A computational workflow for designing silicon donor qubits.

Developing devices that can reliably and accurately demonstrate the principles of superposition and entanglement is an on-going challenge for the quantum computing community. Modeling and simulation offer attractive means of testing early device designs and establishing expectations for operational performance. However, the complex integrated material systems required by quantum device designs are not captured by any single existing computational modeling method. We examine the development and analysis of a multi-staged computational workflow that can be used to design and characterize silicon donor qubit systems with modeling and simulation. Our approach integrates quantum chemistry calculations with electrostatic field solvers to perform detailed simulations of a phosphorus dopant in silicon. We show how atomistic details can be synthesized into an operational model for the logical gates that define quantum computation in this particular technology. The resulting computational workflow realizes a design tool for silicon donor qubits that can help verify and validate current and near-term experimental devices.

Vertically aligned carbon nanofiber as nano-neuron interface for monitoring neural function.

Neural chips, which are capable of simultaneous multisite neural recording and stimulation, have been used to detect and modulate neural activity for almost thirty years. As neural interfaces, neural chips provide dynamic functional information for neural decoding and neural control. By improving sensitivity and spatial resolution, nano-scale electrodes may revolutionize neural detection and modulation at cellular and molecular levels as nano-neuron interfaces. We developed a carbon-nanofiber neural chip with lithographically defined arrays of vertically aligned carbon nanofiber electrodes and demonstrated its capability of both stimulating and monitoring electrophysiological signals from brain tissues in vitro and monitoring dynamic information of neuroplasticity. This novel nano-neuron interface may potentially serve as a precise, informative, biocompatible, and dual-mode neural interface for monitoring of both neuroelectrical and neurochemical activity at the single-cell level and even inside the cell. FROM THE CLINICAL EDITOR: The authors demonstrate the utility of a neural chip with lithographically defined arrays of vertically aligned carbon nanofiber electrodes. The new device can be used to stimulate and/or monitor signals from brain tissue in vitro and for monitoring dynamic information of neuroplasticity both intracellularly and at the single cell level including neuroelectrical and neurochemical activities.

Characterization of a reversible thermally-actuated polymer-valve: A potential dynamic treatment for congenital diaphragmatic hernia.

BACKGROUND: Congenital diaphragmatic hernia (CDH) is a fetal defect comprising an incomplete diaphragm and the herniation of abdominal organs into the chest cavity that interfere with fetal pulmonary development. Though the most promising treatment for CDH is via interventional fetoscopic tracheal occlusion (TO) surgery in-utero, it has produced mixed results due to the static nature of the inserted occlusion. We hypothesize that a suitable noninvasively-actuatable, cyclic-release tracheal occlusion device can be developed to enable dynamic tracheal occlusion (dTO) implementation. OBJECTIVE: To conduct an in-vitro proof-of-concept investigation of the construction of thermo-responsive polymer valves designed for targeted activation within a physiologically realizable temperature range as a first step towards potential development of a noninvasively-actuatable implantable device to facilitate dynamic tracheal occlusion (dTO) therapy. METHODS: Six thermo-responsive polymer valves, with a critical solution temperature slightly higher than normal physiological body temperature of 37°C, were fabricated using a copolymer of n-isopropylacrylamide (NIPAM) and dimethylacrylamide (DMAA). Three of the valves underwent ethylene oxide (EtO) sterilization while the other three served as controls for EtO-processing compatibility testing. Thermal response actuation of the valves and their steady-state flow performances were evaluated using water and caprine amniotic fluid. RESULTS: All six valves consisting of 0.3-mole fraction of DMAA were tested for thermal actuation of caprine amniotic fluid flow at temperatures ranging from 30-44°C. They all exhibited initiation of valve actuation opening at ~40°C with full completion at ~44°C. The overall average coefficient of variation (CV) for the day-to-day flow performance of the valves tested was less than 12%. Based on a Student t-test, there was no significant difference in the operational characteristics for the EtO processed versus the non-EtO processed valves tested. CONCLUSIONS: We successfully fabricated and demonstrated physiological realizable temperature range operation of thermo-responsive polymer valves in-vitro and their suitability for standard EtO sterilization processing, a prerequisite for future in-vivo surgical implantation testing.

