Subject: NA Digest, V. 16, # 13 NA Digest Wednesday, March 30, 2016 Volume 16 : Issue 13 Today's Editor: Daniel M. Dunlavy Sandia National Labs [log in to unmask] Today's Topics: StochSS Version 1.7 Release Honoring Elias Houstis's 70th Birthday, Greece, Jun 2016 Mathematical Imaging, Osnabrueck, Jun 2016 Numerical Optimisation Methods for Eng Design, Germany, Jul 2016 Fluids under Pressure, Czech Republic, Aug-Sep 2016 International Meshing Roundtable (IMR), USA, Sep 2016 Researcher Position, Optimization, Mitsubishi Electric Research Laboratories Software Developer Position, Linear Equation Solver University Assistant Position, Univ of Graz Postdoc Position, Mathematical Model for Systems Involving Uncertainty Postdoc Position, Parallel Algorithms to Protein Structure Determination Postdoc Positions, Inria Bordeaux (France) CFP, Special Issue, Inverse Problems CFP, Special Issue, Molecular Bioscience and Biophysics SISC Copper Mountain Special Section Contents, Information and Inference, 5 (1) Contents, Journal of Scientific Computing, 67 (1) 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: Linda Petzold [log in to unmask] Date: March 23, 2016 Subject: StochSS Version 1.7 Release StochSS: Stochastic Simulation Service, is an integrated development environment for modeling and simulation of discrete stochastic biochemical systems. An easy to use GUI enables researchers to quickly develop and simulate biological models on a desktop or laptop, which can then be expanded or combined to incorporate increasing levels of complexity. As the demand for computational power increases, StochSS is able to seamlessly scale up by deploying cloud computing resources. The software currently supports simulation of ODE and well-mixed discrete stochastic models, parameter estimation of discrete stochastic models, and simulation of spatial stochastic models. New capabilities of Version 1.7 include: - Volume rendering visualization for spatial jobs. - StochSS-launcher uses docker containers to run StochSS. Includes support for newest OSX and Windows operating systems. - Added RSS feed to front page - Many bug fixes and stability enhancements For more details and instructions on how to obtain the code, visit us at http://www.StochSS.org . Linda Petzold and Chandra Krintz, University of California Santa Barbara Per Lötstedt and Andreas Hellander, Uppsala University ------------------------------------------------------- From: Manolis Vavalis [log in to unmask] Date: March 22, 2016 Subject: Honoring Elias Houstis's 70th Birthday, Greece, Jun 2016 Computational and Informational Science and Engineering Conference Portaria, Volos, Greece, Jun 2016 Web Page: http://enh2016.uth.gr The University of Thessaly and the Centre for Research and Technology-Hellas proudly organize an International Conference Honoring Elias N. Houstis. This conference will bring together teachers, friends, colleagues and students to honor Elias Houstis's 70th birthday, recognize his broader impact in the areas of Computational and Informational Sciences and Engineering and exhibit his overall scientific and social influence to very many scientists, entrepreneurs and engineers around the globe. The first two days of this International Conference will be devoted to high quality scientific presentations delivered by both well recognized scientists and talented young students in diverse thematic areas of Computational and Informational Sciences and Engineering that utilize both theoretical results and emerging technologies. These include but are not limited to: - Numerical Analysis - Scientific Computation - High Performance Computing - Artificial Intelligence - Information and Knowledge Management - Electrical Engineering - Programming - Education A special session during the second day is devoted to presentations by Elias's PhD students associated with their past and recent activities and accomplishments. The third day is devoted to presentations by Elias's teachers, collaborators and friends. The fourth day involves social activities only. ------------------------------------------------------- From: Stefan Kunis [log in to unmask] Date: March 23, 2016 Subject: Mathematical Imaging, Osnabrueck, Jun 2016 The Workshop on Mathematical Imaging and Emerging Modalities takes place from June 27 - 30, 2016, in Osnabrueck, Germany, and hosts the Annual Meeting of the GAMM-Activity Group "Mathematical Signal and Image Processing". Confirmed plenary speakers are - Kristian Bredies: Variational Approaches for New Techniques in Magnetic