Modelling of some biological materials using continuum mechanics

Continuum mechanics provides a mathematical framework for modelling the physical stresses experienced by a material. Recent studies show that physical stresses play an important role in a wide variety of biological processes, including dermal wound healing, soft tissue growth and morphogenesis. Thus, continuum mechanics is a useful mathematical tool for modelling a range of biological phenomena. Unfortunately, classical continuum mechanics is of limited use in biomechanical problems. As cells refashion the �bres that make up a soft tissue, they sometimes alter the tissue's fundamental mechanical structure. Advanced mathematical techniques are needed in order to accurately describe this sort of biological `plasticity'. A number of such techniques have been proposed by previous researchers. However, models that incorporate biological plasticity tend to be very complicated. Furthermore, these models are often di�cult to apply and/or interpret, making them of limited practical use. One alternative approach is to ignore biological plasticity and use classical continuum mechanics. For example, most mechanochemical models of dermal wound healing assume that the skin behaves as a linear viscoelastic solid. Our analysis indicates that this assumption leads to physically unrealistic results. In this thesis we present a novel and practical approach to modelling biological plasticity. Our principal aim is to combine the simplicity of classical linear models with the sophistication of plasticity theory. To achieve this, we perform a careful mathematical analysis of the concept of a `zero stress state'. This leads us to a formal de�nition of strain that is appropriate for materials that undergo internal remodelling. Next, we consider the evolution of the zero stress state over time. We develop a novel theory of `morphoelasticity' that can be used to describe how the zero stress state changes in response to growth and remodelling. Importantly, our work yields an intuitive and internally consistent way of modelling anisotropic growth. Furthermore, we are able to use our theory of morphoelasticity to develop evolution equations for elastic strain. We also present some applications of our theory. For example, we show that morphoelasticity can be used to obtain a constitutive law for a Maxwell viscoelastic uid that is valid at large deformation gradients. Similarly, we analyse a morphoelastic model of the stress-dependent growth of a tumour spheroid. This work leads to the prediction that a tumour spheroid will always be in a state of radial compression and circumferential tension. Finally, we conclude by presenting a novel mechanochemical model of dermal wound healing that takes into account the plasticity of the healing skin.

Continuum mechanics modelling of microfilament networks with different architectures based on molecular investigation of single F-actin

The actin microfilament plays a critical role in many cellular processes including embryonic development, wound healing, immune response, and tissue development. It is commonly organized in the form of networks whose mechanical properties change with changes in their architecture due to cell evolution processes. This paper presents a new nonlinear continuum mechanics model of single filamentous actin (F-actin) that is based on nanoscale molecular simulations. Following this continuum model of the single F-actin, mechanical properties of differently architected lamellipodia are studied. The results provide insight that can contribute to the understanding of the cell edge motions of living cells.

Critical buckling temperature of single-walled carbon nanotubes embedded in a one-parameter elastic medium based on nonlocal continuum mechanics

In this paper, the critical budding temperature of single-walled carbon nanotubes (SWCNTs), which are embedded in one-parameter elastic medium (Winkler foundation) is estimated under the umbrella of continuum mechanics theory. Nonlocal continuum theory is incorporated into Timoshenko beam model and the governing differential equations of motion are derived. An explicit expression for the non-dimensional critical buckling temperature is also derived in this work. The effect of the nonlocal small scale coefficient, the Winkler foundation parameter and the ratio of the length to the diameter on the critical buckling temperature is investigated in detail. It can be observed that the effects of nonlocal small scale parameter and the Winkler foundation parameter are significant and should be considered for thermal analysis of SWCNTs. The results presented in this paper can provide useful guidance for the study and design of the next generation of nanodevices that make use of the thermal buckling properties of embedded single-walled carbon nanotubes. (C) 2011 Elsevier B.V. All rights reserved.

Spectral Finite Element Formulation for Nanorods via Nonlocal Continuum Mechanics

In this article, the Eringen's nonlocal elasticity theory has been incorporated into classical/local Bernoulli-Euler rod model to capture unique properties of the nanorods under the umbrella of continuum mechanics theory. The spectral finite element (SFE) formulation of nanorods is performed. SFE formulation is carried out and the exact shape functions (frequency dependent) and dynamic stiffness matrix are obtained as function of nonlocal scale parameter. It has been found that the small scale affects the exact shape functions and the elements of the dynamic stiffness matrix. The results presented in this paper can provide useful guidance for the study and design of the next generation of nanodevices that make use of the wave dispersion properties of carbon nanotubes.