In-silico and in-vitro investigation of a photonic monitor for intestinal perfusion and oxygenation.

The quantification of visceral organ oxygenation after trauma-related systemic hypovolemia and shock is critical to enable effective resuscitation. In this work, a photoplethysmography-based (PPG) sensor was specifically designed for probing the perfusion and oxygenation condition of intestinal tissue with the ultimate goal to monitor patients post trauma to guide resuscitation. Through Monte Carlo modeling, suitable optofluidic phantoms were determined, the wavelength and separation distance for the sensor was optimized, and sensor performance for the quantification of tissue perfusion and oxygenation was tested on the in-vitro phantom. In particular, the Monte Carlo simulated both a standard block three-layer model and a more realistic model including villi. Measurements were collected on the designed three layer optofluidic phantom and the results taken with the small form factor PPG device showed a marked improvement when using shorter visible wavelengths over the more conventional longer visible wavelengths. Overall, in this work a Monte Carlo model was developed, an optofluidic phantom was built, and a small form factor PPG sensor was developed and characterized using the phantom for perfusion and oxygenation over the visible wavelength range. The results show promise that this small form factor PPG sensor could be used as a future guide to shock-related resuscitation.

Resident neuroelectrochemical interfacing using carbon nanofiber arrays.

Carbon nanofiber electrode architectures are used to provide for long-term, neuroelectroanalytical measurements of the dynamic processes of intercellular communication between excitable cells. Individually addressed, vertically aligned carbon nanofibers are incorporated into multielement electrode arrays upon which excitable cell matrixes of both neuronal-like derived cell lines (rat pheochromocytoma, PC-12) and primary cells (dissociated cells from embryonic rat hippocampus) are cultured over extended periods (days to weeks). Electrode arrays are characterized with respect to their response to easily oxidized neurotransmitters, including dopamine, norepinephrine, and 5-hydroxytyramide. Electroanalysis at discrete electrodes following long-term cell culture demonstrates that this platform remains responsive for the detection of easily oxidized species generated by the cultured cells. Preliminary data also suggests that quantal release of easily oxidized transmitters can be observed at nanofiber electrodes following direct culture and differentiation on the arrays for periods of at least 16 days.

Real-time separation of perfusion and oxygenation signals for an implantable sensor using adaptive filtering.

In this paper, an adaptive filtering algorithm to separate signals due to perfusion and oxygenation has been developed using an 810-nm source, in addition to 660-nm and 940-nm sources, as an internal reference due to its limited oxygen sensitivity. The newly developed algorithm was tested using Monte Carlo simulated data to prove the effectiveness of the 810-nm reference and adaptive algorithm. Following the simulation, an in vitro model was developed to test the algorithm that used a blood flow through system wrapped with tissue. The system had the ability to isolate the effects of perfusion and oxygenation and the algorithm accurately captured the changes in these signals with reliable consistency. Using the serosal surface of the swine jejunum, in vivo data was also taken to analyze the algorithms response to fluctuating perfusion levels like that seen in hemorrhaging or failing transplants. The algorithm was able to extract the perfusion information from the oxygenation information in this in vivo study. Overall, it was shown that an adaptive filtering algorithm using an 810-nm reference has provided a means to separate oxygenation and perfusion.

Processing of pulse oximeter data using discrete wavelet analysis.

A wavelet-based signal processing technique was employed to improve an implantable blood perfusion monitoring system. Data was acquired from both in vitro and in vivo sources: a perfusion model and the proximal jejunum of an adult pig. Results showed that wavelet analysis could isolate perfusion signals from raw, periodic, in vitro data as well as fast Fourier transform (FFT) methods. However, for the quasi-periodic in vivo data segments, wavelet analysis provided more consistent results than the FFT analysis for data segments of 50, 10, and 5 s in length. Wavelet analysis has thus been shown to require less data points for quasi-periodic data than FFT analysis making it a good choice for an indwelling perfusion monitor where power consumption and reaction time are paramount.

