, surfaces and volumes; approximation of scalar, vector and tensor field data; topological analysis of scalar, vector and tensor fields; best approximation; data reduction and compression; hierarchical or multi-resolution data representation; data tessellations and triangulations; efficient volume rendering, slicing and contouring of three-dimensional data sets.

EEC 201 (Winter 2012): Digital Signal Processing
Theory and design of digital filters. Classification of digital filters, linear phase systems, all-pass functions, FIR and IIR filter design methods and optimality measures, DFT, FFT implementations. EEC201 requires only some working knowledge of continuous and discrete-time Fourier analysis. This is a first-year grad course with final exam

EEC 263 (Spring 2012): Optimal and Adaptive Filtering
Geometric formulation of least-square estimation problems. Theory and applications of optimum Wiener and Kalman filtering. Adaptive filtering algorithms, properties and applications. EEC263 requires both some knowledge of random processes and of DSP. This course is more advanced than EEC 201 and requires a term paper or project.

MAT 280 (Winter 2012): Introduction to Random Matrices
The class is devoted to the spectral properties of large random matrices with independent entries.

ECI 212A (Winter 2012): Finite Element Procedures in Applied Mechanics
The focus in this course is to provide students a sound understanding of the variational basis and tools required to develop Galerkin finite elements for linear elliptic boundary-value problems in applied mechanics. Students will be introduced to good programming practices for finite elements, and through computer assignments, they will program finite elements for the purpose of computer simulations in structural and solid mechanics.

BIM 271 (Fall 2011): Gene Circuit Theory: Analysis of Function and Design
Nonlinear ODEs are used to model gene circuits. Students taking this course learn strategies for the formulation of mathematical and computer models, gain experience in the interpretation of modeling results, and acquire an appreciation for how models contribute to the understanding of function, design and evolution of natural and synthetic gene circuits.

ECS 227 (Winter 2012): Modern Cryptography
Encryption, authentication, and protocols, with an emphasis on definitional foundations and reductions.

EME 254 (Spring 2012): Engineering Software Design
Principle and design of engineering software. Advanced topics in engineering software design, such as object-oriented design, real-time multi-thread computing and sensor fusion, embedded computing, mobile agent-based computing, grid computing, and design of graphical user interface.

NPB/NSC 287AB (Fall 2011/Winter 2012): Topics in Theoretical Neuroscience
Topics in Theoretical Neuroscience* (graduate seminar). The topic this year is Neural Dynamics, including introduction to the analysis of nonlinear dynamics, synchrony, and noise analysis.

NSC 267 (Fall 2011): Computational Neuroscience
This is a lecture course with computer programming laboratory). This course provides a broad introduction to the field of Computational Neuroscience, including models of single-neuron biophysics, neural coding, spike train statistics, and learning

MAT 280 (Spring 2012): Quantum Phase Transitions
In this course we will explore the structural properties of gapped ground state phases of quantum many-body systems and the critical points that separate distinct phases. The emphasis will be on models that are or might become amenable to mathematical analysis. Prerequisite: some background in basic quantum mechanics or statistical mechanics preferred.

STA 223 (Winter 2012): Generalized Linear Models
The class requires STA131ABC and STA232A or familiarity with exponential family, maximum likelihood and asymptotic statistical inference. It provides an advanced graduate level introduction to statistical regression analysis and biostatistical applications, emphasizing the generalized linear model and related topics.

MAT 280 (Fall 2011): Introduction to ramified optimal transportation
This topic course aims at introducing ramified optimal transportation to graduate students in both pure and applied mathematics.
Ramified transportation formally formulates the concept of transport economy of scale in group transportation observed widely in both nature (e.g. trees, blood vessels, river channel networks, lightning) and efficiently designed transport systems of branching structures (e.g. railway configurations and postage delivery networks). Motivations of this theory originate from the study of minimal surfaces in geometry as well as designing optimal communication networks. During the course, we will first study mathematical formulations of the problem. Our attention will be focused on studying analytical as well as geometric properties of an optimal transport path. Then, we will study its applications in both pure mathematics (e.g. metric geometry) and applied mathematics (e.g. formation of tree leaves, fractals, mathematical economics). Suitable audiences include those who are interested in geometry, combinatorics, analysis, optimization, complex structures, fractals, math biology, mathematical economics etc, and in particularly those who are amazed by the beauty of the nature.
Here is the link of the course website: .

EME 263 (Winter 2012): Introduction to Computational Fluid Dynamics
The course deals with numerical simulations of basic flows (boundary layers and potential and Euler flows with shocks) using simple grids and standard finite difference schemes and solvers. Prerequisites are undergraduate Flow Physics and Numerics.

