MolComp

Molecular Computing

MolComp is for studying biomolecules and their usage in technical applications.

Introduction

Molecular computing is a relatively new field of science where novel computing approaches are searched from the domain of molecules and atoms. More specifically, the aim is to understand how to control molecular reactions for information processing. Despite the fact that the Moore's "law"~still holds, these studies are motivated by the increasing technical difficulties to further develop the CMOS transistors as the building blocks of computing devices. These difficulties are already realising because the microelectronics industry has already pushed multicore and other parallel architectures to the market.

Biomolecules offer several advantages over synthetic ones. In their natural environment, their functionality and robustness is usually close to optimal due to evolutionary steps during the development of their structure and function. Therefore, many things can be learned from nature by studying the biomolecules and their interactions. Most of the studies concerning information processing using biomolecules have concentrated in DNA and photoactive biomolecules, for example, rhodopsins, chloroplasts, photosynthetic reaction centers and light-harvesting complexes, and retinal proteins. Bacteriorhodopsin (BR) is a retinal protein which has been intensively studied and proposed for various applications.

Molecular computing has been studied in Lappeenranta from the year 1995, and the research group has participated to the national nanotechnology research program funded by the Academy of Finland, and material science technology program funded by the Finnish Funding Agency for Technology and Innovation during 1997-1999. The most important results up till now are as follows:

  1. Cultivation of the archaea, Halobacterium salinarum as the source of bacteriorhodopsin, and preparation of bacteriorhodopsin-in-polyvinylalcohol thick films
  2. Single-element optoelectronic sensors based on wild-type BR and its variants

    Single-element optoelectronic element based on wild-type BR

  3. Colour-sensitive digital camera based on three types of BR

    Camera matrix based on wild-type BR Camera matrix based on three types of BR

  4. Models for colour vision systems based on, e.g., BR
  5. Simulation environment for the reduced photocycle of BR

Goals

The purpose of MolComp is to study biomolecules and their usage in technical applications and information processing. The goal of MolComp is to understand especially the photoelectric functionality of bacteriorhodopsin and its applicability to implement colour-sensitive artificial retina.

News

Contact information

Lappeenranta University of Technology (LUT)
Teemu Tukiainen WWW Researcher
Lasse Lensu WWW DSc 2002, LUT, Post-doc researcher
University of Joensuu (UJo)
Jussi Parkkinen e-mail WWW Project leader
Timo Jääskeläinen e-mail WWW Project leader
Sinikka Parkkinen e-mail WWW Post-doc researcher
Alumni
Marko Palviainen e-mail WWW MSc 1998, LUT
Veli-Pekka Leppänen e-mail WWW PhD 1999, UJo
Michael Frydrych e-mail WWW PhD 1999, LUT
Jarmo Vanhanen e-mail WWW PhD 2001, UJo
Lasse Lensu WWW LicSc 2001, DSc 2002, LUT
Teemu Tukiainen WWW MSc 2008, LUT
Visitors
To be announced

This project is partially under the research in the Machine Vision and Pattern Recognition Research Group.

