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

Rezultaty

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.

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.

Publikacje

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

Autorzy: Cordula Reuther, Sönke Steenhusen, Christoph Robert Meinecke, Pradheebha Surendiran, Aseem Salhotra, Frida W Lindberg, Alf Månsson, Heiner Linke and Stefan Diez
Opublikowane w: New Journal of Physics, Numer 23, 2021, Strona(/y) 125002, ISSN 1367-2630
Wydawca: 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

Autorzy: Ayyappasamy Sudalaiyadum Perumal, Zihao Wang, Giulia Ippoliti, Falco C M J M van Delft, Lila Kari and Dan V Nicolau
Opublikowane w: New Journal of Physics, Numer 23, 2021, Strona(/y) 125001, ISSN 1367-2630
Wydawca: 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

Autorzy: Eduard Zenkevich, Thomas Blaudeck, Vladimir Sheinin, Olga Kulikova, Oleksandr Selyshchev, Volodymyr Dzhagan, Oscar Koifman, Christian von Borczyskowski, Dietrich R.T. Zahn
Opublikowane w: Journal of Molecular Structure, Numer 1244, 2021, Strona(/y) 131239, ISSN 0022-2860
Wydawca: Elsevier BV
DOI: 10.1016/j.molstruc.2021.131239

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

Autorzy: Venukumar Vemula, Tamás Huber, Marko Ušaj, Beáta Bugyi, Alf Månsson
Opublikowane w: Journal of Biological Chemistry, Numer 296, 2021, Strona(/y) 100181, ISSN 0021-9258
Wydawca: 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

Autorzy: Sara-Jane Dunn; Hillel Kugler; Boyan Yordanov
Opublikowane w: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Numer vol. 18, no. 1, 2021, Strona(/y) 261-271, ISSN 1557-9964
Wydawca: IEEE COMPUTER SOC
DOI: 10.1109/tcbb.2019.2948157

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

Autorzy: Aseem Salhotra, Jingyuan Zhu, Pradheebha Surendiran, Christoph Robert Meinecke, Roman Lyttleton, Marko Ušaj, Frida W Lindberg, Marlene Norrby, Heiner Linke and Alf Månsson
Opublikowane w: New Journal of Physics, Numer 23, 2021, Strona(/y) 085005, ISSN 1367-2630
Wydawca: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac1809

Physical requirements for scaling up network-based biocomputation

Autorzy: Jingyuan Zhu, Till Korten, Hillel Kugler, Falco van Delft, Alf Månsson, Danny Reuter, Stefan Diez and Heiner Linke
Opublikowane w: New Journal of Physics, Numer 23, 2021, Strona(/y) 105004, ISSN 1367-2630
Wydawca: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac2a5d

Design and fabrication of networks for bacterial computing

Autorzy: 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
Opublikowane w: New Journal of Physics, Numer 23, 2021, Strona(/y) 085009, ISSN 1367-2630
Wydawca: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac1d38

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

Autorzy: Mario Baum, Christoph Meinecke, Thomas Blaudeck, Christian Helke, Danny Reuter, Karla Hiller, Sascha Hermann, Stefan E. Schulz, and Harald Kuhn
Opublikowane w: Journal of Vacuum Science & Technology B, Numer 39, 2021, Strona(/y) 062805, ISSN 2166-2746
Wydawca: A V S AMER INST PHYSICS
DOI: 10.1116/6.0001299

Solving the 3‐Satisfiability Problem Using Network‐Based Biocomputation

Autorzy: Jingyuan Zhu; Aseem Salhotra; Christoph Robert Meinecke; Pradheebha Surendiran; Roman Lyttleton; Danny Reuter; Hillel Kugler; Stefan Diez; Alf Månsson; Heiner Linke; Till Korten
Opublikowane w: Adv. Intell. Syst., Numer 4, 2022, Strona(/y) 2200202, ISSN 2640-4567
Wydawca: Wiley-VCH GmbH
DOI: 10.1002/aisy.202200202

