A workflow for the hybrid modelling and simulation of multi-timescale biological systems
With the steady advance of in-silico biological experimentation, model construction and
simulation becomes a ubiquitous tool to understand and predict the behaviour of many …
simulation becomes a ubiquitous tool to understand and predict the behaviour of many …
A hybrid stochastic model of the budding yeast cell cycle
The growth and division of eukaryotic cells are regulated by complex, multi-scale networks.
In this process, the mechanism of controlling cell-cycle progression has to be robust against …
In this process, the mechanism of controlling cell-cycle progression has to be robust against …
[HTML][HTML] Efficient Finite-Difference Estimation of Second-Order Parametric Sensitivities for Stochastic Discrete Biochemical Systems
F Jabeen, S Ilie - Mathematical and Computational Applications, 2024 - mdpi.com
Biochemical reaction systems in a cell exhibit stochastic behaviour, owing to the
unpredictable nature of the molecular interactions. The fluctuations at the molecular level …
unpredictable nature of the molecular interactions. The fluctuations at the molecular level …
Analysis and remedy of negativity problem in hybrid stochastic simulation algorithm and its application
The hybrid stochastic simulation algorithm, proposed by Haseltine and Rawlings, can
significantly improve the simulation efficiency for multiscale biochemical networks. However …
significantly improve the simulation efficiency for multiscale biochemical networks. However …
Stochastic simulation of biochemical systems: In memory of Dan T. Gillespie's contributions
Y Cao, P Linda, E Seitaridou - Bulletin of Mathematical Biology, 2019 - Springer
On April 19, 2017, sad news hit all of us in the research communities of computational
biology, stochastic simulation and applied physics. Our beloved friend, Dan T. Gillespie, a …
biology, stochastic simulation and applied physics. Our beloved friend, Dan T. Gillespie, a …
A hybrid stochastic model of the budding yeast cell cycle
The growth and division of eukaryotic cells are regulated by complex, multi-scale networks.
In this process, the mechanism of controlling cell-cycle progression has to be robust against …
In this process, the mechanism of controlling cell-cycle progression has to be robust against …
[HTML][HTML] Finding acceptable parameter regions of stochastic Hill functions for multisite phosphorylation mechanism
Multisite phosphorylation plays an important role in regulating switch-like protein activity and
has been used widely in mathematical models. With the development of new experimental …
has been used widely in mathematical models. With the development of new experimental …
Stochastic Modeling and Simulation of Multiscale Biochemical Systems
M Chen - 2019 - vtechworks.lib.vt.edu
Numerous challenges arise in modeling and simulation as biochemical networks are
discovered with increasing complexities and unknown mechanisms. With the improvement …
discovered with increasing complexities and unknown mechanisms. With the improvement …