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A System for Tracking the Dynamics of Social Preference Behavior in Small Rodents
Published on: November 21, 2019
Slow sites in an exclusion process with limited resources
Chris A Brackley1, M Carmen Romano, Marco Thiel
1Institute for Complex Systems and Mathematical Biology, SUPA, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom.
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|January 15, 2011
Summary
We modeled protein production with dynamic resource availability, finding that depleted amino acid-transfer-RNA (aa-tRNA) complexes can paradoxically reduce translation queues.
Area of Science:
- Biophysics
- Computational Biology
- Biochemistry
Background:
- The totally asymmetric exclusion process models systems with excluded volume and directed transport.
- Resource availability dynamically influences reaction rates in biological and chemical systems.
- Messenger RNA (mRNA) translation relies on amino acid-transfer-RNA (aa-tRNA) complexes as essential resources.
Purpose of the Study:
- To investigate the impact of slow bottleneck sites on resource-dependent hopping rates in a modified exclusion process.
- To model messenger RNA (mRNA) translation dynamics with a focus on amino acid-transfer-RNA (aa-tRNA) availability.
- To explore emergent behaviors in translation queues under resource depletion conditions.
Main Methods:
- Introduction of slow bottleneck sites into a dynamic totally asymmetric exclusion process.
- Simulation of a simplified mRNA sequence with a central defect codon.
- Analysis of queuing behavior and queue severity as a function of aa-tRNA concentration.
Main Results:
- Observed standard queuing behavior in the translation model.
- Identified a novel regime within the queuing phase where queue severity decreases with aa-tRNA depletion.
- Demonstrated that bottleneck sites significantly influence translation dynamics under varying resource levels.
Conclusions:
- Dynamic resource availability can lead to counterintuitive queuing phenomena in biological translation.
- The model provides insights into how cellular resource fluctuations affect protein synthesis efficiency.
- Slow bottleneck sites play a critical role in modulating the response of translation to resource scarcity.
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