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Yimin Luo

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cond-mat.soft Biological Physics Applications Computer Vision eess.IV Machine Learning physics.data-an

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preprint2026arXiv

A framework for modeling and inferring tracer diffusion in crowded environments

Tracer diffusion in crowded environments is central to many biological and soft matter systems, but quantitative frameworks for linking tracer motion to environmental structure remain limited. Here, we study the transport of rigid tracers in suspensions of soft particles and within living cells. Experiments reveal a transition from diffusive to confined motion as the matrix area fraction increases. We develop a minimal simulation that incorporates steric exclusion and hydrodynamic hindrance to reproduce the observed mean-squared displacements (MSDs). Using simulation outputs, we train a parallel partial Gaussian process (PPGP) model that rapidly predicts MSDs from matrix geometric variables, including area fraction, particle size, and polydispersity. The PPGP model accelerates predictions by several orders of magnitude relative to simulation and experiments. Analysis reveals that tracer transport is primarily governed by accessible pore sizes and that distinct global structures can produce indistinguishable MSDs. We find that the minimal model can also capture the MSDs of internalized tracer particles in cells. The framework enables rapid inference of structural properties in crowded environments, including transport in the intracellular environment.

preprint2026arXiv

Proliferating Nematic That Collectively Senses an Anisotropic Substrate

Motivated by recent experiments on growing fibroblasts, we examine the development of nematic order in a colony of elongated cells proliferating on a nematic elastomer substrate. After sparse seeding, the cells divide and grow into locally ordered, but randomly oriented, domains that then interact with each other and the substrate. Global alignment with the substrate is only achieved above a critical density, suggesting a collective mechanism for the sensing of substrate anisotropy. The system jams at high density, where both reorientation and proliferation stop. Using a continuum model of a proliferating nematic liquid crystal, we examine the competition between growth-driven alignment and substrate-driven alignment in controlling the density and structure of the final jammed state. We propose that anisotropic traction forces and the tendency of cells to align perpendicular to the direction of density gradients act in concert to provide a mechanism for collective cell alignment.

preprint2022arXiv

Nematic colloidal micro-robots as physically intelligent systems

Physically intelligent micro-robotic systems exploit information embedded in micro-robots, their colloidal cargo, and their milieu to interact, assemble and form functional structures. Nonlinear anisotropic fluids like nematic liquid crystals (NLCs) provide untapped opportunities to embed interactions via their topological defects, complex elastic responses, and their ability to dramatically restructure in dynamic settings. Here we design and fabricate a 4-armed ferromagnetic micro-robot to embed and dynamically reconfigure information in the nematic director field, generating a suite of physical interactions for cargo manipulation. The micro-robot shape and surface chemistry are designed to generate a nemato-elastic energy landscape in the domain that defines multiple modes of emergent, bottom-up interactions with passive colloids. Micro-robot rotation expands the ability to sculpt interactions; the energy landscape around a rotating micro-robot is dynamically reconfigured by complex far-from-equilibrium dynamics of the micro-robot's companion topological defect. These defect dynamics allow transient information to be programmed into the domain and exploited for top-down cargo manipulation. We demonstrate robust micro-robotic manipulation strategies that exploit these diverse modes of nemato-elastic interaction to achieve cargo docking, transport, release, and assembly of complex reconfigurable structures at multi-stable sites. Such structures are of great interest to future developments of LC-based advanced optical device and micro-manufacturing in anisotropic environments.

preprint2022arXiv

Uncertainty quantification and estimation in differential dynamic microscopy

Differential dynamic microscopy (DDM) is a form of video image analysis that combines the sensitivity of scattering and the direct visualization benefits of microscopy. DDM is broadly useful in determining dynamical properties including the intermediate scattering function for many spatiotemporally correlated systems. Despite its straightforward analysis, DDM has not been fully adopted as a routine characterization tool, largely due to computational cost and lack of algorithmic robustness. We present statistical analysis that quantifies the noise, reduces the computational order and enhances the robustness of DDM analysis. We propagate the image noise through the Fourier analysis, which allows us to comprehensively study the bias in different estimators of model parameters, and we derive a different way to detect whether the bias is negligible. Furthermore, through use of Gaussian process regression (GPR), we find that predictive samples of the image structure function require only around 0.5%-5% of the Fourier transforms of the observed quantities. This vastly reduces computational cost, while preserving information of the quantities of interest, such as quantiles of the image scattering function, for subsequent analysis. The approach, which we call DDM with uncertainty quantification (DDM-UQ), is validated using both simulations and experiments with respect to accuracy and computational efficiency, as compared with conventional DDM and multiple particle tracking. Overall, we propose that DDM-UQ lays the foundation for important new applications of DDM, as well as to high-throughput characterization. We implement the fast computation tool in a new, publicly available MATLAB software package.

preprint2020arXiv

Multi-Scale Progressive Fusion Network for Single Image Deraining

Rain streaks in the air appear in various blurring degrees and resolutions due to different distances from their positions to the camera. Similar rain patterns are visible in a rain image as well as its multi-scale (or multi-resolution) versions, which makes it possible to exploit such complementary information for rain streak representation. In this work, we explore the multi-scale collaborative representation for rain streaks from the perspective of input image scales and hierarchical deep features in a unified framework, termed multi-scale progressive fusion network (MSPFN) for single image rain streak removal. For similar rain streaks at different positions, we employ recurrent calculation to capture the global texture, thus allowing to explore the complementary and redundant information at the spatial dimension to characterize target rain streaks. Besides, we construct multi-scale pyramid structure, and further introduce the attention mechanism to guide the fine fusion of this correlated information from different scales. This multi-scale progressive fusion strategy not only promotes the cooperative representation, but also boosts the end-to-end training. Our proposed method is extensively evaluated on several benchmark datasets and achieves state-of-the-art results. Moreover, we conduct experiments on joint deraining, detection, and segmentation tasks, and inspire a new research direction of vision task-driven image deraining. The source code is available at \url{https://github.com/kuihua/MSPFN}.

preprint2015arXiv

Curvature-driven, One-step Assembly of Reconfigurable Smectic Liquid Crystal "Compound Eye" Lenses

Confined smectic A liquid crystals (SmA LCs) form topological defects called focal conic domains (FCDs) that focus light as gradient-index lenses. Here, we exploit surface curvature to self-assemble FCDs in a single step into a hierarchical structure (coined "flower pattern") molded by the fluid interface that is pinned at the top of a micropillar. The structure resembles the compound eyes of some invertebrates, which consist of hundreds of microlenses on a curved interface, able to focus and construct images in three dimensions. Here we demonstrate that these flowers are indeed "compound eyes" with important features which have not been demonstrated previously in the literature. The eccentric FCDs gradually change in size with radial distance from the edge of the micropillar, resulting in a variable microlens focal length that ranges from a few microns to a few tens of microns within a single "flower". We show that the microlenses can construct a composite 3D image from different depth of field. Moreover, the smectic "compound eye" can be reconfigured by heating and cooling at the LC phase transition temperature; its field of view can be manipulated by tuning the curvature of the LC interface, and the lenses are sensitive to light polarization.