Project Management during the Period (Months 13-24) · where all the partners produced a...

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Project Management during the Period (Months 13-24)

Publications (or work in progress), events, activities

There has been no problem regarding the management of the activities for the consortium.

The coordinator has been monitoring the activities progress and the project objectives and that the FOCUS budget is used in an optimal way in respect to the achievement of the objectives/tasks of the project.

Most of the Deliverables and Milestones expected so far have been achieved and there is a slight delay of a couple of months related to deliverables D7.3 and D7.5 as explained in the Scientific Report (WP7) and related to D8.1 mainly due to the recent contributions arrived that did not leave sufficient time to update the website by month 26. It will be done over the next weeks.

There was also a delay in completing Task 2.2 due to an unexpected low reactivity of the functional groups initially considered, which was based on recent publications. In order to overcome this difficulty IBEC decided to widen their choice of functional groups to be tested, which forced us to redesign the synthetic strategy using a convergent approach. This measure was fruitful and only added a 6-month delay in Deliverable 2.2, which was successfully completed.

Regarding the Milestones, also in this case most of them have been achieved and a couple are experiencing a slight delay of one or two months.

The partners have been in constant contact since before the beginning of the project and they all know each other quite well now.

There are many collaborations taking place as demonstrated also by the travels indicated in the Resources tables, visits to and from the institutions within the consortium. There are obviously further plans for the future year that involve more exchanges of knowledge and techniques.

The first review meeting took place on March 12th 2012 at the EC Headquarters in Brussels. The Consortium presented the First Year’s Results and the Reviewers gave the following suggestions in order to keep the project running on schedule: they recommended

1 - the organization of the expected Workshop 2 - deliverables The Consortium needs to keep focused and send good quality deliverables, always on the expected deadline. 3- decide on proposed options and stop evaluating different ways to proceed. Make decisions. The Consortium has followed the suggestions and 1 – the workshop was organized and took place in Venice on October 13th -14th 2013. The event was rather successful. The reason why we chose the Istituto Veneto di Scienze Lettere e Arti as the ideal location was also related to the fact that – apart from Venice being a very attractive spot for anyone, the Istituto was the venue for another Workshop that took place two days earlier (October 11th and 12th) “The first NEMB Venice workshop on Cancer Nanotechnology” http://nemb2012.cism.it/ which had some speakers and participants in common with our FOCUS event.

The publication of the FOCUS Workshop Proceedings on a book entitled "Novel approaches for Single Molecule Activation and Detection" is now taking shape. The book will be part of the series “Advances in Atom and Single Molecule Machines” edited by Christian Joachim and published by Springer. Partner IIT is currently collecting titles and the authors’ list for each chapter.

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2- The Deliverables: The Consortium had 19 Deliverables to meet for this Period and 17 Milestones. Most of them have been reached and a few are still in progress, but, considering the status of the project, activities are proceeding rather successfully. 3 – We decided to concentrate our effort to produce narrow spots of lights using tapered optical fibers and matrices of nanoholes. The Second Annual Meeting took place at the Municon Centre in Munich airport on February 20th 2013 where all the partners produced a presentation of their progress over the last months.

SISSA organized the meeting and the catering. There was no need for accommodation to be arranged since the choice for the location was strategic in this sense: have a full day and fruitful meeting allowing everybody to be back in their lab already the following day.

Regarding the website, most of the information referring to the project objectives is still kept in a private section, always due to IP issues related to some of the objectives. As mentioned last year, the Consortium is trying to solve this problem and in these next months it will certainly move most of the contents from the private to the public section. There is still a high hope for patents that might be damaged by the fact that too much information is put on the web.

The coordinator uses Netscience to manage the deadlines of the project and to update the website.

FOCUS has the logo that is being used in public occasions and that gives an identity to the project.

Also the two templates created for powerpoint presentations and posters or other dissemination material are being used by the Consortium partners.

