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Parallel network-based biocomputation: technological baseline, scale-up and innovation ecosystem

Deliverables

Report on the establishment of a Community Portal

The basic structure of a Community Portal, integrating the project web site, will be established. Content will be added throughout the duration of the project.

Report on the performance of EXACT COVER devices

Results of iterative process of device testing and optimization with contributions from LnU for for actin filaments and from TUD for microtubules.

Report on the suitability of different bio-agents for future NBC devices

A detailed report comparing and contrasting the suitability of cytoskeletal filaments of different types, bacteria of different species and other potential bio-agents for use in network biocomputing devices, in terms of velocity, error rates, energy use, ability to replicate or divide and other parameters.

Fabrication of 3-SAT devices

Following tests and iterations, functional 3-SAT devices for Milestone IV delivered.

Fabrication of EXACT COVER devices

Following tests and iterations, functional EXACT COVER devices for Milestone II delivered.

Logotype and Website

Our project website will be online latest by the end of M2.

Data Management Plan

Establishment of a data management plan that fully complies with legal requirements. Links to open-data repositories will be made available at the Community Portal.

Searching for OpenAIRE data...

Publications

Myosin and gelsolin cooperate in actin filament severing and actomyosin motor activity

Author(s): Venukumar Vemula, Tamás Huber, Marko Ušaj, Beáta Bugyi, Alf Månsson
Published in: Journal of Biological Chemistry, Issue 296, 2021, Page(s) 100181, ISSN 0021-9258
DOI: 10.1074/jbc.ra120.015863

Regeneration of Assembled, Molecular-Motor-Based Bionanodevices

Author(s): Mohammad A. Rahman, Cordula Reuther, Frida W. Lindberg, Martina Mengoni, Aseem Salhotra, Georg Heldt, Heiner Linke, Stefan Diez, Alf Månsson
Published in: Nano Letters, Issue 19/10, 2019, Page(s) 7155-7163, ISSN 1530-6984
DOI: 10.1021/acs.nanolett.9b02738

Discovering Essential Multiple Gene Effects through Large Scale Optimization: an Application to Human Cancer Metabolism

Author(s): Annalisa Occhipinti, Youssef Hamadi, Hillel Kugler, Christoph Wintersteiger, Boyan Yordanov, Claudio Angione
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020, Page(s) 1-1, ISSN 1545-5963
DOI: 10.1109/tcbb.2020.2973386

Covalent and non-covalent chemical engineering of actin for biotechnological applications

Author(s): Saroj Kumar, Alf Mansson
Published in: Biotechnology Advances, Issue 35/7, 2017, Page(s) 867-888, ISSN 0734-9750
DOI: 10.1016/j.biotechadv.2017.08.002

Label-Free Detection of Microvesicles and Proteins by the Bundling of Gliding Microtubules

Author(s): Samata Chaudhuri, Till Korten, Slobodanka Korten, Gloria Milani, Tobia Lana, Geertruy te Kronnie, Stefan Diez
Published in: Nano Letters, Issue 18/1, 2017, Page(s) 117-123, ISSN 1530-6984
DOI: 10.1021/acs.nanolett.7b03619

Tetrazine– trans -cyclooctene Mediated Conjugation of Antibodies to Microtubules Facilitates Subpicomolar Protein Detection

Author(s): Samata Chaudhuri, Till Korten, Stefan Diez
Published in: Bioconjugate Chemistry, Issue 28/4, 2017, Page(s) 918-922, ISSN 1043-1802
DOI: 10.1021/acs.bioconjchem.7b00118

Highly-Efficient Guiding of Motile Microtubules on Non-Topographical Motor Patterns

Author(s): Cordula Reuther, Matthäus Mittasch, Sundar R. Naganathan, Stephan W. Grill, Stefan Diez
Published in: Nano Letters, Issue 17/9, 2017, Page(s) 5699-5705, ISSN 1530-6984
DOI: 10.1021/acs.nanolett.7b02606

Nanowires for Biosensing: Lightguiding of Fluorescence as a Function of Diameter and Wavelength

Author(s): Damiano Verardo, Frida W. Lindberg, Nicklas Anttu, Cassandra S. Niman, Mercy Lard, Aleksandra P. Dabkowska, Tommy Nylander, Alf Månsson, Christelle N. Prinz, Heiner Linke
Published in: Nano Letters, Issue 18/8, 2018, Page(s) 4796-4802, ISSN 1530-6984
DOI: 10.1021/acs.nanolett.8b01360

Controlled Surface Silanization for Actin-Myosin Based Nanodevices and Biocompatibility of New Polymer Resists