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Source code

  1. No public releases

Researchers

Publications

  1. Articles in refereed scientific journals
    1. Khodonov A.A., Demina O.V., Khitrina L.V., Kaulen A.D., Silfsten P., Parkkinen S., Parkkinen J. and Jaaskelainen T.: Modified bacteriorhodopsins as a basis for new optical devices. Sensors and Actuators B, 38-39, 1997, pp. 218-221.
    2. Vanhanen J., Leppanen V.P., Jaaskelainen T., Parkkinen S., and Parkkinen J.P.S.: Photochromic properties of photoactive yellow protein. Optics Communications, 153, 1998, pp.289-294.
    3. Vanhanen J., Leppanen V.P., Haring T., Kettunen V., Jaaskelainen T., Parkkinen S., Parkkinen J.P.S.: Nonlinear refractive index change of photoactive yellow protein. Optics Communications, 155, 1998, pp. 327-331.
    4. Leppanen V.P., Haring T., Jaaskelainen T., Vartiainen E., Parkkinen S., and Parkkinen J.P.S.: The intensity dependent refractive index change of photochromic proteins. Optics Communications, 163, 1999, pp. 189-192.
    5. Vanhanen J., Leppanen V.P., Jaaskelainen T., Parkkinen S., Parkkinen J.P.S.: Nonlinear transmittance of the 4-keto bacteriorhodopsin. Optical Materials, 12, 1999, pp. 473-480.
    6. Frydrych M., Silfsten P., Parkkinen S., Parkkinen J., and Jaaskelainen T.: Color sensitive retina based on bacteriorhodopsin. BioSystems, vol. 54, no. 3, 2000, pp. 131-140.
    7. Vanhanen J., Leppänen V.P., Jaaskelainen T., Parkkinen S., and Parkkinen J.P.S.: Optical anisotropy in photoactive yellow protein film. Optics Communications, vol. 187, no. 1-3, Jan 2001, pp. 283-288.
    8. Vanhanen J., Parkkinen S., Leppanen V. P., Jaaskelainen T., and Parkkinen J.P.S.: Grating Formation in 13-demethyl Bacteriorhodopsin Film. Optical Review, vol. 8, no. 5, 2001, pp. 368-372.
    9. Lensu L., Parkkinen J., Parkkinen S., Frydrych M., and Jaaskelainen T.: Photoelectrical properties of protein-based optoelectronic sensor. Optical Materials, Vol. 21, No. 4, Feb 2003, pp. 783-788.
    10. Lensu, L., Frydrych, M., Parkkinen, J., Parkkinen, S. and Jaaskelainen, T.: Photoelectric properties of bacteriorhodopsin analogs for color-sensitive optoelectronic device. Optical Materials, Volume 27, Issue 1, October 2004, pp. 57-62.
  2. Articles in scientific edited volumes with referee or invitation practise
    1. Lensu L., Frydrych M., Parkkinen J., Parkkinen S. and Jaaskelainen T.: Color-Sensitive Biosensors for Imaging Applications. In: Knopf G.K., Bassi A.S. (Eds.): Smart Biosensor Technology, CRC Press, Boca Raton, FL, USA, 2007.
  3. Articles in refereed scientific conference proceedings
    1. Silfsten P., Parkkinen S., Luostarinen J., Khodonov A., Jaaskelainen T. and Parkkinen J.: Color sensitive biosensors for imaging. Proceedings of 13th International Conference on Pattern Recognition, August 25-30, 1996, Vienna, Austria. Vol. III, pp. 331-335.
    2. Frydrych M., Parkkinen J., Parkkinen S., Silfsten P. and Jaaskelainen T.: Model for color perception system with learning capabilities. Proceedings of the International Symposium on Optical Information Science and Technology, August 26-30,1997, Moscow, Russia. SPIE Conference.
    3. Frydrych M., Silfsten P., Parkkinen S., Parkkinen J. and Jaaskelainen T.: Color recognition with Bacteriorhodopsin. Pacific Symposium on Biocomputing, January 4-9, 1998, Hawaii, USA.
    4. Frydrych M. and Parkkinen J.: Uniform Color Spaces for Color Sensors. 11th Scandinavian Conference on Image Analysis, SCIA'99, Kangerlussuaq, Greenland, June 7-11, 1999, Vol. I, pp. 465-470.
    5. Lensu L., Parkkinen J., Parkkinen S., Palviainen M., and Jaaskelainen T.: Basic photoelectrical properties of protein based artificial retina. Proceedings of Intelligent Systems and Applications, ISA'2000, Wollongong, Australia, 12-15 December 2000, pp. 1001-1005.
    6. Frydrych M., Lensu L., and Parkkinen J.: Model of photovoltage response of bacteriorhodopsin in pva films. Technical Proceedings of the 2001 International Conference on Computational Nanoscience, ICCN'2001, Hilton Head Island, South Carolina, U.S.A., March 19-21, 2001, pp. 17-20.
    7. Lensu L., Frydrych M., Aschi C., Parkkinen J., Parkkinen S., and Jaaskelainen T.: Towards color sensitivity of protein based artificial retina. Technical Proceedings of the 2001 International Conference on Computational Nanoscience, ICCN'2001, Hilton Head Island, South Carolina, U.S.A., March 19-21, 2001, pp. 5-8.
    8. Frydrych M., Lensu L., Parkkinen S., Parkkinen J., and Jaaskelainen T.: Photoelectric response of bacteriorhodopsin in thin PVA films and its model. In M. De Gregorio, V. Di Maio, M. Frucci, and C. Musio, editors, Brain, Vision, and Artificial Intelligence: First International Symposium, BVAI 2005 Naples, Italy, October 19-21, 2005 Proceedings, volume 3704 of LNCS, pages 126-135, Berlin Heidelberg, 2005. Springer.
    9. Tukiainen T., Lensu L., and Parkkinen J.: Temporal characteristics of colour sensitive artificial retina based on bacteriorhodopsin. In F. Mele, G. Ramella, S. Santillo, and F. Ventriglia, editors, Advances in Brain, Vision, and Artificial Intelligence: Second International Symposium, BVAI 2007, Naples, Italy, October 10-12, 2007 Proceedings, volume 4729 of LNCS, pages 94-103, Berlin Heidelberg, 2007. Springer.
  4. Monographs published
    1. Leppänen, Veli-Pekka: Optical properties of bio-optical materials, University of Joensuu, 1999.
    2. Frydrych, Michael: Color Vision System Based on Bacteriorhodopsin, Lappeenranta University of Technology, 1999.
    3. Vanhanen, Jarmo: Studies on Three Different Types of Organic Non-linear Optical Materials, University of Joensuu, 2001.
    4. Lensu, Lasse: Photoelectric Properties of Bacteriorhodopsin Films for Photosensing and Information Processing, Lappeenranta University of Technology, 2002.
  5. Other scientific publications
    1. Silfsten P., Parkkinen S., Luostarinen J., Khodonov A., Demina O., Jaaskelainen T. and Parkkinen J.: Opto-electrical properties of bacteriorhodopsin and its analogs in polyvinylalchohol films. Proceedings of the 7th International Conference on Retinal Proteins, Zichron Yaacov, Israel, June 23-28, 1996.
    2. Silfsten P., Jaaskelainen T., Leppanen V.-P., Parkkinen S. and Parkkinen J.: Photochromic properties of 4-keto bacteriorhodopsin. Proceedings of the 7th International Conference on Retinal Proteins, Zichron Yaacov, Israel, June 23-28, 1996.
    3. Frydrych M., Parkkinen S., Silfsten P., Jaaskelainen T. and Parkkinen J.: Designing of protein based color sensitive retina. The 7th International Conference on Molecular Electronics and Biocomputing, Nanjing, China, November 10-12, 1997.
    4. Tukiainen T., Lensu L., and Parkkinen J.: Simulation Environment for Bacteriorhodopsin Sensors. NanoBionics IV - from Molecules to Applications, Marburg (Germany), September 17-21, 2007. Extended abstract.