An Autonomous Molecular Bioluminescent Reporter (AMBER) for Voltage Imaging in Freely Moving Animals.

Genetically encoded reporters have greatly increased our understanding of biology. While fluorescent reporters have been widely used, photostability and phototoxicity have hindered their use in long-term experiments. Bioluminescence overcomes some of these challenges but requires the addition of an exogenous luciferin limiting its use. Using a modular approach, Autonomous Molecular BioluminEscent Reporter (AMBER), an indicator of membrane potential is engineered. Unlike other bioluminescent systems, AMBER is a voltage-gated luciferase coupling the functionalities of the Ciona voltage-sensing domain (VSD) and bacterial luciferase, luxAB. When co-expressed with the luciferin-producing genes, AMBER reversibly switches the bioluminescent intensity as a function of membrane potential. Using biophysical and biochemical methods, it is shown that AMBER switches its enzymatic activity from an OFF to an ON state as a function of the membrane potential. Upon depolarization, AMBER switches from a low to a high enzymatic activity state, showing a several-fold increase in the bioluminescence output (ΔL/L). AMBER in the pharyngeal muscles and mechanosensory touch neurons of Caenorhabditis elegans is expressed. Using the compressed sensing approach, the electropharingeogram of the C. elegans pharynx is reconstructed, validating the sensor in vivo. Thus, AMBER represents the first fully genetically encoded bioluminescent reporter without requiring exogenous luciferin addition.

Instantaneous tension measurements in droplet interface bilayers using an inexpensive, integrated pendant drop camera.

Recently, droplet interface bilayers (DIBs) have been used to determine bilayer tension and thickness in situ by automated image analysis using a microscope and an applied voltage. In this paper, we demonstrate improvements to these measurements by integrating an inexpensive pendant drop setup onto the microscope stage, which allows for simultaneous imaging of DIBs from both the bottom and side. By using pendant drop shape analysis in situ to determine the monolayer tension of the droplets, we avoid the reliance on applied voltages to determine tension. The integrated system also allows for direct measurement of both the major and minor diameter of the elliptical contact region, which produces a more direct measurement of the bilayer specific capacitance. Additionally, we demonstrate a technique for measuring the instantaneous monolayer tension of DIBs using shape analysis despite the assumed requirement for axial symmetry in pendant drop tensiometry. Compared to previous DIB measurements, the integrated pendant drop-microscope system provides improved accuracy accompanied by a fivefold to twentyfold improvement in precision while considerably decreasing the experiment time.

Multi-wavelength selective crossbar switch.

Here we demonstrate an 8x4 multi-wavelength selective ring resonator based crossbar switch matrix implemented in a 220-nm silicon photonics foundry for interconnecting electronic packet switches in scalable data centers. This switch design can dynamically assign up to two wavelength channels for any port-port connection, providing almost full connectivity with significant reduction in latency, cost and complexity. The switch unit cell insertion loss was measured at 0.8 dB, with an out-of-band rejection of 32 dB at 400 GHz channel separation. All the ring resonator heaters were thermally tuned, with heaters controlled by a custom 64-channel DAC driver. Detailed measurements on the whole switch showed standard deviation of 2 dB in losses across different paths, standard deviation of 0.33 nm in resonant wavelength and standard deviation of 0.01 nm/mW in ring heater tuning efficiency. Data transmission experiments at 40 Gbps showed negligible penalty due to crosstalk paths through the switch.

Orchestrating cells on a chip: Employing surface acoustic waves towards the formation of neural networks.

