The slime mould Physarum polycephalum displays adaptive transport dynamics and network formation that have inspired its use as a model of biological computation. We develop a Lagrangian formulation of Physarum's adaptive dynamics on predefined graphs, showing that steady states arise as extrema of a least-action functional balancing metabolic dissipation and transport efficiency. The organism's apparent ability to find optimal paths between nutrient sources and sinks emerges from minimizing global energy dissipation under predefined boundary conditions that specify the problem to be solved. Applied to ring, tree, and lattice geometries, the framework accurately reproduces the optimal conductance and flux configurations observed experimentally. These results show that Physarum's problem-solving on constrained topologies follows a physics-based variational principle, revealing least-action dynamics as the foundation of its adaptive organization.
AbstractWe present an updated determination of the values of $$\vert V_{cb} \vert ,$$ | V cb | , $$R(D^*)$$ R ( D ∗ ) and $$\vert V_{ub} \vert /\vert V_{cb} \vert $$ | V ub | / | V cb | based on the new data on semileptonic $$B \rightarrow D^* \ell \nu _\ell $$ B → D ∗ ℓ ν ℓ decays by the Belle and Belle-II Collaborations and on the recent theoretical progress in the calculation of the form factors relevant for semileptonic $$B \rightarrow D^* \ell \nu _\ell $$ B → D ∗ ℓ ν ℓ and $$B_s \rightarrow K \ell \nu _\ell $$ B s → K ℓ ν ℓ decays. In particular we present results derived by applying either the Dispersive Matrix (DM) method of Di Carlo et al. (Phys Rev D 104:054502, 2021), Martinelli et al. (Phys Rev D 104:094512, 2021), Martinelli et al. (Phys Rev D 105:034503, 2022), Martinelli et al. (Eur Phys J C 82:1083, 2022), Martinelli et al. (JHEP 08:022, 2022) and Martinelli et al. (Phys Rev D 106:093002, 2022) or the more standard Boyd–Grinstein–Lebed (BGL) (Boyd et al. in Phys Rev D 56:6895, 1997) approach to the most recent values of the form factors determined in lattice QCD. Using all the available lattice results for the form factors from the DM method we get the theoretical value $$R^{\textrm{th}}(D^*) = 0.262 \pm 0.009$$ R th ( D ∗ ) = 0.262 ± 0.009 and we extract from a bin-per-bin analysis of the experimental data the value $$\vert V_{cb} \vert = (39.92 \pm 0.64) \cdot 10^{-3}.$$ | V cb | = ( 39.92 ± 0.64 ) · 10 - 3 . Our result for $$R(D^*)$$ R ( D ∗ ) is consistent with the latest experimental world average $$R^{\textrm{exp}}(D^*) = 0.284 \pm 0.012$$ R exp ( D ∗ ) = 0.284 ± 0.012 (HFLAV Collaboration in Preliminary average of R(D) and $$R(D^*)$$ R ( D ∗ ) as for Summer 2023. See https://hflav-eos.web.cern.ch/hflav-eos/semi/summer23/html/RDsDsstar/RDRDs.html) at the $$\simeq 1.5\,\sigma $$ ≃ 1.5 σ level. Our value for $$\vert V_{cb} \vert $$ | V cb | is compatible with the latest inclusive determinations $$\vert V_{cb} \vert ^{\textrm{incl}} = (41.97 \pm 0.48) \cdot 10^{-3}$$ | V cb | incl = ( 41.97 ± 0.48 ) · 10 - 3 (Finauri and Gambino in The $$q^2$$ q 2 moments in inclusive semileptonic B decays. arXiv:2310.20324) and $$\vert V_{cb} \vert ^{\textrm{incl}} = (41.69\pm 0.63) \cdot 10^{-3}$$ | V cb | incl = ( 41.69 ± 0.63 ) · 10 - 3 (Bernlochner et al. in JHEP 10:068, 2022) within $$\simeq 2.6$$ ≃ 2.6 and $$\simeq 2.0$$ ≃ 2.0 standard deviations, respectively. From a reappraisal of the calculations of $$\vert V_{ub} \vert / \vert V_{cb} \vert ,$$ | V ub | / | V cb | , we also obtain $$\vert V_{ub} \vert / \vert V_{cb} \vert = 0.087\pm 0.009$$ | V ub | / | V cb | = 0.087 ± 0.009 in good agreement with the result $$\vert V_{ub} \vert / \vert V_{cb} \vert = 0.0844\pm 0.0056$$ | V ub | / | V cb | = 0.0844 ± 0.0056 from the latest FLAG review (Flavour Lattice Averaging Group (FLAG) Collaboration in Phys J C 82:869, 2022).
