Analysis of Reaction Network Systems Using Tropical Geometry

We discuss a novel analysis method for reaction network systems with polynomial or rational rate functions. This method is based on computing tropical equilibrations defined by the equality of at least two dominant monomials of opposite signs in the differential equations of each dynamic variable. In algebraic geometry, the tropical equilibration problem is tantamount to finding tropical prevarieties, that are finite intersections of tropical hypersurfaces. Tropical equilibrations with the same set of dominant monomials define a branch or equivalence class. Minimal branches are particularly interesting as they describe the simplest states of the reaction network. We provide a method to compute the number of minimal branches and to find representative tropical equilibrations for each branch.Comment: Proceedings Computer Algebra in Scientific Computing CASC 201

Connectivity, Coverage and Placement in Wireless Sensor Networks

Wireless communication between sensors allows the formation of flexible sensor networks, which can be deployed rapidly over wide or inaccessible areas. However, the need to gather data from all sensors in the network imposes constraints on the distances between sensors. This survey describes the state of the art in techniques for determining the minimum density and optimal locations of relay nodes and ordinary sensors to ensure connectivity, subject to various degrees of uncertainty in the locations of the nodes

Topology Control, Routing Protocols and Performance Evaluation for Mobile Wireless Ad Hoc Networks

A mobile ad-hoc network (MANET) is a collection of wireless mobile nodes forming a temporary network without the support of any established infrastructure or centralized administration. There are many potential applications based the techniques of MANETs, such as disaster rescue, personal area networking, wireless conference, military applications, etc. MANETs face a number of challenges for designing a scalable routing protocol due to their natural characteristics. Guaranteeing delivery and the capability to handle dynamic connectivity are the most important issues for routing protocols in MANETs. In this dissertation, we will propose four algorithms that address different aspects of routing problems in MANETs. Firstly, in position based routing protocols to design a scalable location management scheme is inherently difficult. Enhanced Scalable Location management Service (EnSLS) is proposed to improve the scalability of existing location management services, and a mathematical model is proposed to compare the performance of the classical location service, GLS, and our protocol, EnSLS. The analytical model shows that EnSLS has better scalability compared with that of GLS. Secondly, virtual backbone routing can reduce communication overhead and speedup the routing process compared with many existing on-demand routing protocols for routing detection. In many studies, Minimum Connected Dominating Set (MCDS) is used to approximate virtual backbones in a unit-disk graph. However finding a MCDS is an NP-hard problem. In the dissertation, we develop two new pure localized protocols for calculating the CDS. One emphasizes forming a small size initial near-optimal CDS via marking process, and the other uses an iterative synchronized method to avoid illegal simultaneously removal of dominating nodes. Our new protocols largely reduce the number of nodes in CDS compared with existing methods. We show the efficiency of our approach through both theoretical analysis and simulation experiments. Finally, using multiple redundant paths for routing is a promising solution. However, selecting an optimal path set is an NP hard problem. We propose the Genetic Fuzzy Multi-path Routing Protocol (GFMRP), which is a multi-path routing protocol based on fuzzy set theory and evolutionary computing

Optimal Transmission Radius for Energy Efficient Broadcasting Protocols in Ad Hoc and Sensor Networks

International audienceWe investigate the problem of minimum energy broadcasting in ad hoc networks where nodes have capability to adjust their transmission range. The minimal transmission energy needed for correct reception by neighbor at distance r is proportional to r^alpha + c_e, alpha and c_e being two environment-dependent constants. We demonstrate the existence of an optimal transmission radius, computed with a hexagonal tiling of the network area, that minimizes the total power consumption for a broadcasting task. This theoretically computed value is experimentally confirmed. The existing localized protocols are inferior to existing centralized protocols for dense networks. We present two localized broadcasting protocols, based on derived 'target' radius, that remain competitive for all network densities. The first one, TR-LBOP, computes the minimal radius needed for connectivity and increases it up to the target one after having applied a neighbor elimination scheme on a reduced subset of direct neighbors. In the second one, TR-DS, each node first considers only neighbors whose distance is no greater than the target radius (which depends on the power consumption model used), and neighbors in a localized connected topological structure such as RNG or LMST. Then, a connected dominating set is constructed using this subgraph. Nodes not selected for the set may be sent to sleep mode. Nodes in selected dominating set apply TR-LBOP. This protocol is the first one to consider both activity scheduling and minimum energy consumption as one combined problem. Finally, some experimental results for both protocols are given, as well as comparisons with other existing protocols. Our analysis and protocols remain valid if energy needed for packet receptions is charged

A geometric method for model reduction of biochemical networks with polynomial rate functions

Model reduction of biochemical networks relies on the knowledge of slow and fast variables. We provide a geometric method, based on the Newton polytope, to identify slow variables of a biochemical network with polynomial rate functions. The gist of the method is the notion of tropical equilibration that provides approximate descriptions of slow invariant manifolds. Compared to extant numerical algorithms such as the intrinsic low dimensional manifold method, our approach is symbolic and utilizes orders of magnitude instead of precise values of the model parameters. Application of this method to a large collection of biochemical network models supports the idea that the number of dynamical variables in minimal models of cell physiology can be small, in spite of the large number of molecular regulatory actors