Biochemical interactions in systems and synthetic biology are often modeled with chemical
reaction networks (CRNs). CRNs provide a principled modeling environment capable of …

Biological membranes consist of a lipid bilayer in which integral membrane proteins are
embedded. Based on the compositional complexity of the lipid species found in membranes …

Many goals in synthetic biology, including the elucidation and refactoring of biosynthetic
pathways and the engineering of regulatory circuits and networks, require knowledge of …

Abstract Motivation This article introduces Vivarium—software born of the idea that it should
be as easy as possible for computational biologists to define any imaginable mechanistic …

The malachite green aptamer (MGapt) is known for its utility in RNA measurement in vivo
and in lysate-based cell-free protein systems. However, MGapt fluorescence dynamics do …

Can a micron sized sack of interacting molecules understand, and adapt to a constantly-
fluctuating environment? Cellular life provides an existence proof in the affirmative, but the …

Cell-free expression systems provide a method for rapid DNA circuit prototyping and
functional protein synthesis. While crude extracts remain a black box with many components …

Modeling and simulating gene regulatory networks (GRNs) is crucial for understanding
biological processes, predicting system behavior, guiding the design of synthetic biological …

The successful advancement and deployment of technologies in the field of synthetic
biology will require sophisticated computational infrastructure coupled with new theoretical …

Molecular feedback control circuits can improve robustness of gene expression at single cell-
level. This achievement can be offset by requirements of rapid protein expression, that may …