Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

An introduction to Biomodel engineering, illustrated for signal transduction pathways

BioModel Engineering is the science of designing, constructing and analyzing computational models of biological systems. It is inspired by concepts from software engineering and computing science. This paper illustrates a major theme in BioModel Engineering, namely that identifying a quantitative model of a dynamic system means building the structure, finding an initial state, and parameter fitting. In our approach, the structure is obtained by piecewise construction of models from modular parts, the initial state is obtained by analysis of the structure and parameter fitting comprises determining the rate parameters of the kinetic equations. We illustrate this with an example in the area of intracellular signalling pathways

A photodissociation model for the morphology of the HI near OB associations in M33

We present an approach for analysing the morphology and physical properties of Hi features near giant OB asso- ciations in M33, in the context of a model whereby the Hi excess arises from photodissociation of the molecular gas in remnants of the parent Giant Molecular Clouds (GMCs). Examples are presented here in the environs of NGC604 and CPSDPZ204, two prominent Hii regions in M33. These are the first results of a detailed analysis of the environs of a large number of OB associations in that galaxy. We present evidence for "diffusion" of the far-UV radiation from the OB association through a clumpy remnant GMC, and show further that enhanced CO(1-0) emission appears preferentially associated with GMCs of higher volume density.Comment: Accepted to Ap

Atomic Hydrogen produced in M33 Photodissociation Regions

We derive total (atomic + molecular) hydrogen densities in giant molecular clouds (GMCs) in the nearby spiral galaxy M33 using a method that views the atomic hydrogen near regions of recent star formation as the product of photodissociation. Far-UV photons emanating from a nearby OB association produce a layer of atomic hydrogen on the surfaces of nearby GMCs. Our approach provides an estimate of the total hydrogen density in these GMCs from observations of the excess far-UV emission that reaches the GMC from the OB association, and the excess 21-cm radio HI emission produced after these far-UV photons convert H2 into HI on the GMC surface. The method provides an alternative approach to the use of CO emission as a tracer of H2 in GMCs, and is especially sensitive to a range of density well below the critical density for CO(1-0) emission. We describe our "PDR method" in more detail and apply it using GALEX far-UV and VLA 21-cm radio data to obtain volume densities in a selection of GMCs in the nearby spiral galaxy M33. We have also examined the sensitivity of the method to the linear resolution of the observations used; the results obtained at 20 pc are similar to those for the larger set of data at 80 pc resolution. The cloud densities we derive range from 1 to 500 cm-3, with no clear dependence on galactocentric radius; these results are generally similar to those obtained earlier in M81, M83, and M101 using the same method.Comment: Accepted for publication in MNRAS. 25 figures, 16 tables, including online-only material

Realization of a feedback controlled flashing ratchet

A flashing ratchet transports diffusive particles using a time-dependent, asymmetric potential. Particle speed is predicted to increase when a feedback algorithm based on particle positions is used. We have experimentally realized such a feedback ratchet using an optical line trap, and observed that use of feedback increases velocity by up to an order of magnitude. We compare two different feedback algorithms for small particle numbers, and find good agreement with simulations. We also find that existing algorithms can be improved to be more tolerant to feedback delay times

Multi-directional sorting modes in deterministic lateral displacement devices

Deterministic lateral displacement (DLD) devices separate micrometer-scale particles in solution based on their size using a laminar microfluidic flow in an array of obstacles. We investigate array geometries with rational row-shift fractions in DLD devices by use of a simple model including both advection and diffusion. Our model predicts novel multi-directional sorting modes that could be experimentally tested in high-throughput DLD devices containing obstacles that are much smaller than the separation between obstacles

Nutrient supply to anticyclonic meso-scale eddies off western Australia estimated with artificial tracers released in a circulation model

The phytoplankton distribution off western Australia in the period from April to October is unique in that high biomass is generally associated with anticyclonic eddies and not with cyclonic eddies. As the western Australian region is oligotrophic this anomalous feature must be related to differing nutrient supply pathways to the surface mixed layer of cyclonic and anticyclonic eddies. A suite of modelled abiotic tracers suggests that cyclonic eddies are predominantly supplied by diapycnal processes that remain relatively weak until June–July, when they rapidly increase because of deepening surface mixed layers, which start to tap into the nutrient-replete waters below the euphotic zone. To the contrary, we find that anticyclonic eddies are predominantly supplied by injection of shelf waters, which carry elevated levels of inorganic nutrients and biomass. These injections start with the formation of the eddies in April–May, continue well into the austral winter and reach as far as several hundred kilometers offshore. The diapycnal supply of nutrients is suppressed in anticyclonic eddies since the injection of warm, low-salinity shelf waters delays the erosion of the density gradient at the base of the mixed layer. Our results are consistent with the observed seasonal cycles of chlorophyll a and observation of particulate organic matter export out of the surface mixed layer of an anticyclonic eddy in the region