# Publications using Octave

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## Contents

# Books

- GNU Octave Manual Version 3, 2011, ISBN 0-9546120-6-X
- Scientific Computing with MATLAB and Octave, 2010, ISBN 978-3-642-12429-7
- Numerical Methods for the Life Scientist, 2011, ISBN 978-3-642-20819-5
- GNU Octave Beginners Guide, 2011, ISBN 1849513325
- Chemical Reactor Analysis and Design Fundamentals, 2009, ISBN 978-0-615-11884-0
- Model Predictive Control: Theory and Design, 2009, ISBN 978-0-9759377-0-9

# Articles

The following list contains articles that used GNU Octave. Older articles were collected automatically and they might appear in the list only because they cite the GNU Octave Manual, we are checking these publications manually, those that have been checked and confirmed are marked with "!" those marked with a "?" could not be checked due to access restrictions.

## 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

- Journal of Process Control, 2012, GNU Octave and reproducible research !
- 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 !
- Biophysical Journal Locomotion control of Caenorhabditis elegans through confinement !
- 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 !
- 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 !
- 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 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 !
- IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum p2 Matlab: Productive parallel matlab for the exascale
- Physics of Fluids Relaminarisation of Re τ = 100 channel flow with globally stabilising linear feedback control
- Journal of Machine Learning Research Lightweight implementations of probabilistic programming languages via transformational compilation
- Proceedings of the ASME Design Engineering Technical Conference uBlasCL: Architecture agnostic massively parallel Linear Algebra system
- Proceedings - 2011 IEEE Electronics, Robotics and Automotive Mechanics Conference, CERMA 2011 Analysis of AVI files for mice behavior experiments in the Morris water maze
- Earthquake and Structures Reconstruction of missing response data for identification of higher modes
- Advances in Engineering Software GeoPDEs: A research tool for Isogeometric Analysis of PDEs
- 2011 IEEE International Conference on Robotics and Biomimetics, ROBIO 2011 From walking to running a natural transition in the SLIP model using the hopping gait
- Applied Bionics and Biomechanics Teletactile system based on mechanical properties estimation
- Proceedings of the National Academy of Sciences of the United States of America Mean-field modeling of thalamocortical dynamics and a model-driven approach to EEG analysis
- Nucleic Acids Research A quantitative model of nucleosome dynamics
- ACM Transactions on Graphics Steady affine motions and morphs
- Wiener Medizinische Wochenschrift Role of optimization criterion in static asymmetric analysis of lumbar spine load
- Journal of Composite Materials Micro-mechanical prediction of UD laminates behavior under combined compression up to failure: Influence of matrix degradation
- Proceedings - 2011 IEEE International Symposium on Assembly and Manufacturing, ISAM 2011 Importance sampling based on adaptive principal component analysis
- International Journal for Numerical Methods in Engineering RK-Slim: Embedded Runge-Kutta without the excess baggage
- Journal of Neuroscience Methods Calcium signals: Analysis in time and frequency domains
- IFIP Advances in Information and Communication Technology Architecture of a Pan-European framework for integrated soil water erosion assessment
- Proceedings - Annual Workshop on Interaction between Compilers and Computer Architectures, INTERACT MATLAB parallelization through scalarization
- 2011 Promotion and Innovation with New Technologies in Engineering Education, FINTDI 2011, Conference Proceedings A review of teaching power system harmonics
- Physical Review E - Statistical, Nonlinear, and Soft Matter Physics Automatic recovery of missing amplitudes and phases in tilt-limited electron crystallography of two-dimensional crystals
- Communications in Computer and Information Science Analysis of time measurements in network systems using decomposition on subprocesses
- Proceedings of the ACM SIGPLAN Conference on Programming Language Design and Implementation (PLDI) Automatic compilation of MATLAB programs for synergistic execution on heterogeneous processors
- Journal of Aerospace Engineering Experiments and cohesive zone model parameters for T650/AFR-PE-4/FM680-1 at high temperatures
- Proceedings of the IEEE Enabling accurate cross-layer PHY/MAC/NET simulation studies of vehicular communication networks
- Journal of Mathematics and Music A few more words about James Tenney: Dissonant counterpoint and statistical feedback
- Applied Optics On the importance of path for phase unwrapping in synthetic aperture radar interferometry
- Physical Review E - Statistical, Nonlinear, and Soft Matter Physics Exploiting the passive dynamics of a compliant leg to develop gait transitions
- BMC Systems Biology Automated Bayesian model development for frequency detection in biological time series
- Journal of Wind Engineering and Industrial Aerodynamics Fractional spectral moments for digital simulation of multivariate wind velocity fields
- Advances in Applied Probability Approximation of bounds on mixed-level orthogonal arrays
- IEEE Transactions on Antennas and Propagation Demonstration of a dual-polarized phased-array feed
- Electrochimica Acta Reducing error and measurement time in impedance spectroscopy using model based optimal experimental design
- Biomacromolecules Infrared linear dichroism spectroscopy on amyloid fibrils aligned by molecular combing
- Chemical Science Conformational states of nucleic acid-peptide complexes monitored by acoustic wave propagation and molecular dynamics simulation
- Journal of the Acoustical Society of America Estimating the control parameters of an articulatory model from electromagnetic articulograph data ?
- Fuzzy Sets and Systems Decision tree based fuzzy classifier of 1H magnetic resonance spectra from cerebrospinal fluid samples !
- Computational Management Science Shape-based scenario generation using copulas !
- 2011 4th IFIP International Conference on New Technologies, Mobility and Security, NTMS 2011 - Proceedings Adaptive fuzzy-MAC for power reduction in Wireless Sensor Networks !
- Communications in Computational Physics Reduction of linear systems of ODEs with optimal replacement variables !
- Optics Express Longitudinal mode multistability in Ring and Fabry-Pérot lasers: The effect of Spatial Hole Burning !
- Journal of Chemical Physics Photoelectron imaging of several 5d and 6p Rydberg states Xe 2 and improving the Xe 2 + I(12g) potential ?
- Chemical Physics Letters Analysis of motion features for molecular dynamics simulation of proteins !
- Journal of Physical Chemistry B In silico predictions of the temperature-dependent viscosities and electrical conductivities of functionalized and nonfunctionalized ionic liquids !
- Journal of Molecular Biology Probing designability via a generalized model of helical bundle geometry !