Deviation requests:

In month 22, METU’s e-beam lithography instrument in the central laboratories has undergone a break-down due to a necessary building reinforcement construction which left the instrument in a sub-optimally operable condition. They have therefore experienced a 2 months set-back in fabrication part of the tasks in this period. The instrument has come back into an operable condition after 2 months on the 25th month. Because of this reason METU would like to have the review committee’s agreement on rescheduling the due date of the follow-up task T9.2 and its deliverable D9.2 from month 34 to month 36 of the project.

In addition, they have made visits as long as one month to CBM to perform experiments in WP9. Another similar visit might be necessary for the remaining WP9 and WP3 tasks. Because of these planned visits METU are short in travel budget to enable further stays at other partners’ locations. So they ask for permission for an adjustment of €3000 shift to the travel budget from the consumables budget.

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Publications Conferences, Meetings and other events

The main event for the Consortium has certainly been the Workshop in Venice:

INTERNATIONAL WORKSHOP

SINGLE MOLECULE ACTIVATION AND DETECTION

IN MOLECULAR DEVICES

Istituto Veneto di Scienze, Lettere ed Arti

Palazzo Franchetti, Sala del Portego

Venezia (Italy), October 13-14, 2012

Organizing Committee: V. Torre, E. Di Fabrizio, F. Benfenati

Sponsored by EU FET Proactive 7

Proceedings published by Springer

TOPICS: Session 1: SINGLE MOLECULE TECHNOLOGIES IN NEUROSCIENCE Session 2: SINGLE MOLECULE ACTIVATION AND DETECTION IN MOLECULAR DEVICES Session 3: NEW FRONTIERS IN SUPERRESOLUTION TECHNOLOGIES

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Invited Speakers (in alphabetical order): Christian Amatore (Paris, France) Andrea Barberis (Genoa, Italy) Achim Hartshuh (Munchen, Germany) Anne Marie Pucci (Heidelberg, Germany) Daniel Choquet (Bordeaux, France) Alberto Diaspro (Genova, Italy) Ljljiana Fruk (Karlsruhe, Germany) Pau Gorostiza (Barcelona, Spain) Duncan Graham (Glasgow, UK) Peter Hegemann (Berlin, Germany) Fedor Jelezko (Ulm, Germany) Christian Joachim (Toulouse, France) Mark Lamy de la Chapelle (Paris, France) Marco Lazzarino & Alpan Bek (Trieste, Italy & Ankara, Turkey) Vincenzo Lombardi (Florence, Italy) Arto Nurmikko (Providence, USA) Remo Proietti & Marco Dal Maschio (Genoa, Italy) Giampietro Schiavo (Glasgow, UK)

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Publications: Please note that Publications marked with an * are mentioned by more than one partner.

SISSA:

* E. Migliorini, J. Ban, G.Grenci, L. Andolfi, A. Pozzato, M. Tormen, V. Torre and M. Lazzarino Nanomechanics controls neuronal precursors adhesion and differentiation.. Biotech and Bioeng 2013 Feb 22. doi: 10.1002/bit.24880.

G De Palo, G Facchetti, M Mazzolini, A Menini, V Torre, C Altafini Common dynamical features of sensory adaptation in photoreceptors and olfactory sensory neurons. Sci Rep. 2013;3:1251. doi: 10.1038/srep01251. Epub 2013 Feb 13. PMID: 23409242 [PubMed - in process] FREE ACCESS G.Pinato, D.Cojoc, LT Lien, A Ansuini, J Ban, E D'Este, V Torre. Less than 5 Netrin-1 molecules initiate attraction but 200 Sema3A molecules are necessary for repulsion. Sci Rep. 2012;2:675. Epub 2012 Sep 20. PMID: 22997549 FREE ACCESS A Marchesi, M Mazzolini, V Torre. Gating of cyclic nucleotide-gated channels is voltage dependent. Nat Commun. 2012 Jul 24;3:973. doi: 10.1038/ncomms1972. PMID: 22828633 [PubMed - indexed for MEDLINE] A Marchesi, M Mazzolini, V Torre. A ring of threonines in the inner vestibule of the pore of CNGA1 channels constitutes a binding site for permeating ions. J Physiol. 2012 Oct 15;590(Pt 20):5075-90. doi: 10.1113/jphysiol.2012.238352. Epub 2012 Aug 6. PMID: 22869010 [PubMed - in process]

