stochastic logic

Utilizing stochastic model checking to analyze genetic circuits

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 …

Erlang-delayed stochastic chemical kinetic formalism for efficient analysis of biological systems with non-elementary reaction effects

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 …

Effecient Stochastic Simulation to Analyze Targeted Properties of Biological Systems

Open access peer-reviewed chapter

Stochastic Control

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 …

Design and analysis of a robust genetic Muller C-element

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 …

iSSA: An incremental stochastic simulation algorithm for genetic circuits

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 …

Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction

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 …

Genetic design automation

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 …

Production-passage-time approximation: a new approximation method to accelerate the simulation process of enzymatic reactions

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 …

Model Abstraction and Temporal Behavior Analysis of Genetic Regulatory Networks

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 …