NA Digest Monday, April 21, 2014 Volume 14 : Issue 11

Today's Editor:
Daniel M. Dunlavy
Sandia National Labs

Submissions for NA Digest:


From: Jan G. Korvink
Date: April 14, 2014
Subject: SYMPLER - an open source SYmbolic ParticLE simulatoR

If you are in need of a unified flexible and modular simulation tool
allowing for the investigation of structural, thermodynamic, and
dynamical properties of fluids and solids, and you want to cover
microscopic, mesoscopic, and macroscopic time and length scales, then
consider to give SYMPLER a try. SYMPLER allows to choose freely
between particle based simulation methods such as molecular dynamics,
dissipative particle dynamics or smoothed particle
hydrodynamics. SYMPLER is published under the GNU Public License and
is hence absolutely free. SYMPLER has a modular object oriented
structure that is passed to the user level and allows to easily switch
among different integration algorithms, particle interaction forces,
boundary conditions, etc. It allows for an arbitrary number of
particle-species for the simulation of complex multi-component systems
and an arbitrary number of additional user-defined degrees of freedom
per particle-species. Symbolic definition of runtime compiled
mathematical expressions for particle interactions is possible and
there is the possibility to import CAD-geometries in the STL-
format. SYMPLER is hosted on GitHub to provide a platform for both
users and contributors, most easily accessible from


From: W. E. Schiesser
Date: April 17, 2014
Subject: New Books, Computational ODE/PDEs

Two recent books in computational ODE/PDEs:

Differential Equation Analysis in Biomedical Science and Engineering

Vol 1: Ordinary Differential Equation Applications with R
- Introduction to Ordinary Differential Equation Analysis: Bioreactor
- Diabetes Glucose Tolerance Test
- Apoptosis
- Dynamic Neuron Model
- Stem Cell Differentiation
- Acetylcholine Neurocycle
- Tuberculosis with Differential Infectivity
- Corneal Curvature
- Appendix A1: Stiff ODE Integration

Vol 2: Partial Differential Equation Applications with R
- Introduction to Partial Differential Equation Analysis: Chemotaxis
- Pattern Formation
- Belousov-Zhabotinskii Reaction System
- Hodgkin-Huxley and Fitzhugh-Nagumo Models
- Anesthesia Spatiotemporal Distribution
- Influenza with Vaccination and Diffusion
- Drug Release Tracking
- Temperature Distributions in Cryosurgery

The programming is in R, an open source (no cost) scientific
programming system that can be easily downloaded from any
Internet connection. A link for the R routines is available
on request from


From: Homer Walker
Date: April 20, 2014
Subject: Image-based Cardiovascular Modeling, USA, Jul 2014

A workshop entitled "Vulnerable Plaques: Data, Modeling, Predictions,
and Translation to Clinical Applications" will be held at Worcester
Polytechnic Institute next July 12-13 following the World Conference
on Biomechanics in Boston July 6-11. The organizers are David Ku,
Danny Bluestein, Frank Gijsen, and Dalin Tang.

The objective of the workshop is to gather researchers from different
disciplines related to image-based cardiovascular computational
modeling to exchange state-of-the-art techniques in their respective
fields and to identify challenges and critical needs.

For more information about the workshop, please contact Dalin Tang,


From: Przemyslaw Stpiczynski
Date: April 18, 2014
Subject: Computer Aspects of Numerical Algorithms, Poland, Sep 2014

7th Workshop on Computer Aspects of Numerical Algorithms (CANA'14)
Warsaw, Poland, 7-10 September, 2014 (
in conjunction with Federated Conference of Computer Science and
Information Systems

Numerical algorithms are widely used by scientists engaged in various
areas. There is a special need of highly efficient and easy-to-use
scalable tools for solving large scale problems. The workshop is
devoted to numerical algorithms with the particular attention to the
latest scientific trends in this area and to problems related to
implementation of libraries of efficient numerical algorithms.

Topics (including but not limited to): Parallel numerical algorithms;
Novel data formats for dense and sparse matrices; Libraries for
numerical computations; Numerical algorithms testing and benchmarking;
Analysis of rounding errors of numerical algorithms; Languages, tools
and environments for programming numerical algorithms; Numerical
algorithms on GPUs; Paradigms of programming numerical algorithms;
Contemporary computer architectures; Heterogeneous numerical
algorithms; Applications of numerical algorithms in science and

Authors should submit draft papers (as Postscript, PDF of MSWord



From: Pamela Bye
Date: April 16, 2014
Subject: IMA Math Modelling of Fluid Systems, UK, Sep 2014

10 - 12 September 2014 Engineers’ House, Bristol

As the most versatile medium for transmitting signals and power, fluid
(gas or liquid) have wide usage in industry. Fluid systems are used in
machine tool applications, vehicle control systems, where high power
to weight ratio, accuracy and quick response are required. Fluid
systems for industrial processes often involve networks consisting of
tanks, pipes, orifices, valves, pumps and other flow devices. It is
important to develop a systematic method to mathematically model
different types of fluid systems for safe and optimal operations.

