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Living Architecture

Deliverables

Model reactor array

The production of a 2D array of bioreactors with sensors and controllers that collectively perceives its environment makes decision about reconfiguration of the reactors contents and performs basic computational primitives with their closest neighbours

LIAR hardware

LIAR hardware, of MFCs running in both large partition panels and active wall sections capable of performing wastewater treatment, generating electricity and producing biomass.

ODACS part 2 and updates

These goals extend the project objectivesExploitationQuality control advisory board checksevaluation process and troubleshooting strategyOutreach launch website event schedule professional and publicDesign intentions update hardware software wetware

Progress Report Period 1

Period 1 progress report

Bioreactor Implementation Report

Final Report

Progress Report Period 2

Period 2 progress report

ODACS part 3

Addition to ODACS with schedule for integration of bioreactors (and evaluation of progress) through design/computation/experimental work

ODACS part 1

Outline Design and Contact Specification Document these goals build the team objectivesDesign intentions hardware software wetwareImplementation strategy meeting rota procurement assemblyManagement website document management system communications system

Final Report

Compiling of final report

Publications

FLYCOP: metabolic modeling-based analysis and engineering microbial communities

Author(s): Beatriz García-Jiménez, José Luis García, Juan Nogales
Published in: Bioinformatics, Issue 34/17, 2018, Page(s) i954-i963, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty561

Quantifying dynamic mechanisms of auto-regulation in Escherichia coli with synthetic promoter in response to varying external phosphate levels

Author(s): Cansu Uluşeker, Jesús Torres-Bacete, José L. García, Martin M. Hanczyc, Juan Nogales, Ozan Kahramanoğulları
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-38223-w

Living architecture: workshop report from the European Conference on Artificial Life, Lyon, France, 4 September 2017

Author(s): Martin M Hanczyc, Barbara Imhof, Andrew Adamatzky
Published in: Adaptive Behavior, Issue 26/2, 2018, Page(s) 85-88, ISSN 1059-7123
Publisher: SAGE Publications
DOI: 10.1177/1059712318761518

Regenerated silk fibroin membranes as separators for transparent microbial fuel cells

Author(s): Grzegorz Pasternak, Yuejiao Yang, Bruno Bosquiroli Santos, Federico Brunello, Martin M. Hanczyc, Antonella Motta
Published in: Bioelectrochemistry, Issue 126, 2019, Page(s) 146-155, ISSN 1567-5394
Publisher: Elsevier BV
DOI: 10.1016/j.bioelechem.2018.12.004

Novel method for detecting and quantifying phenol with transient response of glycolytic oscillations of synchronised yeast cells

Author(s): Grzegorz Pasternak, Martin M. Hanczyc
Published in: Sensing and Bio-Sensing Research, Issue 22, 2019, Page(s) 100259, ISSN 2214-1804
Publisher: Elsevier BV
DOI: 10.1016/j.sbsr.2019.100259

Artificial neural network simulating microbial fuel cells with different membrane materials and electrode configurations

Author(s): Michail-Antisthenis Tsompanas, Jiseon You, Lauren Wallis, John Greenman, Ioannis Ieropoulos
Published in: Journal of Power Sources, Issue 436, 2019, Page(s) 226832, ISSN 0378-7753
Publisher: Elsevier BV
DOI: 10.1016/j.jpowsour.2019.226832

Modelling the energy harvesting from ceramic-based microbial fuel cells by using a fuzzy logic approach

Author(s): Alberto de Ramón-Fernández, M.J. Salar-García, Daniel Ruiz-Fernández, J. Greenman, I. Ieropoulos
Published in: Applied Energy, Issue 251, 2019, Page(s) 113321, ISSN 0306-2619
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.apenergy.2019.113321

Modelling Microbial Fuel Cells using lattice Boltzmann methods

Author(s): Michail-Antisthenis Tsompanas, Andy Adamatzky, Ioannis Ieropoulos, Neil Phillips, Georgios Ch. Sirakoulis, John Greenman
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018, Page(s) 1-1, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/tcbb.2018.2831223

Cellular non-linear network model of microbial fuel cell

Author(s): Michail-Antisthenis Tsompanas, Andrew Adamatzky, Ioannis Ieropoulos, Neil Phillips, Georgios Ch. Sirakoulis, John Greenman
Published in: Biosystems, Issue 156-157, 2017, Page(s) 53-62, ISSN 0303-2647
Publisher: Elsevier BV
DOI: 10.1016/j.biosystems.2017.04.003

