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

Risultati finali

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.

Roadmap for NBC

The finalized roadmap for networkbased biocomputation that coordinating research efforts of the growing stakeholder community and charting the remaining path to commercial application of NBC

Report on the establishment of a stakeholder community

The report will account for our stakeholder workshops format attendees and outcomes the overall structure and reach of the interdisciplinary community training periods beneficiaries contents outcomes the Community Portal and the outcome of the Bio4Comp awards

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.

Release of open source version of software package for simulating NBC

The software will be made available to the community through our Community Portal.

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.

Pubblicazioni

Molecular motor-driven filament transport across three-dimensional, polymeric micro-junctions

Autori: Cordula Reuther, Sönke Steenhusen, Christoph Robert Meinecke, Pradheebha Surendiran, Aseem Salhotra, Frida W Lindberg, Alf Månsson, Heiner Linke and Stefan Diez
Pubblicato in: New Journal of Physics, Numero 23, 2021, Pagina/e 125002, ISSN 1367-2630
Editore: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac39b4

As good as it gets: a scaling comparison of DNA computing, network biocomputing, and electronic computing approaches to an NP-complete problem

Autori: Ayyappasamy Sudalaiyadum Perumal, Zihao Wang, Giulia Ippoliti, Falco C M J M van Delft, Lila Kari and Dan V Nicolau
Pubblicato in: New Journal of Physics, Numero 23, 2021, Pagina/e 125001, ISSN 1367-2630
Editore: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac3883

Self-assembly of semiconductor quantum dots with porphyrin chromophores: Energy relaxation processes and biomedical applications

Autori: Eduard Zenkevich, Thomas Blaudeck, Vladimir Sheinin, Olga Kulikova, Oleksandr Selyshchev, Volodymyr Dzhagan, Oscar Koifman, Christian von Borczyskowski, Dietrich R.T. Zahn
Pubblicato in: Journal of Molecular Structure, Numero 1244, 2021, Pagina/e 131239, ISSN 0022-2860
Editore: Elsevier BV
DOI: 10.1016/j.molstruc.2021.131239

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

Autori: Venukumar Vemula, Tamás Huber, Marko Ušaj, Beáta Bugyi, Alf Månsson
Pubblicato in: Journal of Biological Chemistry, Numero 296, 2021, Pagina/e 100181, ISSN 0021-9258
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.ra120.015863

Formal Analysis of Network Motifs Links Structure to Function in Biological Programs

Autori: Sara-Jane Dunn; Hillel Kugler; Boyan Yordanov
Pubblicato in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Numero vol. 18, no. 1, 2021, Pagina/e 261-271, ISSN 1557-9964
Editore: IEEE COMPUTER SOC
DOI: 10.1109/tcbb.2019.2948157

Prolonged function and optimization of actomyosin motility for upscaled network-based biocomputation

Autori: Aseem Salhotra, Jingyuan Zhu, Pradheebha Surendiran, Christoph Robert Meinecke, Roman Lyttleton, Marko Ušaj, Frida W Lindberg, Marlene Norrby, Heiner Linke and Alf Månsson
Pubblicato in: New Journal of Physics, Numero 23, 2021, Pagina/e 085005, ISSN 1367-2630
Editore: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac1809

Physical requirements for scaling up network-based biocomputation

Autori: Jingyuan Zhu, Till Korten, Hillel Kugler, Falco van Delft, Alf Månsson, Danny Reuter, Stefan Diez and Heiner Linke
Pubblicato in: New Journal of Physics, Numero 23, 2021, Pagina/e 105004, ISSN 1367-2630
Editore: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac2a5d

Design and fabrication of networks for bacterial computing

Autori: Falco C M J M van Delft, Ayyappasamy Sudalaiyadum Perumal, Anja van Langen-Suurling, Charles de Boer, Ondřej Kašpar, Viola Tokárová, Frank W A Dirne and Dan V Nicolau
Pubblicato in: New Journal of Physics, Numero 23, 2021, Pagina/e 085009, ISSN 1367-2630
Editore: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac1d38

Bridging the gap: Perspectives of nanofabrication technologies for application-oriented research

Autori: Mario Baum, Christoph Meinecke, Thomas Blaudeck, Christian Helke, Danny Reuter, Karla Hiller, Sascha Hermann, Stefan E. Schulz, and Harald Kuhn
Pubblicato in: Journal of Vacuum Science & Technology B, Numero 39, 2021, Pagina/e 062805, ISSN 2166-2746
Editore: A V S AMER INST PHYSICS
DOI: 10.1116/6.0001299

