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Chemical Reaction Networks: signal amplification, spatiotemporal control, and materials

Deliverables

Short articles in newspapers, magazines, newsletter, etc. online

UNISTRA will collect interesting results gathered by all ESR's and encourage all beneficiaries to engage to disseminate in popular media such as newspapers, magazines, etc.

Full Implementation of mentoring system

The TTC headed by the TC (Aldo JESORKA, CHALMERS) will make sure the mentoring program is implemented. Specifically, each ESR will be assigned a second mentor from a different node in addition to their direct local supervisor to broaden possible guidance during the research tasks. Bi-annual (during the scheduled ESR gatherings or more if necessary; see Gantt chart) meetings between the ESR, supervisor, and mentor will take place, during which the ESR will present detailed progress reports. During these meetings, overall progress of the research project, secondments programme, and complementary skills of the ESR fellow will be evaluated, and progress will be monitored based on the PCDP drafted at the start of the ESR project. All graduate schools also have arrangements in place for problem solving, including mediators, should conflicts arise.

Website: ESR profiles and projects online

The Creanet website should be fully operational. It will be hosted at https://H2020crea.net and https://creanet.u-strasbg.fr

Social media (Facebook, Twitter, etc.) operational

All social media accounts should be functional.

Completed secondment program

All ESR's have finished all their secondments or in case of delays will (in agreement with the TCC) wrap up their secondments as soon as possible.

ETN Open doors event (during summer school at USFD)

An evening ETN OPEN DOORS event with a keynote lecture aiming at the general public will be open to the general public. The ESRs can put their skills on communication to test and will present posters representing the scope of the ETN, ETNs in general, and the four scientific and training work packages. Again, the ESRs will be reminded of the CReaNet Communication Strategy.

15 x 36-month PhD training and research programmes

All ESRs have completed their 36 month training and research programmes.

Summer school

CRN modelling/design and further professional development (USFD): This will be a five-day summer school organised by USFD with local speakers and externally invited speakers, e.g., Christophe Flamm, Harold Fellerman, and Raphael Plasson. Taylor (USFD) was one of the lecturers at the Systems Chemistry Summer School as part of COST action (CM1304); she has taught modules involving CRN modelling and currently leads the 2nd year laboratory module at USFD, delivering computational modelling workshops to 180 undergraduates. She was also on the advisory board of Chaos (an AIP journal). Therefore, she is well placed to organise this summer school, which is intended for newcomers to CRN modelling/design and will comprise a series of lectures and workshops where students will solve problems in groups using available software. It will be open to non-Network members and will host 15 ESRs + 16 external applicants. The aims of the sessions are: i) to introduce students to the tools available for modeling chemical reaction networks, ii) to provide insight into how to build reaction network models for certain types of behaviour, iii) to explore methods for finding behaviour, and iv) to give experience in parameter estimation and kinetic data fitting. The topics covered will include: Solving ODEs, integration methods; Kinetics: mass-action, Michaelis-Menten etc.; Reaction network design and behaviour (oscillations etc.); Signal response curves; DNA based systems; Stochastic modelling; Reaction diffusion systems and PDEs; Data fitting.

Workshops completed

There are 6 workshops (W1) in total:W1 due in month 3 (UNISTRA)W2 due in month 12 (WEIZMANN)W3 due in month 15 (CHALMERS)W4 due in month 24 (ALU-FR)W5 due in month 30 (CHALMERS)W6 due in month 36 (TU Delft)

Publications

Redox-Controlled Shunts in a Synthetic Chemical Reaction Cycle

Author(s): Anastasiia Sharko; Benjamin Spitzbarth; Thomas M. Hermans; Rienk Eelkema
Published in: Journal of the American Chemical Society, Issue 145/17, 2023, Page(s) 9672-9678, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.3c00985

Improving Fatigue Resistance of Dihydropyrene by Encapsulation within a Coordination Cage

Author(s): Martina Canton, Angela B. Grommet, Luca Pesce, Julius Gemen, Shiming Li, Yael Diskin-Posner, Alberto Credi, Giovanni M. Pavan, Joakim Andréasson, Rafal Klajn
Published in: Journal of the American Chemical Society, Issue 142/34, 2020, Page(s) 14557-14565, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.0c06146

Protocells: Milestones and Recent Advances

Author(s): Irep Gözen, Elif Senem Köksal, Inga Põldsalu, Lin Xue, Karolina Spustova, Esteban Pedrueza-Villalmanzo, Ruslan Ryskulov, Fanda Meng, Aldo Jesorka
Published in: Small, 2022, ISSN 1613-6810
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.202106624

Modulating the Optical Properties of BODIPY Dyes by Noncovalent Dimerization within a Flexible Coordination Cage

Author(s): Julius Gemen, Johannes Ahrens, Linda J. W. Shimon, Rafal Klajn
Published in: Journal of the American Chemical Society, Issue 142/41, 2020, Page(s) 17721-17729, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.0c08589

pH-feedback systems to program autonomous self-assembly and material lifecycles

Author(s): Charu Sharma, Indrajit Maity, Andreas Walther
Published in: Chemical Communications, Issue 12, 2022, ISSN 1364-548X
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2cc06402b

