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.

Dynamic regulation of the tryptophan operon: A modeling study and comparison with experimental data

A mathematical model for regulation of the tryptophan operon is presented. This model takes into account repression, feedback enzyme inhibition, and transcriptional attenuation. Special attention is given to model parameter estimation based on experimental data. The model's system of delay differential equations is numerically solved, and the results are compared with experimental data on the temporal evolution of enzyme activity in cultures of Escherichia coli after a nutritional shift (minimal + tryptophan medium to minimal medium). Good agreement is obtained between the numeric simulations and the experimental results for wild-type E. coli, as well as for two different mutant strains.

Implementation of non-local boundary layer schemes in the Regional Atmospheric Modeling System and its impact on simulated mesoscale circulations

This paper proposes the implementation of different non-local Planetary Boundary Layer schemes within the Regional Atmospheric Modeling System (RAMS) model. The two selected PBL parameterizations are the Medium-Range Forecast (MRF) PBL and its updated version, known as the Yonsei University (YSU) PBL. YSU is a first-order scheme that uses non-local eddy diffusivity coefficients to compute turbulent fluxes. It is based on the MRF, and improves it with an explicit treatment of the entrainment. With the aim of evaluating the RAMS results for these PBL parameterizations, a series of numerical simulations have been performed and contrasted with the results obtained using the Mellor and Yamada (MY) scheme, also widely used, and the standard PBL scheme in the RAMS model. The numerical study carried out here is focused on mesoscale circulation events during the summer, as these meteorological situations dominate this season of the year in the Western Mediterranean coast. In addition, the sensitivity of these PBL parameterizations to the initial soil moisture content is also evaluated. The results show a warmer and moister PBL for the YSU scheme compared to both MRF and MY. The model presents as well a tendency to overestimate the observed temperature and to underestimate the observed humidity, considering all PBL schemes and a low initial soil moisture content. In addition, the bias between the model and the observations is significantly reduced moistening the initial soil moisture of the corresponding run. Thus, varying this parameter has a positive effect and improves the simulated results in relation to the observations. However, there is still a significant overestimation of the wind speed over flatter terrain, independently of the PBL scheme and the initial soil moisture used, even though a different degree of accuracy is reproduced by RAMS taking into account the different sensitivity tests.

User's guide to the Shoreline Modeling System (SMS) /

At head of title: "Shore Protection and Restoration Program."

Traffic safety demonstration program modeling system. Volume III: citizens band radio model. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Traffic safety demonstration program modeling system. Volume IV: appendices.

National Highway Traffic Safety Administration, Washington, D.C.

Traffic safety demonstration program modeling system. Volume I: technical summary. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Traffic safety demonstration program modeling system. Volume II: system manual. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Local information retrieval for the simulation and modeling system /

COO-1469-0174.

An interactive graphic modeling system,

"Supported in part by Grant U.S. AEC AT(11-1)1469."

DMS : Diagnostic Modeling System.

Includes bibliographical references (p. 52-53).

Regional multipliers : a user handbook for the regional input-output modeling system (RIMS II) /

"May 1986."

Integrating multiple taxa in a biological stream rating system.

"This report is based largely on work done by Leslie Bol and Leon Hinz of the Illinois Natural History Survey, and Ann Marie Holtrop of the IDNR. Their work was funded by IDNR through the Illinois State Wildlife Grant Program (T-20-P-001)." -- acknowledgments.

Organizational maintenance repair parts and special tools lists for shelter system, collective protection, chemical-biological, inflatable, traiiler-transported, M51, (NSN 4240-00-854-4144).

Includes index.

Direct support and general support maintenance repair parts and special tools lists for shelter system, collective protection, chemical-biological, inflatable, trailer-transported, M51, (NSN 4240-00-854-4144).

"November 1975."