pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells.

SUMMARY: pyCapsid is a Python package developed to facilitate the characterization of the dynamics and quasi-rigid mechanical units of protein shells and other protein complexes. The package was developed in response to the rapid increase of high-resolution structures, particularly capsids of viruses, requiring multiscale biophysical analyses. Given a protein shell, pyCapsid generates the collective vibrations of its amino-acid residues, identifies quasi-rigid mechanical regions associated with the disassembly of the structure, and maps the results back to the input proteins for interpretation. pyCapsid summarizes the main results in a report that includes publication-quality figures. AVAILABILITY AND IMPLEMENTATION: pyCapsid's source code is available under MIT License on GitHub. It is compatible with Python 3.8-3.10 and has been deployed in two leading Python package-management systems, PIP and Conda. Installation instructions and tutorials are available in the online documentation and in the pyCapsid's YouTube playlist. In addition, a cloud-based implementation of pyCapsid is available as a Google Colab notebook. pyCapsid Colab does not require installation and generates the same report and outputs as the installable version. Users can post issues regarding pyCapsid in the repository's issues section.

High density vertical optical interconnects for passive assembly.

The co-packaging of optics and electronics provides a potential path forward to achieving beyond 50 Tbps top of rack switch packages. In a co-packaged design, the scaling of bandwidth, cost, and energy is governed by the number of optical transceivers (TxRx) per package as opposed to transistor shrink. Due to the large footprint of optical components relative to their electronic counterparts, the vertical stacking of optical TxRx chips in a co-packaged optics design will become a necessity. As a result, development of efficient, dense, and wide alignment tolerance chip-to-chip optical couplers will be an enabling technology for continued TxRx scaling. In this paper, we propose a novel scheme to vertically couple into standard 220 nm silicon on insulator waveguides from 220 nm silicon nitride on glass waveguides using overlapping, inverse double tapers. Simulation results using Lumerical's 3D Finite Difference Time Domain solver are presented, demonstrating insertion losses below -0.13 dB for an inter-chip spacing of 1 µm; 1 dB vertical and lateral alignment tolerances of approximately 2.6 µm and ± 2.8 µm, respectively; a greater than 300 nm 1 dB bandwidth; and 1 dB twist and tilt tolerances of approximately ± 2.3 degrees and 0.4 degrees, respectively. These results demonstrate the potential of our coupler for use in co-packaged designs requiring high performance, high density, CMOS compatible out of plane optical connections.

C-band operating plasmonic sensor with a high Q-factor/figure of merit based on a silicon nano-ring.

In this paper, we take advantage of the high refractive index property of silicon to design a practical and sensitive plasmonic sensor on a photonic integrated circuit (PIC) platform. It has been demonstrated that a label-free refractive index sensor with sensitivity up to 1124 nm/RIU can be obtained using a simple design of a silicon nano-ring with a concentric hexagonal plasmonic cavity. It has also been shown that, with optimum structural parameters, a quality factor (Q-factor) of 307 and a figure of merit (FOM) of 234R I U -1 can be achieved, which are approximately 8 times and 5 times higher than the proposed sensors counterparts, respectively. In addition, the resonance mode of the hexagonal cavity with Si nano-ring (HCS) sensor can be adjusted to operate in the C-band, which is a highly desirable wavelength range in terms of compatibility with devices in PIC technology.

Hands-On Photonic Education Kits: empowering the integrated photonics workforce through practical training.

The Hands-On Photonic Education (HOPE) Kits, developed with AIM Photonics, address the need for skilled workers in integrated photonics. This paper highlights the role of the HOPE Kits in advancing the training ecosystem and bridging the skills gap. The kits include fully packaged photonic integrated circuits (PICs), enabling instructors to educate and train students on PIC testing and characterization. Covering a wide range of devices and circuits, from waveguides to wavelength division multiplexing for data communication, the kits offer a hands-on experience. Engaging with actual PICs, students gain practical insights, enhancing their understanding of key principles, and preparing them for real-world skill sets in integrated photonics.

Preventing Risks of Infections and Medication Errors in IV therapy (PRIME): a patient safety initiative.

