National Repository of Grey Literature 3 records found  Search took 0.00 seconds. 
Systems biology analysis of a drug metabolism (with slow-fast. . . )
Papáček, Štěpán ; Lynnyk, Volodymyr ; Rehák, Branislav
In the systems biology literature, complex systems of biochemical reactions (in form of ODEs) have become increasingly common. This issue of complexity is often making the modelled processes (e.g. drug metabolism, XME induction, DDI) difficult to intuit or to be computationally tractable, discouraging their practical use.
Mathematics and Optimal control theory meet Pharmacy: Towards application of special techniques in modeling, control and optimization of biochemical networks
Papáček, Štěpán ; Matonoha, Ctirad ; Duintjer Tebbens, Jurjen
Similarly to other scienti c domains, the expenses related to in silico modeling in pharmacology need not be extensively apologized. Vis a vis both in vitro and in vivo experiments, physiologically-based pharmacokinetic (PBPK) and pharmacodynamic models represent an important tool for the assessment of drug safety before its approval, as well as a viable option in designing dosing regimens. In this contribution, some special techniques related to the mathematical modeling, control and optimization of biochemical networks are presented on a paradigmatic example of enzyme kinetics.
Stochastic dynamics and energetics of biomolecular systems
Ryabov, Artem ; Chvosta, Petr (advisor) ; Novotný, Tomáš (referee) ; Papáček, Štěpán (referee)
Title: Stochastic dynamics and energetics of biomolecular systems Author: Artem Ryabov Department: Department of Macromolecular Physics Supervisor: prof. RNDr. Petr Chvosta, CSc., Department of Macromolecular Physics Abstract: The thesis comprises exactly solvable models from non-equilibrium statistical physics. First, we focus on a single-file diffusion, the diffusion of particles in narrow channel where particles cannot pass each other. After a brief review, we discuss open single-file systems with absorbing boundaries. Emphasis is put on an interplay of absorption process at the boundaries and inter-particle entropic repulsion and how these two aspects affect the dynam- ics of a given tagged particle. A starting point of the discussions is the exact distribution for the particle displacement derived by order-statistics argu- ments. The second part of the thesis is devoted to stochastic thermodynam- ics. In particular, we present an exactly solvable model, which describes a Brownian particle diffusing in a time-dependent anharmonic potential. The potential has a harmonic component with a time-dependent force constant and a time-independent repulsive logarithmic barrier at the origin. For a particular choice of the driving protocol, the exact work characteristic func- tion is obtained. An asymptotic analysis of...

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