ACDC – Artificial Cells with Distributed Cores to Decipher Protein Function
At a glance
- Project leader : Prof. Dr. Rudolf Marcel Füchslin
- Deputy of project leader : Dr. Dandolo Flumini
- Project team : Dr. Johannes Josef Schneider, Mathias Weyland
- Project budget : CHF 730'000
- Project status : completed
- Funding partner : EU and other international programmes (Horizon 2020 / Projekt Nr. 824060)
- Contact person : Rudolf Marcel Füchslin
Description
ACDC will employ a rapidly expanding living technology platform of transformational artificial cell technologies towards the next generation of small molecule drug discovery, protein biophysics, and biochemical energy production. This will be executed through a future paradigm of sensory and synthesis regimes, based on programmable and re-configurable, (bio)chemical processes, built with precision, order, and as hierarchical cellular constructs, in a design mirrored in living systems. In effect, we aim to emulate the structure and dynamics of living cells and cellular tissues by embedding biochemical and biophysical systems capable of sensing, reconfiguration, synthesis, electrochemical gradient production and biochemical energy production - all essential processes of living cells - built from the bottom up and middle-out approaches. We will accomplish this by producing microscale, liquid-based, chemical compartmentalisation (cores), with inter-compartmental (core-core) communication, just as one finds in organelles, cells and tissues. In the future, the resulting technology will enable creation of simplified artificial cell technologies based on cores as a platform for technical innovation, precisely for 1) the high throughput screening of small molecule libraries against defined protein targets, such as membrane proteins, 2) the definition of precise biophysical aspects of targeted protein systems, 3) the elucidation of targets for future antibiotics, 4) the definition of a scale-up of this core technology, and 5) the development of the multi-level mathematics underpinning the complexity of such artefacts of living technology but also of natural living systems. ACDC will focus on developing this next generation technology through a detailed workplan that heavily involves the nontrivial tasks of integrating diverse state of the art technologies including microfluidics, microwave resonators, DNA-based supramolecular assembly, in vitro gene expression and the integration of membrane channels into a functional platform. To exemplify the future potential of this integrated platform we will perform initial tests using high throughput screening of a small molecule library against the membrane protein target FeoB in phospholipid vesicles. Once demonstrated, a future implementation includes genetic mutation screening of ion channels for high value targets. The development of in situ protein expression systems for expressing target proteins, will be further applicable beyond screening and biophysical characterisation, to repurposing as bespoke sensing and communication components. This will enable the creation of modular pathways within programmable capsules for applications, in a future embodiment of this project, that includes using artificial cell technology as programmable and reconfigurable matter for specific applications including theranostics and personalized medicine, sensing and actuation in the environments for bioremediation, and discovery of potential antibiotics from complex soil environments. All of these future applications will rely on the fundamental functionalities developed in ACDC including modular functional capsules, reconfiguration, remote read-out, core-core and core-environment communication. We have assembled an international, interdisciplinary team from academia, industry and public engagement including expertise in engineering, physics, computer science, and chemical biology, to undertake this work. Our outreach and engagement programme will define the impact in both the public and economic sectors. Further, building upon 55 years of collective start-up enterprise experience, we will explore a new, agile, innovative vehicle to accelerate the translation of new intellectual property generated into commercial advantage and job creation for the European Union. The overall objective of the ACDC project is to manufacture compartmentalised, liquid-based chemistries, as discrete, yet interactive and multifunctional cores, within micro-scale containment capsules as communicating micro-laboratories. Analogous to current ICT, we imagine the tremendous opportunities and potentialities that exist when chemical and biochemical processes are miniaturized in programmable discrete units that provide on demand functionality. For example, we hope one day to be able to produce biochemical apps that could be installed in a portable chemical laboratory the size of a mobile phone that can then produce insulin, antibiotics or other high value medicines on demand. Another app could in principle detect toxins or disease in the environment or user. Another app would monitor daily nutritional parameters including mental or physical performance. As the first steps towards that future vision, we aim to produce an artificial technological construct and process that recapitulates some aspects of living systems on the microscale, and therefore this project will produce exemplars of secondary living technologies concentrating on the wetware class [1] but also a multi-level mathematical framework.
Publications
-
Schneider, Johannes Josef; Barrow, David Anthony; Li, Jin; Weyland, Mathias; Flumini, Dandolo; Eggenberger Hotz, Peter; Füchslin, Rudolf Marcel,
2023.
Bidisperse extension of the kissing number problem.
In:
28th International Conference on Statistical Physics (Statphys28), Tokyo, Japan, 7-11 August 2023.
-
Weyland, Mathias S.; Flumini, Dandolo; Schneider, Johannes J.; Faggian, Alessia; Patiño Diaz, Aitor; Füchslin, Rudolf Marcel,
2023.
In:
ALIFE 2023: Ghost in the Machine : Proceedings of the 2023 Artificial Life Conference.
International Conference on Artificial Life (ALIFE), Sapporo, Japan, 24-28 July 2023.
Cambridge:
MIT Press.
pp. 105.
