arXiv subjects

Nicholas A. Battista

Publications and source records attributed to Nicholas A. Battista.

17 recordsLinked to original sources

arXiv2021

Hopscotching Jellyfish: combining different duty cycle kinematics can lead to enhanced swimming performance

Jellyfish (Medusozoa) have been deemed the most energy-efficient animals in the world. Their bell morphology and relatively simple nervous systems make them attractive to robotocists. Although, the science community has devoted much attention to understanding their swimming performance, there is still much to be learned about the jet propulsive locomotive gait displayed by prolate jellyfish. Traditionally, computational scientists have assumed uniform duty cycle kinematics when computationally modeling jellyfish locomotion. In this study we used fluid-structure interaction modeling to determine possible enhancements in performance from shuffling different duty cycles together across multiple Reynolds numbers and contraction frequencies. Increases in speed and reductions in cost of transport were observed as high as 80% and 50%, respectively. Generally, the net effects were greater for cases involving lower contraction frequencies. Overall, robust duty cycle combinations were determined that led to enhanced or impeded performance.

physics.flu-dyn↗

arXiv2020

Swimming through parameter subspaces of a simple anguilliform swimmer

Computational scientists have investigated swimming performance across a multitude of different systems for decades. Most models depend on numerous model parameters and performance is sensitive to those parameters. In this paper, parameter subspaces are qualitatively identified in which there exists enhanced swimming performance for an idealized, simple swimming model that resembles a C. elegans, an organism that exhibits an anguilliform mode of locomotion. The computational model uses the immersed boundary method to solve the fluid-interaction system. The 1D swimmer propagates itself forward by dynamically changing its preferred body curvature. Observations indicate that the swimmer's performance appears more sensitive to fluid scale and stroke frequency, rather than variations in the velocity and acceleration of either its upstroke or downstroke as a whole. Pareto-like optimal fronts were also identified within the data for the cost of transport and swimming speed. While this methodology allows one to locate robust parameter subspaces for desired performance in a straight-forward manner, it comes at the cost of simulating orders of magnitude more simulations than traditional fluid-structure interaction studies.

physics.flu-dyn↗

arXiv2020

Don't be jelly: Exploring effective jellyfish locomotion

Jellyfish have been called one of the most energy-efficient animals in the world due to the ease in which they move through their fluid environment, by product of their morphological, muscular, and material properties. We investigated jellyfish locomotion by conducting \textit{in silico} comparative studies and explored swimming performance across different fluid scales (e.g., Reynolds Number), bell contraction frequencies, and contraction phase kinematics for a jellyfish with a fineness ratio of 1 (ratio of bell height to bell diameter). To study these relationships, an open source implementation of the immersed boundary method was used (\textit{IB2d}) to solve the fully coupled fluid-structure interaction problem of a flexible jellyfish bell in a viscous fluid. Thorough 2D parameter subspace explorations illustrated optimal parameter combinations in which give rise to enhanced swimming performance. All performance metrics indicated a higher sensitivity to bell actuation frequency than fluid scale or contraction phase kinematics, via Sobol sensitivity analysis, on a high performance parameter subspace. Moreover, Pareto-like fronts were identified in the overall performance space involving the cost of transport and forward swimming speed. Patterns emerged within these performance spaces when highlighting different parameter regions, which complemented the global sensitivity results. Lastly, an open source computational model for jellyfish locomotion is offered to the science community that can be used as a starting place for future numerical experimentation.

physics.flu-dyn↗

arXiv2020

Diving into a simple anguilliform swimmer's sensitivity

Computational models of aquatic locomotion range from individual modest simple swimmers in 2D to sophisticated 3D individual swimmers to complex multi-swimmer models that attempt to parse collective behavioral dynamics. Each of these models contain a multitude of model input parameters to which the model outputs are inherently dependent, i.e., various swimming performance metrics. In this work, the swimming performance's sensitivity to parameters is investigated for an idealized, simple anguilliform swimming model in 2D. The swimmer considered here propagates forward by dynamically varying its body curvature, similar to motion of a \textit{C. elegan}. The parameter sensitivities were explored with respect to the fluid scale (Reynolds number, Re), stroke (undulation) frequency, as well as a kinematic parameter controlling the velocity and acceleration of each upstroke and downstroke. In total, 5000 fluid-structure interaction simulations were performed, each with a unique parameter combination selected via a Sobol sequence. Thus, global sensitivity analysis was performed using Sobol sensitivity analysis. Results indicate that the swimmer's performance is most sensitive to variation in its stroke frequency. Trends in swimming performance were discovered by projecting the performance metrics from the overall 3D parameter space onto particular 2D subspaces and Pareto-like optimal fronts were identified for swimming efficiency. This work is a natural extension of the parameter explorations of the same model from [1].

physics.flu-dyn↗

arXiv2020

Fluid-Structure Interaction for the Classroom: Interpolation, Hearts, and Swimming!

