Publications of Thomas J. Naughton

Publications [Compressed PostScript files and PDF files can be viewed using Ghostview . Compressed PostScript files can also be decompressed using gzip or WinZip. Comments welcome at ]

Journal papers

Damien Woods and Thomas J. Naughton, "Optical computing: Photonic neural networks," Nature Physics, vol. 8, no. 4, pp. 257-259, April 2012. (News & Views) (© Nature Publishing Group.)
Risto Näsänen, Tristan Colomb, Yves Emery, and Thomas J. Naughton, "Enhancement of three-dimensional perception of numerical hologram reconstructions of real-world objects by motion and stereo," Optics Express, vol. 19, no. 17, pp. 16075-16086, August 2011. [plus 2 multimedia files] (© OSA.) Selected for republication in Virtual Journal for Biomedical Optics, vol. 6, no. 9, October 2011.
Tomi Pitkäaho and Thomas J. Naughton, "Calculating depth maps from digital holograms using stereo disparity," Optics Letters, vol. 36, no. 11, pp. 2035-2037, June 2011. (© OSA.)
Naveen K. Nishchal and Thomas J. Naughton, "Flexible optical encryption with multiple users and multiple security levels," Optics Communications, vol. 284, no. 3, pp. 735-739, February 2011. (© Elsevier.)
Andrew J. Page, Thomas M. Keane, and Thomas J. Naughton, "Multi-heuristic dynamic task allocation using genetic algorithms in a heterogeneous distributed system," Journal of Parallel and Distributed Computing, vol. 70, no. 7, pp. 758-766, July 2010. (© Elsevier.)
Melania Paturzo, Pasquale Memmolo, Andrea Finizio, Risto Näsänen, Thomas J. Naughton, and Pietro Ferraro, "Holographic display of synthetic 3D dynamic scene," 3D Research, vol. 1, no. 2, pp. 31-35, June 2010. (Invited.) [plus 3 multimedia files] (© 3D Research Center and Springer.)
Melania Paturzo, Pasquale Memmolo, Andrea Finizio, Risto Näsänen, Thomas J. Naughton, and Pietro Ferraro, "Synthesis and display of dynamic holographic 3D scenes with real-world objects," Optics Express, vol. 18, no. 9, pp. 8806-8815, April 2010. [plus 8 multimedia files] (© OSA.)
Karen M. Molony, Bryan M. Hennelly, Damien P. Kelly, and Thomas J. Naughton, "Reconstruction algorithms applied to in-line Gabor digital holographic microscopy," Optics Communications, vol. 283, no. 6, pp. 903-909, March 2010. (© Elsevier.)
Emmanouil Darakis, Taslima Khanama, Arvind Rajendran, Vinay Kariwala, Thomas J. Naughton, and Anand K. Asundi, "Microparticle characterization using digital holography," Chemical Engineering Science, vol. 65, no. 2, pp. 1037-1044, January 2010. (© Elsevier.)
Damien Woods and Thomas J. Naughton, "Optical computing," Applied Mathematics and Computation, Special Issue on Physics and Computation, vol. 215, no. 4, pp. 1417-1430, October 2009. (© Elsevier.)
Damien P. Kelly, Bryan M. Hennelly, Nitesh Pandey, Thomas J. Naughton, and William T. Rhodes, "Resolution limits in practical digital holographic systems," Optical Engineering, vol. 48, article no. 095801, September 2009. (© SPIE.)
David S. Monaghan, Unnikrishnan Gopinathan, Guohai Situ, Thomas J. Naughton, and John T. Sheridan, "Statistical investigation of the double random phase encoding technique," Journal of the Optical Society of America A, vol. 26, no. 9, pp. 2033-2042, September 2009. (© OSA.)