## 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 !

- Algebraic and Geometric Topology Symmetric homology of algebras
- ICFC 2010 ICNC 2010 - Proceedings of the International Conference on Fuzzy Computation and International Conference on Neural Computation [ Development of a fuzzy calculator for continuous functions of non-interactive fuzzy variables]
- Journal of Computational and Applied Mathematics Modeling of an insurance system and its large deviations analysis
- 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10 Real-time Experiment Interface for biological control applications
- INFORMS Journal on Computing A heuristic for nonlinear global optimization
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) Probabilistic semantics and program analysis
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) Performance aware reconfiguration of software systems
- Biotechnology, Agronomy and Society and Environment Comparison of two drying models applied to corn drying in fluidized bed [Comparaison d'un modèle empirique et d'un modèle physique de séchage de grains de maïs en lit fluidisé]
- Spectroscopy Letters Quantitative infrared spectroscopy in the undergraduate laboratory via multivariate mixture analysis of a simulated analgesic
- European Radiology Longitudinal study of a mouse model of chronic pulmonary inflammation using breath hold gated micro-CT
- Chemical Physics A classical Master equation approach to modeling an artificial protein motor
- ACM Transactions on Mathematical Software Increasing the reliability of adaptive quadrature using explicit interpolants
- Computer Applications in Engineering Education Teaching differential equations in different environments: A first approach
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) The qnetworks toolbox: A software package for queueing networks analysis
- Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences Stochastically forced water waves in a circular basin
- Performance Evaluation Review RSIO: Automatic user interaction detection and scheduling
- Journal of High Energy Physics Quasinormal modes of massive charged avor branes
- Langmuir Viscoelastic modeling with interfacial slip of a protein monolayer electrode-adsorbed on an acoustic wave biosensor
- Journal of Biological Chemistry Biochemical basis of the interaction between cystic fibrosis transmembrane conductance regulator and immunoglobulin-like repeats of filamin
- Computers and Chemical Engineering Data smoothing and numerical differentiation by a regularization method
- Physical Review A - Atomic, Molecular, and Optical Physics Resonant trapping in the transport of a matter-wave soliton through a quantum well
- High Pressure Research Raman spectroscopy of triolein under high pressures
- Journal of Physics A: Mathematical and Theoretical Relaxation dynamics of perturbed regular hyperbranched fractals
- Bulletin of the Polish Academy of Sciences: Technical Sciences Extending scientific computing system with structural quantum programming capabilities
- Communications in Computational Physics Simulation of spherulite growth using a comprehensive approach to modeling the first-order isotropic/smectic-a mesophase transition
- Computational Statistics and Data Analysis Grapham: Graphical models with adaptive random walk Metropolis algorithms
- Autonomous Robots HERB: A home exploring robotic butler
- International Journal of Electrical Engineering Education Experience with PSAT (Power System Analysis Toolbox) as free and open-source software for power system education and research

