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Satellite-derived attributes of cloud vortex systems and their application to climate studies
Defense Meteorological Satellite Program (DMSP) visible and infrared mosaics are analyzed in conjunction with synoptic meteorological observations of sea level pressure (SLP) and upper-air height to derive composite patterns of cyclonic cloud vortices for the Northern Hemisphere. The patterns reveal variations in the structure and implied dynamics of cyclonic systems at different stages of development that include: (1) increasing vertical symmetry of the lower-level and upper-air circulations and (2) decreasing lower-tropospheric thicknesses and temperature advection, associated with increasing age of the vortex. Cloud vortices are more intense in winter than in summer and typically reach maximum intensity in the short-lived prespiral signature stage. There are major structural differences among frontal wave, polar air, and 'instant occlusion' cyclogenesis types. Cyclones in the dissipation stage may reintensify (deepen), as denoted by the appearance in the imagery of an asymmetric cloud band or a tightened spiral vortex. The satellite-derived statistics on cloud vortex intensity, which are seasonal- and latitude- as well as type-dependent, are applied to a preliminary examination of the synoptic manifestations of seasonal climate variability. An apparently close relationship is found, for two winter and spring seasons, between Northern Hemisphere cyclonic activity and variations in cryosphere variables, particularly the extent of Arctic sea ice. The results may indicate that increased snow and ice extent accompany a southward displacement of cyclonic activity and/or a predominance of deeper systems. However, there is also a strong regional dependence to the ice-synoptics feedback. This study demonstrates the utility of high resolution meteorological satellite imagery for studies of climate variations (climate dynamics).
Carleton, Andrew M.↗
A New Approach to using a Cloud-Resolving Model to Study the Interactions between Clouds, Precipitation and Aerosols
Numerical cloud models, which are based the non-hydrostatic equations of motion, have been extensively applied to cloud-scale and mesoscale processes during the past four decades. Because cloud-scale dynamics are treated explicitly, uncertainties stemming from convection that have to be parameterized in (hydrostatic) large-scale models are obviated, or at least mitigated, in cloud models. Global models will use the non-hydrostatic framework when their horizontal resolution becomes about 10 kilometers, the theoretical limit for the hydrostatic approximation. This juncture will be reached one to two decades from now. Over the past generation, voluminous datasets on atmospheric convection have been accumulated from radar, instrumented aircraft, satellites, and rawinsonde measurements in field campaigns, enabling the detailed evaluation of models. Improved numerical methods have resulted in more accurate and efficient dynamical cores in models. Improvements have been made in the parameterizations of microphysical processes, radiation, boundary-layer effects, and turbulence; however, microphysical parameterizations remain a major source of uncertainty in all classes of atmospheric models. In recent years, exponentially increasing computer power has extended cloud-resolving-model integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-kilometer scales are resolved in horizontal domains as large as 10,000 kilometers in two dimensions, and 1,000 x 1,000 square kilometers in three-dimensions. Cloud models now provide statistical information useful for developing more realistic physically-based parameterizations for climate models and numerical weather prediction models. A review of developments and applications of cloud models in the past, present and future will be presented in this talk. In particular, a new approach to using cloud-resolving models to study the interactions between clouds, precipitation and aerosols will be presented.
Tao, Wei-Kuo↗
A New Approach to Using a Cloud-resolving Model to Study the Interactions Between Clouds, Precipitation and Aerosols
Numerical cloud models, which are based the non-hydrostatic equations of motion, have been extensively applied to cloud-scale and mesoscale processes during the past four decades. Because cloud-scale dynamics are treated explicitly, uncertainties stemming from convection that have to be parameterized in (hydrostatic) large-scale models are obviated, or at least mitigated, in cloud models. Global models will use the non-hydrostatic framework when their horizontal resolution becomes about 10 km, the theoretical limit for the hydrostatic approximation. This juncture will be reached one to two decades from now. Over the past generation, voluminous datasets on atmospheric convection have been accumulated from radar, instrumented aircraft, satellites, and rawinsonde measurements in field campaigns, enabling the detailed evaluation of models. Improved numerical methods have resulted in more accurate and efficient dynamical cores in models. Improvements have been made in the parameterizations of microphysical processes, radiation, boundary-layer effects, and turbulence; however, microphysical parameterizations remain a major source of uncertainty in all classes of atmospheric models. In recent years, exponentially increasing computer power has extended cloud-resolving-model integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as l0,OOO km in two-dimensions, and 1,OOO x 1,OOO km2 in three-dimensions. Cloud models now provide statistical information useful for developing more realistic physically-based parameterizations for climate models and numerical weather prediction models. A review of developments and applications of cloud models in the past, present and future will be presented in this talk. In particular, a new approach to using cloud-resolving models to study the interactions between clouds, precipitation and aerosols will be presented.
