# Publications using Octave

## Contents

# 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.

- IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum p 2Matlab: 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]
- SEKE 2011 - Proceedings of the 23rd International Conference on Software Engineering and Knowledge Engineering [ SC-xScript: An embedded script language for scientific computation in embedded systems]
- 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
- WSEAS Transactions on Information Science and Applications [ Matlab-like scripting for the Java platform with the jLab environment]
- WSEAS Transactions on Information Science and Applications [ Scientific programming with an environment that combines effectively compiled and interpreted scripting at the Java platform]
- 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
- WSEAS Transactions on Information Science and Applications [ The design and implementation of a Java based open source mathematical programming environment]
- 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

## 2002

- International Polymer Processing [ Modelling of the flow in the distribution plate of a spin pack]
- Journal of Magnetic Resonance Specification and visualization of anisotropic interaction tensors in polypeptides and numerical simulations in biological solid-state NMR

# 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