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Accurate and reliable registration of longitudinal spine images is essential for assessment of disease progression and surgical outcome. Implementing a fully automatic and robust registration is crucial for clinical use, however, it is challenging due to substantial change in shape and appearance due to lesions. In this paper we present a novel method to automatically align longitudinal spine CTs and accurately assess lesion progression. Our method follows a two-step pipeline where vertebrae are first automatically localized, labeled and 3D surfaces are generated using a deep learning model, then longitudinally aligned using a Gaussian mixture model surface registration. We tested our approach on 37 vertebrae, from 5 patients, with baseline CTs and 3, 6, and 12 months follow-ups leading to 111 registrations. Our experiment showed accurate registration with an average Hausdorff distance of 0.65 mm and average Dice score of 0.92., Comment: Paper accepted for publication at SPIE Medical Imaging 2024

Nanopore-based sensing platforms have transformed single-molecule detection and analysis. The foundation of nanopore translocation experiments lies in conductance measurements, yet existing models, which are largely phenomenological, are inaccurate in critical experimental conditions such as thin and tightly fitting pores. Of the two components of the conductance blockade, channel and access resistance, the access resistance is poorly modeled. We present a comprehensive investigation into the access resistance and associated conductance blockade in thin nanopore membranes. By combining a first-principles approach, multi-scale modeling, and experimental validation, we propose a unified theoretical modeling framework. The analytical model derived as a result surpasses current approaches across a broad parameter range. Beyond advancing theoretical understanding, our framework's versatility enables analyte size inference and predictive insights into conductance blockade behavior. Our results will facilitate the design and optimization of nanopore devices for diverse applications, including nanopore base calling and data storage.

Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast. Restriction enzymes, that cleave DNA at sequence-specific sites, are used to selectively cut and remove rings from the network and hence tune the molecular topology while maintaining overall structural integrity. We find that topology has minimal effects over the spatial extension of the 2D network, however, it significantly affects the relaxation behavior. The shape fluctuations of the network are governed by two distinct characteristic time scales attributed to the thermal fluctuations and confinement of the network. The relationship between the time constant of thermal relaxation and the amplitude of anisotropy fluctuations yields a universal scaling. Interestingly, this scaling is independent of the detailed arrangements of rings and/or perforation within the catenated networks. This study provides a route to tune the elastic properties of 2D catenated DNA networks by modifying the underlying topology in a rational and highly controllable manner., Comment: 4+ pages, 4 figures

Phase separation in a low-density gas-like phase and a high-density liquid-like one is a common trait of biological and synthetic self-propelling particles' systems. The competition between motility and stochastic forces is assumed to fix the boundary between the homogeneous and the phase-separated phase. Here we demonstrate that motility does also promote the homogeneous phase allowing particles to resolve their collisions. This new understanding allows quantitatively predicting the spinodal-line of hard self-propelling Brownian particles, the prototypical model exhibiting a motility induced phase separation. Furthermore, we demonstrate that frictional forces control the physical process by which motility promotes the homogeneous phase. Hence, friction emerges as an experimentally variable parameter to control the motility induced phase diagram., Comment: Physical Review Research, to appear. In the revised manuscript, the theoretical model is validated against simulations spanning a larger range of parameters

Frictional forces affect the rheology of hard-sphere colloids, at high shear rate. Here we demonstrate, via numerical simulations, that they also affect the dynamics of active Brownian particles, and their motility induced phase separation. Frictional forces increase the angular diffusivity of the particles, in the dilute phase, and prevent colliding particles from resolving their collision by sliding one past to the other. This leads to qualitatively changes of motility-induced phase diagram in the volume-fraction motility plane. While frictionless systems become unstable towards phase separation as the motility increases only if their volume fraction overcomes a threshold, frictional system become unstable regardless of their volume fraction. These results suggest the possibility of controlling the motility induced phase diagram by tuning the roughness of the particles.

Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such excitation can occur with the level of DNA bending in these experiments remains unclear. Intriguingly, the DNA contained preexisting nicks in most of these experiments but whether nicks might play a role in flexibility has never been considered in the interpretation of experimental results. Here, using full-atom molecular dynamics simulations, we show that nicks promote DNA basepair disruption at the nicked sites, which drastically reduces DNA bending energy. In addition, lower temperatures suppress the nick-dependent basepair disruption. In the absence of nicks, basepair disruption can also occur but requires a higher level of DNA bending. Therefore, basepair disruption inside B-form DNA can be suppressed if the DNA contains preexisting nicks. Overall, our results suggest that the reported mechanical anomaly of sharply bent DNA is likely dependent on preexisting nicks, therefore the intrinsic mechanisms of sharply bent nick-free DNA remain an open question., Comment: 39 pages, 11 figures, 1 supporting material