Research publications


2017-


Lloyd, H. & Amos, M. (2017, to appear). Analysis of independent roulette selection in parallel ant colony optimization. Accepted for presentation at The Genetic and Evolutionary Computation Conference (GECCO), July 15-19 2017, Berlin, Germany.

2016


Richards, D. & Amos, M. (2016c). Shape optimization with surface-mapped CPPNs. IEEE Transactions on Evolutionary Computation. doi: 10.1109/TEVC.2016.2606040.

Goñi-Moreno, A, Carcajona, M., Kim, J., Martinez-García, E., Amos, M. & de Lorenzo, V. (2016). An implementation-focused bio/algorithmic workflow for synthetic biology. ACS Synthetic Biology 5:10, 1127-1135. doi: 10.1021/acssynbio.6b00029.

LLanes, A., Cecilia, J., Sanchez, A., Garcia, J.M., Amos, M. & Ujaldon, M. (2016). Dynamic load balancing on heterogenous clusters for parallel ant colony optimization. Cluster Computing 19:1, 1-11. doi: 10.1007/s10586-016-0534-4.

LLoyd, H. & Amos, M. (2016). A highly parallelized and vectorized implementation of Max-Min Ant System on Intel Xeon Phi. IEEE Symposium Series on Computational Intelligence (SSCI), December 6-9 2016, Athens, Greece. doi: 10.1109/SSCI.2016.7850085.

Richards, D. & Amos, M. (2016b). Regulatory representations in architectural design. In Iba, H. & Noman, N. (Eds.), Evolutionary Computation in Gene Regulatory Network Research, pp. 362-397, Wiley.

Richards, D. & Amos, M. (2016a). Encoding multi-materiality. In Grigoriadis, K. (Ed.), Mixed Matter: A Multi-Material Design Compendium, pp. 40-49, Jovis.

Amos, M. & Condon, E. (Eds.) (2016). Unconventional Computation and Natural Computation: 15th International Conference (UCNC 2016), Manchester, UK, July 11-15, 2016, Proceedings. Lecture Notes in Computer Science (LNCS) Vol. 9726, Springer.

2015


Amos, M., Axmann, I., Bluethgen, N., de la Cruz, F., Jaramillo, A., Rodriguez-Paton, A. & Simmel, F. (2015). Bacterial computing with engineered populations. Philosophical Transactions of the Royal Society A 373:2046. doi: 10.1098/rsta.2014.0218.

Goñi-Moreno, A. & Amos, M. (2015). DiSCUS: A simulation platform for conjugation computing. In Calude, C.S. & Dineen, M.J. (Eds), Unconventional and Natural Computation (UCNC 2015), Auckland, New Zealand, August 31-September 4, 2015. Springer, p.p. 181-191.

Amos, M., Rasmussen, S., McCaskill, J. & Dittrich, P. (Eds.) (2015). Special issue of Artificial Life, dedicated to the Second Workshop on Biological and Chemical Computing (BioChemIT), Volume 21: 1-2 (Editorial).

Amos, M. (Ed.) (2015). Special issue of International Journal of Unconventional Computing 11:1 (Editorial).

2014


Guerrero, G.D., Cecilia, J.M., Llanes, A., Garcia, J.M., Amos, M. & Ujaldon, M. (2014) Comparative evaluation of platforms for parallel Ant Colony Optimization. Journal of Supercomputing 69:1, 318-329. doi: 10.1007/s11227-014-1154-5.

Amos, M. (2014) Population-based microbial computing: A third wave of synthetic biology? International Journal of General Systems 43:7, 770-782. doi:10.1080/03081079.2014.921001.

Richards, D. & Amos, M. (2014a) Evolving morphologies with CPPN-NEAT and a dynamic substrate. In Proceedings of ALIFE 14, the Fourteenth International Conference on the Synthesis and Simulation of Living Systems, July 30-August 2, 2014, New York, USA. Edited by Hiroki Sayama, John Rieffel, Sebastian Risi, René Doursat and Hod Lipson, p.p. 255-262, MIT Press. doi: 10.7551/978-0-262-32621-6-ch042.

Richards, D. & Amos, M. (2014b) Designing with gradients: bio-inspired computation for digital fabrication. In Proceedings of the 34th Annual Conference of the Association for Computer Aided Design in Architecture (ACADIA 14: Design Agency), October 23-25, 2014, University of Southern California, Los Angeles, USA, p.p. 101-110.