Rapid Growth and Fusion of Protocells in Surface‐Adhered Membrane Networks

Author(s): Elif S. Köksal, Susanne Liese, Lin Xue, Ruslan Ryskulov, Lauri Viitala, Andreas Carlson, Irep Gözen
Published in: Small, Issue 16/38, 2020, Page(s) 2002529, ISSN 1613-6810
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.202002529

Transient co-assemblies of micron-scale colloids regulated by ATP-fueled reaction networks

Author(s): Charu Sharma, Aritra Sarkar, Andreas Walther
Published in: Chemical Sciences, 2023, ISSN 2041-6539
Publisher: Royal Society of Chemistry
DOI: 10.1039/d3sc04017h

Colony-like Protocell Superstructures

Author(s): Chinmay Katke, Esteban Pedrueza-Villalmanzo, Karolina Spustova, Ruslan Ryskulov, C. Nadir Kaplan, Irep Gözen
Published in: ACS Nano, 2023, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.2c08093

A microfluidic double emulsion platform for spatiotemporal control of pH and particle synthesis

Author(s): Maheen Rana, Raheel Ahmad, Annette F. Taylor
Published in: Lab on a Chip, 2023, Page(s) 4504-4513, ISSN 1473-0189
Publisher: RSC
DOI: 10.1039/d3lc00711a

Self‐Regulating Colloidal Co‐Assemblies That Accelerate Their Own Destruction via Chemo‐Structural Feedback

Author(s): Charu Sharma; Andreas Walther
Published in: Angewandte Chemie International Edition in English, Issue 4, 2022, ISSN 0044-8249
Publisher: Wiley-VCH
DOI: 10.1002/anie.202201573

Naked-Eye Thiol Analyte Detection via Self-Propagating, Amplified Reaction Cycle

Author(s): Benjamin Klemm, Ardeshir Roshanasan, Irene Piergentili, Jan H. van Esch, Rienk Eelkema
Published in: Journal of the American Chemical Society, 2023, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.3c02937

Chemically Fueled Self-Sorted Hydrogels

Author(s): Nishant Singh, Alvaro Lopez-Acosta, Georges J. M. Formon, and Thomas M. Hermans
Published in: Journal of the American Chemical Society, Issue 144, 2021, Page(s) 410-415, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.1c10282

Dissipative Self-Assembly: Fueling with Chemicals versus Light

Author(s): Maren Weißenfels, Julius Gemen, Rafal Klajn
Published in: Chem, Issue 7/1, 2021, Page(s) 23-37, ISSN 2451-9294
Publisher: Cell Press
DOI: 10.1016/j.chempr.2020.11.025

On‐Demand Release of Secondary Amine Bases for the Activation of Catalysts and Crosslinkers

Author(s): Benjamin Spitzbarth; Rienk Eelkema
Published in: Chemistry: A European Journal, Issue 29/17, 2023, Page(s) e202203028, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.202203028

Feedback and Communication in Active Hydrogel Spheres with pH Fronts: Facile Approaches to Grow Soft Hydrogel Structures

Author(s): Indrajit Maity, Charu Sharma, Francisco Lossada, Andreas Walther
Published in: Angewandte Chemie International Edition, 2021, ISSN 1521-3773
Publisher: Wiley VCH
DOI: 10.1002/anie.202109735

Insights into Chemically Fueled Supramolecular Polymers

Author(s): Anastasiia Sharko, Dimitri Livitz, Serena De Piccoli, Kyle J. M. Bishop, Thomas M. Hermans
Published in: Chemical Reviews, 2022, ISSN 0009-2665
Publisher: American Chemical Society
DOI: 10.1021/acs.chemrev.1c00958

DNA-Based Signaling Networks for Transient Colloidal Co-Assemblies

Author(s): Charu Sharma, Avik Samanta, Ricarda Sophia Schmidt, and Andreas Walther*
Published in: Journal of the American Chemical Society, Issue 4, 2023, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.3c04807

Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures

Author(s): Tong Bian, Andrea Gardin, Julius Gemen, Lothar Houben, Claudio Perego, Byeongdu Lee, Nadav Elad, Zonglin Chu, Giovanni M. Pavan, Rafal Klajn
Published in: Nature Chemistry, 2021, ISSN 1755-4330
Publisher: Nature Publishing Group
DOI: 10.1038/s41557-021-00752-9

Autonomous Soft Robots Empowered by Chemical Reaction Networks

Author(s): Giorgio Fusi, Daniele Del Giudice, Oliver Skarsetz, Stefano Di Stefano, Andreas Walther
Published in: Advanced Materials, 2022, ISSN 0935-9648
Publisher: United Nations Industrial Developement Organization
DOI: 10.1002/adma.202209870

Chemical reaction networks based on conjugate additions on β′-substituted Michael acceptors

Author(s): Benjamin Spitzbarth; Rienk Eelkema
Published in: Chemical Communications, Issue 59, 2023, Page(s) 11174-11187, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/d3cc02126b

Sensitive fluorescence spectroscopic based techniques to study tau assemblies implicated in neurodegenerative diseases

Author(s): Lacey Chunilal
Published in: 2023
Publisher: Johannes Gutenberg-Universität Mainz
DOI: 10.25358/openscience-9721

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