An autocorrelation-based time domain analysis technique for monitoring perfusion and oxygenation in transplanted organs.

In designing an implantable sensor for perfusion monitoring of transplant organs the ability of the sensor to gather perfusion information with limited power consumption and in near real time is paramount. The following work was performed to provide a processing method that is able to predict perfusion and oxygenation change within the blood flowing through a transplanted organ. For this application, an autocorrelation-based algorithm was used to reduce the acquisition time required for fast Fourier transform (FFT) analysis while retaining the accuracy inherent to FFT analysis. In order to provide data proving that the developed method is able to predict perfusion as accurately as FFT two experiments were developed isolating both periodic and quasi-periodic cardiac frequencies. It was shown that the autocorrelation-based method was able to perform comparably with FFT (limited to a sampling frequency of 300 Hz) and maintain accuracy down to acquisition times as low as 4 s in length.

Wireless monitoring of liver hemodynamics in vivo.

Liver transplants have their highest technical failure rate in the first two weeks following surgery. Currently, there are limited devices for continuous, real-time monitoring of the graft. In this work, a three wavelengths system is presented that combines near-infrared spectroscopy and photoplethysmography with a processing method that can uniquely measure and separate the venous and arterial oxygen contributions. This strategy allows for the quantification of tissue oxygen consumption used to study hepatic metabolic activity and to relate it to tissue stress. The sensor is battery operated and communicates wirelessly with a data acquisition computer which provides the possibility of implantation provided sufficient miniaturization. In two in vivo porcine studies, the sensor tracked perfusion changes in hepatic tissue during vascular occlusions with a root mean square error (RMSE) of 0.135 mL/min/g of tissue. We show the possibility of using the pulsatile wave to measure the arterial oxygen saturation similar to pulse oximetry. The signal is also used to extract the venous oxygen saturation from the direct current (DC) levels. Arterial and venous oxygen saturation changes were measured with an RMSE of 2.19% and 1.39% respectively when no vascular occlusions were induced. This error increased to 2.82% and 3.83% when vascular occlusions were induced during hypoxia. These errors are similar to the resolution of a commercial oximetry catheter used as a reference. This work is the first realization of a wireless optical sensor for continuous monitoring of hepatic hemodynamics.

Quantifying tissue mechanical properties using photoplethysmography.

Photoplethysmography (PPG) is a non-invasive optical method that can be used to detect blood volume changes in the microvascular bed of tissue. The PPG signal comprises two components; a pulsatile waveform (AC) attributed to changes in the interrogated blood volume with each heartbeat, and a slowly varying baseline (DC) combining low frequency fluctuations mainly due to respiration and sympathetic nervous system activity. In this report, we investigate the AC pulsatile waveform of the PPG pulse for ultimate use in extracting information regarding the biomechanical properties of tissue and vasculature. By analyzing the rise time of the pulse in the diastole period, we show that PPG is capable of measuring changes in the Young's Modulus of tissue mimicking phantoms with a resolution of 4 KPa in the range of 12 to 61 KPa. In addition, the shape of the pulse can potentially be used to diagnose vascular complications by differentiating upstream from downstream complications. A Windkessel model was used to model changes in the biomechanical properties of the circulation and to test the proposed concept. The modeling data confirmed the response seen in vitro and showed the same trends in the PPG rise and fall times with changes in compliance and vascular resistance.

Intestinal perfusion monitoring using photoplethysmography.

