Simulating spatially-explicit crop dynamics of agricultural landscapes: The ATLAS simulator

The spatially-explicit AgriculTural LandscApe Simulator (ATLAS) simulates realistic spatial-temporal crop availability at the landscape scale through crop rotations and crop phenology. Intended to be linked to organism population dynamics, the simulator is developed in a multi-agent platform. The model relies on initial GIS inputs for landscape composition and configuration. Users define typical rotations and crop phenology stages to be included, according to their objectives. In the study, we present two applications to contrasting landscapes, where ATLAS is capable of simulating accurate composition (crop area) and configuration (crop clustering) dynamics. ATLAS has potential applicability to a range of contrasting agricultural landscapes. The benefits of such a simulator are the possibility to study the effects of various simulated management scenarios of crop spatial-temporal availability in relation to target organisms and/or specific ecological processes (e.g. pest, biological control), within a single model framework.     

Simulation of fretting wear at orthopaedic implant interfaces

Osteolysis due to wear debris is a primary cause of failure of total joint replacements. Although debris produced by the joint articulating surfaces has been studied and simulated extensively, fretting wear debris, produced at nonarticulating surfaces, has not received adequate attention. We developed a three-station fretting wear simulator to reproduce in vivo motion and stresses at the interfaces of total joint replacements. The simulator is based on the beam bending theory and is capable of producing cyclic displacement from 3 to 1000 microns, under varying magnitudes of contact stresses. The simulator offers three potential advantages over previous studies: The ability to control the displacement by load, the ability to produce very small displacements, and dynamic normal loads as opposed to static. A pilot study was designed to test the functionality of the simulator, and verify that calculated displacements and loads produced the predicted differences between two commonly used porous ingrowth titanium alloy surfaces fretting against cortical bone. After 1.5 million cycles, the simulator functioned as designed, producing greater wear of bone against the rougher plasma-sprayed surface compared to the fiber-mesh surface, as predicted. A novel pin-on-disk apparatus for simulating fretting wear at orthopaedic implant interfaces due to micromotion is introduced. The test parameters measured with the fretting wear simulator were as predicted by design calculations, and were sufficient to measure differences in the height and weight of cortical bone pins rubbing against two porous ingrowth surfaces, plasma-sprayed titanium and titanium fiber mesh.     

Dynamic finite element knee simulation for evaluation of knee replacement mechanics

In vitro pre-clinical testing of total knee replacement (TKR) devices is a necessary step in the evaluation of new implant designs. Whole joint knee simulators, like the Kansas knee simulator (KKS), provide a controlled and repeatable loading environment for comparative evaluation of component designs or surgical alignment under dynamic conditions. Experimental testing, however, is time and cost prohibitive for design-phase evaluation of tens or hundreds of design variations. Experimentally-verified computational models provide an efficient platform for analysis of multiple components, sizes, and alignment conditions. The purpose of the current study was to develop and verify a computational model of a dynamic, whole joint knee simulator. Experimental internal-external and valgus-varus laxity tests, followed by dynamic deep knee bend and gait simulations in the KKS were performed on three cadaveric specimens. Specimen-specific finite element (FE) models of posterior-stabilized TKR were created from magnetic resonance images and CAD geometry. The laxity data was used to optimize mechanical properties of tibiofemoral soft-tissue structures on a specimen-specific basis. Each specimen was subsequently analyzed in a computational model of the experimental KKS, simulating both dynamic activities. The computational model represented all joints and actuators in the experimental setup, including a proportional-integral-derivative (PID) controller to drive quadriceps actuation. The computational model was verified against six degree-of-freedom patellofemoral (PF) and tibiofemoral (TF) kinematics and actuator loading during both deep knee bend and gait activities, with good agreement in trends and magnitudes between model predictions and experimental kinematics; differences were less than 1.8 mm and 2.2° for PF and TF translations and rotations. The whole joint FE simulator described in this study can be applied to investigate a wide range of clinical and research questions.     

Flocculation in brewing yeasts: a computer simulation study

A new simulator, INDISIM-FLOC, based on the individual-based simulator INDISIM, is used to examine the predictions of two different models of yeast flocculation. The first, proposed by Calleja is known as the "addition" model. The second, proposed by Stratford is known as the "cascade" model. The simulations show that the latter exhibits a better qualitative agreement with available experimental data.     