Tao, Wei-Kuo↗
A New Approach to using a Cloud-Resolving Model to Study the Interactions between Clouds, Precipitation and Aerosols
Numerical cloud models, which are based the non-hydrostatic equations of motion, have been extensively applied to cloud-scale and mesoscale processes during the past four decades. Because cloud-scale dynamics are treated explicitly, uncertainties stemming from convection that have to be parameterized in (hydrostatic) large-scale models are obviated, or at least mitigated, in cloud models. Global models will use the non-hydrostatic framework when their horizontal resolution becomes about 10 km, the theoretical limit for the hydrostatic approximation. This juncture will be reached one to two decades from now. Over the past generation, voluminous datasets on atmospheric convection have been accumulated from radar, instrumented aircraft, satellites, and rawinsonde measurements in field campaigns, enabling the detailed evaluation of models. Improved numerical methods have resulted in more accurate and efficient dynamical cores in models. Improvements have been made in the parameterizations of microphysical processes, radiation, boundary-layer effects, and turbulence; however, microphysical parameterizations remain a major source of uncertainty in all classes of atmospheric models. In recent years, exponentially increasing computer power has extended cloud-resolving-model integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 square kilometers in three-dimensions. Cloud models now provide statistical information useful for developing more realistic physically-based parameterizations for climate models and numerical weather prediction models. A review of developments and applications of cloud models in the past, present and future will be presented in this talk. In particular, a new approach to using cloud-resolving models to study the interactions between clouds, precipitation and aerosols will be presented.
Tao, Wei-Kuo↗
A cloud classification scheme applied to the breakup region of marine stratocumulus
A major goal of the marine stratocumulus (MSc) segment of FIRE is to describe and explain the temporal and spatial variability in fractional cloud cover. The challenge from a theoretical standpoint is to correctly represent the mechanisms leading to the transitions between solid stratus, stratocumulus and trade wind cumulus. The development and testing of models accounting for fractional cloudiness require an observational data base that will come primarily from satellites. This, of course, is one of the missions of the ISCCP. There are a number of satellite cloud analysis programs that are being undertaken as part of FIRE. One that has already produced data from the FIRE MSc experiment is the spatial coherence method (COAKLEY and Baldwin, 1984). This method produces information on fractional cloud coverage and cloud heights. It may be possible, however, to extract more information on cloud structure from satellite data that might be of use in describing the transitions in the marine stratocumulus cloud deck. Potential applications are explored of a cloud analysis scheme relying on more detailed analysis of visible and infrared cloud radiance statistics. For this preliminary study, data is examined from three days during the 1987 FIRE MSc field work. These case studies provide a basis for comparison and evaluation of the technique.
Khalsa, Siri Jodha Singh↗
A Deterministic Self-Organizing Map Approach and its Application on Satellite Data based Cloud Type Classification
A self-organizing map (SOM) is a type of competitive artificial neural network, which projects the high dimensional input space of the training samples into a low dimensional space with the topology relations preserved. This makes SOMs supportive of organizing and visualizing complex data sets and have been pervasively used among numerous disciplines with different applications. Notwithstanding its wide applications, the self-organizing map is perplexed by its inherent randomness, which produces dissimilar SOM patterns even when being trained on identical training samples with the same parameters every time, and thus causes usability concerns for other domain practitioners and precludes more potential users from exploring SOM based applications in a broader spectrum. Motivated by this practical concern, we propose a deterministic approach as a supplement to the standard self-organizing map. In accordance with the theoretical design, the experimental results with satellite cloud data demonstrate the effective and efficient organization as well as simplification capabilities of the proposed approach.
Initialization method↗
Analytical Solutions for Precipitation Size Distributions at Steady State
Analytical solutions are derived for the steady-state size distributions of precipitating rain and snow particles assuming growth via collection of suspended cloud particles. Application of the Liouville equation to the transfer of precipitating mass through size bins in a “cascade” yields a characteristic gamma distribution with a Marshall–Palmer exponential tail with respect to particle diameter. For rain, the principle parameters controlling size distribution shape are cloud droplet liquid water path and cloud updraft speed. Stronger updrafts lead to greater concentrations of large precipitating drops and a peak in the size distribution. The solutions provide a means for relating size distributions measured in the air or on the ground to cloud bulk microphysical and dynamic properties.
