Professorship Orponen P.

Organisational unit: Research group

Research outputs

  1. 2019
  2. Published

    A computational framework for DNA sequencing microscopy

    Hoffecker, I. T., Yang, Y., Bernardinelli, G., Orponen, P. & Högberg, B., 4 Sep 2019, In : Proceedings of the National Academy of Sciences. 116, 39, p. 19282-19287 6 p., 1821178116.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Published

    A Critical Comparison of Rejection-Based Algorithms for Simulation of Large Biochemical Reaction Networks

    Thanh, V. H., 1 Aug 2019, In : Bulletin of Mathematical Biology. 81, 8, p. 3053-3073 21 p.

    Research output: Contribution to journalArticleScientificpeer-review

  4. Published

    Kohti avointa tiedettä

    Orponen, P., 2019, Kaikenlaista rohkeutta. Hetemäki, I., Koskinen, H., Pulkkinen, T. & Väliverronen, E. (eds.). Tallinna: Gaudeamus Oy, p. 64-65

    Research output: Chapter in Book/Report/Conference proceedingChapterGeneral public

  5. 2018
  6. Published

    Efficient finite-difference method for computing sensitivities of biochemical reactions

    Thanh, V. H., Zunino, R. & Priami, C., 1 Oct 2018, In : Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 474, 2218, p. 1-20

    Research output: Contribution to journalArticleScientificpeer-review

  7. Published

    Effects of design choices on the stiffness of wireframe DNA origami structures

    Benson, E., Mohammed, A., Rayneau-Kirkhope, D., Gådin, A., Orponen, P. & Högberg, B., 25 Sep 2018, In : ACS Nano. 12, 9, p. 9291-9299 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  8. Published

    Efficient anticorrelated variance reduction for stochastic simulation of biochemical reactions

    Vo, T., Sep 2018, In : IET SYSTEMS BIOLOGY.

    Research output: Contribution to journalArticleScientificpeer-review

  9. Published

    Algorithmic design of cotranscriptionally folding 2D RNA origami structures

    Mohammed, A., Orponen, P. & Pai, S., 31 May 2018, Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings. Stepney, S. & Verlan, S. (eds.). p. 159-172 (Lecture Notes in Computer Science; vol. 10867).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  10. Published

    Design methods for 3D wireframe DNA nanostructures

    Orponen, P., Mar 2018, In : Natural Computing. 17, 1, p. 147-160

    Research output: Contribution to journalArticleScientificpeer-review

  11. Published

    Algorithmic Design of Biomolecular Nanostructures

    Mohammed, A., 2018, Aalto University. 168 p.

    Research output: ThesisDoctoral ThesisCollection of Articles

  12. 2017
  13. Published

    Computational modelling of the kinetic Tile Assembly Model using a rule-based approach

    Mohammed, A., Czeizler, E. & Czeizler, E., Nov 2017, In : Theoretical Computer Science. 701, p. 203-215

    Research output: Contribution to journalArticleScientificpeer-review

  14. Published

    A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tileset synthesis

    Johnsen, A., Kao, M. Y. & Seki, S., 2017, In : JOURNAL OF COMBINATORIAL OPTIMIZATION. 33, 2, p. 496–529 34 p.

    Research output: Contribution to journalArticleScientificpeer-review

  15. Published

    Binary Pattern Tile Set Synthesis Is NP-Hard

    Kari, L., Kopecki, S., Meunier, P. É., Patitz, M. J. & Seki, S., 2017, In : Algorithmica. 78, 1, p. 1-46 46 p.

