Dipteran insect flight dynamics. Part 1 Longitudinal motion about hover

This paper presents a reduced-order model of longitudinal hovering flight dynamics for dipteran insects. The quasi-steady wing aerodynamics model is extended by including perturbation states from equilibrium and paired with rigid body equations of motion to create a nonlinear simulation of a Drosophila-like insect. Frequency-based system identification tools are used to identify the transfer functions from biologically inspired control inputs to rigid body states. Stability derivatives and a state space linear system describing the dynamics are also identified. The vehicle control requirements are quantified with respect to traditional human pilot handling qualities specification. The heave dynamics are found to be decoupled from the pitch/fore/aft dynamics. The haltere-on system revealed a stabilized system with a slow (heave) and fast subsidence mode, and a stable oscillatory mode. The haltere-off (bare airframe) system revealed a slow (heave) and fast subsidence mode and an unstable oscillatory mode, a modal structure in agreement with CFD studies. The analysis indicates that passive aerodynamic mechanisms contribute to stability, which may help explain how insects are able to achieve stable locomotion on a very small computational budget.     

Synthetic,Multi-Layer,Self-Oscillating Vocal Fold Model Fabrication

Sound for the human voice is produced via flow-induced vocal fold vibration. The vocal folds consist of several layers of tissue, each with differing material properties ¹. Normal voice production relies on healthy tissue and vocal folds, and occurs as a result of complex coupling between aerodynamic, structural dynamic, and acoustic physical phenomena. Voice disorders affect up to 7.5 million annually in the United States alone ² and often result in significant financial, social, and other quality-of-life difficulties. Understanding the physics of voice production has the potential to significantly benefit voice care, including clinical prevention, diagnosis, and treatment of voice disorders.Existing methods for studying voice production include in vivo experimentation using human and animal subjects, in vitro experimentation using excised larynges and synthetic models, and computational modeling. Owing to hazardous and difficult instrument access, in vivo experiments are severely limited in scope. Excised larynx experiments have the benefit of anatomical and some physiological realism, but parametric studies involving geometric and material property variables are limited. Further, they are typically only able to be vibrated for relatively short periods of time (typically on the order of minutes).Overcoming some of the limitations of excised larynx experiments, synthetic vocal fold models are emerging as a complementary tool for studying voice production. Synthetic models can be fabricated with systematic changes to geometry and material properties, allowing for the study of healthy and unhealthy human phonatory aerodynamics, structural dynamics, and acoustics. For example, they have been used to study left-right vocal fold asymmetry ^3,4, clinical instrument development ⁵, laryngeal aerodynamics ^6-9, vocal fold contact pressure ¹⁰, and subglottal acoustics ¹¹ (a more comprehensive list can be found in Kniesburges et al. ¹²)Existing synthetic vocal fold models, however, have either been homogenous (one-layer models) or have been fabricated using two materials of differing stiffness (two-layer models). This approach does not allow for representation of the actual multi-layer structure of the human vocal folds ¹ that plays a central role in governing vocal fold flow-induced vibratory response. Consequently, one- and two-layer synthetic vocal fold models have exhibited disadvantages ^3,6,8 such as higher onset pressures than what are typical for human phonation (onset pressure is the minimum lung pressure required to initiate vibration), unnaturally large inferior-superior motion, and lack of a "mucosal wave" (a vertically-traveling wave that is characteristic of healthy human vocal fold vibration).In this paper, fabrication of a model with multiple layers of differing material properties is described. The model layers simulate the multi-layer structure of the human vocal folds, including epithelium, superficial lamina propria (SLP), intermediate and deep lamina propria (i.e., ligament; a fiber is included for anterior-posterior stiffness), and muscle (i.e., body) layers ¹. Results are included that show that the model exhibits improved vibratory characteristics over prior one- and two-layer synthetic models, including onset pressure closer to human onset pressure, reduced inferior-superior motion, and evidence of a mucosal wave.     

