Journal Articles

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    Nigel W.T. Quinn, Olga Epshtein
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    ABSTRACT: One major challenge in water resource management is the estimation of evapotranspiration losses from seasonally managed wetlands. Quantifying these losses is complicated by the dynamic nature of the wetlands’ areal footprint during the periods of flood-up and drawdown. We present a data-lean solution to problem using an example application in the San Joaquin Basin, California. Through analysis of high-resolution Landsat Enhanced Thematic Mapper Plus (ETMþ) satellite imagery, we develop a metric to better capture the extent of total flooded wetland area. The procedure is validated using year-long, continuously-logged field datasets for two wetlands within the study area. The proposed classification which uses a Landsat ETM þ Band 5 (mid-IR wavelength) to Band 2 (visible green wavelength) ratio improves estimates by 30e50% relative to previous wetland delineation studies. Requiring modest ancillary data, the study results provide a practical and efficient option for wetland management in data sparse regions or un-gauged watersheds.
    Environmental Modelling and Software 04/2014; 54(April):9-23. · 3.48 Impact Factor
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    ABSTRACT: Real-time salinity management (RTSM) has been advocated as a means of improving compliance with San Joaquin River salinity objectives by improving the coordination of west-side agricultural and wetland dischargers of salt with reservoir releases flows made along east-side tributaries. RTSM is a concept that relies upon access to real-time flow and electrical conductivity data from networks of sensors located along the San Joaquin River and its major tributaries. RTSM provides timely decision support to agricultural water districts and seasonal wetland managers - allowing them to improve the coordination of salt load export with the available assimilative capacity of the San Joaquin River . An Environmental Decision Support System is under development which combines watershed flow and water quality monitoring, modelling, salt assimilative capacity forecasting and web-based information dissemination and sharing.
    12/2013;
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    ABSTRACT: In 2010, the California Energy Commission, via its PIER program, commissioned a study to evaluate the potential impact of large-scale CO2 sequestration in California, with specific focus on the water resources in the southern San Joaquin River Valley. The study work comprised two distinct, but related projects: The first project utilized production and pressure data from oil reservoirs in the San Joaquin Valley as a reverse analog to the potential pressure impact of CO2 injection. Results from this project are summarized in a companion report. The second project investigated (via simulation studies) whether the basin-scale pressure changes and brine displacement caused by future CO2 storage in the deep sediments could have an impact on the groundwater-surface water systems in the area. The current report summarizes the simulation studies conducted in the second project. The objective of this second project was to address the following questions: • Will vertical pressure propagation through thick layers of shale and sands have a significant impact on shallow water resources? • Is brine displacement an issue through thick layers of shale and sands for shallow water resources? • What deformations are to be expected from deep CO2 storage, and would land surface uplift be a concern for shallow water resources? In 2010, the California Energy Commission, via its PIER program, commissioned a study to evaluate the potential impact of large-scale CO2 sequestration in California, with specific focus on the water resources in the southern San Joaquin River Valley. The study work comprised two distinct, but related projects: The first project utilized production and pressure data from oil reservoirs in the San Joaquin Valley as a reverse analog to the potential pressure impact of CO2 injection. Results from this project are summarized in a companion report. The second project investigated (via simulation studies) whether the basin-scale pressure changes and brine displacement caused by future CO2 storage in the deep sediments could have an impact on the groundwater-surface water systems in the area. The current report summarizes the simulation studies conducted in the second project. The objective of this second project was to address the following questions: • Will vertical pressure propagation through thick layers of shale and sands have a significant impact on shallow water resources? • Is brine displacement an issue through thick layers of shale and sands for shallow water resources? • What deformations are to be expected from deep CO2 storage, and would land surface uplift be a concern for shallow water resources? In 2010, the California Energy Commission, via its PIER program, commissioned a study to evaluate the potential impact of large-scale CO2 sequestration in California, with specific focus on the water resources in the southern San Joaquin River Valley. The study work comprised two distinct, but related projects: The first project utilized production and pressure data from oil reservoirs in the San Joaquin Valley as a reverse analog to the potential pressure impact of CO2 injection. Results from this project are summarized in a companion report. The second project investigated (via simulation studies) whether the basin-scale pressure changes and brine displacement caused by future CO2 storage in the deep sediments could have an impact on the groundwater-surface water systems in the area. The current report summarizes the simulation studies conducted in the second project.In 2010, the California Energy Commission, via its PIER program, commissioned a study to evaluate the potential impact of large-scale CO2 sequestration in California, with specific focus on the water resources in the southern San Joaquin River Valley. The study work comprised two distinct, but related projects: The first project utilized production and pressure data from oil reservoirs in the San Joaquin Valley as a reverse analog to the potential pressure impact of CO2 injection. Results from this project are summarized in a companion report. The second project investigated (via simulation studies) whether the basin-scale pressure changes and brine displacement caused by future CO2 storage in the deep sediments could have an impact on the groundwater-surface water systems in the area.
