A Life Cycle for Modeling Biology at Different Scales

Modeling has become a popular tool for inquiry and discovery across biological disciplines. Models allow biologists to probe complex questions and to guide experimentation. Modeling literacy among biologists, however, has not always kept pace with the rise in popularity of these techniques and the relevant advances in modeling theory. The result is a lack of understanding that inhibits communication and ultimately, progress in data gathering and analysis. In an effort to help bridge this gap, we present a blueprint that will empower biologists to interrogate and apply models in their field. We demonstrate the applicability of this blueprint in two case studies from distinct subdisciplines of biology; developmental-biomechanics and evolutionary biology. The models used in these fields vary from summarizing dynamical mechanisms to making statistical inferences, demonstrating the breadth of the utility of models to explore biological phenomena.

Developmental biodynamics: the development of coordination in children

Human movement is brought about by the musculoskeletal system under the control of the nervous system. By coordinated activity between the various muscle groups, forces generated by the muscles are transmitted by the bones and joints to enable the individual to maintain an upright or partially upright posture and bring about voluntary controlled movements. Biomechanics of human movement is the study of the relationship between the external forces (due to body weight and physical contact with the external environment) and internal forces (active forces generated by muscles and passive forces exerted on other structures) that act on the body and the eff ect of these forces on the movement of the body. This chapter specifically addresses developmental biomechanics as it relates to the development of coordination in children.

INTEGRATING MECHANICAL CONTROL THEORY INTO MODELS OF BIOLOGICAL DEVELOPMENT — ANALYTICAL REVIEW

This paper presents both a general review on developmental biomechanics and a concrete proposition for the computation of a symmetry breaking instability of a model of biological development in terms of self-organization theory. The necessary biological and physical facts taken from the literature are described and discussed in the context of a unified statement of the problems for mathematical modeling of pattern formation. This is then applied to planar cell polarization (PCP) of the Drosophila wing. In this way, the process is modeled by an elastopolarization equation. In terms of this statement, the mechanical specificity (interaction with basal plate) of wing PCP is characterized. Some aspects of modeling somite formation as well as other developmental processes are also concerned.

FEM Voxel Modeling of the Tubular Embryonic Chick Heart for Finite Strain Analysis

Significant progress has been made in the study of the developmental biomechanics of the embryonic chick heart through the use of the finite element method (FEM) [1, 2, 3]. Our work focuses on the geometry of the Hamburger-Hamilton stages 9–12 embryonic chick heart, approximately the time when the heart begins to function and undergoes drastic morphological changes, such as c-looping. Our objective is to devise a method for building an accurate 3D solid FEM mesh used for nonlinear analysis of the myocardium (MY) and cardiac jelly (CJ). The models are based on the extraction of voxels from optical coherence tomography (OCT) images of an arrested developing heart. To alleviate the problem of jagged edges introduced by the hexahedral voxel structure, we present a method for geometric smoothing and mesh coarsening. The performance of the voxel and smoothed models are tested given physiological loading conditions (pressure, biological growth, muscle contraction), to ascertain which model should be used for modeling the c-looping process.