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Augustinas Sukys

Publications and source records attributed to Augustinas Sukys.

2 recordsLinked to original sources

The Origins of Transient Bimodality

Many dynamical systems exhibit diverse modes of behavior. In biology, such modes can represent individual or cell fates. While the emergence of multimodality is commonly studied, transient bimodality is much less well understood. Under transient bimodality, a system moving from a well-defined initial to a final state transiently undergoes a bifurcation into multiple probability modes. This noise-driven phenomenon can significantly impact processes such as cell differentiation and speciation in the presence of changing environmental conditions. We detail a theoretical approach for understanding transient bimodality connecting results from ecology, optics, chemical reaction networks and cell biology, propose a ``minimal model'' of transient bimodality and derive a general criterion for its presence. We show that fast-to-slow dynamics can lead to transient bimodality in addition to the well-known case of slow-to-fast dynamics. Finally, we discuss the role of transient bimodality across the scientific literature, with emphasis on biochemical kinetics and gene regulation.

q-bio.SC

MomentClosure.jl: automated moment closure approximations in Julia

MomentClosure.jl is a Julia package providing automated derivation of the time-evolution equations of the moments of molecule numbers for virtually any chemical reaction network using a wide range of moment closure approximations. It extends the capabilities of modelling stochastic biochemical systems in Julia and can be particularly useful when exact analytic solutions of the chemical master equation are unavailable and when Monte Carlo simulations are computationally expensive. MomentClosure.jl is freely accessible under the MIT license. Source code and documentation are available at https://github.com/augustinas1/MomentClosure.jl

q-bio.MN