Resonance Imaging - Carlos Fernandez-Granda: From Seismology to Compressed Sensing and Back, a Brief History of Optimization-Based Signal Processing - Per Christian Hansen: ART* Performance (*Algebraic Reconstruction Technique) - Rainer Heintzmann: Structured Illumination and the Analysis of Single Molecules in Cells - Tobias Knopp: Matrix Compression Techniques and Multi-Spectral Reconstruction in Magnetic Particle Imaging - Veniamin Morgenshtern: Super-Resolution of Positive Sources Registration is free of charge but mandatory. Deadline is May 15, 2016. For more information, we refer to http://www.math.uni-luebeck.de/mitarbeiter/erb/miem2016. With best regards, Christina Brandt, Wolfgang Erb, Stefan Kunis, Andreas Weinmann ------------------------------------------------------- From: Jens-Dominik Mueller [log in to unmask] Date: March 22, 2016 Subject: Numerical Optimisation Methods for Eng Design, Germany, Jul 2016 Multi-disciplinary and adjoint-based design optimisation methods are providing powerful and systematic model-based processes for the optimisation of increasingly complex engineering systems, including many important examples in the aerospace and automotive industries. ASMO UK/ISSMO, the EU Marie Curie Initial Training Networks About Flow and Amedeo are jointly organising an international conference on this topic at the Technical University of Munich, 18-20 July 2016. http://aboutflow.sems.qmul.ac.uk/events/munich2016/ Inited speakers are JJR Martins (UMich), Christoph Hinterberger (Faurecia), E. Chaput (Airbus) Call for Papers: The deadline for 2pp abstract submissions is 15th April 2016, see http://aboutflow.sems.qmul.ac.uk/events/munich2016/papers/ The areas of particular relevance and interest include, but are not limited to: Industrial Flow Optimisation; Continuous Adjoint Solvers; Automatic Differentiation Tools and Discrete Adjoint Solvers; Adjoint Optimisation of Unsteady Flows; Shape and topology optimisation approaches for Adjoint-based Optimisation Workflows; Multi-Fidelity and Multi-Objective Optimisation Methods; Computational and Parametrisation Methods for Large-scale Optimisation Problems; Metamodel-based Multi-Disciplinary Optimisation Frameworks; and Structural and Composite Optimisation Methods. ------------------------------------------------------- From: Tomas Bodnar [log in to unmask] Date: March 26, 2016 Subject: Fluids under Pressure, Czech Republic, Aug-Sep 2016 Fluids under Pressure Summer School August 29 - September 2, 2016 and Workshop on August 31 http://prague-sum.com The aim of the summer school is to present a comprehensive series of lectures on various aspects of problems related to pressure and its role in mathematical analysis and numerical simulation of various types of flows. It is organized as a multidisciplinary event with topics ranging from theoretical and numerical mathematics up to physics and applications. The emphasize will be on models related to topics originating in environmental, biomedical and industrial applications. The summer course is prepared for graduate students, young scientists, and other interested specialists. Besides of the course lectures, the program will include a one day workshop (on Wednesday, August 31) dedicated to short, more advanced lectures given by attending scientists. Main Speakers - Matthias Hieber - Technische Universität Darmstadt, Germany - Didier Bresch - Université de Savoie, France - Giovanni Paolo Galdi - University of Pittsburgh, USA - Jiří Neustupa - Institute of Mathematics, ASCR Prague, Czech Republic - Yoshihiro Shibata - Waseda University, Japan - Milovan Perić - Continuum Mechanics Technologies GmbH, Germany - Miroslav Bulíček - Charles University, Prague, Czech Republic - Volker John - Weierstrass Institute, Berlin, Germany Main Topics - pressure in incompressible and compressible flows - role of pressure in regularity of Navier-Stokes eqn. - constitutive laws of viscous fluids - pressure role in the equations of state - numerical methods for pressure resolution - shock related pressure effects - physical background of pressure ------------------------------------------------------- From: Hang Si [log in to unmask] Date: March 26, 2016 Subject: International Meshing Roundtable (IMR), USA, Sep 2016 The 25th International Meshing Roundtable (IMR) and User Forum will be held September 26-30, 2016 at the Doubletree, Washington DC - Crystal City. We solicit technical papers that present original results on meshing, gridding and related technology. In addition, the 25th IMR