Regeneration of Assembled, Molecular-Motor-Based Bionanodevices

Autorzy: Mohammad A. Rahman, Cordula Reuther, Frida W. Lindberg, Martina Mengoni, Aseem Salhotra, Georg Heldt, Heiner Linke, Stefan Diez, Alf Månsson
Opublikowane w: Nano Letters, Numer 19/10, 2019, Strona(/y) 7155-7163, ISSN 1530-6984
Wydawca: American Chemical Society
DOI: 10.1021/acs.nanolett.9b02738

Fundamental energy cost of finite-time parallelizable computing

Autorzy: Michael Konopik; Till Korten; Eric Lutz; Heiner Linke
Opublikowane w: Nat Commun, Numer 14, 2023, Strona(/y) 447, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-023-36020-2

Solving the subset sum problem with a nonideal biological computer

Autorzy: Michael Konopik, Till Korten, Heiner Linke and Eric Lutz
Opublikowane w: New Journal of Physics, Numer 23, 2021, Strona(/y) 095007, ISSN 1367-2630
Wydawca: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac2005

Roadmap for network-based biocomputation

Autorzy: 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
Opublikowane w: Nano Futures, Numer 6, 2022, Strona(/y) 032002, ISSN 2399-1984
Wydawca: IOP Publishing
DOI: 10.1088/2399-1984/ac7d81

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

Autorzy: Annalisa Occhipinti, Youssef Hamadi, Hillel Kugler, Christoph Wintersteiger, Boyan Yordanov, Claudio Angione
Opublikowane w: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020, Strona(/y) 1-1, ISSN 1545-5963
Wydawca: IEEE Computer Society
DOI: 10.1109/tcbb.2020.2973386

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

Autorzy: Saroj Kumar, Alf Mansson
Opublikowane w: Biotechnology Advances, Numer 35/7, 2017, Strona(/y) 867-888, ISSN 0734-9750
Wydawca: Elsevier BV
DOI: 10.1016/j.biotechadv.2017.08.002

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

Autorzy: Samata Chaudhuri, Till Korten, Slobodanka Korten, Gloria Milani, Tobia Lana, Geertruy te Kronnie, Stefan Diez
Opublikowane w: Nano Letters, Numer 18/1, 2017, Strona(/y) 117-123, ISSN 1530-6984
Wydawca: American Chemical Society
DOI: 10.1021/acs.nanolett.7b03619

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

Autorzy: Samata Chaudhuri, Till Korten, Stefan Diez
Opublikowane w: Bioconjugate Chemistry, Numer 28/4, 2017, Strona(/y) 918-922, ISSN 1043-1802
Wydawca: American Chemical Society
DOI: 10.1021/acs.bioconjchem.7b00118

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

Autorzy: Cordula Reuther, Matthäus Mittasch, Sundar R. Naganathan, Stephan W. Grill, Stefan Diez
Opublikowane w: Nano Letters, Numer 17/9, 2017, Strona(/y) 5699-5705, ISSN 1530-6984
Wydawca: American Chemical Society
DOI: 10.1021/acs.nanolett.7b02606

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

Autorzy: Damiano Verardo, Frida W. Lindberg, Nicklas Anttu, Cassandra S. Niman, Mercy Lard, Aleksandra P. Dabkowska, Tommy Nylander, Alf Månsson, Christelle N. Prinz, Heiner Linke
Opublikowane w: Nano Letters, Numer 18/8, 2018, Strona(/y) 4796-4802, ISSN 1530-6984
Wydawca: American Chemical Society
DOI: 10.1021/acs.nanolett.8b01360

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

Autorzy: Frida W. Lindberg, Marlene Norrby, Mohammad A. Rahman, Aseem Salhotra, Hideyo Takatsuki, Sören Jeppesen, Heiner Linke, Alf Månsson
Opublikowane w: Langmuir, Numer 34/30, 2018, Strona(/y) 8777-8784, ISSN 0743-7463
Wydawca: American Chemical Society
DOI: 10.1021/acs.langmuir.8b01415