BACKGROUND: Two major avoidable reasons for adverse events in hospital are medication errors and intravenous therapy-induced infections or complications. Training for clinical staff and compliance to patient safety principles could address these. METHODS: Joint Commission International (JCI) consultants created a standardised, 6-month training programme for clinical staff in hospitals. Twenty-one tertiary care hospitals from across south-east Asia took part. JCI trained the clinical consultants, who trained hospital safety champions, who trained nursing staff. Compliance and knowledge were assessed, and monthly audits were conducted. RESULTS: There was an overall increase of 29% in compliance with parameters around medication preparation and vascular access device management. CONCLUSION: The programme improved safe practice around preparing medications management and managing vascular access devices. The approach could be employed as a continuous quality improvement initiative for the prevention of medication errors and infusion-associated complications.

Large-area optical metasurface fabrication using nanostencil lithography.

We demonstrate a large-area fabrication process for optical metasurfaces utilizing reusable SiN on Si nanostencils. To improve the yield of the nanostencil fabrication, we partially etch the front-side SiN layer to transfer the metasurface pattern from the resist to the nanostencil membrane, preserving the integrity of the membrane during the subsequent potassium hydroxide etch. To enhance the reliability and resolution of metasurface fabrication using the nanostencil, we spin coat a sacrificial layer of resist to precisely determine the gap between the nanostencil and the metasurface substrate for the subsequent liftoff. 1.5 mm diameter PbTe meta-lenses on ${\rm{Ca}}{{\rm{F}}_2}$ fabricated using nanostencils show diffraction-limited focusing and focusing efficiencies of 42% for a 2 mm focal length lens and 53% for a 4 mm focal length lens. The nanostencils can also be cleaned using chemical cleaning methods for reuse.

Single-Element Diffraction-Limited Fisheye Metalens.

Wide field-of-view (FOV) optical functionality is crucial for implementation of advanced imaging and image projection devices. Conventionally, wide FOV operation is attained with complicated assembly of multiple optical elements known as "fisheye lenses". Here we present a novel metalens design capable of performing diffraction-limited focusing and imaging over an unprecedented near 180° angular FOV. The lens is monolithically integrated on a one-piece flat substrate and involves only a single layer of metasurface that corrects third-order Seidel aberrations including coma, astigmatism, and field curvature. The metalens further features a planar focal surface, which enables considerably simplified system architectures for applications in imaging and projection. We fabricated the metalens using Huygens meta-atoms operating at 5.2 µm wavelength and experimentally demonstrated aberration-free focusing and imaging over the entire FOV. The design concept is generic and can be readily adapted to different meta-atom geometries and wavelength ranges to meet diverse application demands.

Deep learning modeling approach for metasurfaces with high degrees of freedom.

Metasurfaces have shown promising potentials in shaping optical wavefronts while remaining compact compared to bulky geometric optics devices. The design of meta-atoms, the fundamental building blocks of metasurfaces, typically relies on trial and error to achieve target electromagnetic responses. This process includes the characterization of an enormous amount of meta-atom designs with varying physical and geometric parameters, which demands huge computational resources. In this paper, a deep learning-based metasurface/meta-atom modeling approach is introduced to significantly reduce the characterization time while maintaining accuracy. Based on a convolutional neural network (CNN) structure, the proposed deep learning network is able to model meta-atoms with nearly freeform 2D patterns and different lattice sizes, material refractive indices and thicknesses. Moreover, the presented approach features the capability of predicting a meta-atom's wide spectrum response in the timescale of milliseconds, attractive for applications necessitating fast on-demand design and optimization of a meta-atom/metasurface.

Mycobacterium chimaera: A novel pathogen with potential risk to cardiac surgical patients.

Mycobacterium chimaera was first described in 2004, coming to prominence in 2011 with reports from across the globe of invasive infections following cardiac surgery. This outbreak was linked to a specific type of heater cooler machine used for cardiac surgery by whole-genome sequencing. We briefly outline what is currently known about this pathogen, highlighting the importance of clinical vigilance and the diagnostic options for the clinician.

Mid-IR supercontinuum generated in low-dispersion Ge-on-Si waveguides pumped by sub-ps pulses.