While students may find spline interpolation quite digestible, based on their familiarity with continuity of a function and its derivatives, some of its inherent value may be missed when students only see it applied to standard data interpolation exercises. In this paper, we offer alternatives where students can qualitatively and quantitatively witness the resulting dynamical differences when objects are driven through a fluid using different spline interpolation methods. They say, seeing is believing; here we showcase the differences between linear and cubic spline interpolation using examples from fluid pumping and aquatic locomotion. Moreover, students can define their own interpolation functions and visualize the dynamics that unfold. To solve the fluid-structure interaction system, the open-source fluid dynamics software IB2d is used. In that vein, all simulation codes, analysis scripts, and movies are provided for streamlined use.

math.HO↗

arXiv2019

Naut your everyday jellyfish model: Exploring how tentacles and oral arms impact locomotion

Jellyfish - majestic, energy efficient, and one of the oldest species that inhabits the oceans. It is perhaps the second item, their efficiency, that has captivated scientists for decades into investigating their locomotive behavior. Yet, no one has specifically explored the role that their tentacles and oral arms may have on their potential swimming performance, arguably the very features that give jellyfish their beauty while instilling fear into their prey (and beach-goers). We perform comparative in silico experiments to study how tentacle/oral arm number, length, placement, and density affect forward swimming speeds, cost of transport, and fluid mixing. An open source implementation of the immersed boundary method was used (IB2d) to solve the fully coupled fluid-structure interaction problem of an idealized flexible jellyfish bell with poroelastic tentacles/oral arms in a viscous, incompressible fluid. Overall tentacles/oral arms inhibit forward swimming speeds, by appearing to suppress vortex formation. Non-linear relationships between length and fluid scale (Reynolds Number) as well as tentacle/oral arm number, density, and placement are observed, illustrating that small changes in morphology could result in significant decreases in swimming speeds, in some cases by downwards of 400% between cases with to without tentacles/oral arms.

physics.flu-dyn↗

arXiv2019

Fluid-Structure Interaction for the Classroom: Speed, Accuracy, Convergence, and Jellyfish!

When is good, good enough? This question lingers in approximation theory and numerical methods as a competition between accuracy and practicality. Numerical Analysis is traditionally where the rubber meets the road: students begin to use numerical algorithms to compute approximate solutions to non-trivial problems. However, it is difficult for students to understand that more accuracy is not always the goal, but rather enough accuracy for practical use and meaningful interpretation. This compromise between accuracy and computational time/resources can be explored through the use of convergence plots. We offer a variety of classroom activities that allow students to discover the usefulness of convergence plots, including a contemporary example involving jellyfish locomotion using fluid-structure interaction modeling. These examples will additionally illustrate subtleties of convergence analysis: the same numerical scheme can exhibit different convergence rates, and the definition of `error' may change the convergence properties. To solve the fluid-structure interaction system, the open source software IB2d is used. All numerical codes, scripts, and movies are provided for streamlined integration into a classroom setting.

math.HO↗

arXiv2018

Vortex dynamics in trabeculated embryonic ventricles

Proper heart morphogenesis requires a delicate balance between hemodynamic forces, myocardial activity, morphogen gradients, and epigenetic signaling, all of which are coupled with genetic regulatory networks. Recently both in vivo and in silico studies have tried to better understand hemodynamics at varying stages of vertebrate cardiogenesis. In particular, the intracardial hemodynamics during the onset of trabeculation is notably complex - the inertial and viscous fluid forces are approximately equal at this stage and small perturbations in morphology, scale, and steadiness of the flow can lead to significant changes in bulk flow structures, shear stress distributions, and chemical morphogen gradients. The immersed boundary method was used to solve the computational fluid dynamics problem involving fluid flow moving through the trabeculated ventricles of 72, 80, and 120 hours post fertilization wild type zebrafish embryos and ErbB2-inhibited embryos at 7 days post fertilization. An idealized trabeculated ventricular model was explored to map the bifurcations in flow structure that occur as a result of the unsteadiness of flow, trabeculae height, and fluid scale ($Re$). Vortex formation occurred in intertrabecular regions for biologically relevant parameter spaces, wherein flow velocities increased. This indicates that trabecular morphology may alter intracardial flow patterns and hence ventricular shear stresses and morphogen gradients. A potential implication of this work is that the onset of vortical (disturbed) flows can upregulate Notch1 expression in endothelial cells in vitro and hence impacts chamber morphogensis, valvulogenesis, and the formation of the trabeculae themselves.