A Kin I-Independent Pacman: Flux Mechanism for Anaphase A

Anaphase A chromatid-to-pole motion is fundamental for proper chromosome segregation in most systems. During the past several decades, two models for the mechanism of anaphase A have come to prominence. The Pacman model posits that chromatids induce the depolymerization of microtubule plus-ends embedded in kinetochores, thereby ‘chewing’ their way poleward. Alternatively, the Poleward-flux model posits that chromatids are ‘reeled-in’ to poles by the continual depolymerization of the minus-ends of kinetochore-associated microtubules, which are focused at spindle poles. In a recent study, we reported that anaphase A in Drosophila requires the depolymerization of both ends of kinetochore-associated microtubules, simultaneously. This is driven by two members of the Kin I subfamily of kinesins, termed KLP59C and KLP10A, which target specifically to chromatids and spindle poles, respectively. We have termed this hybrid of Pacman and Poleward flux the Kin I-dependent Pacman-flux mechanism for anaphase A. Here, we discuss the implications of these findings and explore potential additional components required to drive chromatid-to-pole motion by such a mechanism.     

Computational fluid dynamics analysis of cyclist aerodynamics: Performance of different turbulence-modelling and boundary-layer modelling approaches

This study aims at assessing the accuracy of computational fluid dynamics (CFD) for applications in sports aerodynamics, for example for drag predictions of swimmers, cyclists or skiers, by evaluating the applied numerical modelling techniques by means of detailed validation experiments. In this study, a wind-tunnel experiment on a scale model of a cyclist (scale 1:2) is presented. Apart from three-component forces and moments, also high-resolution surface pressure measurements on the scale model’s surface, i.e. at 115 locations, are performed to provide detailed information on the flow field. These data are used to compare the performance of different turbulence-modelling techniques, such as steady Reynolds-averaged Navier–Stokes (RANS), with several k–ε and k–ω turbulence models, and unsteady large-eddy simulation (LES), and also boundary-layer modelling techniques, namely wall functions and low-Reynolds number modelling (LRNM). The commercial CFD code Fluent 6.3 is used for the simulations. The RANS shear-stress transport (SST) k–ω model shows the best overall performance, followed by the more computationally expensive LES. Furthermore, LRNM is clearly preferred over wall functions to model the boundary layer. This study showed that there are more accurate alternatives for evaluating flow around bluff bodies with CFD than the standard k–ε model combined with wall functions, which is often used in CFD studies in sports.     

Does the anthropometric model influence whole-body center of mass calculations in gait?

Examining whole-body center of mass (COM) motion is one of method being used to quantify dynamic balance and energy during gait. One common method for estimating the COM position is to apply an anthropometric model to a marker set and calculate the weighted sum from known segmental COM positions. Several anthropometric models are available to perform such a calculation. However, to date there has been no study of how the anthropometric model affects whole-body COM calculations during gait. This information is pertinent to researchers because the choice of anthropometric model may influence gait research findings and currently the trend is to consistently use a single model. In this study we analyzed a single stride of gait data from 103 young adult participants. We compared the whole-body COM motion calculated from 4 different anthropometric models (Plagenhoef et al., 1983; Winter, 1990; de Leva, 1996; Pavol et al., 2002). We found that anterior-posterior motion calculations are relatively unaffected by the anthropometric model. However, medial-lateral and vertical motions are significantly affected by the use of different anthropometric models. Our findings suggest that the researcher carefully choose an anthropometric model to fit their study populations when interested in medial-lateral or vertical motions of the COM. Our data can provide researchers a priori information on the model determination depending on the particular variable and how conservative they may want to be with COM comparisons between groups.     

