People
Pekka Orponen

Pekka Orponen

Professor
Department of Computer Science

Background:

Pekka Orponen is Professor of Computer Science at the Aalto University School of Science. He received his MSc and PhD degrees in Computer Science at the University of Helsinki in 1983 and 1986, respectively. After a postdoctoral period at the University of Toronto, he held assistant and associate professorships at the University of Helsinki, before moving first to the University of Jyväskylä (1996-2001) and then to the Helsinki University of Technology, now Aalto University (2001-present). He served as the founding Head of the Aalto Department of Information and Computer Science for 2008-2014, and then as Vice-Head for Research of the newly-established Aalto Department of Computer Science for 2015-2016.

His general research area is algorithms and complexity, with specific contributions spanning computational complexity theory, foundations of neural network and analog computation, stochastic algorithms and distributed sensor networks, and the computational theory and algorithmic design of nucleic acid nanostructures. His Nature 2015 article on the algorithmic design of 3D wireframe DNA nanostructures (with co-authors in Aalto and at the Karolinska Institutet) is currently listed as an ISI highly-cited paper, i.e. within the top 1% from its publication year in the areas of biology and biochemistry.

In addition to his academic activities, Pekka Orponen served in 2003-2021 on the Association and Supervisory Boards of the Finnish Cultural Foundation, which is one of the largest private foundations for arts and science in Europe. Since 2018 he has been a member of the Board of Informatics Europe, the association of European Computer Science departments. He is also a member of the Finnish Academy of Science and Letters, and served in 2015-2022 as the founding Chair of the Academies' joint National Committee for Research Data, representing Finland in CODATA, the Data Committee of the International Science Council. He was awarded Knight First Class of the Order of the White Rose of Finland in 2021.

 Research interests:

  • Algorithmics of self-organisation
  • DNA nanotechnology
  • Stochastic algorithms
  • Computational complexity theory

Research group page: https://research.cs.aalto.fi/nc/

Personal web page: https://users.ics.aalto.fi/orponen/

Full researcher profile
https://research.aalto.fi/...
Email
[email protected]
Phone number
+358500819491

Areas of expertise

Algorithms, Complexity, DNA nanotechnology, 113 Computer and information sciences, Theoretical computer science

Honors and awards

Algorithmic design methods and tools for DNA nanotechnology

Granted funding (personal grants) Computer Science Professors Feb 2023

Knight First Class of the Order of the White Rose of Finland

Award or honor granted for academic or artistic career Computer Science Professors Dec 2021

Best Paper Award, UCNC 2018

Award or honor granted for a specific work Professorship Orponen P. Jun 2018

Research groups

  • Computer Science Professors, Professor
  • Computer Science - Computational Life Sciences (CSLife), Professor
  • Professorship Orponen P., Professor
  • Computer Science - Algorithms and Theoretical Computer Science (TCS), Professor

Publications

A General Design Method for Scaffold-Free DNA Wireframe Nanostructures

Antti Elonen, Abdulmelik Mohammed, Pekka Orponen 2024 Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings

Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops

Antti Elonen, Pekka Orponen 2024 30th International Conference on DNA Computing and Molecular Programming, DNA 30 2024

DNAforge : a design tool for nucleic acid wireframe nanostructures

Antti Elonen, Leon Wimbes, Abdulmelik Mohammed, Pekka Orponen 2024 Nucleic Acids Research

Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots

Małgorzata Nowicka, Vinay K. Gautam, Pekka Orponen 2024 Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings

OVI-3 : A NoSQL visual query system supporting efficient anti-joins

Sami El-Mahgary, Eljas Soisalon-Soininen, Pekka Orponen, Petri Rönnholm, Hannu Hyyppä 2023 Journal of Intelligent Information Systems

Algorithmic design of 3D wireframe RNA polyhedra

Antti Elonen, Ashwin Karthick Natarajan, Ibuki Kawamata, Lukas Oesinghaus, Abdulmelik Mohammed, Jani Seitsonen, Yuki Suzuki, Friedrich C. Simmel, Anton Kuzyk, Pekka Orponen 2022 ACS Nano

RNA secondary structure prediction with convolutional neural networks

Mehdi Saman Booy, Alexander Ilin, Pekka Orponen 2022 BMC Bioinformatics

Unconventional Computation and Natural Computation - 19th International Conference, UCNC 2021, Espoo, Finland, October 18-22, 2021, Proceedings

