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We report on investigations that illustrate the interaction between the specific immune system and a young avascular tumor growing due to a diffusive nutrient supply. We formulate a hybrid cellular automata-partial differential equation (CA-PDE) model which includes cell cycle dynamics and allows for tracking the spatial and temporal evolution of this elaborate biological system. We present results of two dimensional numerical simulations that, specifically in this work, include special cases of the spherical and papillary tumor growth, the infiltration of immune system cells into the tumor and the escape of tumor cells from the regime of the immune cells.
Stereotactic frame systems are widely used in neurosurgery. The accuracy of frame devices is considered as a gold standard to which the accuracy of new frameless stereotactic navigation systems is compared. The purpose of this study is to develop a general approach for the prediction of the application accuracy of stereotactic systems. The approach will be applied to the frame‐based biopsy performed with three frame devices: Leksell G, Cosman–Roberts–Wells (CRW), and Brown–Roberts–Wells (BRW). A work‐flow analysis will be carried out demonstrating that the accuracy relevant for a clinical application comprises several error sources including imaging, target and entry point selection, image to frame coordinates registration, and the setting of mechanical parameters of the frame. These error sources will be postulated to obey a Gaussian distribution probability density. The linear, i.e., Gaussian, error propagation, will be used to link all error contributions thus to calculate the cumulative accuracy of the frame used in the application. Although the Gaussian approach is an approximation, it allows for an analytical treatment of the accuracy. Both the accuracy at the target point and the accuracy of the probe needle guidance along the planned trajectory have been investigated. Of great significance is the relationship found between accuracy, pixel dimension, and image slice thickness, the latter being the dominant factor for slices of more than 1.5 mm thickness, yielding inaccuracies larger than 1.5 mm. For target points the predictions for the application accuracy have been compared to the results of measurements, showing good agreement with the experimental data.
A qualitative work‐flow analysis of a neurosurgical procedure indicates that the resolution of the image used to plan the intervention is the major source of inaccuracy. Quantitative experimental measurements confirm this observation. They fail, however, to explain the relationship between the accuracy of the frame components involved in a stereotactic procedure and the overall application accuracy. This investigation shows that the novel Gaussian approach is a flexible framework for the calculation of the application accuracy of frame systems. Therefore, the Gaussian approach provides a detailed understanding of the interplay between the various factors affecting accuracy. The basic ideas and limitations of the Gaussian approach are briefly explained. The effect of fiducial marker distribution and registration is investigated and shown to introduce a spatial dependence to the accuracy. The results of the Gaussian approach are compared with experimental data for three stereotactic frame devices: Leksell G, Cosman–Roberts–Wells, and Brown–Roberts–Wells. Although the Gaussian approach is an approximation, it reproduces the accuracy measured in the experiment within the statistical error of that experiment. Comp Aid Surg 4:77–86 (1999). © 1999 Wiley‐Liss, Inc.
An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer-monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory-Huggins parameters and isotropic particle-particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLSAA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach.
SPICES (Simplified Particle Input ConnEction Specification) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims at supporting tedious and error-prone molecular structure definitions for particle-based mesoscopic simulation techniques like Dissipative Particle Dynamics by allowing for an interplay of different molecular encoding levels that range from topological line notations and corresponding particle-graph visualizations to 3D structures with support of their spatial mapping into a simulation box. An open Java library for SPICES structure handling and mesoscopic simulation support in combination with an open Java Graphical User Interface viewer application for visual topological inspection of SPICES definitions are provided.
Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The new kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated “all-in-one” simulation systems.
CIP is an open-source high-level function library for (non-linear) curve fitting and data smoothing (with cubic splines), clustering (k-medoids, ART-2a) and machine learning (multiple linear/polynomial regression, feed-forward perceptron-type shallow and deep neural networks and support vector machines). In addition it provides several heuristics for the selection of training and test data or methods to estimate the relevance of data input components. CIP is built on top of the computing platform Mathematica to exploit its algorithmic and graphical capabilities.
CIP is an open-source high-level function library for (non-linear) curve fitting and data smoothing (with cubic splines), clustering (k-medoids, ART-2a) and machine learning (multiple linear/polynomial regression, feed-forward perceptron-type shallow and deep neural networks and support vector machines). In addition it provides several heuristics for the selection of training and test data or methods to estimate the relevance of data input components. CIP is built on top of the computing platform Mathematica to exploit its algorithmic and graphical capabilities.
The algorithm for automated functional groups detection and extraction of organic molecules developed by Peter Ertl is implemented on the basis of the Chemistry Development Kit (CDK).
Folder Basic contains the basic ErtlFunctionalGroupsFinder code and test code for integration in Java projects.
Folder CDK contains CDK library jar file cdk-2.2.jar that ErtlFunctionalGroupsFinder works with.
Folder Evaluation contains sample code for evaluation of functional groups with ErtlFunctionalGroupsFinder.
Folder JUnit 4 contains library jar files for unit testing.
Folder Performance contains a jar library for performance tests.
ErtlFunctionalGroupsFinder is described in the scientific literature