A multiscale computational framework for the development of spines in molluscan shells.

From mathematical models of growth to computer simulations of pigmentation, the study of shell formation has given rise to an abundant number of models, working at various scales. Yet, attempts to combine those models have remained sparse, due to the challenge of combining categorically different approaches. In this paper, we propose a framework to streamline the process of combining the molecular and tissue scales of shell formation. We choose these levels as a proxy to link the genotype level, which is better described by molecular models, and the phenotype level, which is better described by tissue-level mechanics. We also show how to connect observations on shell populations to the approach, resulting in collections of molecular parameters that may be associated with different populations of real shell specimens. The approach is as follows: we use a Quality-Diversity algorithm, a type of black-box optimization algorithm, to explore the range of concentration profiles emerging as solutions of a molecular model, and that define growth patterns for the mechanical model. At the same time, the mechanical model is simulated over a wide range of growth patterns, resulting in a variety of spine shapes. While time-consuming, these steps only need to be performed once and then function as look-up tables. Actual pictures of shell spines can then be matched against the list of existing spine shapes, yielding a potential growth pattern which, in turn, gives us matching molecular parameters. The framework is modular, such that models can be easily swapped without changing the overall working of the method. As a demonstration of the approach, we solve specific molecular and mechanical models, adapted from available theoretical studies on molluscan shells, and apply the multiscale framework to evaluate the characteristics of spines from three distinct populations of Turbo sazae.

Minimal Design of the Elephant Trunk as an Active Filament.

One of the key problems in active materials is the control of shape through actuation. A fascinating example of such control is the elephant trunk, a long, muscular, and extremely dexterous organ with multiple vital functions. The elephant trunk is an object of fascination for biologists, physicists, and children alike. Its versatility relies on the intricate interplay of multiple unique physical mechanisms and biological design principles. Here, we explore these principles using the theory of active filaments and build, theoretically, computationally, and experimentally, a minimal model that explains and accomplishes some of the spectacular features of the elephant trunk.

Active shape control by plants in dynamic environments.

Plants are a paradigm for active shape control in response to stimuli. For instance, it is well known that a tilted plant will eventually straighten vertically, demonstrating the influence of both an external stimulus, gravity, and an internal stimulus, proprioception. These effects can be modulated when a potted plant is additionally rotated along the plant's axis, as in a rotating clinostat, leading to intricate shapes. We use a previously derived rod model to study the response of a growing plant and the joint effects of both stimuli at all rotation speeds. In the absence of rotation, we identify a universal planar shape towards which all shoots eventually converge. With rotation, we demonstrate the existence of a stable family of three-dimensional dynamic equilibria where the plant axis is fixed in space. Further, the effect of axial growth is to induce steady behaviors, such as solitary waves. Overall, this study offers insight into the complex out-of-equilibrium dynamics of a plant in three dimensions and further establishes that internal stimuli in active materials are key for robust shape control.

An automated method for tendon image segmentation on ultrasound using grey-level co-occurrence matrix features and hidden Gaussian Markov random fields.

BACKGROUND: Despite knowledge of qualitative changes that occur on ultrasound in tendinopathy, there is currently no objective and reliable means to quantify the severity or prognosis of tendinopathy on ultrasound. OBJECTIVE: The primary objective of this study is to produce a quantitative and automated means of inferring potential structural changes in tendinopathy by developing and implementing an algorithm which performs a texture based segmentation of tendon ultrasound (US) images. METHOD: A model-based segmentation approach is used which combines Gaussian mixture models, Markov random field theory and grey-level co-occurrence (GLCM) features. The algorithm is trained and tested on 49 longitudinal B-mode ultrasound images of the Achilles tendons which are labelled as tendinopathic (24) or healthy (25). Hyperparameters are tuned, using a training set of 25 images, to optimise a decision tree based classification of the images from texture class proportions. We segment and classify the remaining test images using the decision tree. RESULTS: Our approach successfully detects a difference in the texture profiles of tendinopathic and healthy tendons, with 22/24 of the test images accurately classified based on a simple texture proportion cut-off threshold. Results for the tendinopathic images are also collated to gain insight into the topology of structural changes that occur with tendinopathy. It is evident that distinct textures, which are predominantly present in tendinopathic tendons, appear most commonly near the transverse boundary of the tendon, though there was a large variability among diseased tendons. CONCLUSION: The GLCM based segmentation of tendons under ultrasound resulted in distinct segmentations between healthy and tendinopathic tendons and provides a potential tool to objectively quantify damage in tendinopathy.