Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets

An integrated understanding of molecular and developmental biology must consider the large number of molecular species involved and the low concentrations of many species in vivo. Quantitative stochastic models of molecular interaction networks can be expressed as stochastic Petri nets (SPNs), a mathematical formalism developed in computer science. Existing software can be used to define molecular interaction networks as SPNs and solve such models for the probability distributions of molecular species. This approach allows biologists to focus on the content of models and their interpretation, rather than their implementation. The standardized format of SPNs also facilitates the replication, extension, and transfer of models between researchers. A simple chemical system is presented to demonstrate the link between stochastic models of molecular interactions and SPNs. The approach is illustrated with examples of models of genetic and biochemical phenomena where the UltraSAN package is used to present results from numerical analysis and the outcome of simulations.

Case-based reasoning to support decision making for managing drinking water quality events in distribution systems

Peer reviewed

A numerical strategy for efficient modeling of the equatorial wave guide

Convection in the tropics is observed to involve a wide-ranging hierarchy of scales from a few kilometers to the planetary scales and also has a profound impact on short-term climate. The mechanisms responsible for this behavior present a major unsolved problem. A promising emerging approach to address these issues is cloud-resolving modeling. Here a family of numerical models is introduced specifically to model the feedback of small-scale deep convection on tropical planetary waves and tropical circulation in a highly efficient manner compatible with the approach through cloud-resolving modeling. Such a procedure is also useful for theoretical purposes. The basic idea in the approach is to use low-order truncation in the meriodonal direction through Gauss–Hermite quadrature projected onto a simple discrete radiation condition. In this fashion, the cloud-resolving modeling of equatorially trapped planetary waves reduces to the solution of a small number of purely zonal two-dimensional wave systems along a few judiciously chosen meriodonal layers that are coupled only by some additional source terms. The approach is analyzed in detail with full mathematical rigor for linearized equatorial primitive equations with source terms.

From cell death to embryo arrest: Mathematical models of human preimplantation embryo development

Human preimplantation embryos exhibit high levels of apoptotic cells and high rates of developmental arrest during the first week in vitro. The relation between the two is unclear and difficult to determine by conventional experimental approaches, partly because of limited numbers of embryos. We apply a mixture of experiment and mathematical modeling to show that observed levels of cell death can be reconciled with the high levels of embryo arrest seen in the human only if the developmental competence of embryos is already established at the zygote stage, and environmental factors merely modulate this. This suggests that research on improving in vitro fertilization success rates should move from its current concentration on optimizing culture media to focus more on the generation of a healthy zygote and on understanding the mechanisms that cause chromosomal and other abnormalities during early cleavage stages.

Effect of water vapour condensation on the radon content in subsurface air in a hypogeal inactive-volcanic environment in Galdar cave, Spain

Fluctuations of trace gas activity as a response to variations in weather and microclimate conditions were monitored over a year in a shallow volcanic cave (Painted Cave, Galdar, Canary Islands, Spain). 222Rn concentration was used due to its greater sensitivity to hygrothermal variations than CO2 concentration. Radon concentration in the cave increases as effective vapour condensation within the porous system of the rock surfaces inside the cave increases due to humidity levels of more than 70%. Condensed water content in pores was assessed and linked to a reduction in the direct passage of trace gases. Fluctuations in radon activity as a response to variations in weather and microclimate conditions were statistically identified by clustering entropy changes on the radon signal and parameterised to predict radon concentration anomalies. This raises important implications for other research fields, including the surveillance of shallow volcanic and seismic activity, preventive conservation of cultural heritage in indoor spaces, indoor air quality control and studies to improve understanding of the role of subterranean terrestrial ecosystems as reservoirs and/or temporary sources of trace gases.

Water quality : Western Fish Toxicology Station and western Oregon rivers /

Mode of access: Internet.

Agricultural land use water quality interaction : problem abatement, project monitoring, and monitoring strategies /

Mode of access: Internet.

Surface water quality parameters for monitoring oil shale development /

Mode of access: Internet.

Ion selective electrodes in water quality analysis /

Mode of access: Internet.

Automated In Situ Water Quality Sensor Workshop, February 14-16, 1978 : [proceedings] /

Mode of access: Internet.

Integrated land use/air quality/water quality control study for Sonoma County, California /

Mode of access: Internet.

Data base system for State water quality management information system /

Mode of access: Internet.

Sampling strategies for water quality in the Great Lakes /

Mode of access: Internet.

Forest chemicals and water quality.

Mode of access: Internet.