David G. Ackerman | Searcharxiv

arXiv2024

DaCapo: a modular deep learning framework for scalable 3D image segmentation

DaCapo is a specialized deep learning library tailored to expedite the training and application of existing machine learning approaches on large, near-isotropic image data. In this correspondence, we introduce DaCapo's unique features optimized for this specific domain, highlighting its modular structure, efficient experiment management tools, and scalable deployment capabilities. We discuss its potential to improve access to large-scale, isotropic image segmentation and invite the community to explore and contribute to this open-source initiative.

cs.CV↗

arXiv2011

Limited Perturbation of a DPPC Bilayer by Fluorescent Lipid Probes: A Molecular Dynamics Study

The presence and the properties of lipid bilayer nanometer-scale domains might be important for understanding the membranes of living cells. We used molecular dynamics (MD) simulations to investigate perturbations of a small patch of fluid-phase DPPC bilayer upon incorporation of fluorescent indocarbocyanine lipid probes commonly used to study membranes (DiI-C12:0, DiI-C18:0, or DiI-C18:2). In simulations containing 1 probe per 64 total lipids in each leaflet, an 8 - 12% decrease in chain order is observed for DPPC molecules in the solvation shell closest to the probe, relative to a pure DPPC bilayer. A ~5% increase in chain order is seen in the next three shells, resulting in a small overall increase in average DPPC chain order. In simulations with 1 probe per 256 total lipids in each leaflet, average DPPC chain order is unaffected by the probe. Thus, these DiI probes cause an oscillatory perturbation of their local environment but do not strongly influence the average properties of even "nanoscopic" lipid phase domains.

cond-mat.soft↗