SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: AnyLogic

165

BACKGROUND: Despite the multiple advantages of active travel to school, only a small percentage of US children and adolescents walk or bicycle to school. Intervention studies are in a relatively early stage and evidence of their effectiveness over long periods is limited. The purpose of this study was to illustrate the utility of agent-based models in exploring how various policies may influence children’s active travel to school. METHODS: An agent-based model was developed to simulate children’s school travel behavior within a hypothetical city. The model was used to explore the plausible implications of policies targeting two established barriers to active school travel: long distance to school and traffic safety. The percent of children who walk to school was compared for various scenarios. RESULTS: To maximize the percent of children who walk to school the school locations should be evenly distributed over space and children should be assigned to the closest school. In the case of interventions to improve traffic safety, targeting a smaller area around the school with greater intensity may be more effective than targeting a larger area with less intensity. CONCLUSIONS: Despite the challenges they present, agent based models are a useful complement to other analytical strategies in studying the plausible impact of various policies on active travel to school.

Concepts: AnyLogic, Agent-based model

164

Focal degradation of extracellular matrix (ECM) is the first step in the invasion of cancer cells. MT1-MMP is a potent membrane proteinase employed by aggressive cancer cells. In our previous study, we reported that MT1-MMP was preferentially located at membrane protrusions called invadopodia, where MT1-MMP underwent quick turnover. Our computer simulation and experiments showed that this quick turnover was essential for the degradation of ECM at invadopodia (Hoshino, D., et al., (2012) PLoS Comp. Biol., 8: e1002479). Here we report on characterization and analysis of the ECM-degrading activity of MT1-MMP, aiming at elucidating a possible reason for its repetitive insertion in the ECM degradation. First, in our computational model, we found a very narrow transient peak in the activity of MT1-MMP followed by steady state activity. This transient activity was due to the inhibition by TIMP-2, and the steady state activity of MT1-MMP decreased dramatically at higher TIMP-2 concentrations. Second, we evaluated the role of the narrow transient activity in the ECM degradation. When the transient activity was forcibly suppressed in computer simulations, the ECM degradation was heavily suppressed, indicating the essential role of this transient peak in the ECM degradation. Third, we compared continuous and pulsatile turnover of MT1-MMP in the ECM degradation at invadopodia. The pulsatile insertion showed basically consistent results with the continuous insertion in the ECM degradation, and the ECM degrading efficacy depended heavily on the transient activity of MT1-MMP in both models. Unexpectedly, however, low-frequency/high-concentration insertion of MT1-MMP was more effective in ECM degradation than high-frequency/low-concentration pulsatile insertion even if the time-averaged amount of inserted MT1-MMP was the same. The present analysis and characterization of ECM degradation by MT1-MMP together with our previous report indicate a dynamic nature of MT1-MMP at invadopodia and the importance of its transient peak in the degradation of the ECM.

Concepts: Cell membrane, Thermodynamics, Computer graphics, Monte Carlo method, Computer simulation, Mathematical model, AnyLogic, Computational science

156

We present an agent-based model (ABM) to simulate a hepatic inflammatory response (HIR) in a mouse infected by Salmonella that sometimes progressed to problematic proportions, known as “sepsis”. Based on over 200 published studies, this ABM describes interactions among 21 cells or cytokines and incorporates 226 experimental data sets and/or data estimates from those reports to simulate a mouse HIR in silico. Our simulated results reproduced dynamic patterns of HIR reported in the literature. As shown in vivo, our model also demonstrated that sepsis was highly related to the initial Salmonella dose and the presence of components of the adaptive immune system. We determined that high mobility group box-1, C-reactive protein, and the interleukin-10: tumor necrosis factor-α ratio, and CD4+ T cell: CD8+ T cell ratio, all recognized as biomarkers during HIR, significantly correlated with outcomes of HIR. During therapy-directed silico simulations, our results demonstrated that anti-agent intervention impacted the survival rates of septic individuals in a time-dependent manner. By specifying the infected species, source of infection, and site of infection, this ABM enabled us to reproduce the kinetics of several essential indicators during a HIR, observe distinct dynamic patterns that are manifested during HIR, and allowed us to test proposed therapy-directed treatments. Although limitation still exists, this ABM is a step forward because it links underlying biological processes to computational simulation and was validated through a series of comparisons between the simulated results and experimental studies.

Concepts: Immune system, Inflammation, Infection, Adaptive immune system, Simulation, Operations research, Computational sociology, AnyLogic

119

The extent to which leaf-lobing influences the interception of direct solar radiation by individual plants was studied by means of computer simulations. The morphology, size and orientation ofAmbrosia artemisiifolia L. leaves were measured and used to construct a prototypeAmbrosia plant upon which a computer simulation was based. The leaf geometries of this simulation were then varied, and daily integrated irradiances (DII) were calculated for each variant plant simulation. Data indicate that lobedAmbrosia leaves do not confer an advantage to light-interception based upon values of DII. Simulated plants identical in all respects to the prototype, but with simple, elliptic leaves, had equivalent DII values to the prototype. Simulations with leaves in which gaps between lobes were “filledin” had reduced light-interception efficiencies compared to the prototype and to a simulation with elliptic-leaves. Lightinterception was maximized when leaves on distal nodes wereAmbrosia-like and leaves on proximal nodes were elliptic. The data are interpreted to indicate that lobingperse is not functionally advantageous to light-interception; however, gradients of leaf-lobing along the length of shoots may be very significant in terms of overall light interception.

