An Introduction to Rule-based Modeling of Immune Receptor Signaling

Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory response) depending on the type and number of receptor molecules on the cell surface and the specific intracellular signaling pathways activated by those receptors. Explicitly modeling and simulating kinetic interactions between molecules allows us to pose questions about the dynamics of a signaling network under various conditions. However, the application of chemical kinetics to biochemical signaling systems has been limited by the complexity of the systems under consideration. Rule-based modeling (BioNetGen, Kappa, Simmune, PySB) is an approach to address this complexity. In this chapter, by application to the Fc$\varepsilon$RI receptor system, we will explore the origins of complexity in macromolecular interactions, show how rule-based modeling can be used to address complexity, and demonstrate how to build a model in the BioNetGen framework. Open source BioNetGen software and documentation are available at http://bionetgen.org.Comment: 5 figure

Parametric investigation of nonlinear fluctuations in a dc glow discharge plasma

Glow discharge plasmas exhibit various types of self excited oscillations for different initial conditions like discharge voltages and filling pressures. The behavior of such oscillations associated with the anode glow have been investigated using nonlinear techniques like correlation dimension, largest Lyapunov exponent etc. It is seen that these oscillations go to an ordered state from a chaotic state with increase in input energy i.e. with discharge voltages implying occurrence of inverse bifurcations. These results are different from the other observations wherein the fluctuations have been observed to go from ordered to chaotic state.Comment: Submitted to Chao

Kerjasama Antar Daerah Dalam Sektor Persampahan Berbasis Pembangunan Berkelanjutan (Studi Di Sekretariat Bersama Kartamantul, DI YOGYAKARTA)

: Urban development which grows rapidly along with population growth triggers waste problem. This waste problem can be managed if there is inter-regional cooperation. The form and the program of inter-regional cooperation is reflected in handling waste sector in Sekretariat Bersama Kartamantul, Yogyakarta. The inter-regional cooperation is formed to build regions based on administrative development, especially sustainable development. The research aims to find out inter-regional cooperation in waste sector based on sustainable development in Sekretariat Bersama Kartamantul, Yogyakarta. This research uses qualitative research type. In building inter-regional cooperation, there are form and programs in waste sector that are intertwined. Inter-regional cooperation aims to be able to fulfil mutual needs of other regions in developing the regions. Inter-regional cooperation in waste sector has brought beneficial result and the result of developing the regions which is based on the principles of sustainable development. Inter-regional relationship requires inter-regional management to achieve the objective of inter-regional cooperation. The types of inter-regional cooperation which are built in Sekretariat Bersama Kartamantul, Yogyakarta has become a role model of inter-regional cooperation by other regions