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 …

Fully automated attractor analysis of cyanobacteria models

N Beneš, L Brim, S Pastva, D Šafránek… - … on System Theory …, 2018 - ieeexplore.ieee.org
Complex dynamics arising in biological systems can be characterised by various kinds of
attractors. To that end, the task of determining attractors becomes important in modern …

Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications

E Šmijáková, S Pastva, D Šafránek, L Brim - Computational Methods in …, 2020 - Springer
We consider the parameter synthesis problem for multi-affine hybrid systems and properties
specified using a hybrid extension of CTL (HCTL). The goal is to determine the sets of …

[PDF][PDF] Discrete Bifurcation Analysis

S Pastva, RNDL BRIM - 2019 - is.muni.cz
When trying to describe and understand real-world phenomena, science often relies on a
model-based approach, where the true nature of the system is described in some simplified …

[PDF][PDF] Formal methods for model selection in systems biology

M Hajnal - Master's thesis, Masaryk University, Brno, Czech …, 2018 - is.muni.cz
We address the problem of selecting model from candidate list in the field of systems
biology. The selection is based on model behaviour specified in temporal logic rather than …

[PDF][PDF] Discrete Bifurcation Analysis

M Samuel, RND Luboš - is.muni.cz
When trying to describe and understand real-world phenomena, science often relies on a
model-based approach, where the true nature of the system is described in some simplified …

The modelling and synthesis of chemical reaction networks

M Whitby - 2020 - ora.ox.ac.uk
Biochemical systems have been influenced, altered, and engineered to produce a myriad of
complex behaviours that have far reaching consequences in the realization of computational …

Multi-approaches to achieve an advanced cognitive agent in a new type of parallel processing computer

X Yuan - 2020 - hekyll.services.adelaide.edu.au
In this work, we addressed the problem of developing an agent-based artificial general
intelligence that can be implemented in compact and power-efficient electronic hardware …