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

Autorzy: Till Korten, Elena Tavkin, Lara Scharrel, Vandana Singh Kushwaha, Stefan Diez
Opublikowane w: Lab on a Chip, Numer 18/20, 2018, Strona(/y) 3196-3206, ISSN 1473-0197
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c8lc00547h

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

Autorzy: Mohammad A. Rahman, Marko Ušaj, Dilson E. Rassier, Alf Månsson
Opublikowane w: Biophysical Journal, Numer 115/2, 2018, Strona(/y) 386-397, ISSN 0006-3495
Wydawca: Biophysical Society
DOI: 10.1016/j.bpj.2018.05.037

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

Autorzy: Alf Månsson, Marko Ušaj, Luisa Moretto, Dilson Rassier
Opublikowane w: International Journal of Molecular Sciences, Numer 19/7, 2018, Strona(/y) 1863, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms19071863

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

Autorzy: Frida W Lindberg, Till Korten, Anette Löfstrand, Mohammad A Rahman, Mariusz Graczyk, Alf Månsson, Heiner Linke, Ivan Maximov
Opublikowane w: Materials Research Express, Numer 6/2, 2019, Strona(/y) 025057, ISSN 2053-1591
Wydawca: 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

Autorzy: Mohammad A. Rahman, Aseem Salhotra, Alf Månsson
Opublikowane w: Journal of Muscle Research and Cell Motility, Numer 39/5-6, 2018, Strona(/y) 175-187, ISSN 0142-4319
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10974-019-09505-1

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

Autorzy: Mercy Lard, Heiner Linke, Christelle N Prinz
Opublikowane w: Nanotechnology, Numer 30/21, 2019, Strona(/y) 214003, ISSN 0957-4484
Wydawca: 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

Autorzy: 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
Opublikowane w: Interface Focus, Numer 8/6, 2018, Strona(/y) 20180034, ISSN 2042-8898
Wydawca: Royal Society Publishing
DOI: 10.1098/rsfs.2018.0034

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

Autorzy: Marko Ušaj, Luisa Moretto, Venukumar Vemula, Aseem Salhotra, Alf Månsson
Opublikowane w: Communications Biology, Numer 4/1, 2021, ISSN 2399-3642
Wydawca: Nature Research
DOI: 10.1038/s42003-020-01574-0

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

Autorzy: Cordula Reuther, Rachele Catalano, Aseem Salhotra, Venukumar Vemula, Till Korten, Stefan Diez and Alf Månsson
Opublikowane w: New Journal of Physics, Numer 23, 2021, Strona(/y) 075007, ISSN 1367-2630
Wydawca: Institute of Physics Publishing
DOI: 10.1088/1367-2630/ac10ce

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

Autorzy: 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
Opublikowane w: Macroheterocycles, Numer 13, 2020, Strona(/y) 311-467, ISSN 1998-9539
Wydawca: Ivanovo State University of Chemistry and Technology
DOI: 10.6060/mhc200814k

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

Autorzy: Ani Amar, E. Jane Albert Hubbard, Hillel Kugler
Opublikowane w: BioSystems, Numer 217, 2022, Strona(/y) 104672, ISSN 0303-2647
Wydawca: Elsevier BV
DOI: 10.1016/j.biosystems.2022.104672

Multiplication of Motor-Driven Microtubules for Nanotechnological Applications

Autorzy: Cordula Reuther, Paula Santos-Otte, Rahul Grover, Georg Heldt, Günther Woehlke, and Stefan Diez
Opublikowane w: Nano Letters, Numer 22, 3, 2022, Strona(/y) 926–934, ISSN 1530-6992
Wydawca: ACS
DOI: 10.1021/acs.nanolett.1c03619