Conference topics include the following and are invited to be
presented in oral and poster sessions: Analysis and computational
methods of fluid systems; Computational fluid dynamics (CFD) approach
to engineering systems; Fluid power systems; Multiphase flow;
Modelling and design of fluid system components; Control design
methodologies and techniques for fluid systems and applications; Novel
fluid system configurations; New approaches to system modelling and
system design; Pressure surge; Hydraulic systems; Medical applications

Papers will be accepted for the conference based on a 250 word
abstract. Abstracts should be submitted by Friday 25 April by e- mail
to Please state whether your title is intended
for oral or poster presentation. Notification of acceptance of
abstracts will be Friday 30 May 2014 and the deadline for final papers
will be Thursday 31 July 2014.

For further information on this conference, please visit the
conference webpage:


From: Kirsten Wilden
Date: April 14, 2014
Subject: ACM-SIAM Symposium on Discrete Algorithms, USA, Jan 2015

ACM-SIAM Symposium on Discrete Algorithms (SODA15)
Westin San Diego Gaslamp Quarter, San Diego, California, USA
January 4-6, 2015
Twitter hashtag: #SIAMDA15

Algorithm Engineering and Experiments (ALENEX15) and Analytic
Algorithmics and Combinatorics (ANALCO15) will take place at the
same location, and will hold sessions during the SODA conference.

SODA is jointly sponsored by the ACM Special Interest Group on
Algorithms and Computation Theory and the SIAM Activity Group on
Discrete Mathematics.


July 2, 2014, 4:59 PM EDT - Deadline - Short Abstract Submission
and Paper Registration Deadline

July 7, 2014, 4:59 PM EDT - Deadline - Full Paper Submission

Acceptance/rejection notices will be sent to authors via email in
mid-September 2014.

For additional information, contact the SIAM Conference Department


From: Michael Ruzicka
Date: April 14, 2014
Subject: Faculty Position, Numerics and Theory of PDEs, Uni Freiburg, Germany

The Institute of Mathematics of the Faculty of Mathematics and
Physics at the University of Freiburg invites applications for a

Professorship (W3) of Applied Mathematics (Early succession of
Prof. Kröner)

to be filled as soon as possible.

We are looking for outstanding candidates whose research has a
focus on a current field in the theory and numerics of partial
differential equations which complements the department's
research profile. Particular attention is paid to the candidate's
willingness to cooperate closely with members of the institute and
to contribute actively to the success of future collaborative
research activities. Furthermore she or he will be expected to
bear an appropriate share of the teaching duties of the Institute
of Mathematics as well as of the academic self-administration
(government). Candidates should possess the German Habilitation in
mathematics or an equivalent research qualification. Applicants
with a physical handicap will be given preference over other
candidates provided they are equally qualified.

The University of Freiburg seeks to increase the number of female
scientific faculty members and therefore especially encourages
suitably qualified women to apply.

Applications should be submitted using the application formular
together with the usual references (curriculum vitae, a list of
lecture courses and publications, a list of their 3 to 5 most
prominent papers, copies of academic degree certificates and awards)
and a portfolio of their teaching competence (see
(Lehrkompetenzportfolio-formblatt). Please don't send original
documents, since no documents will be sent back.

Please send your application referring to Kennziffer before April 25th
2014 either as a pdf-file to or via
mail to the Dean of the Faculty of Mathematics and Physics, University
of Freiburg, Eckerstr. 1, D-79104 Freiburg, Germany.

For further information, please contact Prof. Dr. M. Růžička under
Tel. +49 (0)761 203 5680 or via E-Mail


From: Zhiliang Xu
Date: April 14, 2014
Subject: Postdoc Position, Math/Comput Bio, Univ of Notre Dame

We invite applications for an NIH funded postdoctoral research
position in the mathematical and computational biology group in the
Department of Applied and Computational Mathematics and Statistics
(ACMS), University of Notre Dame. We are aiming to develop novel,
multi-scale computational models to study bacterial swarming, biofilms
and blood clot formation. Models will be calibrated using experimental
data. Priority will be given to candidates with research interests and
experience in biological modeling and parallel implementation of
computational models. The salary is competitive. This position is for
1 year with possible extension to a second year.

Applications, including curriculum vitae, should be sent
electronically to Mark Alber at: Applicants should
also arrange for at least three letters of recommendation to be sent
to the same email address. The evaluation of candidates will begin
immediately and continue until the position is filled.