2013


Verran, J., Crossley, M., Carolan, K., Jacobs, N. & Amos, M. (2013) Monsters, microbiology and mathematics: the epidemiology of a zombie apocalypse. Journal of Biological Education 48:2, 98-104. doi: 10.1080/00219266.2013.849283.

Dorrian, H., Borresen, J. & Amos, M. (2013) Community structure and multi-modal oscillations in complex networks. PLOS ONE 8(10): e75569. doi: 10.1371/journal.pone.0075569.

Goñi-Moreno, A., Amos, M. & de la Cruz, F. (2013) Multicellular computation using conjugation for wiring. PLOS ONE 8(6): e65986. doi:10.1371/journal.pone.0065986.

Cecilia, J.M., Nisbet, A., Amos, M., Garcia, J.M. & Ujaldon, M. (2013) Enhancing GPU parallelism in nature-inspired algorithms. Journal of Supercomputing 63:3, p.p. 773-789. doi:10.1007/s11227-012-0770-1.

Cecilia, J.M., Garcia, J.M., Nisbet, A., Amos, M. & Ujaldon, M. (2013) Enhancing data parallelism for ant colony optimisation on GPUs. Journal of Parallel and Distributed Computing 73:1, p.p. 42-51. doi:10.1016/j.jpdc.2012.01.002.

Crossley, M., Nisbet, A. & Amos, M. (2013) Quantifying the impact of parameter tuning on nature-inspired algorithms. In Advances in Artificial Life, ECAL2013, September 2-6, 2013, Taormina, Italy, p.p. 925-932. MIT Press.doi: 10.7551/978-0-262-31709-2-ch138

Crossley, M., Nisbet, A. & Amos, M. (2013) Fitness landscape-based characterisation of nature-inspired algorithms. In Proceedings of the 11th International Conference on Adaptive and Natural Computing Algorithms (ICANNGA’13), Lausanne, Switzerland, April 4-6, 2013. Tomassini, M., Antonioni, A., Daolio, F. & Buesser, P. (Eds.) Lecture Notes in Computer Science (LNCS), Volume 7824, p.p. 110-119, Springer.

2012


Goñi-Moreno, A. & Amos, M. (2012a) A reconfigurable NAND/NOR genetic logic gate. BMC Systems Biology 6:126. doi:10.1186/1752-0509-6-126.

Goñi-Moreno, A. & Amos, M. (2012) Continuous computation in engineered gene circuits. BioSystems 109:1, p.p. 52-56. doi: 10.1016/j.biosystems.2012.02.001.

Houston, R., White, J. & Amos, M. (2012) Zen Puzzle Garden is NP-complete. Information Processing Letters 112:3, p.p. 106-108. doi:10.1016/j.ipl.2011.10.016.

Amos, M. & Coldridge, J. (2012) A genetic algorithm for the Zen Puzzle Garden game. Natural Computing 11:3, p.p. 353-359. doi:10.1007/s11047-011-9284-7.

Amos, M., Stepney, S., Doursat, R., Vico, F.J. & Rasmussen, S. (2012) TRUCE: A coordination action for unconventional computation. International Journal of Unconventional Computing 8:4, p.p., 333-337.

Richards, D., Dunn, N. & Amos, M. (2012) An evo-devo approach to architectural design. Proc. Genetic and Evolutionary Computation Conference (GECCO), July 7-11 2012, Philadelphia, USA, p.p. 569-576. ACM Press.

Amos, M. & Dittrich, P. (Eds.) (2012) Special issue of BioSystems 109:1, p.p. 1-86, dedicated to the COBRA Workshop on Biological and Chemical Information Technologies (BioChemIT), European Conference on Artificial Life, Paris, France, August 8 2011. Editorial: 10.1016/j.biosystems.2012.05.008.

Jacobs, N. & Amos, M. (2012) NanoInfoBio: A case-study in interdisciplinary research. In Kettunen, J., Hyrkkanen, U. & Lehto, A. (Eds.) Applied Research and Professional Education, p.p. 289-309. Turku University of Applied Sciences.

Amos, M., Calow, A., Jacobs, N., Jung, H.Y., Linton, T. & Verran, J. (2012) Manchester DIYbio. In Bowater, L. & Yeoman, K., Science Communication: A Practical Guide for Scientists, p.p. 250-251, Wiley-Blackwell.

