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In this paper, we present the design, optimization, and implementation of a sub-wavelength grating (SWG) multi-mode interference coupler (MMI) on the silicon nitride photonic integrated circuit (PIC) platform with a significantly enhanced bandwidth compared to the conventional MMI. We extend the SWG MMI theory, previously presented for the silicon-on-insulator platform, to the Si₃N₄/SiO₂platform. Our approach involves an initial parameter optimization for a non-paired design, followed by a shift to a paired design that offers a smaller footprint and a broader bandwidth. The optimized SWG MMI exhibits a 1 dB bandwidth of 300 nm for both the insertion loss and power imbalance, making it a significant addition to silicon nitride photonics.

Mitochondrial morphology provides unique insights into their integrity and function. Among fluorescence microscopy techniques, 3D super-resolution microscopy uniquely enables the analysis of mitochondrial morphological features individually. However, there is a lack of tools to extract morphological parameters from super-resolution images of mitochondria. We report a quantitative method to extract mitochondrial morphological metrics, including volume, aspect ratio, and local protein density, from 3D single-molecule localization microscopy images, with single-mitochondrion sensitivity. We validated our approach using simulated ground-truth SMLM images of mitochondria. We further tested our morphological analysis on mitochondria that have been altered functionally and morphologically in controlled manners. This work sets the stage to quantitatively analyze mitochondrial morphological alterations associated with disease progression on an individual basis.

RNAs are fundamental in living cells and perform critical functions determined by their tertiary architectures. However, accurate modeling of 3D RNA structure remains a challenging problem. We present a novel method, DRfold, to predict RNA tertiary structures by simultaneous learning of local frame rotations and geometric restraints from experimentally solved RNA structures, where the learned knowledge is converted into a hybrid energy potential to guide RNA structure assembly. The method significantly outperforms previous approaches by >73.3% in TM-score on a sequence-nonredundant dataset containing recently released structures. Detailed analyses showed that the major contribution to the improvements arise from the deep end-to-end learning supervised with the atom coordinates and the composite energy function integrating complementary information from geometry restraints and end-to-end learning models. The open-source DRfold program with fast training protocol allows large-scale application of high-resolution RNA structure modeling and can be further improved with future expansion of RNA structure databases.

We developed a multiscale optical imaging workflow, integrating and correlating visible-light optical coherence tomography, confocal laser scanning microscopy, and single-molecule localization microscopy to investigate mouse cornea damage from thein-vivotissue level to the nanoscopic single-molecule level. We used electron microscopy to validate the imaged nanoscopic structures. We imaged wild-type mice and mice with acute ocular hypertension and examined the effects of Rho-kinase inhibitor application. We defined four types of intercellular tight junction structures as healthy, compact, partially-distorted, and fully-distorted types by labeling the zonula occludens-1 protein in the corneal endothelial cell layer. We correlated the statistics of the four types of tight junction structures with cornea thickness and intraocular pressure. We found that the population of fully-distorted tight junctions correlated well with the level of corneal edema, and applying Rho-kinase inhibitor reduced the population of fully-distorted tight junctions under acute ocular hypertension. Together, these data point to the utility of multiscale optical imaging in revealing fundamental biology relevant to disease and therapeutics.

Leveraging iterative alignment search through genomic and metagenome sequence databases, we report the DeepMSA2 pipeline for uniform protein single- and multichain multiple-sequence alignment (MSA) construction. Large-scale benchmarks show that DeepMSA2 MSAs can remarkably increase the accuracy of protein tertiary and quaternary structure predictions compared with current state-of-the-art methods. An integrated pipeline with DeepMSA2 participated in the most recent CASP15 experiment and created complex structural models with considerably higher quality than the AlphaFold2-Multimer server (v.2.2.0). Detailed data analyses show that the major advantage of DeepMSA2 lies in its balanced alignment search and effective model selection, and in the power of integrating huge metagenomics databases. These results demonstrate a new avenue to improve deep learning protein structure prediction through advanced MSA construction and provide additional evidence that optimization of input information to deep learning-based structure prediction methods must be considered with as much care as the design of the predictor itself.

