NA Digest, V. 16, # 24

NA Digest Thursday, June 16, 2016 Volume 16 : Issue 24

Today's Editor:

Daniel M. Dunlavy
Sandia National Labs

Today's Topics: Subscribe, unsubscribe, change address, or for na-digest archives:

Submissions for NA Digest:

From: Vincent Acary
Date: June 14, 2016
Subject: Siconos 4.0.0 Release

A brand new Siconos 4.0.0 is out !! Siconos is now distributed under
Apache 2.0 license.

Siconos is an open-source scientific software primarily targeted at
modeling and simulating nonsmooth dynamical systems in C++ and in
- Mechanical systems (rigid or solid) with unilateral contact and
Coulomb friction and impact (nonsmooth mechanics, contact dynamics,
multibody systems dynamics or granular materials).
- Switched Electrical Circuit such as electrical circuits with ideal
and piecewise linear components: power converter, rectifier,
Phase-Locked Loop (PLL) or Analog-to-Digital converter.
- Sliding mode control systems.
- Biology (Gene regulatory network).

Other applications are found in Systems and Control (hybrid systems,
differential inclusions, optimal control with state constraints),
Optimization (Complementarity systems and Variational inequalities),
Fluid Mechanics, and Computer Graphics.

The source code (zip and tar.gz) can be found on github:

We are now working on the release candidate 4.1.0 that can be forked
from our github repo master branch. We have also improved our
documentation at even if it still lacks
some polish. As usual, your feedback comments are welcome.

We have also started to feed our YouTube channel, So, if you
have any nice applications made with Siconos, please do not hesitate
to contribute. We are interested in showcasing Siconos at work!

From: Gilbert Strang
Date: June 07, 2016
Subject: New Book, Introduction to Linear Algebra, Fifth Edition

Announcing the June 2016 publication of this widely used textbook by
Gilbert Strang: Introduction to Linear Algebra with new chapters on
singular values and probability/statistics.

574 pages / Hardcover / 978-09802327-7-6 / Wellesley-Cambridge Press,
70.00 at and member price 67.50 at

I am writing to announce the new Fifth Edition of Introduction to
Linear Algebra. This textbook is available from and
from (which shows the Table of Contents and
offers several sections to download). This is the book that goes with
my video lectures on OpenCourseWare It is the text for a
large number of universities and colleges and now high schools.

This edition has become more than a textbook for the basic
course. That will always be its first purpose. The new Chapter 7
presenting the SVD along with Principal Components in finance and data
analysis, and Chapter 12 about Probability/Statistics, make it also a
text for a graduate course and a resource at work. I hope you will
look at and also at the approach in the
book itself.

From: Steven Kleinstein
Date: June 14, 2016
Subject: Influenza Immunology: Data, Systems and Models, USA, Jun 2016

Registration is now open for the 11th-annual Symposium in
Computational Immunology taking place June 24, 2016 at Yale University
School of Medicine on: Influenza Immunology: Data, Systems and Models

This one-day symposium will cover recent advances in the development
and application of systems biology approaches to understand influenza
infection and vaccination at the molecular, cellular, organism, and
population levels.Speakers include: Rustom Antia (Emory University),
Sarah Cobey (University of Chicago), James Crowe (Vanderbilt
University School of Medicine), Adolfo Garcia-Sastre (Icahn School of
Medicine at Mount Sinai), Tom Kepler (Boston University), Purvesh
Khatri (Stanford University), Rahul Satija (New York Genome Center),
John Tsang (Laboratory of Systems Biology, NIH).

