Analyzing Linear Communication Networks using the Ribosome Flow Model

The Ribosome Flow Model (RFM) describes the unidirectional movement of interacting particles along a one-dimensional chain of sites. As a site becomes fuller, the effective entry rate into this site decreases. The RFM has been used to model and analyze mRNA translation, a biological process in which ribosomes (the particles) move along the mRNA molecule (the chain), and decode the genetic information into proteins. Here we propose the RFM as an analytical framework for modeling and analyzing linear communication networks. In this context, the moving particles are data-packets, the chain of sites is a one dimensional set of ordered buffers, and the decreasing entry rate to a fuller buffer represents a kind of decentralized backpressure flow control. For an RFM with homogeneous link capacities, we provide closed-form expressions for important network metrics including the throughput and end-to-end delay. We use these results to analyze the hop length and the transmission probability (in a contention access mode) that minimize the end-to-end delay in a multihop linear network, and provide closed-form expressions for the optimal parameter values

A Deterministic Model for One-Dimensional Excluded Flow with Local Interactions

Natural phenomena frequently involve a very large number of interacting molecules moving in confined regions of space. Cellular transport by motor proteins is an example of such collective behavior. We derive a deterministic compartmental model for the unidirectional flow of particles along a one-dimensional lattice of sites with nearest-neighbor interactions between the particles. The flow between consecutive sites is governed by a soft simple exclusion principle and by attracting or repelling forces between neighboring particles. Using tools from contraction theory, we prove that the model admits a unique steady-state and that every trajectory converges to this steady-state. Analysis and simulations of the effect of the attracting and repelling forces on this steady-state highlight the crucial role that these forces may play in increasing the steady-state flow, and reveal that this increase stems from the alleviation of traffic jams along the lattice. Our theoretical analysis clarifies microscopic aspects of complex multi-particle dynamic processes

Synthetic Gene Circuits: Design with Directed Evolution

Synthetic circuits offer great promise for generating insights into nature's underlying design principles or forward engineering novel biotechnology applications. However, construction of these circuits is not straightforward. Synthetic circuits generally consist of components optimized to function in their natural context, not in the context of the synthetic circuit. Combining mathematical modeling with directed evolution offers one promising means for addressing this problem. Modeling identifies mutational targets and limits the evolutionary search space for directed evolution, which alters circuit performance without the need for detailed biophysical information. This review examines strategies for integrating modeling and directed evolution and discusses the utility and limitations of available methods

A tractable analytical model for large-scale congested protein synthesis networks

This paper presents an analytical model, based on finite capacity queueing network theory, to evaluate congestion in protein synthesis networks. These networks are modeled as a set of single server bufferless queues in a tandem topology. This model proposes a detailed state space formulation, which provides a fine description of congestion and contributes to a better understanding of how the protein synthesis rate is deteriorated. The model approximates the marginal stationary distributions of each queue. It consists of a system of linear and quadratic equations that can be decoupled. The numerical performance of this method is evaluated for networks with up to 100,000 queues, considering scenarios with various levels of congestion. It is a computationally efficient and scalable method that is suitable to evaluate congestion for large-scale networks. Additionally, this paper generalizes the concept of blocking: blocking events can be triggered by an arbitrary set of queues. This generalization allows for a variety of blocking phenomena to be modeled.Swiss National Science Foundation (Grant 205320-117581