scholarly journals Efficient computation of exact solutions for quantitative model checking

2012 ◽  
Vol 85 ◽  
pp. 17-32 ◽  
Author(s):  
Sergio Giro
1990 ◽  
Vol 258 (3) ◽  
pp. C563-C577 ◽  
Author(s):  
T. Yoshida ◽  
M. Dembo

We propose a quantitative model of the thermodynamics of hemoglobin in contact with its five major ligands (O2, CO2, Cl-, 2,3-bisphosphoglycerate, and H+). Our model incorporates the two-state formalism of J. Monod, J. Wyman, and J.P. Changeux (J. Mol. Biol. 12: 88-118, 1965) for treatment of quanternary transitions and also the mean field formalism of K. Linderstrom-Lang (C. R. Trav. Lab. Carlsberg Ser. Chim. 15: 1-30, 1924) for treatment of electrostatic interactions. On the basis of this approach, we develop an algorithm for the efficient computation of observable quantities, such as the occupancy of various ligand binding sites, and an objective statistical procedure for determining both maximum likelihood values and confidence limits of all the intrinsic thermodynamic parameters of hemoglobin. Finally, we show that the predictions of our theory are in good agreement with independent experimental observations.


2021 ◽  
Author(s):  
Polyxeni Tsompanoglou ◽  
Sophia Petridou ◽  
Petros Nicopolitidis ◽  
Georgios Papadimitriou

Author(s):  
Maximilian A. Köhl ◽  
Michaela Klauck ◽  
Holger Hermanns

AbstractJANI-model [6] is a model interchange format for networks of interacting automata. It is well-entrenched in the quantitative model checking community and allows modeling a variety of systems involving concurrency, probabilistic and real-time aspects, as well as continuous dynamics. Python is a general purpose programming language preferred by many for its ease of use and vast ecosystem. In this paper, we present Momba, a flexible Python framework for dealing with formal models centered around the JANI-model format and formalism. Momba strives to deliver an integrated and intuitive experience for experimenting with formal models making them accessible to a broader audience. To this end, it provides a pythonic interface for model construction, validation, and analysis. Here, we demonstrate these capabilities.


Author(s):  
YoungMin Kwon ◽  
Eunhee Kim ◽  
Seonghwan Jeong ◽  
Arthur H. Lee

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