The increase of distributed embedded systems has enabled pervasive sensing, actuation, and information displays across buildings and surrounding environments, yet also entreats huge cost expenditure for energy and human labor for maintenance. Our daily interactions, from opening a window to closing a drawer to twisting a doorknob, are great potential sources of energy but are often neglected. Existing commercial devices to harvest energy from these ambient sources are unaffordable, and DIY solutions are left with inaccessibility for non-experts preventing fully imbuing daily innovations in end-users. We present E3D, an end-to-end fabrication toolkit to customize self-powered smart devices at low cost. We contribute to a taxonomy of everyday kinetic activities that are potential sources of energy, a library of parametric mechanisms to harvest energy from manual operations of kinetic objects, and a holistic design system for end-user developers to capture design requirements by demonstrations then customize augmentation devices to harvest energy that meets unique lifestyle.

Metals with kagome lattice provide bulk materials to host both the flat-band and Dirac electronic dispersions. A new family of kagome metals is recently discovered inAV₆Sn₆. The Dirac electronic structures of this material needs more experimental evidence to confirm. In the manuscript, we investigate this problem by resolving the quantum oscillations in both electrical transport and magnetization in ScV₆Sn₆. The revealed orbits are consistent with the electronic band structure models. Furthermore, the Berry phase of a dominating orbit is revealed to be aroundπ, providing direct evidence for the topological band structure, which is consistent with calculations. Our results demonstrate a rich physics and shed light on the correlated topological ground state of this kagome metal.

Whenever a user interacts with a device, mechanical work is performed to actuate the user interface elements; the resulting energy is typically wasted, dissipated as sound and heat. Previous work has shown that many devices can be powered entirely from this otherwise wasted user interface energy. For these devices, wires and batteries, along with the related hassles of replacement and charging, become unnecessary and onerous. So far, these works have been restricted to proof-of-concept demonstrations; a specific bespoke harvesting and sensing circuit is constructed for the application at hand. The challenge of harvesting energy while simultaneously sensing fine-grained input signals from diverse modalities makes prototyping new devices difficult. To fill this gap, we present a hardware toolkit which provides a common electrical interface for harvesting energy from user interface elements. This facilitates exploring the composability, utility, and breadth of enabled applications of interaction-powered smart devices. We design a set of energy as input harvesting circuits, a standard connective interface with 3D printed enclosures, and software libraries to enable the exploration of devices where the user action generates the energy needed to perform the device's primary function. This exploration culminated in a demonstration campaign where we prototype several exemplar popular toys and gadgets, including battery-free Bop-It--- a popular 90s rhythm game, an electronic Etch-a-sketch, a Simon-Says-style memory game, and a service rating device. We run exploratory user studies to understand how generativity, creativity, and composability are hampered or facilitated by these devices. These demonstrations, user study takeaways, and the toolkit itself provide a foundation for building interactive and user-focused gadgets whose usability is not affected by battery charge and whose service lifetime is not limited by battery wear.

Timely and accurate bearing fault detection plays an important role in various industries. Data-driven deep learning methods have recently become a prevailing approach for bearing fault detection. Despite the success of deep learning, fault diagnosis performance is hinged upon the size of labeled data, the acquisition of which oftentimes is expensive in actual practice. Unlabeled data, on the other hand, are inexpensive. To fully utilize a large amount of unlabeled data together with limited labeled data to enhance fault detection performance, in this research, we develop a semi-supervised learning method built upon the autoencoder. In this method, a joint loss is established to account for the effects of both the labeled and unlabeled data, which is subsequently used to direct the backpropagation training. Systematic case studies using the Case Western Reserve University (CWRU) rolling bearing dataset are carried out, in which the effectiveness of this new method is verified by comparing it with other benchmark models.