Overview | Research directions | Group members | Collaborations | Selected Publications

Overview

The research of the Hanczyc Lab at the University of Trento seeks to integrate various functional aspects of artificial life, synthetic life, and natural life.  We have expertise in interfacial dynamics, modeling of complex chemistry, optimization strategies, robot-chemistry interfaces, fundamentals of intelligent materials, synthetic biology, and new bio-inspired materials for architecture and engineering.

Research directions

  • Artificial Cells
    We are currently developing several distinct types of artificial cells in the laboratory, based on lipid bilayer interfaces and droplet-based emulsions.  Several life-like characteristics are explored including self-movement, self-division, biochemical transformation, group dynamics and self-identity.  In parallel with developing new artificial cell technologies we are exploring the use of artificial cells in natural cell ecologies such as microbial fuel cells (see below) and in directed theranostics.
  • Robot Interfaces
    We will develop artificial, technological evolution and use it to design functional ecosystems consisting of up to three forms of living technology, namely, artificial chemical life, living microorganisms, and reconfigurable robotics for the purpose of improved treatment and cleanup of wastewater for energy generation.
    The goals of this project are i) develop a general, robotic platform, which by using artificial evolution can optimize the performance of a physicochemical or microbial system and its environment and ii) use the robotic platform to evolve improved microbial fuel cells in terms of robustness, longevity, or adaptability. The robot evolutionary platform will take the form of an open-source 3D printer extended with functionality for handling liquids and reaction vessels, and for obtaining feedback from the reaction vessels either using computer vision or task-specific sensors in real-time. The robot platform will optimize parameters such as the environment, hydraulics or real-time interaction with experiments (for instance, timing of injection of nutrients, removal of metabolic products, stirring, etc.) to maximize a desired functionality. Initially, we investigate processes such as fluid-structure-interaction driving bio-aggregate structure and in turn metabolic activity as well as the interaction of nanoparticles and bacterial cells by analyzing the outcome of the evolutionary process using state-of-the-art imaging techniques. We then seek to exploit synergies between these technologies to significantly improve the ability of the living technology, in the form of optimized microbial fuel cells, to cleanup wastewater. Overall, this is a cross-disciplinary project involving state-of-the-art chemistry, imaging, robotics, artificial life, microbiology and bio-energy harvesting for the purpose of enhancing our understanding of living technologies and how to best design and exploit groundbreaking bio-hybrid systems.
  • Complex Chemistry ad Massive Chemical Flow
    Polymers of hydrogen cyanide and their hydrolysis products constitute a plausible, but still poorly understood proposal for early prebiotic chemistry on Earth. HCN polymers are generated by the interplay of more than a dozen distinctive reaction mechanisms and form a highly complex mixture. Here we use a computational model based on graph grammars as a means of exploring the chemical spaces of HCN polymerization and hydrolysis. A fundamental issue is to understand the combinatorial explosion inherent in large, complex chemical systems. We demonstrate that experimental data, here obtained by mass spectrometry, and computationally predicted free energies together can be used to guide the exploration of the chemical space and makes it feasible to investigate likely pathways and chemical motifs even in potentially open-ended chemical systems.

Group members

  • Martin M. Hanczyc, PI
  • Valter Bavastrello, postdoctoral fellow
  • Jitka Cejkova, postdoctoral fellow
  • Silvia Holler, PhD student

Collaborations

  • Rachel Armstrong, University of Greenwich, London
  • Jitka Čejková, Institute of Chemical Technology, Prague
  • Lee Cronin, University of Glasgow
  • Christoph Flamm, University of Vienna
  • Harald Horn, Karlsruhe Institute of Technolog
  • Ioannis Ieropoulos, Bristol Robotics Laboratory
  • Takashi Ikegami, University of Tokyo
  • Christian Kerrigan, London
  • Daniel Merkle, University of Southern Denmark
  • Norman Packard, ProtoLife, San Francisco
  • Peter Stadler, Max Planck Institute for Mathematics, Leipzig
  • Kasper Støy, IT University of Copenhagen
  • Tadashi Sugawara, Kanagawa University
  • Taro Toyota, University of Tokyo

Selected publications

Andersen JK, Andersen T, Flamm C, Hanczyc MM, Merkle D, Stadler PF.  2013.  Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data. Entropy. 15(10), 4066-4083.

Armstrong R, Hanczyc MM. 2013.  Bütschli Dynamic Droplet System. Artificial Life, 19(3-4): 331-346.

Caschera F, Rasmussen S, Hanczyc MM.  2013. An Oil Droplet Division-Fusion Cycle, ChemPlusChem, 78: 52–54. doi: 10.1002/cplu.201200275.

Hadorn M, Boenzli E, Sørensen KT, Fellermann H, Eggenberger Hotz P, Hanczyc MM. 2012. Specific and Reversible DNA-directed Self-Assembly of Oil-in-Water Emulsion Droplets. PNAS, doi: 10.1073/pnas.1214386109.

Hadorn M, Boenzli E, Eggenberger Hotz P, Hanczyc MM. 2012. Hierarchical Unilamellar Vesicles of Controlled Compositional Heterogeneity, PLoS ONE, 7 (11) e50156.