## 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 !
- Journal of Physical Chemistry B Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis
- IEEE Transactions on Semiconductor Manufacturing A novel approach to analyze and model feature size effects in CMP
- Performance Evaluation System-theoretical algorithmic solution to waiting times in semi-Markov queues
- Computer Languages, Systems and Structures jLab: Integrating a scripting interpreter with Java technology for flexible and efficient scientific computation
- Journal of Geophysical Research B: Solid Earth NW Australian intraplate seismicity and stress regime
- Journal of Chemometrics A comparison of nine PLS1 algorithms
- Measurement Science and Technology Determining membrane permeability of giant phospholipid vesicles from a series of videomicroscopy images
- Mathematical Methods of Statistics A Bayesian approach to the estimation of maps between Riemannian manifolds. II: Examples
- Physical Review Special Topics - Accelerators and Beams Tracking studies of the Compact Linear Collider collimation system
- Biological Cybernetics Predictive feedback in human simulated pendulum balancing
- Bulletin of the Russian Academy of Sciences: Physics Regions of excessive flux of PeV cosmic rays
- Computing in Science and Engineering Scientific scripting for the java platform with jlab
- International Journal of Control Constrained intermittent model predictive control
- Journal of Chromatography A Suppressing the charged coupled device noise in univariate thin-layer videoscans: A comparison of several algorithms
- ACM Transactions on Mathematical Software Algorithm 892: DISPMODULE, a Fortran 95 module for pretty-printing matrices
- Stochastic Processes and their Applications Importance sampling for a Markov modulated queuing network

## 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 !
- Journal of Biological Chemistry Monitoring light-induced structural changes of channelrhodopsin-2 by UV-visible and Fourier transform infrared spectroscopy
- Journal of Applied Physics Electro-optical modeling of bulk heterojunction solar cells !
- Clinical and Experimental Ophthalmology Fourier analysis of digital retinal images in estimation of cataract severity
- Numerische Mathematik Approximating optimization problems over convex functions
- Medical Engineering and Physics Cervical spine biomechanics following implantation of a disc prosthesis
- IEEE Power and Energy Society 2008 General Meeting: Conversion and Delivery of Electrical Energy in the 21st Century, PES Towards a common model for studying critical infrastructure interdependencies
- 3rd International Symposium on Wireless Pervasive Computing, ISWPC 2008, Proceedings A novel low-complexity algorithm for linear MMSE MIMO receivers
- Studies in Computational Intelligence Visualization and interactive exploration of large, multidimensional data sets
- Studies in Computational Intelligence A versatile surrogate-assisted memetic algorithm for optimization of computationally expensive functions and its engineering applications
- IEEE Transactions on Education An open source power system virtual laboratory: The PSAT case and experience
- Applied Mechanics Reviews A review of H∞ robust control of piezoelectric smart structures
- IEEE Transactions on Biomedical Engineering Image analysis for microelectronic retinal prosthesis
- Composite Structures Finite element modeling and optimization of load transfer in multi-fastener joints using structural elements