Dynamic Modeling, Testing, and Stability Analysis of an Ornithoptic Blimp

In order to study omithopter flight and to improve a dynamic model of flapping propulsion,a series of tests are conducted on a flapping-wing blimp.The blimp is designed and constructed from mylar plastic and balsa wood as a test platform for aerodynamics and flight dynamics.The blimp,2.3 meters long and 420 gram mass,is propelled by its flapping wings.Due to buoyancy the wings have no lift requirement so that the distinction between lift and propulsion can be analyzed in a flight platform at low flight speeds.The blimp is tested using a Vicon motion tracking system and various initial conditions are tested including accelerating flight from standstill,decelerating from an initial speed higher than its steady state,and from its steady-state speed but disturbed in pitch angle.Test results are used to estimate parameters in a coupled quasi-steady aerodynamics/Newtonian flight dynamics model.This model is then analyzed using Floquet theory to determine local dynamic modes and stability.It is concluded that the dynamic model adequately describes the vehicle's nonlinear behavior near the steady-state velocity and that the vehicle's linearized modes are akin to those of a fixed-wing aircraft.     

Stochastic Models for Phototaxis

This work studies two mathematical models for describing the motion of phototactic bacteria, i.e., bacteria that move toward light. Based on experimental observations, we conjecture that the motion of the colony toward light depends on certain group dynamics. These group dynamics are hypothesized to be coordinated through an individual property of each bacterium, which we refer to as excitation. The excitation of each individual bacterium is assumed to change based on the excitation of the neighboring bacteria. Under these assumptions, we propose a (discrete) cellular automaton model and derive an analogous stochastic model for describing the evolution in time of the location of bacteria, the excitation of individual bacteria, and a surface memory effect. We provide simulation results and discuss in detail the role of the various model parameters in controlling the emerging dynamics.     

Simulation of nitrogen in agro-ecosystems: Criteria for model selection and use

Available simulation models for describing nitrogen behavior in agro-ecosystems vary in two characteristics:(i) conceptual completeness in terms of the number of processes considered, and(ii) thelevel of detail at which each process is modeled. These model characteristics are determined by both the objectives that the model is designed to meet and the current state-of-the-art understanding of the various processes included in the model. The levels of conceptual completeness and detail in a model govern the potential applications for which the model may be used. Applications of models may be research-oriented, management-oriented, or planning-oriented. A model suitable for a given application should have an appropriate level of completeness and detail to accomplish the stated objective. Criteria to aid in the selection and evaluation of nitrogen simulation models for a particular application include: i) the availability of computational facilities, ii) the spatial and temporal scales of application, iii) the intended use of the simulations, iv) the availability of model input data, and v) the confidence regions associated with the model output.     

Mechanism for Anaphase B: Evaluation of “Slide-and-Cluster” versus “Slide-and-Flux-or-Elongate” Models

Elongation of the mitotic spindle during anaphase B contributes to chromosome segregation in many cells. Here, we quantitatively test the ability of two models for spindle length control to describe the dynamics of anaphase B spindle elongation using experimental data from Drosophila embryos. In the slide-and-flux-or-elongate (SAFE) model, kinesin-5 motors persistently slide apart antiparallel interpolar microtubules (ipMTs). During pre-anaphase B, this outward sliding of ipMTs is balanced by depolymerization of their minus ends at the poles, producing poleward flux, while the spindle maintains a constant length. Following cyclin B degradation, ipMT depolymerization ceases so the sliding ipMTs can push the poles apart. The competing slide-and-cluster (SAC) model proposes that MTs nucleated at the equator are slid outward by the cooperative actions of the bipolar kinesin-5 and a minus-end-directed motor, which then pulls the sliding MTs inward and clusters them at the poles. In assessing both models, we assume that kinesin-5 preferentially cross-links and slides apart antiparallel MTs while the MT plus ends exhibit dynamic instability. However, in the SAC model, minus-end-directed motors bind the minus ends of MTs as cargo and transport them poleward along adjacent, parallel MT tracks, whereas in the SAFE model, all MT minus ends that reach the pole are depolymerized by kinesin-13. Remarkably, the results show that within a narrow range of MT dynamic instability parameters, both models can reproduce the steady-state length and dynamics of pre-anaphase B spindles and the rate of anaphase B spindle elongation. However, only the SAFE model reproduces the change in MT dynamics observed experimentally at anaphase B onset. Thus, although both models explain many features of anaphase B in this system, our quantitative evaluation of experimental data regarding several different aspects of spindle dynamics suggests that the SAFE model provides a better fit.     