From: Malte Braack
Date: April 14, 2014
Subject: Postdoc Position, Numerical Mathematics, Kiel Univ

The University of Kiel offers a PostDoc position at the interface
between Numerical Mathematics and Ocean Sciences.

The applicant is expected to have a Ph.D. in Mathematics or Ocean
Sciences with a background in Numerical Analysis or Numerical
Modelling. He/she should have a knowledge in at least one Ocean
Sciences model or another numerical software library for partial
differential equations. The candidate should be familiar with the
development and enhancement of existing simulation software, have a
thorough knowledge of programming languages such as C, C++, Fortran90,
and experience in using parallel computer codes. Adequate language
skills in English are required. Didactic skills should also be

The candidate will work in an interdisciplinary team with close
contacts to scientists from the Departments of Mathematics, Computer
Science and Ocean Sciences. The position will be filled as soon as
possible until end of 2016. It is a full-time position with a salary
according to TV-L 13. Women are especially encouraged to
apply. Severely handicapped people will be referentially considered in
case of equivalent qualifications. Applications and contact: Please
submit your application in both paper and electronic format including
a cover letter that indicates your main area of interest, your CV,
publication list, information on previous research, university
diplomas before April 30th, 2014 to:

Prof. Dr. Malte Braack
Mathematical Seminar
University of Kiel
Ludewig-Meyn-Str. 4
24098 Kiel, Germany


From: Shan Zhao
Date: April 18, 2014
Subject: Postdoc Position, Scientific Computing, Univ of Alabama

The University of Alabama Department of Mathematics invites
applications for a non-tenure-track, Postdoctoral Research Associate
position in Scientific Computing, beginning the fall term of 2014. The
initial appointment will be for one year and is renewable for up to
two years, depending on performance. The Postdoctoral Fellow will work
with Dr. Shan Zhao on Computational Molecular Biology. A Ph.D. in
Computational Mathematics, Mathematical Biology or a related field is
required. Strong programming skills are also required. Candidates with
expertise in immersed interface/boundary methods, high order methods
for PDEs, PDE models for molecular biology, mathematical biophysics,
or parallel/GPU computing are encouraged to apply. Applications should
include the following: 1) curriculum vitae, 2) cover letter, 3)
one-page research statement, and 4) copies of up to 3 selected
publications. All application materials must be submitted online at Applicants must also
arrange for three letters of recommendation to be sent to The University of Alabama is an Equal Opportunity
Affirmative Action Employer. Women and minorities are encouraged to


From: Bubacarr Bah
Date: April 15, 2014
Subject: Postdoc Positions, Lab for Information & Inference Systems, EPFL

The Laboratory for Information and Inference Systems
( at Ecole Polytechnique Federale de Lausanne
(EPFL) has multiple openings for energetic postdoctoral fellows in the
broad fields of Applied Mathematics, Theoretical Computer Science, and
Statistics as part of Prof. Volkan Cevher's 5-year European Research
Council project.

Topics of interest include, but are not limited to Analysis and design
of advanced convex and non-convex optimization methods with
applications to inverse problems; Analysis and design of advanced
discrete optimization methods with particular emphasis on sublinear,
submodular, and approximation algorithms; Learning theory and methods
for non-parametric, sparse additive models; Encoder design for
compressive and adaptive measurement schemes, including information
extractors (e.g., polar codes) and expanders; Advanced linear algebra
methods for optimized information extraction from very large
dimensional datasets; Analysis and applications of non-iid
probabilistic models.

Applicants are expected to have finished, or are about to finish their
Ph.D. degrees. They must have an exceptional background at least in
one of the following topics: numerical convex optimization,
combinatorial optimization, statistics, coding theory, and
algorithms. A track record of relevant publications at top applied
mathematics, theoretical computer science, statistics, or engineering
journals or conferences is essential. The working language at EPFL is

Starting date: available immediately

For informal enquiries, please contact Gosia Baltaian

The application letter including a curriculum vitae with a list of
publications, statement of research, contact details for 3 references
should be sent via email to Gosia Baltaian


From: Borek Patzak
Date: April 14, 2014
Subject: Postdoc/PhD Position, Dept of Mechanics, Czech Technical Univ

Department of Mechanics of the Czech Technical University offers
PostDoc/PhD position in the frame of EU funded research project
Multiscale Modelling Platform: Smart design of nanoenabled products in
green technologies ( )

Description: The development and design of advanced and ntelligent
materials and products requires understanding of underlying physical
phenomena and development and use of advanced simulation tools. One of
the important goals of the project is the development of open-source
framework for integration of existing simulation tools. This framework
will be developed in Python and will provide distributed environment
for interactive simulations build from independent components
supporting transparent data exchange, steering, and
visualization. This environment will be used to design new advanced
ligth LED sources (in cooperation with Philips) and design of new
photo-voltaic cells (CelSian).

