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—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)
We introduce a graph-theoretic formalism suitable for mod-eling 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(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)
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)
Previous models of the cerebrovascular smooth muscle cell have not addressed the interaction between the electrical, chemical, and mechanical components of cell function during the development of active tension. These models are primarily electrical, biochemical or mechanical in their orientation, and do not permit a full exploration of how the smooth(More)
N-Methyl-D-aspartate receptors (NMDARs) composed of NR1 and NR3 subunits differ from other NMDAR subtypes in that they require glycine alone for activation. However, little else is known about the activation mechanism of these receptors. Using NMDAR glycine-site agonists/antagonists in conjunction with functional mutagenesis of the NR1 and NR3(More)
Protein synthesis is highly regulated throughout nervous system development, plasticity and regeneration. However, tracking the distributions of specific new protein species has not been possible in living neurons or at the ultrastructural level. Previously we created TimeSTAMP epitope tags, drug-controlled tags for immunohistochemical detection of specific(More)