Global Motion Percept Mediated through Integration of Barber Poles Presented in Bilateral Visual Hemifields

How is motion information that has been obtained through multiple viewing apertures integrated to form a global motion percept? We investigated the mechanisms of motion integration across apertures in two hemifields by presenting gratings through two rectangles (that form the dual barber poles) and recording the perceived direction of motion by human observers. To this end, we presented dual barber poles in conditions with various inter-component distances between the apertures and evaluated the degree to which the hemifield information was integrated by measuring the magnitude of the perceived barber pole illusion. Surprisingly, when the inter-component distance between the two apertures was short, the perceived direction of motion of the dual barber poles was similar to that of a single barber pole formed by the concatenation of the two component barber poles, indicating motion integration is achieved through a simple concatenation mechanism. We then presented dual barber poles in which the motion and contour properties of the two component barber poles differed to characterize the constraints underlying cross-hemifield integration. We found that integration is achieved only when phase, speed, wavelength, temporal frequency, and duty cycle are identical in the two barber poles, but can remain robust when the contrast of the two component barber poles differs substantially. We concluded that a motion stimulus presented in bilateral hemifields tends to be integrated to yield a global percept with a substantial tolerance for spatial distance and contrast difference.     

Critical analysis of musculoskeletal modelling complexity in multibody biomechanical models of the upper limb

The inverse dynamics technique applied to musculoskeletal models, and supported by optimisation techniques, is used extensively to estimate muscle and joint reaction forces. However, the solutions of the redundant muscle force sharing problem are sensitive to the detail and modelling assumptions of the models used. This study presents four alternative biomechanical models of the upper limb with different levels of discretisation of muscles by bundles and muscle paths, and their consequences on the estimation of the muscle and joint reaction forces. The muscle force sharing problem is solved for the motions of abduction and anterior flexion, acquired using video imaging, through the minimisation of an objective function describing muscle metabolic energy consumption. While looking for the optimal solution, not only the equations of motion are satisfied but also the stability of the glenohumeral and scapulothoracic joints is preserved. The results show that a lower level of muscle discretisation provides worse estimations regarding the muscle forces. Moreover, the poor discretisation of muscles relevant to the joint in analysis limits the applicability of the biomechanical model. In this study, the biomechanical model of the upper limb describing the infraspinatus by a single bundle could not solve the complete motion of anterior flexion. Despite the small differences in the magnitude of the forces predicted by the biomechanical models with more complex muscular systems, in general, there are no significant variations in the muscular activity of equivalent muscles.     

Technique and preliminary findings for in vivo quantification of brain motion during injurious head impacts

Computational models of the human brain are widely used in the evaluation and development of helmets and other protective equipment. These models are often attempted to be validated using cadaver tissue displacements despite studies showing neural tissue degrades quickly after death. Addressing this limitation, this study aimed to develop a technique for quantifying living brain motion in vivo using a closed head impact animal model of traumatic brain injury (TBI) called CHIMERA. We implanted radiopaque markers within the brain of three adult ferrets and resealed the skull while the animals were anesthetized. We affixed additional markers to the skull to track skull kinematics. The CHIMERA device delivered controlled, repeatable head impacts to the head of the animals while the impacts were fluoroscopically stereo-visualized. We observed that 1.5 mm stainless steel fiducials (∼8 times the density of the brain) migrated from their implanted positions while neutral density targets remained in their implanted position post-impact. Brain motion relative to the skull was quantified in neutral density target tests and showed increasing relative motion at higher head impact severities. We observed the motion of the brain lagged behind that of the skull, similar to previous studies. This technique can be used to obtain a comprehensive dataset of in vivo brain motion to validate computational models reflecting the mechanical properties of the living brain. The technique would also allow the mechanical response of in vivo brain tissue to be compared to cadaveric preparations for investigating the fidelity of current human computational brain models.     