Pekka Orponen, Irina Kostitsyna 2021

Cotranscriptional kinetic folding of RNA secondary structures including pseudoknots

Hong Thanh Vo, Dani Korpela, Pekka Orponen 2021 Journal of Computational Biology

RuleDSD: A rule-based modelling and simulation tool for DNA strand displacement systems

Vinay Gautam, Shiting Long, Pekka Orponen 2020 Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies

A computational framework for DNA sequencing microscopy

Ian T. Hoffecker, Yunshi Yang, Giulio Bernardinelli, Pekka Orponen, Björn Högberg 2019 Proceedings of the National Academy of Sciences

Kohti avointa tiedettä

Pekka Orponen 2019 Kaikenlaista rohkeutta

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

Erik Benson, Abdulmelik Mohammed, Daniel Rayneau-Kirkhope, Andreas Gådin, Pekka Orponen, Björn Högberg 2018 ACS Nano

Algorithmic design of cotranscriptionally folding 2D RNA origami structures

Abdulmelik Mohammed, Pekka Orponen, Sachith Pai 2018 Unconventional Computation and Natural Computation

Design methods for 3D wireframe DNA nanostructures

Pekka Orponen 2018 Natural Computing

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

Erik Benson, Abdulmelik Mohammed, Alessandro Bosco, Ana I. Teixeira, Pekka Orponen, Björn Högberg 2016 Angewandte Chemie

DNA rendering of polyhedral meshes at the nanoscale

Erik Benson, Abdulmelik Mohammed, Johan Gardell, Sergej Masich, Eugen Czeizler, Pekka Orponen, Björn Högberg 2015 Nature

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

Eugen Czeizler, Pekka Orponen 2015 IEEE Transactions on Nanotechnology

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

Amotz Bar-Noy, Thomas Erlebach, Magnus M. Halldorsson, Sotiris Nikoletseas, Pekka Orponen 2014 Theoretical Computer Science

Special Issue on Algorithms for Sensor Systems, Wireless Ad Hoc Networks and Autonomous Mobile Entities

Amotz Bar-Noy, Thomas Erlebach, Magnus M. Halldorsson, Sotiris Nikoletseas, Pekka Orponen 2014 Theoretical Computer Science

Search methods for tile sets in patterned DNA self-assembly

Mika Göös, Tuomo Lempiäinen, Eugen Czeizler, Pekka Orponen 2014 Journal of Computer and System Sciences

Online bin packing with delay and holding costs

Lauri Ahlroth, André Schumacher, Pekka Orponen 2013 Operations Research Letters

Yield optimization strategies for DNA staged tile assembly systems

Eugen Czeizler, Pekka Orponen 2013 2nd International Conference on the Theory and Practice of Natural Computing (TPNC 2013), Cáceres, Spain, 3-5 December 2013

Witness of unsatisfiability for a random 3-satisfiability formula

Lu-Lu Wu, Hai-Jun Zhou, Mikko Alava, Erik Aurell, Pekka Orponen 2013 Physical Review E

Unordered constraint satisfaction games

Lauri Ahlroth, Pekka Orponen 2012 MFCS 37th International Symposium on Mathematical Foundations of Computer Science (MFCS 2012) MFCS, Bratislava, Slovakia, August 27-31, 2012

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

Thomas Erlebach, Sotiris Nikoletseas, Pekka Orponen 2012

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

Eugen Czeizler, Tuomo Lempiäinen, Pekka Orponen 2011 FNANO Proceedings of the 8th Annual Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO11) FNANO, Snowbird UT, April 2011

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

Eugen Czeizler, Tuomo Lempiäinen, Pekka Orponen 2011 Proceedings of the Workshop on Language Theory in Biocomputing

Synthesizing minimal tile sets for patterned DNA self-assembly

Mika Göös, Pekka Orponen 2011 The 16th Conference on DNA Computing and Molecular Programming (DNA16) DNA, (Hong Kong, China, June 2010)

Synthesizing small and reliable tile sets for patterned DNA self-assembly

Tuomo Lempiäinen, Eugen Czeizler, Pekka Orponen 2011 DNA Computing and Molecular Programming - 17 th International Conference, DNA 17, Pasadena, CA, USA, September 19-23, 2011. Proceedings

Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday

Tapio Elomaa, Heikki Mannila, Pekka Orponen 2010

Distributed algorithms for lifetime maximization in sensor networks via min-max spanning subgraphs

Harri Haanpää, André Schumacher, Pekka Orponen 2010 Wireless Networks

Synthesizing minimal tile sets for patterned DNA self-assembly

Mika Göös, Pekka Orponen 2009 arXiv.org

Circumspect descent prevails in solving random constraint satisfaction problems

Mikko Alava, John Ardelius, Erik Aurell, Petteri Kaski, Supriya Krishnamurthy, Pekka Orponen 2008 Proceedings of the National Academy of Sciences of the United States of America

Locally computable approximations for spectral clustering and absorption times of random walks

Pekka Orponen, Satu Elisa Schaeffer, Vanesa Avalos Gaytán 2008

Balanced multipath source routing

Shreyas Prasad, André Schumacher, Harri Haanpää, Pekka Orponen 2008 The 21st International Conference on Information Networking (ICOIN'07)

Lifetime maximization in wireless sensor networks by distributed binary search

Andre Schumacher, Pekka Orponen, Thorn Thaler, Harri Haanpää 2008 5th European Conference on Wireless Sensor Networks, EWSN 2008, Jan 30-Feb 1 2008

Distributed computation of maximum lifetime spanning subgraphs in sensor networks

Harri Haanpää, André Schumacher, Thorn Thaler, Pekka Orponen 2007 The 3rd International Conference on Mobile Ad-Hoc and Sensor Networks (MSN'07, Beijing, China, December 2007)

Security Topics and Mobility Management in Hierarchical Ad Hoc Networks (Samoyed): Final Report

Maarit Hietalahti, Mikko Särelä, Antti Tuominen, Pekka Orponen 2007

"P = NP" -ongelma ja laskennan vaativuusteoria

Pekka Orponen 2007 Tietojenkäsittelytiede

Load balancing by distributed optimisation in ad hoc networks

André Schumacher, Harri Haanpää, Satu Elisa Schaeffer, Pekka Orponen 2006 Mobile Ad-hoc and Sensor Networks Second International Conference, MSN 2006 Hong Kong, China, December 13-15, 2006

Exact and approximate balanced data gathering in energy-constrained sensor networks

Patrik Floréen, Petteri Kaski, Jukka Kohonen, Pekka Orponen 2005 Theoretical Computer Science

Lifetime maximization for multicasting in energy-constrained wireless networks

Patrik Floréen, Petteri Kaski, Jukka Kohonen, Pekka Orponen 2005 IEEE Journal on Selected Areas in Communications

Optimization, block designs and No Free Lunch theorems

Evan Griffiths, Pekka Orponen 2005 Information Processing Letters

Local clustering of large graphs by approximate Fiedler vectors

Pekka Orponen, Satu Elisa Schaeffer 2005 4th International Workshop on Efficient and Experimental Algorithms, Santorini, Kreikka, 10.-13.5.2005

Focused local search for random 3-satisfiability.

Sakari Seitz, Mikko Alava, Pekka Orponen 2005 Journal of Statistical Mechanics: Theory and Experiment

Threshold behaviour of WalkSAT and focused Metropolis search on random 3-satisfiability

Sakari Seitz, Mikko Alava, Pekka Orponen 2005 8th International Conference on Theory and Applications of Satisfiability Testing, St. Andrews, Skotlanti, 20.-23.6.2005

Balanced data gathering in energy-constrained sensor networks

Emil Falck, Patrik Floréen, Petteri Kaski, Jukka Kohonen, Pekka Orponen 2004 ALGOSENSORS'04, First International Workshop on Algorithmic Aspects of Wireless Sensor Networks, Turku, Suomi, 16.7.2004

Multicast time maximization in energy constrained wireless networks

Patrik Floréen, Petteri Kaski, Jukka Kohonen, Pekka Orponen 2003 DIALM-POMC '03 Joint Workshop on Foundations of Mobile Computing, San Diego, CA, USA, 19.9.2003

Mitä tietojenkäsittelyteoriaan kuuluu?