L Amin, E Ercolini, R Shahapure, E Migliorini, Torre. The role of membrane stiffness and actin turnover on the force exerted by DRG lamellipodia. Biophys J. 2012 Jun 6;102(11):2451-60. doi: 10.1016/j.bpj.2012.04.036. Epub 2012 Jun 5. PMID: 22713560

IIT:

Nanostructures Group T. Limongi, F. Cesca, F.Gentile, R. Marotta, R. Ruffilli, A. Barberis, M. Dal Maschio, E.M. Petrini, S. Santoriello, F. Benfenati and E. Di Fabrizio (2012) Nanostructured superhydrophobic substrates trigger the development of three-dimensional neuronal networks. Small. 2012 Oct 2. doi: 10.1002/smll.201201377. R. Proietti Zaccaria, F. De Angelis, A. Toma, L. Razzari, A. Alabastri, G. Das, C. Liberale, and E. Di Fabrizio Surface plasmon polariton compression through radially and linearly polarized source, Optics Letters 37, 1 (2012).

R. Proietti Zaccaria, A. Alabastri, F. De Angelis, G. Das, C. Liberale, A. Toma, A. Giugni, L. Razzari, M. Malerba, H. Bo Sun, and E. Di Fabrizio, Fully analytical description of adiabatic compression in dissipative polaritonic structures. Physical Review B 86, 035410 (2012).

M. Moretti, R. Proietti Zaccaria, E. Descrovi, G. Das, M. Leoncini, C. Liberale, F. De Angelis, and E. Di Fabrizio. Reflection-mode TERS on insulin amyloid fibrils with top-visual AFM probes. Plasmonics, DOI 10.1007/s11468-012-9385-x.

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M. Chirumamilla, G. Das, A. Toma, A. Gopalakrishnan, R.Proietti Zaccaria, C. Liberale, F. De Angelis, E. Di Fabrizio,Optimization and characterization of Au cuboid nanostructures as a SERS device for sensing applications, Microelectronic Engineering 97, 189 ( 2012).

L.Razzari, A.Toma, M. Clerici, M. Shalaby, G. Das, C. Liberale, M. Chirumamilla, R. Proietti Zaccaria, F. De Angelis, M. Peccianti, R. Morandotti and E. Di Fabrizio , “Terahertz Dipole Nanoantenna Arrays: Resonance Characteristics”, Plasmonics. DOI 10.1007/s11468-012-9439-0.