The symposium is a part of the NIH-funded Modeling Immunity for
Biodefense program. This year the symposium is organized by PRiME
(Program for Research on Immune Modeling and Experimentation

For more information and to register for the FREE symposium, please
refer to the attached poster or visit:

When: June 24, 2016 (9am - 5:30pm)
Where: TAC Auditorium, 300 Cedar Street, New Haven, CT


From: Scott MacLachlan
Date: June 06, 2016
Subject: Singularly Perturbed DEs, Canada, Jul 2016

Registration is now open for a short course and workshop on the
numerical analysis of singularly perturbed differential equations,
organized by the Atlantic Association for Research in the Mathematical
Sciences Collaborative Research Group in Numerical Analysis and
Scientific Computing, from July 25th-29th, 2016 in Halifax, NS,
Canada. Early bird registration fees are available until June 17th,

The meeting will consist of a 2-day short course on Numerical Analysis
of Singularly Perturbed Differential Equations taught by leading
expert Dr. Niall Madden (National University of Ireland, Galway),
research level talks by experts in the field, and talks by academic
and industrial researchers with applied problems who have an interest
in applying these techniques. The final part of the workshop will be
interactive, linking the applied researchers with numerical analysis
experts to investigate the process of introducing parameter-robust
techniques to their simulations.

Confirmed speakers include Andrew Bernoff (Harvey Mudd College),
Adriana Dawes (Ohio State University), Natalia Kopteva (University of
Limerick), Alan Lindsey (University of Notre Dame), Torsten Linß
(University of Hagen), and Martin Stynes (Beijing Computational
Science Research Centre).

We invite participation from researchers who are interested in either
the development of advanced algorithms for simulation of singularly
perturbed differential equations or the use of these algorithms in
their work. Partial funding to support travel and/or local expenses
for students and early- career researchers is available.

For more information, please see

From: Michael Heroux
Date: June 10, 2016
Subject: Sustainable Software for Science, UK, Sep 2016

4th Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE4)

School of Computer Science, Kilburn and IT Buildings, University of
Manchester, Manchester, UK, Sept. 12th noon - Sept. 14th 5 pm, 2016

Progress in scientific research is dependent on the quality and
accessibility of research software at all levels. It is now critical
to address many new challenges related to the development, deployment,
maintenance, and sustainability of open-use research software.

In addition, it is essential that scientists, researchers, and
students are able to learn and adopt a new set of software-related
skills and methodologies. WSSSPE provides a forum for discussion of
these challenges, including both positions and experiences, and a
forum for the community to assemble and act.

Important Dates:
- Submission of lightning talks: July 10
- Submission of Track 1 idea papers: July 10
- Submission of Track 2 position papers, experience papers,
presentations of previously published works, and demos: July 10
- Submission of travel support requests: July 10
- Lightning talk decisions announced: Aug 1
- Track 1 idea papers decisions announced: Aug 1
- Track 2 position papers, experience papers, presentations of
previously published works, and demo decisions announced: Aug 1
- Travel support decisions announced: Aug 2

From: Matti Heikkurinen
Date: June 13, 2016
Subject: Environmental Computing, USA, Oct 2016

Call for Papers: Environmental Computing Workshop (ECW)
Organised in conjunction with eScience 2016 conference
October 23 - 27 2016 Baltimore, Maryland, USA,
Submission deadline 27th June (extended)

This workshop will bring together practitioners, policymakers, and
environmental modelling experts to present the latest developments in
Environmental Computing. Submissions by groups working on related - or
potentially related - fields are also encouraged in order to uncover
new opportunities for interdisciplinary collaboration.

The topics of interest include: Case studies in environmental
computing related domains; Environmental modelling and optimisation
techniques; Novel environmental computing applications; Multi-scale,
multi-model and multi-physics systems; Civil protection and related
engineering challenges; Scalability of environmental HPC and Big Data
applications; Risk analysis, assessment, management, and mitigation;
Interdisciplinary and stakeholder collaboration; Dynamic
multi-directional model coupling approaches; Multifaceted data and
metadata frameworks; Urgent computing and probabilistic models; Data
visualisation and interactive analysis; Uncertainty quantification and

From: Anand Panangadan
Date: June 10, 2016
Subject: High Performance Computing, Data, and Analytics, India, Dec 2016

23rd IEEE International Conference on High Performance Computing,
Data, and Analytics, HiPC 2016
December 19-22, 2016, Hyderabad, India