A Comparison of Bimolecular Reaction Models for Stochastic Reaction–Diffusion Systems

Stochastic reaction–diffusion models have become an important tool in studying how both noise in the chemical reaction process and the spatial movement of molecules influences the behavior of biological systems. There are two primary spatially-continuous models that have been used in recent studies: the diffusion limited reaction model of Smoluchowski, and a second approach popularized by Doi. Both models treat molecules as points undergoing Brownian motion. The former represents chemical reactions between two reactants through the use of reactive boundary conditions, with two molecules reacting instantly upon reaching a fixed separation (called the reaction-radius). The Doi model uses reaction potentials, whereby two molecules react with a fixed probability per unit time, λ, when separated by less than the reaction radius. In this work, we study the rigorous relationship between the two models. For the special case of a protein diffusing to a fixed DNA binding site, we prove that the solution to the Doi model converges to the solution of the Smoluchowski model as λ→∞, with a rigorous $O(\lambda^{-\frac{1}{2} + \epsilon})$ error bound (for any fixed ?>0). We investigate by numerical simulation, for biologically relevant parameter values, the difference between the solutions and associated reaction time statistics of the two models. As the reaction-radius is decreased, for sufficiently large but fixed values of λ, these differences are found to increase like the inverse of the binding radius.     

The Min system as a general cell geometry detection mechanism: branch lengths in Y-shaped Escherichia coli cells affect Min oscillation patterns and division dynamics

In Escherichia coli, division site placement is regulated by the dynamic behavior of the MinCDE proteins, which oscillate from pole to pole and confine septation to the centers of normal rod-shaped cells. Some current mathematical models explain these oscillations by considering interactions among the Min proteins without recourse to additional localization signals. So far, such models have been applied only to regularly shaped bacteria, but here we test these models further by employing aberrantly shaped E. coli cells as miniature reactors. The locations of MinCDE proteins fused to derivatives of green fluorescent protein were monitored in branched cells with at least three conspicuous poles. MinCDE most often moved from one branch to another in an invariant order, following a nonreversing clockwise or counterclockwise direction over the time periods observed. In cells with two short branches or nubs, the proteins oscillated symmetrically from one end to the other. The locations of FtsZ rings were consistent with a broad MinC-free zone near the branch junctions, and Min rings exhibited the surprising behavior of moving quickly from one possible position to another. Using a reaction-diffusion model that reproduces the observed MinCD oscillations in rod-shaped and round E. coli, we predict that the oscillation patterns in branched cells are a natural response of Min behavior in cellular geometries having different relative branch lengths. The results provide further evidence that Min protein oscillations act as a general cell geometry detection mechanism that can locate poles even in branched cells.     

Determining the location of the body׳s center of mass for different groups of physically active people

The purpose of the present study was to compare the location of the body center of mass (CoM) determined by using a high accuracy reaction board (RB) and two different segment parameter models for motion analysis (Dempster, 1955, DEM and de Leva, 1996 adjusted from Zatsiorsky and Seluyanov, ZAT). The body CoM (expressed as percentage of the total body height) was determined from several subjects including athletes as well as physically active students and sedentary people. Some significant differences were found in the location of the body CoM between the used segment models and the reaction board method for all male subjects (n=58, 57.03±0.79%, 56.20±0.76% and 57.60±0.76% for RB, ZAT and DEM, respectively) and separately for male (n=12, RB 57.02±0.41%, ZAT 56.74±0.62%, DEM 58.19±0.60%) and female (n=12, RB 55.91±0.88%, ZAT 57.24±0.77%) students of physical activity. The ZAT model was a good match with RB for high jumpers (56.26±0.94% and 56.63±0.56%) whereas the DEM model was better for gymnasts (57.38±0.46% and 57.89±0.49%) and throwers (58.19±0.69% and 57.79±0.45%). For ice hockey players (IH) and ski jumpers (SJ) both segment models, ZAT and DEM, differed significantly from the reaction board results. The results of the present study showed that careful attention should be paid while selecting the proper model for motion analysis of different type of athletes.     