Towards implementation of cellular automata in Microbial Fuel Cells

Author(s): Michail-Antisthenis I. Tsompanas, Andrew Adamatzky, Georgios Ch. Sirakoulis, John Greenman, Ioannis Ieropoulos
Published in: PLOS ONE, Issue 12/5, 2017, Page(s) e0177528, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0177528

Genexput: A rapid and standarised method for large genome expansion of Pseudomonas putida

Author(s): Mesa-Galán, A., Blázquez, B., Nogales, J.
Published in: Biosaia: Revista de los másteres de Biotecnología Sanitaria y Biotecnología Ambiental, Industrial y Alimentaria, Issue vol. 1, no 8, 2019, ISSN 2254-3821
Publisher: Universidad Pablo de Olavide

Engineering self-regulated synthetic gene expression systems and its application on controlled protein expression

Author(s): Ronco-Campaña, A.; Torres-Bacete, J.; Nogales, J.
Published in: Biosaia: Revista de los másteres de Biotecnología Sanitaria y Biotecnología Ambiental, Industrial y Alimentaria, Issue vol. 1, no 8., 2019, ISSN 2254-3821
Publisher: Universidad Pablo de Olavide

The inclusion of side metabolic reactions in the genome-scale metabolic model of Pseudomonas putida highlights to underground metabolism as key player in metabolic robustness

Author(s): Canalejo, F. J.; Nogales, J.
Published in: Biosaia: Revista de los másteres de Biotecnología Sanitaria y Biotecnología Ambiental, Industrial y Alimentaria, Issue vol. 1, no 8, 2019, ISSN 2254-3821
Publisher: Universidad Pablo de Olavide

Soft Living Architecture - An Alternative View of Bio-informed Practice

Author(s): Armstrong,R
Published in: 2018, ISBN 978-1-3500-1133-5
Publisher: BLOOMSBURY ACADEMIC
DOI: 10.5040/9781350011366

Liquid Life: On Nonlinear Materiality

Author(s): Armstrong, R., Ferracina, S., Hughes, R.
Published in: 2019
Publisher: Punctum
DOI: 10.21983/p3.0246.1.00

Experimental Architecture - Designing the Unknown

Author(s): Armstrong, R
Published in: 2019, ISBN 9781-351272483
Publisher: ROUTLEDGE
DOI: 10.4324/9781351272483

Quantifying Information Flow in Chemical Reaction Networks

Author(s): Ozan Kahramanoğulları
Published in: Algorithms for Computational Biology, Issue 10252, 2017, Page(s) 155-166, ISBN 978-3-319-58162-0
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-58163-7_11

Living Architecture (LIAR): Metabolically engineered building units

Author(s): Armstrong R, Ferracina S, Caldwell G, Ieropoulos I, Rimbu G, Adamatzky A, Phillips N, De Lucrezia D, Imhof B, Hanczyc MM, Nogales J, Garcia J.
Published in: In: Heisel, F; Hebel, D, ed. Cultivated Building Materials: Industrialized Natural Resources for Architecture and Construction., 2017
Publisher: Birkhauser

A dynamic model of the phosphate response system with synthetic promoters in Escherichia coli

Author(s): Cansu Uluşeker, Jesus Torres, José L. García, Martin M. Hanczyc, Juan Nogales, Ozan Kahramanoğulları
Published in: Proceedings of the 14th European Conference on Artificial Life ECAL 2017, 2017, Page(s) 412-419, ISBN 978-0-262-34633-7
Publisher: MIT Press
DOI: 10.7551/ecal_a_069

Mechanisms of Switching Response to External Phosphate Levels in Escheria coli

Author(s): Cansu Uluşeker, Martin M. Hanczyc, Ozan Kahramanoğulları
Published in: The 2018 Conference on Artificial Life, 2018, Page(s) 633-640
Publisher: MIT Press
DOI: 10.1162/isal_a_00116

QUANTIFYING MECHANISMS OF BACTERIAL PHOSPHATE ECONOMY FOR SYNTHETIC APPS

Author(s): Kahramanog ̆ulları O.,. Hanczyc M.M.
Published in: enth Conference Dynamical Systems Applied to Biology and Natural Sciences DSABNS, 2019, ISBN 978-989-98750-6-7
Publisher: DSABNS

Enumerating Dominant Pathways in Biological Networks by Information Flow Analysis

Author(s): Kahramanoğulları O.
Published in: International Conference on Algorithms for Computational Biology, Issue 11488, 2019, Page(s) 39-51, ISBN 978-3-030-18173-4
Publisher: Springer
DOI: 10.1007/978-3-030-18174-1_3

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