Solving the 3‐Satisfiability Problem Using Network‐Based Biocomputation

Autori: Jingyuan Zhu; Aseem Salhotra; Christoph Robert Meinecke; Pradheebha Surendiran; Roman Lyttleton; Danny Reuter; Hillel Kugler; Stefan Diez; Alf Månsson; Heiner Linke; Till Korten
Pubblicato in: Adv. Intell. Syst., Numero 4, 2022, Pagina/e 2200202, ISSN 2640-4567
Editore: Wiley-VCH GmbH
DOI: 10.1002/aisy.202200202

Regeneration of Assembled, Molecular-Motor-Based Bionanodevices

Autori: Mohammad A. Rahman, Cordula Reuther, Frida W. Lindberg, Martina Mengoni, Aseem Salhotra, Georg Heldt, Heiner Linke, Stefan Diez, Alf Månsson
Pubblicato in: Nano Letters, Numero 19/10, 2019, Pagina/e 7155-7163, ISSN 1530-6984
Editore: American Chemical Society
DOI: 10.1021/acs.nanolett.9b02738

Fundamental energy cost of finite-time parallelizable computing

Autori: Michael Konopik; Till Korten; Eric Lutz; Heiner Linke
Pubblicato in: Nat Commun, Numero 14, 2023, Pagina/e 447, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-36020-2

Solving the subset sum problem with a nonideal biological computer

Autori: Michael Konopik, Till Korten, Heiner Linke and Eric Lutz
Pubblicato in: New Journal of Physics, Numero 23, 2021, Pagina/e 095007, ISSN 1367-2630
Editore: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac2005

Roadmap for network-based biocomputation

Autori: Falco C M J M van Delft, Alf Månsson, Hillel Kugler, Till Korten, Cordula Reuther, Jingyuan Zhu, Roman Lyttleton, Thomas Blaudeck, Christoph Robert Meinecke, Danny Reuter, Stefan Diez and Heiner Linke
Pubblicato in: Nano Futures, Numero 6, 2022, Pagina/e 032002, ISSN 2399-1984
Editore: IOP Publishing
DOI: 10.1088/2399-1984/ac7d81

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

Autori: Annalisa Occhipinti, Youssef Hamadi, Hillel Kugler, Christoph Wintersteiger, Boyan Yordanov, Claudio Angione
Pubblicato in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020, Pagina/e 1-1, ISSN 1545-5963
Editore: IEEE Computer Society
DOI: 10.1109/tcbb.2020.2973386

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

Autori: Saroj Kumar, Alf Mansson
Pubblicato in: Biotechnology Advances, Numero 35/7, 2017, Pagina/e 867-888, ISSN 0734-9750
Editore: Elsevier BV
DOI: 10.1016/j.biotechadv.2017.08.002

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

Autori: Samata Chaudhuri, Till Korten, Slobodanka Korten, Gloria Milani, Tobia Lana, Geertruy te Kronnie, Stefan Diez
Pubblicato in: Nano Letters, Numero 18/1, 2017, Pagina/e 117-123, ISSN 1530-6984
Editore: American Chemical Society
DOI: 10.1021/acs.nanolett.7b03619

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

Autori: Samata Chaudhuri, Till Korten, Stefan Diez
Pubblicato in: Bioconjugate Chemistry, Numero 28/4, 2017, Pagina/e 918-922, ISSN 1043-1802
Editore: American Chemical Society
DOI: 10.1021/acs.bioconjchem.7b00118

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

Autori: Cordula Reuther, Matthäus Mittasch, Sundar R. Naganathan, Stephan W. Grill, Stefan Diez
Pubblicato in: Nano Letters, Numero 17/9, 2017, Pagina/e 5699-5705, ISSN 1530-6984
Editore: American Chemical Society
DOI: 10.1021/acs.nanolett.7b02606

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

Autori: Damiano Verardo, Frida W. Lindberg, Nicklas Anttu, Cassandra S. Niman, Mercy Lard, Aleksandra P. Dabkowska, Tommy Nylander, Alf Månsson, Christelle N. Prinz, Heiner Linke
Pubblicato in: Nano Letters, Numero 18/8, 2018, Pagina/e 4796-4802, ISSN 1530-6984
Editore: American Chemical Society
DOI: 10.1021/acs.nanolett.8b01360

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

Autori: Frida W. Lindberg, Marlene Norrby, Mohammad A. Rahman, Aseem Salhotra, Hideyo Takatsuki, Sören Jeppesen, Heiner Linke, Alf Månsson
Pubblicato in: Langmuir, Numero 34/30, 2018, Pagina/e 8777-8784, ISSN 0743-7463
Editore: American Chemical Society
DOI: 10.1021/acs.langmuir.8b01415

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

Autori: Till Korten, Elena Tavkin, Lara Scharrel, Vandana Singh Kushwaha, Stefan Diez
Pubblicato in: Lab on a Chip, Numero 18/20, 2018, Pagina/e 3196-3206, ISSN 1473-0197
Editore: Royal Society of Chemistry
DOI: 10.1039/c8lc00547h

