In this paper, we propose a new protocol for efficiently managing large ad hoc networks, i.e., networks in which all nodes can be mobile. We observe that, since nodes in such networks are not necessarily equal in that they may have different resources, not all of them should be involved in basic network operations such as packet forwarding, flooding, etc. In the proposed protocol, a small subse...

Computational protein design relies on a number of approximations to efficiently search the huge sequence space available to proteins. The fixed backbone and rotamer approximations in particular are important for formulating protein design as a discrete combinatorial optimization problem. However, the resulting coarse-grained sampling of possible side-chain terminal positions is problematic for...

In this paper, we present the implementation issues of a virtual backbone that supports the operations of the Uniform Quorum System (UQS) and the Randomized Database Group (RDG) mobility management schemes in an ad hoc network. The virtual backbone comprises nodes that are dynamically selected to contain databases that store the location information of the network nodes. Together with the UQS a...

We propose a stable backbone tree construction algorithm using multi-hop clusters for wireless sensor networks (WSNs). The hierarchical cluster structure has advantages in data fusion and aggregation. Energy consumption can be decreased by managing nodes with cluster heads. Backbone nodes, which are responsible for performing and managing multi-hop communication, can reduce the communication ov...

In this paper, we overview our approaches and methods to the topological synthesis and management of Mobile Backbone Network (MBN) based architectures. Such backbone networks are intended to aid in the support of multimedia applications across mobile ad hoc wireless networks. An MBN based ad hoc network employs backbone nodes, operating in a manner similar to that used by base-stations in a cel...

Recommender systems are designed to effectively support individuals' decision-making process on various web sites. It can be naturally represented by a user-object bipartite network, where a link indicates that a user has collected an object. Recently, research on the information backbone has attracted researchers' interests, which is a sub-network with fewer nodes and links but carrying most o...

Computational protein design attempts to create protein sequences that fold stably into pre-specified structures. Here we compare alignments of designed proteins to alignments of natural proteins and assess how closely designed sequences recapitulate patterns of sequence variation found in natural protein sequences. We design proteins using RosettaDesign, and we evaluate both fixed-backbone des...

Given an integer λ ≥ 2, a graph G = (V,E) and a spanning subgraph H of G (the backbone of G), a λ-backbone coloring of (G,H) is a proper vertex coloring V → {1, 2, . . .} of G, in which the colors assigned to adjacent vertices in H differ by at least λ. We study the case where the backbone is either a collection of pairwise disjoint stars or a matching. We show that for a star backbone S of G t...

This paper studies the techniques a backbone ISP can employ to reduce unwanted traffic on its network. For this purpose, we extract likely sources of exploit (thus unwanted) traffic from packet traces collected on backbone links using an Internet traffic behavior profiling methodology we developed earlier. We first study the characteristics of exploit traffic from several aspects, such as netwo...

In this paper, we use Genetic Algorithms to find the Minimum Connected Dominating Set (MCDS) of Unit Disk Graphs (UDG). UDGs are used for modeling ad-hoc networks and finding MCDS in such graphs is a promising approach to construct an efficient virtual backbone in wireless ad-hoc networks. The MCDS problem is proved to be NP-complete. The simulation results show that the proposed algorithm outp...