q-bio.TO↗

arXiv2018

Modeling the prescription opioid epidemic

Opioid addiction has become a global epidemic and a national health crisis in recent years, with the number of opioid overdose fatalities steadily increasing since the 1990s. In contrast to the dynamics of a typical illicit drug or disease epidemic, opioid addiction has its roots in legal, prescription medication - a fact which greatly increases the exposed population and provides additional drug accessibility for addicts. In this paper, we present a mathematical model for prescription drug addiction and treatment with parameters and validation based on data from the opioid epidemic. Key dynamics considered include addiction through prescription, addiction from illicit sources, and treatment. Through mathematical analysis, we show that no addiction-free equilibrium can exist without stringent control over how opioids are administered and prescribed, effectively transforming the dynamics of the opioid epidemic into those found in a purely illicit drug model. Numerical sensitivity analysis suggests that relatively low states of endemic addiction can be obtained by primarily focusing on medical prevention followed by aggressive treatment of remaining cases - even when the probability of relapse from treatment remains high. Further empirical study focused on understanding the rate of illicit drug dependence versus overdose risk, along with the current and changing rates of opioid prescription and treatment, would shed significant light on optimal control efforts and feasible outcomes for this epidemic and drug epidemics in general.

q-bio.PE↗

arXiv2017

Under the sea: Pulsing corals in ambient flow

While many organisms filter feed and exchange heat or nutrients in flow, few benthic organisms also actively pulse to enhance feeding and exchange. One example is the pulsing soft coral (Heteroxenia fuscescens). Pulsing corals live in colonies, where each polyp actively pulses through contraction and relaxation of their tentacles. The pulses are typically out of phase and without a clear pattern. These corals live in lagoons and bays found in the Red Sea and Indian Ocean where they at times experience strong ambient flows. In this paper, $3D$ fluid-structure interaction simulations are used to quantify the effects of ambient flow on the exchange currents produced by the active contraction of pulsing corals. We find a complex interaction between the flows produced by the coral and the background flow. The dynamics can either enhance or reduce the upward jet generated in a quiescent medium. The pulsing behavior also slows the average horizontal flow near the polyp when there is a strong background flow. The dynamics of these flows have implications for particle capture and nutrient exchange.

q-bio.QM↗

arXiv2017

Bifurcations in valveless pumping techniques from a coupled fluid-structure-electrophysiology model in heart development

We explore an embryonic heart model that couples electrophysiology and muscle-force generation to flow induced using a $2D$ fluid-structure interaction framework based on the immersed boundary method. The propagation of action potentials are coupled to muscular contraction and hence the overall pumping dynamics. In comparison to previous models, the electro-dynamical model does not use prescribed motion to initiate the pumping motion, but rather the pumping dynamics are fully coupled to an underlying electrophysiology model, governed by the FitzHugh-Nagumo equations. Perturbing the diffusion parameter in the FitzHugh-Nagumo model leads to a bifurcation in dynamics of action potential propagation. This bifurcation is able to capture a spectrum of different pumping regimes, with dynamic suction pumping and peristaltic-like pumping at the extremes. We find that more bulk flow is produced within the realm of peristaltic-like pumping.

q-bio.TO↗

arXiv2017

Pulsing corals: A story of scale and mixing

Effective methods of fluid transport vary across scale. A commonly used dimensionless number for quantifying the effective scale of fluid transport is the Reynolds number, Re, which gives the ratio of inertial to viscous forces. What may work well for one Re regime may not produce significant flows for another. These differences in scale have implications for many organisms, ranging from the mechanics of how organisms move through their fluid environment to how hearts pump at various stages in development. Some organisms, such as soft pulsing corals, actively contract their tentacles to generate mixing currents that enhance photosynthesis. Their unique morphology and intermediate scale where both viscous and inertial forces are significant make them a unique model organism for understanding fluid mixing. In this paper, 3D fluid-structure interaction simulations of a pulsing soft coral are used to quantify fluid transport and fluid mixing across a wide range of Re. The results show that net transport is negligible for $Re<10$, and continuous upward flow is produced for $Re\geq 10$.

q-bio.QM↗

arXiv2017

Three-dimensional low Reynolds number flows near biological filtering and protective layers

