Quantifying the impact of electric fields on single-cell motility.

Cell motility in response to environmental cues forms the basis of many developmental processes in multicellular organisms. One such environmental cue is an electric field (EF), which induces a form of motility known as electrotaxis. Electrotaxis has evolved in a number of cell types to guide wound healing and has been associated with different cellular processes, suggesting that observed electrotactic behavior is likely a combination of multiple distinct effects arising from the presence of an EF.

Ribo-attenuators: novel elements for reliable and modular riboswitch engineering.

Riboswitches are structural genetic regulatory elements that directly couple the sensing of small molecules to gene expression. They have considerable potential for applications throughout synthetic biology and bio-manufacturing as they are able to sense a wide range of small molecules and regulate gene expression in response. Despite over a decade of research they have yet to reach this considerable potential as they cannot yet be treated as modular components.

A Synthetic Recombinase-Based Feedback Loop Results in Robust Expression.

Accurate control of a biological process is essential for many critical functions in biology, from the cell cycle to proteome regulation. To achieve this, negative feedback is frequently employed to provide a highly robust and reliable output. Feedback is found throughout biology and technology, but due to challenges posed by its implementation, it is yet to be widely adopted in synthetic biology.

Designing Conservation Relations in Layered Synthetic Biomolecular Networks.

In Synthetic Biology, biomolecular networks are designed and constructed to perform specified tasks. Design strategies for these networks tend to center on tuning the parameters of mathematical models to achieve a specified behavior, and implementing these parameters experimentally. This design strategy often assumes a fixed network structure that defines the possible behaviors, which may be too restrictive for our purposes.

Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering.

Large, naturally evolved biomolecular networks typically fulfil multiple functions. When modelling or redesigning such systems, functional subsystems are often analysed independently first, before subsequent integration into larger-scale computational models. In the design and analysis process, it is therefore important to quantitatively analyse and predict the dynamics of the interactions between integrated subsystems; in particular, how the incremental effect of integrating a subsystem into a network depends on the existing dynamics of that network.

Layered decomposition for the model order reduction of timescale separated biochemical reaction networks.

Biochemical reaction networks tend to exhibit behaviour on more than one timescale and they are inevitably modelled by stiff systems of ordinary differential equations. Singular perturbation is a well-established method for approximating stiff systems at a given timescale. Standard applications of singular perturbation partition the state variable into fast and slow modules and assume a quasi-steady state behaviour in the fast module.

Guaranteed error bounds for structured complexity reduction of biochemical networks.

Biological systems are typically modelled by nonlinear differential equations. In an effort to produce high fidelity representations of the underlying phenomena, these models are usually of high dimension and involve multiple temporal and spatial scales. However, this complexity and associated stiffness makes numerical simulation difficult and mathematical analysis impossible.