Bayesian Multiple Emitter Fitting using Reversible Jump Markov Chain Monte Carlo.
ABSTRACT: In single molecule localization-based super-resolution imaging, high labeling density or the desire for greater data collection speed can lead to clusters of overlapping emitter images in the raw super-resolution image data. We describe a Bayesian inference approach to multiple-emitter fitting that uses Reversible Jump Markov Chain Monte Carlo to identify and localize the emitters in dense regions of data. This formalism can take advantage of any prior information, such as emitter intensity and density. The output is both a posterior probability distribution of emitter locations that includes uncertainty in the number of emitters and the background structure, and a set of coordinates and uncertainties from the most probable model.
Project description:Mass spectrometry (MS) is the enabling technology for proteomics and metabolomics. However, dramatic improvements in both sensitivity and throughput are still required to achieve routine MS-based single cell proteomics and metabolomics. Here, we report the silicon-based monolithic multinozzle emitter array (MEA) and demonstrate its proof-of-principle applications in high-sensitivity and high-throughput nanoelectrospray mass spectrometry. Our MEA consists of 96 identical 10-nozzle emitters in a circular array on a 3 in. silicon chip. The geometry and configuration of the emitters, the dimension and number of the nozzles, and the micropillar arrays embedded in the main channel can be systematically and precisely controlled during the microfabrication process. Combining electrostatic simulation and experimental testing, we demonstrated that sharpened-end geometry at the stem of the individual multinozzle emitter significantly enhanced the electric fields at its protruding nozzle tips, enabling sequential nanoelectrospray for the high-density emitter array. We showed that electrospray current of the multinozzle emitter at a given total flow rate was approximately proportional to the square root of the number of its spraying-nozzles, suggesting the capability of high MS sensitivity for multinozzle emitters. Using a conventional Z-spray mass spectrometer, we demonstrated reproducible MS detection of peptides and proteins for serial MEA emitters, achieving sensitivity and stability comparable to the commercial capillary emitters. Our robust silicon-based MEA chip opens up the possibility of a fully integrated microfluidic system for ultrahigh-sensitivity and ultrahigh-throughput proteomics and metabolomics.
Project description:On-chip twisted light emitters are essential components of orbital angular momentum (OAM) communication devices1, 2. These devices address the growing demand for high-capacity communication systems by providing an additional degree of freedom for wavelength/frequency division multiplexing (WDM/FDM). Although whispering-gallery-mode-enabled OAM emitters have been shown to possess some advantages3, 4, 5, such as compactness and phase accuracy, their inherent narrow bandwidths prevent them from being compatible with WDM/FDM techniques. Here, we demonstrate an ultra-broadband multiplexed OAM emitter that utilizes a novel joint path-resonance phase control concept. The emitter has a micron-sized radius and nanometer-sized features. Coaxial OAM beams are emitted across the entire telecommunication band from 1,450 to 1,650 nm. We applied the emitter to an OAM communication with a data rate of 1.2 Tbit/s assisted by 30-channel optical frequency combs (OFCs). The emitter provides a new solution to further increase capacity in the OFC communication scenario.
Project description:The rate at which a given site in a gene sequence alignment evolves over time may vary. This phenomenon--known as heterotachy--can bias or distort phylogenetic trees inferred from models of sequence evolution that assume rates of evolution are constant. Here, we describe a phylogenetic mixture model designed to accommodate heterotachy. The method sums the likelihood of the data at each site over more than one set of branch lengths on the same tree topology. A branch-length set that is best for one site may differ from the branch-length set that is best for some other site, thereby allowing different sites to have different rates of change throughout the tree. Because rate variation may not be present in all branches, we use a reversible-jump Markov chain Monte Carlo algorithm to identify those branches in which reliable amounts of heterotachy occur. We implement the method in combination with our 'pattern-heterogeneity' mixture model, applying it to simulated data and five published datasets. We find that complex evolutionary signals of heterotachy are routinely present over and above variation in the rate or pattern of evolution across sites, that the reversible-jump method requires far fewer parameters than conventional mixture models to describe it, and serves to identify the regions of the tree in which heterotachy is most pronounced. The reversible-jump procedure also removes the need for a posteriori tests of 'significance' such as the Akaike or Bayesian information criterion tests, or Bayes factors. Heterotachy has important consequences for the correct reconstruction of phylogenies as well as for tests of hypotheses that rely on accurate branch-length information. These include molecular clocks, analyses of tempo and mode of evolution, comparative studies and ancestral state reconstruction. The model is available from the authors' website, and can be used for the analysis of both nucleotide and morphological data.
