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We present a kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalently, definitions of reaction classes. A rule identifies the molecular components involved in a transformation, how these components change, conditions that affect whether a(More)
This paper proposes an approach to optimally synthesize quantum circuits by symbolic reachability analysis, where the primary inputs and outputs are basis binary and the internal signals can be nonbinary in a multiple-valued domain. The authors present an optimal synthesis method to minimize quantum cost and some speedup methods with nonoptimal quantum(More)
Reversible quantum logic plays an important role in quantum computing. In this paper, we propose an approach to optimally synthesize quantum circuits by symbolic reachability analysis where the primary inputs are purely binary. we use symbolic reachability analysis, a technique most commonly used in model checking (a way of formal verification), to(More)
We introduce a graph-theoretic formalism suitable for modeling biochemical networks marked by combinatorial complexity, such as signal-transduction systems, in which protein-protein interactions play a prominent role. This development extends earlier work by allowing for explicit representation of the connectivity of a protein complex. Within the formalism,(More)
OBJECTIVES Mice deficient in the regulator of G-protein signaling 2 (RGS2) exhibit a strong hypertensive phenotype. We studied whether genetic variations in RGS2 are implicated in hypertension or other phenotypes in Japanese hypertensive individuals and the general population. METHODS We sequenced all exons of RGS2 and the promoter region in 953 and 48(More)
Rule-based modeling provides a means to represent cell signaling systems in a way that captures site-specific details of molecular interactions. For rule-based models to be more widely understood and (re)used, conventions for model visualization and annotation are needed. We have developed the concepts of an extended contact map and a model guide for(More)