Amos, M. (2012) Bacterial computing. In Computational Complexity: Theory, Techniques and Applications, Robert A. Meyers (Ed.), p.p. 228-237, Springer New York. doi: 10.1007/978-1-4614-1800-9_15. (Originally appeared in Encyclopedia of Complexity and Systems Science, 2009).

Amos, M. (2012a) DNA computing. In Computational Complexity: Theory, Techniques and Applications, Robert A. Meyers (Ed.), p.p. 882-896, Springer New York. doi: 10.1007/978-1-4614-1800-9_57.(Originally appeared in Encyclopedia of Complexity and Systems Science, 2009).

2011


Harding, P., Gwynne, S. & Amos, M. (2011) Mutual information for the detection of crush. PLOS ONE 6(12): e28747. doi:10.1371/journal.pone.0028747.

Amos, M., Dittrich, P., McCaskill, J. & Rasmussen, S. (2011) Biological and chemical information technologies. Procedia Computer Science 7, p.p. 56-60. doi:10.1016/j.procs.2011.12.019.

Goñi-Moreno, A. & Amos, M. (2011) Model for a population-based microbial oscillator. BioSystems 105:3, p.p. p.p.286-294. doi:10.1016/j.biosystems.2011.05.011.

Crossley, M. & Amos, M. (2011) SimZombie: a case-study in agent-based simulation construction. In Agent and Multi-Agent Systems: Technologies and Applications, Lecture Notes in Artificial Intelligence (LNAI) Vol. 6682, Springer, 2011, p.p. 514-523. doi:10.1007/978-3-642-22000-5_53.

Cecilia, J.M., Garcia, J.M, Ujaldon, M., Nisbet, A. & Amos, M. (2011) Parallelization strategies for ant colony optimization on GPUs. Proceedings of the 25th IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS 2011), Anchorage, Alaska, USA, 16-20 May 2011, p.p. 334-341.

Amos, M. & the BACTOCOM consortium (2011). BACTOCOM: Bacterial computing with engineered populations. ERCIM News 85, p.p. 38-39.

2010


Gibbons, A. & Amos, M. (2010) Wave propagation in filamental cellular automata. International Journal of Natural Computing Research 1:1, p.p. 56-69. doi: 10.4018/jncr.2010010103.

Harding, P.J., Amos, M. & Gwynne, S. (2010) Prediction and mitigation of crush conditions in emergency evacuations. Pedestrian and Evacuation Dynamics 2008, Klingsch, W.W.F., Rogsch, C., Schadschneider, A. and Schreckenberg, M. (Eds.), p.p. 233-246, Springer. doi: 10.1007/978-3-642-04504-2_18.

Goñi-Moreno, A. & Amos, M. (2010) Engineered microbial communication for population-level behaviour (abstract). Artificial Life XII: Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, Odense, Denmark, 19-23 August 2010, Harold Fellermann, Mark Dörr, Martin M. Hanczyc, Lone Ladegaard Laursen, Sarah Maurer, Daniel Merkle, Pierre-Alain Monnard, Kasper Stoy and Steen Rasmussen (Eds.), p.p. 184-185, MIT Press.

2009


Shasha, D. & Amos, M. (2009) DNA hash pooling and its applications. International Journal of Nanotechnology and Molecular Computation 1:1, p.p. 18-32.

Amos, M. (2009) Bacterial computing. Encyclopedia of Complexity and Systems Science, Robert A. Meyers (Ed.), Part 2, p.p. 417-426, Springer New York. doi: 10.1007/978-0-387-30440-3_28. .

Amos, M. (2009a) DNA computing. Encyclopedia of Complexity and Systems Science, Robert A. Meyers (Ed.), Part 4, p.p. 2089-2104, Springer New York. doi:10.1007/978-0-387-30440-3_131

2008


Amos, M. & Don, O. (2008) Swarm-based spatial sorting. International Journal of Intelligent Computing and Cybernetics 1:3, p.p. 454-473. doi: 10.1108/17563780810893491.

2007


Xiao, R-B., Xu, Y-C. & Amos, M. (2007) Two hybrid compaction algorithms for the layout optimization problem. BioSystems 90:2, p.p. 560--567. doi: 10.1016/j.biosystems.2006.12.007.

Amos, M., Hodgson, D.A. & Gibbons, A. (2007) Bacterial self-organisation and computation. International Journal of Unconventional Computing 3:3, p.p. 199--210.

