Thomas E. Gorochowski

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Enhancing the synchronization of dynamical networks is of great interest to those designing and analyzing many man-made and natural systems. In this work, we investigate how network topology can be evolved to improve this property through the rewiring of edges. A computational tool called NETEVO performs this task using a simulated annealing metaheuristic.(More)
Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we(More)
Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation(More)
Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular resources is dedicated to protein translation. Synthetic biology often exploits these resources in executing orthogonal genetic circuits, yet the burden this places on the cell is rarely considered. Here,(More)
Animal societies rely on interactions between group members to effectively communicate and coordinate their actions. To date, the transmission properties of interaction networks formed by direct physical contacts have been extensively studied for many animal societies and in all cases found to inhibit spreading. Such direct interactions do not, however,(More)
The synthesis of protein from messenger RNA during translation is a highly dynamic process that plays a key role in controlling the efficiency and fidelity of genome-wide protein expression. The availability of aminoacylated transfer RNA (tRNA) is a major factor influencing the speed of ribosomal movement, which depending on codon choices, varies(More)
Networks are widely used to describe many natural and technological systems. Understanding how these evolve over time poses a challenge for existing visualization techniques originally developed for fixed network structures. We describe a method of incorporating the concept of aging into evolving networks, where nodes and edges store information related to(More)
NetEvo is a computational framework designed to help understand the evolution of dy-namical complex networks. It provides flexible tools for the simulation of dynamical processes on networks and methods for the evolution of underlying topological structures. The concept of a supervisor is used to bring together both these aspects in a coherent way. It is(More)
We introduce a computational model describing rat behavior and the interactions of neural populations processing spatial and mnemonic information during a maze-based, decision-making task. The model integrates sensory input and implements working memory to inform decisions at a choice point, reproducing rat behavioral data and predicting the occurrence of(More)