Pierre Gérard-Marchant

Bio: Pierre Gérard-Marchant is an academic researcher from University of Georgia. The author has contributed to research in topics: Surface runoff & Runoff curve number. The author has an hindex of 13, co-authored 16 publications receiving 3757 citations. Previous affiliations of Pierre Gérard-Marchant include Cornell University.

Array programming with NumPy

Abstract: Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves1 and in the first imaging of a black hole2. Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis. NumPy is the primary array programming library for Python; here its fundamental concepts are reviewed and its evolution into a flexible interoperability layer between increasingly specialized computational libraries is discussed.

Array Programming with NumPy

Abstract: Array programming provides a powerful, compact, expressive syntax for accessing, manipulating, and operating on data in vectors, matrices, and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It plays an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, material science, engineering, finance, and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves and the first imaging of a black hole. Here we show how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring, and analyzing scientific data. NumPy is the foundation upon which the entire scientific Python universe is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Because of its central position in the ecosystem, NumPy increasingly plays the role of an interoperability layer between these new array computation libraries.

A soil-water-balance approach to quantify groundwater recharge from irrigated cropland in the North China Plain

Abstract: Rapidly depleting unconfined aquifers are the primary source of water for irrigation on the North China Plain. Yet, despite its critical importance, groundwater recharge to the Plain remains an enigma. We introduce a one-dimensional soil-water-balance model to estimate precipitation- and irrigation-generated areal recharge from commonly available crop and soil characteristics and climate data. To limit input data needs and to simplify calculations, the model assumes that water flows vertically downward under a unit gradient; infiltration and evapotranspiration are separate, sequential processes; evapotranspiration is allocated to evaporation and transpiration as a function of leaf-area index and is limited by soil-moisture content; and evaporation and transpiration are distributed through the soil profile as exponential functions of soil and root depth, respectively. For calibration, model-calculated water contents of I I soil-depth intervals from 0 to 200 cm were compared with measured water contents of loam soil at four sites in Luancheng County, Hebei Province, over 3 years (1998-2001). Each 50-m(2) site was identically cropped with winter wheat and summer maize, but received a different irrigation treatment. Average root mean-squared error between measured and model-calculated water content of the top 180 cm was 4.2 cm, or 9.3% of average total water content. In addition, model-calculated evapotranspiration compared well with that measured by a large-scale lysimeter. To test the model, 12 additional sites were simulated successfully. Model results demonstrate that drainage from the soil profile is not a constant fraction of precipitation and irrigation inputs, but rather the fraction increases as the inputs increase. Because this drainage recharges the underlying aquifer, improving irrigation efficiency by reducing seepage will not reverse water-table declines. Copyright (C) 2003 John Wiley Sons, Ltd.

Using a topographic index to distribute variable source area runoff predicted with the SCS curve-number equation

Abstract: Because the traditional Soil Conservation Service curve-number (SCS-CN) approach continues to be used ubiquitously in water quality models, new application methods are needed that are consistent with variable source area (VSA) hydrological processes in the landscape. We developed and tested a distributed approach for applying the traditional SCS-CN equation to watersheds where VSA hydrology is a dominant process. Predicting the location of source areas is important for watershed planning because restricting potentially polluting activities from runoff source areas is fundamental to controlling non-point-source pollution. The method presented here used the traditional SCS-CN approach to predict runoff volume and spatial extent of saturated areas and a topographic index, like that used in TOPMODEL, to distribute runoff source areas through watersheds. The resulting distributed CN–VSA method was applied to two subwatersheds of the Delaware basin in the Catskill Mountains region of New York State and one watershed in south-eastern Australia to produce runoff-probability maps. Observed saturated area locations in the watersheds agreed with the distributed CN–VSA method. Results showed good agreement with those obtained from the previously validated soil moisture routing (SMR) model. When compared with the traditional SCS-CN method, the distributed CN–VSA method predicted a similar total volume of runoff, but vastly different locations of runoff generation. Thus, the distributed CN–VSA approach provides a physically based method that is simple enough to be incorporated into water quality models, and other tools that currently use the traditional SCS–CN method, while still adhering to the principles of VSA hydrology. Copyright  2004 John Wiley & Sons, Ltd.