ATM 221 (Winter 2012): Advanced Atmospheric Dynamics (subtitle: Geophysical Wave Motions)
Waves are ubiquitous. They occur in liquids, solids, gases and plasmas as well as in interplanetary space. Because waves can communicate information far from their seat of origin, it is important to understand their behavior in order to predict the future state of a system. In this course, I will cover the fundamentals of geophysical wave theory with application to Earth's atmosphere. Among the topics I will cover are: wave kinematics; surface gravity waves; energy and energy propagation; internal gravity waves; group velocity, reflection; WKB theory for internal gravity waves; ray tracing; energy and energy flux; conservation laws for waves (e.g., wave action); instability waves; wave-mean flow interaction.ere we will develop mathematical models of the structure and function of networks, including growth, vulnerability and percolation, and explore their applications to real world systems ranging from the Internet and power gird, to social acquaintance networks and biological networks.

MAT 271 (Winter 2012): Applied & Computational Harmonic Analysis
The course will introduce the student to the mathematical basic building blocks (wavelets, local Fourier basis, and their relatives) useful for diverse fields (signal and image processing, numerical analysis, and statistics. Connections to emerging fields such as sparse representations and compressive sensing will also be discussed.

MAT 280 (Spring 2012): Harmonic Analysis on Graphs and Networks
Graphs and networks have been successfully used in a variety of fields (e.g., machine learning, data mining, image analysis, sensor networks, social sciences, etc.) that are confronted with the analysis and modeling of high-dimensional datasets. Harmonic analysis tools originally developed for Euclidean spaces and regular lattices are now being transferred to the general settings of graphs and networks in order to analyze geometric and topological structures, and data and signals measured on them. In this course, we shall discuss a variety of important theories and interesting applications employing harmonic analysis on graphs and networks. Topics include: graph Laplacians, their eigenvalues and eigenvectors for structural analysis, wavelets on graphs, random walks and diffusion on graphs, spectral clustering, non-local means denoising algorithms, etc. Prerequisite: MAT 129, MAT 167, MAT 271, or consent of instructor.

5. Apply internal and external graduate fellowships

Please consider applying for internal and external graduate fellowships. Although they are very competitive, it helps you and GGAM tremendously. For example, the application process itself, including writing an essay, will be useful training for your future career when you apply for research grants.
An important note to faculty advisers: In past years, the number of our students applying for campus fellowships has been ridiculously low. We need you to light a fire under your students to encourage them in this regard. Every student who brings in funding on his/her own helps our efforts in securing funding for the group as a whole.

Internship Fellowships (NOTE: Deadline is December 1st this year)

Travel Awards - Graduate Studies (deadlines vary)
NOTE: For the current awards cycle, applications are due to departments Friday, Oct 15.

Here is a very convenient list of nationally competitive fellowships sorted in terms of deadline gathered by North Carolina State Univ.:

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

One more thing, I encourage you all to read each announcement that our Student Services Unit sends you via the listserv. Although I realize that most of the information that is sent to you is academically based with respect to upcoming events on campus, I also know that a few of the announcements include valuable information about funding opportunities. Please do not take these messages lightly. Make the most of your resources, and take advantage of these opportunities when they become available.

6. Free SIAM student membership and The UC Davis SIAM Student Chapter

Because UC Davis has a local student chapter of SIAM (Society for Industrial and Applied Mathematics as you know), any UC Davis student is eligible for FREE SIAM membership once he/she becomes a member of the UC Davis student chapter of SIAM. For the benefits of membership, see: .

One of the major activities of
this student chapter of SIAM is the annual UC Davis SIAM Student Research Conference (DSSRC). On May 6-7, 2011, the fourth annual DSSRC was held. Approximately 60 conference attendees from UC Davis and CSU Sacramento were present to welcome this year's distinguished keynote speaker. We were very proud to have Professor Yinyu Ye from Stanford University. Professor Ye gave a presentation on "The Simplex and Policy-Iteration Methods for the Markov Decision Problem with a Fixed Discount Rate." The conference consisted of 12 student talks and poster presentations on applied mathematics related to topics ranging from atmospheric science to mathematical biology to integer optimization. Presenters and attendees included students from CSU Sacramento and the faculty advisor of the CSU Sacramento Student Chapter of SIAM. This was a great networking opportunity for the Davis chapter, which has opened a line of dialogue for future collaboration. The conference was supported by SIAM, an NSF VIGRE mini-grant, and the UCD Mathematics Galois Group. More information including how to join the UC Davis SIAM student chapter 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 and Barbara Gastel: How to Write and Publish a Scientific Paper, 7th Edition, Greenwood Press, 2011. ISBN: 03133919710
On general advise on your career:
  • Peter J. Feibelman: A Ph.D. Is Not Enough! A Guide to Survival in Science, 2nd Edition, Basic Books, 2011. ISBN: 0465022227
  • Richard M. Reis: Tomorrow's Professor: Preparing for Careers in Science and Engineering, IEEE Press, 1997. ISBN: 0780311361
  • Federico Rosei and Tudor Johnston: Survival Skills for Scientists, Imperial College Press, 2006. ISBN: 1860946410
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 and Nancy Sakaduski: Scientific English: A Guide for Scientists and OtherProfessionals, 3rd Edition, Greenwood Press, 2011. 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 assemble your presentation materials, how to get your point across to the audience, and 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. See the above Item 5 on Travel Awards. So, please consider to submit your paper(s) to appropriateconferences. 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:
- Summer Graduate Workshops at MSRI
- 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).