## 2007

- Water Science and Technology Kinetics of autothermal thermophilic aerobic digestion - Application and extension of Activated Sludge Model No 1 at thermophilic temperatures
- Western North American Naturalist Moistened seeds increase rodent trap success
- EUROMICRO 2007 - Proceedings of the 33rd EUROMICRO Conference on Software Engineering and Advanced Applications, SEAA 2007 GridIJ - A dynamic grid service architecture for scientific image processing
- IEEE International Conference on Intelligent Robots and Systems Kernel-based visual servoing
- 2007 IEEE Power Engineering Society General Meeting, PES Application of the PSAT, an open source software, for educational and research purposes
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) Abstract interpretation for worst and average case analysis
- Proceedings - IEEE International Conference on Cluster Computing, ICCC Performance analysis of a user-level memory server
- Proceedings of the Institution of Mechanical Engineers. Part I: Journal of Systems and Control Engineering An adaptive learning algorithm for controlling a two-degree-of-freedom serial ball-and-socket actuator
- Lecture Notes in Control and Information Sciences A nonlinear model predictive control framework as free software: Outlook and progress report
- Collection of Technical Papers - 2007 AIAA InfoTech at Aerospace Conference Airfoil shape optimization by minimization of an expensive and discontinuous black-box function
- Periodica Polytechnica: Chemical Engineering Connection between oxygen uptake rate and carbon dioxide evolution rate in aerobic thermophilic sludge digestion
- Journal of Fluid Mechanics Instability of the buoyancy layer on an evenly heated vertical wall
- Electronic Notes in Theoretical Computer Science On Probabilistic Techniques for Data Flow Analysis
- Collection of Technical Papers - AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics and Materials Conference T650/AFR-PE-4/FM680-1 mode I critical energy release rate at high temperatures: Experiments and numerical models
- Phytochemistry Design of substrate label for steady state flux measurements in plant systems using the metabolic network of Brassica napus embryos
- IET Software Scientific programming with Java classes supported with a scripting interpreter
- Genetics Adaptation of a quantitative trait to a moving optimum
- Water Environment Research Application of activated sludge model no. 3 for the modeling of organic matter biodegradation at thermophilic temperatures
- Computational Statistics Excel :: COM :: R
- IEEE Transactions on Power Delivery Effects of sampling rate and ADC width on the accuracy of amplitude and phase measurements in power-quality monitoring
- Bulletin of the Russian Academy of Sciences: Physics Search for sources of cosmic rays in the region of the knee: Part II

## 2006

- Chemometrics and Intelligent Laboratory Systems How octave can replace Matlab in chemometrics
- 41st International Universities Power Engineering Conference, UPEC 2006, Conference Procedings System requirements of real time continuous data acquisition for power quality monitoring
- e-Science 2006 - Second IEEE International Conference on e-Science and Grid Computing Grid services toolkit for process data processing
- Chemometrics and Intelligent Laboratory Systems Superresolution of hyperspectral images
- Computer Applications in Engineering Education A Web-based tool for control engineering teaching
- ANZIAM Journal Drainage after total knee replacement
- Protein Engineering, Design and Selection Consensus guided mutagenesis of Renilla luciferase yields enhanced stability and light output
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) SCE toolboxes for the development of high-level parallel applications
- Space Science Reviews End-to-end modeling of the solar terrestrial system
- Publications of the Astronomical Society of Japan [ Milliarcsecond-scale spectral properties and jet motions in M 87]
- Nucleic Acids Research Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I
- Physiological Measurement Uses and abuses of EIDORS: An extensible software base for EIT
- International Journal for Numerical and Analytical Methods in Geomechanics Review of validation of the discontinuous deformation analysis (DDA) method
- Physical Review A - Atomic, Molecular, and Optical Physics Maximizing nearest-neighbor entanglement in finitely correlated qubit chains
- Transportation Science Solving noisy, large-scale fixed-point problems and systems of nonlinear equations

## 2005

- Collection of Technical Papers - AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics and Materials Conference Comprehensive rotorcraft analysis: Past, present, and future
- Journal of Geophysical Research A: Space Physics Analysis and visualization of space science model output and data with CISM-DX
- Applied Catalysis A: General Simplified kinetic models of methanol oxidation on silver
- Automatica Data compression for estimation of the physical parameters of stable and unstable linear systems
- IEEE Transactions on Power Systems An open source power system analysis toolbox
- BMC Bioinformatics Computing expectation values for RNA motifs using discrete convolutions
- IEEE Transactions on Signal Processing Design of discrete coefficient FIR filters by a fast entropy-directed deterministic annealing algorithm

## 2004

- Proceedings of the International Conference on Automation Technology for Off-road Equipment, ATOE 2004 [ RTK-GPS based autonomous crawler wagon control]
- Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science) Data analysis of microarrays using SciCraft
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) Self-adaptive scouting-autonomous experimentation for systems biology
- Journal of Engineering Mechanics Time integration in discontinuous deformation analysis

## 2003

- Physical Review Special Topics - Accelerators and Beams Calibration of the Fermilab Booster ionization profile monitor
- SAR and QSAR in Environmental Research Zherlock: An open source data analysis software