NA Digest Sunday, June 5, 2005 Volume 05 : Issue 22

Today's Editor:
Cleve Moler
The MathWorks, Inc.

Submissions for NA Digest:

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Information via e-mail about NA-NET: Mail to


From: Cleve Moler <>
Date: Wed, 1 Jun 2005 23:57:38 -0400
Subject: Trefethen Elected Fellow of the Royal Society

Nick Trefethen of Oxford University has been elected a Fellow of the Royal
Society. The Royal Society is the independent scientific academy of the UK
dedicated to promoting excellence in science. I

The Royal Society elected on 26 May 2005 forty-four new Fellows and six
Foreign Members from the fields of science, engineering and technology.
Fellows are elected for their contributions to science, both in fundamental
research resulting in greater understanding, and also in leading and directing
scientific and technological progress in industry and research establishments.
A maximum of forty-four new Fellows, who must be citizens or residents of
Commonwealth countries or Ireland, may be elected annually.

For more details, see,12243,1494034,00.html


From: Scott Hampton <>
Date: Tue, 31 May 2005 14:27:35 -0500 (EST)
Subject: ProtoMol, Software for Molecular Dynamics

We are pleased to announce the release of ProtoMol v2.0: a free, open
source, object-oriented, component-based framework for molecular dynamics
(MD) simulations. It supports CHARMM 19 and 28a2 force fields and is able
to read and write PDB, PSF, XYZ, DCD, and several common graphics formats.
ProtoMol is designed for high flexibility, ease of extendibility and
maintenance, and high performance and scalability demands. We use MPI to
implement atom- and force-based decompositions in a manner nearly
transparent to both end-users and developers. The use of fast
electrostatic force evaluation algorithms like particle mesh Ewald (PME),
an O(n log n) method, and multigrid summation (MG), an O(n) method,
further improve performance.

ProtoMol contains many novel MD and Monte Carlo (MC) based methods
suitable for simulation in a variety of ensembles. For example, shadow
hybrid Monte Carlo (SHMC) has been shown to scale with system size and MD
timestep by a factor of 10 or more over hybrid Monte Carlo (HMC).
Multiscale simulations take advantage of longer timesteps by coupling
multiple time-stepping algorithms with advanced integrators. Using
targeted Molly, we have achieved stable timesteps of 16fs for solvated
proteins. In addition, ProtoMol has been designed to interact with VMD, a
visualization engine developed at the University of Illinois, which is
used for displaying large biomolecular systems and running simulations in

Highlights of ProtoMol v2.0:
- Average 50% performance increase versus ProtoMol 1.8.3
- Novel integrators including Shadow Hyrid Monte Carlo (SHMC),
isothermal-isobaric MD, and isomolar-semigrand MD.
- An updated interface for adding new forces, integrators, and output methods
- Improved code organization utilizing design patterns

We invite you to visit the ProtoMol home page,, where C++ source code, documentation, and
prebuilt binaries may be found. Operating systems natively supported
include Linux, SunOS, Irix, HP-UX and Windows.

We have also configured a new mailing list to better serve our user base.
Please visit the following link and join the list for support and
development news:

Protomol user and development questions can be sent to the list using the
following email address:

For questions or comments, please feel free to contact the ProtoMol team


From: Heinz W. Engl <>
Date: Mon, 30 May 2005 14:32:12 +0200 (CEST)
Subject: Special Semester at RICAM on Groebner Bases

RICAM Linz, Austria, Special Semester on Groebner Bases
Call for Participation

The Radon Institute for Computational and Applied Mathematics (RICAM), in
close cooperation with the Research Institute for Symbolic Computation
(RISC), is organizing a

Special Semester on Groebner Bases and Related Method, February - July
2006, see

in the frame of the Radon Institute for Computational and
Applied Mathematics (RICAM) in close cooperation with RISC.

This event will bring together key researchers in this area with postdocs
and docs for intensive joint research. Also, tutorials will be offered. If
you are interested in taking part, go to the web site and fill out the
expression of interest. Some limited funds for supporting participation are

If you have any questions, please, write directly to me.