NBT group Papers in ISI peer-reviewed international journals F Gentile, R La Rocca, G Marinaro, A Nicastri, A Toma, F Paonessa, G Cojoc, C Liberale, F Benfenati, E di Fabrizio, P Decuzzi. Differential Cell Adhesion on Mesoporous Silicon Substrates. ACS Appl Mater Interfaces. 2012 May 22. [Epubahead of print] PubMed PMID: 22583790. J Scholz-Starke, F Cesca, G Schiavo, F Benfenati, P Baldelli. Kidins220/ARMSis a novel modulator of short-term synaptic plasticity in hippocampal GABAergicneurons. PLoS One. 2012;7(4):e35785. P Valente, S Casagrande, T Nieus, AM Verstegen, F Valtorta, F Benfenati, P Baldelli. Site-specific synapsin I phosphorylation participates in theexpression of post-tetanic potentiation and its enhancement by BDNF. J Neurosci. 2012 Apr 25;32(17):5868-79. E Marconi, T Nieus, A Maccione, P Valente, A Simi, M Messa, S Dante, P Baldelli, L Berdondini, F Benfenati. Emergent functional properties of neuronal networkswith controlled topology. PLoS One. 2012;7(4):e34648. S Galiani, B Harke, G Vicidomini, G Lignani, F Benfenati, A Diaspro, P Bianchini. Strategies to maximize the performance of a STED microscope. Opt Express. 2012Mar 26;20(7):7362-74. F Succol, H Fiumelli, F Benfenati, L Cancedda, A Barberis. Intracellularchloride concentration influences the GABAA receptor subunit composition. Nat.Commun. 2012 Mar 13;3:738. G Gelsomino, E Menna, F Antonucci, S Rodighiero, L Riganti, C Mulle, F Benfenati, F Valtorta, C Verderio, M Matteoli. Kainate Induces Mobilization of SynapticVesicles at the Growth Cone through the Activation of Protein Kinase A. CerebCortex. 2013 Mar;23(3):531-41. P Farisello, D Boido, T Nieus, L Medrihan, F Cesca, F Valtorta, P Baldelli, F Benfenati. Synaptic and Extrasynaptic Origin of the Excitation/InhibitionImbalance in the Hippocampus of Synapsin I/II/III Knockout Mice. Cereb Cortex.2013 Mar;23(3):581-93. G Lignani, A Raimondi, E Ferrea, A Rocchi, F Paonessa, F Cesca, M Orlando, T Tkatch, F Valtorta, P Cossette, P Baldelli, F Benfenati. EPILEPTOGENIC Q555XSYN1 MUTANT TRIGGERS IMBALANCES IN RELEASE DYNAMICS AND SHORT-TERM PLASTICITY.Hum Mol Genet. 2013 Feb 12. [Epub ahead of print] PubMed PMID: 23406870. L Bragina, G Fattorini, S Gioved√¨ , F Bosco, F Benfenati, F Conti. Heterogeneity of presynaptic proteins: do not forget isoforms. Front CellNeurosci. 2013;7:8. E Ferrea, A Maccione, L Medrihan, T Nieus, D Ghezzi, P Baldelli, F Benfenati, L Berdondini. Large-scale, high-resolution electrophysiological imaging of field potentials in brain slices with microelectronic multielectrode arrays. FrontNeural Circuits. 2012;6:80.

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L Zullo, M Chiappalone, S Martinoia, F Benfenati. A "spike-based" grammarunderlies directional modification in network connectivity: effect on burstingactivity and implications for bio-hybrids systems. PLoS One. 2012;7(11):e49299. EF Fornasiero, A Raimondi , FC Guarnieri, M Orlando, R Fesce, F Benfenati, F Valtorta. Synapsins contribute to the dynamic spatial organization of synaptic vesicles in an activity-dependent manner. J Neurosci. 2012 Aug29;32(35):12214-27. E M Petrini, T Ravasenga, T C. Jacob, V Racine, J B Sibarita, F Benfenati, M Kneussel, S Moss and A Barberis (2013)Gephyrin upregulation determines GABAAR immobilization at potentiated inhibitory synapses. Submitted Book Chapters F Difato., M Dal Maschio , R Beltramo, A Blau, F Benfenati, T Fellin. (2012) Spatial light modulators for complex spatio-temporal illumination of neuronal networks Neuronal Network Analysis: concepts and experimental approaches, Neuromethods Book Series, Springer. M Dal Maschio, F Difato, A De Stasi, R Beltramo, A Blau, F Benfenati, T Fellin. (2012) Structured light illumination for the optical investigation of brain networks Cellular imaging techniques in neuroscience and beyond, Elsevier.

IBEC:

M Izquierdo-Serra, D Trauner, A Llobet, P. Gorostiza. Optical control of calcium-regulated exocytosis. Biochimica Biophysica Acta. 1830 (3), 2853-2860 (2013). doi: 10.1016/j.bbagen.2012.11.003 http://dx.doi.org/10.1016/j.bbagen.2012.11.003 M.Izquierdo-Serra, D.Trauner, A.Llobet and P.Gorostiza Optical modulation of neurotransmission using calcium photocurrents through the ion channel LiGluR. Frontiers in Molecular Neuroscience, accepted (Feb 2013). http://dx.doi.org/10.3389/fnmol.2013.00003 [1]

KIT:

I.Ahmed, L.Fruk, The power of Light: photosensitive tools for chemical biology, MolBioSys. 2013, Advance article, DOI:10.1039/c2mb25407g. D. Bauer, I. Ahmed, A. Vigovskaya, L. Fruk, Clickable Tyrosine Binding Bifunctional Linkers for Preparation of DNA-protein conjugates, 2013, submitted.