Analysis and simulation of hollow-fiber bioreactor dynamics

A flexible and economical computer simulation model for the process analysis, parameter prediction, and optimal design of hollow-fiber biochemical reactors (HFBRs) has been developed. The validity and predictive capability of the HFBR simulator was successfully tested with two independent laboratory case studies. Of particular interest are the transient transport and bioconversion mechanisms including the effect of radial mass convection on the substrate uptake in the lumen. The portable computer code is an efficient tool to aid in theoretical and experimental investigations. The underlying principles used for the model development are applicable to a broad family of (membrane) bioreactors.     

Computational modeling of cardiovascular response to orthostatic stress.

The objective of this study is to develop a model of the cardiovascular system capable of simulating the short-term (< or = 5 min) transient and steady-state hemodynamic responses to head-up tilt and lower body negative pressure. The model consists of a closed-loop lumped-parameter representation of the circulation connected to set-point models of the arterial and cardiopulmonary baroreflexes. Model parameters are largely based on literature values. Model verification was performed by comparing the simulation output under baseline conditions and at different levels of orthostatic stress to sets of population-averaged hemodynamic data reported in the literature. On the basis of experimental evidence, we adjusted some model parameters to simulate experimental data. Orthostatic stress simulations are not statistically different from experimental data (two-sided test of significance with Bonferroni adjustment for multiple comparisons). Transient response characteristics of heart rate to tilt also compare well with reported data. A case study is presented on how the model is intended to be used in the future to investigate the effects of post-spaceflight orthostatic intolerance.     

CADCS simulation of the closed-loop cardiovascular system

A pulsatile simulator of the closed-loop cardiovascular system, designed to solve simulation, identification and control problems in a research and education context, is presented. Its implimentation makes use of a command-driven interactive program for simulation of non-linear ordinary differential equations. The flexibility of the simulator is demonstrated by the results presented which refer to a basal steady-state circulatory condition as well as a transient induced by an abrupt change in peripheral resistance.     

Perturbation of a circadian rhythm by single and periodic signals and its mathematical simulation

Adaptive characteristics of circadian rhythm are based on their capacity to be synchronized by external signals, particularly light signals. The effect of both single and periodic light signals on the electroretinogram (ERG) circadian rhythm in crayfish is studied. In a previous work (Lara-Aparicioet al., Bull math. Biol. 55, 97–110, 1993) we developed a mathematical model simulating the emergence of the ERG circadian rhythm during the ontogeny of the crayfish. In the present work we have tested the familiar wave-shift behaviour of an oscillator with a single limit cycle. Two new facts, not present in a simpler model, now appear, which simulate adequately the experimental results, i.e. the presence of a transient stage and the shape of the perturbed wave which changes according to the characteristics of the external light signals.     

Simulating genetic networks made easy: network construction with simple building blocks

SUMMARY: We present SIM-plex, a genetic network simulator with a very intuitive interface in which a user can easily specify interactions as simple 'if-then' statements. The simulator is based on the mathematical model of Piecewise Linear Differential Equations (PLDEs). With PLDEs, genetic interactions are approximated as acting in a switch-like manner. AVAILABILITY: The Java program, examples and a tutorial are available at http://www.psb.ugent.be/cbd/ CONTACT: {stcru,makui}@psb.ugent.be     

Mechanobiological model of arterial growth and remodeling

A coupled agent-based model (ABM) and finite element analysis (FEA) computational framework is developed to study the interplay of bio-chemo-mechanical factors in blood vessels and their role in maintaining homeostasis. The agent-based model implements the power of REPAST Simphony libraries and adapts its environment for biological simulations. Coupling a continuum-level model (FEA) to a cellular-level model (ABM) has enabled this computational framework to capture the response of blood vessels to increased or decreased levels of growth factors, proteases and other signaling molecules (on the micro scale) as well as altered blood pressure. Performance of the model is assessed by simulating porcine left anterior descending artery under normotensive conditions and transient increases in blood pressure and by analyzing sensitivity of the model to variations in the rule parameters of the ABM. These simulations proved that the model is stable under normotensive conditions and can recover from transient increases in blood pressure. Sensitivity studies revealed that the model is most sensitive to variations in the concentration of growth factors that affect cellular proliferation and regulate extracellular matrix composition (mainly collagen).     

