ϵ-Semantics computations on biological systems

Domain semantics of possibility computations

A duality between LM-fuzzy possibility computations and their logical semantics

Let X be a dcpo and let L be a complete lattice. The family σL(X) of all Scott continuous mappings from X to L is a complete lattice under pointwise order, we call it the L-fuzzy Scott structure on X. Let E be a dcpo. A mapping g : σL(E) −> M is called an LM-fuzzy possibility valuation of E if it preserves arbitrary unions. Denote by πLM(E) the set of all LM-fuzzy possibility valuations of E. T...

Diacylglycerol Kinase-ε: Properties and Biological Roles

In mammals there are at least 10 isoforms of diacylglycerol kinases (DGK). All catalyze the phosphorylation of diacylglycerol (DAG) to phosphatidic acid (PA). Among DGK isoforms, DGKε has several unique features. It is the only DGK isoform with specificity for a particular species of DAG, i.e., 1-stearoyl-2-arachidonoyl glycerol. The smallest of all known DGK isoforms, DGKε, is also the only DG...

Cooperativity in biological systems

Living organisms can sense and respond to external and internal stimuli. Response isdemonstrated in many forms including modulation of gene expression profiles, motility,secretion, cell death, etc. Nevertheless, all forms share a basic property: they depend on sensingsmall changes in the concentration of an effector molecule or subtle conformational changes ina protein and invoking the appropri...

CTL Model Update: Semantics, Computations and Implementation

Minimal change is a fundamental principle for modeling system dynamics. In this paper, we study the issue of minimal change for Computational Tree Logic (CTL) model update. We first propose five primitive operations which capture the basic update of the CTL model, and then define the minimal change criteria for CTL model update based on these primitive operations. We provide essential semantic ...