Search

Flow cytometry (FC) is a pivotal tool for studying the physical and chemical properties of particles. State-of-the-art FC systems are highly advanced, yet they are expensive, bulky, and require high sample volume, qualified operators, and periodic maintenance. The manipulation of particles suspended in viscoelastic fluids has received increasing attention, especially for miniaturized flow cytometry technologies. This study presents a miniaturized optical capillary FC device using the viscoelastic focusing technique. A straight, one inlet/outlet microcapillary device is precisely aligned to a fiber-coupled laser source and detectors. Forward scattered, side scattered, and fluorescently emitted light signals are collected and analyzed in a real-time environment. The developed platform fits onto an inverted microscope stage enabling real-time microscopy imaging of the particles of interest together with the flow cytometry analysis. We achieved stable viscoelastic focusing and performed FC measurements for rigid polystyrene beads (diameters: 2 - 15 μm), non-spherical human erythrocytes, and canonical shape metaphase human chromosomes. We performed cytometry measurements with a throughput of 100 events/s yielding a coefficient of variation of 2%. This newly developed FC device is a versatile tool and can be operated with any inverted microscope to get the mutual benefits of optical and imaging FC measurements. Furthermore, it is possible to extend these benefits by adding more back-end tools, such as optical trapping and Raman spectroscopy.

Plasmonic color metasurfaces enable high resolution, ink-free color decoration and sensing devices. This work presents a full solution from design of plasmonic color elements suitable for master origination by 248 nm Deep Ultraviolet (DUV) lithography to production grade manufacture of plasmonic color metasurfaces on plastic substrates. Design of hybrid aluminum disk-hole structures with hybridized multiple resonances, which are controlled by the disk-hole distance, enables plasmonic color generation across the visible spectrum with larger sized nanostructures, above 160 nm. Such larger structures can be defined by 248 nm DUV lithography as a cost-efficient and high throughput alternative to, e.g., electron beam lithography.

The advent of resonant dielectric nanomaterials has provided a new path for concentrating and manipulating light on the nanoscale. Such high-refractive-index materials support a diverse set of low-loss optical resonances, including Mie resonances, anapole states, and bound states in the continuum. Through these resonances, high-refractive-index materials can be used to engineer the optical near field, both inside and outside the nanostructures, which opens up new opportunities for Raman spectroscopy. In this review, we discuss the impact of high-refractive-index nano-optics on Raman spectroscopy. In particular, we consider the intrinsic Raman enhancement produced by different dielectric resonances and their theoretical description. Using the optical reciprocity theorem, we derive an expression which links the Raman enhancement to the enhancement of the stored electric energy. We also address recent results on surface-enhanced Raman spectroscopy based on high-refractive-index dielectric materials along with applications in stimulated Raman scattering and nanothermometry. Finally, we discuss the potential of Raman spectroscopy as a tool for detecting the optical near-fields produced by dielectric resonances, complementing reflection and transmission measurements.

Disclosed is a method for self-organization of a nanostructure, comprising the steps of, providing a narrow-band light source having a center wavelength; providing a film on a substrate, said thin film having a film thickness, said film thickness being in the range from 0.9 to 1.1 times a Fabry Perot resonance condition thickness for said center wavelength; and irradiating said film, the irradiating comprises using said narrow-band light source to induce self-organization of said film, thereby obtaining nanostructures. A product comprising a substrate and nanostructures produced by said method is further disclosed.

Plasmonic color generation from metal nanostructures has attracted intensive attention because of their excellence in achieving high spatial resolution, strong color contrast, and long‐term durability. The limited area of plasmonic patterns anchored on substrates and produced by current top‐down methods, however, severely restricts the advanced developments and potential applications in structural color display. Herein a robust method for realizing the laser printing of plasmonic colors inside transparent gold nanodisk‐embedded poly(dimethylsiloxane) matrices is presented. It is found that various colors can not only be easily generated by embedding gold nanodisks of different sizes, but also finely varied by adjusting the laser pulse intensity during printing. It is further demonstrated that multiple color layers can be laser‐printed at different depths. Stereoscopic images in the 3D matrices are laser‐printed with sizes as large as 12 × 15 mm2 and a resolution of 4600 dots per inch.