    Research output: Contribution to journalArticleScientificpeer-review

  16. Published

    Unknotted strand routings of triangulated meshes

    Mohammed, A. & Hajij, M., 2017, DNA Computing and Molecular Programming: 23rd International Conference, DNA 23, Austin, TX, USA, September 24–28, 2017, Proceedings. Brijder, R. & Qian, L. (eds.). Springer International Publishing AG, p. 46-63 ( Lecture Notes in Computer Science; vol. 10467).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  17. 2016
  18. Published

    Computer-aided production of scaffolded DNA nanostructures from flat sheet meshes

    Benson, E., Mohammed, A., Bosco, A., Teixeira, A. I., Orponen, P. & Högberg, B., 2016, In : Angewandte Chemie. 55, 31, p. 8869-8872 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  19. Published

    Programming biomolecules that fold greedily during transcription

    Geary, C., Meunier, P-É., Schabanel, N. & Seki, S., 2016, 41st International Symposium on Mathematical Foundations of Computer Science, MFCS 2016, August 22-26, 2016 - Kraków, Poland. Faliszewski, P., Muscholl, A. & Niedermaier, R. (eds.). Germany: Schloss Dagstuhl - Leibniz Center for Informatics, p. 1-14 14 p. 43. (LIPIcs - Leibniz International Proceedings in Informatics; vol. 58).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  20. 2015
  21. Published

    3-color bounded patterned self-assembly

    Kari, L., Kopecki, S. & Seki, S., 2015, In : Natural Computing. 14, 2, p. 279-292

    Research output: Contribution to journalArticleScientificpeer-review

  22. Published

    An Excursion Through Quantitative Model Refinement

    Azimi, S., Czeizler, E., Gratie, C., Gratie, D-E., Iancu, B., Ibssa, N., Petre, I., Rogojin, V., Shadbahr, T. & Shokri, F., 2015, 16th International Conference, CMC 2015, Valencia, Spain, August 17-21, 2015. p. 25-47

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  23. Published

    Binary pattern tile set synthesis is NP-hard

    Kari, L., Kopecki, S., Meunier, P-É., Patitz, M. J. & Seki, S., 2015, 42nd International Colloquium on Automata, Languages and Programming, ICALP 2015, Kyoto, Japan, July 6-10, 2015. Springer Berlin Heidelberg, p. 1022-1034

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  24. Published

    DNA rendering of polyhedral meshes at the nanoscale

    Benson, E., Mohammed, A., Gardell, J., Masich, S., Czeizler, E., Orponen, P. & Högberg, B., 2015, In : Nature. 523, 7561, p. 441-444

    Research output: Contribution to journalArticleScientificpeer-review

  25. Published

    Dynamic Simulation of 1D Cellular Automata in the Active aTAM

    Jonoska, N., Karpenko, D. & Seki, S., 2015, In : NEW GENERATION COMPUTING. 33, 3, p. 271-295

    Research output: Contribution to journalArticleScientificpeer-review

  26. Published

    Fault tolerant design and analysis of carbon nanotube circuits affixed on DNA origami tiles

    Czeizler, E. & Orponen, P., 2015, In : IEEE TRANSACTIONS ON NANOTECHNOLOGY. 14, 5, p. 817-877

    Research output: Contribution to journalArticleScientificpeer-review

  27. Published

    Program Size and Temperature in Self-Assembly

    Chen, H-L., Doty, D. & Seki, S., 2015, In : Algorithmica. 72, 3, p. 884-899

    Research output: Contribution to journalArticleScientificpeer-review

  28. Published

    Semilinear Sets and Counter Machines: a Brief Survey

    Ibarra, O. H. & Seki, S., 2015, In : Fundamenta Informaticae. 138, 1-2, p. 61-76

    Research output: Contribution to journalArticleScientificpeer-review

  29. Published

    Square-Density Increasing Mappings

    Manea, F. & Seki, S., 2015, 10th International Conference, WORDS 2015, Kiel, Germany, September 14-17, 2015. Springer-verlag Berlin, p. 160-169

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  30. 2014
  31. Published

    Editorial for Algorithms for Sensor Systems, Wireless Ad Hoc Networks and Autonomous Mobile Entities

    Bar-Noy, A., Erlebach, T., Halldorsson, M. M., Nikoletseas, S. & Orponen, P., 9 Oct 2014, In : Theoretical Computer Science. 553, p. 1-1 1 p.

