Ozan Kahramanoğulları

Ozan Kahramanoğulları is an assistant professor 
at the Department of Mathematics, University of Trento.

His research focuses on theoretical aspects of computer science
with practical problems in
 biology in perspective, in particular 
  • modeling and simulation languages, 
  • stochastic simulation and analysis, 
  • automated reasoning and proof theory, 
  • and their applications in computational biology.


July 2018 - Cansu's recent results are now published in the proceedings of ALIFE 2018 in Tokyo.

     Mechanisms of Switching Response to External Phosphate Levels in Escherichia coli[LINK]
     C. Uluseker, M. M. Hanczyc and O. Kahramanoğulları 

     Artificial Life 

Conference Proceedings, 23-27 July, 2018, Tokyo.


Keywords: Systems Biology, Synthetic Biology, Artificial Life, Modelling, E. coli ] 

October 2017 - We have built microbial fuel cells and droplet cells at the IT University of Copenhagen, Autumn School on DIY Liquid Handling Robots, Microbial Fuel Cells, and Artificial Chemical Life.

September 2017 - We had a workshop on modelling in Trento for H2020 LIAR - Living Architecture project.

September 2017 - We presented the preliminary results of Cansu's PhD work at the ECAL'17 Conference.

     A Dynamic Model of the Phosphate Response System with Synthetic Promoters in E. coli[LINK]
     C. Uluseker, J. Torres, J. L. Garcia, M. M. Hanczyc, J. Nogales and O. Kahramanoğulları 

     Proc. of the International Conference on Artificial Life, 4-8 September, 2017, Lyon.


Keywords: Synthetic Biology, Artificial Life, Systems Biology, Modelling, E. coli ]

March 2017: This one should ease the applications of our previous work with James Lynch on stochastic simulation fluxes by introducing a simple algorithm that extends Gillespie's direct method.

     Quantifying Information Flow in Chemical Reaction Networks.    [PDF]     [TALK-PDF]   
     Ozan Kahramanoğulları
     Proceedings of 4th International Conference on Algorithms for Computational Biology
     AlCoB 2017, Aveiro, Portugal, June 5-6, LNCS 10252, Springer, 2017.

Stochastic Flux Analysis of Chemical Reaction Networks, [LINK]
Ozan Kahramanoğulları, James Lynch, 

BMC Systems Biology, 7: 133,



Among 100 most viewed articles of 2014 at BMC Systems Biology.

March 2017:  Back to the future: I could finally put together some new ideas on old thoughts. 

     Deep Proof Search iMELL.   [LINK]     [TALK-PDF]   
     Ozan Kahramanoğulları
     Logic for Programming, Artificial Intelligence, and Reasoning, 21st International Conference,
     Maun Botswana, May 7-12, 2017. 
     Proceedings of LPAR'17, EPiC Series in Computing, Volume 46.

The social event of the conference was a safari at the Okavango delta.

January 2017 - Federico's PhD work is now published at the Nature Scientific Reports Journal.

     Mechanistic interplay between ceramide and insulin resistance[LINK]
     F. Reali, M. Morine, O. Kahramanoğulları, S. Raichur

, H. Schneider, 

D. Crowther, C. Priami



Nature Scientific Reports 


      [ Keywords: Computational Biology, Systems Biology, Modelling, Ceramides, Insulin resistance ]

October 2017 - With Cansu (left) and Martin (right), we participated in our European project meeting in Venice on Living Architecture (LIAR).  And then again we met in Madrid at the Spanish National Research Council (CSIC) with a hands-on workshop on synthetic biology.

LIAR is a modular bioreactor-wall, which is based on the operational principles of microbial fuel cell technology and synthetic ‘consortia’ of microbes. The project establishes:

• Foundational concepts through which ‘designed’ metabolisms can computationally process, recycle, remediate and synthesize valuable compounds from waste water.

• Transferable principles by which synthetic ecosystems can shape the environmental performance of our living spaces to increase our health, productivity and ecosystems impact.

• New standards for synthetic ‘ecosystems’ through consortia design, engineering and optimization.

December 2016 - Some ideas on merging modeling technologies at different biological levels on a single platform.

     Simulating Stochastic Dynamic Interactions with Spatial Information and Flux. [PDF]
     Ozan Kahramanoğulları
     Proceedings of 5th International Conference on the Theory and Practice of Natural Computing
     TPNC 2016, Sendai, Japan December 12-13, LNCS 10071, Springer, 2016.

We are visiting with the conference crowd one of the monuments of Sendai overlooking the city.

August 2016: Is it possible to look at proofs as truly-concurrent processes? Yes, and this can also mean faster proof search.

     True Concurrency of Deep Inference Proofs. [PDF]
     Ozan Kahramanoğulları
     Proceedings of 23rd Workshop on Logic, Language, Information and Computation,
    WoLLIC 2016, August 16-19, 2016, Puebla, Mexico, Springer, 2016.

     Gener: A minimal programming module for chemical controllers based on DNA strand displacement.
     Ozan Kahramanoğulları, Luca Cardelli






       * Gener is a tool for performing reductions on DNA strands wrt. a strand displacement algebra.

        * Rendering 3D Process Models: Actin


         Process Modeling and Rendering of Biochemical Structures: Actin.  
         Ozan Kahramanoğulları, Andrew Phillips, Federico Vaggi 

         Biomechanics of cells and tissues: experiments, models and simulations


Lecture Notes in Computational Vision and Biomechanics,  Volume 9, 2013