Simulation Model Development and Analysis in UNITY

We evaluate UNITY – a computational model, specification language and proof system defined by Chandy and Misra [5] for the development of parallel and distributed programs – as a platform for simulation model specification and analysis. We describe a UNITY-based methodology for the construction, analysis and execution of simulation models. The methodology starts with a simulation model specification in the form of a set of coupled state transition systems. Mechanical methods for mapping the transition systems first into a set of formal assertions, permitting formal verification of the transition systems, and second into an executable program are described. The methodology provides a means to independently verify the correctness of the transition systems: one can specify properties formally that the model should obey and prove them as theorems using the formal specification. The methodology is illustrated through generation of a simulation program solving the machine interference problem using the Time Warp protocol on a distributed memory parallel architecture.     

A hybrid approach for addressing ring flexibility in 3D database searching

A hybrid approach for flexible 3D database searching is presented that addresses the problemof ring flexibility. It combines the explicit storage of up to 25 multiple conformations ofrings, with up to eight atoms, generated by the 3D structure generator CORINA with thepower of a torsional fitting technique implemented in the 3D database system UNITY. Acomparison with the original UNITY approach, using a database with about 130,000 entriesand five different pharmacophore queries, was performed. The hybrid approach scored, on anaverage, 10–20% more hits than the reference run. Moreover, specific problems withunrealistic hit geometries produced by the original approach can be excluded. In addition, theinfluence of the maximum number of ring conformations per molecule was investigated. Anoptimal number of 10 conformations per molecule is recommended.