Computational wear simulation of patellofemoral articular cartilage during in vitro testing

Though changes in normal joint motions and loads (e.g., following anterior cruciate ligament injury) contribute to the development of knee osteoarthritis, the precise mechanism by which these changes induce osteoarthritis remains unknown. As a first step toward identifying this mechanism, this study evaluates computational wear simulations of a patellofemoral joint specimen wear tested on a knee simulator machine. A multibody dynamic model of the specimen mounted in the simulator machine was constructed in commercial computer-aided engineering software. A custom elastic foundation contact model was used to calculate contact pressures and wear on the femoral and patellar articular surfaces using geometry created from laser scan and MR data. Two different wear simulation approaches were investigated--one that wore the surface geometries gradually over a sequence of 10 one-cycle dynamic simulations (termed the "progressive" approach), and one that wore the surface geometries abruptly using results from a single one-cycle dynamic simulation (termed the "non-progressive" approach). The progressive approach with laser scan geometry reproduced the experimentally measured wear depths and areas for both the femur and patella. The less costly non-progressive approach predicted deeper wear depths, especially on the patella, but had little influence on predicted wear areas. Use of MR data for creating the articular and subchondral bone geometry altered wear depth and area predictions by at most 13%. These results suggest that MR-derived geometry may be sufficient for simulating articular cartilage wear in vivo and that a progressive simulation approach may be needed for the patella and tibia since both remain in continuous contact with the femur.     

Development of computational wear simulation of metal-on-metal hip resurfacing replacements

As one of the alternatives to traditional metal-on-polyethylene total hip replacements, metal-on-metal hip resurfacing prostheses demonstrating lower wear have been introduced for younger and more active patients during the past decade. However, in vitro hip simulator testing for the predicted increased lifetime of these surface replacements is time-consuming and costly. Computational wear modelling based on the Archard wear equation and finite element contact analysis was developed in this study for artificial hip joints and particularly applied to metal-on-metal resurfacing bearings under simulator testing conditions to address this issue. Wear factors associated with the Archard wear equation were experimentally determined and based on the short-term hip simulator wear results. The computational wear simulation was further extended to a long-term evaluation up to 50 million cycles assuming that the wear rate stays constant. The prediction from the computational model shows good agreement with the corresponding simulator study in terms of volumetric wear and the wear geometry. The simulation shows the progression of linear wear penetrations, and the complexity of contact stress distribution on the worn bearing surfaces. After 50 million cycles, the maximum linear wear was predicted to be approximately 6 and 8 microm for the cup and head, respectively, and no edge contact was found.     

Simulating dynamic activities using a five-axis knee simulator

This work describes the design and capabilities of the Purdue Knee Simulator: Mark II and a sagittal-plane model of the machine. This five-axis simulator was designed and constructed to simulate dynamic loading activities on either cadaveric knee specimens or total knee prostheses mounted on fixtures. The purpose of the machine was to provide a consistent, realistic loading of the knee joint, allowing the kinematics and specific loading of the structures of the knee to be determined based on condition, articular geometry, and simulated activity. The sagittal-plane model of the knee simulator was developed both to predict the loading at the knee from arbitrary inputs and to generate the necessary inputs required to duplicate specified joint loading. Measured tibio-femoral compressive force and quadriceps tension were shown to be in good agreement with the predicted loads from the model. A controlled moment about the ankle-flexion axis was also shown to change the loading on the quadriceps.     

Experimental-theoretical study of the force-interval relationship in the developing chicken myocardium]

The force-interval relationship was studied on myocardium preparations from chick embryos and hatched chickens. It is shown that the force-interval relationships of myocardium change during ontogenesis. A negative staircase (a decrease in the isometric force with increasing stimulation rate) in the chick embryo myocardium and a positive steady-state relationship in hatched stage myocardium were revealed. Changes in the force after switching from one stimulation frequency to another, the effects of poststimulation potentiation, as well as responses to the introduction of pauses and extrasystols at a constant stimulation rate were recorded. All the effects observed in the transient processes in preparations from hatched stage myocardium were more pronounced than in embryo myocardium. Our previous mathematical model of calcium recirculation in cardiomyocytes was adapted for simulating the main features of force-interval relationships in embryonal and relatively developed myocardium. The main source of regulatory calcium in the model of hatched stage myocardium is sarcoplasmic reticulum. In the model of embryo myocardium, it was postulated, based on data available in literature, that the main regulator of contractile response of the muscle is calcium that enters cardiomyocytes from extracellular medium. To describe force-interval relationships, by this model, the decreasing dependence of the entry of extracellular calcium on the intervals between stimuli was introduced.     

