Digest of the Non Linear Science Network, Volume 05, Number 11 June 15, 2005 Editor: Angel Jorba Topics: School, Neural Networks in Classification, Regression and Data Mining PhD studentship available at the University of Aberdeen Chairs at University of Edinburgh Lecturer Position at University of the Witwatersrand ProtoMol, Software for Molecular Dynamics Contents, Nonlinear Analysis: Modelling and Control Contents, Physica D: Nonlinear Phenomena, 205:1-4 Contents, Physica D: Nonlinear Phenomena, 206:1-2 Submissions to nls-net must be addressed to: Comments and suggestions are also welcome. General information about nls-net can be found at: http://www.maia.ub.es/cgi-bin/mailman/listinfo/nls-net/ This is a service created and maintained in collaboration with the American Institute of Mathematical Sciences (AIMS) http://www.aimsciences.org/ ------ From: "Jorge M. Santos" Subject: School, Neural Networks in Classification, Regression and Data Mining Date: Mon, 6 Jun 2005 22:49:40 +0100 FINAL ANNOUNCEMENT ============================================================= SUMMER SCHOOL NN2005 - with a special poster session and workshop (bring your data sets). NEURAL NETWORKS in CLASSIFICATION, REGRESSION and DATA MINING July 4-8, 2005, ISEP - Porto, Portugal; http://www.nn.isep.ipp.pt/ nn-2005@isep.ipp.pt ============================================================= GENERAL INFORMATION The Summer School will be held at Porto, Portugal, jointly organized by the Polytechnic School of Engineering of Porto (ISEP) and the Faculty of Engineering, Porto University (FEUP). This year's edition, NN2005, includes a special WORKSHOP SESSION providing a discussion forum where the participants can obtain peer guidance for their projects. For more details, visit: http://www.nn.isep.ipp.pt/ ------ Subject: PhD studentship available at the University of Aberdeen From: K Nakkeeran Date: Thu, 2 Jun 2005 10:29:07 +0100 PhD studentship available at the University of Aberdeen, UK Project title: Transmission performance improvement of dispersion managed fibre systems using non-linear optional loop mirrors Supervisor: Dr K Nakkeeran (Engineering) 3R (re-shaping, re-timing and re-amplification) regeneration of return to zero (RZ) format optical pulses in dispersion-managed (DM) optical fibre transmission systems is an important issue in improving transmission performance. In this research using numerical simulations & analysis, various factors have to be investigated for the utilisation of nonlinear optical loop mirrors (NOLMs) for 2R regeneration in DM fibre transmission to improve the transmission performance. Applicants should have upper second class honours undergraduate Engineering, Physics or Applied Mathematics degree. The project start date is 1st October 2005. Studentship comprises: Fees: at Home/EU rate GBP 3,085 and Subsistence GBP 12,000 per annum for three years, International students must arrange for the international fee difference of GBP 8000 per annum Contact for further information about the project: Dr K Nakkeeran e-mail: k.nakkeeran@abdn.ac.uk More details about studentship and the application details (@ end of the URL) could be found at the URL http://www.abdn.ac.uk/studentships/ Contact for further information about the studentship: Postgraduate Office, Department of Engineering, University of Aberdeen, Fraser Noble Building, Aberdeen AB24 3UE Tel: 01224 272513 Fax: 01224 273895 e-mail: p.waterworth@abdn.ac.uk ------ Subject: Chairs at University of Edinburgh From: Douglas Heggie Date: Thu, 9 Jun 2005 08:38:17 +0100 (BST) University of Edinburgh School of Mathematics The School seeks to fill two established Chairs following the impending retirement of the present incumbents, Professors David Parker and Elmer Rees. Chair of Applied Mathematics