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

Autori: Mohammad A. Rahman, Marko Ušaj, Dilson E. Rassier, Alf Månsson
Pubblicato in: Biophysical Journal, Numero 115/2, 2018, Pagina/e 386-397, ISSN 0006-3495
Editore: Biophysical Society
DOI: 10.1016/j.bpj.2018.05.037

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

Autori: Alf Månsson, Marko Ušaj, Luisa Moretto, Dilson Rassier
Pubblicato in: International Journal of Molecular Sciences, Numero 19/7, 2018, Pagina/e 1863, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms19071863

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

Autori: Frida W Lindberg, Till Korten, Anette Löfstrand, Mohammad A Rahman, Mariusz Graczyk, Alf Månsson, Heiner Linke, Ivan Maximov
Pubblicato in: Materials Research Express, Numero 6/2, 2019, Pagina/e 025057, ISSN 2053-1591
Editore: Institute of Physics Publishing
DOI: 10.1088/2053-1591/aaed10

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

Autori: Mohammad A. Rahman, Aseem Salhotra, Alf Månsson
Pubblicato in: Journal of Muscle Research and Cell Motility, Numero 39/5-6, 2018, Pagina/e 175-187, ISSN 0142-4319
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10974-019-09505-1

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

Autori: Mercy Lard, Heiner Linke, Christelle N Prinz
Pubblicato in: Nanotechnology, Numero 30/21, 2019, Pagina/e 214003, ISSN 0957-4484
Editore: Institute of Physics Publishing
DOI: 10.1088/1361-6528/ab0326

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

Autori: 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
Pubblicato in: Interface Focus, Numero 8/6, 2018, Pagina/e 20180034, ISSN 2042-8898
Editore: Royal Society Publishing
DOI: 10.1098/rsfs.2018.0034

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

Autori: Marko Ušaj, Luisa Moretto, Venukumar Vemula, Aseem Salhotra, Alf Månsson
Pubblicato in: Communications Biology, Numero 4/1, 2021, ISSN 2399-3642
Editore: Nature Research
DOI: 10.1038/s42003-020-01574-0

Comparison of actin- and microtubule-based motility systems for application in functional nanodevices

Autori: Cordula Reuther, Rachele Catalano, Aseem Salhotra, Venukumar Vemula, Till Korten, Stefan Diez and Alf Månsson
Pubblicato in: New Journal of Physics, Numero 23, 2021, Pagina/e 075007, ISSN 1367-2630
Editore: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac10ce

Macroheterocyclic Compounds - a Key Building Block in New Functional Materials and Molecular Devices

Autori: Koifman O.I., Ageeva T.A., Beletskaya I.P., Averin A.D., Yakushev A.A., Tomilova L.G.,.Dubinina T.V., Tsivadze A.Yu., Gorbunova Yu.G., Martynov A.G., Konarev D.V., Khasanov S.S., Lyubovskaya R.N., Lomova T.N., Korolev V.V., Zenkevich E.I., Blaudeck T. , Ch. von Borczyskowski, Zahn D.R.T., Mironov A.F., Bragina N.A., Ezhov A.V., Zhdanova K.A., Stuzhin P.A., Pakhomov G.L., Rusakova N.V., Semenishyn
Pubblicato in: Macroheterocycles, Numero 13, 2020, Pagina/e 311-467, ISSN 1998-9539
Editore: Ivanovo State University of Chemistry and Technology
DOI: 10.6060/mhc200814k

Modeling the C. elegans germline stem cell genetic network using automated reasoning

Autori: Ani Amar, E. Jane Albert Hubbard, Hillel Kugler
Pubblicato in: BioSystems, Numero 217, 2022, Pagina/e 104672, ISSN 0303-2647
Editore: Elsevier BV
DOI: 10.1016/j.biosystems.2022.104672

Multiplication of Motor-Driven Microtubules for Nanotechnological Applications

Autori: Cordula Reuther, Paula Santos-Otte, Rahul Grover, Georg Heldt, Günther Woehlke, and Stefan Diez
Pubblicato in: Nano Letters, Numero 22, 3, 2022, Pagina/e 926–934, ISSN 1530-6992
Editore: ACS
DOI: 10.1021/acs.nanolett.1c03619

Solving Exact Cover Instances with Molecular-Motor-Powered Network-Based Biocomputation

Autori: Pradheebha Surendiran, Christoph Robert Meinecke, Aseem Salhotra, Georg Heldt, Jingyuan Zhu, Alf Månsson, Stefan Diez, Danny Reuter, Hillel Kugler, Heiner Linke, and Till Korten
Pubblicato in: ACS Nanoscience Au, Numero XXXX, 2022, Pagina/e XXXX, ISSN 2694-2496
Editore: ACS Publications
DOI: 10.1021/acsnanoscienceau.2c00013

