Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop

. In this paper we will attempt to give convincing arguments for why we believe it is time for the formal methods community to shift some of its attention towards the analysis of programs written in modern programming languages. In keeping with this philosophy we have developed a verification and testing

Several recent studies have introduced lightweight versions of Java: reduced languages in which complex features like threads and reflection are dropped to enable rigorous arguments about key properties such as type safety. We carry this process a step further, omitting almost all features

the most prevalent type of evaluation carried out. We also include a summary of TRECVid as an example of a system evaluation benchmarking campaign and this allows us to discuss whether such campaigns are a good thing or a bad thing. There are arguments for and against these campaigns and we present some

Informal arguments that cryptographic protocols are secure can be made rigorous using inductive definitions. The approach is based on ordinary predicate calculus and copes with infinite-state systems. Proofs are generated using Isabelle/HOL. The human effort required to analyze a protocol can

fraction of the nodes crash or the network partitions. But current overlays are not secure; even a small fraction of malicious nodes can prevent correct message delivery throughout the overlay. This prob-lem is particularly serious in open peer-to-peer systems, where many diverse, autonomous parties

was considered by Hamilton [H 5,§4,5]; unfortunately, his argument, as written, contains an unjustified statement (RMAX = Γ, on page 62, lines 7-10 from the bottom), which I was unable to fix. Our approach is somewhat different, and is aimed at eventually constructing a canonical Ricci flow, defined on a largest

common, systems with very small numbers of molecules are important in some applications (e.g., in small biological cells or in surface processes). In both views, most complicated systems with multiple reaction channels and multiple chemical species cannot be solved analytically. There are exact numerical

The Penn Treebank has recently implemented a new syntactic annotation scheme, designed to highlight aspects of predicate-argument structure. This paper discusses the implementation of crucial aspects of this new annotation scheme. It incorporates a more consistent treatment of a wide range

Conflict resolution is a critical problem in distributed and collaborative multi-agent systems. Argumentation-based negotiation, where agents provide explicit arguments or justifications for their proposals for resolving conflicts, is an effective approach to resolve conflicts. However, while small-scale