The School wishes to appoint a world-class applied mathematician with the vision to lead its Applied Mathematics group in a changing environment. In addition to pursuing his or her own research, the successful candidate will be expected to help the School stimulate its research income, establish collaborative research opportunities within and beyond the University, and develop its undergraduate and postgraduate teaching programmes. Ref: 3004446 Chair of Mathematics The School seeks to appoint a mathematician with a research record of international eminence who will provide imaginative research leadership within the School and University. Candidates should also be able to contribute creatively to the undergraduate and postgraduate programmes offered by the School. The ability to enhance the work of one or more of the existing research groups within the School would be welcome, although outstanding candidates in any area of Mathematics are encouraged to apply. Ref: 3004448 Each position will be available at a mutually agreed date after 1st October 2005. Informal enquiries about the positions may be made to Professor T.A. Gillespie: telephone 0131 650 5062, fax 0131 650 6553 or e-mail hos@maths.ed.ac.uk . Further information about the School is available at http://www.maths.ed.ac.uk (click on "Job vacancies" for further details about the positions and application procedures; alternatively, go to http://www.jobs.ed.ac.uk and quote the relevant reference number or phone the recruitment line 0131 650 2511). ------ Subject: Lecturer Position at University of the Witwatersrand From: Montaz Ali Date: Mon, 6 Jun 2005 13:25:07 +0200 (SAST) UNIVERSITY OF THE WITWATERSRAND, JOHANNESBURG, FACULTY OF SCIENCE LECTURER School of Computational and Applied Mathematics Applications are invited for the above permanent position. The School has particular interests in the fields of optimization, control, numerical analysis, computational mathematics, differential equations, continuum mechanics, mathematics of finance, infectious disease modeling, astronomy, industrial mathematics. Qualifications and Experience: The successful applicant must have a PhD, preferably in Computational and /or Applied Mathematics. Lecturing experience will be a strong advantage. School Website: www.cam.wits.ac.za Living in South Africa: www.wits.ac.za/international, www.joburg.co.za, www.safrica.info Best Regards Dr Montaz Ali mali@cam.wits.ac.za Centre for Control Theory and Optimization School of Computational and Applied Maths Witwatersrand University, Johannesburg ------ Subject: ProtoMol, Software for Molecular Dynamics From: Scott Hampton Date: Tue, 31 May 2005 14:27:35 -0500 (EST) We are pleased to announce the release of ProtoMol v2.0: a free, open source, object-oriented, component-based framework for molecular dynamics (MD) simulations. It supports CHARMM 19 and 28a2 force fields and is able to read and write PDB, PSF, XYZ, DCD, and several common graphics formats. ProtoMol is designed for high flexibility, ease of extendibility and maintenance, and high performance and scalability demands. We use MPI to implement atom- and force-based decompositions in a manner nearly transparent to both end-users and developers. The use of fast electrostatic force evaluation algorithms like particle mesh Ewald (PME), an O(n log n) method, and multigrid summation (MG), an O(n) method, further improve performance. ProtoMol contains many novel MD and Monte Carlo (MC) based methods suitable for simulation in a variety of ensembles. For example, shadow hybrid Monte Carlo (SHMC) has been shown to scale with system size and MD timestep by a factor of 10 or more over hybrid Monte Carlo (HMC). Multiscale simulations take advantage of longer timesteps by coupling multiple time-stepping algorithms