When designing and analyzing genetic circuits, researchers are often interested in the probability of the system reaching a given state within a certain amount of time. Usually, this involves simulating the system to produce some time series data and …
Stochastic chemical kinetics (SCK) has become an important formalism for modeling and analysis of complex biological systems as it can capture the discreteness and the randomness of underlying biochemical reactions. One of the assumptions made by SCK …
Uncertainty presents significant challenges in the reasoning about and controlling of complex dynamical systems. To address this challenge, numerous researchers are developing improved methods for stochastic analysis. This book presents a diverse …
This paper presents results on the design and analysis of a robust genetic Muller C-element. The Muller C-element is a standard logic gate commonly used to synchronize independent processes in most asynchronous electronic circuits. Synthetic …
Researchers are now developing synthetic genetic circuits to manipulate the biochemical processes within living cells. In order to model and predict the behavior of these circuits, the designer must account for numerous reactions among many chemical …
Uropathogenic Escherichia coli (UPEC) represent the predominant cause of urinary tract infections (UTIs). A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA …
Electronic design automation (EDA) tools have facilitated the design of ever more complex integrated circuits each year. Synthetic biology would also benefit from the development of genetic design automation (GDA) tools. Existing GDA tools require …
Given the substantial computational requirements of stochastic simulation, approximation is essential for efficient analysis of any realistic biochemical system. This paper introduces a new approximation method to reduce the computational cost of …
With advances in technologies such as high throughput data collection and genome sequencing methods, the Human Genome Project which, among other things, determined the human DNA sequence and identified all the genes in human DNA was completed at …