Amos, M. & Don, O. (2007) An ant-based algorithm for annular sorting. Proc. IEEE Congress on Evolutionary Computation (CEC'07), Singapore, September 25-28, 2007, p.p. 142-148, IEEE Press.

Xu, Y-C., Xiao, R-B. & Amos, M. (2007) A novel genetic algorithm for the layout optimization problem. Proc. IEEE Congress on Evolutionary Computation (CEC'07), Singapore, September 25-28, 2007, p.p. 3938-3942, IEEE Press.

Xu, Y-C., Xiao, R-B. & Amos, M. (2007a) Particle swarm algorithm for weighted rectangle placement. Proc. Third International Conference on Natural Computation (ICNC'07), Haikou, China, August 24-27, 2007, Volume 4, p.p. 728-732, IEEE Press.

2006


Timmis, J., Amos, M., Banzhaf, W. & Tyrrell, A. (2006) "Going back to our roots": Second generation biocomputing. International Journal of Unconventional Computing 2:4, p.p. 349-378.

2005


Amos, M. (2005) Theoretical and Experimental DNA Computation. Research monograph in the Natural Computing Series, Springer, ISBN 3-540-65773-8.

Amos, M. & Hodgson, D.A. (Eds.) (2005) Selected papers from the First International Symposium on Cellular Computing. Special issue of Natural Computing 4:4, p.p. 293-451.

Amos, M. (2005a) Cellular computing. Proc. Montpellier Spring School on Modelling Complex Biological Systems in the Context of Genomics, P. Amar, F. Kepes, F. Molina & V. Norris (Eds.), p.p. 3-6, ISBN 2-86883-947-9.

2004


Amos, M. (Ed.) (2004) Cellular Computing. Series in Systems Biology, Oxford University Press, ISBN 0195155394.

Sant, P. & Amos, M. (2004) Models of recombination in ciliates. In Computation in Cells and Tissues: Perspectives and Tools of Thought, Paton, R., Bolouri, H., Holcombe, M., Parish, J. H., Tateson, R. (Eds.). Collected volume in the Natural Computing Series, Springer-Verlag, ISBN 3-540-00358-4, p.p. 269-276.

Amos, M. & Owenson, G. (2004) An introduction to cellular computing. In Cellular Computing, Amos, M. (Ed.), p.p. 1-10, Oxford University Press.

2003


Hodgson, D.A., Owenson, G., Amos, M. & Gibbons, A. (2003) Towards molecular computation. Electronics Information and Planning 31:7-8, p.p. 159-165.

2002


Amos, M., Paun, G., Rozenberg, G. & Salomaa, A. (2002) Topics in the theory of DNA computing. Theoretical Computer Science 287:1, 3-38. doi: 10.1016/S0304-3975(02)00134-2.

Amos, M. (2002) Molecular computing. In Macmillan's Computer Sciences Encyclopedia, Volume 4, Roger Flynn (Ed.), p.p. 167-168, Macmillan Reference USA.

2001


Owenson, G.G., Amos, M., Hodgson, D.A. & Gibbons, A. (2001) DNA-based logic. Soft Computing 5:2, 102-105. doi: 10.1007/s005000000073.

Amos, M. (2001) Theoretical and experimental DNA computation. In Current Trends in Theoretical Computer Science - Entering the 21st Century, Gheorge Paun, Grzegorz Rozenberg & Arto Salomaa (Eds.), p.p. 614--630, World Scientific Publishing, Singapore, ISBN 981-02-4473-8.

2000


Amos, M. & Owenson, G.G. (2000) Cellular computing. ERCIM News 43, p.p. 36-37, October 2000.

Amos, M., Sant, P. & Gibbons, A. (2000) Report on the Sixth International Meeting on DNA Based Computers, Leiden, The Netherlands, 13-17 June 2000. Bulletin of the EATCS 72, 213-214.

Amos, M. & Dunne, P.E. (2000) Report on the Sixteenth Annual Meeting of the British Colloquium for Theoretical Computer Science (BCTCS16), 10-12 April 2000 Liverpool, United Kingdom. Bulletin of the EATCS 72, 203-213.

1999


Owenson, G.G., Amos, M., Hodgson, D.A. & Gibbons, A. (1999) Molecular implementation of computational components. Proc. Congress on Evolutionary Computation (CEC99), Washington D.C., USA, 6-9 July 1999, p.p. 967-971, IEEE.

Amos, M. (1999) Review of DNA Based Computers III, Harvey Rubin & David Harlan Wood (Eds.). ACM SIGACT News 30:4, 10-12.