In abdominal trauma patients, monitoring intestinal perfusion and oxygen consumption is essential during the resuscitation period. Photoplethysmography is an optical technique potentially capable of monitoring these changes in real time to provide the medical staff with a timely and quantitative measure of the adequacy of resuscitation. The challenges for using optical techniques in monitoring hemodynamics in intestinal tissue are discussed, and the solutions to these challenges are presented using a combination of Monte Carlo modeling and theoretical analysis of light propagation in tissue. In particular, it is shown that by using visible wavelengths (i.e., 470 and 525 nm), the perfusion signal is enhanced and the background contribution is decreased compared with using traditional near-infrared wavelengths leading to an order of magnitude enhancement in the signal-to-background ratio. It was further shown that, using the visible wavelengths, similar sensitivity to oxygenation changes could be obtained (over 50% compared with that of near-infrared wavelengths). This is mainly due to the increased contrast between tissue and blood in that spectral region and the confinement of the photons to the thickness of the small intestine. Moreover, the modeling results show that the source to detector separation should be limited to roughly 6 mm while using traditional near-infrared light, with a few centimeters source to detector separation leads to poor signal-to-background ratio. Finally, a visible wavelength system is tested in an in vivo porcine study, and the possibility of monitoring intestinal perfusion changes is showed.

Optofluidic phantom mimicking optical properties of porcine livers.

One strategy for assessing efficacy of a liver transplant is to monitor perfusion and oxygenation after transplantation. An implantable optical sensor is being developed to overcome inadequacies of current monitoring approaches. To facilitate sensor design while minimizing animal use, a polydimethylsiloxane (PDMS)-based liver phantom was developed to mimic the optical properties of porcine liver in the 630-1000 nm wavelength range and the anatomical geometry of liver parenchyma. Using soft lithography to construct microfluidic channels in pigmented elastomer enabled the 2D approximation of hexagonal liver lobules with 15mm sinusoidal channels, which will allow perfusion with blood-mimicking fluids to facilitate the development of the liver perfusion and oxygenation monitoring system.

Optimizing probe design for an implantable perfusion and oxygenation sensor.

In an effort to develop an implantable optical perfusion and oxygenation sensor, based on multiwavelength reflectance pulse oximetry, we investigate the effect of source-detector separation and other source-detector characteristics to optimize the sensor's signal to background ratio using Monte Carlo (MC) based simulations and in vitro phantom studies. Separations in the range 0.45 to 1.25 mm were found to be optimal in the case of a point source. The numerical aperture (NA) of the source had no effect on the collected signal while the widening of the source spatial profile caused a shift in the optimal source-detector separation. Specifically, for a 4.5 mm flat beam and a 2.4 mm × 2.5 mm photodetector, the optimal performance was found to be when the source and detector are adjacent to each other. These modeling results were confirmed by data collected from in vitro experiments on a liver phantom perfused with dye solutions mimicking the absorption properties of hemoglobin for different oxygenation states.

Isolated photosystem I reaction centers on a functionalized gated high electron mobility transistor.

In oxygenic plants, photons are captured with high quantum efficiency by two specialized reaction centers (RC) called Photosystem I (PS I) and Photosystem II (PS II). The captured photon triggers rapid charge separation and the photon energy is converted into an electrostatic potential across the nanometer-scale (~6 nm) reaction centers. The exogenous photovoltages from a single PS I RC have been previously measured using the technique of Kelvin force probe microscopy (KFM). However, biomolecular photovoltaic applications require two-terminal devices. This paper presents for the first time, a micro-device for detection and characterization of isolated PS I RCs. The device is based on an AlGaN/GaN high electron mobility transistor (HEMT) structure. AlGaN/GaN HEMTs show high current throughputs and greater sensitivity to surface charges compared to other field-effect devices. PS I complexes immobilized on the floating gate of AlGaN/GaN HEMTs resulted in significant changes in the device characteristics under illumination. An analytical model has been developed to estimate the RCs of a major orientation on the functionalized gate surface of the HEMTs.

Vertically aligned carbon nanofiber arrays record electrophysiological signals from hippocampal slices.

Vertically aligned carbon nanofiber (VACNF) electrode arrays were tested for their potential application in recording neuro-electrophysiological activity. We report, for the first time, stimulation and extracellular recording of spontaneous and evoked neuroelectrical activity in organotypic hippocampal slice cultures with ultramicroelectrode VACNF arrays. Because the electrodes are carbon-based, these arrays have potential advantages over metal electrodes and could enable a variety of future applications as precise, informative, and biocompatible neural interfaces.