Estimating crop yield using a satellite-based light use efficiency model

Satellite-based techniques that provide temporally and spatially continuous information over vegetated surfaces have become increasingly important in monitoring the global agriculture yield. In this study, we examine the performance of a light use efficiency model (EC-LUE) for simulating the gross primary production (GPP) and yield of crops. The EC-LUE model can explain on average approximately 90% of the variability in GPP for 36 FLUXNET sites globally. The results indicate that a universal set of parameters, independent of crop species (except for C4 crops), can be adopted in the EC-LUE model for simulating crops’ GPP. At both irrigated and rainfed sites, the EC-LUE model exhibits a similar level of performance. However, large errors are found when simulating yield based on crop harvest index. This analysis highlights the need to improve the representation of the harvest index and carbon allocation for improving crop yield estimations from satellite-based methods.     

A stochastic simulator of a blood product donation environment with demand spikes and supply shocks

The availability of an adequate blood supply is a critical public health need. An influenza epidemic or another crisis affecting population mobility could create a critical donor shortage, which could profoundly impact blood availability. We developed a simulation model for the blood supply environment in the United States to assess the likely impact on blood availability of factors such as an epidemic. We developed a simulator of a multi-state model with transitions among states. Weekly numbers of blood units donated and needed were generated by negative binomial stochastic processes. The simulator allows exploration of the blood system under certain conditions of supply and demand rates, and can be used for planning purposes to prepare for sudden changes in the public's health. The simulator incorporates three donor groups (first-time, sporadic, and regular), immigration and emigration, deferral period, and adjustment factors for recruitment. We illustrate possible uses of the simulator by specifying input values for an 8-week flu epidemic, resulting in a moderate supply shock and demand spike (for example, from postponed elective surgeries), and different recruitment strategies. The input values are based in part on data from a regional blood center of the American Red Cross during 1996-2005. Our results from these scenarios suggest that the key to alleviating deficit effects of a system shock may be appropriate timing and duration of recruitment efforts, in turn depending critically on anticipating shocks and rapidly implementing recruitment efforts.     

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.     

Computational modeling of a dynamic knee simulator for reproduction of knee loading

As a first step towards reproducing desired three-dimensional joint loading and motion on a dynamic knee simulator, the goal of this study was to develop and verify a three-dimensional computational model that generated control profiles for the simulator using desired knee loading and motion as model inputs. The developed model was verified by predicting tibio-femoral loading on an instrumented analog knee for given actuator forces and the ability to generate simulator control profiles was demonstrated using a three-dimensional walking profile. The model predicted axial tibia loading for a sagittal-plane dual-limb squat within 1% of measured peak loading. Adding out-of-sagittal-plane forces decreased the accuracy of load prediction. The model generated control profiles to the simulator that produced axial tibia loading within 16% of desired for walking. Discrepancies in predicted and measured quadriceps forces influenced the accuracy of the generated control profiles. Future work will replace the analog knee in both the model and machine with a prosthetic knee.     

Non-linear elastic deformable models for real-time surgery simulation

In this article, we describe the latest developments of the minimally invasive hepatic surgery simulator prototype developed at INRIA. A key problem with such a simulator is the physical modelling of soft tissues. We propose a new deformable model based on non-linear elasticity and the finite element method. This model is valid for large displacements, which means in particular that it is invariant with respect to rotations. This property improves the realism of the deformations and solves the problems related to the shortcomings of linear elasticity, which is only valid for small displacements. We also address the problem of volume variations by adding to our model incompressibility constraints. Finally, we demonstrate the relevance of this approach for the real-time simulation of laparoscopic surgical gestures on the liver.