with advanced integrators. Using targeted Molly, we have achieved stable timesteps of 16fs for solvated proteins. In addition, ProtoMol has been designed to interact with VMD, a visualization engine developed at the University of Illinois, which is used for displaying large biomolecular systems and running simulations in 3-D. Highlights of ProtoMol v2.0: - Average 50% performance increase versus ProtoMol 1.8.3 - Novel integrators including Shadow Hyrid Monte Carlo (SHMC), isothermal-isobaric MD, and isomolar-semigrand MD. - An updated interface for adding new forces, integrators, and output methods - Improved code organization utilizing design patterns We invite you to visit the ProtoMol home page, http://protomol.sourceforge.net, where C++ source code, documentation, and prebuilt binaries may be found. Operating systems natively supported include Linux, SunOS, Irix, HP-UX and Windows. We have also configured a new mailing list to better serve our user base. Please visit the following link and join the list for support and development news: http://lists.sourceforge.net/lists/listinfo/protomol-users Protomol user and development questions can be sent to the list using the following email address: protomol-users@lists.sourceforge.net For questions or comments, please feel free to contact the ProtoMol team at protomol@cse.nd.edu ------ Subject: Contents, Nonlinear Analysis: Modelling and Control From: Romas Baronas Date: Mon, 06 Jun 2005 07:57:42 +0300 Nonlinear Analysis: Modelling and Control, ISSN 1392-5113, Volume 10, Number 2, 2005 A free on-line edition is available at: http://www.lana.lt/journal/issues.php TABLE OF CONTENTS Neural Predictive Control of Unknown Chaotic Systems, Pages 95-106 A. Boukabou, N. Mansouri Application of the Total Approximation Method for the Investigation of the Temperature Regime of a Polychromatic Solid-State Lamp, Pages 107-117 J. Dabulyte, F. Ivanauskas Pulse Shape Influence on the Accuracy of Z-scan Measurements, Pages 119-136 A. Dement'ev, A. Jovaisa Mathematical Modelling on RLCG Transmission Lines, Pages 137-149 Y.-L. Jiang Influence of Yield Strength Variability over Cross-Section to Steel Beam Load-Carrying Capacity, Pages 151-160 J. Kala, Z. Kala On Some Extremal Problems on Linearly Invariant Classes, Pages 161-170 E.G. Kiriyatzkii, J. Kirjackis Detecting and Locating a Changed Segment in a Binomial Sequence: Comparison of Tests, Pages 171-192 D. Zuokas Nonlinear Analysis: Modelling and Control, an official journal of the Lithuanian Association of Nonlinear Analysts (LANA), welcomes contributions from the international community. For a paper submission, please refer to http://www.lana.lt/journal Dr. Romas Baronas, Journal Secretary, Nonlinear Analysis: Modelling and Control, ------ Subject: Contents, Physica D: Nonlinear Phenomena, 205:1-4 From: cdmailer@elsevier.co.uk Date: Mon, 6 Jun 2005 14:57:55 +0100 (BST) For more information about this journal visit: http://www.elsevier.com/locate/physd Synchronization and pattern recognition in a pulse-coupled neural net H. Haken pp 1-6 On stochastic evolution equations for chaos and turbulence H. Mori pp 7-14 The role of sampling time in measurements of the CO"2 kinetics of the bistable reaction CO+O"2->CO"2 on Ir(1@?1@?1) surfaces Y. Hayase, S. Wehner, J. Kuppers, H.R. Brand pp 15-24 Effects of microscopic disorder on the collective dynamics of globally coupled maps S. De Monte, F. d'Ovidio, H. Chate, E. Mosekilde pp 25-40 Chaotic phase synchronization and phase diffusion H. Fujisaka, T. Yamada, G. Kinoshita, T. Kono pp 41-47 Langevin equation with Coulomb friction H. Hayakawa pp 48-56 Extracting order parameters from global measurements with application to coupled electrochemical oscillators Y. Zhai, I.Z. Kiss, H. Daido, J.L. Hudson pp 57-69 The effects