Lukas Ahrenberg, Andrew J. Page, Bryan M. Hennelly, John B. McDonald, and Thomas J. Naughton, "Using commodity graphics hardware for real-time digital hologram view-reconstruction," Journal of Display Technology, vol. 5, no. 4, pp. 111-119, April 2009. (© IEEE.)
Michel Kempkes, Emmanouil Darakis, Taslima Khanam, Arvind Rajendran, Vinay Kariwala, Marco Mazzotti, Thomas J. Naughton, and Anand K. Asundi, "Three dimensional digital holographic profiling of micro-fibers," Optics Express, vol. 17, no. 4, pp. 2938-2943, February 2009. (© OSA.)
David S. Monaghan, Guohai Situ, Unnikrishnan Gopinathan, Thomas J. Naughton, and John T. Sheridan, "Analysis of phase encoding for optical encryption," Optics Communications, vol. 282, no. 4, pp. 482-492, February 2009. (© Elsevier.)
David S. Monaghan, Unnikrishnan Gopinathan, Damien P. Kelly, Thomas J. Naughton, and John T. Sheridan, "Systematic errors of an optical encryption system due to the discrete values of a spatial light modulator," Optical Engineering, vol. 48, article no. 027001, February 2009. (© SPIE.)
Andrew J. Page, Thomas M. Keane, and Thomas J. Naughton, "Scheduling in a dynamic heterogeneous distributed system using estimation error," Journal of Parallel and Distributed Computing, vol. 68, no. 11, pp. 1452-1462, November 2008. (© Elsevier.)
Thomas J. Naughton, Bryan M. Hennelly, and Tom Dowling, "Introducing secure modes of operation for optical encryption," Journal of the Optical Society of America A, vol. 25, no. 10, pp. 2608-2617, October 2008. (© OSA.)
Guohai Situ, David S. Monaghan, Thomas J. Naughton, John T. Sheridan, Giancarlo Pedrini, and Wolfgang Osten, "Collision in double random phase encoding," Optics Communications, vol. 281, no. 20, pp. 5122-5125, October 2008. (© Elsevier.)
David S. Monaghan, Guohai Situ, Unnikrishnan Gopinathan, Thomas J. Naughton, and John T. Sheridan, "Role of phase keys in the double random phase encoding technique: an error analysis," Applied Optics, vol. 47, no. 21, pp. 3808-3816, July 2008. (© OSA.)
Conor P. Mc Elhinney, Bryan M. Hennelly, and Thomas J. Naughton, "Extended focused imaging for digital holograms of macroscopic three-dimensional objects," Applied Optics, vol. 47, no. 19, pp. D71-D79, July 2008. (© OSA.)
Unnikrishnan Gopinathan, David S. Monaghan, Bryan M. Hennelly, Conor P. Mc Elhinney, Damien P. Kelly, John B. McDonald, Thomas J. Naughton, and John T. Sheridan, "A projection system for real world three-dimensional objects using spatial light modulators," Journal of Display Technology, vol. 4, no. 2, pp. 254-261, June 2008. (© IEEE.)
Andrew J. Page, Lukas Ahrenberg, and Thomas J. Naughton, "Low memory distributed reconstruction of large digital holograms," Optics Express, vol. 16, no. 3, pp. 1990-1995, February 2008. (© OSA.)
Unnikrishnan Gopinathan, Guohai Situ, Thomas J. Naughton, and John T. Sheridan, "Noninterferometric phase retrieval using a fractional Fourier system," Journal of the Optical Society of America A, vol. 25, no. 1, pp. 108-115, January 2008. (© OSA.) Selected for republication in Virtual Journal for Biomedical Optics, vol. 3, no. 2, February 2008.