Project description:Coupling nano-emitters to plasmonic antennas is a key milestone for the development of nanoscale quantum light sources. One challenge, however, is the precise nanoscale positioning of the emitter in the structure. Here, we present a laser etching protocol that deterministically positions a single colloidal CdSe/CdS core/shell quantum dot emitter inside a subwavelength plasmonic patch antenna with three-dimensional nanoscale control. By exploiting the properties of metal-insulator-metal structures at the nanoscale, the fabricated single-emitter antenna exhibits a very high-Purcell factor (>72) and a brightness enhancement of a factor of 70. Due to the unprecedented quenching of Auger processes and the strong acceleration of the multiexciton emission, more than 4 photons per pulse can be emitted by a single quantum dot, thus increasing the device yield. Our technology can be applied to a wide range of photonic nanostructures and emitters, paving the way for scalable and reliable fabrication of ultra-compact light sources.
Project description:Tandem repeats occur frequently in biological sequences. They are important for studying genome evolution and human disease. A number of methods have been designed to detect a single tandem repeat in a sliding window. In this article, we focus on the case that an unknown number of tandem repeat segments of the same pattern are dispersively distributed in a sequence. We construct a probabilistic generative model for the tandem repeats, where the sequence pattern is represented by a motif matrix. A Bayesian approach is adopted to compute this model. Markov chain Monte Carlo (MCMC) algorithms are used to explore the posterior distribution as an effort to infer both the motif matrix of tandem repeats and the location of repeat segments. Reversible jump Markov chain Monte Carlo (RJMCMC) algorithms are used to address the transdimensional model selection problem raised by the variable number of repeat segments. Experiments on both synthetic data and real data show that this new approach is powerful in detecting dispersed short tandem repeats. As far as we know, it is the first work to adopt RJMCMC algorithms in the detection of tandem repeats.
Project description:The application of plasmonics to thermal emitters is generally assisted by absorptive losses in the metal because Kirchhoff's law prescribes that only good absorbers make good thermal emitters. Based on a designed plasmonic crystal and exploiting a slow-wave lattice resonance and spontaneous thermal plasmon emission, we engineer a tungsten-based thermal emitter, fabricated in an industrial CMOS process, and demonstrate its markedly improved practical use in a prototype non-dispersive infrared (NDIR) gas-sensing device. We show that the emission intensity of the thermal emitter at the CO(2) absorption wavelength is enhanced almost 4-fold compared to a standard non-plasmonic emitter, which enables a proportionate increase in the signal-to-noise ratio of the CO(2) gas sensor.
Project description:One approach to super-resolution fluorescence microscopy, termed stochastic localization microscopy, relies on the nanometer scale spatial localization of individual fluorescent emitters that stochastically label specific features of the specimen. The precision of emitter localization is an important determinant of the resulting image resolution but is insufficient to specify how well the derived images capture the structure of the specimen. We address this deficiency by considering the inference of specimen structure based on the estimated emitter locations. By using estimation theory, we develop a measure of spatial resolution that jointly depends on the density of the emitter labels, the precision of emitter localization, and prior information regarding the spatial frequency content of the labeled object. The Nyquist criterion does not set the scaling of this measure with emitter number. Given prior information and a fixed emitter labeling density, our resolution measure asymptotes to a finite value as the precision of emitter localization improves. By considering the present experimental capabilities, this asymptotic behavior implies that further resolution improvements require increases in labeling density above typical current values. Our treatment also yields algorithms to enhance reliable image features. Overall, our formalism facilitates the rigorous statistical interpretation of the data produced by stochastic localization imaging techniques.
