Biology subjects

Moulton, D. E.

Publications and source records attributed to Moulton, D. E..

4 recordsLinked to original sources

bioRxiv2024

Ultra-fast physics-based modeling of the elephant trunk

With more than 90,000 muscle fascicles, the elephant trunk is a complex biological structure and the largest known muscular hydrostat. It achieves an unprecedented control through intricately orchestrated contractions of a wide variety of muscle architectures. Fascinated by the elephant trunks unique performance, scientists of all disciplines are studying its anatomy, function, and mechanics, and use it as an inspiration for biomimetic soft robots. Yet, to date, there is no precise mapping between microstructural muscular activity and macrostructural trunk motion, and our understanding of the elephant trunk remains incomplete. Specifically, no model of the elephant trunk employs formal physics-based arguments that account for its complex muscular architecture, while preserving low computational cost, to enable fast screening of its configuration space. Here we create a reduced-order model of the elephant trunk that can-within a fraction of a second- predict the trunks motion as a result of its muscular activity. To ensure reliable results in the finite deformation regime, we integrate first principles of continuum mechanics and the theory of morphoelasticity for fibrillar activation. We employ dimensional reduction to represent the trunk as an active slender structure, which results in closed-form expressions for its curvatures and extension as functions of muscle activation and anatomy. We create a high-resolution digital representation of the trunk from magnetic resonance images to quantify the effects of different muscle groups. We propose a general solution method for the inverse motion problem and apply it to extract the muscular activations of three representative trunk motions: picking a fruit; lifting a log; and lifting a log asymmetrically. For each task, we identify key features in the muscle activation profiles. Our results suggest that, upon reaching maximum contraction in select muscle groups, the elephant trunk autonomously reorganizes muscle activation to perform specific tasks. Our study provides a complete quantitative characterization of the fundamental science behind elephant trunk biomechanics, with potential applications in the material science of flexible structures, the design of soft robots, and the creation of flexible prosthesis and assist devices.

bioengineering↗

bioRxiv2023

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. Author summaryConnecting genotype to phenotype is a fundamental goal in developmental biology. While many studies examine this link in model organisms for which gene regulatory networks are well known, for non-model organisms, different techniques are required, and multiscale computational modeling offers a promising direction. In this paper, we develop a framework linking molecular-scale interactions to tissue-level growth and mechanics to organism-level characteristics in order to investigate spine formation in T. sazae, a species of mollusc that displays remarkable phenotypic plasticity in spine form. Our analysis uncovers a subtle but statistically significant difference in spine form between shell specimens collected from three different localities in Japan. Moreover, by tracing the difference in form through parametric differences in the multiscale framework, we provide mechanistic insight as to how environmental differences may translate to a change in form. The methodology we present may readily be extended to more detailed modeling of this system, and the conceptual framework is amenable for multiscale analysis in other systems.

systems biology↗

bioRxiv2023

Mechanics reveals the role of peristome geometry in prey capture in carnivorous pitcher plants (Nepenthes)

Carnivorous pitcher plants (Nepenthes) are a striking example of a natural pitfall trap. The traps slippery rim, or peristome, plays a critical role in insect capture via an aquaplaning mechanism that is well documented. Whilst the peristome has received significant research attention, the conspicuous variation in peristome geometry across the genus remains unexplored. We examined the mechanics of prey capture using Nepenthes pitcher plants with divergent peristome geometries. Inspired by living materials, we developed a mathematical model that links the peristomes three-dimensional geometries to the physics of prey capture under the laws of Newtonian mechanics. Linking form and function enables us to test hypotheses related to the function of features such as shape and ornamentation, orientation in a gravitational field, and the presence of teeth, while analysis of the energetic costs and gains of a given geometry provides a means of inferring potential evolutionary pathways. In a separate modeling approach, we show how prey size may correlate with peristome dimensions for optimal capture. Our modeling framework provides a physical platform to understand how divergence in peristome morphology may have evolved in the genus Nepenthes in response to shifts in prey diversity, availability, and size. Significance StatementPitcher plants (Nepenthes) produce an astonishing array of leaf-derived traps into which preys (typically insects) slide from a rim (the peristome). How prey capture varies across this varied genus is a mystery. We hypothesized that insects behave differently depending on peristome size and geometry. We examined the physics of prey capture under the laws of Newtonian mechanics to show that prey size and behavior correlate with peristome shape. We conclude that a diversity of peristomes in Nepenthes evolved in response to variation in prey capture.

plant biology↗

bioRxiv2020

Multiscale integration of environmental stimuli in plant tropism produces complex behaviors

Plant tropism refers to the directed movement of an organ or organism in response to external stimuli. Typically, these stimuli induce hormone transport that triggers cell growth or deformation. In turn, these local cellular changes create mechanical forces on the plant tissue that are balanced by an overall deformation of the organ, hence changing its orientation with respect to the stimuli. This complex feedback mechanism takes place in a three-dimensional growing plant with varying stimuli depending on the environment. We model this multiscale process in filamentary organs for an arbitrary stimulus by linking explicitly hormone transport to local tissue deformation leading to the generation of mechanical forces and the deformation of the organ in three dimensions. We show, as examples, that the gravitropic, phototropic, nutational, and thigmotropic dynamic responses can be easily captured by this framework. Further, the integration of evolving stimuli and/or multiple contradictory stimuli can lead to complex behavior such as sun following, canopy escape, and plant twining. Significance StatementTo survive and to thrive, plants rely on their ability to sense multiple environmental signals, such as gravity or light, and respond to them by growing and changing their shape. To do so, the signals must be transduced down to the cellular level to create the physical deformations leading to shape changes. We propose a multiscale theory of tropism that takes multiple stimuli and transforms them into auxin transport that drives tissue-level growth and remodeling, thus modifying the plant shape and position with respect to the stimuli. This feedback loop can be dynamically updated to understand the response to individual stimuli or the complex behavior generated by multiple stimuli such as canopy escape or pole wrapping for climbing plants.

plant biology↗