CBM: * E. Migliorini, J. Ban, G.Grenci, L. Andolfi, A. Pozzato, M. Tormen, V. Torre and M. Lazzarino Nanomechanics controls neuronal precursors adhesion and differentiation.. Biotech and Bioeng 2013 Feb 22. doi: 10.1002/bit.24880.

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METU: 3 manuscripts which are related to the project have been submitted to scientific journals: H. Nasser, Z. M. Saleh, E. Ozkol, M. Gunoven, A. Bek, R. Turan, “Fabrication of Ag nanoparticles embedded in Al:ZnO as potential light-trapping plasmonic interface for thin film solar cells”, submitted to Plasmonics I. Tanyeli, H. Nasser, F. Es, A. Bek, R. Turan, “Effect of surface type on structural and optical properties of Ag nanoparticles formed by dewetting”, submitted to Optics Express M. C. Gunendi, I. Tanyeli, G. B. Akguc, A. Bek, R. Turan and O. Gulseren, “Understanding the realistic plasmonic properties of dewetting formed Ag nanoparticles in large area solar cell applications”, submitted to Nanoscale

Meetings and Conferences attended:

SISSA:

* Biophysical Society Meeting, USA, San Diego, USA, 26. – 28. February 2012

* Focus First Meeting 2012 – State of the Art of the Project | Analysis of deviation | Plans for the following year. SISSA, Trieste, 23-24 Jan 2012.

* Focus Review Meeting 2012 – State of the Art of the Project | Analysis of deviation | Plans for the following year. European Commission, Brussels, 12 Mar 2012

* International Workshop – Single Molecule Activation and Detection in Molecular Devices. Palazzo Loredan, Venezia, 13-14 Oct 2012. OWLS 12 Conference “Optics within life Sciences”, Genoa, Italy 4-7 July 2012

IIT:



* International Workshop – Single Molecule Activation and Detection in Molecular Devices. Palazzo Loredan, Venezia, 13-14 Oct 2012. Annual Meeting Young Researchers, Sestri Levante, May 30th – June 1st 2012

Colloids and Nanomedicine, Amsterdam, The Netherlands, 15-17th July 2012

At the Interface between Applied Physics and Medicine, Catanzaro, Italy, Feb. 6th 2012

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IBEC:

“Single protein transistors”. Pau Gorostiza. Oral Communication. Architecture & Design of Molecule Logic Gates and Atom Circuits - AtMol International Workshop 2012, Barcelona (Spain), 12-13 January 2012. “Optical control of exocytosis”. Pau Gorostiza. Oral Communication. International workshop on single molecule activation and detection in molecular devices, Venice (Italy), 13-14 October 2012. “Remote control of biological processes by optogenetics and optopharmacology”. Pau Gorostiza. Oral Communication. Rethinking Nano Workshop, Barcelona (Spain), 8 October 2012.



* International Workshop – Single Molecule Activation and Detection in Molecular Devices. Palazzo Loredan, Venezia, 13-14 Oct 2012.

•

RAPP:

* Biophysical Society Meeting, USA, San Diego, USA, 26. – 28. February 2012

ELMI, European Light Microscopy Initiative, Leuven, Belgium, 5. – 8. June 2012

FENS, European Neuroscience Meeting, Barcelona, Spain, 12. – 17. July 2012

DGfB, German Biophysical Society Meeting, Göttingen, Germany, 23. – 25. September 2012

SFN, Society for Neuroscience, USA, New Orleans, USA, 13. – 17. October 2012




•

KIT:


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* International Workshop – Single Molecule Activation and Detection in Molecular Devices. Palazzo Loredan, Venezia, 13-14 Oct 2012. NT-MDT: * Focus First Meeting 2012 – State of the Art of the Project | Analysis of deviation | Plans for the following year. SISSA, Trieste, 23-24 Jan 2012.



CBM:

1st international conference on enhanced spectroscopy (ICES 2012) October 3-5, 2012, Porquerolle Island ,France * Focus First Meeting 2012 – State of the Art of the Project | Analysis of deviation | Plans for the following year. SISSA, Trieste, 23-24 Jan 2012.