    10/2013;
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    Nigel W T Quinn, Lisa Holm
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    ABSTRACT: The San Joaquin River is a salinity impaired water-body and one of the most highly regulated rivers in the nation. An innovative option promoted by the salinity TMML (Total Maximum Monthly Load) for the lower San Joaquin River Basin requires continuous forecasting of salt assimilative capacity and real-time coordination of salt load discharges and east-side tributary dilution flow releases in order to improve compliance with downstream salinity objectives. This paper discusses four key elements of real-time salinity management which address (a) sensor and data acquisition technology -sensors, telemetry, remote sensing; (b) information technology -databases, water quality simulation modeling, flow and salinity forecasting, quality assurance procedures; (c) technology transfer -adaptive decision support system development, stakeholder adoption, coordination and cooperation activities; and (d) sustainability – long-term implementation, governance and institutional issues. The paper reviews progress to date and discusses some of the challenges, successes and failures in developing the conceptual model for real-time salinity monitoring and management and the implications for future TMMLs (and TMDLs) for other pollutants of concern in the San Joaquin River Basin (SJRB).
    ASCE EWRI Conference, Cincinnatti, OH. May 19-23, 2013. Berkeley National Laboratory Topical Report - LBL -. 05/2013;
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    ABSTRACT: Integrated environmental modeling (IEM) is inspired by modern environmental problems, decisions, and policies and enabled by transdisciplinary science and computer capabilities that allow the environment to be considered in a holistic way. The problems are characterized by the extent of the environmental system involved, dynamic and interdependent nature of stressors and their impacts, diversity of stakeholders, and integration of social, economic, and environmental considerations. IEM provides a science-based structure to develop and organize relevant knowledge and information and apply it to explain, explore, and predict the behavior of environmental systems in response to human and natural sources of stress. During the past several years a number of workshops were held that brought IEM practitioners together to share experiences and discuss future needs and directions. In this paper we organize and present the results of these discussions. IEM is presented as a landscape containing four interdependent elements: applications, science, technology, and community. The elements are described from the perspective of their role in the landscape, current practices, and challenges that must be addressed. Workshop participants envision a global scale IEM community that leverages modern tech-nologies to streamline the movement of science-based knowledge from its sources in research, through its organization into databases and models, to its integration and application for problem solving purposes. Achieving this vision will require that the global community of IEM stakeholders transcend social, and organizational boundaries and pursue greater levels of collaboration. Among the highest priorities for community action are the development of standards for publishing IEM data and models in forms suitable for automated discovery, access, and integration; education of the next generation of environmental stakeholders, with a focus on transdisciplinary research, development, and decision making; and providing a web-based platform for community interactions (e.g., continuous virtual workshops).
    Environmental Modelling and Software 01/2013; 39:3-23. · 3.48 Impact Factor
  • N.W.T. Quinn, O. Epshtein
    Journal of Environmental Modeling and Software. 01/2013;
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    Olga Epshtein, Nigel W.T. Quinn
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    ABSTRACT: Seasonally managed wetlands experience an annual cycle of inundation and drainage driving multiple ecohydrologic fluxes; while the effects of this seasonality propagate through the watershed, spatial changes in the wetland tract itself remain poorly quantified at large scales and for spatially irregular wetland networks. Remote sensing offers the potential to track temporal changes in wetland hydrology, chemistry, and vegetation dynamics, thereby accounting for fluxes in water and constituent cycling.