Bruno Buchberger
Director of the Special Semester

Research Institute for Symbolic Computation
Johannes Kepler University, A 4232 Castle of Hagenberg, Austria
Phone office: ++ 43 732 2468 9921
Mobile phone: ++ 43 664 4211646
Fax: ++ 43 732 2468 9930
home page:


From: Christiane Frougny <>
Date: Mon, 30 May 2005 17:20:38 +0200
Subject: Special Issue on Real Numbers

The dead-line has been postponed to June 15th 2005

Special issue of the journal

Theoretical Informatics and Applications

Guest editors: Vasco Brattka, Christiane Frougny, Norbert Mueller

Efficient manipulation of real numbers in computers is still a
challenge. Many interesting theoretical and algorithmic problems are
linked with that topic and belong to quite distant fields such as
computer science, number theory, numerical analysis, computer algebra
and logics. Several special issues on real numbers and
computers have been previously published in the journal Theoretical
Computer Science, as follow-up to the RNC meetings on these topics.

The last meeting was RNC6 which took place in Dagstuhl, Germany,
in November 2004, see

However, this call for papers is open to authors who did not attend RNC6.

Scientists working on questions related to real computer arithmetic
are encouraged to present the theoretical or algorithmic aspects of
their results, even if they did not attend the RNC6 conference. Survey
and tutorial articles may be suitable if clearly identified as
such. Topics include (but are not restricted to) the following list:

* Foundation and properties of number systems
* Computability and complexity
* Formal aspects and automatic proof checking
* Links with number theory and automata theory
* Basic arithmetic operations
* Implementation of the standard and special functions
* Engineering of floating and fixed point algorithms
* Symbolic manipulation of numbers
* Accuracy and reliability for applications and industry
* Robust geometric algorithms and exact geometric computation
* Hardware design support and implementations

Prepare a PostScript or PDF version of your full 10-20 pages paper
preferably using the latex style
LaTeX2e class for RAIRO -Theoretical Informatics and Applications

The file should be sent by e-mail to
before June 15th 2005.


From: David F Griffiths <>
Date: Fri, 3 Jun 2005 17:15:37 +0100
Subject: Conference at Dundee on Numerical Analysis

Tuesday 28 June - Friday 1 July, 2005

Final call for registrations

A draft timetable will be posted on our web site by Tuesday, 7 June.
We have accepted over 100 contributed talks covering differential equations,
linear algebra, optimization, integral equations, approximation theory,
and more.

The closing date for registrations is 10 June.

The conference will be preceded on Monday, 27 June, by talks given by
the finalists of the Leslie Fox Prize.

Our web site

is open for registration and reservation of accommodation. Please
consult the web site for a list of invited speakers and other
information regarding the conference.

Conference Secretaries:
David Griffiths
Alistair Watson


From: Denis Sidorov <>
Date: Thu, 2 Jun 2005 19:49:10 +0800
Subject: Conference in Baikal, Russia on Optimisation Methods

This is the Thirteenth Triennial Baikal International Conference on
Optimisation Methods & their Applications, which traditionally (since 1969)
brings together the engineers and the scientists working in the general
area of optimisation.

The conference will cover all topics related to optimisation and
include the following sessions:
Mathematical programming
Interval analysis
Optimal control
Inverse and ill-posed problems in applied mathematics
Modelling of technical and nature systems

The special attention will be paid to the following topics:
equilibrium programming, parallel computations, interior point
methods, and models of imperfect competition.

The Conference will include Plenary sessions, Invited sessions, Regular
sessions, Poster sessions, Workshops and Two Satellite conferences:
'Equilibrium models of economics and energetics' and 'IT in Power Industry'.

For further information, visit the web-site

Organised by the Energy Systems Institute of Russian Academy of Sciences (SB).

Venue: Irkutsk-Severobaikalsk, Lake Baikal Northern Shore, RUSSIA,
July, 2-8, 2005.


