Final Activity Report Summary - NAPS (Nano-Scale Analysis, Prototyping and Self-Assembly Processes) The NAPS project had the primary goal to train six young researchers in nanotechnology and biophysical modelling, aiming for a technology leap from purely silicon to new and more advanced technologies in the future Europe. A broad interdisciplinary training program was carried out in the field of optics, nanotechnology and biophysical modelling, covering four areas, namely electron beam analysis and prototyping, biosensors, neurotechnology and biophysical modelling. More specifically, the aims were to: 1. study and improve electron beam deposition to deposit material with dimensions that came close to the atomic resolution; 2. analyse the interaction of bio-molecules with spherical magnetic particles (beads) and the way they could be used in biosensors; 3. progress the understanding of the mechanisms behind neuro-stimulation and therapeutic neuro-stimulation in the particular case of Parkinson disease by elaborating models describing the influence of electrical fields on networks of connected neurons and developing microfluidic systems that mimicked existing neural pathways to study the in vitro behaviour of neurons; 4. study light propagation in breast tissue for mammography for non-invasive breast scan; 5. develop spectroscopic analysis of light collected from tissue in a biopsy. Regarding electron beam deposition, several new purification methods for platinum and gold nanostructures deposited with the Evidence-based individual decision (EBID) technique were demonstrated and published. Detailed experiments were performed to study the physical processes behind deposition events in the EBID technique. Considerable evidence for a single model was advanced and contributed to a further understanding of how to exploit the mechanism to the advantage of improving application development. Finally, several practical applications of the technique were investigated, which were actively pursued by the research and development department of the FEI company. The rotational behaviour of an individual cluster in a magnetic biosensor aggregation assay was studied in depth. Two different techniques to accurately characterise the particles in terms of susceptibility and magnitude of the permanent moment were developed and a novel technique to break a specific particle cluster was found. Regarding the work on neurostimulation, we evaluated functional properties of thalamocortical relay cells during 'normal', 'Parkinsonian' and 'deep brain stimulation' conditions using computational models and tools. The model predictions were validated by in vitro experiments which were conducted at the University of Amsterdam (UvA). Furthermore, these single cell biophysical models were extended to network models of thalamus - reticular nucleus, sub-thalamic nucleus, external part of globus pallidus and basal ganglia network model connected to thalamocortical relay neurons. Neural cell culture Microsystems were designed and fabricated and critical factors for cell death were identified. Improvements in cell culture conditions led to neural network survival beyond 21 days in vitro, with spontaneous, healthy electrical network activity. The study of light propagation in breast tissue for mammography included a clinical trial with a three-dimensional full breast ultrasound prototype in the Leiden University medical centre. Data obtained from the Philips optical mammography system (POMS) underwent statistical analysis for the classification of healthy and tumourous tissue. POMS data led to the development and improvement of a method to combine different breast tissue parameters in order to improve breast tissue analysis and exploration of new dyes for breast cancer imaging. Finally, regarding the activities around the spectroscopic analysis of light collected from tissue during biopsy, algorithms were developed to extract optical properties from a reflectance spectrum measured on tissue. A data clustering tool was available, by the time of the project completion, to discriminate between different kinds of tissues based on their optical signature.