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Foldy: An open-source web application for interactive protein structure analysis
Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy’s interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy’s interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.
Cloud Scaling Properties and Cloud Parameterization
Cloud liquid and cloud traction variability is studied as a function of horizontal scale in the ECMWF forecast model during several 10-day runs at the highest available model resolution, recently refined from approximately 60 km (T213) down to approximately 20 km (T639). At higher resolutions, model plane-parallel albedo biases are reduced, so that models may be tuned to have larger, more realistic, cloud liquid water amounts, However, the distribution of cloud liquid assumed -within- each gridbox, for radiative and thermodynamic computations, depends on ad hoc assumptions that are not necessarily consistent with observed scaling properties, or with scaling properties produced by the model at larger scales. To study the larger-scale cloud properties, ten locations on the Earth are chosen to coincide with locations having considerable surface data available for validation, and representing a variety of climatic regimes, scaling exponents are determined from a range or scales down to model resolution, and are re-computed every three hours, separately for low, medium and high clouds, as well as column-integrated cloudiness. Cloud variability fluctuates in time, due to diurnal, synoptic and other' processes, but scaling exponents are found to be relatively stable. various approaches are considered for applying computed cloud scaling to subgrid cloud distributions used for radiation, beyond simple random or maximal overlap now in common use. Considerably more work is needed to compare model cloud scaling with observations. This will be aided by increased availability of high-resolution surface, aircraft and satellite data, and by the increasing resolution of global models,
Cloud Structure and Cloud-Radiation Interaction: From Smallest Observable Scales (Less than 10 m) to GCM Grid Scales (More than 100 km)
In this presentation we review the fractal nature of internal cloud structure from cm- to km-scales as captured by in-situ probes during long horizontal penetrations by aircraft. We uncover the non-Poissonian spatial distribution of cloud droplets at submeter scales and confirm scale-invariant behavior for large scales. Based on these structural characteristics, we generate simple fractal cloud models that reproduce statistical scaling properties of real clouds. These stochastic models represent a link between nonlinear science, in general, and cloud-radiation interaction, in particular. Next we run three-dimensional radiative transfer computations on these synthetic fractal clouds and compare the structure of the resulting radiation fields with the known structure of the cloud model and with satellite images of real clouds. The different behaviors observed for small and large-scale variabilities will be discussed in detail. We find that while the large-scale fluctuations of the resulting radiation fields resemble those in the original scale-invariant cloud structure, the radiation at small scales is much smoother than its cloud liquid water counterpart. This violates scale-invariance and produces a scale-break at 0.2-0.5 km that is clearly observed in high-resolution satellite data such as from Landsat. Finally, we show how radiative transfer Green function theory in the photon diffusion limit explains (and predicts) the above phenomena of "radiative smoothing."
Precipitation Processes Developed During ARM (1997), TOGA COARE (1992) GATE (1974), SCSMEX (1998), and KWAJEX (1999): Consistent 3D, Semi-3D and 3D Cloud Resolving Model Simulations
Real clouds and cloud systems are inherently three-dimensional (3D). Because of the limitations in computer resources, however, most cloud-resolving models (CRMs) today are still two-dimensional (2D) have been used to study the response of clouds to large-scale forcing. IN these 3D simulators, the model domain was small, and the integration time was 6 hours. Only recently have 3D experiments been performed for multi-day periods for tropical clouds systems with large horizontal domains at the National Center of Atmospheric Research (NCAR) and at NASA Goddard Space Center. At Goddard, a 3D cumulus Ensemble (GCE) model was used to simulate periods during TOGA COARE, GATE, SCSMEX, ARM, and KWAJEX using a 512 by 512 km domain (with 2-km resolution). The result indicate that surface precipitation and latent heating profiles are very similar between the 2D and 3D GCE model simulation. The major objective of this paper are: (1) to assess the performance of the super-parametrization technique, (2) calculate and examine the surface energy (especially radiation) and water budget, and (3) identify the differences and similarities in the organization and entrainment rates of convection between simulated 2D and 3D cloud systems.