    Office of Science, Summer Undergraduate Laboratory Internship (SULI) Program. 08/2012;
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    ABSTRACT: We demonstrate a simple high-throughput single-cell approach that exploits the ultrahigh brightness and non-invasive nature of synchrotron infrared beam to characterize strains of the cyanobacterium Synechocystis 6803 (S. 6803) constructed with altered metabolic traits affecting the acyl-CoA pool. Their metabolic responses to the modified traits were phenotyped by single-cell synchrotron radiation Fourier transform infrared (SR-FTIR) spectromicroscopy and multivariate analysis. SR-FTIR difference spectra and cluster vector plots segregated the strains as phenotypic populations based on signals in the hydrocarbon and biomolecular fingerprint regions, although each population incorporated a stochastic distribution of cells with different metabolic properties. All engineered strains exhibited an increase in FTIR features attributed to functional groups in hydrocarbon, fatty acid (FA), and/or FA ester chains, and a decrease in polysaccharide features. The metabolic signatures obtained by SR-FTIR were consistent with detailed qualitative and quantitative metabolic information provided in GC/MS/NMR data. A strain with extra copies of the FAR and FAD genes, encoding, respectively, the fatty acyl-ACP reductase and fatty aldehyde decarbonylase enzymes in the alkane biosynthesis pathway, showed up to a fivefold increase in the intracellular levels of heptadecane, a threefold increase in 9-heptadecene, and a significant increase in secreted 16:0 and 18:0 free FAs (FFAs). Inactivation of the AAS gene, encoding acyl-ACP synthetase, prevented re-thioesterification of FFAs generated from membrane lipid recycling and led to elevated levels and of intracellular FFAs of an altered composition, and a decrease in heptadecane and secreted FFAs. Introduction of a FatB gene, encoding a thioesterase (TE), which catalyzes the liberation of FFAs from acyl-ACP, yielded little effect in itself. However, the activity of the TE enzyme was clearly manifested in combination with AAS inactivation; A TE-containing train lacking AAS showed a dramatic (30-fold) increase in intracellular FFAs (with the majority being 16:0) and increases in heptadecane and secreted FFAs.
    Applied Energy. 01/2012;
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    International Journal of Remote Sensing 01/2012; 33(16):4902-4918. · 1.36 Impact Factor
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    Nigel William Trevelyan Quinn, Ric Ortega, Patrick Rahilly, Charles B. Johnson
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    ABSTRACT: The project has provided science-based tools for the long-term management of salinity in drainage discharges from wetlands to the SJR. The results of the project are being used to develop best management practices (BMP) and a decision support system to assist wetland managers adjust the timing of salt loads delivered to the San Joaquin River during spring drawdown. Adaptive drainage management scheduling has the potential to improve environmental compliance with salinity objectives in the Lower San Joaquin River by reducing the frequency of violation of Vernalis salinity standards, especially in dry and critically dry years. The paired approach to project implementation whereby adaptively managed and traditional practices were monitored in a side-by-side fashion has provided a quantitative measure of the impacts of the project on the timing of salt loading to the San Joaquin River. The most significant accomplishments of the project has been the technology transfer to wetland biologists, ditch tenders and water managers within the Grasslands Ecological Area. This “learning by doing” has build local community capacity within the Grassland Water District and California Department of Fish and Game providing these institutions with new capability to assess and effectively manage salinity within their wetlands while simultaneously providing benefits to salinity management of the San Joaquin River.
    LBNL Report; Final Report - California Department of Water Resources under Agreement No. 4600003430. 12/2011;
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    ABSTRACT: Despite the perceived value of DSS in informing environmental and natural resource management, DSS tools often fail to be adopted by intended end users. By drawing together the experience of a global group of EDSS developers, we have identified and assessed key challenges in EDSS development and offer recommendations to resolve them. Challenges related to engaging end users in EDSS development emphasise the need for a participatory process that embraces end users and stakeholders throughout the design and development process. Adoption challenges concerned with individual and organisational capacities to use EDSS and the match between EDSS and organisational goals can be overcome through the use of an internal champion to promote the EDSS at different levels of a target organisation; co-ordinate and build capacity within the organisation, and; ensure that developers maintain focus on developing EDSS which are relatively easy and inexpensive to use and update (and which are perceived as such by the target users). Significant challenges exist in relation to ensuring EDSS longevity and financial sustainability. Such business challenges may be met through planning and design that considers the long-term costs of training, support, and maintenance; revenue generation and licensing by instituting processes which support communication and interactions; and by employing software technology which enables easy model expansion and re use to gain an economy of scale and reduce development costs. A final group of perhaps more problematic challenges relate to how the success of EDSS ought to be evaluated. Whilst success can be framed relatively easily in terms of interactions with end users, difficulties of definition and measurability emerge in relation to the extent to which EDSS achieve intended outcomes. To tackle the challenges described, the authors provide a set of best practice recommendations concerned with promoting design for ease of use, design for usefulness, establishing trust and credibility, promoting EDSS acceptance, and starting simple and small in functionality terms. Following these recommendations should enhance the achievement of successful EDSS adoption, but more importantly, help facilitate the achievement of desirable social and environmental outcomes.
