A new method for the visualization of state transition graphs is presented. Visual information is reduced by clustering nodes, forming a tree structure of related clusters. This structure is visualized in three dimensions with concepts from cone trees and emphasis on symmetry. The resulting visualization makes it easier to relate features in the visualization of the state transition graph to se...

Human DNA methyltransferase 1 (DNMT1) maintains the epigenetic state of DNA by replicating CpG methylation signatures from parent to daughter strands, producing heritable methylation patterns through cell divisions. The proposed catalytic mechanism of DNMT1 involves nucleophilic attack of Cys(1226) to cytosine (Cyt) C6, methyl transfer from S-adenosyl-l-methionine (SAM) to Cyt C5, and proton ab...

For the treatment of equilibrated molecular systems in a heat bath we propose a transition state theory that is based on conformation dynamics. In general, a set-based discretization of a Markov operator P does not preserve the Markov property. In this article, we propose a discretization method which is based on a Galerkin approach. This discretization method preserves the Markov property of t...

ab initio calculation at hf/6-31g* level of theory for geometry optimization and mp2/6-31g*//hf/6-31g* for a single point total energy calculation are reported for the important energyminimumconformations and transition-state geometries of of cyclodeca-1,2,3-triene (1). the mostfavorable conformation of 1 is a unsymmetrical twist-chair (1-tc) structure. degenerateinterconversion of 1-tc with it...

In this paper, we present a general concept of state transition diagrams well-suited for various modeling purposes. Our notation is tailored for the description of asynchronous time-independent agents. We start by proposing a graphical and textual syntax, and deene an abstract syntax for both notations. The semantics of state transition diagrams deened by translating the abstract syntax into ti...

This paper describes the design and implementation of a passive scanner for Modbus networks. The tool integrates packet parsing and passive scanning functionality to interpret Modbus transactions and provide accurate network representations. In particular, the scanner monitors Modbus messages to maintain and update state table entries associated with field devices. Entries in the state tables r...

Dynamic configuration is the ability to modify the structure of an application as a concurrent activity to the application providing service. Society has placed great reliance on complex computer systems; this trend looks set to continue with expectations for non-stop and adaptive applications. Research to date has produced a pool of mechanisms and theory regarding dynamic configuration. Our re...