Stochastic models for regulatory networks of the genetic toggle switch

Bistability arises within a wide range of biological systems from the λ phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. In this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks.

A regulatory framework for short-term stochastic maintenance outage scheduling in smart grids

The current regulatory framework for maintenance outage scheduling in distribution systems needs revision to face the challenges of future smart grids. In the smart grid context, generation units and the system operator perform new roles with different objectives, and an efficient coordination between them becomes necessary. In this paper, the distribution system operator (DSO) of a microgrid receives the proposals for shortterm (ST) planned outages from the generation and transmission side, and has to decide the final outage plans, which is mandatory for the members to follow. The framework is based on a coordination procedure between the DSO and other market players. This paper undertakes the challenge of optimization problem in a smart grid where the operator faces with uncertainty. The results show the effectiveness and applicability of the proposed regulatory framework in the modified IEEE 34- bus test system.

Stochastic models of road geometry and wind condition for vehicle energy management and control

Modeling and simulation is commonly used to improve vehicle performance, to optimize vehicle system design, and to reduce vehicle development time. Vehicle performances can be affected by environmental conditions and driver behavior factors, which are often uncertain and immeasurable. To incorporate the role of environmental conditions in the modeling and simulation of vehicle systems, both real and artificial data are used. Often, real data are unavailable or inadequate for extensive investigations. Hence, it is important to be able to construct artificial environmental data whose characteristics resemble those of the real data for modeling and simulation purposes. However, to produce credible vehicle simulation results, the simulated environment must be realistic and validated using accepted practices. This paper proposes a stochastic model that is capable of creating artificial environmental factors such as road geometry and wind conditions. In addition, road geometric design principles are employed to modify the created road data, making it consistent with the real-road geometry. Two sets of real-road geometry and wind condition data are employed to propose probability models. To justify the distribution goodness of fit, Pearson's chi-square and correlation statistics have been used. Finally, the stochastic models of road geometry and wind conditions (SMRWs) are developed to produce realistic road and wind data. SMRW can be used to predict vehicle performance, energy management, and control strategies over multiple driving cycles and to assist in developing fuel-efficient vehicles.

Stochastic scheduling - A flow shop no wait application and solutions

Minimizing the makespan of a flow-shop no-wait (FSNW) schedule where the processing times are randomly distributed is an important NP-Complete Combinatorial Optimization Problem. In spite of this, it can be found only in very few papers in the literature. By considering the Start Interval Concept, this problem can be formulated, in a practical way, in function of the probability of the success in preserve FSNW constraints for all tasks execution. With this formulation, for the particular case with 3 machines, this paper presents different heuristics solutions: by integrating local optimization steps with insertion procedures and by using genetic algorithms for search the solution space. Computational results and performance evaluations are commented. Copyright (C) 1998 IFAC.

PERFORMANCE EVALUATION OF RESOURCE-AWARE BUSINESS PROCESSES USING STOCHASTIC AUTOMATA NETWORKS

In this work, we study the performance evaluation of resource-aware business process models. We define a new framework that allows the generation of analytical models for performance evaluation from business process models annotated with resource management information. This framework is composed of a new notation that allows the specification of resource management constraints and a method to convert a business process specification and its resource constraints into Stochastic Automata Networks (SANs). We show that the analysis of the generated SAN model provides several performance indices, such as average throughput of the system, average waiting time, average queues size, and utilization rate of resources. Using the BP2SAN tool - our implementation of the proposed framework - and a SAN solver (such as the PEPS tool) we show through a simple use-case how a business specialist with no skills in stochastic modeling can easily obtain performance indices that, in turn, can help to identify bottlenecks on the model, to perform workload characterization, to define the provisioning of resources, and to study other performance related aspects of the business process.

Stochastic models for regulatory networks of the genetic toggle switch

Bistability arises within a wide range of biological systems from the A phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. in this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks.

Quality assurance of aerial applications of larvicides for mosquito control : effects of granule and catch tray size on field monitoring programs

Aerial applications of granular insecticides are preferable because they can effectively penetrate vegetation, there is less drift, and no loss of product due to evaporation. We aimed to 1) assess the field efficacy ofVectoBac G to control Aedes vigilax (Skuse) in saltmarsh pools, 2) develop a stochastic-modeling procedure to monitor application quality, and 3) assess the distribution of VectoBac G after an aerial application. Because ground-based studies with Ae. vigilax immatures found that VectoBac G provided effective control below the recommended label rate of 7 kg/ha, we trialed a nominated aerial rate of 5 kg/ha as a case study. Our distribution pattern modeling method indicated that the variability in the number of VectoBac G particles captured in catch-trays was greater than expected for 5 kg/ha and that the widely accepted contour mapping approach to visualize the deposition pattern provided spurious results and therefore was not statistically appropriate. Based on the results of distribution pattern modeling, we calculated the catch tray size required to analyze the distribution of aerially applied granular formulations. The minimum catch tray size for products with large granules was 4 m2 for Altosid pellets and 2 m2 for VectoBac G. In contrast, the minimum catch-tray size for Altosid XRG, Aquabac G, and Altosand, with smaller granule sizes, was 1 m2. Little gain in precision would be made by increasing the catch-tray size further, when the increased workload and infrastructure is considered. Our improved methods for monitoring the distribution pattern of aerially applied granular insecticides can be adapted for use by both public health and agricultural contractors.