Pekka Orponen 2003 Tietojenkäsittelytiede

Tietotekniikkaa ennen tietokoneita - Alan Turing ja tietotekniikan kiehtovat alkuvaiheet

Pekka Orponen 2003 Tietoa

An efficient local search method for random 3-satisfiability

Sakari Seitz, Pekka Orponen 2003 IEEE LICS'03 Workshop on Typical Case Complexity and Phase Transitions, Ottawa, Canada, June 2003

An efficient local search method for random 3-satisfiability

Sakari Seitz, Pekka Orponen 2003 Electronic Notes in Discrete Mathematics

Continuous-time symmetric Hopfield nets are computationally universal

Jiri Sima, Pekka Orponen 2003 Neural Computation

Exponential transients in continuous-time Liapunov systems

Jiri Sima, Pekka Orponen 2003 Theoretical Computer Science

General purpose computation with neural networks: a survey of complexity theoretic results

Jiri Sima, Pekka Orponen 2003 Neural Computation

Computation of the multivariate Oja median

Tommi Ronkainen, Hannu Oja, Pekka Orponen 2002 Developments in robust statistics : International Conference on Robust Statistics ICORS '01, Stift Vorau, Itävalta, heinäkuu 2001

Computing with continuous-time Liapunov systems

Jirí Síma, Pekka Orponen 2001 Proceedings on 33rd Annual ACM Symposium on Theory of Computing, July 6-8, 2001, Heraklion, Crete, Greece

Exponential transients in continuous-time symmetric Hopfield nets

Jirí Síma, Pekka Orponen 2001 Artificial Neural Networks - ICANN 2001, International Conference Vienna, Austria, August 21-25, 2001 Proceedings

Some afterthoughts on Hopfield networks

Jirí Síma, Pekka Orponen, Teemu Antti-Poika 1999 SOFSEM '99, Theory and Practice of Informatics, 26th Conference on Current Trends in Theory and Practice of Informatics, Milovy, Czech Republic, November 27 - December 4, 1999, Proceedings

On the effect of analog noise in discrete-time analog computations

Wolfgang Maass, Pekka Orponen 1998 Neural Computation

On the effect of analog noise in discrete-time analog computations

Wolfgang Maass, Pekka Orponen 1997 Electronic Colloquium on Computational Complexity

A survey of continuous-time computation theory

Pekka Orponen 1997 Advances in Algorithms, Languages, and Complexity - In Honor of Ronald V. Book

Computing with truly asynchronous threshold logic networks

Pekka Orponen 1997 Theoretical Computer Science

Matematiikka ja tietotekniikka

Pekka Orponen 1997 Arkhimedes

The computational power of continuous time neural networks

Pekka Orponen 1997 SOFSEM '97: Theory and Practice of Informatics, 24th Seminar on Current Trends in Theory and Practice of Informatics, Milovy, Czech Republic, November 22-29, 1997, Proceedings

Random strings make hard instances

Harry Buhrman, Pekka Orponen 1996 Journal of Computer and System Sciences

Probably approximately optimal satisficing strategies

Russell Greiner, Pekka Orponen 1996 Artificial Intelligence

On the effect of analog noise in discrete-time analog computations

Wolfgang Maass, Pekka Orponen 1996 Advances in Neural Information Processing Systems 9, NIPS, Denver, CO, USA, December 2-5, 1996

Laskentaongelmien yksittäistapausten vaativuudesta

Pekka Orponen 1996 Logiikka, matematiikka ja tietokone

Parallel programming on Hopfield nets

Pekka Orponen, Frédéric Prost 1996 7th Finnish Artificial Intelligence Conference, Vaasa, Finland, August 20-23, 1996, Proceedings

The computational power of discrete Hopfield nets with hidden units

Pekka Orponen 1996 Neural Computation

Universal computation by finite two-dimensional coupled map lattices

Pekka Orponen, Martin Matamala 1996 4th Workshop on Physics and Computation, PhysComp 96, Boston, MA, USA, November 22-24, 1996, Proceedings

Random strings make hard instances

Harry Buhrman, Pekka Orponen 1994 Proceedings of the Ninth Annual Structure in Complexity Theory Conference, Amsterdam, The Netherlands, June 28 - July 1, 1994