From: Kees Oosterlee <>
Date: Mon, 30 May 2005 17:17:45 +0200
Subject: Conference in The Hague on Multigrid

Dear Colleagues,
The scientific programme of the 8th European Multigrid conference on
multigrid, multilevel and multiscale methods, held in Scheveningen/the Hague,
Netherlands from 27-30 September 2005 is now available under
Early registration at reduced rate is open until 15th June 2005 at


From: Xiaoping Shen <>
Date: Mon, 30 May 2005 23:31:13 -0400 (EDT)
Subject: Workshop in Beijing on Computational Science and its Education

International Workshop on Computational Science and its Education
(IWCSE-2005 Beijing, China)

Time: August 29 ? September 02, 2005
Location: Capital Normal University, Beijing, CHINA

(1) Computational methods and analysis for problems with stochastic nature;
(2) Computational fluid dynamics with multi-physics and multi-scale structures;
(3) Computational methods for problems in nano scale;
(4) Inverse problems with applications;
(5) Topics on integration of computer science, electrical engineering and mathematics;
(6) Interaction between teaching and research in computational science.

Sponsored by

Capital Normal University, China
Ohio University, USA
Beijing Municipal Commission of Science and Technology
Beijing Municipal Commission of Education
National Science Foundation of China
National Science Foundation of United States

Details can be found at the webpage:


From: Miguel Anjos <>
Date: Mon, 30 May 2005 11:29:07 -0400 (EDT)
Subject: Postdoctoral Position at the University of Waterloo

Postdoctoral Position at the University of Waterloo, Canada

Applications are invited for a postdoctoral position at the University of
Waterloo, for research with Professors Miguel Anjos (Management Sciences),
Anthony Vannelli (Electrical & Computer Engineering), and Henry Wolkowicz
(Combinatorics & Optimization). The area of research is the development of
optimization methodologies for solving combinatorial problems arising in
the area of VLSI circuit design.

The successful applicant should have a Ph.D. in Operations Research,
Electrical Engineering, Computer Science, or a related field. Preference
will be given to candidates with documented expertise in computational
optimization, particularly in the application of mathematical programming

The starting date, to be determined by mutual agreement, is as soon as
possible. The initial contract will be for 6-12 months, with a possibility
of extensions up to a maximum of 2 years in total.

Applicants should send as soon as possible a CV and list of referees to
Professor Miguel Anjos (, as a pdf (preferred) or Word
file. Applications are sought immediately and will be accepted until the
position is filled, with no specific deadline.

Further information can be obtained from:
Professor Miguel Anjos
Tel.: +1-509-888-4567 ext 2521


From: Levent Gurel <>
Date: Fri, 3 Jun 2005 15:12:38 -0500
Subject: Postdoctoral Position at Bilkent University

Postdoctoral Position on Parallel Computing at Bilkent University

Research involves fast solution algorithms for computational
electromagnetics (CEM). The goal is to parallelize CEM solvers of
different kinds (such as, the multi-level fast multipole algorithm),
some of which pose parallelization challenges and, thus, research
opportunities. This project also involves hardware issues, such as
the construction of parallel PC clusters.

Familiarity with Linux, Unix, MPI, and Fortran (90) is required.
Familiarity with electromagnetics will be very helpful, but is not
strictly required.

Applications are sought immediately and will be accepted until the
position is filled, with no specific deadline. Modern setting,
friendly environment, satisfactory compensation package. For more info,
please see For applications and further
details, please contact Prof. Levent Gurel, Dept. of Electrical and
Electronics Engineering, Bilkent University, TR-06800, Ankara, Turkey,


From: Steve Sporzynski <>
Date: Fri, 3 Jun 2005 20:06:26 -0700
Subject: Staff Position at PANTA Systems, Cupertino

PANTA Systems, Inc., has an immediate opening for a Senior Principal
Engineer in our Applications Environment Group.

Location: Cupertino, CA

Job Description:

Reporting to the Director of Software Engineering, this position is
responsible for benchmarking and enabling applications in key PANTA
markets, and analyzing hardware and software performance for cutting-edge
computer systems. In addition, the position is responsible for working
with the PANTA Field Operations Organization on key customer opportunities.

The position requires an individual with significant prior experience in
one or more technical application areas either as a systems engineer,
application analyst or application engineer, and a successful track record
as a technical contributing member of an application development team in a
computer system company.

The ideal candidate possesses an M.S., Ph.D. preferred, and 15-20 years
experience working ideally for a tier one corporation with a reputation for
delivering world-class high-performance computer system products. This
position requires an individual who can develop and apply best-practice
application analysis, debugging, and optimization techniques in a
fast-paced environment.

The ideal candidate must possess a verifiable track record of superior
professional accomplishments and have worked as part of a team on
large-scale technical computer systems and customer engagements over
significant periods of very high growth.