This thesis seeks to investigate how Psalm 139, and biblical texts in general, can be interpreted to facilitate a meaningful reading by bereaved parents after the early loss of a child. By using in-depth interviews with bereaved parents, this study emphasises the reader’s perspective in its exegesis to produce a responsible, contemporary interpretation. I applied insights on the existential challenges of bereaved parents to a reader-oriented exegetical approach to Psalm 139, imagining a hypothetical reader’s creative engagement with the biblical text. To investigate the merit of this approach, the resulting interpretation was then compared to findings from interviews conducted with bereaved parents about their experiences of reading the psalm. This study finds that the individual experience of the reader is hugely influential in the creative process of interpretation. Depending on the reader’s past life and personal convictions, Psalm 139 can be immensely comforting or disconcerting. I conclude that the reader-oriented approach to exegesis is a valuable tool for any biblical scholar and minister, as it can unearth a wealth of relevant, contemporary interpretations inaccessible to the historical approach to exegesis. This thesis contends that scholarly biblical studies, homiletics and pastoral would all benefit greatly from an increased focus on the contemporary reader’s perspective.

We demonstrate on-chip, differential DNA and RNA extraction from a single cell using a microfluidic chip and a two-stage lysis protocol. This method enables direct use of the whole extract, without additional washing steps, reducing sample loss. Using this method, the tumor driving pathway in individual cells from a colorectal cancer cell line was determined by applying a Bayesian computational pathway model to sequences obtained from the RNA fraction of a single cell and, the mutations driving the pathway were determined by analyzing sequences obtained from the DNA fraction of the same single cell. This combined functional and mutational pathway assessment of a single cell could be of significant value for dissecting cellular heterogeneity in tumors and analyzing single circulating tumor cells.

The absorption in amorphous silicon nano antennas is engineered for the purpose of post process structural change via resonant laser printing by illumination, thus shifting transmission and reflection spectrum in a controlled manner.

Conventional three-dimensional optics requires curvature to control the wave front of light thus making it difficult to reduce the size of the optical systems. Furthermore, for correction of optical aberrations, complex optical systems comprising more than one lens are used. This adds additional bulk, mass and complexity to the optical systems. Recent development in diffractive optics has enabled new thin lightweight optical elements such as metalenses. We introduce resonant laser printing technique as a flexible photo-thermal technology for metalens fabrication with the ability to control the light with microscale precision. Our laser printed metalenses can be integrated in bio-sensors, bio-imaging systems, and optofluidical devices.

Spatially offset Raman spectroscopy (SORS) enables one to distinguish chemical fingerprints of top and subsurface layers. In this paper, we apply SORS to a microfluidic two-layer system consisting of transparent liquid in a microchannel as the surface layer and microfluidic PDMS chip material as the sublayer. By using an imaging spectrograph connected to a microscope, we perform hyperspectral SORS acquisitions. Furthermore, the focus position z is translated. Thus, we combine the two methods of hyperspectral SORS and defocusing micro-SORS, which leads to an integral characterization of the layered system. The collected top and subsurface layers of Raman scattering at the optical axis (zero spatial offset) largely depends on the focus position z. However, the spatially offset Raman scattered intensity from the subsurface layer is constant for a large range of focus positions z. We claim that there is potential for internal referencing and alignment reproducibility. We demonstrate these findings experimentally in a microfluidic scenario where a 16 mu m deep channel is filled with an aqueous hemoglobin solution. Our observation enables consistent concentration measurements in small-volume liquid samples. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

International audience; The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received 12 million s funding under the European Union Framework Programme 7 from 1st June 2008 to 30th November 2012. The 19 project partners from both academia and industry from in total 7 countries had a project budget of 16 Ms with which they have discovered, created and developed a huge body of insights into nucleic acid analysis. Results have been presented widely in publications and in innumerous public presentations. Results have been moved to spin-offs such as the Olink enrichment kits (now sold by Agilent as Haloplex) and are findingtheir way to the market, such as the Oxford Nanopore MinIon sequencer that was first released to early-access user sites in 2014.

To elucidate cellular diversity and clonal evolution in tissues and tumors, one must resolve genomic heterogeneity in single cells. To this end, we have developed low-cost, mass-producible micro-/nanofluidic chips for DNA extraction from individual cells. These chips have modules that collect genomic DNA for sequencing or map genomic structure directly, on-chip, with denaturation-renaturation (D-R) optical mapping [Marie R, et al. (2013) Proc Natl Acad Sci USA 110:4893-4898]. Processing of single cells from the LS174T colorectal cancer cell line showed that D-R mapping of single molecules can reveal structural variation (SV) in the genome of single cells. In one experiment, we processed 17 fragments covering 19.8 Mb of the cell's genome. One megabase-large fragment aligned well to chromosome 19 with half its length, while the other half showed variable alignment. Paired-end single-cell sequencing supported this finding, revealing a region of complexity and a 50-kb deletion. Sequencing struggled, however, to detect a 20-kb gap that D-R mapping showed clearly in a megabase fragment that otherwise mapped well to the reference at the pericentromeric region of chromosome 4. Pericentromeric regions are complex and show substantial sequence homology between different chromosomes, making mapping of sequence reads ambiguous. Thus, D-R mapping directly, from a single molecule, revealed characteristics of the single-cell genome that were challenging for short-read sequencing.