54 ENVIRONMENTAL SCIENCES↗
Cloud Condensation Nuclei Prediction Error from Application of Kohler Theory: Importance for the Aerosol Indirect Effect
In situ observations of aerosol and cloud condensation nuclei (CCN) and the GISS GCM Model II' with an online aerosol simulation and explicit aerosol-cloud interactions are used to quantify the uncertainty in radiative forcing and autoconversion rate from application of Kohler theory. Simulations suggest that application of Koehler theory introduces a 10-20% uncertainty in global average indirect forcing and 2-11% uncertainty in autoconversion. Regionally, the uncertainty in indirect forcing ranges between 10-20%, and 5-50% for autoconversion. These results are insensitive to the range of updraft velocity and water vapor uptake coefficient considered. This study suggests that Koehler theory (as implemented in climate models) is not a significant source of uncertainty for aerosol indirect forcing but can be substantial for assessments of aerosol effects on the hydrological cycle in climatically sensitive regions of the globe. This implies that improvements in the representation of GCM subgrid processes and aerosol size distribution will mostly benefit indirect forcing assessments. Predictions of autoconversion, by nature, will be subject to considerable uncertainty; its reduction may require explicit representation of size-resolved aerosol composition and mixing state.
Sotiropoulou, Rafaella-Eleni P.↗
Assessing the Reliability of Relevant Tweets and Validation Using Manual and Automatic Approaches for Flood Risk Communication
While Twitter has been touted as a preeminent source of up-to-date information on hazard events, the reliability of tweets is still a concern. Our previous publication extracted relevant tweets containing information about the 2013 Colorado flood event and its impacts. Using the relevant tweets, this research further examined the reliability (accuracy and trueness) of the tweets by examining the text and image content and comparing them to other publicly available data sources. Both manual identification of text information and automated (Google Cloud Vision, application programming interface (API)) extraction of images were implemented to balance accurate information verification and efficient processing time. The results showed that both the text and images contained useful information about damaged/flooded roads/streets. This information will help emergency response coordination efforts and informed allocation of resources when enough tweets contain geocoordinates or location/venue names. This research will identify reliable crowdsourced risk information to facilitate near real-time emergency response through better use of crowdsourced risk communication platforms.
54 ENVIRONMENTAL SCIENCES↗
Targeting accuracy of single-isocenter intensity-modulated radiosurgery for multiple lesions
To investigate the targeting accuracy of intensity-modulated SRS (IMRS) plans designed to simultaneously treat multiple brain metastases with a single isocenter. A home-made acrylic phantom able to support a film (EBT3) in its coronal plane was used. The phantom was CT scanned and three coplanar small targets (a central and two peripheral) were outlined in the Eclipse system. Peripheral targets were 6 cm apart from the central one. A reference IMRS plan was designed to simultaneously treat the three targets, but only a single isocenter located at the center of the central target was used. After positioning the phantom on the linac using the room lasers, a CBCT scan was acquired and the reference plan were mapped on it, by placing the planned isocenter at the intersection of the landmarks used in the film showing the linac isocenter. The mapped plan was then recalculated and delivered. The film dose distribution was derived using a cloud computing application ( (www.radiochromic.com)) that uses a triple-channel dosimetry algorithm. Comparison of dose distributions using the gamma index (5%/1 mm) were performed over a 5 × 5 cm{sup 2} region centered over each target. 2D shifts required to get the best gamma passing rates on the peripheral target regions were compared with the reported ones for the central target. The experiment was repeated ten times in different sessions. Average 2D shifts required to achieve optimal gamma passing rates (99%, 97%, 99%) were 0.7 mm (SD: 0.3 mm), 0.8 mm (SD: 0.4 mm) and 0.8 mm (SD: 0.3 mm), for the central and the two peripheral targets, respectively. No statistical differences (p > 0.05) were found for targeting accuracy between the central and the two peripheral targets. The study revealed a targeting accuracy within 1 mm for off-isocenter targets within 6 cm of the linac isocenter, when a single-isocenter IMRS plan is designed.
61 RADIATION PROTECTION AND DOSIMETRY↗
Foldy v1
We created a cloud-based application for running AlphaFold2 and related structural programs called Foldy. Foldy is built on Helm / Kubernetes, which enables a facile production deployment and a scalable backend. Once set up by an institution, Foldy requires no software expertise from its users. It can be used to predict the structure of large proteins (up to 3000 amino acids), to visualize Pfam and antiSMASH annotations, and to perform ligand docking with Autodock Vina.
