arXiv subjects

Po-Nan Li

Publications and source records attributed to Po-Nan Li.

7 recordsLinked to original sources

arXiv2023

PeakNet: An Autonomous Bragg Peak Finder with Deep Neural Networks

Serial crystallography at X-ray free electron laser (XFEL) and synchrotron facilities has experienced tremendous progress in recent times enabling novel scientific investigations into macromolecular structures and molecular processes. However, these experiments generate a significant amount of data posing computational challenges in data reduction and real-time feedback. Bragg peak finding algorithm is used to identify useful images and also provide real-time feedback about hit-rate and resolution. Shot-to-shot intensity fluctuations and strong background scattering from buffer solution, injection nozzle and other shielding materials make this a time-consuming optimization problem. Here, we present PeakNet, an autonomous Bragg peak finder that utilizes deep neural networks. The development of this system 1) eliminates the need for manual algorithm parameter tuning, 2) reduces false-positive peaks by adjusting to shot-to-shot variations in strong background scattering in real-time, 3) eliminates the laborious task of manually creating bad pixel masks and the need to store these masks per event since these can be regenerated on demand. PeakNet also exhibits exceptional runtime efficiency, processing a 1920-by-1920 pixel image around 90 ms on an NVIDIA 1080 Ti GPU, with the potential for further enhancements through parallelized analysis or GPU stream processing. PeakNet is well-suited for expert-level real-time serial crystallography data analysis at high data rates.

physics.ins-det↗

arXiv2021

An image-incorporated immersed boundary method for diffusion equations

A novel sharp interface ghost-cell based immersed boundary method has been proposed and its parameters have been optimized against an analytical model in diffusion applications. The proposed embedded constrained moving least-squares (ECMLS) algorithm minimizes the error of the interpolated concentration at the image point of the ghost point by applying a moving least-squares method on all internal nodes, near the ghost image point, and the associated mirrored image points of these internal nodes through the corresponding boundary conditions. Using an analytical model as a reference, the ECMLS algorithm is compared to the constrained moving least-squares (CMLS) algorithm and the staircase model using various grid sizes, interpolation basis functions, weight functions, and the penalty parameter of the constraint. It is found that using ECMLS algorithm in the investigated diffusion application, the incomplete quartic basis function yields the best performance while the quadratic, cubic, and bicubic basis functions also produce results better than the staircase model. It is also found that the linear and bilinear basis functions cannot produce results better than the staircase model in diffusion applications. It is shown that the optimal radius of the region of internal nodes used for interpolation scales with the logarithm of the boundary radius of curvature. It is shown that for the diffusion application, the proposed ECMLS algorithm produces lower errors at the boundary with better numerical stability over a wider range of basis functions, weight functions, boundary radius of curvature, and the penalty parameter than the CMLS algorithm.

math.NA↗

arXiv2020

Sequence-guided protein structure determination using graph convolutional and recurrent networks

Single particle, cryogenic electron microscopy (cryo-EM) experiments now routinely produce high-resolution data for large proteins and their complexes. Building an atomic model into a cryo-EM density map is challenging, particularly when no structure for the target protein is known a priori. Existing protocols for this type of task often rely on significant human intervention and can take hours to many days to produce an output. Here, we present a fully automated, template-free model building approach that is based entirely on neural networks. We use a graph convolutional network (GCN) to generate an embedding from a set of rotamer-based amino acid identities and candidate 3-dimensional C$α$ locations. Starting from this embedding, we use a bidirectional long short-term memory (LSTM) module to order and label the candidate identities and atomic locations consistent with the input protein sequence to obtain a structural model. Our approach paves the way for determining protein structures from cryo-EM densities at a fraction of the time of existing approaches and without the need for human intervention.

q-bio.BM↗

arXiv2020

Hybrid real- and reciprocal-space full-field imaging with coherent illumination

We present a novel diffractive imaging method that harnesses a low-resolution real-space image to guide the phase retrieval. A computational algorithm is developed to utilize such prior knowledge as a real-space constraint in the iterative phase retrieval procedure. Numerical simulations and proof-of-concept experiments are carried out, demonstrating our method's capability of reconstructing high-resolution details that are otherwise inaccessible with traditional phasing algorithms. With the present method, we formulate a conceptual design for the coherent imaging experiments at a next-generation X-ray light source.

physics.optics↗

arXiv2019

Dual-Reference Design for Holographic Coherent Diffraction Imaging

A new reference design is introduced for holographic coherent diffraction imaging. This consists in two references - "block" and "pinhole" shaped regions - placed adjacent to the imaging specimen. An efficient recovery algorithm is provided for the resulting holographic phase retrieval problem, which is based on solving a structured, overdetermined linear system. Analysis of the expected recovery error on noisy data, which is contaminated by Poisson shot noise, shows that this simple modification synergizes the individual references and hence leads to uniformly superior performance over single-reference schemes. Numerical experiments on simulated data confirm the theoretical prediction, and the proposed dual-reference scheme achieves a smaller recovery error than leading single-reference schemes.

eess.IV↗

arXiv2019

Holographic Phase Retrieval and Reference Design

A general mathematical framework and recovery algorithm is presented for the holographic phase retrieval problem. In this problem, which arises in holographic coherent diffraction imaging, a "reference" portion of the signal to be recovered via phase retrieval is a priori known from experimental design. A generic formula is also derived for the expected recovery error when the measurement data is corrupted by Poisson shot noise. This facilitates an optimization perspective towards reference design and analysis. We employ this optimization perspective towards quantifying the performance of various reference choices.

cs.IT↗

arXiv2011

Sub-wavelength localization of near-fields in coupled metallic spheres for single emitter polarization analysis

We numerically demonstrate selective near-field localization determined by the polarization state of a single emitter coupled to plasmonic nano-cluster. Seven gold nanospheres are carefully arranged such that up to ten polarization states of the single emitter, including linear, circular, and elliptical polarizations, can be distinguished via the distinct field localization in four gaps. The ability to transform polarization state into field spatial localization may find application for single emitter polarization analysis.

physics.optics↗