For the investigation of cell-cell interaction in general and for neural communication and future applications of neural networks, a controllable and well-defined network structure is crucial. We here propose the implementation of an acoustically driven system for tunable and deliberate stimulation and manipulation of cell growth on a chip. This piezoelectric chip allows us to generate a checkerboard-like standing surface acoustic wave pattern coupled to a fluid layer in a microfluidic chamber on top. Such a dynamically induced patterning lattice is shown to allow for the active positioning of the neurons and subsequent guided neurite outgrowth, thus finally overcoming the limitations of static approaches. After thorough characterization of the resulting tunable potential landscape, we successfully demonstrate cell adhesion and even growth of the such positioned cells within the well-defined pressure nodes. We demonstrate neuron growth at predetermined positions and observe a subsequent neurite outgrowth, even being correlated with the artificial potential landscape. For the very delicate and sensitive primary neural cells, this is a change of paradigm! Our experimental findings give us confidence that our hybrid lab-on-a-chip system in the near future will allow researchers to study cell-cell interaction of primary neurons. If scaled to a true network level, it will enable us to control and study how neural networks connect, interact, and communicate.

An optical-frequency synthesizer using integrated photonics.

Optical-frequency synthesizers, which generate frequency-stable light from a single microwave-frequency reference, are revolutionizing ultrafast science and metrology, but their size, power requirement and cost need to be reduced if they are to be more widely used. Integrated-photonics microchips can be used in high-coherence applications, such as data transmission 1 , highly optimized physical sensors 2 and harnessing quantum states 3 , to lower cost and increase efficiency and portability. Here we describe a method for synthesizing the absolute frequency of a lightwave signal, using integrated photonics to create a phase-coherent microwave-to-optical link. We use a heterogeneously integrated III-V/silicon tunable laser, which is guided by nonlinear frequency combs fabricated on separate silicon chips and pumped by off-chip lasers. The laser frequency output of our optical-frequency synthesizer can be programmed by a microwave clock across 4 terahertz near 1,550 nanometres (the telecommunications C-band) with 1 hertz resolution. Our measurements verify that the output of the synthesizer is exceptionally stable across this region (synthesis error of 7.7 × 10-15 or below). Any application of an optical-frequency source could benefit from the high-precision optical synthesis presented here. Leveraging high-volume semiconductor processing built around advanced materials could allow such low-cost, low-power and compact integrated-photonics devices to be widely used.

From Winner-Takes-All to Winners-Share-All: Exploiting the Information Capacity in Temporal Codes.

In this letter, we have implemented and compared two neural coding algorithms in the networks of spiking neurons: Winner-takes-all (WTA) and winners-share-all (WSA). Winners-Share-All exploits the code space provided by the temporal code by training a different combination of [Formula: see text] out of [Formula: see text] neurons to fire together in response to different patterns, while WTA uses a one-hot-coding to respond to distinguished patterns. Using WSA, the maximum value of [Formula: see text] in order to maximize information capacity using [Formula: see text] output neurons was theoretically determined and utilized. A small proof-of-concept classification problem was applied to a spiking neural network using both algorithms to classify 14 letters of English alphabet with an image size of 15 [Formula: see text] 15 pixels. For both schemes, a modified spike-timing-dependent-plasticity (STDP) learning rule has been used to train the spiking neurons in an unsupervised fashion. The performance and the number of neurons required to perform this computation are compared between the two algorithms. We show that by tolerating a small drop in performance accuracy (84% in WSA versus 91% in WTA), we are able to reduce the number of output neurons by more than a factor of two. We show how the reduction in the number of neurons will increase as the number of patterns increases. The reduction in the number of output neurons would then proportionally reduce the number of training parameters, which requires less memory and hence speeds up the computation, and in the case of neuromorphic implementation on silicon, would take up much less area.

On-chip wavelength locking for photonic switches.

We present an on-chip wavelength reference with a partial drop ring resonator and germanium photodetector. This approach can be used in ring-resonator-based wavelength-selective switches where absolute wavelength alignment is required. We use the temperature dependence of heater resistance as a temperature sensor. Additionally, we discuss locking speed, statistical variation of heater resistances, and tuning speed of the switches.

Solid-state nanopore based biomimetic voltage gated ion channels.