of weak randomness on pulse interactions and four-wave mixing products R.L. Horne, C.K.R.T. Jones, T. Schafer pp 70-79 Global synchronization in two-dimensional lattices of discrete Belousov-Zhabotinsky oscillators H. Fukuda, H. Morimura, S. Kai pp 80-86 Discreteness-induced stochastic steady state in reaction diffusion systems: self-consistent analysis and stochastic simulations Y. Togashi, K. Kaneko pp 87-99 Long dynamo waves J. Mason, E. Knobloch pp 100-124 A coupled-oscillator model with a conservation law for the rhythmic amoeboid movements of plasmodial slime molds A. Tero, R. Kobayashi, T. Nakagaki pp 125-135 Periodic growth of bacterial colonies Y. Yamazaki, T. Ikeda, H. Shimada, F. Hiramatsu, N. Kobayashi, J.i. Wakita, H. Itoh, S. Kurosu, M. Nakatsuchi, T. Matsuyama, M. Matsushita pp 136-153 Birhythmicity, synchronization, and turbulence in an oscillatory system with nonlocal inertial coupling V. Casagrande, A.S. Mikhailov pp 154-169 Interfacial turbulence enhances oxygen transport into shallow liquid layers M.J.B. Hauser, J. Oberender, S. Richter, K. Bartels, S.C. Muller pp 170-180 Mean creep: the soft mode in elastic sheet buckling M. Kucken, A.C. Newell, P.D. Shipman pp 181-188 Statistical pulse dynamics in a reaction-diffusion system T. Ohta, T. Yoshimura pp 189-194 Spatio-temporal structures in sheared polymer systems A. Furukawa, A. Onuki pp 195-206 Some implications of renormalization group theoretical ideas to statistics S. Rajaram, Y.h. Taguchi, Y. Oono pp 207-214 An unfinished tale of nonlinear PDEs: Do solutions of 3D incompressible Euler equations blow-up in finite time? Y. Pomeau, D. Sciamarella pp 215-221 Front instability and pattern dynamics in the phase-field model for crystal growth H. Sakaguchi, S. Tokunaga pp 222-232 Long range spatial correlation between two Brownian particles under external driving S.i. Sasa pp 233-241 Autonomous free-energy transducer working under thermal fluctuations K. Sekimoto pp 242-248 The spectrum of the locked state for the Kuramoto model of coupled oscillators R.E. Mirollo, S.H. Strogatz pp 249-266 Orientational order in buckling elastic membranes N. Uchida pp 267-274 Forced excitations and excitable chaos in the photosensitive Oregonator under periodic sinusoidal perturbations H. Mahara, T. Yamaguchi, Y. Morikawa, T. Amemiya, T. Yamamoto, H. Miike, P. Parmananda pp 275-282 Chemo-mechanical energy transduction through interfacial instability H. Kitahata, K. Yoshikawa pp 283-291 Non-existence of elliptic travelling wave solutions of the complex Ginzburg-Landau equation A.N.W. Hone pp 292-306 ------ Subject: Contents, Physica D: Nonlinear Phenomena, 206:1-2 From: cdmailer@elsevier.co.uk Date: Thu, 9 Jun 2005 19:44:38 +0100 (BST) For more information about this journal visit: http://www.elsevier.com/locate/physd Stochastic heating in ultra high intensity laser-plasma interaction A. Bourdier, D. Patin, E. Lefebvre pp 1-31 Regular dynamics in a delayed network of two neurons with all-or-none activation functions S. Guo, L. Huang, J. Wu pp 32-48 On spectral techniques in analysis of Boolean networks J. Kesseli, P. Ramo, O. Yli-Harja pp 49-61 Renormalization group reduction of pulse dynamics in thermally loaded optical parametric oscillators R.O. Moore, K. Promislow pp 62-81 Homoclinic snaking near a heteroclinic cycle in reversible systems J. Knobloch, T. Wagenknecht pp 82-93 Bubbling bifurcation: Loss of synchronization and shadowing breakdown in complex systems R.L. Viana, C. Grebogi, S.E. de S.Pinto, S.R. Lopes, A.M. Batista, J. Kurths pp 94-108 Some properties of the magnetic fields generated by symmetric configurations of wires F.G. Gascon, D. Peralta-Salas pp 109-120 Localized patterns in homogeneous networks of diffusively coupled reactors P.K. Moore, W. Horsthemke pp 121-144