Complexity issues in discrete Hopfield networks

Patrik Floreen, Pekka Orponen 1994

Computational complexity of neural networks: A survey

Pekka Orponen 1994 Nordic Journal of Computing

Instance complexity

Pekka Orponen, Ker-I Ko, Uwe Schöning, Osamu Watanabe 1994 Journal of the ACM

Attraction radii in binary Hopfield nets are hard to compute

Patrik Floréen, Pekka Orponen 1993 Neural Computation

On the computational power of discrete Hopfield nets

Pekka Orponen 1993 Automata, Languages and Programming, 20nd International Colloquium, ICALP93, Lund, Sweden, July 5-9, 1993, Proceedings

NEULA: A hybrid neural-symbolic expert system shell

Patrik Floreen, Petri Myllymäki, Pekka Orponen, Henry Tirri 1992 Tietojenkäsittelytiede

Integrating symbolic reasoning with neurally represented background knowledge

Petri Myllymäki, Pekka Orponen, Tomi Silander 1992 5th Finnish Artificial Intelligence Conference, Espoo, Finland, June 9-11, 1992, Proceedings

Neural networks and complexity theory

Pekka Orponen 1992 Mathematical Foundations of Computer Science 1992, 17th International Symposium, MFCS'92, Prague, Czechoslovakia, August 24-28, 1992, Proceedings

Probably approximately optimal derivation strategies

Russell Greiner, Pekka Orponen 1991 Proceedings of the 2nd International Conference on Principles of Knowledge Representation and Reasoning (KR'91). Cambridge, MA, USA, April 22-25, 1991.

Compiling object declarations into connectionist networks

Patrik Floréen, Petri Myllymäki, Pekka Orponen, Henry Tirri 1990 AI Communications

Dempster's rule of combination is #P-complete

Pekka Orponen 1990 Artificial Intelligence

On the instance complexity of NP-hard problems

Pekka Orponen 1990 Proceedings: Fifth Annual Structure in Complexity Theory Conference, Universitat Politècnica de Catalunya, Barcelona, Spain, July 8-11, 1990

On the sample complexity of finding good search strategies

Pekka Orponen, Russell Greiner 1990 Proceedings of the Third Annual Workshop on Computational Learning Theory, COLT 1990, University of Rochester, Rochester, NY, USA, August 6-8, 1990.

Programming methods for neural computing

Henry Tirri, Petri Myllymäki, Pekka Orponen, Patrik Floréen 1990 Parallelization in Inference Systems, International Workshop, Dagstuhl Castle, Germany, December 17-18, 1990, Proceedings

On the computational complexity of analyzing Hopfield nets

Patrik Floreen, Pekka Orponen 1989 Complex Systems

Lowness properties of sets in the exponential-time hierarchy

Ronald V. Book, Pekka Orponen, David A. Russo, Osamu Watanabe 1988 SIAM JOURNAL ON COMPUTING

On P-subset structures

David A. Russo, Pekka Orponen 1987 Mathematical systems theory

On exponential lowness

Ronald V. Book, Pekka Orponen, David A. Russo, Osamu Watanabe 1986 Automata, Languages and Programming, 13th International Colloquium, ICALP86, Rennes, France, July 15-19, 1986, Proceedings

What Is a hard instance of a computational problem?

Ker-I Ko, Pekka Orponen, Uwe Schöning, Osamu Watanabe 1986 Structure in Complexity Theory, Proceedings of the Conference hold at the University of California, Berkeley, California, June 2-5, 1986

A classification of complexity core lattices

Pekka Orponen 1986 Theoretical Computer Science

Optimal approximations and polynomially levelable sets

Pekka Orponen, David A. Russo, Uwe Schöning 1986 SIAM JOURNAL ON COMPUTING

The density and complexity of polynomial cores for intractable sets

Pekka Orponen, Uwe Schöning 1986 Information and Computation

Polynomial levelability and maximal complexity cores

Pekka Orponen, David A. Russo, Uwe Schöning 1985 Automata, Languages and Programming, 12th Colloquium, Nafplion, Greece, July 15-19, 1985, Proceedings

The structure of polynomial complexity cores (Extended abstract)

Pekka Orponen, Uwe Schöning 1984 Mathematical Foundations of Computer Science 1984, Praha, Czechoslovakia, September 3-7, 1984, Proceedings

Complexity classes of alternating machines with oracles

Pekka Orponen 1983 Automata, Languages and Programming