Mesoscale filtering and protective layers are replete throughout the natural world. Within the body, arrays of extracellular proteins, microvilli, and cilia can act as both protective layers and mechanosensors. For example, blood flow profiles through the endothelial surface layer determine the amount of shear stress felt by the endothelial cells and may alter the rates at which molecules enter and exit the cells. Characterizing the flow profiles through such layers is therefore critical towards understanding the function of such arrays in cell signaling and molecular filtering. External filtering layers are also important to many animals and plants. Trichomes (the hairs or fine outgrowths on plants) can drastically alter both the average wind speed and profile near the leaf's surface, affecting the rates of nutrient and heat exchange. In this paper, dynamically scaled physical models are used to study the flow profiles outside of arrays of cylinders that represent such filtering and protective layers. In addition, numerical simulations using the Immersed Boundary Method are used to resolve the 3D flows within the layers. The experimental and computational results are compared to analytical results obtained by modeling the layer as a homogeneous porous medium with free flow above the layer. The experimental results show that the bulk flow is well described by simple analytical models. The numerical results show that the spatially averaged flow within the layer is well described by the Brinkman model. The numerical results also demonstrate that the flow can be highly 3D with fluid moving into and out of the layer. These effects are not described by the Brinkman model and may be significant for biologically relevant volume fractions. The results of this paper can be used to understand how variations in density and height of such structures can alter shear stresses and bulk flows.

physics.flu-dyn↗

arXiv2016

IB2d: a Python and MATLAB implementation of the immersed boundary method

The development of fluid-structure interaction (FSI) software involves trade-offs between ease of use, generality, performance, and cost. Typically there are large learning curves when using low-level software to model the interaction of an elastic structure immersed in a uniform density fluid. Many existing codes are not publicly available, and the commercial software that exists usually requires expensive licenses and may not be as robust or allow the necessary flexibility that in house codes can provide. We present an open source immersed boundary software package, IB2d, with full implementations in both MATLAB and Python, that is capable of running a vast range of biomechanics models and is accessible to scientists who have experience in high-level programming environments. IB2d contains multiple options for constructing material properties of the fiber structure, as well as the advection-diffusion of a chemical gradient, muscle mechanics models, and artificial forcing to drive boundaries with a preferred motion.

physics.flu-dyn↗

arXiv2016

Fluid Dynamics in Heart Development: Effects of Hematocrit and Trabeculation

Recent \emph{in vivo} experiments have illustrated the importance of understanding the hemodynamics of heart morphogenesis. In particular, ventricular trabeculation is governed by a delicate interaction between hemodynamic forces, myocardial activity, and morphogen gradients, all of which are coupled to genetic regulatory networks. The underlying hemodynamics at the stage of development in which the trabeculae form is particularly complex, given the balance between inertial and viscous forces. Small perturbations in the geometry, scale, and steadiness of the flow can lead to changes in the overall flow structures and chemical morphogen gradients, including the local direction of flow, the transport of morphogens, and the formation of vortices. The immersed boundary method was used to solve the fluid-structure interaction problem of fluid flow moving through a two chambered heart of a zebrafish (\emph{Danio rerio}), with a trabeculated ventricle, at $96\ hpf$ (hours post fertilization). Trabeculae heights and hematocrit were varied, and simulations were conducted for two orders of magnitude of Womersley number, extending beyond the biologically relevant range ($0.2$ -- $12.0$). Both intracardial and intertrabecular vortices formed in the ventricle for biologically relevant parameter values. The bifurcation from smooth streaming flow to vortical flow depends upon the trabeculae geometry, hematocrit, and $Wo$. This work shows the importance of hematocrit and geometry in determining the bulk flow patterns in the heart at this stage of development.

q-bio.TO↗

arXiv2016

On the dynamic suction pumping of blood cells in tubular hearts

Around the third week after gestation in embryonic development, the human heart consists only of a valvless tube, unlike a fully developed adult heart, which is multi-chambered. At this stage in development, the heart valves have not formed and so net flow of blood through the heart must be driven by a different mechanism. It is hypothesized that there are two possible mechanisms that drive blood flow at this stage - Liebau pumping (dynamic suction pumping or valveless pumping) and peristaltic pumping. We implement the immersed boundary method with adaptive mesh refinement (IBAMR) to numerically study the effect of hematocrit on the circulation around a valveless. Both peristalsis and dynamic suction pumping are considered. In the case of dynamic suction pumping, the heart and circulatory system is simplified as a flexible tube attached to a relatively rigid racetrack. For some Womersley number (Wo) regimes, there is significant net flow around the racetrack. We find that the addition of flexible blood cells does not significantly affect flow rates within the tube for Wo $\leq$ 10. On the other hand, peristalsis consistently drives blood around the racetrack for all Wo and for all hematocrit considered.

q-bio.TO↗

arXiv2015

A comparison of heroin epidemic models

The use of illicit drugs has been on the rise in United States. It is very detrimental on society, as fatal overdose is the fourth leading cause of death in the United States, which is about the same as motor vehicle crashes. Of all illicit drugs, one drug that has an severe adverse effect on a community as a whole is heroin. This paper will discuss two mathematical models- the White and Comiskey model and a newly introduced model proposed by the author, describing heroin use within a fixed community. We will show the existence of stable equilibrium from both models, suggesting both a situation where heroin use is eradicated and one where it remains an endemic.

q-bio.PE↗