According to one aspect, an optoelectric scaffold for accommodating photo- responsive biological components is provided. The scaffold comprises an optical waveguide configured for confining light propagating in a longitudinal direction thereof. The optical waveguide comprises at least one leaky section with enhanced emission of light in a direction transverse or lateral to the longitudinal direction. The scaffold further comprises an electrically conductive layer arranged on an outer surface of the optical waveguide, wherein the electrically conductive layer has an immobilisation or growth support surface for the immobilisation or cultivation of photo-responsive biological components thereon. The electrically conductive layer comprises transparent regions at least partially overlapping the leaky section. The transparent region is configured so as to transmit light from the leaky section of the waveguide to the immobilisation and/or growth support surface. According to a further aspect, an optoelectric device comprises an optoelectric scaffold and a photo-responsive biological component arranged on the immobilisation/growth support surface. The growth support surface is arranged so as to transmit light received from the leaky section of the optical waveguide to the biological component placed thereon.

Traffic accidents are a result of the convergence of hazards, malfunctioning of vehicles and human negligence that have adverse economic and health impacts and effects. Unfortunately, avoiding them completely is very difficult, but with quick response to rescue and first aid, the mortality rate of inflicted persons can be reduced significantly. Smart and innovative technologies can play a pivotal role to respond faster to traffic crash emergencies comparing conventional means of transportation. For instance, Rescue Emergency Drone (RED) can provide faster and real-time crash site risk assessment to emergency medical services, thereby helping them to quickly and accurately assess a situation, dispatch the right equipment and assist bystanders to treat inflicted person properly. To conduct a research in this regard, the case of a traffic roundabout that is prone to frequent traffic accidents on the outskirts of Esbjerg, a town located on western coast of Denmark is hypothetically considered. Along with manual calculations, Emergency Disaster Management Simulation (EDMSIM) has been used to verify the response time of RED from a fire station of the town to the presumed crash site. The results of the study demonstrate the robustness of RED into emergency services to help save lives., {"references":["World Health Organization (2017) \"Road Traffic Injuries\". (Accessed on 29/08/2017), Available at: http://www.who.int/mediacentre/factsheets/fs358/en/.","Frederick B. Rogers (2014) 'The Golden Hour in Trauma: Dogma or Medical Folklore?' MD, MS, FACS Medical Director, Trauma Program, LGH and Katelyn Rittenhouse, BS.","Alec Momont (2016) \"Ambulance Drone\", Delft University of Technology (2016) (Accessed on 07/08/2017). Available at: https://www.tudelft.nl/en/ide/research/research-labs/applied-labs/ambulance-drone/.","Len Watson (2001) \"Platinum Ten, the final countdown in the moments following a serious motor vehicle accident\" Saint Andrews House, 21 Head Street, Halstead, Essex CO) 2SZ, England).","Bartosz Puchalski, Marek Kwasiżur, Anna E. Płatek1, Filip M. Szymański1 (2014) \"The use of an automated external defibrillator in a victim of car accident\" 1st Chair and Department of Cardiology, Medical University of Warsaw, Warsaw, Poland. Volunteer Mountain Rescue Service, Subcarpathian Group, Sanok, Poland.","Statistics Denmark (2017) Living conditions, Traffic Accidents, \"Road Traffic Accidents\" Road Traffic Accidents by type of accidents, Municipality, Urban area and Accident situation (1998-2015) (Accessed on 07/08/2017) Available at: https://www.statbank.dk/statbank5a/SelectVarVal/saveselections.asp.","Iflscience (2017) \" Ambulance Drone' Could Drastically Increase Heart Attack Survival\" (Accessed on 10/08/2017) Available at: http://www.iflscience.com/health-and-medicine/ambulance-drone-could-drastically-increase-heart-attack-survival/.","Sydvestjysk Brandvæsen (2016) \"Generel beredskabsplan 2016 - Esbjerg, Varde og Fanø kommuner\" 128.","Sydvestjysk Brandvæsen (2016) \"Risikobaseret dimensionering Sydvestjysk Brandvæsen 2016.\n[10]\tStatistics Denmark (2017) Living condition. traffic Accidents. \"Road traffic Accidents\". Road traffic accidents by region and time (Accessed on 15/08/2017) Available at: http://www.statbank.dk/statbank5a/default.asp?w=1600.\n[11]\tSaqib Mehmood, Shakeel Ahmed (2017), 'Incorporation of Drones into Fire and Rescue Service of Esbjerg Muncipality for a Robout Response' A MSc Risk and Safety Management Thesis. Aalborg University, Esbjerg Denmark.\n[12]\tAeryon skyranger (2017) \" Aeryon skyranger\" (Online) Available: https://www.aeryon.com/aeryon-skyranger Accessed on 20/09/2017.\n[13]\tEENA / DJI Pilot Project Report (2016) \"The use of Remotely Piloted Aircraft Systems (RPAS) by the Emergency Service\"'. European Emergency Number Association – EENA 112. Avenue de la Toison d'Or 79, Brussels, Belgium.\n[14]\tSchiebel (2017), \"Camcopter S 100\" (Accessed on 16/09/2017) Available at: https://schiebel.net/products/camcopter-s-100/.\n[15]\tDJI (2017) \"Phantom 4 Specs\" (Accessed on 12/08/2017) Available at: https://www.dji.com/phantom-4/info.\n[16]\tWeisfeldt ML, Sitlani CM, Ornato JP, et al (2010). \"Survival after application of automated external defibrillators before arrival of the emergency medical system: Evaluation in the Resuscitation outcomes consortium population of 21 million\". J Am Coll Cardiol. 2010;55(16): 1,713-1,720.\n[17]\tSudden Cardiac Arrest foundation (2017) \"Sudden Cardiac Arrest: A Healthcare Crisis\" (Accessed on 12/08/2017) Available at: http://www.sca-aware.org/about-sca.\n[18]\tDistance Between Cities Places On Map (Aerial Distance) (Accessed on 04/08/2017) Available at: http://www.distancefromto.net/ \n[19]\tEmergency and Disaster Management Simulation (EDMSIM) (Accessed on 12/09/2017) Available at: http://www.c4itrgtech.com/products/edmsim/.\n[20]\tAnne Møller Nielsen et al (11 November 2012) 'Use and benefits of public access defibrillation in a nation-wide network'. Department of Anaesthesia, Centre of Head and Orthopaedics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.\n[21]\tFreddy Lippert (2016) 'Strategic deployment of public Access Defibrillations in Denmark'. Chief Executive, MD. Ass. Professor Emergency Medical Services, Copenhagen University of Copenhagen, Denmark.\n[22]\tUnmanned Systems Australia (2013) \"Schiebel Camcopter® S-100 – Successful Integration with the Flir Systems Polytec Ab Corona 350 Sensor\" (Accessed on 02/09/2017) Available at: http://www.unmannedsystemsaustralia.com.au/latestnews/?p=842."]}