Nonlocal continuum mechanics formulation for axial, flexural, shear and contraction coupled wave propagation in single walled carbon nanotubes

This paper presents the effect of nonlocal scaling parameter on the coupled i.e., axial, flexural, shear and contraction, wave propagation in single-walled carbon nanotubes (SWCNTs). The axial and transverse motion of SWCNT is modeled based on first order shear deformation theory (FSDT) and thickness contraction. The governing equations are derived based on nonlocal constitutive relations and the wave dispersion analysis is also carried out. The studies shows that the nonlocal scale parameter introduces certain band gap region in all wave modes where no wave propagation occurs. This is manifested in the wavenumber plots as the region where the wavenumber tends to infinite or wave speed tends to zero. The frequency at which this phenomenon occurs is called the escape frequency. Explicit expressions are derived for cut-off and escape frequencies of all waves in SWCNT. It is also shown that the cut-off frequencies of shear and contraction mode are independent of the nonlocal scale parameter. The results provided in this article are new and are useful guidance for the study and design of the next generation of nanodevices that make use of the coupled wave propagation properties of single-walled carbon nanotubes.

Thermal vibration analysis of orthotropic nanoplates based on nonlocal continuum mechanics

This paper presents the thermal vibration analysis of orthotropic nanoplates such as graphene, using the two variable refined plate theory and nonlocal continuum mechanics for small scale effects. The nanoplate is modeled based on two variable refined plate theory and the axial stress caused by the thermal effects is also considered. The two variable refined plate theory takes account of transverse shear effects and parabolic distribution of the transverse shear strains through the thickness of the plate, hence it is unnecessary to use shear correction factors. Nonlocal governing equations of motion for the nanoplate are derived from the principle of virtual displacements. The closed form solution for thermal-vibration frequencies of a simply supported rectangular nanoplate has been obtained by using Navier's method of solution. Numerical results obtained by the present theory are compared with available solutions in the literature and the molecular dynamics results. The influences of the small scale coefficient, the room or low temperature, the high temparature, the half wave number and the aspect ratio of nanoplate on the natural frequencies are considered and discussed in detail. It can be concluded that the present theory, which does not require shear correction factor, is not only simple but also comparable to the first-order and higher order shear deformation theory. The present analysis results can be used for the design of the next generation of nanodevices that make use of the thermal vibration properties of the nanoplates. (C) 2012 Elsevier B.V. All rights reserved.

Nonlocal continuum mechanics based ultrasonic flexural wave dispersion characteristics of a monolayer graphene embedded in polymer matrix

Wave propagation in graphene sheet embedded in elastic medium (polymer matrix) has been a topic of great interest in nanomechanics of graphene sheets, where the equivalent continuum models are widely used. In this manuscript, we examined this issue by incorporating the nonlocal theory into the classical plate model. The influence of the nonlocal scale effects has been investigated in detail. The results are qualitatively different from those obtained based on the local/classical plate theory and thus, are important for the development of monolayer graphene-based nanodevices. In the present work, the graphene sheet is modeled as an isotropic plate of one-atom thick. The chemical bonds are assumed to be formed between the graphene sheet and the elastic medium. The polymer matrix is described by a Pasternak foundation model, which accounts for both normal pressure and the transverse shear deformation of the surrounding elastic medium. When the shear effects are neglected, the model reduces to Winkler foundation model. The normal pressure or Winkler elastic foundation parameter is approximated as a series of closely spaced, mutually independent, vertical linear elastic springs where the foundation modulus is assumed equivalent to stiffness of the springs. For this model, the nonlocal governing differential equations of motion are derived from the minimization of the total potential energy of the entire system. An ultrasonic type of flexural wave propagation model is also derived and the results of the wave dispersion analysis are shown for both local and nonlocal elasticity calculations. From this analysis we show that the elastic matrix highly affects the flexural wave mode and it rapidly increases the frequency band gap of flexural mode. The flexural wavenumbers obtained from nonlocal elasticity calculations are higher than the local elasticity calculations. The corresponding wave group speeds are smaller in nonlocal calculation as compared to local elasticity calculation. The effect of y-directional wavenumber (eta(q)) on the spectrum and dispersion relations of the graphene embedded in polymer matrix is also observed. We also show that the cut-off frequencies of flexural wave mode depends not only on the y-direction wavenumber but also on nonlocal scaling parameter (e(0)a). The effect of eta(q) and e(0)a on the cut-off frequency variation is also captured for the cases of with and without elastic matrix effect. For a given nanostructure, nonlocal small scale coefficient can be obtained by matching the results from molecular dynamics (MD) simulations and the nonlocal elasticity calculations. At that value of the nonlocal scale coefficient, the waves will propagate in the nanostructure at that cut-off frequency. In the present paper, different values of e(0)a are used. One can get the exact e(0)a for a given graphene sheet by matching the MD simulation results of graphene with the results presented in this article. (c) 2012 Elsevier Ltd. All rights reserved.