Available from: https://doi.org/10.1162/isal_a_00648
-
Schneider, Johannes Josef; Faggian, Alessia; Jamieson, William David; Weyland, Mathias Sebastian; Li, Jin; Castell, Oliver; Matuttis, Hans-Georg; Barrow, David Anthony; Patiño Diaz, Aitor; Sanahuja, Lorena Cebolla; Holler, Silvia; Casiraghi, Federica; Hanczyc, Martin Michael; Flumini, Dandolo; Eggenberger Hotz, Peter; Füchslin, Rudolf Marcel,
2023.
Artificial chemistry performed in an agglomeration of droplets with restricted molecule transfer [paper].
In:
De Stefano, Claudio; Fontanella, Francesco; Vanneschi, Leonardo, eds.,
Artificial Life and Evolutionary Computation.
XVI Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Gaeta, Italy, 14-16 September 2022.
Cham:
Springer.
pp. 107-118.
Communications in Computer and Information Science ; 1780.
Available from: https://doi.org/10.1007/978-3-031-31183-3_9
-
Matuttis, Hans-Georg; Schneider, Johannes Josef; Li, Jin; Barrow, David Anthony; Faggian, Alessia; Patiño Diaz, Aitor; Holler, Silvia; Casiraghi, Federica; Sanahuja, Lorena Cebolla; Hanczyc, Martin Michael; Weyland, Mathias Sebastian; Flumini, Dandolo; Eggenberger Hotz, Peter; Dimitriou, Pantelitsa; Jamieson, William David; Castell, Oliver; Füchslin, Rudolf Marcel,
2023.
Computational investigation of the clustering of droplets in widening pipe geometries [paper].
In:
De Stefano, Claudio; Fontanella, Francesco; Vanneschi, Leonardo, eds.,
Artificial Life and Evolutionary Computation.
XVI Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Gaeta, Italy, 14-16 September 2022.
Cham:
Springer.
pp. 82-93.
Communications in Computer and Information Science ; 1780.
Available from: https://doi.org/10.1007/978-3-031-31183-3_7
-
Schneider, Johannes Josef; Faggian, Alessia; Patiño Diaz, Aitor; Li, Jin; Holler, Silvia; Casiraghi, Federica; Sanahuja, Lorena Cebolla; Matuttis, Hans-Georg; Hanczyc, Martin Michael; Barrow, David Anthony; Weyland, Mathias Sebastian; Flumini, Dandolo; Eggenberger Hotz, Peter; Dimitriou, Pantelitsa; Jamieson, William David; Castell, Oliver; Eschle, Patrik; Füchslin, Rudolf Marcel,
2023.
Network creation during agglomeration processes of polydisperse and monodisperse systems of droplets [paper].
In:
De Stefano, Claudio; Fontanella, Francesco; Vanneschi, Leonardo, eds.,
Artificial Life and Evolutionary Computation.
XVI Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Gaeta, Italy, 14-16 September 2022.
Cham:
Springer.
pp. 94-106.
Communications in Computer and Information Science ; 1780.
Available from: https://doi.org/10.1007/978-3-031-31183-3_8
-
Füchslin, Rudolf Marcel; Ambühl, Jacques; Faggian, Alessia; Fellermann, Harold M.; Flumini, Dandolo; Geller, Armando; Hanczyc, Martin M.; Klinkert, Andreas; Krütli, Pius; Matuttis, Hans-Georg; Ott, Thomas; Scheidegger, Stephan; Schmid, Gary Bruno; Smieszek, Timo; Schneider, Johannes J.; Steiner, Albert; Weyland, Mathias S.,
2023.
Ethical aspects of computational modelling in science, decision support and communication [paper].
In:
Artificial Life and Evolutionary Computation.
XV Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Winterthur, Switzerland, 15-17 September 2021.
Cham:
Springer.
Communications in Computer and Information Science ; 1722.
Available from: https://doi.org/10.1007/978-3-031-23929-8_24
-
Schneider, Johannes Josef; Weyland, Mathias Sebastian; Flumini, Dandolo; Füchslin, Rudolf Marcel,
2023.
Exploring the three-dimensional arrangement of droplets [paper].
In:
Artificial Life and Evolutionary Computation.
XV Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Winterthur, Switzerland, 15-17 September 2021.
Cham:
Springer.
Communications in Computer and Information Science ; 1722.
Available from: https://doi.org/10.1007/978-3-031-23929-8_6
-
Schneider, Johannes Josef; Barrow, David Anthony; Li, Jin; Weyland, Mathias Sebastian; Flumini, Dandolo; Eggenberger Hotz, Peter; Füchslin, Rudolf Marcel,
2023.
Geometric restrictions to the agglomeration of spherical particles [paper].
In:
Artificial Life and Evolutionary Computation.
XV Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Winterthur, Switzerland, 15-17 September 2021.
Cham:
Springer.
Communications in Computer and Information Science ; 1722.
Available from: https://doi.org/10.1007/978-3-031-23929-8_7
-
Schneider, Johannes Josef; Faggian, Alessia; Matuttis, Hans-Georg; Barrow, David Anthony; Li, Jin; Holler, Silvia; Casiraghi, Federica; Cebolla Sanahuja, Lorena; Hanczyc, Martin Michael; Eschle, Patrik; Weyland, Mathias Sebastian; Flumini, Dandolo; Eggenberger Hotz, Peter; Füchslin, Rudolf Marcel,
2023.
