A model checking approach to discrete bifurcation analysis

N Beneš, L Brim, M Demko, S Pastva… - FM 2016: Formal Methods …, 2016 - Springer
Bifurcation analysis is a central task of the analysis of parameterised high-dimensional
dynamical systems that undergo transitions as parameters are changed. The classical …

Parallel SMT-based parameter synthesis with application to piecewise multi-affine systems

N Beneš, L Brim, M Demko, S Pastva… - Automated Technology for …, 2016 - Springer
We propose a novel scalable parallel algorithm for synthesis of interdependent parameters
from CTL specifications for non-linear dynamical systems. The method employs a symbolic …

Detecting attractors in biological models with uncertain parameters

J Barnat, N Beneš, L Brim, M Demko, M Hajnal… - … Methods in Systems …, 2017 - Springer
Complex behaviour arising in biological systems is typically characterised by various kinds
of attractors. An important problem in this area is to determine these attractors. Biological …

Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway

M Demko, L Chrást, P Dvořák, J Damborský… - Microorganisms, 2019 - mdpi.com
In our previous work, we designed and implemented a synthetic metabolic pathway for 1, 2,
3-trichloropropane (TCP) biodegradation in Escherichia coli. Significant effects of metabolic …

Pithya: a parallel tool for parameter synthesis of piecewise multi-affine dynamical systems

N Beneš, L Brim, M Demko, S Pastva… - … Aided Verification: 29th …, 2017 - Springer
We present a novel tool for parameter synthesis of piecewise multi-affine dynamical systems
from specifications expressed in a hybrid branching-time temporal logic. The tool is based …

[HTML][HTML] Parallel parameter synthesis algorithm for hybrid CTL

N Beneš, L Brim, S Pastva, D Šafránek - Science of Computer …, 2020 - Elsevier
Parametrised models of dynamical systems arise in various areas of science. In this work,
we focus on models described as parametrised Kripke structures with properties formulated …

Model checking approach to the analysis of biological systems

N Beneš, L Brim, S Pastva, D Šafránek - Automated Reasoning for …, 2019 - Springer
Formal verification techniques together with other computer science formal methods have
been recently tailored for applications to biological and biomedical systems. In contrast to …

Probabilistic reachability for multi-parameter bifurcation analysis of cardiac alternans

MA Islam, R Cleaveland, FH Fenton, R Grosu… - Theoretical Computer …, 2019 - Elsevier
Using a probabilistic reachability-based approach, we present a multi-parameter bifurcation
analysis of electrical alternans in the two-current Mitchell–Schaeffer (MS) cardiac-cell model …

Toward modelling and analysis of transient and sustained behaviour of signalling pathways

M Hajnal, D Šafránek, M Demko, S Pastva… - Hybrid Systems Biology …, 2016 - Springer
Signalling pathways provide a complex cellular information processing machinery that
evaluates particular input stimuli and transfers them into the genome by means of regulation …

Bifurcation analysis of cardiac alternans using-decidability

MA Islam, G Byrne, S Kong, EM Clarke… - … Methods in Systems …, 2016 - Springer
We present a bifurcation analysis of electrical alternans in the two-current Mitchell-Schaeffer
(MS) cardiac-cell model using the theory of δ-decidability over the reals. Electrical alternans …