Precipitation Processes developed during ARM (1997), TOGA COARE (1992), GATE (1974), SCSMEX (1998), and KWAJEX (1999), Consistent 2D, semi-3D and 3D Cloud Resolving Model Simulations
Real clouds and cloud systems are inherently three-dimensional (3D). Because of the limitations in computer resources, however, most cloud-resolving models (CRMs) today are still two-dimensional (2D). A few 3D CRMs have been used to study the response of clouds to large-scale forcing. In these 3D simulations, the model domain was small, and the integration time was 6 hours. The major objectives of this paper are: (1) to assess the performance of the super-parameterization technique (i.e. is 2D or semi-3D CRM appropriate for the super-parameterization?); (2) calculate and examine the surface energy (especially radiation) and water budgets; (3) identify the differences and similarities in the organization and entrainment rates of convection between simulated 2D and 3D cloud systems.
Precipitation Processes Developed During ARM (1997), TOGA COARE (1992), GATE (1974), SCSMEX (1998), and KWAJEX (1999): Consistent 2D, Semi-3D and 3D Cloud Resolving Model Simulations
Real clouds and cloud systems are inherently three-dimensional (3D). Because of the limitations in computer resources, however, most cloud-resolving models (CRMs) today are still two-dimensional (2D). A few 3D CRMs have been used to study the response of clouds to large-scale forcing. In these 3D simulations, the model domain was small, and the integration time was 6 hours. Only recently have 3D experiments been performed for multi-day periods for tropical cloud systems with large horizontal domains at the National Center for Atmospheric Research (NACAR) and at NASA Goddard Space Flight Center . At Goddard, a 3D Goddard Cumulus Ensemble (GCE) model was used to simulate periods during TOGA COARE, SCSMEX and KWAJEX using 512 by 512 km domain (with 2 km resolution). The results indicate that surface precipitation and latent heating profiles are very similar between the 2D and 3D GCE model simulations. The reason for the strong similarity between the 2D and 3D CRM simulations is that the same observed large-scale advective tendencies of potential temperature, water vapor mixing ratio, and horizontal momentum were used as the main focusing in both the 2D and 3D models. Interestingly, the 2D and 3D versions of the CRM used at CSU showed significant differences in the rainfall and cloud statistics for three ARM cases. The major objectives of this paper are: (1) to assess the performance of the super-parameterization technique, (2) calculate and examine the surface energy (especially radiation) and water budgets, and (3) identify the differences and similarities in the organization and entrainment rates of convection between simulated 2D and 3D cloud systems.
The Impact of Model Configuration and Large-Scale, Upper-Level Forcing on CRM- Simulated Convective Systems
Real clouds and cloud systems are inherently three-dimensional (3D). Because of the limitations in computer resources, however, most cloud-resolving models (CRMs) today are still two-dimensional (2D, see a brief review by Tao 2003). Only recently have 3D experiments been performed for multi-day periods for tropical cloud systems with large horizontal domains at the National Center for Atmospheric Research, at NOAA GFDL, at the U. K. Met. Office, at Colorado State University and at NASA Goddard Space Flight Center (Tao 2003). At Goddard, a 3D Goddard Cumulus Ensemble (GCE) model was used to simulate periods during TOGA COARE (December 19-27, 1992), GATE (September 1-7, 1974), SCSMEX (June 2-11, 1998), ARM (June 26-30, 1997) and KWAJEX (August 7-13, August 18-21, and August 29-September 12, 1999) using a 512 by 512 km domain (with 2-km resolution). The results indicate that surface precipitation and latent heating profiles are similar between the 2D and 3D GCE model simulations. However, there are difference in radiation, surface fluxes and precipitation characteristics. The 2D GCE model was used to perform a long-term integration on ARM/GCSS case 4 (22 days at the ARM Southern Great Plains site in March 2000). Preliminary results showed a large temperature bias in the upper troposphere that had not been seen in previous tropical cases. The major objectives of this paper are: (1) to determine the sensitivities to model configuration (i.e., 2D in west-east, south-north or 3D), (2) to identify the differences and similarities in the organization and entrainment rates of convection between 2D- and 3D-simulated ARM cloud systems, and (3) assess the impact of upper tropospheric forcing on tropical and ARM case 4 cases.