Author(s): Frida W. Lindberg, Marlene Norrby, Mohammad A. Rahman, Aseem Salhotra, Hideyo Takatsuki, Sören Jeppesen, Heiner Linke, Alf Månsson
Published in: Langmuir, Issue 34/30, 2018, Page(s) 8777-8784, ISSN 0743-7463
DOI: 10.1021/acs.langmuir.8b01415

An automated in vitro motility assay for high-throughput studies of molecular motors

Author(s): Till Korten, Elena Tavkin, Lara Scharrel, Vandana Singh Kushwaha, Stefan Diez
Published in: Lab on a Chip, Issue 18/20, 2018, Page(s) 3196-3206, ISSN 1473-0197
DOI: 10.1039/c8lc00547h

Blebbistatin Effects Expose Hidden Secrets in the Force-Generating Cycle of Actin and Myosin

Author(s): Mohammad A. Rahman, Marko Ušaj, Dilson E. Rassier, Alf Månsson
Published in: Biophysical Journal, Issue 115/2, 2018, Page(s) 386-397, ISSN 0006-3495
DOI: 10.1016/j.bpj.2018.05.037

Do Actomyosin Single-Molecule Mechanics Data Predict Mechanics of Contracting Muscle?

Author(s): Alf Månsson, Marko Ušaj, Luisa Moretto, Dilson Rassier
Published in: International Journal of Molecular Sciences, Issue 19/7, 2018, Page(s) 1863, ISSN 1422-0067
DOI: 10.3390/ijms19071863

Design and development of nanoimprint-enabled structures for molecular motor devices

Author(s): Frida W Lindberg, Till Korten, Anette Löfstrand, Mohammad A Rahman, Mariusz Graczyk, Alf Månsson, Heiner Linke, Ivan Maximov
Published in: Materials Research Express, Issue 6/2, 2019, Page(s) 025057, ISSN 2053-1591
DOI: 10.1088/2053-1591/aaed10

Comparative analysis of widely used methods to remove nonfunctional myosin heads for the in vitro motility assay

Author(s): Mohammad A. Rahman, Aseem Salhotra, Alf Månsson
Published in: Journal of Muscle Research and Cell Motility, Issue 39/5-6, 2018, Page(s) 175-187, ISSN 0142-4319
DOI: 10.1007/s10974-019-09505-1

Biosensing using arrays of vertical semiconductor nanowires: mechanosensing and biomarker detection

Author(s): Mercy Lard, Heiner Linke, Christelle N Prinz
Published in: Nanotechnology, Issue 30/21, 2019, Page(s) 214003, ISSN 0957-4484
DOI: 10.1088/1361-6528/ab0326

Something has to give: scaling combinatorial computing by biological agents exploring physical networks encoding NP-complete problems

Author(s): Falco C. M. J. M. van Delft, Giulia Ipolitti, Dan V. Nicolau, Ayyappasamy Sudalaiyadum Perumal, Ondřej Kašpar, Sara Kheireddine, Sebastian Wachsmann-Hogiu, Dan V. Nicolau
Published in: Interface Focus, Issue 8/6, 2018, Page(s) 20180034, ISSN 2042-8898
DOI: 10.1098/rsfs.2018.0034

Single molecule turnover of fluorescent ATP by myosin and actomyosin unveil elusive enzymatic mechanisms

Author(s): Marko Ušaj, Luisa Moretto, Venukumar Vemula, Aseem Salhotra, Alf Månsson
Published in: Communications Biology, Issue 4/1, 2021, ISSN 2399-3642
DOI: 10.1038/s42003-020-01574-0

Synthetic biology approaches to dissecting linear motor protein function: towards the design and synthesis of artificial autonomous protein walkers

Author(s): Heiner Linke, Birte Höcker, Ken’ya Furuta, Nancy R. Forde, Paul M. G. Curmi
Published in: Biophysical Reviews, Issue 12/4, 2020, Page(s) 1041-1054, ISSN 1867-2450
DOI: 10.1007/s12551-020-00717-1

Formal Semantics and Verification of Network-Based Biocomputation Circuits

Author(s): Michelle Aluf-Medina, Till Korten, Avraham Raviv, Dan V. Nicolau, Hillel Kugler
Published in: Verification, Model Checking, and Abstract Interpretation - 22nd International Conference, VMCAI 2021, Copenhagen, Denmark, January 17–19, 2021, Proceedings, Issue 12597, 2021, Page(s) 464-485
DOI: 10.1007/978-3-030-67067-2_21