Hierarchical biomechanics: student engagement activities with a focus on biological physics

Hierarchical structure and mechanics are crucial in biological systems as they allow for smaller molecules, such as proteins and sugars, to be used in the construction of large scale biological structures exhibiting properties such as structural support functionality. By exploring the fundamental principles of structure and mechanics at the macroscale, this general theme provides a clear insight into how physics can be applied to the complex questions of biology. With a focus on biopolymer networks and hydrogels, we present a series of interactive activities which cover a range of biophysical concepts at an introductory level, such as viscoelasticity, biological networks and ultimately, hierarchical biomechanics. These activities enable us to discuss multidisciplinary science with a general audience and, given the current trends of research science, this conceptualisation of science is vital for the next generation of scientists

Localized energy absorbers in Hertzian chains

Energy absorbers and energy-harvesting devices have been under the scope of scientists and engineers for decades to fulfill specific technological needs, mainly concerned with sound and vibration absorbers, and efficient mechanical energy converters. In this paper, as a proof of concept, we build a mass-in-mass device to study the response of a linear absorber immersed in one of the spheres composing a linear array of equal elastic spheres. Spheres barely touch one another and can thus sustain nonlinear solitary wave propagation only. The linear intruder absorbs a given amount of energy depending on the frequency content of the incident solitary wave. A numerical simulation is developed to account for the experimental finding. The validation of the numerical model allows for the theoretical study of the energy absorbed by any number of intruders, and to demonstrate that the former increases exponentially with the latter, indicating that only ten of the intruders is enough to absorb the system energy. A detailed study of the transmitted energy from an external source into the chain reveals that, due to nonlinearity, the array of spheres is able to convert almost any mechanical shock to a well defined solitary or trains of solitary waves, whose frequency content is nearly independent on the excitation amplitude. This property leads to the design of a device, which is optimized to absorb energy over a broad frequency range

Shaken Baby Syndrome: Retinal Hemorrhaging. A Biomechanical Approach to Understanding the Mechanism of Causation

Shaken Baby Syndrome (SBS) is a form of abuse where typically an infant, age six months or less, is held and shaken. There may or may not be direct impact associated with this action. Further, there is very little agreement on the actual mechanism of SBS. Clinical studies are limited in showing the exact mechanism of injury and only offer postulations and qualitative descriptions. SBS has received much attention in the media, has resulted in a great deal of litigation and can be the source of unfounded accusations. Therefore, it is necessary to try to quantify the forces that may cause injury due to SBS. The physiology of infants makes injury due to SBS more likely. Infants have relatively large heads supported by weak necks that simply act as tethers (Prange et al., 2003). Therefore, there is minimal resistance to shaking. In addition, the cerebrospinal fluid (CSF) layer surrounding the infant\u27s brain is up to 10 mm thick as opposed to 1–2 mm in older children and adults (Morison, 2002). This thick layer reduces the resistance in rotation of the brain and can cause shearing injuries to the brain tissue. In addition, retinal hemorrhaging has been reported in SBS. The infant\u27s eyes have a vitreous that is typically more gelatinous and with a higher viscosity than in adult eyes. In addition, this vitreous is firmly attached to the retina and is difficult to remove (Levin, 2000). A preliminary parametric model of an infant eye will be presented so that resultant nodal retinal force of the posterior retina can be investigated and compared with a documented shaking frequency and a documented impact pulse. Retinal forces are then compared with various studies that investigate retinal detachment or adhesive strength. This eye model is built using a variety of material properties that have been reported for the sclero-cornea shell, choroids, retina, vitreous, aqueous, lens, ciliary, optic nerve, tendons, extra ocular muscles, optic nerve, and orbital fatty tissue. The geometry of the eye has been carefully optimized for this parametric model based on scaling to an infant from an adult using idealized eye globe geometry and transverse slice tracings of The Visible Human Project. This model shows promise in investigating the forces and kinematics of the infant eye exposed to harmonic shaking and further bolsters some of the few biomechanical studies investigating SBS. However, improvements are necessary to complete the eye model presented. Specifically, improvements on the mechanical properties for the components of the eye and especially the infant eye are needed. There is currently a deficit of biomechanical studies of the materials needed for the infant eye that is specifically geared for use in an explicit finite element code package. Conversions and adaptations of available materials are used in this first version of the infant eye model presented here and are in fair agreement with some of the clinical studies concerning SBS

Modeling electrospinning process and a numerical scheme using Lattice Boltzmann method to simulate viscoelastic fluid flows