Niall Murphy, Thomas J. Naughton, Damien Woods, Beverley Henley, Kieran McDermott, Elaine Duffy, Peter J. M. van der Burgt, and Niamh Woods, "Implementations of a model of physical sorting," International Journal of Unconventional Computing, vol. 4, no. 1, pp. 3-12, January 2008. (Invited.) (© Old City Publishing, Inc.)
David S. Monaghan, Unnikrishnan Gopinathan, Thomas J. Naughton, and John T. Sheridan, "Key-space analysis of double random phase encryption technique," Applied Optics, vol. 46, no. 26, pp. 6641-6647, September 2007. (© OSA.)
Yann Frauel, Albertina Castro, Thomas J. Naughton, and Bahram Javidi, "Resistance of the double random phase encryption against various attacks," Optics Express, vol. 15, no. 16, pp. 10253-10265, August 2007. (© OSA.)
Thomas M. Keane, Thomas J. Naughton, and James O. McInerney, "MultiPhyl: a high-throughput phylogenomics webserver using distributed computing," Nucleic Acids Research, vol. 35, pp. W33-W37, July 2007. (© The Authors)
Emmanouil Darakis, Thomas J. Naughton, and John J. Soraghan, "Compression defects in different reconstructions from phase-shifting digital holographic data," Applied Optics, vol. 46, no. 21, pp. 4579-4586, July 2007. (© OSA.)
Alison E. Shortt, Thomas J. Naughton, and Bahram Javidi, "Histogram approaches for lossy compression of digital holograms of three-dimensional objects," IEEE Transactions on Image Processing, vol. 16, no. 6, pp. 1548-1556, June 2007. (© IEEE.)
Jonathan Maycock, Bryan M. Hennelly, John B. McDonald, Yann Frauel, Albertina Castro, Bahram Javidi, and Thomas J. Naughton, "Reduction of speckle in digital holography by discrete Fourier filtering," Journal of the Optical Society of America A, vol. 24, no. 6, pp. 1617-1622, June 2007. (© OSA.)
Conor P. Mc Elhinney, John B. McDonald, Albertina Castro, Yann Frauel, Bahram Javidi, and Thomas J. Naughton, "Depth-independent segmentation of macroscopic three-dimensional objects encoded in single perspectives of digital holograms," Optics Letters, vol. 32, no. 10, pp. 1229-1231, May 2007. (© OSA.)
Bryan M. Hennelly, Thomas J. Naughton, John B. McDonald, John T. Sheridan, Gopinathan Unnikrishnan, Damien P. Kelly, and Bahram Javidi, "Spread space spread spectrum technique for secure multiplexing," Optics Letters, vol. 32, no. 9, pp. 1060-1062, May 2007. (© OSA.)
Alison E. Shortt, Thomas J. Naughton, and Bahram Javidi, "Compression of optically encrypted digital holograms using artificial neural networks," Journal of Display Technology, vol. 2, no. 4, pp. 401-410, December 2006. (© IEEE.)
Unnikrishnan Gopinathan, Thomas J. Naughton, and John T. Sheridan, "Polarization encoding and multiplexing of two-dimensional signals: application to image encryption," Applied Optics, vol. 45, no. 22, pp. 5693-5700, August 2006. (© OSA.)
Thomas M. Keane, Andrew J. Page, Thomas J. Naughton, Simon A.A. Travers, and James O. McInerney, "Building large phylogenetic trees on coarse-grained parallel machines," Algorithmica, Special issue on Coarse Grained Parallel Algorithms for Scientific Applications, vol. 45, no. 3, pp. 285-300, July 2006. (© Springer.)
Alison E. Shortt, Thomas J. Naughton, and Bahram Javidi, "A companding approach for nonuniform quantization of digital holograms of three-dimensional objects," Optics Express, vol. 14, no. 12, pp. 5129-5134, June 2006. (© OSA.)