The Impact of Model Configuration and Large-Scale, Upper-Level Forcing on CRM-Simulated Convective Systems
Real clouds and cloud systems are inherently three-dimensional (3D). Because of the limitations in computer resources, however, most cloud-resolving models (CRMs) today are still two-dimensional (2D, see a brief review by Tao 2003). Only recently have 3D experiments been performed for multi-day periods for tropical cloud systems with large horizontal domains at the National Center for Atmospheric Research, at NOAA GFDL, at the U. K. Met. Office, at Colorado State University and at NASA Goddard Space Flight Center (Tao 2003). At Goddard, a 3D Goddard Cumulus Ensemble (GCE) model was used to simulate periods during TOGA COARE (December 19-27, 1992), GATE (September 1-7, 1974), SCSMEX (June 2-11, 1998), ARM (June 26-30, 1997) and KWAJEX (August 7-13, August 18-21, and August 29-September 12, 1999) using a 512 km domain (with 2-kilometer resolution). The results indicate that surface precipitation and latent heating profiles are similar between the 2D and 3D GCE model simulations. However, there are difference in radiation, surface fluxes and precipitation characteristics. The 2D GCE model was used to perform a long-term integration on ARM/GCSS case 4 (22 days at the ARM southern Great Plains site in March 2000). Preliminary results showed a large temperature bias in the upper troposphere that had not been seen in previous tropical cases. The major objectives of this paper are: (1) to determine the sensitivities to model configuration (ie., 2D in west-east, south-north or 3D), (2) to identify the differences and similarities in the organization and entrainment rates of convection between 2D- and 3D-simulated ARM cloud systems, and (3) assess the impact of upper tropospheric forcing on tropical and ARM case 4 cases.
Precipitation processes developed during TOGA COARE (1992), GATE (1974), SCSMEX (1998), and KWAJEX (1999): 3D Cloud Resolving Model Simulation
Real clouds and cloud systems are inherently three-dimensional (3D). Because of the limitations in computer resources, however, most cloud-resolving models (CRMs) today are still two-dimensional (2D). A few 3D CRMs have been used to study the response of clouds to large-scale forcing. In these 3D simulations, the model domain was small, and the integration time was 6 hours. Only recently have 3D experiments been performed for multi-day periods for tropical cloud systems with large horizontal domains at the National Center for Atmospheric Research (NCAR), NOAA GFDL, the U.K. Met. Office, Colorado State University and NASA Goddard Space Flight Center. An improved 3D Goddard Cumulus Ensemble (GCE) model was recently used to simulate periods during TOGA COARE (December 19-27, 1992), GATE (september 1-7, 1974), SCSMEX (May 18-26, June 2-11, 1998) and KWAJEX (August 7-13, August 18-21, and August 29-September 12, 1999) using a 512 by 512 km domain and 41 vertical layers. The major objectives of this paper are: (1) to identify the differences and similarities in the simulated precipitation processes and their associated surface and water energy budgets in TOGA COARE, GATE, KWAJEX, and SCSMEX, and (2) to asses the impact of microphysics, radiation budget and surface fluxes on the organization of convection in tropics.
Fragmentation in a rotating protostar - A comparison of two three-dimensional computer codes
The collapse of an isothermal protostellar cloud with pressure, gravity, and rotation included is followed with two independent computer codes. For the initial condition, a nonaxisymmetric perturbation of mode m = 2 and 50% amplitude is introduced into a cloud of 1 solar mass with a mean density of 1.44 x 10 to the -17g/cu cm and a uniform angular velocity of 1.6 x 10 to the -12 rad/sec. The collapse is followed through an increase in density of over four orders of magnitude to the point where a binary protostar forms. The agreement between the results of the two calculations is good.
Design and verification of a cloud field optical simulator
A concept and an apparatus designed to investigate the reflected and transmitted distributions of light from optically thick clouds is presented. The Cloud Field Optical Simulator (CFOS) is a laboratory device which utilizes an array of incandescent lamps as a source, simulated clouds made from cotton or styrofoam as targets, and an array of silicon photodiodes as detectors. The device allows virtually any source-target-detector geometry to be examined. Similitude between real clouds and their CFOS cotton or styrofoam counterparts is established by relying on a linear relationship between optical depth and the ratio of reflected to transmitted light for a semiinfinite layer. Comparisons of principal plane radiances observed by the CFOS with Monte Carlo computations for a water cloud at 0.7 micron show excellent agreement. Initial applications of the CFOS are discussed.
Design and verification of a cloud field optical simulator
A concept and an apparatus designed to investigate the reflected and transmitted distributions of light from optically thick clouds is presented. The Cloud Field Optical Simulator (CFOS) is a laboratory device which utilizes an array of incandescent lamps as a source, simulated clouds made from cotton or styrofoam as targets, and an array of silicon photodiodes as detectors. The device allows virtually any source-target-detector geometry to be examined. Similitude between real clouds and their CFOS cotton or styrofoam counterparts is established by relying on a linear relationship between optical depth and the ratio of reflected to transmitted light for a semi-infinite layer. Comparisons of principal plane radiances observed by the CFOS with Monte Carlo computations for a water cloud at 0.7 microns show excellent agreement.
The Radiometric Scaling of the MODIS and VIIRS Imagers to a Common Reference and Stability Analysis for the Next Edition of CERES Products
The NASA CERES project has provided the climate quality observed TOA and computed surface fluxes to the scientific community. CERES uses MODIS and VIIRS imagers to retrieve cloud properties needed to convert Terra, Aqua, NPP, and NOAA-20 CERES footprint radiance observations into fluxes. The imagers are also used to radiometrically scale the geostationary sensors (GEO) radiances to the imager calibration reference to ensure that the GEO derived cloud properties and broadband TOA fluxes are consistent in both space and time. Both the imager and GEO retrieved cloud properties are used to compute the surface fluxes. The CERES imager and GEO calibration team uses ray-matched radiance pairs to radiometrically scale the SNPP and NOAA-20 VIIRS sensors to the Aqua-MODIS calibration reference. The radiometric scaling is further validated using geostationary imagers as transfer radiometers. The team will rely primarily on deep convective clouds to monitor the imager channel calibration stability and to correct for short term calibration drifts. The DSCOVR satellite was launched on February 25, 2015 and orbits around the L1 Lagrange point directly between the Earth and the sun. The EPIC sensor contains no onboard calibration systems. However, multiple inter-calibration studies have shown that the EPIC imager is very stable in time. The excellent radiometric stability of EPIC allows the use of EPIC observations as a stable reference to validate both the short term drift corrections of the imagers, as well as to validate the radiometric scaling factors between them. Examples of the imager relative calibration using EPIC before and after radiometric scaling will be shown along with the results from the use of invariant targets to remove imager calibration drifts.
The globus compute dataset: An open function-as-a-service dataset from the edge to the cloud
Here we present a unique function-as-a-service (FaaS) dataset capturing the use of the Globus Compute (previously funcX) platform. Globus Compute implements a federated model via which users may deploy endpoints on arbitrary remote computers, from the edge to high performance computing (HPC) cluster, and they may then invoke Python functions on those endpoints via a reliable cloud -hosted service. The dataset covers 31 weeks and includes 2121472 task submissions from 252 users executed on 580 remote computing endpoints. It includes 277386 registered functions. We describe the dataset and various observations, some that are similar to other FaaS datasets, for example, that 74% of tasks run for less than 1 s, and some that are unique to Globus Compute, for example, that endpoints are used in different ways and that the majority of functions are related to scientific computing and machine learning. To the best of our knowledge, this dataset represents the first federated FaaS dataset that includes user workloads, distributed computing endpoints, and analysis of registered function bodies. We expect the dataset to be useful for researching FaaS architectures, workload modeling, container warming, and other distributed computing architectures.
PipeSight: A High-Performance Computing Platform for Pipeline Integrity Management
The Phase I feasibility study completed as part of this project has led to a number of innovative technologies being developed and has laid the foundation for a successful Phase II effort to commercialize a platform for managing the integrity of pipelines for the damage mechanisms of the new, hybrid-energy based economy. To ground the development efforts and direction of the project, an extensive market research and customer discovery effort was undertaken early in Phase I. Through this effort, a number of pipeline owners and operators were interviewed, and the following key findings were discovered about the pipeline industry: • Small pipeline operators do not have the central engineering groups necessary to perform their own independent analysis of inspection data, but instead rely on summarized tally sheets provided to them by inspection service providers. • The time it takes to go from an inspection to a completed engineering assessment, even for small segments of pipeline, can take anywhere from 30-120 days. During this delay, critical threats can (and have been known to) cause failures. • Uncertainty is often not accounted for in the assessment of pipeline integrity. The tally sheets provided by third-party service providers are almost always deterministic in nature, identifying threats that present a concern only to the current (not the future) integrity of the pipeline. • It is uncommon to apply the latest technologies to perform advanced assessments of damaged pipelines. There is a desire to use more advanced analysis capabilities to assess threats. Many pipeline operators indicated that they would often excavate a pipeline to perform an inspection and find that the damage was not as bad as they anticipated, thus using limited resources unnecessarily. Companies are not consistent in their use of inspection data to determine corrosion rates, and those that do only calculate deterministic corrosion rates. • The industry has prominently relied on time-based inspections but has recently started to transition to risk-based inspections. However, there appears to be no uniform guidance on how to do so while properly accounting for all sources of uncertainty. • Companies are not storing inspection data in a manner that allows for the ready determination of temporal trends. • Predictive maintenance principles and practices are beginning to be used by early adopters • Some pipelines are being re-purposed to transport different process fluids than they were designed for, e.g., H 2 and CO 2 rich process streams to serve the new hybrid-energy based economy, which are presenting new integrity concerns for the existing pipeline network that crisscrosses the United States. As a result of these discoveries, we were able to target the development efforts in Phase I to best serve the needs of the industry. In Phase I, we developed a way to correlate multiple large-scale scans of the pipeline to determine a probabilistic corrosion rate that accounts for all sources of error and uncertainty in the inspection process. This probabilistic corrosion rate can be used to predict the future thickness distribution of the pipe wall. We demonstrate how this analysis may be performed in an analytical fashion and has been implemented in such a manner that it can be readily distributed using GPU computing through integration of the Kokkos programming model. We also make a very novel extension of the analytical corrosion rate model to Bayesian Networks (an explainable AI technique) that can account for non-parametric distributions of corrosion rates. With the predictions made above for the probabilistic corrosion rate and corresponding future distribution of the pipe wall thickness, we can assess the integrity of the pipeline through the use of a probabilistic engineering assessment. We developed a novel screening data analysis approach that can rapidly identify ‘hotspots’ (local thin areas) where the integrity of the pipeline is a concern. Once more, we implemented this screening approach in C++ to leverage GPU computing via the Kokkos programming model. After the critical hotspots are identified, we developed a program that can automatically generate an advanced finite element model of the damaged regions. Since the number of damaged regions that require advanced analysis can number in the thousands, we integrated an open-source container-native workflow engine for orchestrating parallel jobs on the cloud. Initially, these advanced numerical models were only designed to account for loading due to internal pressure. However, in a slight pivot from the initial Phase I proposal, we developed a complete pipe stress analysis program (called Simflex) which can simulate the complete pipeline and its response to thermal expansion, pressure, thermal bowing, weight, wind, earthquake, support displacement, support friction and external forces. This pipe stress analysis program was written generically, to handle any piping system, but contains the features needed to model long pipelines (i.e., it incorporates a model for soil mechanics and can account for the nonlinear boundary conditions necessary to simulate long underground pipelines). This pipe stress analysis program can simulate any segment of the pipeline (simple or complex) under any set of conditions and loads, to determine the supplemental loads (axial forces and bending moments) at the location of damage. This enables the most accurate state of stress to be accounted for in the pipeline, which can prove critical when evaluating the integrity of a damaged region. In the process of developing the technologies to perform the integrity assessment of the pipeline, we also extended one of the industry standard approaches for performing the assessment of local thin areas that extend more in the circumferential direction than the longitudinal direction of the pipeline. This approach was presented to the API 579-1/AS ME FFS-1 steering committee in November 2021 for consideration in the next edition of the industry standard for Fitness-For-Service (expected to be released in 2023). To help pipeline operators make decisions with the results on any integrity assessment, we developed a new approach to the life-cycle management of pipelines which uses a Bayesian Decision Network. The network is designed to help pipeline operators plan and prioritize inspection activities and ultimately make smarter, more cost-effective decisions. The Bayesian approach accounts for all sources of uncertainty and carries them through to the final optimal decisions, providing a probabilistic framework for optimizing inspection intervals. The proof-of-concept networks developed in the feasibility study are complete, verified, and are focused on a subset of the pipeline. To expand this novel approach to the scale necessary for an entire network of pipelines in Phase II, we will leverage the DOE-funded Bengi solver for industrial-scale decision making with Bayesian Networks [22]. Once implemented, we will be able to provide the pipeline industry with a much-needed tool for optimal inspection planning using truly explainable artificial intelligence (XAI). To handle all of these advanced capabilities into a cloud-based platform, the architecture of the Equity Engineering Cloud (EEC) was extended to include Argo Workflows, a framework capable of distributing and managing a massive number of jobs that consume their own resources, such that thousands of serial finite element simulations can be run in parallel. As part of this substantial undertaking, we also integrated Argo Continuous Delivery (CD) into the EEC, to aid with the rapid prototyping and iterations that will be imperative to the success of the PipeSight platform’s Agile development process in Phase II. As part of the pipe stress analysis program, we also developed a custom visualizer that leverages the DOE-funded VTK visualization library. We added custom contouring capabilities and a means for interacting visually with both the inputs and outputs of the pipe stress analysis program. We also developed routines for automating the post-processing of the finite element simulations to determine if any failure criteria are met and to visualize the deformations, stresses and strains in ParaView using the exodus II file format (a subset of netCDF).
RACORO Continental Boundary Layer Cloud Investigations: 1. Case Study Development and Ensemble Large-Scale Forcings
Observation-based modeling case studies of continental boundary layer clouds have been developed to study cloudy boundary layers, aerosol influences upon them, and their representation in cloud- and global-scale models. Three 60 h case study periods span the temporal evolution of cumulus, stratiform, and drizzling boundary layer cloud systems, representing mixed and transitional states rather than idealized or canonical cases. Based on in situ measurements from the Routine AAF (Atmospheric Radiation Measurement (ARM) Aerial Facility) CLOWD (Clouds with Low Optical Water Depth) Optical Radiative Observations (RACORO) field campaign and remote sensing observations, the cases are designed with a modular configuration to simplify use in large-eddy simulations (LES) and single-column models. Aircraft measurements of aerosol number size distribution are fit to lognormal functions for concise representation in models. Values of the aerosol hygroscopicity parameter, kappa, are derived from observations to be approximately 0.10, which are lower than the 0.3 typical over continents and suggestive of a large aerosol organic fraction. Ensemble large-scale forcing data sets are derived from the ARM variational analysis, European Centre for Medium-Range Weather Forecasts, and a multiscale data assimilation system. The forcings are assessed through comparison of measured bulk atmospheric and cloud properties to those computed in "trial" large-eddy simulations, where more efficient run times are enabled through modest reductions in grid resolution and domain size compared to the full-sized LES grid. Simulations capture many of the general features observed, but the state-of-the-art forcings were limited at representing details of cloud onset, and tight gradients and high-resolution transients of importance. Methods for improving the initial conditions and forcings are discussed. The cases developed are available to the general modeling community for studying continental boundary clouds.
Simulating nuclear cloud rise within a realistic atmosphere using the Weather Research and Forecasting model
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