HiPC serves as a forum for researchers from around the world to
present current work in high performance computing and to highlight
activities in Asia. In keeping pace with new computing trends, HiPC
has added two new areas of interest to its name: Data and
Analytics. Authors are invited to submit original unpublished research
manuscripts that demonstrate current research in all areas of high
performance computing,data, and analytics. Topics include (but are not
limited to): Algorithms for Mobile and Wireless Networks; Big Data
Processing and the 4 V's (Volume, Variety, Velocity, Veracity); Big
Data and Data Analytics Systems and Software Architectures; Compiler
Technologies for High-Performance Computing; Concurrent Algorithms
such as Concurrent Data Structures; Cross-Cutting Methods: Co-Design
of Algorithms, Software, and Architectures; Dealing with
Uncertainties, Resilient/Fault-Tolerant Algorithms and Systems;
Emerging Applications such as Biotechnology, Nanotechnology; Exascale
Computing, Cloud Platforms, Data Center Architectures and Services;
High Performance/Scalable Storage Systems; Hybrid Parallel Programming
with GPUs and Accelerators; Interconnection Networks and
Architectures; Large Scale Recommendation Systems, Graph Analytics &
Computing Challenges; Load Balancing, Scheduling and Resource
Management; Operating Systems for Scalable High-Performance Computing;
Parallel Languages, Programming Environments, and Performance
Assessment; Power-Efficient and Reconfigurable Architectures; Quantum
and Bio-Inspired Algorithms and Architectures;
Scientific/Engineering/Commercial Applications and Workloads; Software
Support and Advanced Micro-architecture Techniques; Streaming
Algorithms; Visualization

From: Svetozar Margenov
Date: June 13, 2016
Subject: Large-Scale Scientific Computations, Bulgaria, Jun 2017

The 11th International Conference on Large-Scale Scientific
Computations will take place in June 5-9, 2017, Sozopol,
Bulgaria. LSSC'17 is organized by the Department of Scientific
Computations, Institute of Information and Communication Technologies,
Bulgarian Academy of Sciences.

A detailed information is available at:

Following the tradition, the topics of interest include: Hierarchical,
adaptive, domain decomposition and local refinement methods; Robust
preconditioning algorithms; Monte Carlo methods and algorithms;
Numerical linear algebra; Control systems; Parallel algorithms and
performance analysis; Large-scale computations of environmental,
biomedical and engineering problems.

Applications for organizing special sessions are welcome till the end
of September.

From: Stig Larsson
Date: June 15, 2016
Subject: Tenure Track Positions, Chalmers Univ

Chalmers University of Technology in Gothenburg, Sweden, advertises
tenure track positions in the Basic Sciences (including Mathematics).
The positions are for four years with the possibility of obtaining a
permanent position after a tenure assessment. They also come with
funding for a PhD student and other expenses.

For more information follow this link:

From: Mario Ohlberger
Date: June 07, 2016
Subject: Junior Professor Positions, MATHRIX, Muenster Univ

At the Department for Mathematics and Computer Sciences at the
University of Muenster, Germany, we are seeking for two W1 Junior-
Professors -MATHRIX - in Mathematics that contribute to gender
equality. One of the positions is offered in applied mathematics and
one in pure mathematics.

For further information please see the call at

From: Mike Kirby
Date: June 07, 2016
Subject: Postdoc Position, Application of UQ Multiscale Systems

The Scientific Computing and Imaging (SCI) Institute at the University
of Utah and the Center for Multiscale Modeling of Electronic Materials
(MSME) invites applications for one post-doctoral researcher for
interdisciplinary work spanning applied mathematics, computer science
and material sciences. The successful candidate will perform research
in the application of uncertainty quantification (UQ) techniques to
multiscale algorithms developed at both the continuum level and
molecular dynamics level, and will work closely with SCI Institute
researchers and external collaborators to integrate research into SCI
Institute software applications and apply this software to compelling
problems in science and engineering. Previous postdocs who have held
this position benefited from its interdisciplinary nature: placing
individuals with strong applied mathematics and computing skills at
the interface of realistic and compelling engineering problems
involving electronic storage devices (batteries and fuel cells) and
electronic devices and methodologies (such as optimization of
plasmonic nanoparticles).