* International Workshop – Single Molecule Activation and Detection in Molecular Devices. Palazzo Loredan, Venezia, 13-14 Oct 2012. METU: NanoTR8 - Nanoscience and Nanotechnology Congress, 25-29 June, 2012 (Ankara) * Focus First Meeting 2012 – State of the Art of the Project | Analysis of deviation | Plans for the following year. SISSA, Trieste, 23-24 Jan 2012.



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Regarding the Other Activities planned in the DoW:

FET molecular symposium organized by each project and attached (or not) to well-known conferences.

This is the list of the events we were supposed to have, but we were informed only about the first one, then, even though during the FOCUS Workshop organization we officially invited (also as speakers) the other Consortia Coordinators, only one of the four replied and actually participated (Christian Joachim from ATMOL).

—- ATMOL (Year 2011): Spring 2011 (Toulouse): Main topic: “Trends in calculating and computing with a molecule(s) or a few atoms”.

—- DIAMANT (year 2012): Symposium part of German Physical Society Symposium (tentatively scheduled for March 2012). Main topic: “Control of single quantum objects in condensed matter”.

—- ELFOS (year 2012 or 2013): Lorentz Centre (Leiden). Main topic: “Single-molecule devices”

—-FOCUS (year 2012): Satellite symposium to the Advanced Nano-optics Conference for Interdisciplinary Applications. The Conference will be organized either at Varenna or Genova and will be held in collaboration with the Italian Physical Society (SIF). The most likely date is late May or early June of 2012. Main Topics: “Photonics and Molecular devices”.

As already mentioned, our workshop took place in Venice on October 13th-14th 2012. Title of the event: SINGLE MOLECULE ACTIVATION AND DETECTION IN MOLECULAR DEVICES.

—- ATMOL (year 2014): Main Topic: “Atom tech for Molecular computing” symposium tentatively attached to the Trends in Nanotechnology TNT 2014 (www.tntconf.org) or to the International Meeting on Molecular Electronics 2014 (www.elecmol.com)

Collaborative Tasks

These Joint collaborative tasks among the Molecular Scale Devices and Systems FET funded projects are meant to enhance the FET proactive initiative visibility.

—These tasks covering activities such as clustering and inter-project collaboration, initiative-level promotion activities and contribution to FET-wide events and publications have partially developed during the Focus project lifetime. From the FOCUS Consortium’s point of view, the major problem has been the non-involvement of two of the other projects, leaving only FOCUS and ATMOL in contact.

—joint scientific publications: Proceedings of our Workshop in Venice (Springer), supervised by IIT

—joint press-releases

—joint events and or symposia (FET label): our Workshop in Venice

The FET Molecular computing and atom tech board was created to provide inputs to the program and suggest invited speakers for the FET Molecular symposia.

—- To participate in the preparation of the next calls (i.e. the meeting in Brussels in December 2011)

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—-To implement (special issues dedicated to research topics of interest for the FET proactive). These joint

publications are meant to help to enhance/promote the FET proactive initiative visibility worldwide

In November 2012 the Project Officer asked our coordinator to provide a successful story of the FOCUS project for the FET newsletter. So, thanks to Ljiljana Fruck’s contribution, the following piece of news was sent to the EC just before Christmas 2012.

FOCUS on tools for molecular manipulation and computation

Biology can inspire the design of novel light triggered devices that can shed light on complex biological processes and serve as a platform for computation at the molecular level.

The core of the FOCUS project is to address a long standing issue of programmable assembly, which Nature masters at a fine molecular level, but scientists have not yet achieved: Nature has developed highly sophisticated systems able to detect single photons and molecules and to perform reliable computations in a noisy environment dominated by thermal motion. Can we design and assemble molecular devices with similar properties?