Jonathan Maycock, Conor P. McElhinney, Bryan M. Hennelly, Thomas J. Naughton, John B. McDonald, and Bahram Javidi, "Reconstruction of partially occluded objects encoded in three-dimensional scenes using digital holograms," Applied Optics, vol. 45, no. 13, pp. 2975-2985, May 2006. (© OSA.)
Unnikrishnan Gopinathan, David S. Monaghan, Thomas J. Naughton, and John T. Sheridan, "A known-plaintext heuristic attack on the Fourier plane encryption algorithm," Optics Express, vol. 14, no. 8, pp. 3181-3186, April 2006. (© OSA.)
Alison E. Shortt, Thomas J. Naughton, and Bahram Javidi, "Compression of digital holograms of three-dimensional objects using wavelets," Optics Express, vol. 14, no. 7, pp. 2625-2630, April 2006. (© OSA.)
Thomas M. Keane, Christopher J. Creevey, Melissa M. Pentony, Thomas J. Naughton, and James O. McInerney, "Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified," BMC Evolutionary Biology, vol. 6, p. 29, March 2006. [HTML] (© Keane et al.)
Yann Frauel, Thomas J. Naughton, Osamu Matoba, Enrique Tajahuerce, and Bahram Javidi, "Three-dimensional imaging and processing using computational holographic imaging," Proceedings of the IEEE, vol. 94, no. 3, pp. 636-653, March 2006. (Invited.) (© IEEE.) Winner of 2008 IEEE Donald G. Fink Prize Paper Award for most outstanding review paper in preceding year from all IEEE journals.
Andrew J. Page and Thomas J. Naughton, "Framework for task scheduling in heterogeneous distributed computing using genetic algorithms," Artificial Intelligence Review, vol. 24, no. 3-4, pp. 415-429, November 2005. (© Springer.)
Damien Woods and Thomas J. Naughton, "An optical model of computation," Theoretical Computer Science, vol. 334, no. 1-3, pp. 227-258, April 2005. (© Elsevier.)
Thomas M. Keane and Thomas J. Naughton, "DSEARCH: sensitive database searching using distributed computing," Bioinformatics, vol. 21, no. 8, pp. 1705-1706, April 2005. [HTML] (© Oxford University Press.)
Thomas M. Keane, Thomas J. Naughton, Simon A.A. Travers, James O. McInerney, and Grace P. McCormack, "DPRml: distributed phylogeny reconstruction by maximum likelihood," Bioinformatics, vol. 21, no. 7, pp. 969-974, April 2005. [HTML] (© Oxford University Press.)
Thomas J. Naughton and Bahram Javidi, "Compression of encrypted three-dimensional objects using digital holography," Optical Engineering, vol. 43, no. 10, pp. 2233-2238, October 2004. (Invited.) (© SPIE.)
Thomas J. Naughton, John B. Mc Donald, and Bahram Javidi, "Efficient compression of Fresnel fields for Internet transmission of three-dimensional images," Applied Optics, vol. 42, no. 23, pp. 4758-4764, August 2003. (© OSA.)
Osamu Matoba, Thomas J. Naughton, Yann Frauel, Nicolas Bertaux, and Bahram Javidi, "Real-time three-dimensional object reconstruction by use of a phase-encoded digital hologram," Applied Optics, vol. 41, no. 29, pp. 6187-6192, October 2002. (© OSA.)
Thomas J. Naughton, Yann Frauel, Bahram Javidi, and Enrique Tajahuerce, "Compression of digital holograms for three-dimensional object reconstruction and recognition," Applied Optics, vol. 41, no. 20, pp. 4124-4132, July 2002. (© OSA.)
Thomas Naughton, Zohreh Javadpour, John Keating, Milos Klíma, and Jirí Rott, "General-purpose acousto-optic connectionist processor," Optical Engineering, vol. 38, no. 7, pp. 1170-1177, July 1999. (© SPIE.)