Niranjan Sarpangala, Brooke Randell, Ajay Gopinathan
et al.
A common type of cytoskeletal morphology involves multiple converging microbutubules with their minus ends collected and stabilized by a microtubule organizing center (MTOC) in the interior of the cell. This arrangement enables the ballistic transport of cargo bound to microtubules, both dynein mediated transport towards the MTOC and kinesin mediated transport away from it, interspersed with diffusion for unbound cargo-motor complexes. Spatial and temporal positioning of the MTOC allows for bidirectional transport towards and away from specific organelles and locations within the cell and also the sequestering and subsequent dispersal of dynein transported cargo. The general principles governing dynamics, efficiency and tunability of such transport in the MTOC vicinity is not fully understood. To address this, we develop a one-dimensional model that includes advective transport towards an attractor (such as the MTOC), and diffusive transport that allows particles to reach absorbing boundaries (such as cellular membranes). We calculated the mean first passage time (MFPT) for cargo to reach the boundaries as a measure of the effectiveness of sequestering (large MFPT) and diffusive dispersal (low MFPT). The MFPT experiences a dramatic growth in magnitude, transitioning from a low to high MFPT regime (dispersal to sequestering) over a window of cargo attachment/detachment rates that is close to in vivo values. We find that increasing either the attachment or detachment rate, while fixing the other, can result in optimal dispersal when the attractor is placed asymmetrically. Finally, we describe a rare event regime, where the escape location is exponentially sensitive to the attractor positioning. Our results suggest that structures such as the MTOC allow for the sensitive control of the spatial and temporal features of transport and corresponding function under physiological conditions.
Binghao Chai, Christoforos Efstathiou, Haoran Yue
et al.
With the growth of artificial intelligence (AI), there has been an increase in the adoption of computer vision and deep learning (DL) techniques for the evaluation of microscopy images and movies. This adoption has not only addressed hurdles in quantitative analysis of dynamic cell biological processes, but it has also started supporting advances in drug development, precision medicine and genome-phenome mapping. Here we survey existing AI-based techniques and tools, and open-source datasets, with a specific focus on the computational tasks of segmentation, classification, and tracking of cellular and subcellular structures and dynamics. We summarise long-standing challenges in microscopy video analysis from the computational perspective and review emerging research frontiers and innovative applications for deep learning-guided automation for cell dynamics research.
A general model is presented for coupling of high-Q whispering-gallery modes in optical microsphere resonators with coupler devices that possess a discrete and continuous spectrum of propagating modes. By contrast to conventional high-Q optical cavities, in microspheres the independence of high intrinsic quality-factor and controllable parameters of coupling via an evanescent field offer a variety of regimes similar to those that are already available in rf devices. The theory is applied to data reported earlier on different types of couplers to microsphere resonators and is complemented by the experimental demonstration of enhanced coupling efficiency (∼80%) and variable loading regimes with Q>108 fused-silica microspheres.
Kenneth Blahut, Christian Quirouette, Jordan J. Feld
et al.
Experiments have shown that hepatitis C virus (HCV) infections in vitro disseminate both distally via the release and diffusion of cell-free virus through the medium, and locally via direct, cell-to-cell transmission. To determine the relative contribution of each mode of infection to HCV dissemination, we developed an agent-based model (ABM) that explicitly incorporates both distal and local modes of infection. The ABM tracks the concentration of extracellular infectious virus in the supernatant and the number of intracellular HCV RNA segments within each infected cell over the course of simulated in vitro HCV infections. Experimental data for in vitro HCV infections conducted in the presence and absence of free-virus neutralizing antibodies was used to validate the ABM and constrain the value of its parameters. We found that direct, cell-to-cell infection accounts for 99% (84%$-$100%, 95% credible interval) of infection events, making it the dominant mode of HCV dissemination in vitro. Yet, when infection via the free-virus route is blocked, a 57% reduction in the number of infection events at 72 hpi is observed experimentally; a result consistent with that found by our ABM. Taken together, these findings suggest that while HCV spread via cell-free virus contributes little to the total number of infection events in vitro, it plays a critical role in enhancing cell-to-cell HCV dissemination by providing access to distant, uninfected areas, away from the already established large infection foci.