Thermal vibration analysis of monolayer graphene embedded in elastic medium based on nonlocal continuum mechanics

This paper presents the thermal vibration analysis of single-layer graphene sheet embedded in polymer elastic medium, using the plate theory and nonlocal continuum mechanics for small scale effects. The graphene is modeled based on continuum plate theory and axial stress caused by the thermal effects is also considered. Nonlocal governing equation of motion for this graphene sheet system is derived from the principle of virtual displacements. The closed form solution for thermal-vibration frequencies of a simply supported rectangular nanoplate has been obtained by using the Navier's method of solution. Numerical results obtained by the present theory are compared with available solutions in the literature and the molecular dynamics results. The influences of the small scale coefficient, the room or low temperature, the high temperature, the half wave number and the aspect ratio of nanoplate on the natural frequencies are considered and discussed in detail. The thermal vibration analysis of single- and double-layer graphene sheets are considered for the analysis. The mode shapes of the respective graphene system are also captured in this work. The present analysis results can be used for the design of the next generation of nanodevices that make use of the thermal vibration properties of the graphene.

Part I. On the breaking of nonlinear dispersive waves. Part II. Variational principles in continuum mechanics

A model equation for water waves has been suggested by Whitham to study, qualitatively at least, the different kinds of breaking. This is an integro-differential equation which combines a typical nonlinear convection term with an integral for the dispersive effects and is of independent mathematical interest. For an approximate kernel of the form e^(-b|x|) it is shown first that solitary waves have a maximum height with sharp crests and secondly that waves which are sufficiently asymmetric break into "bores." The second part applies to a wide class of bounded kernels, but the kernel giving the correct dispersion effects of water waves has a square root singularity and the present argument does not go through. Nevertheless the possibility of the two kinds of breaking in such integro-differential equations is demonstrated.

Difficulties arise in finding variational principles for continuum mechanics problems in the Eulerian (field) description. The reason is found to be that continuum equations in the original field variables lack a mathematical "self-adjointness" property which is necessary for Euler equations. This is a feature of the Eulerian description and occurs in non-dissipative problems which have variational principles for their Lagrangian description. To overcome this difficulty a "potential representation" approach is used which consists of transforming to new (Eulerian) variables whose equations are self-adjoint. The transformations to the velocity potential or stream function in fluids or the scaler and vector potentials in electromagnetism often lead to variational principles in this way. As yet no general procedure is available for finding suitable transformations. Existing variational principles for the inviscid fluid equations in the Eulerian description are reviewed and some ideas on the form of the appropriate transformations and Lagrangians for fluid problems are obtained. These ideas are developed in a series of examples which include finding variational principles for Rossby waves and for the internal waves of a stratified fluid.

Development of a continuum mechanics model of passive skeletal muscle

Skeletal muscle force evaluation is difficult to implement in a clinical setting. Muscle force is typically assessed through either manual muscle testing, isokinetic/isometric dynamometry, or electromyography (EMG). Manual muscle testing is a subjective evaluation of a patient’s ability to move voluntarily against gravity and to resist force applied by an examiner. Muscle testing using dynamometers adds accuracy by quantifying functional mechanical output of a limb. However, like manual muscle testing, dynamometry only provides estimates of the joint moment. EMG quantifies neuromuscular activation signals of individual muscles, and is used to infer muscle function. Despite the abundance of work performed to determine the degree to which EMG signals and muscle forces are related, the basic problem remains that EMG cannot provide a quantitative measurement of muscle force. Intramuscular pressure (IMP), the pressure applied by muscle fibers on interstitial fluid, has been considered as a correlate for muscle force. Numerous studies have shown that an approximately linear relationship exists between IMP and muscle force. A microsensor has recently been developed that is accurate, biocompatible, and appropriately sized for clinical use. While muscle force and pressure have been shown to be correlates, IMP has been shown to be non-uniform within the muscle. As it would not be practicable to experimentally evaluate how IMP is distributed, computational modeling may provide the means to fully evaluate IMP generation in muscles of various shapes and operating conditions. The work presented in this dissertation focuses on the development and validation of computational models of passive skeletal muscle and the evaluation of their performance for prediction of IMP. A transversly isotropic, hyperelastic, and nearly incompressible model will be evaluated along with a poroelastic model.