The SCI Institute is seeking a highly talented and committed
individual with a demonstrated ability to work well with minimal
supervision in a multi-disciplinary research environment. Backgrounds
in the engineering sciences, applied mathematics, physics and
computational sciences will be considered. Individuals comfortable
with uncertainty quantification (sensitivity analysis, reduced-order
modeling, etc.), probability theory, multiscale theory, and
statistical mechanics preferred. The candidate selected will
contribute to the Institute's world-class research and software
development efforts and have the opportunity to develop their
research, publication, and presentation skills under mentorship from
established faculty investigators. Please contact Mike Kirby
( for further information, and send all applications
to both Prof. Kirby and Ms. Dawn Porter (,
executive administrator for the MSME Center.

Position Posting:

From: Mike Kirby
Date: June 07, 2016
Subject: Postdoc Position, Interface of Computational and Data Science

The Scientific Computing and Imaging (SCI) Institute at the University
of Utah invites applications for one post-doctoral researcher for
interdisciplinary work spanning applied mathematics, computer science,
computational science and data science. Candidates will work as part
of an interdisciplinary team developing and implementing algorithms
that span the imaging, meshing, simulation and visualization pipeline.
Backgrounds in the engineering sciences, applied mathematics, physics
and computational and/or computer science will be considered.
Individuals comfortable with one or more of the following areas is
preferred: imagine analysis, computer vision, data science (e.g.
machine learning), meshing, computational methods for PDEs,
uncertainty quantification or scientific visualization. The candidate
selected will contribute to the Institute’s world-class research and
software development efforts and have the opportunity to develop their
research, publication, and presentation skills under mentorship from
established faculty investigators. Please contact Ross Whitaker
( and/or Mike Kirby ( for
further information.

From: Heike Emmerich
Date: June 07, 2016
Subject: Postdoc Position, Simulation of Materials, Univ of Bayreuth

The chair of Materials and Process Simulation at the University of
Bayreuth offers a post-doc position within the joint project
"ParaPhase: space-time-parallel adaptive simulation of phase field
models on supercomputers". The project is funded within assistance
measures by IKT 2020 - Supercomuting as a DLR project executing
organization for a period of 3 years. In our project, we seek to
conduct systematic studies in order to optimize optoelectronic devices
by means of advanced microstructure models and their simulation on

Applicants must hold a PhD/doctoral degree and be able to adapt to and
carry out novel research projects. They have gained fundamental
experience in modeling and simulation in physics, chemistry,
mathematics, or material science. Furthermore, they have good skills
in at least one of the topics mentioned above. We especially encourage
applications by young scientists who have just recently accomplished
their PhD/doctoral degree or enthusiastically want to pursue it on an
emerging topic with perspectives.

Please send your application (and any inquiries) to with the indication "Postdoc position
4356" in the subject field of the message.

From: MM
Date: June 14, 2016
Subject: Postdoc Position, Univ Graz

POSTDOC POSITION within the FWF funded project "Regularization Graphs
for Variational Imaging"

Institute of Mathematics and Scientific Computing, University of Graz

About the project: The project aims at developing a unified
comprehensive analytical and numerical framework for regularization
functionals in variational imaging, centered around the concept of
regularization graphs. Its goal is to provide a common and rigorous
mathematical basis for recent approaches as well as to pave way for
novel developments in that area. A main part of the project is also
devoted to carrying this concept into application, making it
accessible for non-specialists and practitioners. For this purpose, a
unified numerical optimization framework in form of a freely available
and easily extendible software package will be developed.

Professional qualifications: Doctoral degree in a mathematical branch
of study. Solid knowledge in applied mathematics, with experience in
one or more of the following topics: Variational image processing,
continuous optimization, convex analysis, functional analysis.
Programming skills and experience, e.g., in Python, MATLAB or C++. A
research background covering different regularization approaches in
imaging and applications in the context of inverse problems is very

Contact person and grant holder:
Prof. Kristian Bredies,

Starting date: As soon as possible (contract duration: 3 years)

From: Kees Vuik
Date: June 13, 2016
Subject: PhD Position, Numerical Analysis, Delft Univ of Technology

Currently, there is an open position for a PhD student at the Delft
University of Technology, Department of Applied Mathematics in the
Numerical Analysis group of Prof. Kees Vuik.

