COOKIES: By using this website you agree that we can place Google Analytics Cookies on your device for performance monitoring. |

University of Cambridge > Talks.cam > Isaac Newton Institute Seminar Series > Hybrid modelling of stochastic chemical kinetics

## Hybrid modelling of stochastic chemical kineticsAdd to your list(s) Download to your calendar using vCal - Konstantinos Zygalakis (University of Edinburgh)
- Wednesday 03 February 2016, 15:00-16:00
- Seminar Room 1, Newton Institute.
If you have a question about this talk, please contact INI IT. SDB - Stochastic dynamical systems in biology: numerical methods and applications It is well known that stochasticity can play a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be adequately modelled by Markov processes and, for such systems, methods such as Gillespie's algorithm are typically employed. While such schemes are easy to implement and are exact, the computational cost of simulating such systems can become prohibitive as the frequency of the reaction events increases. This has motivated numerous coarse grained schemes, where the ``fast'' reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation for systems where all reactants are present in large concentrations, the approximation breaks down when the fast chemical species exist in small concentrations, giving rise to significant errors in the simulation. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as computing observables of cell cycle models. In this talk, we present a hybrid scheme for simulating well-mixed stochastic kinetics, using Gillepsie—type dynamics to simulate the network in regions of low reactant concentration, and chemical langevin dynamics when the concentrations of all species is large. These two regimes are coupled via an intermediate region in which a ``blended'' jump-diffusion model is introduced. Examples of gene regulatory networks involving reactions occurring at multiple scales, as well as a cell-cycle model are simulated, using the exact and hybrid scheme, and compared, both in terms weak error, as well as computational cost. This talk is part of the Isaac Newton Institute Seminar Series series. ## This talk is included in these lists:- All CMS events
- Featured lists
- INI info aggregator
- Isaac Newton Institute Seminar Series
- School of Physical Sciences
- Seminar Room 1, Newton Institute
- bld31
Note that ex-directory lists are not shown. |
## Other listsHistory of Modern Medicine and Biology Computer Laboratory Computer Architecture Group Meeting Cambridge Peace and Education Research Group Advances and Controversies in Lipid Lowering Cambridge Conversations in Translation Cambridge Ukrainian Studies Lecture Series## Other talksSolving the Reproducibility Crisis Religion, revelry and resistance in Jacobean Lancashire CANCELLED: The Loxbridge Triangle: Integrating the East-West Arch into the London Mega-region Fukushima and the Law How India Became Democratic: Comparative Perspectives (Panel discussion led by Gary Gerstle and Tim Harper) Ethics for the working mathematician, seminar 10: Mathematicians being leaders. |