Ge-on-Si is an attractive material platform for mid-IR broadband sources on a chip because of its wide transparency window, high Kerr nonlinearity and CMOS compatibility. We present a low-loss Ge-on-Si waveguide with flat and low dispersion from 3 to 11 µm, which enables a coherent supercontinuum from 2 to 12 µm, generated using a sub-ps pulsed pump. We show that 700-fs pump pulses with a low peak power of 400 W are needed to generate such a wide supercontinuum, and the waveguide length is around 5.35 mm.

Gamma radiation effects in amorphous silicon and silicon nitride photonic devices.

Understanding radiation damage is of significant importance for devices operating in radiation-harsh environments. In this Letter, we present a systematic study on gamma radiation effects in amorphous silicon and silicon nitride guided wave devices. It is found that gamma radiation increases the waveguide modal effective indices by as much as 4×10-3 in amorphous silicon and 5×10-4 in silicon nitride at 10 Mrad dose. This Letter further reveals that surface oxidation and radiation-induced densification account for the observed index change.

Loss reduction of silicon-on-insulator waveguides for deep mid-infrared applications.

We report that propagation loss of optical waveguides based on a silicon-on-insulator (SOI) material platform can be greatly reduced. Our simulations show that the loss, including SiO2 absorption and substrate leakage, but no scattering loss, is 0.024 and 0.53 dB/cm in the deep mid-infrared at 4.8 and 7.1 µm wavelengths, where the material absorption in SiO2 is 100 and 1000 dB/cm, respectively. The loss becomes negligible, compared to scattering loss in Si waveguides. This is enabled by using the TE10 mode in a pedestal waveguide. We also show that the TE10 mode can be excited in the proposed waveguide by the fundamental mode with a coupling efficiency of >94%. Low propagation loss, high coupling efficiency, and fabrication-friendly design would make it promising for practical use of SOI devices in the deep mid-infrared.

Gamma radiation effects on silicon photonic waveguides.

To support the use of integrated photonics in harsh environments, such as outer space, the hardness threshold to high-energy radiation must be established. Here, we investigate the effects of gamma (γ) rays, with energy in the MeV-range, on silicon photonic waveguides. By irradiation of high-quality factor amorphous silicon core resonators, we measure the impact of γ rays on the materials incorporated in our waveguide system, namely amorphous silicon, silicon dioxide, and polymer. While we show the robustness of amorphous silicon and silicon dioxide up to an absorbed dose of 15 Mrad, more than 100× higher than previous reports on crystalline silicon, polymer materials exhibit changes with doses as low as 1 Mrad.

Nonlinear conversion efficiency in Kerr frequency comb generation.

We analytically and numerically investigate the nonlinear conversion efficiency in ring microresonator-based mode-locked frequency combs under different dispersion conditions. Efficiency is defined as the ratio of the average round trip energy values for the generated pulse(s) to the input pump light. We find that the efficiency degrades with growth of the comb spectral width and is inversely proportional to the number of comb lines. It depends on the cold-cavity properties of a microresonator only and can be improved by increasing the coupling coefficient. Also, it can be increased in the multi-soliton state.

Mid-infrared materials and devices on a Si platform for optical sensing.

In this article, we review our recent work on mid-infrared (mid-IR) photonic materials and devices fabricated on silicon for on-chip sensing applications. Pedestal waveguides based on silicon are demonstrated as broadband mid-IR sensors. Our low-loss mid-IR directional couplers demonstrated in SiN x waveguides are useful in differential sensing applications. Photonic crystal cavities and microdisk resonators based on chalcogenide glasses for high sensitivity are also demonstrated as effective mid-IR sensors. Polymer-based functionalization layers, to enhance the sensitivity and selectivity of our sensor devices, are also presented. We discuss the design of mid-IR chalcogenide waveguides integrated with polycrystalline PbTe detectors on a monolithic silicon platform for optical sensing, wherein the use of a low-index spacer layer enables the evanescent coupling of mid-IR light from the waveguides to the detector. Finally, we show the successful fabrication processing of our first prototype mid-IR waveguide-integrated detectors.

Generation of two-cycle pulses and octave-spanning frequency combs in a dispersion-flattened micro-resonator.