Next-generation sequencing (NGS) has caused a revolution, yet left a gap: long-range genetic information from native, non-amplified DNA fragments is unavailable. It might be obtained by optical mapping of megabase-sized DNA molecules. Frequently only a specific genomic region is of interest, so here we introduce a method for selection and enrichment of megabase-sized DNA molecules intended for single-molecule optical mapping: DNA from a human cell line is digested by the NotI rare-cutting enzyme and size-selected by pulsed-field gel electrophoresis. For demonstration, more than 600 sub-megabase- to megabase-sized DNA molecules were recovered from the gel and analysed by denaturation-renaturation optical mapping. Size-selected molecules from the same gel were sequenced by NGS. The optically mapped molecules and the NGS reads showed enrichment from regions defined by NotI restriction sites. We demonstrate that the unannotated genome can be characterized in a locus-specific manner via molecules partially overlapping with the annotated genome. The method is a promising tool for investigation of structural variants in enriched human genomic regions for both research and diagnostic purposes. Our enrichment method could potentially work with other genomes or target specified regions by applying other genomic editing tools, such as the CRISPR/Cas9 system.

We show how a bird’s-eye view of genomic structure can be obtained at ∼1-kb resolution from long (∼2 Mb) DNA molecules extracted from whole chromosomes in a nanofluidic laboratory-on-a-chip. We use an improved single-molecule denaturation mapping approach to detect repetitive elements and known as well as unique structural variation. Following its mapping, a molecule of interest was rescued from the chip; amplified and localized to a chromosome by FISH; and interrogated down to 1-bp resolution with a commercial sequencer, thereby reconciling haplotype-phased chromosome substructure with sequence.

Knowledge about the Holocene evolution of the Greenland ice sheet (GrIS) is important to put the recent observations of ice loss into a longer-term perspective. In this study, we use six new threshold lake records supplemented with two existing lake records to reconstruct the Holocene ice marginal fluctuations of the Qassimiut lobe (QL) – one of the most dynamic parts of the GrIS in South Greenland. Times when the ice margin was close to present extent are characterized by clastic input from the glacier meltwater, whereas periods when the ice margin was behind its present day extent comprise organic-rich sediments. We find that the overall pattern suggests that the central part of the ice lobe in low-lying areas experienced the most prolonged ice retreat from ~9–0.4 cal. ka BP, whereas the more distal parts of the ice lobe at higher elevation re-advanced and remained close to the present extent during the Neoglacial between ~4.4 and 1.8 cal. ka BP. These results demonstrate that the QL was primarily driven by Holocene climate changes, but also emphasises the role of local topography on the ice marginal fluctuations.