Implications of local lifecycle analyses and low carbon fuel standard design on gasohol transportation fuels

State and regional policies, such as low carbon fuel standards (LCFSs), increasingly mandate that transportation fuels be examined according to their greenhouse gas (GHG) emissions. We investigate whether such policies benefit from determining fuel carbon intensities (FCIs) locally to account for variations in fuel production and to stimulate improvements in FCI. In this study, we examine the FCI of transportation fuels on a lifecycle basis within a specific state, Minnesota, and compare the results to FCIs using national averages. Using data compiled from 18 refineries over an 11-year period, we find that ethanol production is highly variable, resulting in a 42% difference between carbon intensities. Historical data suggests that lower FCIs are possible through incremental improvements in refining efficiency and the use of biomass for processing heat. Stochastic modeling of the corn ethanol FCI shows that gains in certainty due to knowledge of specific refinery inputs are overwhelmed by uncertainty in parameters external to the refiner, including impacts of fertilization and land use change. The LCA results are incorporated into multiple policy scenarios to demonstrate the effect of policy configurations on the use of alternative fuels. These results provide a contrast between volumetric mandates and LCFSs. © 2011 Elsevier Ltd.

渤海海域河流相油藏精细描述技术及应用研究

Aiming at the character of Bohaii Sea area and the heterogeneity of fluvial facies reservoir, litho-geophysics experiments and integrated research of geophysical technologies are carried out. To deal with practical problems in oil fields of Bohai area, such as QHD32-6, Southern BZ25-1 and NP35-2 et al., technology of reservoir description based on seismic data and reservoir geophysical methods is built. In this dissertation, three points are emphasized: ①the integration of multidiscipline; ②the application of new methods and technologies; ③the integration of quiescent and dynamic data. At last, research of geology modeling and reservoir numerical simulation based on geophysical data are integrated. There are several innovative results and conclusion in this dissertation: (1)To deal with problems in shallow sea area where seismic data is the key data, a set of technologies for fine reservoir description based on seismic data in Bohai Sea area are built. All these technologies, including technologies of stratigraphic classification, sedimentary facies identification, structure fine characterization, reservoir description, fluid recognition and integration of geological modeling& reservoir numerical simulation, play an important role in the hydrocarbon exploration and development. In the research of lithology and hydrocarbon-bearing condition, petrophysical experiment is carried out. Outdoors inspection and experiment test data are integrated in seismic forward modeling& inversion research. Through the research, the seismic reflection rules of fluid in porosity are generated. Based on all the above research, seismic data is used to classify rock association, identify sedimentary facies belts and recognition hydrocarbon-bearing condition of reservoir. In this research, the geological meaning of geophysical information is more clear and the ambiguity of geophysical information is efficiently reduced, so the reliability in hydrocarbon forecasting is improved. The methods of multi-scales are developed in microfacies research aiming at the condition of shallow sea area in Bohai Sea: ① make the transformation from seismic information to sedimentary facies reality by discriminant analysis; ②in research of planar sedimentary facies, make microfacies research on seismic scale by technologies integration of seismic multi-attributes analysis& optimization, strata slicing and seismic waveform classification; ③descript the sedimentary facies distribution on scales below seismic resolution with the method of stochastic modeling. In the research of geological modeling and reservoir numerical simulation, the way of bilateral iteration between modeling and numerical simulation is carried out in the geological model correction. This process include several steps: ①make seismic forward modeling based on the reservoir numerical simulation results and geological models; ②get trend residual of forward modeling and real seismic data; ③make dynamic correction of the model according to the above trend residual. The modern integration technology of reservoir fine description research in Bohai Sea area, which is developed in this dissertation, is successfully used in (1)the reserve volume evaluation and development research in BZ25-1 oil field and (2)the tracing while drilling research in QHD32-6 oil field. These application researches show wide application potential in hydrocarbon exploration and development research in other oil fields.

