ABSTRACT: Discriminating the low-abundance hydroxylated proline from hydroxylated proline is crucial for monitoring diseases and evaluating therapeutic outcomes that require single-molecule sensors. While the plasmonic nanopore sensor can detect the hydroxylation with single-molecule sensitivity by surface enhanced Raman spectroscopy (SERS), it suffers from intrinsic fluctuations of single-molecule signals as well as strong interference from citrates. Here, we used the occurrence frequency histogram of the single-molecule SERS peaks to extract overall dataset spectral features, overcome the signal fluctuations and investigate the citratereplaced plasmonic nanopore sensors for clean and distinguishable signals of proline and hydroxylated proline. By ligand exchange of the citrates by analyte molecules, the representative peaks of citrates decreased with incubation time, proving occupation of the plasmonic hot spot by the analytes. As a result, the discrimination of the single-molecule SERS signals of proline and hydroxylated proline was possible with the convolutional neural network model with 96.6% accuracy.

During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how every single cell decides to position itself relative to its neighboring cells. Despite its importance, it remains a major challenge to understand and predict the behavior of every cell within the living tissue over time during such intricate processes. To tackle this question, we propose a geometric deep learning model that can predict multicellular folding and embryogenesis, accurately capturing the highly convoluted spatial interactions among cells. We demonstrate that multicellular data can be represented with both granular and foam-like physical pictures through a unified graph data structure, considering both cellular interactions and cell junction networks. We successfully use our model to achieve two important tasks, interpretable 4-D morphological sequence alignment, and predicting local cell rearrangements before they occur at single-cell resolution. Furthermore, using an activation map and ablation studies, we demonstrate that cell geometries and cell junction networks together regulate local cell rearrangement which is critical for embryo morphogenesis. This approach provides a novel paradigm to study morphogenesis, highlighting a unified data structure and harnessing the power of geometric deep learning to accurately model the mechanisms and behaviors of cells during development. It offers a pathway toward creating a unified dynamic morphological atlas for a variety of developmental processes such as embryogenesis.

Due to the lack of phase information, determining the physical parameters of multilayer thin films from measured neutron and X-ray reflectivity curves is, on a fundamental level, an underdetermined inverse problem. This so-called phase problem poses limitations on standard neural networks, constraining the range and number of considered parameters in previous machine learning solutions. To overcome this, we present an approach that utilizes prior knowledge to regularize the training process over larger parameter spaces. We demonstrate the effectiveness of our method in various scenarios, including multilayer structures with box model parameterization and a physics-inspired special parameterization of the scattering length density profile for a multilayer structure. By leveraging the input of prior knowledge, we can improve the training dynamics and address the underdetermined ("ill-posed") nature of the problem. In contrast to previous methods, our approach scales favorably when increasing the complexity of the inverse problem, working properly even for a 5-layer multilayer model and an N-layer periodic multilayer model with up to 17 open parameters.

Staring through a microscope at samples of material for hours on end, attempting to locate monolayers, is one of the most laborious and intimidating tasks for undergraduate assistants in university research laboratories. As a result of their unique properties, these two-dimensional materials -- which are less than 1/100,000th the width of a human hair -- are in high demand for use in photonics, electronics, and optoelectronic devices. Research labs hire armies of undergraduates to do nothing but look for monolayers. It's very tedious, and if you get tired, you might miss some of the monolayers or you might start making misidentifications. Jesús Sánchez Juárez, a Ph.D. student in the Cardenas Lab, has made work simpler for undergraduates, their research facilities, and companies that have difficulty identifying monolayers.