Transition state theory (TST) provides a simple interpretation of many thermally activated processes. It applies successfully on timescales and length scales that differ several orders of magnitude: to chemical reactions, breaking of chemical bonds, unfolding of proteins and RNA structures and polymers crossing entropic barriers. Here we apply TST to out-of-equilibrium transport through confined environments: the thermally activated translocation of single DNA molecules over an entropic barrier helped by an external force field. Reaction pathways are effectively one dimensional and so long that they are observable in a microscope. Reaction rates are so slow that transitions are recorded on video. We find sharp transition states that are independent of the applied force, similar to chemical bond rupture, as well as transition states that change location on the reaction pathway with the strength of the applied force. The states of equilibrium and transition are separated by micrometres as compared with angstroms/nanometres for chemical bonds., Transition state theory has proven to be a powerful tool for the analysis of a number of processes, perhaps most commonly chemical reactions. Here, the authors use transition state theory to model a directly observable, micron scale process—the transport of DNA molecules in a confined environment.

Nitrogen-vacancy (NV) centers in diamonds are interesting due to their remarkable characteristics that are well suited to applications in quantum-information processing and magnetic field sensing, as well as representing stable fluorescent sources. Multiple NV centers in nanodiamonds (NDs) are especially useful as biological fluorophores due to their chemical neutrality, brightness and room-temperature photostability. Furthermore, NDs containing multiple NV centers also have potential in high-precision magnetic field and temperature sensing. Coupling NV centers to propagating surface plasmon polariton (SPP) modes gives a base for lab-on-a-chip sensing devices, allows enhanced fluorescence emission and collection which can further enhance the precision of NV-based sensors. Here, we investigate coupling of multiple NV centers in individual NDs to the SPP modes supported by silver surfaces protected by thin dielectric layers and by gold V-grooves (VGs) produced via the self-terminated silicon etching. In the first case, we concentrate on monitoring differences in fluorescence spectra obtained from a source ND, which is illuminated by a pump laser, and from a scattering ND illuminated only by the fluorescence-excited SPP radiation. In the second case, we observe changes in the average NV lifetime when the same ND is characterized outside and inside a VG. Fluorescence emission from the VG terminations is also observed, which confirms the NV coupling to the VG-supported SPP modes., 22 pages, 13 figures

An optical two-beam trap, composed from two counter propagating laser beams, is an interesting setup due to the ability of the system to trap, hold, and stretch soft biological objects like vesicles or single cells. Because of this functionality, the system was also named "the optical stretcher" by Jochen Guck, Josep Kas and co-workers some 15 years ago. In a favorable setup, the two opposing laser beams meet with equal intensities in the middle of a fluidic channel in which cells may flow past, be trapped, stretched, and allowed to move on, giving the promise of a high throughput device. Yet, single beam optical traps, aka optical tweezers, by far outnumber the existing optical stretchers in research labs throughout the world. The ability to easily construct an optical stretcher setup in a low-cost material would possibly imply more frequent use of the optical stretching technique. Here, we will outline the design, the production procedures, and results obtained in a fiber-based experimental setup built within an injection molded microfluidic polymer chip. The microfluidic chip is constructed with a three layer technology in which we ensure both horizontal and vertical focusing of the cells we wish to trap, thereby preventing too many cells to flow below the line of focus of the two counter propagating laser beams that are positioned perpendicular to the direction of flow of the cells. Results will be compared to that from other designs from previous work in the group.

We determine the nonuniform stretching of and tension in a mega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA---e.g., native DNA extracted from human cells or bacteria---must be stretched with ease for inspection, this method applies.

Colour generation by plasmonic nanostructures and metasurfaces has several advantages over dye technology: reduced pixel area, sub-wavelength resolution and the production of bright and non-fading colours. However, plasmonic colour patterns need to be pre-designed and printed either by e-beam lithography (EBL) or focused ion beam (FIB), both expensive and not scalable processes that are not suitable for post-processing customization. Here we show a method of colour printing on nanoimprinted plasmonic metasurfaces using laser post-writing. Laser pulses induce transient local heat generation that leads to melting and reshaping of the imprinted nanostructures. Depending on the laser pulse energy density, different surface morphologies that support different plasmonic resonances leading to different colour appearances can be created. Using this technique we can print all primary colours with a speed of 1 ns per pixel, resolution up to 127,000 dots per inch (DPI) and power consumption down to 0.3 nJ per pixel.

