The mechanics of a chain or ring of spherical magnets

Strong magnets, such as neodymium-iron-boron magnets, are increasingly being manufactured as spheres. Because of their dipolar characters, these spheres can easily be arranged into long chains that exhibit mechanical properties reminiscent of elastic strings or rods. While simple formulations exist for the energy of a deformed elastic rod, it is not clear whether or not they are also appropriate for a chain of spherical magnets. In this paper, we use discrete-to-continuum asymptotic analysis to derive a continuum model for the energy of a deformed chain of magnets based on the magnetostatic interactions between individual spheres. We find that the mechanical properties of a chain of magnets differ significantly from those of an elastic rod: while both magnetic chains and elastic rods support bending by change of local curvature, nonlocal interaction terms also appear in the energy formulation for a magnetic chain. This continuum model for the energy of a chain of magnets is used to analyse small deformations of a circular ring of magnets and hence obtain theoretical predictions for the vibrational modes of a circular ring of magnets. Surprisingly, despite the contribution of nonlocal energy terms, we find that the vibrations of a circular ring of magnets are governed by the same equation that governs the vibrations of a circular elastic ring

Calculus from the past: multiple delay systems arising in cancer cell modelling

Non-local calculus is often overlooked in the mathematics curriculum. In this paper we present an interesting new class of non-local problems that arise from modelling the growth and division of cells, especially cancer cells, as they progress through the cell cycle. The cellular biomass is assumed to be unstructured in size or position, and its evolution governed by a time-dependent system of ordinary differential equations with multiple time delays. The system is linear and taken to be autonomous. As a result, it is possible to reduce its solution to that of a nonlinear matrix eigenvalue problem. This method is illustrated by considering case studies, including the model of the cell cycle developed in Simms K, Bean N, & Koeber A. [10]. The paper concludes by explaining how asymptotic expressions for the distribution of cells across the compartments can be determined and used to assess the impact of different chemotherapeutic agents

Microfluidic immunomagnetic multi-target sorting – a model for controlling deflection of paramagnetic beads

We describe a microfluidic system that uses a magnetic field to sort paramagnetic beads by deflecting them in the direction normal to the flow. Our experiments systematically study the dependence of the beads’ deflection on: bead size and susceptibility, magnet strength, fluid speed and viscosity, and device geometry. We also develop a design parameter that can aid in the design of microfluidic devices for immunomagnetic multi-target sorting

Dynamics of mechanically induced fiber reorientation in\ud the material reinforced by two families of fibers

The specific fiber alignment and its content in biological tissues are created and maintained by the cells, which respond to mechanical stimuli arising from properties of the surrounding material. This coupling between mechanical anisotropy and tissue remodeling can be modeled in the theory of nonlinear elasticity as a fiber-reinforced hyperelastic material where the remodeling is represented as the change in the fiber orientation and/or amount. Here, we study analytically a simple model of fiber reorientation in a rectangular elastic tissue reinforced by two symmetrically arranged families of fibers subject to constant external loads. In this model, the fiber direction tends to align with the maximum principal stretch. We characterize the global behaviour of the system for all material parameters and applied loads, and show that provided the fibers are tensile initially, the system converges to a stable equilibrium, which corresponds to either complete or intermediate fiber alignment

On-lattice agent-based simulation of populations of cells within the open-source chaste framework

Over the years, agent-based models have been developed that combine cell division and reinforced random walks of cells on a regular lattice, reaction-diffusion equations for nutrients and growth factors and ordinary differential equations (ODEs) for the subcellular networks regulating the cell cycle. When linked to a vascular layer, this multiple scale model framework has been applied to tumour growth and therapy. Here we report on the creation of an agent-based multiscale environment amalgamating the characteristics of these models within a Virtual Pysiological Human (VPH) Exemplar Project. This project enables re-use, integration, expansion and sharing of the model and relevant data. The agent-based and reactiondiffusion parts of the multiscale model have been implemented and are available for download as part of the latest public release of Chaste (“Cancer, Heart and Soft Tissue Environment”), (http://www.cs.ox.ac.uk/chaste/) version 3.1, part of the VPH Toolkit (http://toolkit.vph-noe.eu/). The environment functionalities are verified against the original models, in addition to extra validation of all aspects of the code. In this work, we present the details of the implementation of the agent-based environment, including the system description, the conceptual model, the development of the simulation model and the processes of verification and validation of the simulation results. We explore the potential use of the environment by presenting exemplar applications of the “what if” scenarios that can easily be studied in the environment. These examples relate to tumour growth, cellular competition for resources and tumour responses to hypoxia. We conclude our work by summarising the future steps for the expansion of the current system

Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana

Regulation of gene expression is crucial for organism growth, and it is one of the challenges in Systems Biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyse two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants to infer their regulatory network. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale-free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation

Multiscale stochastic reaction-diffusion modelling: application to actin dynamics in filopodia

Two multiscale (hybrid) stochastic reaction-diffusion models of actin dynamics in a filopodium are investigated. Both hybrid algorithms combine compartment-based and molecular-based stochastic reaction-diffusion models. The first hybrid model is based on the models previously\ud developed in the literature. The second hybrid model is based on the application of recently developed two-regime method (TRM) to a fully molecular-based model which is also developed in this paper. The results of hybrid models are compared with the results of the molecular-based model. It is shown that both approaches give comparable results, although the TRM model better agrees quantitatively with the molecular-based model

Magnetic chains: From self-buckling to self-assembly

Spherical neodymium-iron-boron magnets are perman-ent magnets that can be assembled into a variety of structures due to their high magnetic strength. A one-dimensional chain of these magnets responds to mechanical loadings in a manner reminiscent of an elastic rod. We investigate the macroscopic mechanical properties of assemblies of ferromagnetic spheres by considering chains, rings, and chiral cylinders of magnets. Based on energy estimates and simple experiments, we introduce an effective magnetic bending stiffness for a chain of magnets and show that, used in conjunction with classic results for elastic rods, it provides excellent estimates for the buckling and vibration dynamics of magnetic chains. We then use this estimate to understand the dynamic self-assembly of a cylinder from an initially straight chain of magnets.Comment: Final version, as publishe

Axisymmetric bifurcations of thick spherical shells under inflation and compression

Incremental equilibrium equations and corresponding boundary conditions for an isotropic, hyperelastic and incompressible material are summarized and then specialized to a form suitable for the analysis of a spherical shell subject to an internal or an external pressure. A thick-walled spherical shell during inflation is analyzed using four different material models. Specifically, one and two terms in the Ogden energy formulation, the Gent model and an I1 formulation recently proposed by Lopez-Pamies. We investigate the existence of local pressure maxima and minima and the dependence of the corresponding stretches on the material model and on shell thickness. These results are then used to investigate axisymmetric bifurcations of the inflated shell. The analysis is extended to determine the behavior of a thick-walled spherical shell subject to an external pressure. We find that the results of the two terms Ogden formulation, the Gent and the Lopez-Pamies models are very similar, for the one term Ogden material we identify additional critical stretches, which have not been reported in the literature before

Rotation, inversion, and perversion in anisotropic elastic cylindrical tubes and membranes

Cylindrical tubes and membranes are universal structural elements found in biology and engineering over a wide range of scales. Working in the framework of nonlinear elasticity we consider the possible deformations of elastic cylindrical shells reinforced by one or two families of anisotropic fibers. We consider both small and large deformations and the reduction from thick cylindrical shells (tubes) to thin shells (cylindrical membranes). In particular, a number of universal regimes can be identified including the possibility of inversion and perversion of rotation