We show that octave-spanning Kerr frequency combs with improved spectral flatness of comb lines can be generated in dispersion-flattened microring resonators. The resonator is formed by a strip/slot hybrid waveguide, exhibiting a flat and low anomalous dispersion between two zero-dispersion wavelengths that are separated by one octave from near-infrared to mid-infrared. Such flattened dispersion profiles allow for the generation of mode-locked frequency combs, using relatively low pump power to obtain two-cycle cavity solitons on a chip, associated with the octave-spanning comb bandwidth. The wavelength dependence of the optical loss and of the coupling coefficient and thus wavelength dependent Q-factor are also considered.

Inverse design of photonic meta-structure for beam collimation in on-chip sensing.

Designed or patterned structured surfaces, metasurfaces, enable the miniaturization of complex arrangements of optical elements on a plane. Most of the existing literature focuses on miniaturizing the optical detection; little attention is directed to on-chip optical excitation. In this work, we design a metasurface to create a planar integrated photonic source beam collimator for use in on-chip optofluidic sensing applications. We use an iterative inverse design approach in order to optimize the metasurface to achieve a target performance using gradient descent method. We then fabricate beam collimators and experimentally compare performance characteristics with conventional uniform binary grating-based photonic beam diffractors. The optimal design enhances the illumination power by a factor of 5. The reinforced beam is more uniform with 3 dB beam spot increased almost ~ 3 times for the same device footprint area. The design approach will be useful in on-chip applications of fluorescence imaging, Raman, and IR spectroscopy and will enable better multiplexing of light sources for high throughput biosensing.

High spectro-temporal compression on a nonlinear CMOS-chip.

Optical pulses are fundamentally defined by their temporal and spectral properties. The ability to control pulse properties allows practitioners to efficiently leverage them for advanced metrology, high speed optical communications and attosecond science. Here, we report 11× temporal compression of 5.8 ps pulses to 0.55 ps using a low power of 13.3 W. The result is accompanied by a significant increase in the pulse peak power by 9.4×. These results represent the strongest temporal compression demonstrated to date on a complementary metal-oxide-semiconductor (CMOS) chip. In addition, we report the first demonstration of on-chip spectral compression, 3.0× spectral compression of 480 fs pulses, importantly while preserving the pulse energy. The strong compression achieved at low powers harnesses advanced on-chip device design, and the strong nonlinear properties of backend-CMOS compatible ultra-silicon-rich nitride, which possesses absence of two-photon absorption and 500× larger nonlinear parameter than in stoichiometric silicon nitride waveguides. The demonstrated work introduces an important new paradigm for spectro-temporal compression of optical pulses toward turn-key, on-chip integrated systems for all-optical pulse control.

Reconfigurable all-dielectric metalens with diffraction-limited performance.

Active metasurfaces, whose optical properties can be modulated post-fabrication, have emerged as an intensively explored field in recent years. The efforts to date, however, still face major performance limitations in tuning range, optical quality, and efficiency, especially for non-mechanical actuation mechanisms. In this paper, we introduce an active metasurface platform combining phase tuning in the full 2π range and diffraction-limited performance using an all-dielectric, low-loss architecture based on optical phase change materials (O-PCMs). We present a generic design principle enabling binary switching of metasurfaces between arbitrary phase profiles and propose a new figure-of-merit (FOM) tailored for reconfigurable meta-optics. We implement the approach to realize a high-performance varifocal metalens operating at 5.2 µm wavelength. The reconfigurable metalens features a record large switching contrast ratio of 29.5 dB. We further validate aberration-free and multi-depth imaging using the metalens, which represents a key experimental demonstration of a non-mechanical tunable metalens with diffraction-limited performance.

Resonant-cavity-enhanced mid-infrared photodetector on a silicon platform.

In this paper, we demonstrate high optical quantum efficiency (90%) resonant-cavity-enhanced mid-infrared photodetectors fabricated monolithically on a silicon platform. High quality photoconductive polycrystalline PbTe film is thermally evaporated, oxygen-sensitized at room temperature and acts as the infrared absorber. The cavity-enhanced detector operates in the critical coupling regime and shows a peak responsivity of 100 V/W at the resonant wavelength of 3.5 microm, 13.4 times higher compared to blanket PbTe film of the same thickness. Detectivity as high as 0.72 x 10(9) cmHz(1/2)W(-1) has been measured, comparable with commercial polycrystalline mid-infrared photodetectors. As low temperature processing (< 160 degrees C) is implemented in the entire fabrication process, our detector is promising for monolithic integration with Si readout integrated circuits.