Nanofluidics enables the imaging of stretched single molecules with potential applications for single molecule sequence mapping. Lab-on-a-chip devices for single cell trapping and lyzing, genomic DNA extraction from single cells, and optical mapping of genomic length DNA has been demonstrated separately. Yet the pursuit for applying DNA optical mapping to solve real genomics challenges is still to come. We review lab-on-a-chip devices from literature that could be part of a complete system for the sequence mapping of single DNA molecules.

The invention relates to a surface refractive index scanning system for characterization of a sample. The system comprises a grating device for holding or receiving the sample, the device comprising at least a first grating region having a first grating width along a transverse direction, and a second grating region having a second grating width in the transverse direction. The first grating region and the second grating region are adjacent in the transverse direction, wherein the first grating region has a grating period Λ1 in a longitudinal direction, and the second grating region has a grating period Λ2 in the longitudinal direction, where the longitudinal direction is orthogonal to the transverse direction. A grating period spacing ΔΛ = Λ1 - Λ2 is finite. Further, the first and second grating periods are chosen to provide optical resonances for light respectively in a first wavelength band and a second wavelength band, light is being emitted, transmitted, or reflected in an out-of-plane direction, wherein the first wavelength band and the second wavelength band are at least partially non-overlapping in wavelength. The system further comprises a light source for illuminating at least a part of the grating device with light at an illumination wavelength band. Additionally, the system comprises an imaging system for imaging the emitted, transmitted or reflected light from the grating device. The imaging system comprises an optical element, such as a cylindrical lens or a bended mirror, configured for focusing light in a transverse direction and for being invariant in an orthogonal transverse direction, the optical element being oriented such that the longitudinal direction of the grating device is oriented to coincide with the invariant direction of the optical element, and an imaging spectrometer comprising an entrance slit having a longitudinal direction oriented to coincide with the invariant direction of the optical element. The imaging spectrometer further comprises a 2-dimensional image sensor. The invention further relates to a method.

We present a method for making polymer chips with a narrow-band near-infrared absorber layer that enables light-induced local heating of liquids inside fluidic micro- and nanochannels fabricated by thermal imprint in polymethyl methacrylate. We have characterized the resulting liquid temperature profiles in microchannels using the temperature dependent fluorescence of the complex [Ru(bpy)(3)](2+). We demonstrate thermophoretic manipulation of individual YOYO-1 stained T4 DNA molecules inside micro- and nanochannels.

A chip scale tunable laser in the visible spectral band is realized by generating a periodic droplet array inside a microfluidic channel. Combined with a gain medium within the droplets, the periodic structure provides the optical feedback of the laser. By controlling the pressure applied to two separate inlets we can change the period of the droplet array. As a result, the lasing frequency is tuned over a broad spectral range. Using this configuration, we demonstrate wavelength tunability of about 70 nm and lasing threshold of about 15 μJ/mm2.

We demonstrate all-polymer injection molded devices for optical mapping of denaturation–renaturation (DR) patterns on long, single DNA-molecules from the human genome. The devices have channels with ultra-low aspect ratio, only 110 nm deep while 20 μm wide, and are superior to the silica devices used previously in the field. With these polymer devices, we demonstrate on-chip recording of DR images of DNA-molecules stretched to more than 95% of their contour length. The stretching is done by opposing flows Marie et al (2013 Proc. Natl Acad. Sci. USA 110 4893–8). The performance is validated by mapping 20 out of 24 Mbp-long DNA fragments to the human reference genome. We optimized fabrication of the devices to a yield exceeding 95%. This permits a substantial economies-of-scale driven cost-reduction, leading to device costs as low as 3 USD per device, about a factor 70 lower than the cost of silica devices. This lowers the barrier to a wide use of DR mapping of native, megabase-size DNA molecules, which has a huge potential as a complementary method to next-generation sequencing.

We demonstrate the highly efficient (>50%) conversion of freely propagating light to channel plasmon-polaritons (CPPs) in gold V-groove waveguides using compact 1.6 mu m long waveguide-termination coupling mirrors. Our straightforward fabrication process, involving UV-lithography and crystallographic silicon etching, forms the coupling mirrors innately and ensures exceptional-quality, wafer-scale device production. We tailor the V-shaped profiles by thermal silicon oxidation in order to shift initially wedge-located modes downward into the V-grooves, resulting in well-confined CPPs suitable for nanophotonic applications. We demonstrate the highly efficient (>50%) conversion of freely propagating light to channel plasmon-polaritons (CPPs) in gold V-groove waveguides using compact 1.6 mu m long waveguide-termination coupling mirrors. Our straightforward fabrication process, involving UV-lithography and crystallographic silicon etching, forms the coupling mirrors innately and ensures exceptional-quality, wafer-scale device production. We tailor the V-shaped profiles by thermal silicon oxidation in order to shift initially wedge-located modes downward into the V-grooves, resulting in well-confined CPPs suitable for nanophotonic applications.