�

�

�

�

�

�

� Diagram of the Molecular Device

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� The FOCUS project has gathered biologists, chemists and nanotechnologists so to develop a prototype of a new molecular device, inspired by Biology, able to perform single molecule computation using thermal motion as an essential component. The strength of FOCUS lies in the orthogonal expertise of the partners. FOCUS is developing a prototype of a new generation of molecular devices based on the use of DNA as molecular anchor to allow precise positioning of photoactivable molecules. Nanotechnologists are developing tools to obtain strong plasmonic enhancements needed for studies at the molecular level. Physicists involved are developing photonic devices able to create a highly focused beam of light based on the use of nano-tips or tapered plasmonic wave guides mounted on i.e. AFM cantilever. Chemists are testing the synthetic procedures to design photoswitchable protein models that can be studied in a single molecule experimental setup. To achieve that, the catalytic centre of the model protein is modified with photoswitchable molecules, which enable ON and OFF control over the protein activity with light of certain wavelengths. At the same time, when working with biological models, one needs to take into account their sensitivity to environmental changes and to develop mild strategies for their immobilisation onto plasmonic surfaces. Next, thoreticians involved need to analyse the advantages and limitations of single molecule computations and formalise the input-output relationship when a

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single or limited number of molecules are activated at well defined spatial locations. They also need to provide the theoretical background on signal output and molecular diffusion to troubleshoot the experimental design. Finally, once the model system is complete and functional, new devices combined with optogenetic tools, can be used to address biological problems such as the signal transfer and exchange across a synapse, the processing of the electrical signals within neurons when one or few inputs such as receptors are activated at specific sites.

Single molecule computation and processing in a biological environment has not yet been demonstrated and the methodologies developed within FOCUS will have wider implications not only to study biological processes but also in the fields of photonics, single molecule manipulation and detection, chemical modification and programmable assembly.

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Deliverables and milestones tables

Deliverables

For this Second Period 19 Deliverables were expected and 16 were reached while 3 are still in progress. The

delay consists in a couple of months.

Del. Nr

Deliverable Title Version WP n.

Lead Benef. Nature* Dissem Level**

Deliv. Date From AnnexI

Actual Forecast Delivery date dd/mm/ yyyy

Status Not submitted/

Submitted

D1.2 Coupling to the external laser

Final 1 2 R PP 18 14/01/12 YES

D1.3 Technology transfer

Final 1 4 R PU 24 28/02/13

YES

D2.2 Development of photoswitchable tethered ligand

Final 2 3 R PP 18 10/12/12

YES

D2.3 Characterization of photoswitcha le tethered ligand or Alternative Development

Final 2 3 R PP 24 28/02/13

YES

D3.1 Simultaneous activation of two rhodopsins

Final 3 1 R PP 18 27/09/12

YES

D3.2 Activation of two rhodopsins at different times and sites

Final 3 1 R PP 24 22/02/13

YES

D4.2 Receptor trafficking in dendrites during plasticity

Final 4 2 R PP 18 29/09/12

YES

D4.3 Processing of multiple pre-synaptic activation

Final 4 2 R PP 24 13/02/2013

YES

D5.2 Reliability, accuracy and reproducibility of single molecule computation

Final 5 1 R PU 18 10/01/13

YES

D5.3 Beyond Boolean logics by Receptor Trafficking

Final 5 1 R PP 24 28/02/13

YES

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D6.2 Detection strategy evaluation

Final 6 6 R PP 24 28/02/13

YES

D7.3 Report on Photoswitchable protein/cofactor immobilisation

Final 7 5 R PP 18 20/12/12

YES

D7.4 Final design of photoswtichable molecular devices

Not finalized yet

7 5 R CO 24 IN PROGRESS

D7.5 Report on the effect of tether length

Not finalized yet

7 5 R PP 24 IN PROGRESS

D8.1 Publication and main update of the project web site and intranet

Not finalized yet

8 1 O PU 24 IN PROGRESS

D8.2 List of articles published on high impact scientific journals and international conferences

Final 8 1 O PU 24 07/03/13

YES

D8.3 Cooperation activities with other EU projects

Final 8 1 O PU 24 13&14/10/12

YES

D8.5 FET Molecular Symposium

Final 8 1 O PU 24 13&14/10/12

YES

D9.1 nonlinear optical field generation in interparticle gaps

Final 9 8 R CO 24 27/02/13

YES

*Nature of reports:

R = Report, P = Prototype, D = Demonstrator, O = Other

**Dissemination Level:

• PU = Public

• PP = Restricted to other programme participants (including the Commission Services)

• RE = Restricted to a group specified by the consortium (including the Commission Services)

• CO = Confidential, only for members of the consortium (including the Commission Services)

• Restreint UE = Classified with the classification level "Restreint UE" according to Commission Decision 2001/844 and amendments

• Confidentiel UE = Classified with the mention of the classification level "Confidentiel UE" according to Commission Decision 2001/844 and amendments

• Secret UE = Classified with the mention of the classification level "Secret UE" according to Commission Decision 2001/844 and amendments

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Milestones

17 Milestones were expected for this Second Period and 15 were achieved

Milestone Number

Milestone Name

WP Number

Lead Benef. Nr

Delivery Date from Annex I

Achieved Yes/No

Actual / Forecast achievement date

dd/mm/yyyy

Comments

MS6 Biological

Analysis as

planned

WP3 1 18 YES 01/07/2012 also linked to

WP4. The

biological

Analysis in WP 3-

4 is proceeding as

planned

MS8 Assessment of

new Molecular

Devices


WP7. The

assessment of the

new Molecular

Devices to be

constructed in

WP6-7 has been

performed

MS9 Assembly of

nanowires and

new devices

transferred

WP1 2 18 YES 28/12/2012 The assembly of

nanowires

necessary for the

biological testing

and analysis has

been made and

the new devices

have been

transferred to the

other Partners

MS10 Photoaffinity

procedures

accomplished

and protocols

transferred

WP2 3 18 YES 09/01/2013 Photoaffinity

procedures in

WP2 have

accomplished and

the scientific and

technological

protocols have

been transferred

to the other

Partners

MS11 Biological

Analysis

proceeding as

planned


WP4. The

biological

Analysis in WP 3-

4 is proceeding as

planned

MS12 Computational

analysis and

theoretical

framework for

molecular

computation

WP5 1 18 YES 30/07/2012 The

computational

analysis and the

new theoretical

framework for

molecular

17

computation

planned in WP5

has been obtained

MS13 Fabrication and

development of

Molecular

Devices as

planned

WP6 6 24 In progress

28/02/2013 also linked to

WP7. The

fabrication and

development of

the new

Molecular Devices

in WP6-7 is

proceeding as

planned

MS14 Photonic

devices

fabricated

WP1 2 18 YES 18/12/2012 The new Photonic

devices planned

in WP1 have been

fabricated as

planned

MS15 Chemistry

performed and

transferred to

partners

WP2 3 24 YES 28/02/2012 All chemistry

planned in WP2

has been

performed and

transferred to the

other partners

MS16 Biological

Analysis

produced

expected results


WP4. The

biological

Analysis in WP 3-

4 has produced

the expected

results

MS17 Computational

paradigm for

molecular

computing

WP5 1 24 28/02/2012 The new

computational

paradigm for

molecular

computing has

been produced

MS18 First prototypes

of MDs

constructed

WP7 2 24 In progress

The first

prototypes of the

new Molecular

Devices have been

constructed

MS22 First Annual Meeting

WP8 1 14 YES 23&24/01/2012

MS23 First Periodic Report

WP8 1 14 YES 29/02/2012

MS24 FET Projects 1st

Workshop/

Symposium

WP8 1 14 YES 13&14/10/2013

MS25 Website Update WP8 1 14 YES 31/03/2012

MS34 Measurement

technique for

function of

molecular gap

WP9 8 24 YES //201 Measurement

technique able to

provide

information of the

plasmonic field as

a function of

18

molecular gap is

developed

Explanation of the use of the resources

Related to FORMs C (Months 13-24)

SISSA

19

IIT

20

IBEC

22

RAPP

KIT

23

NT-MDT

CBM

24

METU

26

Financial statements – Form C and Summary financial report

Please see documents online.

Project Management during the Period (Months 13-24) · where all the partners produced a...

Documents

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