In the recent years, researchers have discovered a multitude of applications using nanofibers in fields like composites, biotechnology, environmental engineering, defense, optics and electronics. This increase in nanofiber applications needs a higher rate of nanofiber production. Electrospinning has proven to be the best nanofiber manufacturing process because of simplicity and material compatibility. Study of effects of various electrospinning parameters is important to improve the rate of nanofiber processing. In addition, several applications demand well-oriented nanofibers. Researchers have experimentally tried to control the nanofibers using secondary external electric field. In the first study, the electrospinning process is modeled and the bending instability of a viscoelastic jet is simulated. For this, the existing discrete bead model is modified and the results are compared, qualitatively, with previous works in literature. In this study, an attempt is also made to simulate the effect of secondary electric field on electrospinning process and whipping instability. It is observed that the external secondary field unwinds the jet spirals, reduces the whipping instability and increases the tension in the fiber. Lattice Boltzmann method (LBM) has gained popularity in the past decade as the method is easy implement and can also be parallelized. In the second part of this thesis, a hybrid numerical scheme which couples lattice Boltzmann method with finite difference method for a Oldroyd-B viscoelastic solution is proposed. In this scheme, the polymer viscoelastic stress tensor is included in the equilibrium distribution function and the distribution function is updated using SRT-LBE model. Then, the local velocities from the distribution function are evaluated. These local velocities are used to evaluate local velocity gradients using a central difference method in space. Next, a forward difference scheme in time is used on the Maxwell Upper Convected model and the viscoelastic stress tensor is updated. Finally, using the proposed numerical method start-up Couette flow problem for Re = 0.5 and We = 1.1, is simulated. The velocity and stress results from these simulations agree very well with the analytical solutions

Microrheology to explore protein and cell dynamics

In this thesis, I explore the applications of optical tweezers and passive video particle tracking microrheology for bioanalytical applications. Microrheology is a branch of rheology that has the same principles as conventional bulk rheology, but which works on micron length scales. Microrheological techniques relate the free or the driven motion of micron-sized tracer particles suspended in the fluid under investigation to the ‘elastic’ and ‘viscous’ components of the material. These components can be related to the dynamics of the molecules that make up the fluid, and thus microrheology has the potential to reveal new information about the microscopic properties of complex materials. Optical tweezers are sensitive instruments that have been used to apply forces on the order of pN and to measure the displacements down to nm of objects ranging in size from 10 nm to over 100μm, making them an essential tool for microrheology. Here, we have developed a new set of analytical methods for microrheological measurements of biological and bio-analytical systems. In particular, we have developed two new self-consistent procedures for measuring the linear viscoelastic properties of materials across the widest frequency range achievable with optical tweezers (Phys.Review E. (2010) 81:2, and J. Optics (2011) 13:4). Furthermore, we present a straightforward procedure for measuring the in vivo linear viscoelastic properties of single cells via passive video particle tracking microrheology of single beads attached to the cells’ exterior. Notably, the procedure presented here represents an alternative methodology that can be extended to many experimental formats and provides a simple addition to existing cellular physiology studies. In addition, we introduce new methodologies for deriving the concentration scaling laws of polymer and biopolymer solutions from microrheological measurements carried out with optical tweezers. These methods have been adopted to investigate the concentration scaling laws of in vitro reconstituted actin solutions and actin/myosin solution

Biplanar High-Speed Fluoroscopy of Pony Superficial Digital Flexor Tendon (SDFT)-An In Vivo Pilot Study.

The superficial digital flexor tendon (SDFT) is the most frequently injured structure of the musculoskeletal system in sport horses and a common cause for early retirement. This project's aim was to visualize and measure the strain of the sound, injured, and healing SDFTs in a pony during walk and trot. For this purpose, biplanar high-speed fluoroscopic kinematography (FluoKin), as a high precision X-ray movement analysis tool, was used for the first time in vivo with equine tendons. The strain in the metacarpal region of the sound SDFT was 2.86% during walk and 6.78% during trot. When injured, the strain increased to 3.38% during walk and decreased to 5.96% during trot. The baseline strain in the mid-metacarpal region was 3.13% during walk and 6.06% during trot and, when injured, decreased to 2.98% and increased to 7.61%, respectively. Following tendon injury, the mid-metacarpal region contributed less to the overall strain during walk but showed increased contribution during trot. Using this marker-based FluoKin technique, direct, high-precision, and long-term strain measurements in the same individual are possible. We conclude that FluoKin is a powerful tool for gaining deeper insight into equine tendon biomechanics

A comparison between the FENE-P and sPTT constitutive models in Large Amplitude Oscillatory Shear (LAOS)

The FENE-P and sPTT viscoelastic models are widely used for modelling of complex fluids. Although they are derived from distinct micro-structural theories, these models can become mathematically identical in steady and homogeneous flows with a particular choice of the value of the model parameters. However, even with this choice of parameter values, the model responses are known to differ from each other in transient flows. In this work, we investigate the responses of the FENE-P and sPTT constitutive models in Large Amplitude Oscillatory Shear (LAOS). In steady-shear, the shear stress scales with the non-dimensional group $Wi/(aL) \ (Wi\sqrt{\epsilon})$ for the FENE-P (sPTT) model, where $Wi$ is the Weissenberg number, $L^2$ is the limit of extensibility in the FENE-P model ($a$ being $L^2/(L^2-3)$) and $\epsilon$ is the extensibility parameter in the sPTT model. Our numerical and analytical results show that, in LAOS, the FENE-P model only shows this universality for large values of $L^2$ whereas the sPTT model shows this universality for all values of$\epsilon$. In the strongly non-linear region, there is a drastic difference between the responses of the two models, with the FENE-P model exhibiting strong shear stress overshoots which manifest as self-intersecting secondary loops in the viscous Lissajous curves. We quantify the non-linearity exhibited by each constitutive model using the Sequence of Physical Processes framework. Despite the high degree of non-linearity exhibited by the FENE-P model, we also show using fully non-linear 1D simulations that it does not shear band in LAOS within the range of conditions studied.Comment: Submitted to Journal of Fluid Mechanic