We are looking for a strategic-thinking individual with strong analytical
and tactical skills. Commitment to an open, high-integrity, hard-working
culture with a real sense of urgency and a make it happen attitude is a
must. This individual must have excellent communications, interpersonal,
and influencing skills, as this position requires significant interaction
with groups within the PANTA Product Development Organization, Field
Operations and internal executive level of management.

This position requires the ability to travel as required.

Please fax or email your resume to:

PANTA Systems, Inc.
20450 Stevens Creek Blvd.
Suite 400
Cupertino, CA 95014
Fax: 408-996-7569
(No agency resumes please.)

PANTA is an equal opportunity employer. We administer all human resources
actions and policies without regard to race, color, religion, sex, national
origin, ancestry, age, mental or physical disability, sexual orientation or
any other category protected under the law. All employment decisions are
administered in accordance with and in furtherance of the principle of
equal employment opportunity.


From: Charlotte Smith <>
Date: Tue, 31 May 2005 09:48:55 +0100
Subject: Lectureship at Oxford in Computational Biology

Mathematical and Physical Sciences Division
Computing Laboratory
in association with St John's College


Applications are invited for a University Lecturership in Computational Biology.

The successful candidate will join the Computational Biology Group within
the Computing Laboratory, which is led by Professor David Gavaghan.
Applicants should have an internationally leading research record in an area
complementary to the current interests of the group. These focus on the
numerical analysis, software engineering and (parallel) scientific
programming research issues arising in the multiscale modelling of complex
physiological and biological systems. Current application areas include
heart, cancer and respiratory modelling, and the modelling of clinical
monitoring techniques, particularly in medical image analysis. Strong
collaborative links exist with internationally leading experimental groups
in each of these areas, and the successful candidate would be expected to
support and extend this collaborative research programme. Informal enquiries
should be addressed to Professor Gavaghan by e-mail
or telephone on 01865 281840.Further details of the research of the group
are available at: Computational
<> Biology Group

In addition, the successful candidate will be expected to lecture, supervise
graduate students and perform other departmental duties under the direction
of the Head of Department.

The successful candidate will be appointed to a non-stipendiary Fellowship
at St John's College. Further allowances may be payable from the college as
detailed in its associated Further Particulars. The salary will be on a
scale up to :45,707 (pay award pending).

Further <> Particulars
of the post, including selection criteria and application method, together
with more detailed descriptions of the departmental and college duties are
available, by telephone request to +44 (0)1865 273831 or by email request to The closing date for receipt of applications
is 20th June 2005.

Please note that applicants should request that three referees consider the
further particulars and write directly to the above address (fax or email is
sufficient) so that references arrive by the closing date.


From: Romas Baronas <>
Date: Tue, 31 May 2005 11:44:20 +0300
Subject: Contents, Nonlinear Analysis: Modelling and Control

Nonlinear Analysis: Modelling and Control, ISSN 1392-5113,
Volume 10, Number 2, 2005

A free on-line edition is available at:


Neural Predictive Control of Unknown Chaotic Systems, Pages 95-106
A. Boukabou, N. Mansouri

Application of the Total Approximation Method for the Investigation of the
Temperature Regime of a Polychromatic Solid-State Lamp, Pages 107-117
J. Dabulyte, F. Ivanauskas

Pulse Shape Influence on the Accuracy of Z-scan Measurements, Pages 119-136
A. Dement'ev, A. Jovaisa

Mathematical Modelling on RLCG Transmission Lines, Pages 137-149
Y.-L. Jiang

Influence of Yield Strength Variability over Cross-Section to Steel Beam
Load-Carrying Capacity, Pages 151-160
J. Kala, Z. Kala

On Some Extremal Problems on Linearly Invariant Classes, Pages 161-170
E.G. Kiriyatzkii, J. Kirjackis

Detecting and Locating a Changed Segment in a Binomial Sequence: Comparison of
Tests, Pages 171-192
D. Zuokas

Nonlinear Analysis: Modelling and Control, an official journal of
the Lithuanian Association of Nonlinear Analysts (LANA),
welcomes contributions from the international community.

For a paper submission, please refer to

Dr. Romas Baronas, Journal Secretary,
Nonlinear Analysis: Modelling and Control,


End of NA Digest