Design of network-based biocomputation circuits for the exact cover problem

Autori: Till Korten, Stefan Diez, Heiner Linke, Dan V Nicolau Jr and Hillel Kugler
Pubblicato in: New Journal of Physics, Numero 23, 2021, Pagina/e 085004, ISSN 1367-2630
Editore: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac175d

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

Autori: Heiner Linke, Birte Höcker, Ken’ya Furuta, Nancy R. Forde, Paul M. G. Curmi
Pubblicato in: Biophysical Reviews, Numero 12/4, 2020, Pagina/e 1041-1054, ISSN 1867-2450
Editore: Springer Verlag
DOI: 10.1007/s12551-020-00717-1

The potential of myosin and actin in nanobiotechnology

Autori: Alf Månsson
Pubblicato in: J Cell Sci, Numero 136 (5), 2023, Pagina/e jcs261025, ISSN 1477-9137
Editore: The Company of Biologists
DOI: 10.1242/jcs.261025

Prospects for single-molecule electrostatic detection in molecular motor gliding motility assays

Autori: M Sanchez Miranda, R Lyttleton, P H Siu, S Diez, H Linke and A P Micolich
Pubblicato in: New Journal of Physics, Numero 23, 2021, Pagina/e 065003, ISSN 1367-2630
Editore: Institute of Physics Publishing
DOI: 10.1088/1367-2630/abfdf5

Low-Temperature Parylene-Based Adhesive Bonding Technology for 150 and 200 mm Wafers for Fully Biocompatible and Highly Reliable Microsystems

Autori: Franz Selbmann; Mario Baum; Christoph Meinecke; Maik Wiemer; Harald Kuhn; Yvonne Joseph
Pubblicato in: ECS Journal of Solid State Science and Technology, Numero 10, 2021, Pagina/e 074010, ISSN 2162-8777
Editore: IOP Publishing Limited
DOI: 10.1149/2162-8777/ac12b6

Formal Semantics and Verification of Network-Based Biocomputation Circuits

Autori: Michelle Aluf-Medina, Till Korten, Avraham Raviv, Dan V. Nicolau, Hillel Kugler
Pubblicato in: Verification, Model Checking, and Abstract Interpretation - 22nd International Conference, VMCAI 2021, Copenhagen, Denmark, January 17–19, 2021, Proceedings, Numero 12597, 2021, Pagina/e 464-485, ISBN 978-3-030-67066-5
Editore: Springer International Publishing
DOI: 10.1007/978-3-030-67067-2_21

Biocomputation Using Molecular Agents Moving in Microfluidic Channel Networks: An Alternative Platform for Information Technology.

Autori: Thomas Blaudeck, Christoph R. Meinecke, Danny Reuter, Sönke Steenhusen, Archa Jain, Sascha Hermann, Stefan E. Schulz, Eduard I. Zenkevich, Till Korten & Heiner Linke
Pubblicato in: In: Kravets, A.G., Bolshakov, A.A., Shcherbakov, M. (eds) Cyber-Physical Systems: Intelligent Models and Algorithms. Studies in Systems, Decision and Control, Springer, Cham., Numero vol 417., 2022, ISBN 978-3-030-95116-0
Editore: Springer, Cham
DOI: 10.1007/978-3-030-95116-0_2

Solving the 3-SAT problem using network-based biocomputation

Autori: Jingyuan Zhu, Aseem Salhotra, Christoph Robert Meinecke, Pradheebha Surendiran, Roman Lyttleton, Danny Reuter, Hillel Kugler, Stefan Diez, Alf Månsson, Heiner Linke, Till Korten
Pubblicato in: arXiv:2203.17154 [physics.bio-ph], 2022
Editore: arxiv
DOI: 10.48550/arxiv.2203.17154

TEMPO: Thermal-Efficient Management of Power in High-Throughput Network Switches

Autori: Tom Munk; Hillel Kugler; Ofir Maori; Adam Teman
Pubblicato in: 2019 International Symposium on VLSI Design, Automation and Test (VLSI-DAT), 2019, Pagina/e 1-4, ISBN 978-1-7281-0655-7
Editore: IEEE
DOI: 10.1109/vlsi-dat.2019.8741684

Approach to combine electron-beam lithography and two-photon polymerization for enhanced nano-channels in network-based biocomputation devices

Autori: G. Heldt, Ch. Meinecke, S. Steenhusen, T. Korten, M. Groß, G. Domann, F. Lindberg, D. Reuter, St. Diez, H. Linke, St. E. Schulz
Pubblicato in: Proceedings Volume 10775, 34th European Mask and Lithography Conference, Numero Vol. 10775, 2018, Pagina/e 1077517, ISSN 1996-756X
Editore: SPIE-INT SOC OPTICAL ENGINEERING
DOI: 10.1117/12.2326598

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