New perspectives have been developed to understand the processes of modeling heterogeneous membranes. These are crucial steps prior to applying advanced techniques like molecular dynamic simulations of whole membrane systems. Lipid, protein, and membrane packing problems are addressed based on biochemical properties in combination with computational optimization techniques. The CELLmicrocosmos 2.2 MembraneEditor (CmME) is introduced as an appropriate framework to handle such problems by offering diverse algorithmic approaches. Its algorithm plug-in-interface enables modelers to generate problem-specific algorithms. Good solutions concerning runtime and lipid density are realized by focusing on the outer shapes of the PDB-based molecules. Application cases are presented like the publication-based modeling of inner and outer mitochondrial membrane-fragments, semiautomatic incorporation of proteins, and the assembly of rafts. Concerning geometrical aspects of the lipids, the achieved results are consistent with experimental observations related to lipid densities and distributions. Finally, two membranes simulated with GROMACS are analyzed and compared: the first is generated with conventional scripting techniques, the second with the CmME Distributor algorithm. The examples prove that CmME is a valuable and versatile tool for a broad set of applications in analysis and visualization of biomembranes.
The understanding of the molecular mechanism of cell-to-cell communication is fundamental for system biology. Up to now, the main objectives of bioinformatics have been reconstruction, modeling and analysis of metabolic, regulatory and signaling processes, based on data generated from high-throughput technologies. Cell-to-cell communication or quorum sensing (QS), the use of small molecule signals to coordinate complex patterns of behavior in bacteria, has been the focus of many reports over the past decade. Based on the quorum sensing process of the organism Aliivibrio salmonicida, we aim at developing a functional Petri net, which will allow modeling and simulating cell-to-cell communication processes. Using a new editor-controlled information system called VANESA (http://vanesa.sf.net), we present how to combine different fields of studies such as life-science, database consulting, modeling, visualization and simulation for a semi-automatic reconstruction of the complex signaling quorum sensing network. We show how cell-to-cell communication processes and information-flow within a cell and across cell colonies can be modeled using VANESA and how those models can be simulated with Petri net network structures in a sophisticated way. is one of the main tasks in integrative bioinformatics. To trim down data to a manageable yet relevant size and to analyze and identify new as well as altered versions of interaction patterns we have implemented a new editor-controlled information system called VANESA (http://vanesa.sf.net).VANESA provides new bioinformatics methods and visualization approaches to analyze dynamic interacting networks. The idea of VANESA is to extend any molecular data based network by new targets and interacting elements. Using VANESA we aim at developing sophisticated network structures for the modeling and simulation of coordinated cell actions based on the quorum sensing system of the bacteria Aliivibrio salmonicida.Coordinated cell actions and basic cellular activities are controlled by cell signaling and communication processes. The study of individual parts of cell signaling pathways has become a major objective in bioinformatics. Bacterial cells are able to adapt their behavior to the environment and its conditions [Schauder et al., 2001]. In biology and medicine, investigating how cells perceive and respond to their microenvironment adapting processes such as development, growth, tissue repair, virulence production and other complex actions can lead to a better understanding of molecular interactions and the causes of diseases [Visick et al., 2005].It is necessary to understand the gene-controlled cell differentiation processes to be able to modify the metabolic behavior, which will be the elementary operation of synthetic biology. Until now methods of biotechnology could not control the cell differentiation process, which is based on fundamental gene regulation events. One aspect related to cell differentiation is cell-to-cell communication. Although cell-to-cell communication is not string...
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