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

Autorzy: Pradheebha Surendiran, Christoph Robert Meinecke, Aseem Salhotra, Georg Heldt, Jingyuan Zhu, Alf Månsson, Stefan Diez, Danny Reuter, Hillel Kugler, Heiner Linke, and Till Korten
Opublikowane w: ACS Nanoscience Au, Numer XXXX, 2022, Strona(/y) XXXX, ISSN 2694-2496
Wydawca: ACS Publications
DOI: 10.1021/acsnanoscienceau.2c00013

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

Autorzy: Till Korten, Stefan Diez, Heiner Linke, Dan V Nicolau Jr and Hillel Kugler
Opublikowane w: New Journal of Physics, Numer 23, 2021, Strona(/y) 085004, ISSN 1367-2630
Wydawca: 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

Autorzy: Heiner Linke, Birte Höcker, Ken’ya Furuta, Nancy R. Forde, Paul M. G. Curmi
Opublikowane w: Biophysical Reviews, Numer 12/4, 2020, Strona(/y) 1041-1054, ISSN 1867-2450
Wydawca: Springer Verlag
DOI: 10.1007/s12551-020-00717-1

The potential of myosin and actin in nanobiotechnology

Autorzy: Alf Månsson
Opublikowane w: J Cell Sci, Numer 136 (5), 2023, Strona(/y) jcs261025, ISSN 1477-9137
Wydawca: The Company of Biologists
DOI: 10.1242/jcs.261025

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

Autorzy: M Sanchez Miranda, R Lyttleton, P H Siu, S Diez, H Linke and A P Micolich
Opublikowane w: New Journal of Physics, Numer 23, 2021, Strona(/y) 065003, ISSN 1367-2630
Wydawca: 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

Autorzy: Franz Selbmann; Mario Baum; Christoph Meinecke; Maik Wiemer; Harald Kuhn; Yvonne Joseph
Opublikowane w: ECS Journal of Solid State Science and Technology, Numer 10, 2021, Strona(/y) 074010, ISSN 2162-8777
Wydawca: IOP Publishing Limited
DOI: 10.1149/2162-8777/ac12b6

Formal Semantics and Verification of Network-Based Biocomputation Circuits

Autorzy: Michelle Aluf-Medina, Till Korten, Avraham Raviv, Dan V. Nicolau, Hillel Kugler
Opublikowane w: Verification, Model Checking, and Abstract Interpretation - 22nd International Conference, VMCAI 2021, Copenhagen, Denmark, January 17–19, 2021, Proceedings, Numer 12597, 2021, Strona(/y) 464-485, ISBN 978-3-030-67066-5
Wydawca: 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.

Autorzy: Thomas Blaudeck, Christoph R. Meinecke, Danny Reuter, Sönke Steenhusen, Archa Jain, Sascha Hermann, Stefan E. Schulz, Eduard I. Zenkevich, Till Korten & Heiner Linke
Opublikowane w: 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., Numer vol 417., 2022, ISBN 978-3-030-95116-0
Wydawca: Springer, Cham
DOI: 10.1007/978-3-030-95116-0_2

Solving the 3-SAT problem using network-based biocomputation

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

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

Autorzy: Tom Munk; Hillel Kugler; Ofir Maori; Adam Teman
Opublikowane w: 2019 International Symposium on VLSI Design, Automation and Test (VLSI-DAT), 2019, Strona(/y) 1-4, ISBN 978-1-7281-0655-7
Wydawca: 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

Autorzy: G. Heldt, Ch. Meinecke, S. Steenhusen, T. Korten, M. Groß, G. Domann, F. Lindberg, D. Reuter, St. Diez, H. Linke, St. E. Schulz
Opublikowane w: Proceedings Volume 10775, 34th European Mask and Lithography Conference, Numer Vol. 10775, 2018, Strona(/y) 1077517, ISSN 1996-756X
Wydawca: SPIE-INT SOC OPTICAL ENGINEERING
DOI: 10.1117/12.2326598

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