1998


Amos, M., Gibbons, A. & Dunne, P.E. (1998) Toward feasible and efficient DNA computation. Complexity 4:1, 14-18.

Amos, M., Dunne, P.E. & Gibbons, A. (1998) DNA simulation of Boolean circuits. Genetic Programming 1998: Proc. Third Annual Conference, July 22-25, 1998, University of Wisconsin, Madison, Wisconsin. Koza, John R., Banzhaf, Wolfgang, Chellapilla, Kumar, Deb, Kalyanmoy, Dorigo, Marco, Fogel, David B., Garzon, Max H., Goldberg, David E., Iba, Hitoshi, & Riolo, Rick. (editors), p.p. 679-683, San Francisco, CA: Morgan Kaufmann.

Amos, M., Wilson, S., Hodgson, D.A., Owenson, G. & Gibbons, A. (1998) Practical implementation of DNA computations. Proc. First International Conference on Unconventional Models of Computation, 5-11 January 1998, Auckland, New Zealand. Discrete Mathematics & Theoretical Computer Science, C.S. Calude, J. Casti & M.J. Dinneen (Eds.), p.p. 1-18, Springer-Verlag, Singapore.

Dunne, P.E., Amos, M. & Gibbons, A. (1998) Boolean transitive closure in DNA. In Computing with Bio-Molecules: Theory and Experiments, George Paun (Ed.), p.p. 127-137, Springer-Verlag, Singapore.

Amos, M. & Kari, L. (1998) Report on the Ongoing Workshop on DNA Computing, June 29 - July 3 1998, Leiden, The Netherlands. Bulletin of the EATCS 66, 203-204.

1997


Gibbons, A., Amos, M. & Hodgson, D. (1997) DNA computing. Current Opinion in Biotechnology 8:1, 103-106.

Amos, M., Gibbons, A. & Dunne, P.E. (1997) The complexity and viability of DNA computations. Proc. Bio-computing and Emergent Computation (BCEC97), University of Skovde, Sweden, 1-2 Sep. 1997. Lundh, Olsson & Narayanan (Eds.) p.p. 165-173, World Scientific.

Devine, P., Paton, R. & Amos, M. (1997) Adaptation of evolutionary agents in computational ecologies. Proc. Bio-computing and Emergent Computation (BCEC97), University of Skovde, Sweden, 1-2 Sep. 1997. Lundh, Olsson & Narayanan (Eds.) p.p. 66-75, World Scientific.

Amos, M. (1997) DNA Computation. Thesis submitted to the University of Warwick, UK, for the degree of Doctor of Philosophy. Defended on August 6th, 1997. Conferred on 30th September, 1997.

1996


Gibbons, A., Amos, M. & David Hodgson (1996) Models of DNA computation. Proc. Mathematical Foundations of Computer Science (MFCS), Cracow, Poland, 1996. Lecture Notes in Computer Science 1113, Penczek & Szalas (Eds.) p.p. 18-36, Springer-Verlag.

Amos, M., Gibbons, A. & David Hodgson (1996) Error-resistant implementation of DNA computations. Proc. Second Annual Meeting on DNA Based Computers, Princeton, NJ. DIMACS Series in Discrete Mathematics and Theoretical Computer Science. pp 151-162, Providence, RI: American Mathematical Society.

Zito, M., Pu, I., Amos, M. & Gibbons, A. (1996) RNC algorithms for the uniform generation of combinatorial structures. Proc. Seventh Annual ACM-SIAM Symposium on Discrete Algorithms (SODA '96).

Amos, M. (1996) A new model of DNA computation. 12th British Colloquium on Theoretical Computer Science (BCTCS), University of Kent, UK, 1-4 Apr. 1996. Abstract in Bulletin of the EATCS 61.

1995


Pu, I., Zito, M., Amos, M. & Gibbons, A. (1995) NC and RNC algorithms for the uniform generation of paths and trees in graphs. 11th British Colloquium on Theoretical Computer Science (BCTCS), University of Swansea, UK, 3-5 April, 1995. Abstract in Bulletin of the EATCS 58.

1994


Amos, M., Ravindran, S. & Gibbons, A. (1994) On the analysis of genetic algorithms. 10th British Colloquium on Theoretical Computer Science (BCTCS), Bristol, UK, 28-30 Mar. 1994. Abstract in Bulletin of the EATCS 54.