    Environmental Modelling and Software 12/2011; 26(12):1389–1402. · 3.48 Impact Factor
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    ABSTRACT: Plant-derived oil, whether from terrestrially-produced oilseeds or aquatic algae, represent an 9 important feedstock for liquid fuels. With the advent of the biodiesel industry over the past 10 decade, a supply chain has been established, linking agricultural oilseed production to the 11 transportation fuel market. Largely supply-side driven, and based on the availability and scale of 12 soybean production, this initial supply chain is currently challenged by policy and related 13 economic, environmental, and energy-related performance. These challenges are being met with 14 new approaches coming from research and development. New sources and production methods 15 for plant-derived oils, the creation of regional supply chains matching sources and uses, 16 improvements in conversion of oils-to-fuels to include new classes of “drop in replaceable” 17 fuels, and the creation of a customer-driven pull are all being explored in the creation of 18 sustainable biofuel production.
    Soil and Water Conservation Society. 06/2011;
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    N.W.T. Quinn
    Agricultural Water Management 04/2011; 98:930-940. · 2.33 Impact Factor
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    ABSTRACT: Environmental sensor networks enjoy widespread deployment as monitoring sys-tems have become easier to design and implement in the field and installation costs have fallen. Unfortunately software systems for data quality assurance have not kept pace with the development of these sensor network technologies and risk compromising the potential of these innovative systems by making it difficult to assess the accuracy and consistency of the data. Lingering uncertainty can constrain the willingness of stakeholders to make operational decisions on the basis of the real-time sensor data – a few negative experiences can do irreparable damage to a project which is attempting to change stakeholder behavior. Successful management of river salt loads in complex and highly regulated river basins such as the San Joaquin Valley of California presents significant challenges to Information Technology infrastructure within resource management agencies that have a poor history of coordination and data sharing. Past attempts at developing web-based environmental data resources to address salinity issues have failed in large part due to a fear of loss of autonomy, quality assurance and data reliability issues. This paper describes a new approach to environmental decision support for salinity management in the San Joaquin Basin of California that focuses on web-based data sharing using YSI Econet technology and continuous data quality management using a novel software tool, Aquarius. Commercial turn-key monitoring systems such as YSI EcoNet provide real-time web-access to sensor data as well as providing the owner full control over the way the data is visualized. The same web-sites use GIS to superimpose the monitoring site locations on maps and local hydrography and allow point and click access to the data collected at each environmental monitoring site. This Information Technology suite of software and hardware work together to provide timely, reliable and high quality data in a manner that can used by stakeholder decision makers to better manage salt export to the San Joaquin River and ensure compliance with State water quality objectives.
    Decision Support Systems in Agriculture, Food and the Environment: Trends, Applications and Advances. 01/2011;
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    Nigel W.T. Quinn
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    ABSTRACT: Pollutant trading schemes are market-based strategies that can provide cost-effective and flexible environmental compliance in large river basins. The aim of this paper is to contrast two innovative adaptive strategies for salinity management have been developed in the Hunter River Basin, New South Wales, Australia and in the San Joaquin River Basin, California, USA, respectively. In both instances web-based stakeholder information dissemination has been a key to achieving a high level of stakeholder involvement and the formulation of effective decision support tools for salinity management. A common element to implementation of salinity management strategies in both the Hunter River and San Joaquin River basins has been the concept of river assimilative capacity as a guide for controlling export salt loading and the establishment of a framework for trading of the right to discharge salt load to the Hunter River and San Joaquin River respectively. Both rivers provide basin drainage and the means of exporting salt load to the ocean. The paper compares the opportunities and constraints governing salinity management in the two basins as well as the use of monitoring, modeling and information technology to achieve environmental compliance and sustain irrigated agriculture in an equitable, socially and politically acceptable manner. The paper concludes by placing into broader context some of the issues raised by the comparison of the two approaches to basin salinity management.
