Tunable kinetic proofreading in a model with molecular frustration

In complex systems, feedback loops can build intricate emergent phenomena, so that a description of the whole system cannot be easily derived from the properties of the individual parts. Here we propose that inter-molecular frustration mechanisms can provide non trivial feedback loops which can develop nontrivial specificity amplification. We show that this mechanism can be seen as a more general form of a kinetic proofreading mechanism, with an interesting new property, namely the ability to tune the specificity amplification by changing the reactants concentrations. This contrasts with the classical kinetic proofreading mechanism in which specificity is a function of only the reaction rate constants involved in a chemical pathway. These results are also interesting because they show that a wide class of frustration models exists that share the same underlining kinetic proofreading mechanisms, with even richer properties. These models can find applications in different areas such as evolutionary biology, immunology and biochemistry

Natural parenting : back to basics in infant care

Peer reviewe

Daphnia revisited: Local stability and bifurcation theory for physiologically structured population models explained by way of an example

We consider the interaction between a general size-structured consumer population and an unstructured resource. We show that stability properties and bifurcation phenomena can be understood in terms of solutions of a system of two delay equations (a renewal equation for the consumer population birth rate coupled to a delay differetial equation for the resource concentration). As many results for such systems are available, we can draw rigorous conclusions concerning dynamical behaviour from an analysis of a characteristic equation. We derive the characteristic equation for a fairly general class of population models, including those based on the Kooijman-Metz Daphnia model and a model introduced by Gurney-Nisbet and Jones et al., and next obtain various ecological insights by analytical or numerical studies of special cases

A mesh-free partition of unity method for diffusion equations on complex domains

We present a numerical method for solving partial differential equations on domains with distinctive complicated geometrical properties. These will be called complex domains. Such domains occur in many real-world applications, for example in geology or engineering. We are, however, particularly interested in applications stemming from the life sciences, especially cell biology. In this area complex domains, such as those retrieved from microscopy images at different scales, are the norm and not the exception. Therefore geometry is expected to directly influence the physiological function of different systems, for example signalling pathways. New numerical methods that are able to tackle such problems in this important area of application are urgently needed. In particular, the mesh generation problem has imposed many restrictions in the past. The approximation approach presented here for such problems is based on a promising mesh-free Galerkin method: the partition of unity method (PUM). We introduce the main approximation features and then focus on the construction of appropriate covers as the basis of discretizations. As a main result we present an extended version of cover construction, ensuring fast convergence rates in the solution process. Parametric patches are introduced as a possible way of approximating complicated boundaries without increasing the overall problem size. Finally, the versatility, accuracy and convergence behaviour of the PUM are demonstrated in several numerical examples