    Research output: Contribution to journalEditorialScientific

  32. Published

    Generalized Lyndon-Schützenberger Equations

    Manea, F., Müller, M., Nowotka, D. & Seki, S., 2014, International Symposium on Mathematical Foundations of Computer Science, Budapest, Hungary, August 25-29, 2014. p. 402-413

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  33. Published

    Operational State Complexity under {P}arikh Equivalence

    Lavado, G. J., Pighizzini, G. & Seki, S., 2014, International Workshop on Descriptional Complexity of Formal Systems, Turku, Finland, August 5-8, 2014. p. 294-305

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  34. Published

    Search methods for tile sets in patterned DNA self-assembly

    Göös, M., Lempiäinen, T., Czeizler, E. & Orponen, P., 2014, In : JOURNAL OF COMPUTER AND SYSTEM SCIENCES. 80, 1, p. 297-319

    Research output: Contribution to journalArticleScientificpeer-review

  35. Published

    Special Issue on Algorithms for Sensor Systems, Wireless Ad Hoc Networks and Autonomous Mobile Entities, Theoretical Computer Science, Vol. 553

    Bar-Noy, A., Erlebach, T., Halldorsson, M. M., Nikoletseas, S. & Orponen, P., 2014, Netherlands: Elsevier BV.

    Research output: Book/ReportAnthologyScientificpeer-review

  36. Published

    Strong Square Conjecture on Binary Words

    Jonoska, N., Manea, F. & Seki, S., 2014, Conference on Current Trends in Theory and Practice of Computer Science, Novy Smokovec, Slovakia, January 25-30, 2014. p. 339-350

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  37. Published

    Transfer matrix analysis of one-dimensional majority cellular automata with thermal noise

    Lemoy, R., Mozeika, A. & Seki, S., 2014, In : Journal of Physics A: Mathematical and Theoretical. 47, 10, p. 105001

    Research output: Contribution to journalArticleScientificpeer-review

  38. 2013
  39. Published

    On Computational Complexity of Graph Inference from Counting

    Fazekas, S. Z., Ito, H., Okuno, Y., Seki, S. & Taneishi, K., 2013, In : Natural Computing. 12, 4, p. 589-603

    Research output: Contribution to journalArticleScientificpeer-review

  40. Published

    Online bin packing with delay and holding costs

    Ahlroth, L., Schumacher, A. & Orponen, P., 2013, In : Operations Research Letters. 41, 1, p. 1

    Research output: Contribution to journalArticleScientificpeer-review

  41. Published

    Rule-based modelling as a platform for the analysis of synthetic self-assembled nano-systems

    Mohammed, A. & Czeizler, E., 2013, Proceedings Fourth International Workshop on Computational Models for Cell Processes (Turku, Finland, June 2013). Petre, I. (ed.). Ausralia: Open Publishing Association

    Research output: Chapter in Book/Report/Conference proceedingChapterScientific

  42. Published

    Synthesizing minimal tile sets for complex patterns in the framework of patterned DNA self-assembly

    Czeizler, E. & Popa, A., 2013, In : Theoretical Computer Science. 499, p. 23-37

    Research output: Contribution to journalArticleScientificpeer-review

  43. Published

    Witness of unsatisfiability for a random 3-satisfiability formula

    Wu, L-L., Zhou, H-J., Alava, M., Aurell, E. & Orponen, P., 2013, In : Physical Review E. 87, 5, p. 1-10 052807.

    Research output: Contribution to journalArticleScientificpeer-review

  44. Published

    Yield optimization strategies for DNA staged tile assembly systems

    Czeizler, E. & Orponen, P., 2013, 2nd International Conference on the Theory and Practice of Natural Computing (TPNC 2013), Cáceres, Spain, 3-5 December 2013. Dediu, A-H., Martin-Vide, C., Truthe, B. & Vega-Rodriguez, M. A. (eds.). Berlin Heidelberg, p. 31-44 (Lecture Notes in Computer Science; vol. 8273).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  45. 2012
  46. Published

    Absoluteness of Subword Inequality is Undecidable

    Seki, S., 2012, In : Theoretical Computer Science. 418, p. 116-120

    Research output: Contribution to journalArticleScientificpeer-review

  47. Published

    Algorithms for Sensor Systems - 7th International Symposium on Algorithms for Sensor Systems, Wireless Ad Hoc Networks and Autonomous Mobile Entities, ALGOSENSORS 2011, Saarbrücken, Germany, September 8-9, 2011, Revised Selected Papers