Books/volumes edited

Thomas J. Naughton and John T. Sheridan, Eds., Optics in Information Systems, Special issue on Optical Encryption, vol. 16, no. 1, SPIE Press, Bellingham, Washington, February 2005. (Invited.) (© SPIE.)
M. Aleksy, T. Coffey, A. Fong, R. Gitzel, D. Lewis, F. Masulli, L. Moreno, T. Naughton, D. O'Sullivan, C. Roda, P. Rosso, S. Rovetta, J. Thomas, and J. Waldron, Eds., Proceedings of ISICT 2003 - International Symposium on Information and Communication Technologies, 24-26 September 2003, Computer Science Press, Trinity College Dublin, Ireland, 2003. ISBN: 0-9544145-2-7

Book chapters (incl. LNCS)

Risto Näsänen, Taina M. Lehtimäki, Tomi Pitkäaho, and Thomas J. Naughton, "Presentation and perception of digital hologram reconstructions of real-world objects on conventional stereoscopic displays," in Bahram Javidi and Thierry Fournel, Eds., Information Optics and Photonics: Algorithms, Systems, and Applications, chap. 10, pp. 129-142, Springer, New York, 2010. (Invited.) Thomas J. Naughton and Damien Woods, "Optical computing," in Robert A. Meyers, Ed., Encyclopedia of Complexity and System Science, pp. 6388-6407, Springer, New York, 2009. ISBN: 978-0-387-75888-6 (Invited.)
Conor P. McElhinney, Bryan M. Hennelly, Bahram Javidi, and Thomas J. Naughton, "Extraction of three-dimensional information from reconstructions of in-line digital holograms," in Bahram Javidi, Fumio Okano, Jung-Young Son, Eds., Three-dimensional Imaging, Visualization, and Display, chap. 15, pp. 303-332, Springer-Verlag, New York, 2009. ISBN: 978-0-387-79334-4 (Invited.) Damien Woods and Thomas J. Naughton, "Parallel and sequential optical computing," Optical SuperComputing, Shlomi Dolev, Tobias Haist, and Mihai Oltean, Eds., Springer Lecture Notes in Computer Science vol. 5172, chap. 6, pp. 70-86, Springer-Verlag, Berlin, 2008. ISBN: 978-3-540-85672-6 (© Springer-Verlag.) Alison E. Shortt, Thomas J. Naughton, and Bahram Javidi, "Compression of encrypted digital holograms using artificial neural networks," in Bahram Javidi, Ed., Optical Imaging Sensors and Systems for Homeland Security Applications, chap. 2, pp. 25-46, Springer-Verlag, New York, 2006. ISBN: 978-0-387-26170-6 (Invited.)
Thomas J. Naughton and Bahram Javidi, "Compression of digital holograms for secure three-dimensional image storage and transmission," in Bahram Javidi, Ed., Optical and Digital Techniques for Information Security, chap. 9, pp. 173-191, Springer-Verlag, Berlin, 2005. ISBN: 978-0-387-20616-5 (Invited.) Thomas Keane, Richard Allen, Thomas J. Naughton, James McInerney, and John Waldron, "Distributed Java platform with programmable MIMD capabilities," Scientific Engineering for Distributed Java Applications, Nicolas Guelfi, Egidio Astesiano, and Gianna Reggio, Eds., Springer Lecture Notes in Computer Science vol. 2604, chap. 11, pp. 122-131, Springer-Verlag, Berlin, 2003. ISBN: 3-540-00679-6 (© Springer-Verlag.) Aidan Delaney and Thomas J. Naughton, "Emulation of an unconventional model of computation in Java," in James F. Power and John T. Waldron, Eds., Recent Advances in Java Technology: Theory, Application, Implementation, chap. 1, pp. 1-9, Computer Science Press, Trinity College Dublin, Ireland, 2002. ISBN: 0-9544145-0-0
Thomas Keane, Richard Allen, Thomas J. Naughton, James McInerney, and John Waldron, "Distributed computing for DNA analysis," in James F. Power and John T. Waldron, Eds., Recent Advances in Java Technology: Theory, Application, Implementation, chap. 11, pp. 99-108, Computer Science Press, Trinity College Dublin, Ireland, 2002. ISBN: 0-9544145-0-0 Thomas J. Naughton, Yann Frauel, Osamu Matoba, Bahram Javidi, and Enrique Tajahuerce, "Compression of digital holograms for three-dimensional video," in Bahram Javidi and Fumio Okano, Eds., Three Dimensional Television, Video, and Display Technologies, chap. 13, pp. 273-295, Springer-Verlag, Berlin, 2002. ISBN: 978-3-540-43549-5 (Invited.) Thomas J. Naughton and Damien Woods, "On the computational power of a continuous-space optical model of computation," Third International Conference on Machines, Computations, and Universality, Chisinau, Moldova, 23-27 May 2001, Maurice Margenstern and Yurii Rogozhin, Eds., Springer Lecture Notes in Computer Science vol. 2055, pp. 288-299, Springer-Verlag, Berlin, 2001. ISBN: 3-540-42121-1 (© Springer-Verlag.)