Voltage gating is essential to the computational ability of neurons. We show this effect can be mimicked in a solid-state nanopore by functionalizing the pore interior with a redox active molecule. We study the integration of an active biological molecule-a quinone-into a solid state nanopore, and its subsequent induced voltage gating. We show that the voltage gating effect mimics biological gating systems in its classic sigmoidal voltage response, unlike previous synthetic voltage gating systems. Initially, the quinone undergoes a reduction due to radicals in the bulk solution, and is converted to the hydroquinone state. Upon deprontonation the hydroquinone then acts as a charged nanomechanical arm, which opens the channel under the applied potential. We establish that the quinone gains a single net charge when the pH inside of the nanopore reaches its pKa value, and explore factors that influence the net pH in the middle of the pore. Using a combination of theory, experiment and simulation, we conclude that concentration polarization and a shift of the pH inside of the channel is the main cause of this gating effect.

Tailored Polymeric Membranes for Mycobacterium Smegmatis Porin A (MspA) Based Biosensors.

Nanopores based on protein channels inserted into lipid membranes have paved the way towards a wide-range of inexpensive biosensors, especially for DNA sequencing. A key obstacle in using these biological ion channels as nanodevices is the poor stability of lipid bilayer membranes. Amphiphilic block copolymer membranes have emerged as a robust alternative to lipid membranes. While previous efforts have shown feasibility, we demonstrate for the first time the effect of polymer composition on MspA protein functionality. We show that membrane-protein interaction depends on the hydrophobic-hydrophilic ratio (f-ratio) of the block copolymer. These effects are particularly pronounced in asymmetric protein pores like MspA compared to the cylindrical α-Hemolysin pore. A key effect of membrane-protein interaction is the increased 1/fα noise. After first showing increases in 1/fα behaviour arise from increased substate activity, the noise power spectral density S(f) was used as a qualitative tool for understanding protein-membrane interactions in polymer membranes. Polymer compositions with f-ratios close to lipid membranes caused noise behaviour not observed in lipid membranes. However, by modifying the f-ratio using a modular synthetic approach, we were able to design a block copolymer exhibiting noise properties similar to a lipid membrane, albeit with better stability. Thus, by careful optimization, block copolymer membranes can emerge as a robust alternative for protein-pore based nano-biosensors.

Modeling and Experimental Demonstration of a Hopfield Network Analog-to-Digital Converter with Hybrid CMOS/Memristor Circuits.

The purpose of this work was to demonstrate the feasibility of building recurrent artificial neural networks with hybrid complementary metal oxide semiconductor (CMOS)/memristor circuits. To do so, we modeled a Hopfield network implementing an analog-to-digital converter (ADC) with up to 8 bits of precision. Major shortcomings affecting the ADC's precision, such as the non-ideal behavior of CMOS circuitry and the specific limitations of memristors, were investigated and an effective solution was proposed, capitalizing on the in-field programmability of memristors. The theoretical work was validated experimentally by demonstrating the successful operation of a 4-bit ADC circuit implemented with discrete Pt/TiO2- x /Pt memristors and CMOS integrated circuit components.

Velocity profiles in pores with undulating opening diameter and their importance for resistive-pulse experiments.

Pores with undulating opening diameters have emerged as an analytical tool enhancing the speed of resistive-pulse experiments, with a potential to simultaneously characterize size and mechanical properties of translocating objects. In this work, we present a detailed study of the characteristics of resistive-pulses of charged and uncharged polymer particles in pores with different aspect ratios and pore topography. Although no external pressure difference was applied, our experiments and modeling indicated the existence of local pressure drops, which modified axial and radial velocities of the solution. As a consequence of the complex velocity profiles, pores with undulating pore diameter and low-aspect ratio exhibited large dispersion of the translocation times. Distribution of the pulse amplitude, which is a measure of the object size, was not significantly affected by the pore topography. The importance of tuning pore geometry for the application in resistive-sensing and multipronged characterization of physical properties of translocating objects is discussed.

Rapid Metal -free Macromolecular Coupling via in situ Nitrile Oxide-Activated Alkene Cycloaddition.