准噶尔盆地南缘台13井区侏罗系油藏表征与建模

Junggar Basin has a large amount of recoverable reserves, However, due to the unfavorable factors, such as bad seismic data quality, complex structure with many faults and less wells, the exploration of oil and gas is still relatively limited, so advanced theoretical guidance and effective technical supports are desirable. Based on the theories of sedimentology, as well as comprehensive studies of outcrops, seismic data, drilling data and setting of this area, the paper establishes the isochronous correlation framework, and analyzes the sedimentary facies types and provenance direction, and obtains the profile and plain maps of the sedimentary facies combined with the logging constrained inversion. Then the paper analyzes the reservoir controlling factors, reservoir lithology attribute, 4-property relationship and sensibility based on the sedimentary facies research, and sets up a 3D geological model using facies controlled modeling. Finally, the paper optimizes some target areas with the conclusions of reservoir, structure and reservoir formation.Firstly, the paper establishs the isochronous correlation framework by the seismic data, drilling data and setting of this area. The sedimentary facies in Tai13 well block are braided river and meandering river according to the analysis of the lithology attribute, logging facies and sedimentary structure attribute of outcrop. The concept of “wetland” is put forward for the first time. The provenance direction of Badaowan and Qigu formation is obtained by the geology setting, sedimentary setting and paleocurrent direction. The paper obtains the profile and plain maps of the sedimentary facies from the sand value of the wells and the sand thickness maps from the logging constrained inversion. Then, this paper takes characteristics and control factors of the Jurassic reservoirs analysis on thin section observation, scanning transmission electron microscope observation and find out the petrology characteristics of reservoir, space types of reservoir and lithofacies division. In this area, primary pores dominate in the reservoir pores, which believed that sedimentation played the most important roles of the reservoir quality and diagenesis is the minor factor influencing secondary porosity. Using stochastic modeling technique，the paper builds quantitative 3-D reservoir Parameter. Finally, combined the study of structure and reservoir formation, the reservoir distribution regularity is concluded: (a) structures control the reservoir formation and accumulation. (b) Locating in the favorable sedimentary facies belt. And the area which meets these conditions mentioned above is a good destination for exploration.

胜利油田低渗透砂岩油藏非均质地质建模

Guided by geological theories, the author analyzed factual informations and applied advanced technologies including logging reinterpretation, predicting of fractal-based fracture network system and stochastic modeling to the low permeable sandstone reservoirs in Shengli oilfield. A new technology suitable for precious geological research and 3D heterogeneity modeling was formed through studies of strata precious correlation, relation between tectonic evolution and fractural distribution, the control and modification of reservoirs diagenesis, logging interpretation mathematical model, reservoir heterogeneity, and so on. The main research achievements are as follows: (1) Proposed four categories of low permeable reservoirs, which were preferable, general, unusual and super low permeable reservoir, respectively; (2) Discussed ten geological features of the low permeable reservoirs in Shengli area; (3) Classified turbidite fan of Es_3 member of the Area 3 in Bonan oilfield into nine types of lithological facies, and established the facies sequences and patterns; (4) Recognized that the main diagenesis were compaction, cementation and dissolution, among which the percent compaction was up to 50%~90%; (5) Divided the pore space in ES_3 member reservoir into secondary pores with dissolved carbonate cement and residual intergranular pores strongly compacted and cemented; (6) Established logging interpretation mathematical model guided by facies- control modeling theory; (7) Predicted the fracture distribution in barriers using fractal method; (8) Constructed reservoir structural model by deterministic method and the 3D model of reservoir parameters by stochastic method; (9) Applied permeability magnitudes and directions to describe the fractures' effect on fluid flow, and presented four different fractural configurations and their influence on permeability; (10) Developed 3D modeling technology for the low permeable sandstone reservoirs. The research provided reliable geological foundation for the establishment and modification of development plans in low permeable sandstone reservoirs, improved the development effect and produced more reserves, which provided technical support for the stable and sustained development of Shengli Oilfield.

Explaining young mortality

Stochastic modeling of mortality rates focuses on fitting linear models to logarithmically adjusted mortality data from the middle or late ages. Whilst this modeling enables insurers to project mortality rates and hence price mortality products it does not provide good fit for younger aged mortality. Mortality rates below the early 20's are important to model as they give an insight into estimates of the cohort effect for more recent years of birth. It is also important given the cumulative nature of life expectancy to be able to forecast mortality improvements at all ages. When we attempt to fit existing models to a wider age range, 5-89, rather than 20-89 or 50-89, their weaknesses are revealed as the results are not satisfactory. The linear innovations in existing models are not flexible enough to capture the non-linear profile of mortality rates that we see at the lower ages. In this paper we modify an existing 4 factor model of mortality to enable better fitting to a wider age range, and using data from seven developed countries our empirical results show that the proposed model has a better fit to the actual data, is robust, and has good forecasting ability.

Modelo estocástico para dados GNSS e séries temporais de coordenadas GNSS

Pós-graduação em Ciências Cartográficas - FCT

Contextualização deposicional da formação Rio Claro no município de Paulínia/SP empregando simulações estocásticas

The Rio Claro Formation, Tertiary-Quaternary age, is composed of unconsolidated sediments deposited by fluvial systems. In Paulínia (SP) region geological studies comprising sedimentological, structural and geomorphological aspects indicate that the Rio Claro Formation is constituted by deposits of a meandering fluvial system. Data from SPT drillings were used to obtain sedimentary textural information in order to generate stochastic stratigraphic models. Particle size analysis was carried with the core samples which resulted in the distinction of five litofacies, three of which can be grouped into only one mudstone unit. The other two facies represent channel belt facies, being clayey sands and medium to coarse sands. Geostatistical modeling of the stratigraphic architecture followed together with correlation of analogue outcrop data and conceptual models for this type of depositional system. 100 models were generated with the SPT drillings and 50 models were generated with data from an analogue outcrop, which allowed constraining of both simulation sets to the depositional model given for the region. T-PROGS methodology has good applicability in simulating stratigraphic frameworks and its inherent limitations may be approached with parallel studies, such as stochastic modeling of analogue outcrops or geophysical methods