Mass-action models of regulated degradation

Abstract: A key goal of systems biology is to use predictive models to understand complex regulatory networks in living cells. Mathematical modeling and analysis have been successful in uncovering dynamics and steady-state properties, such as multistability and oscillation, of biologically important reactions networks including multisite phosphorylation cycles. However, it remains unclear how emergent dynamics may arise from other prevalent regulatory networks in nonintuitive ways. In this study, we introduce a family of mass-action models for elementary biochemical reactions involving only binding, production, and degradation. We show that altered degradation rate constants of macromolecules upon the formation of high-order complexes can lead to multistability and limit-cycle oscillation. These models can be used to capture dynamics of RNA transcripts for most human genes, as well as many proteins. Interestingly, multistability and oscillation require the same structurally minimal motif in the context of this model family. In addition, oscillations originating from these models have diverging periods, and we use stochastic simulations to show their utility of robustly generating cell clusters with diverse gene expression patterns in cell populations.

algebraic geometrydynamical systemsprobability

Audience: researchers in the topic

( video )

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Seminar on the Mathematics of Reaction Networks

Series comments: Subscription link: list.ku.dk/postorius/lists/morn.list.ku.dk/

This seminar series focuses on progress in mathematical theory for the study of reaction networks, mainly in biology and chemistry. The scope is broad and accommodates works arising from dynamical systems, stochastics, algebra, topology and beyond.

We aim at providing a common forum for sharing knowledge and encouraging discussion across subfields. In particular we aim at facilitating interactions between junior and established researchers. These considerations will be represented in the choice of invited speakers and we will strive to create an excellent, exciting and diverse schedule.

The seminar runs twice a month, typically on the 2nd and 4th Thursday of the month, at 17:00 Brussels time (observe that this webpage shows the schedule in your current time zone). Each session consists of two 25-minute talks followed by 5-minute questions. After the two talks, longer discussions will take place for those interested. To this end, we will use breakout rooms. For this to work well, you need to have the latest version of Zoom installed (version 5.3.0 or higher), and use the desktop client or mobile app (not supported on ChromeOS).

We look forward hearing about new work and meeting many of you over zoom! Many of the talks are recorded; to see the recording, from Past Talks, open details of the listed talk for a video link.

The organizers.

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