System dynamics and agent based simulation models can both be used to model and understand interactions of entities within a population. Our modeling work presented here is concerned with understanding the suitability of the different types of simulation for the immune system aging problems and comparing their results. We are trying to answer questions such as: How fit is the immune system given a certain age? Would an immune boost be of therapeutic value, e.g. to improve the effectiveness of a simultaneous vaccination? Understanding the processes of immune system aging and degradation may also help in development of therapies that reverse some of the damages caused thus improving life expectancy. Therefore as a first step our research focuses on T cells; major contributors to immune system functionality. One of the main factors influencing immune system aging is the output rate of naive T cells. Of further interest is the number and phenotypical variety of these cells in an individual, which will be the case study focused on in this paper.
The work presented in @cite_12 also compares these modelling approaches and identify a list of likely opportunities for cross-fertilization. The list presented is not exhaustive and should be a starting point to other researchers to take such synergistic views even further.
@cite_12
2093587840 2758941972 2328082688 2040948450
Summary form only given. This work proposes a systematic approach to identify opportunities for cross-fertilization between two modeling paradigms: system dynamics and agent-based modeling. The motivation for this work is the authors' belief that there are gains to be made by crossing the boundaries between different domains of research, or different scientific approaches. This paper presents a comparison between the two modeling approaches, which is brought one step beyond the simple statement of the similarities and differences between them by introducing the novel aspect of taking a synergistic view specifically aimed at identifying a list of likely opportunities for cross-fertilization. The list presented here is not exhaustive and should be regarded more as a starting point than an ending point, and an invitation to other scientists to take such synergistic views even further. Abstract This work presents a data-driven method to simulate, in real-time, the biomechanical behavior of the breast tissues in some image-guided interventions such as biopsies or radiotherapy dose delivery as well as to speed up multimodal registration algorithms. Ten real breasts were used for this work. Their deformation due to the displacement of two compression plates was simulated off-line using the finite element (FE) method. Three machine learning models were trained with the data from those simulations. Then, they were used to predict in real-time the deformation of the breast tissues during the compression. The models were a decision tree and two tree-based ensemble methods (extremely randomized trees and random forest). Two different experimental setups were designed to validate and study the performance of these models under different conditions. The mean 3D Euclidean distance between nodes predicted by the models and those extracted from the FE simulations was calculated to assess the performance of the models in the validation set. The experiments proved that extremely randomized trees performed better than the other two models. The mean error committed by the three models in the prediction of the nodal displacements was under 2 mm, a threshold usually set for clinical applications. The time needed for breast compression prediction is sufficiently short to allow its use in real-time ( 0.2 s). An extremely scalable computational strategy is described for calculations of the potential of mean force (PMF) in multidimensions on massively distributed supercomputers. The approach involves coupling thousands of umbrella sampling (US) simulation windows distributed to cover the space of order parameters with a Hamiltonian molecular dynamics replica-exchange (H-REMD) algorithm to enhance the sampling of each simulation. In the present application, US H-REMD is carried out in a two-dimensional (2D) space and exchanges are attempted alternatively along the two axes corresponding to the two order parameters. The US H-REMD strategy is implemented on the basis of parallel parallel multiple copy protocol at the MPI level, and therefore can fully exploit computing power of large-scale supercomputers. Here the novel technique is illustrated using the leadership supercomputer IBM Blue Gene P with an application to a typical biomolecular calculation of general interest, namely the binding of calcium ions to the ... Malecot's models of isolation by distance seem to assume random distribution in space, Poisson distribution of offspring number, and independent migration of individuals. These assumptions are inconsistent. By calculating the probability of joint occupancy of two locations at a distance x, it is shown that a haploid model embodying the latter two assumptions violates the first, forming larger and larger clumps of individuals separated by greater and greater distances. Thus the model is biologically irrelevant, even though it is possible to use it to calculate probabilities of genetic identity at different distances. The formation of these clumps is verified by computer simulation. The same phenomenon occurs in two- and three-dimensional models. In models of finite regions (a circle or a torus), the formation of clumps takes the form of the certainty of ultimate local extinction of the organism in each region. This does not occur if we hold the number of individuals on the circle or torus constant, but con...