Single Molecule Activation and Computing (FOCUS)

The present project, FOCUS, will build a novel generation of biologically inspired molecular devices (MDs) based on the developments of new photonic tools. These photonic tools will use Plasmon Polariton and two-photon technology, enabling focused light spots with a diameter around 10 nm. FOCUS will also develop new light sensitive molecules that will be selectively activated by our new photonic tools. These new technological innovations will provide a way to control activation of single light sensitive molecules and will allow the investigation of molecular computation in a biological environment and with an unprecedented resolution. On the basis of these investigations and by using the developed new tools, FOCUS will design and test new MDs for amplification and information processing. FOCUS will: i - provide new photonic devices to control single molecules; ii – lay out the basis for understanding molecular computation in biological systems; iii - provide proofs of concept and suggestions for designing new molecular artificial computing systems; iv- build prototypes of these new MDs. FOCUS has formed a highly interdisciplinary consortium composed of nanotechnologists able to fabricate the new photonic devices - i.e. Enzo Di Fabrizio (IIT), Alpan Bek (METU) and Marco Lazzarino (CBM), chemists able to develop the photoswitches and assemble the MDs – i.e. Pau Gorostiza (IBEC) and Ljiljana Fruk (KIT) and biologists able to understand molecular mechanisms – i.e. Vincent Torre (SISSA) and Fabio Benfenati (IIT). The two companies RappOptoElectronic and NT-MDT Europe BV will transform the new tools and devices into marketable products.


Neural networks with piecewise constant argument and impact activation
Yılmaz, Enes; Akhmet, Marat; Department of Scientific Computing (2011)
This dissertation addresses the new models in mathematical neuroscience: artificial neural networks, which have many similarities with the structure of human brain and the functions of cells by electronic circuits. The networks have been investigated due to their extensive applications in classification of patterns, associative memories, image processing, artificial intelligence, signal processing and optimization problems. These applications depend crucially on the dynamical behaviors of the networks. In t...
Computational representation of protein sequences for homology detection and classification
Oğul, Hasan; Mumcuoğlu, Ünal Erkan; Department of Information Systems (2006)
Machine learning techniques have been widely used for classification problems in computational biology. They require that the input must be a collection of fixedlength feature vectors. Since proteins are of varying lengths, there is a need for a means of representing protein sequences by a fixed-number of features. This thesis introduces three novel methods for this purpose: n-peptide compositions with reduced alphabets, pairwise similarity scores by maximal unique matches, and pairwise similarity scores by...
A Cloud Based Architecture for Distributed Real Time Processing of Continuous Queries
Gökalp, Mert Onuralp; Koçyiğit, Altan; Department of Information Systems (2015)
The technological advancements in Internet of Things (IoT) domain have enabled us to reshape the physical world through smart devices, sensors and actuators. The data collected by IoT devices has become a valuable asset to extract knowledge about the environment and other nearby devices. Existing IoT applications mostly store collected data in a central server and allow users to query stored data to notice and react to changes in the environment. Usually cloud and big data technologies are utilized in those...
A Sub-500 mu W Interface Electronics for Bionic Ears
Ulusan, Hasan; Muhtaroglu, Ali; Külah, Haluk (Institute of Electrical and Electronics Engineers (IEEE), 2019-01-01)
This paper presents an ultra-low power current-mode circuit for a bionic ear interface. Piezoelectric (PZT) sensors at the system input transduce sound vibrations into multi-channel electrical signals, which are then processed by the proposed circuit to stimulate the auditory nerves consistently with the input amplitude level. The sensor outputs are first amplified and range-compressed through ultra-low power logarithmic amplifiers (LAs) into AC current waveforms, which are then rectified through custom cur...
Japan and Europe Network for Neutrino and Intensity Frontier Experimental Research (JENNIFER)
Zeyrek, Mehmet Tevfik(2019-3-31)
European particle physics groups interested in searching signals of new physics both with neutrinos, at T2K experiment, and at the intensity frontier, with the Belle-II experiment at the SUPERKEKB machine, want to share between them and with KEK laboratory their knowledge in data analysis and detector technologies. Such knowledge sharing will enhance skills and competences of all participants, will allow Europe to play a primary role in the search for deviations from the actually known fundamental physics i...
Citation Formats
A. Bek, “Single Molecule Activation and Computing (FOCUS),” 2014. Accessed: 00, 2020. [Online]. Available: