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NASA NTRS1993

A global multilevel atmospheric model using a vector semi-Lagrangian finite-difference scheme. I - Adiabatic formulation

An adiabatic global multilevel primitive equation model using a two time-level, semi-Lagrangian semi-implicit finite-difference integration scheme is presented. A Lorenz grid is used for vertical discretization and a C grid for the horizontal discretization. The momentum equation is discretized in vector form, thus avoiding problems near the poles. The 3D model equations are reduced by a linear transformation to a set of 2D elliptic equations, whose solution is found by means of an efficient direct solver. The model (with minimal physics) is integrated for 10 days starting from an initialized state derived from real data. A resolution of 16 levels in the vertical is used, with various horizontal resolutions. The model is found to be stable and efficient, and to give realistic output fields. Integrations with time steps of 10 min, 30 min, and 1 h are compared, and the differences are found to be acceptable.

Bates, J. R.↗

DOE OSTI2019

Predicting sedimentary bedrock subsurface weathering fronts and weathering rates

Although bedrock weathering strongly influences water quality and global carbon and nitrogen budgets, the weathering depths and rates within subsurface are not well understood nor predictable. Determination of both porewater chemistry and subsurface water flow are needed in order to develop more complete understanding and obtain weathering rates. In a long-term field study, we applied a multiphase approach along a mountainous watershed hillslope transect underlain by marine shale. Here we report three findings. First, the deepest extent of the water table determines the weathering front, and the range of annually water table oscillations determines the thickness of the weathering zone. Below the lowest water table, permanently water-saturated bedrock remains reducing, preventing deeper pyrite oxidation. Secondly, carbonate minerals and potentially rock organic matter share the same weathering front depth with pyrite, contrary to models where weathering fronts are stratified. Thirdly, the measurements-based weathering rates from subsurface shale are high, amounting to base cation exports of about 70 kmol c ha -1 y -1 , yet consistent with weathering of marine shale. Finally, by integrating geochemical and hydrological data we present a new conceptual model that can be applied in other settings to predict weathering and water quality responses to climate change.

58 GEOSCIENCES↗

NASA NTRS2010

Atmospheric Risk Assessment for the Mars Science Laboratory Entry, Descent, and Landing System

In 2012, the Mars Science Laboratory (MSL) mission will pioneer the next generation of robotic Entry, Descent, and Landing (EDL) systems, by delivering the largest and most capable rover to date to the surface of Mars. As with previous Mars landers, atmospheric conditions during entry, descent, and landing directly impact the performance of MSL's EDL system. While the vehicle's novel guided entry system allows it to "fly out" a range of atmospheric uncertainties, its trajectory through the atmosphere creates a variety of atmospheric sensitivities not present on previous Mars entry systems and landers. Given the mission's stringent landing capability requirements, understanding the atmosphere state and spacecraft sensitivities takes on heightened importance. MSL's guided entry trajectory differs significantly from recent Mars landers and includes events that generate different atmospheric sensitivities than past missions. The existence of these sensitivities and general advancement in the state of Mars atmospheric knowledge has led the MSL team to employ new atmosphere modeling techniques in addition to past practices. A joint EDL engineering and Mars atmosphere science and modeling team has been created to identify the key system sensitivities, gather available atmospheric data sets, develop relevant atmosphere models, and formulate methods to integrate atmosphere information into EDL performance assessments. The team consists of EDL engineers, project science staff, and Mars atmospheric scientists from a variety of institutions. This paper provides an overview of the system performance sensitivities that have driven the atmosphere modeling approach, discusses the atmosphere data sets and models employed by the team as a result of the identified sensitivities, and introduces the tools used to translate atmospheric knowledge into quantitative EDL performance assessments.

EDL↗

DOE OSTI2022

SDSS-IV MaNGA: pyPipe3D Analysis Release for 10,000 Galaxies

We present here the analysis performed using the pyPipe3D pipeline for the final MaNGA data set included in the Sloan Digital Sky Survey data release 17. This data set comprises more than 10,000 individual data cubes, being the integral field spectroscopic (IFS) galaxy survey with the largest number of galaxies. pyPipe3D processes the IFS data cubes to extract spatially resolved spectroscopic properties of both the stellar population and the ionized gas emission lines. A brief summary of the properties of the sample and the characteristics of the analyzed data are included. The article provides details of: (i) the analysis performed; (ii) a description of the pipeline; (iii) the adopted stellar population library; (iv) the morphological and photometric analysis; (v) the adopted data model for the spatially resolved properties derived; and (vi) the individual integrated and characteristic galaxy properties included in the final catalog. Comparisons with the results from a previous version of the pipeline for earlier data releases and from other tools using this data set are included. A practical example of how to use the full data set and the final catalog illustrates how to handle the delivered product. Our full analysis can be accessed and downloaded from our web page.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

Experimental Design and Laboratory Characterization of a Medium- and High-Efficiency Rooftop Unit for use in Building Energy Simulations

Commercial rooftop units that incorporate variable speed components are quickly entering into the market place; however, the design and modeling tools that calculate the energy benefits of these units cannot properly estimate performance. This is due to two factors: 1) There are insufficient measured performance data of real systems that can be entered into these simulations, and 2) building energy simulators are unable to properly interpret performance data. Therefore, publicly available datasets designed to encompass the entire performance map coupled with control sequence information are needed as inputs for these modelling programs to accurately estimate energy savings and promote variable speed RTUs. As part of the Verification and Uncertainty Characterization for Energy Simulation milestone funded by the Department of Energy, the National Renewable Energy Laboratory recorded and published data across the entire performance range for two commercially available RTUs; one with a two-stage compressor and variable speed supply fan, and another with a fully variable speed compressor, supply fan and condenser fan. This paper details 1) how the design of experiments was created as well as how the units were controlled, and 2) the operational limitations of the two units. The paper will also discuss methods for building energy simulation programs to properly interpret these data sets and integrate them into building energy simulation models.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

NASA NTRSDate not supplied

Atmospheric Variability and Measurement Uncertainty: Pitfalls in Averaging in situ Data

Satellite measurements and atmospheric models, two essential components of the integrated global observing system, provide crucial tools for monitoring and predicting regional and global foci, spanning numerous Earth Science fields. Unfortunately, models can lack the spatial and temporal resolution needed to resolve finer scale structure. Satellite measurements also have similar tempo-spatial restriction issues, but additionally can only measure certain species and can have biases that must be evaluated. Ground measurement networks are critical components of this system, by providing both independent inputs of species needed by models (including those that satellites do not provide) and assisting with investigation of biases in satellite products. Similarly, aircraft measurements play a vital role in closing the gaps between satellite measurements, model products, and ground monitoring networks by providing high accuracy, high-resolution data on local to regional spatial scales. Therefore, both ground-based and airborne observations are widely used to assess model predictions and satellite observations. One of the great challenges in using both ground and aircraft data in this fashion is matching the data temporally and spatially to the model/satellite data. A meaningful comparison with model or satellite requires a solid assessment of the variability of the in-situ measurements, which include both the instrument uncertainty and the statistical uncertainty due to atmospheric variability. While instrument uncertainty is generally more straightforwardly characterized, it can be challenging to accurately capture this variability uncertainty as it often presents in a non-Gaussian manner (e.g. emission plumes, frontal passages). We will present results examining spatial and temporal variability over a selection of scales relevant to satellite measurements and models of several in situ measurement species spanning both airborne and ground measurements. The extent of non-Gaussian variability will be quantified, and we will discuss additional statistical parameters that help assess the fitness of gaussian variability assumption when temporally or spatially averaging.

satellite validation↗

DOE OSTI2026

Regularization by denoising diffusion models for solving inverse PDE problems with application to full waveform inversion

Partial differential equation (PDE)-governed inverse problems are fundamental across various scientific and engineering applications; yet they face significant challenges due to nonlinearity, ill-posedness, and sensitivity to noise. Here, we introduce a computational framework, regularization by denoising using diffusion models for partial differential equations (RED-DiffEq), by integrating physics-driven inversion and data-driven learning. RED-DiffEq leverages pretrained diffusion models as a regularization mechanism for PDE-governed inverse problems. We apply RED-DiffEq to solve the full waveform inversion problem in geophysics, a challenging seismic imaging technique that seeks to reconstruct high-resolution subsurface velocity models from seismic measurement data. Our method shows enhanced accuracy and robustness compared to benchmark methods. Additionally, it exhibits strong generalization and domain decomposition capacity, enabling the inversion of more complex velocity models with larger domains than those used in training the diffusion model. Our framework can also be directly applied to diverse PDE-governed inverse problems.

Shan, Siming [Yale University, New Haven, CT (Unit↗

DOE OSTI2019

A Game-Theoretic Data-Driven Approach for Pseudo-Measurement Generation in Distribution System State Estimation

In this paper, we present an efficient computational framework with the purpose of generating weighted pseudo-measurements to improve the quality of distribution system state estimation (DSSE) and provide observability with advanced metering infrastructure (AMI) against unobservable customers and missing data. The proposed technique is based on a game-theoretic expansion of relevance vector machines (RVMs). This platform is able to estimate the nodal power consumption and quantify its uncertainty while reducing the prohibitive computational burden of model training for large AMI datasets. To achieve this objective, the large training set is decomposed and distributed among multiple parallel learning entities. The resulting estimations from the parallel RVMs are then combined using a game-theoretic model based on the idea of repeated games with vector payoff. It is observed that through this approach and by exploiting the seasonal changes in customers’ behavior the accuracy of pseudo-measurements can be considerably improved, while introducing robustness against bad training data samples. The proposed pseudo-measurement generation model is integrated into a DSSE using a closed-loop information system, which takes advantage of a branch current state estimator (BCSE) to further improve the performance of the designed machine learning framework. This method has been tested on a practical distribution feeder model with smart meter data for verification.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2026

AI-Driven Frameworks for Characterizing Urban Energy Systems

We develop AI-driven frameworks to characterize urban energy systems with the goal of transforming planning by reducing the labor of model generation, scaling scenario exploration, and improving accuracy for localized analysis. The approach integrates top-down and bottom-up data to train different AI models that predict missing information and generate inputs and targeted scenarios for district-scale models. The result is a scalable framework that provides actionable insights for reliable and efficient planning.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

NASA NTRSDate not supplied

Merging Analytic Collaborative Frameworks with New Observing Strategies Toward a Digital Twin: Earth – Episodic Pulse Event Impacts on Ocean Carbon Cycle as an Example

Virtual representations of the Earth will allow us to address some of the most critical environmental issues of our time. Here, we show the first steps toward representation of riverine, estuarine, and coastal carbon processes to enable scenario driven “what-if” analyses of the carbon system and human footprint. Excess sediment and nutrient runoff from land-based human activities impact water quality and can pose serious threats to coastal and marine ecosystems. Episodic pulse events, such as extreme precipitation events, can increase the amount of nutrients entering estuaries and coastal regions, potentially leading to large phytoplankton blooms followed by anoxic conditions. Consequences of coastal runoff are predicted to increase with the higher intensity and frequency of extreme events. Beyond the threat to coastal ecosystems, recent findings suggest these episodic pulses might play a significant role for biological production influencing regional and global carbon fluxes and budgets. An improved understanding of these events through optimal, dynamic observing strategies will increase our knowledge of the land-ocean continuum and how regional events and nutrient fluxes affect the carbon cycle and ocean ecosystem. This conceptual framework enables focused science investigations by pairing data analytics and artificial intelligence tools (otherwise termed an Analytic Center Framework, ACF) with targeted measurement acquisition through distributed sensing and intelligent asset tasking (or New Observing Strategies, NOS). This NOS and ACF iterative approach acquires and integrates complementary and coincident satellite, in-situ and model data to build a more complete and in-depth picture of science phenomena. Specifically, Apache Science Data Analytic Platform (SDAP) is extended to incorporate relevant datasets for data access, harmonized analysis, and anomaly detection. When conditions are met for a likely pulse event, NASA’s D-SHIELD (Distributed Spacecraft with Heuristic Intelligence to Enable Logistical Decisions) tool is triggered to optimize asset overpass frequency and schedule observations for persistent monitoring. Targeted data is ingested by SDAP for enhanced investigation via iterative analysis until the trigger criteria is no longer met - steps toward a digital twin.

Laura Rogers↗

NASA NTRS2019

Fast-Time Simulation for Evaluating the Impact of Estimated Flight Ready Time Uncertainty on Surface Metering

NASA has been developing and demonstrating new concepts and technologies for Integrated Arrival, Departure, and Surface (IADS) traffic management capabilities under the Airspace Technology Demonstration 2 (ATD-2) project. One of the IADS capabilities in the ATD-2 project is surface metering enabled by a tactical surface scheduler to provide controllers with the pushback advisories for departures at gates. The tactical surface scheduler uses the estimated flight ready times provided by airlines, called Earliest Off-Block Times (EOBTs), as input to calculate the target off-block times for pushback advisories. However, the EOBTs are often inaccurate and deviate from the actual flight ready times, which may reduce the benefits of surface metering. In this paper, a linear regression model is developed to model the EOBT uncertainty distribution over time based on actual EOBT data collected at Charlotte airport. This EOBT model is integrated with a tactical surface scheduler and a fast-time simulation tool. To evaluate the impact of the EOBT accuracy on airport surface operations, fast-time simulations are implemented for selected traffic scenarios under different levels of modelled EOBT accuracy. The simulation results show that the EOBT uncertainty affects several performance metrics related to the surface metering, such as gate hold, taxi time reduction, and target takeoff time predictability, which in turn influences ATD-2's scheduler performance.

tactical surface scheduler↗

NASA NTRS2019

Fast-Time Simulation for Evaluating the Impact of Estimated Flight Ready Time Uncertainty on Surface Metering

tactical surface scheduler↗

NASA NTRS1993

Impact of the CO2 and H2O clouds of the Martian polar hood on the polar energy balance

Clouds covering extensive areas above the martian polar caps have regularly been observed during the fall and winter seasons of each hemisphere. These 'polar hoods' are thought to be made of H2O and CO2. In particular, the very cold temperatures observed during the polar night by Viking and Mariner 9 around both poles have been identified as CO2 clouds and several models, including GCM, have indicated that the CO2 can condense in the atmosphere at all polar latitudes. Estimating the impact of the polar hood clouds on the energy balance of the polar regions is necessary to model the CO2 cycle and address puzzling problems like the polar caps assymetry. For example, by altering the thermal radiation emitted to space, CO2 clouds alter the amount of CO2 that condenses during the fall and winter season. The complete set of Viking IRTM data was analyzed to define the spatial and temporal properties of the polar hoods, and how their presence affects the energy radiated by the atmosphere/caps system to space was estimated. The IRTM observations provide good spatial and temporal converage of both polar regions during fall, winter, and spring, when a combination of the first and the second Viking year is used. Only the IRTM brightness temperatures at 11, 15, and 20 microns are reliable at martian polar temperatures. To recover the integrated thermal fluxes from the IRTM data, a simple model of the polar hood, thought to consist of 'warm' H2O clouds lying above colder and opaque CO2 clouds was developed. Such a model is based on the analysis of the IRIS spectra, and is consistent with the IRTM data used.

Forget, Francois↗

DOE OSTI2020

DEEP Solar: Data DrivEn Modeling and Analytics for Enhanced System Layer ImPlementation

Realizing the SETO 2030 mission of reducing solar energy costs to 3-5 c/kWh will require innovative enabling research on effective, cost-efficient integration of local PV within distribution systems. However, the intermittent and variable nature of PVs compels operators to impose conservative hosting capacity constraints. Given the extremely high variability of (intermittent and unpredictable) solar energy generation, relaxing the capacity constraints (which are currently around 15%) and achieving 100% or greater integration of renewables will require a fundamental transformation of the power grid via the utilization of exponentially larger amounts of AMI enabled fine-grained data. To address the challenges in increasing the penetration of renewable energy based DERs, this project envisions an Enhanced System Layer (ESL) at the distribution network level that is reliable, cost-effective and scalable to millions of Distributed Energy Resources (DERs)/devices. This includes developing: 1) Transformative and highly scalable machine learning based predictive analytics tools that plug into distribution system planning and provide real-time situational awareness at the distribution level for short and long-term operational planning. The tools will be built using novel data-driven energy models of millions of active nodes with AMI, 2) Adaptive stochastic analysis and optimization algorithms for real-time grid operations, 3) Dynamic Scenario Analysis using parallel Cloudenabled implementations with < 1 minute computational cycle times.

14 SOLAR ENERGY↗

DOE OSTI2022

IDAC-Bio, A Software for Internal Dosimetry Based on the New ICRP Biokinetic Models and Specific Absorbed Fractions

Radiation dosimetry is central to virtually all radiation safety applications, optimization, and research. It relates to various individuals and population groups and to miscellaneous exposure situations—including planned, existing, and emergency situations. The International Commission on Radiological Protection (ICRP) has developed a new computational framework for internal dose estimations. Important components are more detailed and improved anatomical models and more realistic biokinetic models than before. The ICRP is currently producing new organ dose and effective dose coefficients for occupational intakes of radionuclides (OIR) and environmental intakes of radionuclides (EIR), which supersede the earlier dose coefficients in Publication 68 and the Publication 72 series, respectively. However, the ICRP only publishes dose coefficients for a single acute intake of a radionuclide and for an integration period of 50 years for intake by adults and to age 70 years for intakes by pre-adults. The new software, IDAC-Bio, performs committed absorbed dose and effective dose calculations for a selectable intake scenario, e.g., for a continuous intake or an intake during x hours per day and y days per week, and for any selected integration time. The software uses the primary data and models of the ICRP biokinetic models and numerically solves the biokinetic model and calculates the absorbed doses to organs and tissues in the ICRP reference human phantoms. The software calculates absorbed dose using the nuclear decay data in ICRP publication 107. IDAC-Bio is a further development and an important addition to the internal dosimetry program IDAC-Dose2.1. Here, the results generated by the software were validated against published ICRP dose coefficients. The potential of the software is illustrated by dose calculations for a nuclear power plant worker who had been exposed to varying levels of 60 Co and who had undergone repeated whole-body measurements, and for a hypothetical member of the public subject to future releases of 148 Gd from neutron spallation in tungsten at the European Spallation Source.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2014

Monitoring CO 2 Storage at Cranfield, Mississippi with Time-Lapse Offset VSP – Using Integration and Modeling to Reduce Uncertainty

A time-lapse Offset Vertical Seismic Profile (OVSP) data set was acquired as part of a subsurface monitoring program for geologic sequestration of CO 2 . The storage site at Cranfield, near Natchez, Mississippi, is part of a detailed area study (DAS) site for geologic carbon sequestration operated by the U.S. Dept. of Energy’s Southeast Regional Carbon Sequestration Partnership (SECARB). The DAS site includes three boreholes, an injection well and two monitoring wells. The project team selected the DAS site to examine CO 2 sequestration multiphase fluid flow and pressure at the interwell scale in a brine reservoir. The time-lapse (TL) OVSP was part of an integrated monitoring program that included well logs, crosswell seismic, electrical resistance tomography and 4D surface seismic. The goals of the OVSP were to detect the CO 2 induced change in seismic response, give information about the spatial distribution of CO 2 near the injection well and to help tie the high-resolution borehole monitoring to the 4D surface data. The VSP data were acquired in well CFU 31-F1, which is the ~3200 m deep CO 2 injection well at the DAS site. A preinjection survey was recorded in late 2009 with injection beginning in December 2009, and a post injection survey was conducted in Nov 2010 following injection of about 250 kT of CO 2 . The sensor array for both surveys was a 50-level, 3-component, Sercel MaxiWave system with 15 m (49 ft) spacing between levels. The source for both surveys was an accelerated weight drop, with different source trucks used for the two surveys. Consistent time-lapse processing was applied to both data sets. Time-lapse processing generated difference corridor stacks to investigate CO 2 induced reflection amplitude changes from each source point. Corridor stacks were used for amplitude analysis to maximize the signal-to-noise ratio (S/N) for each shot point. Spatial variation in reflectivity (used to ‘map’ the plume) was similar in magnitude to the corridor stacks but, due to relatively lower S/N, the results were less consistent and more sensitive to processing and therefore are not presented. We examined the overall time-lapse repeatability of the OVSP data using three methods, the NRMS and Predictability (Pred) measures of Kragh and Christie (2002) and the signal-to-distortion ratio (SDR) method of Cantillo (2011). Because time-lapse noise was comparable to the observed change, multiple methods were used to analyze data reliability. The reflections from the top and base reservoir were identified on the corridor stacks by correlation with a synthetic response generated from the well logs. A consistent change in the corridor stack amplitudes from pre- to post-CO 2 injection was found for both the top and base reservoir reflections on all ten shot locations analyzed. In addition to the well-log synthetic response, a finite-difference elastic wave propagation model was built based on rock/fluid properties obtained from well logs, with CO 2 induced changes guided by time-lapse crosswell seismic tomography (Ajo-Franklin, et al., 2013) acquired at the DAS site. Time-lapse seismic tomography indicated that two reservoir zones were affected by the flood. The modeling established that interpretation of the VSP trough and peak event amplitudes as reflectivity from the top and bottom of reservoir is appropriate even with possible tuning effects. Importantly, this top/base change gives confidence in an interpretation that these changes arise from within the reservoir, not from bounding lithology. The modeled time-lapse change and the observed field data change from 10 shotpoints are in agreement for both magnitude and polarity of amplitude change for top and base of reservoir. Therefore, we conclude the stored CO 2 has been successfully detected and, furthermore, the observed seismic reflection change can be applied to Cranfield’s 4D surface seismic for spatially delineating the CO 2 /brine interface.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

2020 Budget Request for the DOE Computational Science Graduate Fellowship (CSGF) Grant

The Department of Energy Computational Science Graduate Fellowship (DOE CSGF) is essential for addressing the increasingly complex national workforce demands stemming from the growth of computational science and engineering challenges. Computational science and engineering (CSE) takes a multidisciplinary approach that utilizes scientific computing to tackle practical problems and provide technical tools across the spectrum of scientific discovery. The DOE CSGF specifically highlights high-performance computing (HPC) as a critical enabling technology in CSE, driving advancements in science and engineering that are vital to both the DOE and the broader economy. Over the past half-century, HPC has been an essential tool for DOE’s success. During this period, important missions, such as nuclear stockpile stewardship, have turned to HPC as an essential technology. Entire science disciplines have been transformed through the augmentation of scientific observation via HPC. At government laboratories, academic institutions, and in industry, DOE CSGF alumni are helping push traditional HPC boundaries while contributing to discoveries in high-energy physics, quantum information systems, fusion-reactor design, machine learning, additive manufacturing, nano materials for next-generation batteries and transistors, and advanced nuclear reactor modeling. In addition, HPC is used to address national health needs that will eventually point to cures both by helping cancer researchers manage and analyze huge troves of data, by simulating biological mechanisms, and by accelerating drug development. A 2023 report from the ASCAC Subcommittee on American Competitiveness and Innovation to the ASCR office, “Can the United States Maintain Its Leadership in High-Performance Computing?” says of the Program, “The CSGF program provides a barometer for disciplines that will be of interest to future DOE computing. Computational biology, machine learning, and quantum computing are among the subjects that began to swell in the ranks of CSGF applicants before the labs were hiring as high a percentage of employees in these categories.” The explosion of scientific and technological data has heightened the demand for advanced high-performance computing (HPC) to transform these data into meaningful scientific insights. As access to vast amounts of data increases, the fields of Machine Learning and Artificial Intelligence are experiencing a resurgence, enhancing the established practices of computational modeling and simulation. In its September 2020 subcommittee report on "AI/ML, Data Intensive Science, and High-Performance Computing," the DOE Advanced Scientific Computing Advisory Committee (ASCAC) specifically called for a fellowship program to train computational and data scientists to address exascale and data-intensive computing challenges. This integration of empirical and theoretical modeling will increasingly guide federal policymakers in making decisions that impact American society and future generations. It demands a workforce of highly skilled and intellectually agile computational scientists capable of navigating the rapid advancements in scientific computing within the DOE National Laboratory research environment. The DOE CSGF program has consistently addressed this critical need.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

59 BASIC BIOLOGICAL SCIENCES↗