# Publications using Octave

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# Articles

## Pre-prints

- Preprint arXiv:1108.3206v2 Modeling and frequency domain analysis of nonlinear compliant joints for a passive dynamic swimmer
- Technical Report UBLCS-2012-02 Queueing Networks Analysis with the qnetworks Toolbox
- Preprint arXiv:1109.0397 Auction-Based Resource Allocation in Digital Ecosystems (Scripts used in the paper)
- Technical Report UBLCS-2011-04 Dynamic Power Management for QoS-Aware Applications (Scripts and data files used in the paper)
- Preprint arXiv:1104.5392 A Framework for QoS-aware Execution of Workflows over the Cloud, to appear in proc. CLOSER 2012 (Script used in the paper)
- Technical Report UBLCS-2010-12 Dynamic Scalability for Next Generation Gaming Infrastructures, to appear in ACM Computers in Entertainment (Script used in the paper)

## 2012

- Comput. Methods Appl. Mech. Engrg., 2012, Multiscale Modeling and Simulation of Organic Solar Cells (Also available at arXiv)
- 12th Int. Conf. on Adaptive Behaviour (2012). Synthesis and Adaptation of Effective Motor Synergies for the Solution of Reaching Tasks. (package used for this publication)
- Communications in Computational Physics System reduction using an LQR-inspired version of Optimal Replacement Variables
- Journal of Computational and Applied Mathematics A Test Set for stiff Initial Value Problem Solvers in the open source software R: Package deTestSet
- Biophysical Journal Locomotion control of Caenorhabditis elegans through confinement
- Behavior Research Methods OpenSesame: An open-source, graphical experiment builder for the social sciences
- Journal of Neural Engineering Stimulus specificity of a steady-state visual-evoked potential-based brain-computer interface
- Nuclear Fusion Detection of geodesic acoustic mode oscillations, using multiple signal classification analysis of Doppler backscattering signal on Tore Supra
- Simulation Modelling Practice and Theory Development and implementation of hydro turbine and governor models in a free and open source software package
- Journal of Biomechanical Engineering Syrinx fluid transport: Modeling pressure-wave-induced flux across the spinal pial membrane
- Biochemistry Testing the nearest neighbor model for canonical RNA base pairs: Revision of GU parameters
- Journal of Chemical Theory and Computation Construction of the free energy landscape of peptide aggregation from molecular dynamics simulations
- Modern Physics Letters B Dynamics on multilayered hyperbranched fractals through continuous time random walks
- IEEE Nuclear Science Symposium Conference Record Dose-free monitoring of radiotherapy treatments with scattered photons: First experimental results at a 6-MV Linac
- Journal of Physics: Conference Series Integration of a neuroimaging processing pipeline into a pan-canadian computing grid
- Journal of Nanomaterials Design and construction of a one-dimensional DNA track for an artificial molecular motor
- Computing in Science and Engineering Applications of computational science: Data-intensive computing for student projects
- Computer Physics Communications Numerical tools to validate stationary points of so (8) -gauged N = 8 D = 4 supergravity
- Advances in OptoElectronics Fundamental issues in manufacturing photovoltaic modules beyond the current generation of materials
- IEEE Transactions on Fuzzy Systems Zadehs extension principle for continuous functions of non-interactive variables: A parallel optimization approach
- Methods in Enzymology Open source tools for fluorescent imaging
- Computer Physics Communications An open-source library for the numerical modeling of mass-transfer in solid oxide fuel cells

## 2011

- Phys. Rev. E 83, 066707 (2011), Exploiting the passive dynamics of a compliant leg to develop gait transitions
- Journal of Fluid Mechanics, volume 681, (2011), pp. 622-638. Perturbations of the coupled Jeffery-Stokes equations.
- International Journal for Numerical Methods in Fluids, 65(11-12):1407–1422, 2011 Isogeometric analysis: Stable elements for the 2d stokes equation.
- Numerical Algorithms, 56(1):107–127, January 2011, A parameter robust Petrov-Galerkin scheme for advection-diffusion-reaction equations.
- Advances in Engineering Software, 42(12):1020–1034, 2011, Geopdes: A research tool for IsoGeometric Analysis of PDEs. (Octave package used discussed in this publication)
- Int. J. of Performability Engineering, 7(5):479–492, 2011 PARSY: Performance-Aware Reconfiguration of Software Systems
- IEEE Trans. Antennas and Propagation, 59(6):2047-2057, 2011, Demonstration of a Dual-Polarized Phased-Array Feed.

## 2010

- Wireless Networks, Vol. 16, No. 2, pp. 355-365, February 2010, Allocating data for broadcasting over wireless channels subject to transmission errors
- Int. J. Numer. Anal. Model., 7(4):444–461, 2010, Interior layers in a reaction–diffusion equation with a discontinuous diffusion coefficient
- Comput. Methods Appl. Mech. Engrg., 199:1722–1732, 2010, Analytical and numerical study of photocurrent transients in organic polymer solar cells (Octave package used to perform the computations)
- Proc. European Performance Engineering Workshop (EPEW), Bertinoro, Italy, sep 2010, Performance-Aware Reconfiguration of Software Systems (Octave script used to perform the computations and produce the plots)
- Proc. Analythical Stochastic Modelling Techniques and Applications (ASMTA'10), Cardiff, UK, jun 2010, The qnetworks Toolbox: A Software Package for Queueing Networks Analysis
- 5th Int. Conf. on Comparing Design in Nature with Science and Engineering (2010). Magneto-mechanical actuation model for fin-based locomotionHTML.

## 2009

- Proceedings of APSIS, Charleston, SC (US), June 2009, Accuracy limits of in-room localisation using RSSI
- J. Comput. Phys., 228:770–1789, 2009, Quantum corrected drift–diffusion models: Solution fixed point map and finite element approximation
- Proceedings of BAIL, Limerick, 2008, volume 69 of LNCSE, 2009, A patched mesh method for singularly perturbed reaction-diffusion equations
- Proceedings of BAIL, Limerick, 2008, volume 69 of LNCSE, 2009, Singularly perturbed reaction-diffusion problem with a boundary turning point
- Proceedings of the 2008 ECMI conference, London, volume 15 of Mathematics in Industry, 2009, Patches of finite elements for singularly-perturbed diffusion reaction equations with discontinuous coefficients

## 2008

- Proceedings of the 79th GAMM meeting, volume 8 of Proc. Appl. Math. Mech. PAMM, pages 10061 – 10064, 2008, Dynamical iteration schemes for multiscale simulation in nanoelectronics
- Proceedings of the 79th GAMM meeting, volume 8 of Proc. Appl. Math. Mech. (PAMM), pages 10065–10068, 2008, Dynamical iteration schemes for coupled simulation in nanoelectronics

# Books

- GNU Octave Manual Version 3, ISBN 0-9546120-6-X
- Scientific Computing with MATLAB and Octave, ISBN 978-3-642-12429-7
- Numerical Methods for the Life Scientist, ISBN 978-3-642-20819-5
- GNU Octave Beginners Guide, ISBN 1849513325