1980 Preface * 1999 Preface * 1999 Acknowledgements * Introduction * 1 Circular Logic * 2 Phase Singularities (Screwy Results of Circular Logic) * 3 The Rules of the Ring * 4 Ring Populations * 5 Getting Off the Ring * 6 Attracting Cycles and Isochrons * 7 Measuring the Trajectories of a Circadian Clock * 8 Populations of Attractor Cycle Oscillators * 9 Excitable Kinetics and Excitable Media * 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways * 11 The Firefly Machine 12 Energy Metabolism in Cells * 13 The Malonic Acid Reagent ('Sodium Geometrate') * 14 Electrical Rhythmicity and Excitability in Cell Membranes * 15 The Aggregation of Slime Mold Amoebae * 16 Numerical Organizing Centers * 17 Electrical Singular Filaments in the Heart Wall * 18 Pattern Formation in the Fungi * 19 Circadian Rhythms in General * 20 The Circadian Clocks of Insect Eclosion * 21 The Flower of Kalanchoe * 22 The Cell Mitotic Cycle * 23 The Female Cycle * References * Index of Names * Index of Subjects

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/596B270197FE27DE5FABB598B6210622/S0025557200150892a.pdf/div-class-title-span-class-italic-the-geometry-of-biological-time-span-by-a-t-winfree-pp-544-dm68-corrected-second-printing-1990-isbn-3-540-52528-9-springer-div.pdf

The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)

Biophysics of Computation

Colon cancer is the third most common cancer worldwide. Most colorectal cancer occurrences are sporadic, not related to genetic predisposition or family history; however, 20–30% of patients with colorectal cancer have a family history of colorectal cancer and 5% of these tumors arise in the setting of a Mendelian inheritance syndrome. In many patients, the development of a colorectal cancer is preceded by a benign neoplastic lesion: either an adenomatous polyp or a serrated polyp. Studies carried out in the last years have characterized the main molecular alterations occurring in colorectal cancers, showing that the tumor of each patient displays from two to eight driver mutations. The ensemble of molecular studies, including gene expression studies, has led to two proposed classifications of colorectal cancers, with the identification of four/five non-overlapping groups. The homeostasis of the rapidly renewing intestinal epithelium is ensured by few stem cells present at the level of the base of intestinal crypts. Various experimental evidence suggests that colorectal cancers may derive from the malignant transformation of intestinal stem cells or of intestinal cells that acquire stem cell properties following malignant transformation. Colon cancer stem cells seem to be involved in tumor chemoresistance, radioresistance and relapse.

Colorectal cancer: genetic abnormalities, tumor progression, tumor heterogeneity, clonal evolution and tumor-initiating cells

We present an experimental observation of an oscillating Kerr cavity soliton, i.e., a time-periodic oscillating one-dimensional temporally localized structure excited in a driven nonlinear fiber cavity with a Kerr-type nonlinearity. More generally, these oscillations result from a Hopf bifurcation of a (spatially or temporally) localized state in the generic class of driven dissipative systems close to the 1 : 1 resonance tongue. Furthermore, we theoretically analyze dynamical instabilities of the one-dimensional cavity soliton, revealing oscillations and different chaotic states in previously unexplored regions of parameter space. As cavity solitons are closely related to Kerr frequency combs, we expect these dynamical regimes to be highly relevant for the field of microresonator-based frequency combs.

Dynamics of one-dimensional Kerr cavity solitons.

The contrast and resolution of images obtained with optical microscopes can be improved by deconvolution and computational fusion of multiple views of the same sample, but these methods are computationally expensive for large datasets Here we describe theoretical and practical advances in algorithm and software design that result in image processing times that are tenfold to several thousand fold faster than with previous methods First, we show that an ‘unmatched back projector’ accelerates deconvolution relative to the classic Richardson–Lucy algorithm by at least tenfold Second, three-dimensional image-based registration with a graphics processing unit enhances processing speed 10- to 100-fold over CPU processing Third, deep learning can provide further acceleration, particularly for deconvolution with spatially varying point spread functions We illustrate our methods from the subcellular to millimeter spatial scale on diverse samples, including single cells, embryos and cleared tissue Finally, we show performance enhancement on recently developed microscopes that have improved spatial resolution, including dual-view cleared-tissue light-sheet microscopes and reflective lattice light-sheet microscopes Microscopy datasets are processed orders-of-magnitude faster with improved algorithms and deep learning

Rapid image deconvolution and multiview fusion for optical microscopy.

