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MOTIVATION Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical(More)
| Network protocols in layered architectures have historically been obtained on an ad hoc basis, and many of the recent cross-layer designs are also conducted through piecemeal approaches. Network protocol stacks may instead be holistically analyzed and systematically designed as distributed solutions to some global optimization problems. This paper(More)
References 197 Preface Striking developments have taken place since 1980 in feedback control theory. The subject has become both more rigorous and more applicable. The rigor is not for its own sake, but rather that even in an engineering discipline rigor can lead to clarity and to methodical solutions to problems. The applicability is a consequence both of(More)
A detailed understanding of the many facets of the Internet's topological structure is critical for evaluating the performance of networking protocols, for assessing the effectiveness of proposed techniques to protect the network from nefarious intrusions and attacks, or for developing improved designs for resource provisioning. Previous studies of topology(More)
This paper considers jointly optimal design of crosslayer congestion control, routing and scheduling for ad hoc wireless networks. We first formulate the rate constraint and scheduling constraint using multicommodity flow variables, and formulate resource allocation in networks with fixed wireless channels (or single-rate wireless devices that can mask(More)
This article reviews the current transmission control protocol (TCP) congestion control protocols and overviews recent advances that have brought analytical tools to this problem. We describe an optimization-based framework that provides an interpretation of various flow control mechanisms, in particular, the utility being optimized by the protocol’s(More)
We introduce a mechanism for generating power law distributions, referred to as highly optimized tolerance (HOT), which is motivated by biological organisms and advanced engineering technologies. Our focus is on systems which are optimized, either through natural selection or engineering design, to provide robust performance despite uncertain environments.(More)
With the advent of faster and cheaper computers, optimization based control methodologies have become a viable candidate for control of nonlinear systems. Over the past twenty years, a group of such control schemes have been successfully used in the process control industry where the processes are either intrinsically stable or have very large time(More)
We present a model for the joint design of congestion control and media access control (MAC) for ad hoc wireless networks. Using contention graph and contention matrix, we formulate resource allocation in the network as a utility maximization problem with constraints that arise from contention for channel access. We present two algorithms that are not only(More)