Project description:Optical cavities can enhance and control light-matter interactions. This level of control has recently been extended to the nanoscale with single emitter strong coupling even at room temperature using plasmonic nanostructures. However, emitters in static geometries, limit the ability to tune the coupling strength or to couple different emitters to the same cavity. Here, we present tip-enhanced strong coupling (TESC) with a nanocavity formed between a scanning plasmonic antenna tip and the substrate. By reversibly and dynamically addressing single quantum dots, we observe mode splitting up to 160 meV and anticrossing over a detuning range of ~100 meV, and with subnanometer precision over the deep subdiffraction-limited mode volume. Thus, TESC enables previously inaccessible control over emitter-nanocavity coupling and mode volume based on near-field microscopy. This opens pathways to induce, probe, and control single-emitter plasmon hybrid quantum states for applications from optoelectronics to quantum information science at room temperature.
Project description:The development of high performance nano-electron-emitter arrays with well reliability still proves challenging. Here, we report a featured integrated nano-electron-emitter. The vertically aligned nano-emitter consists of two segments. The top segment is an intrinsically lightly n-type doped ZnO nano-tip, while the bottom segment is a heavily p-type doped Si nano-pillar (denoted as p-Si/ZnO nano-emitter). The anode voltage not only extracted the electron emission from the emitter apex but also induced the inter-band electron tunneling at the surface of the p-Si/ZnO nano-junction. The designed p-Si/ZnO emitter is equivalent to a ZnO nano-tip individually ballasted by a p-Si/ZnO diode and a parasitic tunneling field effect transistor (TFET) at the surface of the p-Si/ZnO junction. The parasitic TFET provides a channel for the supply of emitting electron, while the p-Si/ZnO diode is benefit for impeding the current overloading and prevent the emitters from a catastrophic breakdown. Well repeatable and stable field emission current were obtained from the p-Si/ZnO nano-emitters. High performance nano-emitters was developed using diamond-like-carbon coated p-Si/ZnO tip array (500?×?500), i.e., 178??A (4.48?mA/cm(2)) at 75.7?MV/m.
Project description:Arrays of chemically etched emitters with individualized sheath gas capillaries were developed to enhance electrospray ionization (ESI) efficiency at subambient pressures. By incorporating the new emitter array in a subambient pressure ionization with nanoelectrospray (SPIN) source, both ionization efficiency and ion transmission efficiency were significantly increased, providing enhanced sensitivity in mass spectrometric analyses. The SPIN source eliminates the major ion losses of conventional ESI-mass spectrometry (MS) interfaces by placing the emitter in the first reduced pressure region of the instrument. The new ESI emitter array design developed in this study allows individualized sheath gas around each emitter in the array making it possible to generate an array of uniform and stable electrosprays in the subambient pressure (10 to 30 Torr) environment for the first time. The utility of the new emitter arrays was demonstrated by coupling the emitter array/SPIN source with a time of flight (TOF) mass spectrometer. The instrument sensitivity was compared under different ESI source and interface configurations including a standard atmospheric pressure single ESI emitter/heated capillary, single emitter/SPIN and multi-emitter/SPIN configurations using an equimolar solution of nine peptides. The highest instrument sensitivity was observed using the multi-emitter/SPIN configuration in which the sensitivity increased with the number of emitters in the array. Over an order of magnitude MS sensitivity improvement was achieved using multi-emitter/SPIN compared with using the standard atmospheric pressure single ESI emitter/heated capillary interface.