Obstacles on the pathway towards chemical programmability using agglomerations of droplets [paper].
In:
Artificial Life and Evolutionary Computation.
XV Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Winterthur, Switzerland, 15-17 September 2021.
Cham:
Springer.
Communications in Computer and Information Science ; 1722.
Available from: https://doi.org/10.1007/978-3-031-23929-8_4
-
Matuttis, Hans-Georg; Holler, Silvia; Casiraghi, Federica; Schneider, Johannes Josef; Faggian, Alessia; Füchslin, Rudolf Marcel; Hanczyc, Martin Michael,
2023.
The good, the bad and the ugly : droplet recognition by a “shootout”-heuristics [paper].
In:
Artificial Life and Evolutionary Computation.
XV Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Winterthur, Switzerland, 15-17 September 2021.
Cham:
Springer.
pp. 51-62.
Communications in Computer and Information Science ; 1722.
Available from: https://doi.org/10.1007/978-3-031-23929-8_5
-
2022.
Applied science : the curse and blessing of applying science.
In:
Talk at Newcastle University, Newcastle, United Kingdom, 15 March 2022.
-
2021.
Modeling social systems at ZHAW.
In:
XV International Workshop on Artificial Life and Evolutionary Computation (WIVACE), Winterthur, Switzerland, 15-17 September 2021.
-
Faggian, Alessia; Schneider, Johannes Josef,
2021.
Available from: https://acdch2020.eu/summer-school
-
2021.
Computational approaches in biology.
In:
ACDC Summer School, online, 26-27 August 2021.
-
Schneider, Johannes Josef; Faggian, Alessia; Holler, Silvia; Casiraghi, Federica; Li, Jin; Cebolla Sanahuja, Lorena; Matuttis, Hans-Georg; Hanczyc, Martin Michael; Barrow, David Anthony; Weyland, Mathias Sebastian; Flumini, Dandolo; Eggenberger Hotz, Peter; Füchslin, Rudolf Marcel,
2021.
In:
ALIFE 2021: The 2021 Conference on Artificial Life.
International Conference on Artificial Life (ALIFE), online, 19-23 July 2021.
Cambridge:
MIT Press.
pp. 71.
Available from: https://doi.org/10.1162/isal_a_00392
-
Schneider, Johannes Josef; Faggian, Alessia; Holler, Silvia; Casiraghi, Federica; Li, Jin; Cebolla Sanahuja, Lorena; Matuttis, Hans-Georg; Hanczyc, Martin Michael; Barrow, David Anthony; Weyland, Mathias Sebastian; Flumini, Dandolo; Eggenberger Hotz, Peter; Füchslin, Rudolf Marcel,
2021.
In:
International Conference on Artificial Life (ALIFE), online, 19-23 July 2021.
Available from: https://www.youtube.com/watch?v=2uSgimAHU4I
-
Schneider, Johannes Josef; Weyland, Mathias Sebastian; Flumini, Dandolo; Füchslin, Rudolf Marcel,
2020.
Investigating three-dimensional arrangements of droplets [paper].
In:
Cicirelli, Franco; Guerrieri, Antonio; Pizzuti, Clara; Socievole, Annalisa; Spezzano, Giandomenico; Vinci, Andrea, eds.,
Artificial Life and Evolutionary Computation.
XIV Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Rende, Italy, 18-20 September 2019.
Cham:
Springer.
pp. 171-184.
Communications in Computer and Information Science ; 1200.
Available from: https://doi.org/10.1007/978-3-030-45016-8_17
-
Schneider, Johannes Josef; Weyland, Mathias Sebastian; Flumini, Dandolo; Matuttis, Hans-Georg; Morgenstern, Ingo; Füchslin, Rudolf Marcel,
2020.
Studying and simulating the three-dimensional arrangement of droplets [paper].
In:
Cicirelli, Franco; Guerrieri, Antonio; Pizzuti, Clara; Socievole, Annalisa; Spezzano, Giandomenico; Vinci, Andrea, eds.,
Artificial Life and Evolutionary Computation.
XIV Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Rende, Italy, 18-20 September 2019.
Cham:
Springer.
Communications in Computer and Information Science ; 1200.
Available from: https://doi.org/10.1007/978-3-030-45016-8_16
-
Flumini, Dandolo; Weyland, Mathias S.; Schneider, Johannes J.; Fellermann, Harold; Füchslin, Rudolf M.,
2020.
Towards programmable chemistries [paper].
In:
Cicirelli, Franco; Guerrieri, Antonio; Pizzuti, Clara; Socievole, Annalisa; Spezzano, Giandomenico; Vinci, Andrea, eds.,
Artificial Life and Evolutionary Computation.
XIV Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Rende, Italy, 18-20 September 2019.
Springer.
Communications in Computer and Information Science ; 1200.
Available from: https://doi.org/10.1007/978-3-030-45016-8_15