📰 "A putative, computationally stable structure of homotrimeric BP180/collagen XVII"
https://arxiv.org/abs/2605.08953 #Physics.Comp-Ph
#Physics.Bio-Ph
#Extracellular #Dynamics #Q-Bio.Qm
#Q-Bio.Bm
A putative, computationally stable structure of homotrimeric BP180/collagen XVII
Background: BP180, also known as collagen XVII and BPAG2 (bullous pemphigoid antigen 2), is a 180-kDa transmembrane protein within the hemidesmosomal plaque complex, and which is known to be a major antigen in bullous pemphigoid, gestational pemphigoid, cicatricial (mucous membrane) pemphigoid, and linear IgA bullous disease.
Objective: At present, the 3D structure of BP180 is not known. The goal is to predict a reasonable structure for BP180 through machine learning and molecular dynamics.
Methods: In this work, we use the recent Boltz-2 model to predict a putative structure for the intracellular, transmembrane, and proximal extracellular domains, including the NC16A antigenic region and a portion of its first extracellular collagenous domain, Col-15. We computationally embed BP180 in a simple phospholipid bilayer, demonstrate that the putative structure is stable using molecular dynamics, and analyze its allosteric properties.
Results: The structures presented satisfy symmetry and secondary structure properties which are expected from homology modelling. Over three 500 ns trajectories, there is minor instability of the predicted globular head domain, but the homotrimer otherwise stays mostly folded. The putative NC16A domain is stiff, whereas the truncated Col-15 domain is highly flexible. There does not appear to be a nearby stable conformation distinct from the initial state.
Conclusion: The structure presented is a useful starting point for targeting BP180 pharmacologically, for further experimental characterization of BP180, and for generating hypotheses regarding the relevant epitopes contributing to bullous disease. Diffusion models such as Boltz-2 and AlphaFold3 are useful, but their results must be evaluated carefully.
📰 "FLUX: Geometry-Aware Longitudinal Flow Matching with Mixture of Experts"
https://arxiv.org/abs/2605.08648 #Dynamics #Q-Bio.Nc
#Cs.Lg
#Cell
FLUX: Geometry-Aware Longitudinal Flow Matching with Mixture of Experts
Many biological systems evolve through continuous local dynamics while switching between latent regimes defined by learning, stimulus context, internal state, or developmental stage. These processes are often observed only as unpaired longitudinal snapshots: the same cells, neurons, or animals are not tracked as matched trajectories, even though population states are sampled across successive stages. This creates two coupled challenges. First, trajectories must respect curved low-dimensional manifolds embedded in high-dimensional biological measurements. Second, the model must identify when the transport mechanism itself changes. We introduce FLUX (FLow matching for Unpaired longitudinal data with miXture-of-experts), a geometry-aware longitudinal flow-matching framework for joint transport modeling and unsupervised regime discovery. FLUX learns a data-dependent metric from pooled labeled and unlabeled observations, uses that metric to construct geometry-aware conditional paths between adjacent marginals, and decomposes the resulting velocity field into sparse expert vector fields selected by a Straight-Through Gumbel-Softmax router. Across manifold controls, a regime-switching Lorenz system, widefield cortical calcium imaging during associative learning, and embryoid body single-cell differentiation, FLUX reconstructs longitudinal transport while recovering interpretable regime structure. Ablations show that mixture-of-experts routing alone is insufficient: FLUX without geometric learning can fit local transport but fails or weakens regime discovery when regimes are encoded in local dynamics. These results suggest that geometry-aware velocity decomposition provides a general strategy for discovering latent biological state transitions from unpaired longitudinal snapshots.
📰 "Coexistence of trapped and flow-transported nuclei enables fast pigeon post communication across multinucleated cell"
https://arxiv.org/abs/2605.09704 #Physics.Bio-Ph
#Dynamics #Q-Bio.Cb
#Cell
Coexistence of trapped and flow-transported nuclei enables fast pigeon post communication across multinucleated cell
Multi-nucleated cells exist in all domains of life, ranging from animals, plants and fungi to single-celled organisms such as the slime mold Physarum polycephalum. The large cell size, in the case of Physarum reaching centimeters and more, challenges the coordination of nuclei activity as signals need to cross large distances. In search for a mechanism for fast long-ranged communication among nuclei, we quantify nuclei dynamics and cytoplasmic flows in Physarum's tubular network. We observe nuclei in two interchangeable, dynamic states: mobile, flowing within the cytoplasmic shuttle flow, or trapped in the tube's porous cell cortex. As we find nuclei to accumulate at the tube's inner fluid-porous interface we theoretically explore and confirm, with physiological parameters, that slowing down of mobile nuclei during flow is sufficient for diffusible signal exchange between mobile and trapped nuclei. We analytically derive that communication akin to pigeon-post with mobile nuclei serving as pigeons shuttling between trapped nuclei acting as waypoints, gives rise to signaling velocities that account for the rapid intracellular reorganization observed in Physarum. Since signal transfer by flow-transported nuclei outcompetes the mere diffusion of signals encoded in cytosolic proteins, pigeon-post communication surpasses alternative signaling mechanisms, even diffusive relay signaling up to twenty-fold in velocity. The key ingredients of pigeon-post communication, namely alternating flows and waypoints, exist in other multi-nucleated cells and may also be generalized beyond intracellular signaling.
📰 "Pushing for survival: Spatial intermixing and indirect resistance enable collective growth"
https://www.biorxiv.org/content/10.64898/2026.05.07.723406v1?rss=1 #Dynamics #CellJeff Mullen | The Authority | Comic Crusaders Podcast #699
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https://comiccrusaders.com/comic-books/comic-book-previews/jeff-mullen-the-authority-comic-crusaders-podcast-699/#Jeff Mullen
#The Authority
#collectibles marketplace
#comic collecting
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#Dynamics Inc
#Comic Crusaders Podcast
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📰 "Learning activator-inhibitor dynamics at the cell cortex with neural likelihood ratio estimation"
https://www.biorxiv.org/content/10.64898/2026.05.06.722433v1?rss=1 #Dynamics #Cell
Frontiers | Electrochemical modulation of host-microbe dynamics in wound healing
Wound healing emerges from a tightly orchestrated bioelectric landscape shaped by ion gradients, membrane potentials, and redox dynamics physical cues that d...
📰 "Temporal dynamics of diffusion kurtosis imaging parallels astroglial GFAP expression in a non-traumatic spinal cord injury animal model of ischemia-reperfusion"
https://doi.org/doi:10.3389/fneur.2026.1776453https://pubmed.ncbi.nlm.nih.gov/42111064/ #Dynamics #Gfap
Frontiers | Temporal dynamics of diffusion kurtosis imaging parallels astroglial GFAP expression in a non-traumatic spinal cord injury animal model of ischemia–reperfusion
ObjectivesSpinal cord ischemia–reperfusion (I/R) injury triggers rapid secondary degeneration, yet sensitive noninvasive markers that reflect early astroglia...
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