We offer a possibility to work in dynamical research group during the
period 01/2014-12/2016, possibility of obtaining PhD, gross salary of
45k CZK, possibility to establish contacts at international level.

Requirements: Communication skills and written/verbal knowledge of the
English language, MSc or PhD degree, knowledge of programming,
motivation. The knowledge of Python, distributed computing, and
numerical modeling is an advantage.

Application: Interested candidates are invited to send their
applications no later than 10 May, 2014. The application must contain
a Curriculum Vitae (one page), a motivation letter (two pages),
stating personal goals and research interests in relation to the
research topic, detailed list of publications, and at least two
recommendation letters.

Prof. Dr. Ing. Bořek Patzák (,
Doc. Ing. Vít Šmilauer, PhD. (


From: Martin Stoll
Date: April 16, 2014
Subject: Postdoc/PhD Positions, Max Planck Inst, Germany

The Max Planck Institute for Dynamics of Complex Technical Systems is
hiring two postdoctoral researchers and one PhD student.

We are seeking two postdoctoral researchers to design and develop
model reduction techniques for different aspects in computational
nanoelectronics. The first position (Ref. nanoCOPS-I) is available
immediately for 2 years, with a research focus on coupled field
simulation. The second position (Ref. nanoCOPS-II) should start
August 1, 2013, and is for 18 months with a focus on uncertainty
quantification. The project is part of the larger consortium NanoCops
funded by the European Union . We expect a PhD
in applied mathematics, numerical analysis, electrical engineering or
related fields.

More information can be found under

Additionally, we are seeking a PhD student (Ref. PhDNDS) to design and
develop numerical methods for problems coming from nonlocal
differential equations.

The PhD student will be part of the research group Numerical Linear
Algebra for Dynamical Systems headed by Martin Stoll within the Max
Planck Institute for dynamics of complex technical systems. The
position is placed within the International Max Planck Research School
and the position is available from September 2014 or afterwards. The
position is equipped with a stipend for up to 4 years and generous
travel support.

More information can be found under

For further information please contact Martin Stoll

Please send you application including a cover letter, CV and the names
of two potential referees to Diana Noatsch-Liebke
( by the 4th of May 2014.


From: Marta Betcke
Date: April 14, 2014
Subject: PhD Position, Image Reconstruction for Photoacoustic Tomography

The majority of biological imaging modalities can either provide high
contrast or high resolution. Photoacoustic Tomography (PAT) is an
example of a new type of imaging utilising coupled physics i.e. where
the contrast induced by one type of wave is read by another kind so
that both high resolution and high contrast are achieved
simultaneously. Many approaches to image reconstruction from
idealised complete data are available including analytic methods based
on the Spherical Mean Radon Transform, (which require the assumption
of uniform sound speed), and time reversal methods (which are able to
accommodate tissue-realistic acoustic attenuation and heterogeneous
sound speed).

In practice, in particular in in vivo applications, it is difficult or
even impossible to measure a complete set of data required for PAT
reconstruction. The data is further degraded by limited penetration of
the optical wave into the tissue. Novel subsampling techniques being
developed in our group pose additional challenge, as the wave field is
captured with non-uniform precision. The goal of the PhD is to develop
mathematical theory and image reconstruction algorithms tailored to
reconstruction from in-prefect data and provide efficient and robust
implementation of the algorithms.

The student will be supervised by Dr Marta Betcke and will be based in
the Department of Computer Science at UCL. The studentship is funded
by the Department of Computer Science for 3.5 years. It covers a
tax-free stipend of approximately £15,863 per annum, other costs of
£1000 per annum and tuition fees (

Application deadline is 31st May 2014.

Further details can be found at:


From: Luca Heltai
Date: April 17, 2014
Subject: SISSA-ICTP Master in High Performance Computing

SISSA and ICTP are pleased to announce that they are now accepting
applications for the inaugural year of the Master in High Performance
Computing (MHPC), which will start in September 2014 in Trieste.

The Master in High Performance Computing (MHPC) is an innovative
degree program that prepares students for exciting careers in the
fast-growing field of HPC. Set in the stimulating research environment
of its co-organizer institutions, SISSA and ICTP, the program combines
lectures with hands-on and applied projects to prepare future HPC
specialists for academia and industry.

Challenging scientific and technical problems that require an HPC
approach will drive MHPC coursework. Lectures will be provided by ICTP
and SISSA staff and highly recognized international experts. Both
institutes have long histories and experience in developing and
applying scientific and research computation models. Students who
successfully complete the program will be able to address problems
requiring advanced computational techniques in multiple domains, and
communicate HPC technological issues in all scientific and industrial

Details about tuition fees, available fellowships and requirements and
more info on how to apply are available at the following link:

Applications deadline is May 19, 2014.

End of Digest