Concepts: Photosynthesis, Computer graphics, Monte Carlo method, Computer simulation, Fern, Plant morphology, Mathematical model, AnyLogic

28

The purpose of the present simulation study is to reveal how confining surfaces with different mechanical properties affect the acoustic response of a contrast agent microbubble. To this end, numerical simulations are carried out for three types of walls: a plastic (OptiCell) wall, an aluminium wall, and a biological tissue. For each wall, the behaviour of contrast microbubbles of three sizes is investigated. The spectral characteristics of the scattered pressure produced by the microbubbles are compared for two cases: the bubble oscillates far away from the wall and the same bubble oscillates in the immediate vicinity of the wall. The results of the simulations allow one to make the following main conclusions. The effect of the OptiCell wall on the acoustic bubble response is stronger than that of the aluminium and tissue walls. Changes in the bubble response near the wall are stronger when bubbles are excited above their resonance frequency. Considering changes in the fundamental and the 2nd harmonic with respect to the peak values of these components at different bubble radii, it is found that the changes are stronger for smaller bubbles and that the changes in the 2nd harmonic are stronger than those in the fundamental. These results allow one to gain an insight into conditions under which the effect of an elastic wall on the acoustic response of a contrast agent microbubble is easier to be detected.

Concepts: Resonator, English-language films, Wave, Acoustics, Sound, Resonance, The Wall, AnyLogic

28

Ultrasonically induced flow is an important phenomenon observed in a sonochemical reactor. It controls the mass transport of sonochemical reaction and enhances the reaction performance. In the present paper, the liquid velocity distribution of ultrasonically induced flow in the sonochemical reactor with a transducer at frequency of 490 kHz has been numerically simulated. From the comparison of simulation results and experimental data, the ultrasonic absorption coefficient in the sonochemical reactor has been evaluated. To simulate the liquid velocity near the liquid surface above the transducer, which is the main sonochemical reaction area, it is necessary to include the acoustic fountain shape into the computational domain. The simulation results indicate that the liquid velocity increases with acoustic power. The variation of liquid height also influences the behavior of liquid velocity distribution and the mean velocity above the transducer centre becomes a maximum when the liquid height is 0.4m. The liquid velocity decreases with increasing the transducer plate radius at the same ultrasonic power.

Concepts: Simulation, Operations research, Monte Carlo method, Simulated reality, Sound, Computational sociology, Mathematical model, AnyLogic

28

For multicomponent vesicles, the line tension of domain boundaries and the component-dependent elastic properties (e.g., spontaneous curvatures) are the most two important factors that mediate the budding behaviors of these vesicles. This paper specially focuses on their effects on the budding number of budding domains and budding types. We found that the budding number is mainly determined by the component-dependent elastic properties while the budding types mediated by line tensions. A phase diagram is also obtained showing three different types of phase regions: (i) partially budding, (ii) partially bud-off and (iii) totally bud-off regions. These inspiring results are, however, derived from a very simple spherical-cap model, and have been tested by computer simulations showing good agreements. We emphasize that besides testing the spherical-cap model, the computer simulation techniques developed in the current work can be easily extended to other systems involving multicomponent vesicles.

Concepts: Psychology, Simulation, Computer graphics, Monte Carlo method, Computer simulation, Mathematical model, AnyLogic, Computational science

25

Agent-based models (ABMs) are computer simulation models which define interactions among agents and simulate emergent behaviors that arise from the ensemble of local decisions. ABMs have been increasingly used to examine trends in infectious disease epidemiology. However, the main limitation of ABMs is the high computational cost for a large-scale simulation. To improve the computational efficiency for large-scale ABM simulations, we built a parallelizable sliding region algorithm (SRA) for ABM and compared it to a non-parallelizable ABM. We developed a complex agent network and performed two simulations to model hepatitis C epidemics based on the real demographic data from Saskatchewan, Canada. The first simulation used the SRA that processed on each postal code subregion subsequently. The second simulation processed the entire population simultaneously. It was concluded that the parallelizable SRA showed computational time saving with comparable results in a province-wide simulation. Using the same method, SRA can be generalized for performing a country-wide simulation. Thus, this parallel algorithm enables the possibility of using ABM for large-scale simulation with limited computational resources.

Concepts: Algorithm, Epidemiology, Infectious disease, Simulation, Computer graphics, Monte Carlo method, Computer simulation, AnyLogic

24

For computational models of microwave ablation (MWA), knowledge of the antenna design is necessary, but the proprietary design of clinical applicators is often unknown. We characterised the specific absorption rate (SAR) during MWA experimentally and compared to a multi-physics simulation.

Concepts: Science, Computer graphics, Monte Carlo method, Computer simulation, Specific absorption rate, Mathematical model, AnyLogic, Computational science

24

Dual-comb system parameters have significant impacts on the ranging accuracy. We present a theoretical model and a numerical simulation method for the parameter optimization of a dual-comb ranging system. With this method we investigate the impacts of repetition rate difference, repetition rate, and carrier-envelope-offset frequency on the ranging accuracy. Firstly, the simulation results suggest a series of discrete zones of repetition rate difference in an optimal range, which are consistent with the experimental results. Secondly, the simulation results of the repetition rate indicate that a higher repetition rate is very favorable to improve the ranging accuracy. Finally, the simulation results suggest a series of discrete optimal ranges of the carrier-envelope-offset frequency for the dual-comb system. The simulated results were verified by our experiments.

Concepts: Mathematics, Experiment, Operations research, Computer graphics, Monte Carlo method, Parameter, Mathematical model, AnyLogic