    Agricultural Water Management 01/2011; 98(6):930-940. · 2.33 Impact Factor
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    ABSTRACT: This report assesses the economics of microalgae biofuels production through an analysis of five production scenarios. These scenarios, or cases, are based on technologies that currently exist or are expected to become available in the near-term, including raceway ponds for microalgae cultivation, bioflocculation for algae harvesting, and hexane for extraction of algae oil. Process flow diagrams, facility site layouts, and estimates for the capital and operations costs of each case were developed de novo. This report also reviews current and developing microalgae biofuel technologies for both oil and biogas production, provides an initial assessment of the US and California resource potential for microalgae biofuels, and recommends specific R&D efforts to advance the feasibility of large-scale algae biofuel production.
    Energy Biosciences Institute Topical Report. 10/2010;
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    Nigel W.T. Quinn
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    ABSTRACT: The mantra that successful Environmental Decision Support Systems (EDSS’s) are those that benefit from a high level of end-user involvement during the design phase and subsequent implementation is well founded. However the practical matter of eliciting the relevant information from stakeholders to develop a useful and robust EDSS is rarely adequate and this weakness contributes to the high rate of failed EDSS’s. Stakeholders sometimes have difficulty articulating the decisions they are called upon to make and cannot definitely describe the bounds of the decision space within which they operate. The EDSS developer is challenged by having to understand the system he/she is attempting to simulate to the same degree as the stakeholder. Environmental Information Management Systems (EIMS’s) have a better record of success than EDSS’s, though the distinction between the two is often blurry since information needs to organized and presented in an appropriate manner to inform decision making. The “handshake” between the stakeholder user of the EDSS and the EDSS itself is one of the most difficult features to determine. In the agricultural salinity management arena EDSS’s do not appear to have a high rate of adoption. However there have been very successful EIMS’s – some of which have user communities that number in the thousands. Perhaps the answer is to use the EIMS as a stepping stone to developing a fully functional EDSS. This paper examines a number of failed EDSS projects and compares and contrasts these systems with successful EIMS projects. The paper suggests some lessons for future EDSS initiatives.
    Proceedings International Environmental Modelling and Software Society, Ottawa, Canada. 07/2010;
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    SWRCB Report. 07/2010;
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    CALFED Report. 06/2010;
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    ABSTRACT: Management of river salt loads in a complex and highly regulated river basin such as the San Joaquin River Basin of California presents significant challenges for current Information Technology. Computer-based numerical models are used as a means of simulating hydrologic processes and water quality within the basin and can be useful tools for organizing Basin data in a structured and readily accessible manner. These models can also be used to extend information derived from environmental sensors within existing monitoring networks to areas outside these systems based on similarity factors – since it would be cost prohibitive to collect data for every channel or pollutant source within the Basin. A common feature of all hydrologic and water quality models is the ability to perform mass balances. This paper describes the use of a number of state-of-the-art sensor technologies that have been deployed to obtain water and salinity mass balances for a 60,000 ha tract of seasonally managed wetlands in the San Joaquin River Basin of California. These sensor technologies are being combined with more traditional environmental monitoring techniques to support real-time salinity management (RTSM) in the River Basin. Two of these new technology applications: YSI-Econet (which supports continuous flow and salinity monitoring of surface water deliveries and seasonal wetland drainage); and electromagnetic salinity mapping (a remote sensing technology for mapping soil salinity in the surface soils) – have not previously been reported in the literature. Continuous sensor deployments that experience more widespread use include: weather station sensor arrays – used to estimate wetland pond evaporation and moist soil plant evapotranspiration; high resolution multi-spectral imagery – used to discriminate between and estimate the area of wetland moist soil plant vegetation; and groundwater level sensors – used primarily to estimate seepage losses beneath a wetland pond during flood-up. Important issues associated with quality assurance of continuous data are discussed and the application of a state-of-the-art software product AQUARIUS, which streamlines the process of data error correction and dissemination, is described as an essential element of ensuring successful RTSM implementation in the San Joaquin River Basin.
    Environmental Modelling & Software. 01/2010;

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