A framework for adaptive e-learning for continuum mechanics and structural analysis

This paper presents a project for providing the students of Structural Engineering with the flexibility to learn outside classroom schedules. The goal is a framework for adaptive E-learning based on a repository of open educational courseware with a set of basic Structural Engineering concepts and fundamentals. These are paramount for students to expand their technical knowledge and skills in structural analysis and design of tall buildings, arch-type structures as well as bridges. Thus, concepts related to structural behaviour such as linearity, compatibility, stiffness and influence lines have traditionally been elusive for students. The objective is to facilitate the student a teachinglearning process to acquire the necessary intuitive knowledge, cognitive skills and the basis for further technological modules and professional development in this area. As a side effect, the system is expected to help the students improve their preparation for exams on the subject. In this project, a web-based open-source system for studying influence lines on continuous beams is presented. It encompasses a collection of interactive user-friendly applications accessible via Web, written in JavaScript under JQuery and Dygraph Libraries, taking advantage of their efficiency and graphic capabilities. It is performed in both Spanish and English languages. The student is enabled to set the geometric, topologic, boundary and mechanic layout of a continuous beam. While changing the loading and the support conditions, the changes in the beam response prompt on the screen, so that the effects of the several issues involved in structural analysis become apparent. This open interaction with the user allows the student to simulate and virtually infer the structural response. Different levels of complexity can be handled, whereas an ongoing help is at hand for any of them. Students can freely boost their experiential learning on this subject at their own pace, in order to further share, process, generalize and apply the relevant essential concepts of Structural Engineering analysis. Besides, this collection is being added to the "Virtual Lab of Continuum Mechanics" of the UPM, launched in 2013 (http://serviciosgate.upm.es/laboratoriosvirtuales/laboratorios/medios-continuos-en-construcci%C3%B3n)

Modelling continuum mechanics phenomena using three dimensional unstructured meshes on massively parallel processors

The difficulties encountered in implementing large scale CM codes on multiprocessor systems are now fairly well understood. Despite the claims of shared memory architecture manufacturers to provide effective parallelizing compilers, these have not proved to be adequate for large or complex programs. Significant programmer effort is usually required to achieve reasonable parallel efficiencies on significant numbers of processors. The paradigm of Single Program Multi Data (SPMD) domain decomposition with message passing, where each processor runs the same code on a subdomain of the problem, communicating through exchange of messages, has for some time been demonstrated to provide the required level of efficiency, scalability, and portability across both shared and distributed memory systems, without the need to re-author the code into a new language or even to support differing message passing implementations. Extension of the methods into three dimensions has been enabled through the engineering of PHYSICA, a framework for supporting 3D, unstructured mesh and continuum mechanics modeling. In PHYSICA, six inspectors are used. Part of the challenge for automation of parallelization is being able to prove the equivalence of inspectors so that they can be merged into as few as possible.

Segregation predictions for a binary mixture of granular material under flow conditions in a continuum mechanics framework

Abstract not available

Trans-Scale Mechanics: Looking For The Missing Links Between Continuum And Micro/Nanoscopic Reality

Problems involving coupled multiple space and time scales offer a real challenge for conventional frameworks of either particle or continuum mechanics. In this paper, four cases studies (shear band formation in bulk metallic glasses, spallation resulting from stress wave, interaction between a probe tip and sample, the simulation of nanoindentation with molecular statistical thermodynamics) are provided to illustrate the three levels of trans-scale problems (problems due to various physical mechanisms at macro-level, problems due to micro-structural evolution at macro/micro-level, problems due to the coupling of atoms/molecules and a finite size body at micro/nano-level) and their formulations. Accordingly, non-equilibrium statistical mechanics, coupled trans-scale equations and simultaneous solutions, and trans-scale algorithms based on atomic/molecular interaction are suggested as the three possible modes of trans-scale mechanics.