    Erlebach, T., Nikoletseas, S. & Orponen, P., 2012, Berlin Heidelberg. 239 p. (Lecture Notes in Computer Science; vol. 7111)

    Research output: Book/ReportAnthologyScientificpeer-review

  48. Published

    Computational Modelling of the kinetic Tile Assembly Model using a rule-based approach

    Mohammed, A., Pletea, D. & Czeizler, E., 2012, DNA Computing and Molecular Programming - 18th International Conference, Aarhus, Denmark, August 14-17, 2012. p. 36

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  49. Published

    Converting Nondeterministic Automata and Context-Free Grammars into Parikh Equivalent Deterministic Automata

    Lavado, G. J., Pighizzini, G. & Seki, S., 2012, DLT The 16th International Conference on Developments in Language Theory (DLT 2012) DLT, (Taipei, Taiwan, August 14-17, 2012). p. 284-295

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  50. Published

    On the Behavior of Tile Assembly System at High Temperatures

    Seki, S. & Okuno, Y., 2012, CiE Turing Centenary Conference - How the World Computes (CiE 2012) CiE, Cambridge, United Kingdom, June 18-23, 2012. p. 550-560

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  51. Published

    Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments from Tetrameric Vimentin

    Czeizler, E., Mizera, A., Czeizler, E., Back, R-J., Eriksson, J. E. & Petre, I., 2012, In : IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 9, 3, p. 885-898

    Research output: Contribution to journalArticleScientificpeer-review

  52. Published

    Quantitative Model Refinement as a Solution to the Combinatorial Size Explosion of Biomodels

    Czeizler, E., Czeizler, E., Iancu, B. & Petre, I., 2012, In : ELECTRONIC NOTES IN THEORETICAL COMPUTER SCIENCE. 284, C, p. 35-53

    Research output: Contribution to journalArticleScientificpeer-review

  53. Published

    Self-assembly models of variable resolution

    Mizera, A., Czeizler, E. & Petre, I., 2012, In : TRANSACTIONS ON COMPUTATIONAL SYSTEMS BIOLOGY. XIV, 7625, p. 181-203

    Research output: Contribution to journalArticleScientificpeer-review

  54. Published

    Synthesizing Minimal Tile Sets for Complex Patterns in the Framework of Patterned DNA Self-Assembly

    Czeizler, E. & Popa, A., 2012, DNA Computing and Molecular Programming - 18th International Conference (DNA 18) DNA, Aarhus, Denmark, August 14-17, 2012. Stefanovic, D. & Turberfield, A. J. (eds.). p. 58-72

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  55. Published

    The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response

    Czeizler, E., Rogojin, V. & Petre, I., 2012, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 9, 5, p. 885-898

    Research output: Contribution to journalArticleScientificpeer-review

  56. Published

    Unordered constraint satisfaction games

    Ahlroth, L. & Orponen, P., 2012, MFCS 37th International Symposium on Mathematical Foundations of Computer Science (MFCS 2012) MFCS, Bratislava, Slovakia, August 27-31, 2012. Rovan, B., Sassone, V. & Widmayer, P. (eds.). p. 64-75

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  57. 2011
  58. Published

    A design framework for carbon nanotube circuits affixed on DNA origami tiles

    Czeizler, E., Lempiäinen, T. & Orponen, P., 2011, FNANO Proceedings of the 8th Annual Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO11) FNANO, Snowbird UT, April 2011. Snowbird, UT, USA, p. 186-187

    Research output: Chapter in Book/Report/Conference proceedingChapterScientific

  59. Published

    Nano architectures for carbon nanotube circuits: design, analysis, and experimental attempts

    Czeizler, E., Lempiäinen, T. & Orponen, P., 2011, Proceedings of the Workshop on Language Theory in Biocomputing. Turku, Finland

    Research output: Chapter in Book/Report/Conference proceedingChapterScientific

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