Subject: NA Digest, V. 14, # 11 NA Digest Monday, April 21, 2014 Volume 14 : Issue 11 Today's Editor: Daniel M. Dunlavy Sandia National Labs [log in to unmask] Today's Topics: SYMPLER - an open source SYmbolic ParticLE simulatoR New Books, Computational ODE/PDEs Image-based Cardiovascular Modeling, USA, Jul 2014 Computer Aspects of Numerical Algorithms, Poland, Sep 2014 IMA Math Modelling of Fluid Systems, UK, Sep 2014 ACM-SIAM Symposium on Discrete Algorithms, USA, Jan 2015 Faculty Position, Numerics and Theory of PDEs, Uni Freiburg, Germany Postdoc Position, Math/Comput Bio, Univ of Notre Dame Postdoc Position, Numerical Mathematics, Kiel Univ Postdoc Position, Scientific Computing, Univ of Alabama Postdoc Positions, Lab for Information & Inference Systems, EPFL Postdoc/PhD Position, Dept of Mechanics, Czech Technical Univ Postdoc/PhD Positions, Max Planck Inst, Germany PhD Position, Image Reconstruction for Photoacoustic Tomography SISSA-ICTP Master in High Performance Computing Subscribe, unsubscribe, change address, or for na-digest archives: http://www.netlib.org/na-digest-html/faq.html Submissions for NA Digest: http://icl.cs.utk.edu/na-digest/ ------------------------------------------------------- From: Jan G. Korvink [log in to unmask] 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 http://sympler.org. ------------------------------------------------------- From: W. E. Schiesser [log in to unmask] Date: April 17, 2014 Subject: New Books, Computational ODE/PDEs Two recent books in computational ODE/PDEs: http://www.wiley.com/WileyCDA/WileyTitle/productCd-1118705483.html http://www.wiley.com/WileyCDA/WileyTitle/productCd-1118705181.html Differential Equation Analysis in Biomedical Science and Engineering Vol 1: Ordinary Differential Equation Applications with R - Introduction to Ordinary Differential Equation Analysis: Bioreactor Dynamics - 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 [log in to unmask] ------------------------------------------------------- From: Homer Walker [log in to unmask] 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, [log in to unmask] ------------------------------------------------------- From: Przemyslaw Stpiczynski [log in to unmask] 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 (http://cana.fedcsis.org/cana) in conjunction with Federated Conference of Computer Science and Information Systems https://fedcsis.org/ 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 technology Authors should submit draft papers (as Postscript, PDF of MSWord file): https://fedcsis.org/hotcrp/ Contact: [log in to unmask] ------------------------------------------------------- From: Pamela Bye [log in to unmask] Date: April 16, 2014 Subject: IMA Math Modelling of Fluid Systems, UK, Sep 2014 IMA CONFERENCE ON MATHEMATICAL MODELLING OF FLUID SYSTEMS 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 [log in to unmask] 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: http://www.ima.org.uk/conferences/conferences_calendar/ima_conferen ce_on_mathematical_modelling_of_fluid_systems.html ------------------------------------------------------- From: Kirsten Wilden [log in to unmask] 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 http://www.siam.org/meetings/da15/ 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. SUBMISSION DEADLINES 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 ([log in to unmask]). ------------------------------------------------------- From: Michael Ruzicka [log in to unmask] 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 (http://www.zuv.unifreiburg.de/formulare/bewerbungsbogen_englisch.pdf) 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 http://www.zuv.uni-freiburg.de/formulare (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 [log in to unmask] 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 [log in to unmask] ------------------------------------------------------- From: Zhiliang Xu [log in to unmask] 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: [log in to unmask] 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 [log in to unmask] 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 established. 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 Email: [log in to unmask] ------------------------------------------------------- From: Shan Zhao [log in to unmask] 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 https://facultyjobs.ua.edu/postings/35006. Applicants must also arrange for three letters of recommendation to be sent to [log in to unmask] The University of Alabama is an Equal Opportunity Affirmative Action Employer. Women and minorities are encouraged to apply. ------------------------------------------------------- From: Bubacarr Bah [log in to unmask] Date: April 15, 2014 Subject: Postdoc Positions, Lab for Information & Inference Systems, EPFL The Laboratory for Information and Inference Systems (http://lions.epfl.ch/) 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 English. Starting date: available immediately For informal enquiries, please contact Gosia Baltaian [log in to unmask] 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 [log in to unmask] ------------------------------------------------------- From: Borek Patzak [log in to unmask] 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 (www.mmp-project.eu ) 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 ([log in to unmask]), Doc. Ing. Vít Šmilauer, PhD. ([log in to unmask]). ------------------------------------------------------- From: Martin Stoll [log in to unmask] 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 http://fp7-nanocops.eu/ . We expect a PhD in applied mathematics, numerical analysis, electrical engineering or related fields. More information can be found under http://www.mpi-magdeburg.mpg.de/2558312/job_full_offer_8138750 http://www.mpi-magdeburg.mpg.de/2558330/job_full_offer_8138773 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 http://www.mpi-magdeburg.mpg.de/2558295/job_full_offer_8137189 For further information please contact Martin Stoll ([log in to unmask]). Please send you application including a cover letter, CV and the names of two potential referees to Diana Noatsch-Liebke ([log in to unmask]) by the 4th of May 2014. ------------------------------------------------------- From: Marta Betcke [log in to unmask] 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 (http://www.ucl.ac.uk/current- students/money/2014-2015_fees/2014-15_postgrad_research). Application deadline is 31st May 2014. Further details can be found at: http://prism.ucl.ac.uk/pgadmissions/apply/new? program=RRDCOMSING01&project=19&advert=55 ------------------------------------------------------- From: Luca Heltai [log in to unmask] 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 environments. Details about tuition fees, available fellowships and requirements and more info on how to apply are available at the following link: http://www.mhpc.it/apply Applications deadline is May 19, 2014. ------------------------------------------------------- End of Digest **************************