Technical magazine articles

Alison E. Shortt, Thomas J. Naughton, and Bahram Javidi, "Compression of encrypted digital holograms using artificial neural networks," Optics in Information Systems, vol. 16, no. 2, pp. 1-8, July 2005. (Invited article.) (© SPIE.)
Thomas J. Naughton, John B. Mc Donald, and Bahram Javidi, "Efficient compression of digital holograms for Internet transmission of three-dimensional images," IEEE Lasers and Electro-Optics Society (LEOS) Newsletter, Special issue on Hot Topics in Electro-Optical Sensors and Systems, vol. 18, no. 1, pp. 9-10, February 2004. (Invited article.) (© IEEE.) [HTML]
Thomas J. Naughton, John B. Mc Donald, and Bahram Javidi, "3D image transmission and the Internet," Optics & Photonics News, vol. 14, no. 8, p. 34, August 2003. (Invited article.) (© OSA.)
Thomas J. Naughton, Yann Frauel, Bahram Javidi, and Enrique Tajahuerce, "Compression of digital holograms for 3D imaging," Optics in Information Systems, Special issue on Integrated Computational Sensors, vol. 13, no. 1, p. 7, May 2002. (Invited article.) (© SPIE.)

Selected conference papers and technical reports

Niall Murphy, Damien Woods, and Thomas J. Naughton, "On the computational power of photosynthesis," Technical Report NUIM-CS-TR-2005-03, Department of Computer Science, National University of Ireland, Maynooth, April 2005.
Andrew Page, Thomas Keane, Richard Allen, Thomas J. Naughton, and John Waldron, "Multi-tiered distributed computing platform," 2nd International Conference on the Principles and Practice of Programming in Java, James F. Power and John T. Waldron, Eds., pp. 191-194, Kilkenny City, Ireland, 16-18 June 2003. (© ACM.)
Aidan Delaney, Thomas J. Naughton, and Damien Woods, "Towards a minimal computational power operating system," British Colloquium for Theoretical Computer Science, no. 19, Leicester, UK, 7-9 April 2003.
Aidan Delaney and Thomas J. Naughton, "Emulation of an unconventional model of computation in Java," Principles and Practice of Programming in Java, James F. Power and John T. Waldron, Eds., pp. 1-6, Dublin, Ireland, 13-14 June 2002.
Thomas J. Naughton, "Continuous-space model of computation is Turing universal," Critical Technologies for the Future of Computing, Sunny Bains and Leo J. Irakliotis, Eds., Proceedings of SPIE vol. 4109, pp. 121-128, San Diego, California, 30 July - 4 August 2000. (© SPIE.)
Thomas J. Naughton, "Fourier optical limits of coherent acousto-optic matrix-vector processor," Optics in Computing 2000, Roger A. Lessard and Tigran Galstian, Eds., Proceedings of SPIE vol. 4089, pp. 181-190, Quebec, Canada, 18-23 June 2000. (© SPIE.)
Thomas J. Naughton, "A model of computation for Fourier optical processors," Optics in Computing 2000, Roger A. Lessard and Tigran Galstian, Eds., Proceedings of SPIE vol. 4089, pp. 24-34, Quebec, Canada, 18-23 June 2000. (© SPIE.)
Thomas J. Naughton, Milos Klíma, and Jirí Rott, "Improved joint transform correlator performance through spectral domain thresholding," Proceedings of Optical Engineering Society of Ireland/Irish Machine Vision and Image Processing Joint Conference, David Vernon, Ed., pp. 199-214, Maynooth, Ireland, 9-10 September 1998.
Milos Klíma, Jirí Rott, Thomas J. Naughton, and John Keating, "Joint transform correlation in security applications," Proceedings of 31st Annual IEEE International Carnahan Conference on Security Technology, Larry D. Sanson, Ed., pp. 77-81, Canberra, Australia, 15-17 October 1997. (© IEEE.)

http://www.cs.nuim.ie/~tomn