also solicits short research notes and posters that describe exploratory research, preliminary results and techniques deemed to be relevant to the field of meshing. The IMR will again host a meshing contest, allowing members of the meshing community to showcase their tools. A detailed description of conference topics can be found at http://imr.sandia.gov/25imr/PaperSubmission.html Important Dates: May 30: Full paper submission deadline June 30: Meshing contest commitment deadline July 31: Meshing contest entry deadline August 15: Research notes and poster submission deadline OpenConf will be used for the paper submissions, details can be found at http://imr.sandia.gov/25imr/PaperSubmission.html . For more details and continued updates, please visit http://www.sandia.gov/imr and also join the LinkedIn Group: International Meshing Roundtable at http://www.linkedin.com/groups/International-Meshing-Roundtable-3890430 . ------------------------------------------------------- From: Stefano Di Cairano [log in to unmask] Date: March 26, 2016 Subject: Researcher Position, Optimization, Mitsubishi Electric Research Laboratories Mitsubishi Electric Research Laboratories in Cambridge, Massachusetts, USA, invites qualified candidates to apply for the position of Member, Research Staff and to join its Mechatronics Group. The candidate is expected to perform research in the area of real-time optimization algorithms, especially for optimization-based control. The candidate is expected to have a strong background in the development and analysis of optimization algorithms, working knowledge of numerical linear algebra, knowledge of system modeling and control theory, and demonstrated capability of implementing the algorithms in Matlab and C/C++. Candidates at all levels of experience will be considered, but at least 1-2 years of experience after completion of Ph.D. is preferred. Responsibilities: - Conducting innovative and relevant research in optimization algorithms, - Applying the research results to company-relevant R&D projects, - Publishing in leading journals, conferences and patent applications, - Transferring results to Mitsubishi Electric corporate research laboratories, - Collaborating with research staff, academic partners, mentoring interns. Qualifications: - A Ph.D. from an internationally-recognized institution in optimization, systems and control or a related discipline, - A strong publication record consistent with experience, - A record of independently proposing and executing research projects - Extensive knowledge of optimization, control, algorithm design and analysis, - Experience and interest in implementing optimization in software, - Strong teamwork, communication, listening and teaching skills. Interested parties can find position details and application at http://www.merl.com/employment/employment.php#ME20 ------------------------------------------------------- From: Sam Guo [log in to unmask] Date: March 28, 2016 Subject: Software Developer Position, Linear Equation Solver CD-adapco is looking for highly qualified and motivated candidate to contribute to the development of our next-generation CFD/CAE tool STAR-CCM+. The successful candidate will be expected to contribute to the architecture and design of the product as well as develop end-user enhancements. The specific area of focus will be the development of matrix linear direct and iterative equation solvers for the simulation software analysis of fluids and structures with finite volume and finite element techniques in a parallel distributed and shared memory environment. The following will be required of all candidates: - MS, PHD or equivalent degree in Computer Science and/or Mathematics, Civil, Mechanical or Aerospace Engineering - Proven expertise in object-oriented C++ software design and development - Experience in development, performance tuning and debugging of parallel code for large scale linear systems (AMG, Krylov based methods) - Familiarity with modern matrix solvers (domain decomposition, multigrid, multi-frontal, sparse solvers, sparse ordering algorithms) - Distributed memory parallel programming - Experience in Intel MPI or Platform MPI - Excellent communication skills - Ability to work as part of a team to meet project goals In addition, experience in one or of the following areas is desired: - Computation Fluid Dynamics / Structural Mechanics or related disciplines - Software development in Java - Client/Server architectures - Design and development of architectural components for large scale