Caschera F, Bernardino de la Serna J, Loffler PMG, Rasmussen TE, Hanczyc MM, Bagatolli LA, Monnard P-A. 2011. Stable Vesicles Composed of Monocarboxylic or Dicarboxylic Fatty Acids and Trimethylammonium Amphiphiles. Langmuir, 27 (23), 14078–14090

 dx.doi.org/10.1021/la203057b.

Caschera F, Sunami T, Matsuura T, Suzuki H,. Hanczyc MM, Yomo T. 2011. Programmed Vesicle Fusion Triggers Gene Expression. Langmuir 2011, 27, 13082–13090.

Hanczyc MM. 2011. Metabolism and motility in prebiotic structures. Phil. Trans. R. Soc. B, 366, 2885-2893. doi: 10.1098/rstb.2011.0141

Caschera F, Bedau MA, Buchanan A, Cawse J, de Lucrezia D, Gazzola G, Hanczyc MM, Packard N. 2011. Coping With Complexity: Machine Learning Optimization of Cell-Free Protein Synthesis. Biotechnology and Bioengineering. 108 (9) 2218–2228.

Horibe N, Hanczyc MM and Ikegami T. 2011. Mode Switching and Collective Behavior in Chemical Oil Droplets. Entropy 13, 709-719; doi:10.3390/e13030709

Hanczyc MM. 2010.  Chapter contribution. In M. A. Bedau, P. Guldborg Hansen, E. Parke, S. Rasmussen, (Eds.) Living Technology, 5 Questions. Automatic  Press. pp 77-84.

Hanczyc MM and Ikegami T. 2010. Emergence of Self-Movement as a Precursor to Darwinian Evolution. OLEB 40(4-5): 383. Conference abstract.

Sunami T, Caschera F, Morita Y, Toyota T, Nishimura K, Matsuura T, Suzuki H, Hanczyc MM, Yomo T. 2010. Detection of Association and Fusion of Giant Vesicles Using a Fluorescence-Activated Cell Sorter, Langmuir 26(19), 15098–15103.

Hanczyc MM and Ikegami T. 2010. Chemical basis for minimal cognition. Artificial Life 16: 233–243.

Caschera F, Gazzola G, Bedau MA, Bosch Moreno C, Buchanan A, Cawse J, Packard N, Hanczyc MM. 2010. Automated Discovery of Novel Drug Formulations Using Predictive Iterated High Throughput Experimentation. PLoS ONE 5(1): e8546.doi:10.1371/journal.pone.0008546

Toyota T, Maru N, Hanczyc MM, Ikegami T, Sugawara T. 2009. Self-Propelled Oil Droplets Consuming “Fuel” Surfactant. J. Am. Chem. Soc., 2009, 131 (14), pp 5012–5013.

Hanczyc MM. 2008. The Early History of Protocells – the search for the recipe of life. In S. Rasmussen, M. A. Bedau, L. Chen, D. Deamer, D. C. Krakauer, N. H. Packard, & P. F. Stadler (Eds.) Protocells: Bridging Nonliving and Living Matter. MIT Press. pp 3-18.  ISBN: 9780262182683

Hanczyc MM, Chen IA, Sazani PL, Szostak JW.  2008. Steps toward a Synthetic Protocell. In S. Rasmussen, M. A. Bedau, L. Chen, D. Deamer, D. C. Krakauer, N. H. Packard, & P. F. Stadler (Eds.) Protocells: Bridging Nonliving and Living Matter. MIT Press.  pp 107-124. ISBN: 9780262182683

Hanczyc MM, Toyota T, Ikegami T, Packard N, Sugawara T.  2007. Fatty Acid Chemistry at the Oil-Water Interface: Self-Propelled Oil Droplets. J Am Chem Soc. 129(30):9386-91.

Hanczyc MM, Mansy SS, Szostak JW. 2006 Mineral surface directed membrane assembly Orig Life Evol Biosph. 37(1):67-82

Chen IA, Hanczyc MM, Sazani PL, Szostak JW.  2006 Protocells: Genetic Polymers Inside Membrane Vesicles, in R.F. Gesteland, T.R. Cech, & J.F. Atkins (Eds.)The RNA World, Third Edition. (pp. 57-88). Cold Spring Harbor, NY: Cold Spring Harbor Press. ISBN 978-0879697396.

Bedau MA, Buchanan A, Gazzola G, Hanczyc MM, Maeke T, McCaskil J, Poli I, Packard NH. 2005. Evolutionary design of a DDPD model of ligation. In Proceedings of the 7th International Conference on Artificial Evolution EA'05. Lecture Notes in Computer Science, Springer Verlag.

Hanczyc MM and Szostak JW. 2004 Replicating vesicles as models of primitive cell growth and division. Curr Opin Chem Biol 8(6):660-4.

Hanczyc MM, Fujikawa SM, and Szostak JW. 2003 Experimental models of primitive cellular compartments: encapsulation, growth and division. Science 302: 618-622.

Hanczyc MM and Dorit RL.2000 Replicability and recurrence in the experimental evolution of a group I ribozyme.. Molecular Biology and Evolution.  17(7): 1050-1060.

Hanczyc MM and Dorit RL. 1998 Experimental evolution of complexity: in vitro emergence of intermolecular ribozyme interactions. RNA 4: 268-275.