Finding the three-dimensional structure of proteins is one of the fundamental problems in molecular biology today. The improvements in throughput of classical methods for determining the structure | e.g., using x-ray di raction analysis or NMR | could not keep up with the ever-increasing speed with which proteins are sequenced. This resulted in a desire for methods for structure prediction sole...

A distributed algorithm is developed that can be used to compute the topology of a network, given that each site starts with information about sites it is adjacent to, the network is strongly connected, and communication channels are unidirectional. The program is derived using assertional reasoning.

Many hierarchical techniques to solve large Markov decision processes (MDPs) are based on the partition of the state space into strongly connected components (SCCs) that can be classified into some levels. In each level, smaller problems named restricted MDPs are solved, and then these partial solutions are combined to obtain the global solution. In this paper, we first propose a novel algorith...

We study ideal languages generated by a single word. We provide an algorithm to construct a strongly connected synchronizing automaton for which such a language serves as the language of synchronizing words. Also we present a compact formula to calculate the syntactic complexity of this language.

We present an algorithm for computing nearly recurrent components, that represent areas of close to circulating or stagnant flow, for 3D piecewise constant (PC) vector fields defined on regular grids. Using a number of analytical and simulated data sets, we demonstrate that nearly recurrent components can provide interesting insight into the topological structure of 3D vector fields. Our approa...

This paper presents an algorithm which solves exponentially fast the average consensus problem on strongly connected network of digital links. The algorithm is based on an efficient zooming-in/zooming-out quantization scheme.

This paper presents an algorithm to statically schedule live and strongly connected Marked Graphs (MG). The proposed algorithm computes the best execution where the execution rate is maximal and place sizes are minimal. The proposed algorithm provides transition schedules represented as binary words. These words are chosen to be balanced. The contributions of this paper is the proposed algorith...

In this article we will present a graph partitioning algorithm which partitions a graph into two different types of components: the well-known ‘strongly connected components’ as well as another type of components we call ‘connected acyclic component’. We will give an algorithm based on Tarjan’s algorithm for finding strongly connected components used to find such a partitioning. We will also sh...