Escherichia coli Survival in,and Release from,White-Tailed Deer Feces

White-tailed deer are an important reservoir for pathogens that can contribute a large portion of microbial pollution in fragmented agricultural and forest landscapes. The scarcity of experimental data on survival of microorganisms in and release from deer feces makes prediction of their fate and transport less reliable and development of efficient strategies for environment protection more difficult. The goal of this study was to estimate parameters for modeling Escherichia coli survival in and release from deer (Odocoileus virginianus) feces. Our objectives were as follows: (i) to measure survival of E. coli in deer pellets at different temperatures, (ii) to measure kinetics of E. coli release from deer pellets at different rainfall intensities, and (iii) to estimate parameters of models describing survival and release of microorganisms from deer feces. Laboratory experiments were conducted to study E. coli survival in deer pellets at three temperatures and to estimate parameters of Chick''s exponential model with temperature correction based on the Arrhenius equation. Kinetics of E. coli release from deer pellets were measured at two rainfall intensities and used to derive the parameters of Bradford-Schijven model of bacterial release. The results showed that parameters of the survival and release models obtained for E. coli in this study substantially differed from those obtained by using other source materials, e.g., feces of domestic animals and manures. This emphasizes the necessity of comprehensive studies of survival of naturally occurring populations of microorganisms in and release from wildlife animal feces in order to achieve better predictions of microbial fate and transport in fragmented agricultural and forest landscapes.     

Perturbation analysis of 6DoF flight dynamics and passive dynamic stability of hovering fruit fly Drosophila melanogaster

Insects exhibit exquisite control of their flapping flight, capable of performing precise stability and steering maneuverability. Here we develop an integrated computational model to investigate flight dynamics of insect hovering based on coupling the equations of 6 degree of freedom (6DoF) motion with the Navier-Stokes (NS) equations. Unsteady aerodynamics is resolved by using a biology-inspired dynamic flight simulator that integrates models of realistic wing-body morphology and kinematics, and a NS solver. We further develop a dynamic model to solve the rigid body equations of 6DoF motion by using a 4th-order Runge-Kutta method. In this model, instantaneous forces and moments based on the NS-solutions are represented in terms of Fourier series. With this model, we perform a systematic simulation-based analysis on the passive dynamic stability of a hovering fruit fly, Drosophila melanogaster, with a specific focus on responses of state variables to six one-directional perturbation conditions during latency period. Our results reveal that the flight dynamics of fruit fly hovering does not have a straightforward dynamic stability in a conventional sense that perturbations damp out in a manner of monotonous convergence. However, it is found to exist a transient interval containing an initial converging response observed for all the six perturbation variables and a terminal instability that at least one state variable subsequently tends to diverge after several wing beat cycles. Furthermore, our results illustrate that a fruit fly does have sufficient time to apply some active mediation to sustain a steady hovering before losing body attitudes.     

Predator-Prey Interactions of Dictyostelium discoideum and Escherichia coli in Continuous Culture

Dictyostelium discoideum and Escherichia coli were aerobically propagated in mixed continuous culture in a predator-prey relationship, and the effects of temperature and holding times were examined. Oscillations developed in the concentration of glucose, the limiting substrate for E. coli, and in the densities of the two populations, but eventually steady-state populations were reached. The experimental data were analyzed according to the Lotka-Volterra model for prey-predator relationships and by the Monod model for saturation kinetics. A comparison of the adequacy of the two models in describing predation is given.     

Assessing Nonsuperiority,Noninferiority, or Equivalence When Comparing Two Regression Models Over a Restricted Covariate Region

Summary In many scientific problems the purpose of the comparison of two regression models, which describe the relationship between a same response variable and several same covariates for two different groups, is to demonstrate that one model is no higher than the other by a negligible amount, or to demonstrate that the models have only negligible differences and so they can be regarded as describing practically the same relationship between the response variable and the covariates. In this article, methods based on one‐sided pointwise confidence bands are proposed for assessing the nonsuperiority of one model to the other and for assessing the equivalence of two regression models. Examples from QT/QTc study and from drug stability study are used to illustrate the methods.