The present invention relates to an optical device having a nano-structured surface capable of providing a structural color to a normal human viewer, the device made being manufactured in one single material. A plurality of nano- structured protrusions (5) is further arranged with a first periodicity (P1) in a first direction and a second periodicity (P2) in a second direction, the first and second periodicity being chosen so that the optical reflection is dominated by specular reflection. The nano-structured protrusions are optionally arranged with a relative spatial randomness (SR) with respect to the average surface positions. The position, size, and randomness of the protrusions are arranged so as to provide, at least up to a maximum angle of incidence (A_in) with respect to a normal to the surface, an angle-independent substantially homogeneous structural color perception for a normal human viewer, at least up to a maximum observation angle (A_obs) with respect to a normal to the surface.

Nanoimprinted distributed feedback dye laser sensors featuring multilayer slab waveguides are presented. A simple yet precise analytical model is used to optimize the lasers in order to give highest sensitivity and it is found that the thickness of a high index TiO2 top layer is the most important parameter for optimization. Using such laser sensors in an imaging spectroscopy setup, real-time label-free monitoring of sugar molecule diffusion in water is demonstrated. This method could potentially pave the way towards the analysis of small molecule diffusion in various media, e.g. protein signaling processes in tissue.

A new surveillance module for monitoring reproduction performances in dairy herd is proposed.The surveillance module includes monitoring of insemination and conception rates.Data are modeled using dynamic linear models and results are monitored using control charts. This application note presents a newly developed surveillance module for monitoring reproduction performances in dairy herds. It is called Critical Control Point and is part of a recently developed management tool, Dairy Management System. This management tool is commercialized as software intended both for farmers, extension officers, breeding advisors and veterinarians. Insemination and conception rates, for cows and heifers, are modeled at the herd level using Dynamic Generalized Linear Models for binomial data. The results are updated and monitored on a weekly basis, using control charts, and alarms are provided when the performances are below target values. Both the number of observed inseminations and pregnancies, and the insemination and pregnancy rates are monitored. The components of the user interface are presented and some comprehensive graphs, accessible to the user, illustrate the herd's performances over the last 52 weeks.

Animal disease epidemics such as the foot-and-mouth disease (FMD) pose recurrent threat to countries with intensive livestock production. Efficient FMD control is crucial in limiting the damage of FMD epidemics and securing food production. Decision making in FMD control involves a hierarchy of decisions made at strategic, tactical, and operational levels. These decisions are interdependent and have to be made under uncertainty about future development of the epidemic. Addressing this decision problem, this paper presents a new decision-support framework based on multi-level hierarchic Markov processes (MLHMP). The MLHMP model simultaneously optimizes decisions at strategic, tactical, and operational levels, using Bayesian forecasting methods to model uncertainty and learning about the epidemic. As illustrated by the example, the framework is especially useful in contingency planning for future FMD epidemics.

Fabrication and electrical properties of silicon quantum point contacts are reported. The devices are fabricated on bonded silicon on insulator (SOI) wafers by combining CMOS process steps and e-beam lithography. Mobility of 9000 cm2 Vs−1 is measured for a 60 nm-thick SOI film at 10 K. Weak localization data is used to estimate the phase coherence length at 4.2 K The point contacts show step like behaviour in linear response conductance at 1.5 K. At 200 mK universal conductance fluctuations begin to dominate the conductance curve. The effective diameter of quantum point constrictions of the devices are estimated to be 30–40 nm. This estimate is based on TEM analysis of test structures and AFM images of the actual device.