The subject is:
Multi-Scale Fluid Flow in DYNamically FRACtured Porous Reservoirs

This is a European Industrial Doctorate project of Schlumberger and
the Delft University of Technology. We are looking for a good PhD
student who has not studied in the Netherlands the previous 3 years
(EU regulations). For more details see:

If you are interested in this position, please send your application,
CV etc to Kees Vuik

From: Adam N. Letchford
Date: June 09, 2016
Subject: PhD Positions, Operational Research and related areas

EPSRC-funded PhD studentships in Operational Research (OR):
Optimisation, Forecasting and Simulation. Stipend £17k to £19k (plus
fe fees paid)

The Department of Management Science is part of Lancaster University
Management School, the most research-intensive business scho school in
the UK (REF, 2014). The department houses one of the larg largest and
most influential OR groups in Europe. We are looking to recruit up to
four researchers who will be excellent doctoral students with a strong
quantitative background ( (including mathematics, physics, computer
science and engineering) a and who satisfy the UK residency
requirement for full EPSRC support (u (usually met by EU students
whose undergraduate studies were in the UK UK); for PhD study in any
area of the department's OR research portfolio. Successful candidates
with a suitable master's degree will be awarded a 3.5 year research
studentship while those with only a bachelor's degree will be admitted
to a 1+3 year programme which incorporates an initial year of research
training (MRes). As part of your doctoral training, you will be able
to access a wide range of opportunities for personal and skills
development, including association with Lancaster's centre for
doctoral training in statistics and OR (STOR-i).

You can access details of some of the areas in which doctoral su
supervision is available by going to:
and then clicking on "Optimisation", "Forecasting" or "Simulation".

Your application should be by covering letter, in which you should
indicate which area is of interest to you (and why) and some possible
topics for research, along with a full CV. We shall then contact
short-listed candidates to put them in touch with potential
supervisors for the development of a fuller research proposal. For
more information go to our webpage and/or contact Gay Bentinck: e
listed candidates to put them in touch with potential supervisors for
the de development of a fuller research proposal. For more information
go to our webpage and/or contact Gay Bentinck: e-mail or phone 01524 592408. Ap Applications will
be processed as soon as they are received. The ap appointment process
will include an interview.

Second round deadline: 30 June 2016.

From: Prof. David G. Yu
Date: June 06, 2016
Subject: Contents, Statistics, Optimization & Information Computing, 4 (2)

Statistics, optimization & information computing, Vol. 4 No. 2,

Efficient Experimental Design Strategies in Toxicology and Bioassay,
Timothy E. O'Brien, DOI: 10.19139/soic.v4i2.192

Estimation Procedure for Reduced Rank Regression, PLSSVD, Willín
Álvarez, Victor John Griffin, DOI: 10.19139/soic.v4i2.146

The Best Model of the Swiss Banknote Data --Validation by the 95% CI
of coefficients and t-test of discriminant scores, Shuichi Shinmura,
DOI: 10.19139/soic.v4i2.178

Morgenstern type bivariate Lindley Distribution, V S Vaidyanathan,
Varghese A. Sharon, DOI: 10.19139/soic.v4i2.183

Memetic Algorithm and its Application to the Arrangement of Exam
Timetable, Wenhua Huang, Guisheng Yi, Sulan He, DOI:

Optimality and duality in set-valued optimization using higher-order
radial derivatives, Guolin Yu, Xiangyu Kong, DOI:

Second-order optimality and duality in vector optimization over cones,
Surjeet Kaur Suneja, Sunila Sharma, Malti Kapoor, DOI:

Two-Step Proximal Gradient Algorithm for Low-Rank Matrix Completion,
Qiuyu Wang, Wenjiao Cao, Zhengfen Jin, DOI: 10.19139/soic.v4i2.201

Relaxed resolvent operator for solving a variational inclusion
problem, Iqbal Ahmad, Mijanur Rahaman, Rais Ahmad, DOI:

End of Digest