Nitrile oxide 1,3 dipolar cycloaddition is a simple and powerful coupling methodology. However, the self-dimerization of nitrile oxides has prevented the widespread use of this strategy for macromolecular coupling. By combining an in situ nitrile oxide generation with a highly reactive activated dipolarophile, we have overcome these obstacles and present a metal-free macromolecular coupling strategy for the modular synthesis of several ABA triblock copolymers. Nitrile oxides were generated in situ from chloroxime terminated poly(dimethylsiloxane) B-blocks and coupled with several distinct hydrophilic (poly(2-methyloxazoline) and poly(ethylene glycol)), and poly(N-isopropylacrylamide) or hydrophobic (poly(L-lactide) A-blocks terminated in activated dipolarophiles in a rapid fashion with high yield. This methodology overcomes many drawbacks of previously reported metal-free methods due to its rapid kinetics, versatility, scalability, and ease of introduction of necessary functionality. Nitrile oxide cycloaddition should find use as an attractive macromolecular coupling strategy for the synthesis of biocompatible polymeric nanostructures.

A CMOS enhanced solid-state nanopore based single molecule detection platform.

Solid-state nanopores have emerged as a single molecule label-free electronic detection platform. Existing transimpedance stages used to measure ionic current nanopores suffer from dynamic range limitations resulting from steady-state baseline currents. We propose a digitally-assisted baseline cancellation CMOS platform that circumvents this issue. Since baseline cancellation is a form of auto-zeroing, the 1/f noise of the system is also reduced. Our proposed design can tolerate a steady state baseline current of 10µA and has a usable bandwidth of 750kHz. Quantitative DNA translocation experiments on 5kbp DNA was performed using a 5nm silicon nitride pore using both the CMOS platform and a commercial system. Comparison of event-count histograms show that the CMOS platform clearly outperforms the commercial system, allowing for unambiguous interpretation of the data.

Stealth polymeric vesicles via metal-free click coupling.

The strain-promoted azide-alkyne cycloaddition represents an optimal metal-free method for the modular coupling of amphiphilic polymer blocks. Hydrophilic poly(oxazoline) (PMOXA) or poly(ethylene glycol) (PEG) A-blocks were coupled with a hydrophobic poly(siloxane) B-block to provide triblock copolymers capable of self-assembling into vesicular nanostructures. Stealth properties investigated via a complement activation assay revealed the superior in vitro stealth attributes of polymeric vesicles synthesized via a metal-free approach to those coupled via the widely used copper-catalyzed click method. Furthermore, the ability to change a single parameter, such as the hydrophilic block, allowed the direct comparison of the biocompatibility properties of triblock copolymers containing PMOXA or PEG. Our studies convincingly demonstrate the need for a metal-free approach, both in preventing cytotoxicity while imparting optimal stealth properties for potential biomedical applications.

Clickable Amphiphilic Triblock Copolymers.

Amphiphilic polymers have recently garnered much attention due to their potential use in drug-delivery and other biomedical applications. A modular synthesis of these polymers is extremely desirable since it offers precise individual block characterization and increased yields. We present here for the first time a modular synthesis of poly(oxazoline)-poly(siloxane)-poly(oxazoline) block copolymers that have been clicked together using the copper-catalyzed azide-alkyne cycloaddition reaction. Various click methodologies for the synthesis of these polymers have been carefully evaluated and optimized. The approach using copper nanoparticles was found to be the most optimal among the methods evaluated. Furthermore, these results were extended to allow for a reactive Si-H group-based siloxane middle block to be successfully clicked. This enables the design of more complex amphiphilic block copolymers that have additional functionality, such as stimuli responsiveness, to be synthesized via a simple hydrosilylation reaction.

Strategies for restoring vision to the blind: current and emerging technologies.

This paper reviews the current state of the art in the design of retinal prostheses that hope to restore vision to the blind. The progress and the challenges faced by electronic implants are discussed. Additionally, the emerging technologies in the field are also reviewed. These include optogenetics and chemical interfaces that interface to the neural system. These emerging fields have made tremendous progress in the last few years and offer new hope in the design of retinal prosthetic devices.

Communication and Control System for a 15-Channel Hermetic Retinal Prosthesis.