Highly accurate protein structure prediction with AlphaFold

Abstract: Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort1–4, the structures of around 100,000 unique proteins have been determined5, but this represents a small fraction of the billions of known protein sequences6,7. Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence—the structure prediction component of the ‘protein folding problem’8—has been an important open research problem for more than 50 years9. Despite recent progress10–14, existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14)15, demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm. AlphaFold predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture.

The Observation of Gravitational Waves from a Binary Black Hole Merger

Abstract: On September 14, 2015 at 09:50:45 UTC the two detectors of the Laser Interferometer Gravitational-Wave Observatory simultaneously observed a transient gravitational-wave signal. The signal sweeps upwards in frequency from 35 to 250 Hz with a peak gravitational-wave strain of 1.0×10(-21). It matches the waveform predicted by general relativity for the inspiral and merger of a pair of black holes and the ringdown of the resulting single black hole. The signal was observed with a matched-filter signal-to-noise ratio of 24 and a false alarm rate estimated to be less than 1 event per 203,000 years, equivalent to a significance greater than 5.1σ. The source lies at a luminosity distance of 410(-180)(+160) Mpc corresponding to a redshift z=0.09(-0.04)(+0.03). In the source frame, the initial black hole masses are 36(-4)(+5)M⊙ and 29(-4)(+4)M⊙, and the final black hole mass is 62(-4)(+4)M⊙, with 3.0(-0.5)(+0.5)M⊙c(2) radiated in gravitational waves. All uncertainties define 90% credible intervals. These observations demonstrate the existence of binary stellar-mass black hole systems. This is the first direct detection of gravitational waves and the first observation of a binary black hole merger.

The Soil and Water Assessment Tool: Historical Development, Applications, and Future Research Directions

Abstract: The Soil and Water Assessment Tool (SWAT) model is a continuation of nearly 30 years of modeling efforts conducted by the USDA Agricultural Research Service (ARS). SWAT has gained international acceptance as a robust interdisciplinary watershed modeling tool as evidenced by international SWAT conferences, hundreds of SWAT-related papers presented at numerous other scientific meetings, and dozens of articles published in peer-reviewed journals. The model has also been adopted as part of the U.S. Environmental Protection Agency (USEPA) Better Assessment Science Integrating Point and Nonpoint Sources (BASINS) software package and is being used by many U.S. federal and state agencies, including the USDA within the Conservation Effects Assessment Project (CEAP). At present, over 250 peer-reviewed published articles have been identified that report SWAT applications, reviews of SWAT components, or other research that includes SWAT. Many of these peer-reviewed articles are summarized here according to relevant application categories such as streamflow calibration and related hydrologic analyses, climate change impacts on hydrology, pollutant load assessments, comparisons with other models, and sensitivity analyses and calibration techniques. Strengths and weaknesses of the model are presented, and recommended research needs for SWAT are also provided.

Soil and Water Assessment Tool: Historical Development, Applications, and Future Research Directions, The

Abstract: The Soil and Water Assessment Tool (SWAT) model is a continuation of nearly 30 years of modeling efforts conducted by the U.S. Department of Agriculture (USDA), Agricultural Research Service. SWAT has gained international acceptance as a robust interdisciplinary watershed modeling tool, as evidenced by international SWAT conferences, hundreds of SWAT-related papers presented at numerous scientific meetings, and dozens of articles published in peer-reviewed journals. The model has also been adopted as part of the U.S. Environmental Protection Agency's BASINS (Better Assessment Science Integrating Point & Nonpoint Sources) software package and is being used by many U.S. federal and state agencies, including the USDA within the Conservation Effects Assessment Project. At present, over 250 peer-reviewed, published articles have been identified that report SWAT applications, reviews of SWAT components, or other research that includes SWAT. Many of these peer-reviewed articles are summarized here according to relevant application categories such as streamflow calibration and related hydrologic analyses, climate change impacts on hydrology, pollutant load assessments, comparisons with other models, and sensitivity analyses and calibration techniques. Strengths and weaknesses of the model are presented, and recommended research needs for SWAT are provided.