We show how to use excitable regimes mediated by localized structures (LSs) to perform AND, OR and NOT logical operations providing full logical functionality. Our scheme is general and can be implemented in any physical system displaying LSs. In particular, LSs in nonlinear photonic devices can be used for all-optical computing applications where several reconfigurable logic gates can be implemented in the transverse plane of a single device, allowing for parallel computing.

/pdf/logical-operations-with-localized-structures-3zueyb1yf4.pdf

Logical operations with localized structures

Dysfunctions of hearing and balance are often irreversible in mammals owing to the inability of cells in the inner ear to proliferate and replace lost sensory receptors. To determine the molecular basis of this deficiency we have investigated the dynamics of growth and cellular proliferation in a murine vestibular organ, the utricle. Based on this analysis, we have created a theoretical model that captures the key features of the organ's morphogenesis. Our experimental data and model demonstrate that an elastic force opposes growth of the utricular sensory epithelium during development, confines cellular proliferation to the organ's periphery, and eventually arrests its growth. We find that an increase in cellular density and the subsequent degradation of the transcriptional cofactor Yap underlie this process. A reduction in mechanical constraints results in accumulation and nuclear translocation of Yap, which triggers proliferation and restores the utricle's growth; interfering with Yap's activity reverses this effect.

Elastic force restricts growth of the murine utricle.

Actively regulated symmetry breaking, which is ubiquitous in biological cells, underlies phenomena such as directed cellular movement and morphological polarization. Here we investigate how an organ-level polarity pattern emerges through symmetry breaking at the cellular level during the formation of a mechanosensory organ. Combining theory, genetic perturbations, and in vivo imaging, we study the development and regeneration of the fluid-motion sensors in the zebrafish's lateral line. We find that two interacting symmetry-breaking events - one mediated by biochemical signaling and the other by cellular mechanics - give rise to precise rotations of cell pairs, which produce a mirror-symmetric polarity pattern in the receptor organ.

Mechanochemical symmetry breaking during morphogenesis of lateral-line sensory organs

The hair bundle, an apical specialization of the hair cell composed of several rows of regularly organized stereocilia and a kinocilium, is essential for mechanotransduction in the ear. Its precise organization allows the hair bundle to convert mechanical stimuli to electrical signals; mutations that alter the bundle’s morphology often cause deafness. However, little is known about the proteins involved in the process of morphogenesis and how the structure of the bundle arises through interactions between these molecules. We present a mathematical model based on simple reaction–diffusion mechanisms that can reproduce the shape and organization of the hair bundle. This model suggests that the boundary of the cell and the kinocilium act as signaling centers that establish the bundle’s shape. The interaction of two proteins forms a hexagonal Turing pattern—a periodic modulation of the concentrations of the morphogens, sustained by local activation and long-range inhibition of the reactants—that sets a blueprint for the location of the stereocilia. Finally we use this model to predict how different alterations to the system might impact the shape and organization of the hair bundle.

https://www.pnas.org/content/pnas/111/43/15444.full.pdf

Reaction–diffusion model of hair-bundle morphogenesis

We show how to exploit excitable regimes mediated by localized structures (LS) to perform AND, OR, and NOT logical operations providing full logical functionality. Our scheme is general and can be implemented in any physical system displaying LS. In particular, LS in nonlinear photonic devices can be used for all-optical computing applications where several reconfigurable logic gates can be implemented in the transverse plane of a single device, allowing for parallel computing.

pdf/logical-operations-with-localized-structures-o7h46xis9g.pdf

Logical operations with Localized Structures

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