A small, hermetic, wirelessy-controlled retinal prosthesis has been developed for pre-clinical studies in Yucatan minipigs. The device was attached conformally to the outside of the eye in the socket and received both power and data wirelessly from external sources. Based on the received image data, the prosthesis drove a subretinal thin-film polyimide array of sputtered iridium oxide stimulating electrodes. The implanted device included a hermetic titanium case containing a 15-channel stimulator and receiver chip and discrete circuit components. Feedthroughs in the hermetic case connected the chip to secondary power- and data-receiving coils, which coupled to corresponding external power and data coils driven by power amplifiers. Power was delivered by a 125 KHz carrier, and data were delivered by amplitude shift keying of a 15.5 MHz carrier at 100 Kbps. Stimulation pulse strength, duration and frequency were programmed wirelessly from an external computer system. The final assembly was tested in vitro in physiological saline and in vivo in two minipigs for up to five and a half months by measuring stimulus artifacts generated by the implant's current drivers.

A hermetic wireless subretinal neurostimulator for vision prostheses.

A miniaturized, hermetically encased, wirelessly operated retinal prosthesis has been developed for preclinical studies in the Yucatan minipig, and includes several design improvements over our previously reported device. The prosthesis attaches conformally to the outside of the eye and electrically drives a microfabricated thin-film polyimide array of sputtered iridium oxide film electrodes. This array is implanted into the subretinal space using a customized ab externo surgical technique. The implanted device includes a hermetic titanium case containing a 15-channel stimulator chip and discrete circuit components. Feedthroughs in the case connect the stimulator chip to secondary power and data receiving coils on the eye and to the electrode array under the retina. Long-term in vitro pulse testing of the electrodes projected a lifetime consistent with typical devices in industry. The final assembly was tested in vitro to verify wireless operation of the system in physiological saline using a custom RF transmitter and primary coils. Stimulation pulse strength, duration, and frequency were programmed wirelessly from a Peripheral Component Interconnect eXtensions for Instrumentation (PXI) computer. Operation of the retinal implant has been verified in two pigs for up to five and a half months by detecting stimulus artifacts generated by the implanted device.

Wafer Scale Integration of CMOS Chips for Biomedical Applications via Self-Aligned Masking.

This paper presents a novel technique for the integration of small CMOS chips into a large area substrate. A key component of the technique is the CMOS chip based self-aligned masking. This allows for the fabrication of sockets in wafers that are at most 5 µm larger than the chip on each side. The chip and the large area substrate are bonded onto a carrier such that the top surfaces of the two components are flush. The unique features of this technique enable the integration of macroscale components, such as leads and microfluidics. Furthermore, the integration process allows for MEMS micromachining after CMOS die-wafer integration. To demonstrate the capabilities of the proposed technology, a low-power integrated potentiostat chip for biosensing implemented in the AMI 0.5 µm CMOS technology is integrated in a silicon substrate. The horizontal gap and the vertical displacement between the chip and the large area substrate measured after the integration were 4 µm and 0.5 µm, respectively. A number of 104 interconnects are patterned with high-precision alignment. Electrical measurements have shown that the functionality of the chip is not affected by the integration process.

Overview of the boston retinal prosthesis: challenges and opportunities to restore useful vision to the blind.

A small, hermetic, wirelessly-controlled retinal prosthesis was developed for pre-clinical studies in Yucatan mini-pigs. The device was implanted on the outside of the eye in the orbit, and it received both power and data wirelessly from external sources. The prosthesis drove a sub-retinal thin-film array of sputtered iridium oxide stimulating electrodes. The implanted device included a hermetic titanium case containing the 16-channel stimulator chip and discrete circuit components. Feedthroughs in the hermetic case connected the chip to secondary power- and data-receiving coils, which coupled to corresponding external power and data coils driven by a power amplifier. Power was delivered by a 500 KHz carrier, and data were delivered by frequency shift keying. Stimulation pulse strength, duration and frequency were programmed wirelessly from an external computer system. Through an 'outbound' telemetry channel, electrode impedances were monitored by an on-board analog to digital converter that sampled the output voltage waveforms. The final assembly was tested in vitro in physiological saline and in vivo in two mini-pigs for up to three months by measuring stimulus artifacts generated by the implant's current drivers.