software systems For more details: visit http://www.cd-adapco.com/jobs/software-developer-linear-equation-solver ------------------------------------------------------- From: Klemens Fellner [log in to unmask] Date: March 23, 2016 Subject: University Assistant Position, Univ of Graz Institute of Mathematics and Scientific Computing is filling an University Assistant with PhD (40 hours a week; fixed-term employment for the period of 6 years; Envisaged Job Starting Date 13 June 2016) For more information follow the link: http://jobs.uni-graz.at/de/MB/66/99/2840 ------------------------------------------------------- From: Paulo José da Silva e Silva [log in to unmask] Date: March 30, 2016 Subject: Postdoc Position, Mathematical Model for Systems Involving Uncertainty Supervisor: Paulo José da Silva e Silva. Abstract: The Research, Innovation and Dissemination Center for Mathematical Sciences Applied to Industry (CeMEAI), hosted by the University of São Paulo, Brazil, and funded by FAPESP (São Paulo Research Foundation, Brazil), is offering a 1 year Postdoctoral fellowship for candidates with outstanding research potential. The candidate will work at the Institute of Mathematics, Statistics and Scientific Computing (IMECC -UNICAMP), Campinas, SP/Brazil. This position focuses on the development of mathematical models for systems involving uncertainty. Candidates with expertise in Fuzzy and Interval Mathematics are welcome. Subjects like Fuzzy Sets, Extensions of Fuzzy Sets, Gradual Numbers, Aggregations and Interval Mathematics are the basic tool for this context of research. Candidates must have received a PhD degree in Applied Mathematics or Computation. Selection criteria will include demonstrated research ability in Applied Mathematics, strong background in computation, commitment to collaborative research, and excellent verbal and written communication skills. The selected candidate will receive FAPESP Post-Doctoral fellowship worth R$ 6819,30 monthly and Technical Reserve. If the selected candidate needs to move to Campinas, (the city where is located the research institution), he/she may be entitled to a financial value to move to the city. To apply please E-mail (only PDF files), up to April 20th, 2016, the following items to Prof. Carlile Lavor ([log in to unmask]): 1. A letter of interest, containing full contact information, year graduated and citizenship/immigration status, concisely responding to the research emphases and criteria above; 2. A CV listing educational background, research experience and publications; 3. A cover letter including names and contact information of two professionals who can recommend the candidate (no letters please). Please indicate "CEPID Postdoc" in the subject field of the message. ------------------------------------------------------- From: José Mário Martinez Perez [log in to unmask] Date: March 30, 2016 Subject: Postdoc Position, Parallel Algorithms to Protein Structure Determination Supervisor: José Mário Martinez Perez Abstract: The Research, Innovation and Dissemination Center for Mathematical Sciences Applied to Industry (CeMEAI), hosted by the University of São Paulo, Brazil, is offering a 1 year Postdoctoral fellowship for candidates with outstanding research potential. The candidate will work at the Institute of Mathematics, Statistics and Scientific Computing (IMECC - UNICAMP), Campinas, SP/Brazil. This position focuses on the development of optimization methods and algorithms to obtain structural resolution of macromolecules using NMR spectroscopy data. Candidates must have received a PhD degree in Applied Mathematics, Computation or Bioinformatics within the last 7 years. Applicants should have a strong background in analysis and implementation of optimization algorithms. Candidates should also be able to demonstrate programming experience in C++, Matlab and high-performance computing (specially OpenMP and MPI). Selection criteria will include demonstrated research ability in Applied Mathematics, Optimization and Bioinformatics, strong background in computation, commitment to collaborative research, and excellent verbal and written communication skills. The selected candidate will receive FAPESP Post-Doctoral fellowship worth R$ 6819,30 monthly and Technical Reserve. If the selected candidate needs to move to Campinas, (the city where is located the research institution), he/she may be entitled to a financial value to move to the city. To apply please E-mail (only PDF files), up to April 20th, 2016, the following items to