Efficient manipulation and generation of Kirchhoff polynomials for the analysis of non-equilibrium biochemical reaction networks.

Kirchhoff polynomials are central for deriving symbolic steady-state expressions of models whose dynamics are governed by linear diffusion on graphs. In biology, such models have been unified under a common linear framework subsuming studies across areas such as enzyme kinetics, G-protein coupled receptors, ion channels and gene regulation. Due to 'history dependence' away from thermodynamic equilibrium, these models suffer from a (super) exponential growth in the size of their symbolic steady-state expressions and, respectively, Kirchhoff polynomials.

BioSwitch: a tool for the detection of bistability and multi-steady state behaviour in signalling and gene regulatory networks.

Motivation: Multi-steady state behaviour, and in particular multi-stability, provides biological systems with the capacity to take reliable decisions (such as cell fate determination). A problem arising frequently in systems biology is to elucidate whether a signal transduction mechanism or a gene regulatory network has the capacity for multi-steady state behaviour, and consequently for a switch-like response to stimuli. Bifurcation diagrams are a powerful instrument in non-linear analysis to study the qualitative and quantitative behaviour of equilibria including bifurcation into different equilibrium branches and bistability.

High-Temperature Thermoelectricity in LaNiO-LaCuO Heterostructures.

Transition metal oxides exhibit a high potential for application in the field of electronic devices, energy storage, and energy conversion. The ability of building these types of materials by atomic layer-by-layer techniques provides a possibility to design novel systems with favored functionalities. In this study, by means of the atomic layer-by-layer oxide molecular beam epitaxy technique, we designed oxide heterostructures consisting of tetragonal KNiF-type insulating LaCuO (LCO) and perovskite-type conductive metallic LaNiO (LNO) layers with different thicknesses to assess the heterostructure-thermoelectric property-relationship at high temperatures.

Steady-State Differential Dose Response in Biological Systems.

In pharmacology and systems biology, it is a fundamental problem to determine how biological systems change their dose-response behavior upon perturbations. In particular, it is unclear how topologies, reactions, and parameters (differentially) affect the dose response. Because parameters are often unknown, systematic approaches should directly relate network structure and function.