Dense Wavelength Division Multiplexing (DWDM) lasers play a major role in today’s long-haul broadband communication. Typical distributed feedback (DFB) laser cavities consist of long half-pitch gratings in InGaAsP on InP substrates with pitches around 240 nm. Lasers are made reliably single mode by including a lambda quarter shift at the center of the grating. The need for phase shifts and multiple wavelengths eliminates some lithography methods such as holography. Typically, these lasers are produced by e-beam lithography (EBL). We present a production method based on thermal nanoimprint lithography (T-NIL), which is potentially less costly and faster than EBL.NIL Technology and NeoPhotonics designed a stamp with the structures shown in Figure 1. The stamp was fabricated using EBL and dry etching. The line width on the stamp was 40 nm to accommodate for line broadening in subsequent processing steps and the structures were placed on mesas on the stamp.T-NIL of these structures presents three major challenges: 1) The imprinted structures must be aligned to the crystallographic direction of the InP substrate within 0.1°; 2) InP is a fragile material that will break under high pressure; 3) InP and Si have different thermal expansion coefficients, so temperatures must be kept low in order to maintain the designed pitches in the final devices.The imprinting was performed using NILT’s CNI tool. The imprint resist used was mr-I7020E spun to a thickness of 160 nm. Imprint pressure, temperature and time were 3 bar, 80°C, and 20 minutes, respectively. The release temperature was 55°C. The residual layer was removed by oxygen plasma. A representative AFM of the imprinted and etched grating structure is shown in Figure 2.The low imprint pressure ensures that the fragile InP substrate is not damaged during the imprint process and the narrow temperature window for imprint and separation (80°C and 55°C) ensures minimal issues with thermal mismatch between the InP substrate and the Si stamp.The imprinted InP wafers were processed in NeoPhotonics standard process line to create working lasers. The fabricated lasers were cleaved and measured. Laser arrays exhibited >40mW optical power in all 12 channels. Figure 3 shows the overlaid spectra of a 12-channel array laser chip with uniform (~3nm) wavelength spacing and good sidemode suppression.

International audience; Enhanced control of diffraction through transparent substrates is achieved via disordered gratings in a silica sol-gel film. Tailoring the degree of disorder allows tuning of the diffractive behavior from discrete orders into broad distributions over large angular range. Gratings of optical quality are formed by silica sol-gel nanoimprint lithography and an optical setup for the measurement of continuous diffraction patterns is presented. Sound agreement is found between measurements and simulation, validating both the approach for redirection of light and the fabrication process. The disordered gratings are presented in the context of improved interior daylighting and may furthermore be suited to a wide variety of applications where controlled angular redirection of light is desired.

Efficient nanoscale patterning of large areas is required for sub-wavelength optics. For example, 200 nm periodic structures are often too small to be made with standard UV- and DUV-equipment. Still, the final product must be made at an economic cost. Here we use a fast-writing strategy described in [1], where electron beam lithography (EBL) with a focused Gaussian beam is used to define shapes directly. The serial technique is optimized for speed and pattern fidelity to a maximum writing speed of around 30 min/cm2 for 200 nm periods in 2D lattices. The overall costs in terms of machine time and feasibility are assessed for different topographies and dimensions.

The magnetoconductivity σ(B) in the two-dimensional (2D) nondegenerate electron fluid and 2D solid has been analyzed theoretically and investigated experimentally, from 60 mK to 1.3 K in magnetic fieldsB up to 8 Tesla. In the fluid phase, σ(B) is described by the Drude model in weak to moderately strong classical fields, including the range βB≫1. At higher fields (depending on the density σ(B) is nonmonotonous and diplays a minimum. This behavior is due to many-electron effects, which can be described in terms of cyclotron orbit diffusion controlled by an internal fluctuational electric field. The squared internal field derived from experiments is in good agreement with computer simulations. In the solid phase electron transport becomes strongly non-linear even for weak driving voltagesV 0. Experimentally we determine, from the losses, the effective AC Corbino conductivity at a frequencyf. We find that σ(BαfV 0/B forV 0 below some threshold voltageV c . In this region the Hall velocity υ H approaches the ripplon phase velocityv 1=w(G 1)/G 1 at the first reciprocal lattice vectorG 1 of the electron solid. We suggest that this behaviour is due to to a resonant drag force from the Bragg-Cerenkov radiation of coherent ripplons by the moving crystal.

The scattering properties of randomly structured antireflective black silicon polymer replica have been investigated. Using a two-step casting process, the structures can be replicated in Ormocomp on areas of up to 3 in. in diameter. Fourier analysis of scanning electron microscopy images of the structures shows that the scattering properties of the surfaces are related to the spatial periods of the nanostructures. Structures with a dominating spatial period of 160 nm, a height of 200 nm, and aspect ratio of 1.3 show insignificant scattering of light with wavelength above 500 nm and lower the reflectance by a factor of two.

Background When inferring phylogenetic trees different algorithms may give different trees. To study such effects a measure for the distance between two trees is useful. Quartet distance is one such measure, and is the number of quartet topologies that differ between two trees. Results We have derived a new algorithm for computing the quartet distance between a pair of general trees, i.e. trees where inner nodes can have any degree ≥ 3. The time and space complexity of our algorithm is sub-cubic in the number of leaves and does not depend on the degree of the inner nodes. This makes it the fastest algorithm so far for computing the quartet distance between general trees independent of the degree of the inner nodes. Conclusions We have implemented our algorithm and two of the best competitors. Our new algorithm is significantly faster than the competition and seems to run in close to quadratic time in practice.