Prof. Carlile Lavor ([log in to unmask]): 1. A letter of interest, containing full contact information, year graduated and citizenship/immigration status, concisely responding to the research emphases and criteria above; 2. A CV listing educational background, research experience and publications; 3. A cover letter including names and contact information of two professionals who can recommend the candidate (no letters please). Please indicate "CEPID Postdoc" in the subject field of the message. ------------------------------------------------------- From: Olivier Coulaud [log in to unmask] Date: March 24, 2016 Subject: Postdoc Positions, Inria Bordeaux (France) Two 16 month post-doc positions are available at Inria Bordeaux Sud- Ouest (France) in the HiePACS project. In that framework, the post-doc will be mainly involved in the research activity dealing with the design and analysis of parallel numerical algorithms. We are looking for candidates at post-doc level with interest, motivation and background in computational science and high performance computing. Applicants should provide a curriculum vitae, a list of refereed papers published and submitted, a brief statement describing his or her research interests. More details on the two applications are available at https://team.inria.fr/hiepacs/job-offers/ Project: Fast tensor arithmetic for large scale computing and applications, Supervisor: Olivier Coulaud Project: Runtime-based sparse direct solvers for large-scale hybrid platforms, Supervisor: Emmanuel Agullo Applicants should also provide the names and contact information for three additional references. The position, which can be starting as early as October, 2016. To ensure a full consideration, applications must be submitted by May 1st, 2016. Applications will be accepted thereafter until the position is filled. Please send your application by email to [log in to unmask] or [log in to unmask] ------------------------------------------------------- From: Yair Censor [log in to unmask] Date: March 30, 2016 Subject: CFP, Special Issue, Inverse Problems DEADLINE EXTENSION: The new submission deadline for the special issue: "Superiorization: Theory and Applications" is April 30, 2016. Guest Editors: Yair Censor and Gabor T. Herman. The special issue is open to all. To view the Announcement and Call for Papers please go to item [44] at: http://math.haifa.ac.il/yair/bib-superiorization-censor.html or to the journal's website at http://iopscience.iop.org/0266-5611/page/Special-issue-superiorization-theory-and- applications . Prof. Yair Censor, Dept. of Mathematics, Univ. of Haifa, Haifa 3498838, Israel. Homepage: http://math.haifa.ac.il/yair/ ------------------------------------------------------- From: Shan Zhao [log in to unmask] Date: March 23, 2016 Subject: CFP, Special Issue, Molecular Bioscience and Biophysics The journal Molecular Based Mathematical Biology (MBMB, http://www.degruyter.com/view/j/mlbmb) will publish a special issue entitled "Molecular biosciences and biophysics: models, methods and applications". Potential topics include, but are not limited to: Geometric and topological modeling of macromolecules; Biomolecular solvation, explicit and implicit solvation models; Electrostatics computing and applications; Structural determination and molecular shape analysis of molecules; Protein folding, protein--protein interactions; Brownian dynamics, molecular dynamics, and Monte Carlo modeling; Modeling and simulation of Ion--channels and membrane; Mathematical analysis of biological macro-molecule Cryo-EM image data; Algorithms and analysis for molecular big data; Biomolecular simulations and software developments; Multiscale modeling; Mathematical methods for molecular imaging and visualization Original papers and high-quality review articles on the aforementioned topics are solicited for this special issue. Please note that the publisher has waived the Article Processing Charges for this special issue, but articles will be open-access in accordance with the overall goals of the journal. Prospective authors should submit their manuscript online at http://mlbmb.edmgr.com/. Manuscript submission Due: August 1, 2016 First Round of Reviews: September 15, 2016 Anticipated Publication Date: December 15, 2016 ------------------------------------------------------- From: Michele Benzi [log in to unmask] Date: March 28, 2016 Subject: SISC Copper Mountain Special Section SISC Copper Mountain Special Section The Fourteenth Copper Mountain Conference on Iterative Methods was held on March 20-25, 2016. The meeting attracted more than 200 participants from around the world, and there were 173 talks covering a broad spectrum of topics related to iterative solvers (http://grandmaster.colorado.edu/~copper/2016/). As in previous even-numbered years, the SIAM Journal on Scientific Computing (SISC) is planning a Special Section, dedicated to recent progress in iterative methods. The window for submission is April 1 - June 30, 2016. Attendees and participants of the conference as well as the general community are invited to submit papers. Papers will be subject to review by a guest Editorial Board. For submission instructions, visit http://www.siam.org/journals/sisc/sisc_special.php or http://grandmaster.colorado.edu/~copper/2016/sisc.php ------------------------------------------------------- From: Suzanne Eves [log in to unmask] Date: March 29, 2016 Subject: Contents, Information and Inference, 5 (1) Contents, Information and Inference: A Journal of the IMA, 05(1) Information and Inference: A Journal of the IMA All Content Free in 2016 For articles in this issue and in our archive: http://www.oxfordjournals.org/page/6856/1 Robust subspace recovery by Tyler's M-estimator, Teng Zhang http://www.oxfordjournals.org/page/6856/2 Super-resolution radar, Reinhard Heckel, Veniamin I. Morgenshtern, and Mahdi Soltanolkotabi http://www.oxfordjournals.org/page/6856/3 A null-space-based weighted l1 minimization approach to compressed sensing, Shenglong Zhou, Naihua Xiu, Yingnan Wang, Lingchen Kong, and Hou-Duo Qi http://www.oxfordjournals.org/page/6856/4 ------------------------------------------------------- From: Chi-Wang Shu [log in to unmask] Date: March 26, 2016 Subject: Contents, Journal of Scientific Computing, 67 (1) Journal of Scientific Computing http://www.springeronline.com/journal/10915 Volume 67, Number 1, April 2016 Image Deblurring Via Total Variation Based Structured Sparse Model Selection, Liyan Ma and Tieyong Zeng. A Mixed Finite Element Discretisation of Thin Plate Splines Based on Biorthogonal Systems, Bishnu P. Lamichhane, Stephen G. Roberts and Linda Stals. Numerical Solutions for Weakly Singular Volterra Integral Equations Using Chebyshev and Legendre Pseudo-Spectral Galerkin Methods, Xianjuan Li, Tao Tang and Chuanju Xu. Galerkin Spectral Approximation of Elliptic Optimal Control Problems with H1-Norm State Constraint, Yanping Chen and Fenglin Huang. High-Order Methods for Turbulent Flows on Three-Dimensional Strand Grids. Oisin Tong, Aaron Katz, Yushi Yanagita, Alex Casey and Robert Schaap. Removing Mixture of Gaussian and Impulse Noise by Patch-Based Weighted Means, Haijuan Hu, Bing Li and Quansheng Liu. Preasymptotic Error Analysis of High Order Interior Penalty Discontinuous Galerkin Methods for the Helmholtz Equation with High Wave Number, Yu Du and Lingxue Zhu. Pointwise Error Estimates and Two-Grid Algorithms of Discontinuous Galerkin Method for Strongly Nonlinear Elliptic Problems, Chunjia Bi, Cheng Wang and Yanping Lin. Comparison of Convective Flux Discretization Schemes in Detached-Eddy Simulation of Turbulent Flows on Unstructured Meshes, Andrey Kozelkov, Vadim Kurulin, Vladislav Emelyanov, Elena Tyatyushkina and Konstantin Volkov. To CG or to HDG: A Comparative Study in 3D, Sergey Yakovlev, David Moxey, Robert M. Kirbyi and Spencer J. Sherwin. An Adaptive Rational Block Lanczos-Type Algorithm for Model Reduction of Large Scale Dynamical Systems, H. Barkouki, A.H. Bentbib and K. Jbilou. Smoothness-Increasing Accuracy-Conserving (SIAC) Filtering and Quasi-Interpolation: A Unified View, Mahsa Mirzargar, Jennifer K. Ryan and Robert M. Kirby. A Sparse Grid Stochastic Collocation Method for Elliptic Interface Problems with Random Input, Qian Zhang, Zhilin Li and Zhiyue Zhang. An Implementable Splitting Algorithm for the l1-norm Regularized Split Feasibility Problem, Hongjin He, Chen Ling and Hong-Kun Xu. Modified Non-linear Weights for Fifth-Order Weighted Essentially Non-oscillatory Schemes, Chang Ho Kim, Youngsoo Ha and Jungho Yoon. Multilevel Preconditioners for Reaction-Diffusion Problems with Discontinuous Coefficients, Tzanio V. Kolev, Jinchao Xu and Yunrong Zhu. A Simplified Formulation of the Flux Reconstruction Method, J. Romero, K. Asthana and A. Jameson. A High-Order Compact Limiter Based on Spatially Weighted Projections for the Spectral Volume and the Spectral Differences Method, Raphael Lamouroux, Jeremie Gressier and Gille. ------------------------------------------------------- End of Digest **************************