Roberts, Jacob↗
Platform for efficient large-scale storage and analysis of multi-omics data in plant and microbial systems (Final Technical Report)
Genomic variation at the sequence level fundamentally affects the phenotypic state of all organisms at all stages of development, while dynamic processes such as changes in the epigenome (e.g. DNA methylation state) and transcriptome regulate the specific phenotype expressed at any given state of development based upon that genomic variation. In plants, DNA methylation is a particularly important mechanism for both regulating transcriptomic expression and for management of genomic variations that could be deleterious to the organism due to the presence of active retrotransposons in plant genomes. While DNA methylation is heritable, it is also dynamic through a given plant’s development and life cycle, particularly during the development from seed to mature specimen suggesting variations in DNA methylation could be critical regulators of biologically and commercially important phenotypes such as time to flowering; in addition, plant DNA methylation is more complex than that of animals, with methylation of CHG and CHH trinucleotides evident in addition to the better-known CG methylation. The complexity of plant DNA methylation and its interplay with genomic sequence variation, transcriptomics and other epigenomic factors demand a storage and analysis framework that can cope with the complexity both within a single specimen and with analyses that span many individuals and even many species, such as attempts to extend models from model organisms to commercially relevant species. In addition to complexity, the rapid development and proliferation of sequencing technology has led to an explosion of data volume that conventional storage and analysis solutions will likely be unable to cope with in the long run. We proposed to study these with suitable distributed storage and computation and therefore for the application of cloud computing to biological analyses; integrate with existing data sources and compatible with virtually any interface use case, from fully automated shell scripts to notebooks and do all these at scale in this STTR grant.
60 APPLIED LIFE SCIENCES↗
Understanding the Design Space of Sparse/Dense Multiphase Dataflows for Mapping Graph Neural Networks on Spatial Accelerators
Graph Neural Networks (GNNs) have garnered a lot of recent interest because of their success in learning representations from graph-structured data across several critical applications in cloud and HPC. Owing to their unique compute and memory characteristics that come from an interplay between dense and sparse phases of computations, the emergence of reconfigurable dataflow (aka spatial) accelerators offers promise for acceleration by mapping optimized dataflows (i.e., computation order and parallelism) for both phases. The goal of this work is to characterize and understand the design-space of dataflow choices for running GNNs on spatial accelerators in order for the compilers to optimize the dataflow based on the workload. Specifically, we propose a taxonomy to describe all possible choices for mapping the dense and sparse phases of GNNs spatially and temporally over a spatial accelerator, capturing both the intra-phase dataflow and the inter-phase (pipelined) dataflow. Using this taxonomy, we do deep-dives into the cost and benefits of several dataflows and perform case studies on implications of hardware parameters for dataflows and value of flexibility to support pipelined execution.
97 MATHEMATICS AND COMPUTING↗
Kullback–Leibler Divergence of an Open-Queuing Network of a Cell-Signal-Transduction Cascade
Queuing networks (QNs) are essential models in operations research, with applications in cloud computing and healthcare systems. However, few studies have analyzed the cell’s biological signal transduction using QN theory. This study entailed the modeling of signal transduction as an open Jackson’s QN (JQN) to theoretically determine cell signal transduction, under the assumption that the signal mediator queues in the cytoplasm, and the mediator is exchanged from one signaling molecule to another through interactions between the signaling molecules. Each signaling molecule was regarded as a network node in the JQN. The JQN Kullback–Leibler divergence (KLD) was defined using the ratio of the queuing time (λ) to the exchange time (μ), λ/μ. The mitogen-activated protein kinase (MAPK) signal-cascade model was applied, and the KLD rate per signal-transduction-period was shown to be conserved when the KLD was maximized. Our experimental study on MAPK cascade supported this conclusion. This result is similar to the entropy-rate conservation of chemical kinetics and entropy coding reported in our previous studies. Thus, JQN can be used as a novel framework to analyze signal transduction.
97 MATHEMATICS AND COMPUTING↗
Field intercomparison of ice nucleation measurements: the Fifth International Workshop on Ice Nucleation Phase 3 (FIN-03)
Abstract. The third phase of the Fifth International Ice Nucleation Workshop (FIN-03) was conducted at the Storm Peak Laboratory in Steamboat Springs, Colorado, in September 2015 to facilitate the intercomparison of instruments measuring ice-nucleating particles (INPs) in the field. Instruments included two online and four offline measurement systems for INPs, which are a subset of those utilized in the laboratory study that comprised the second phase of FIN (FIN-02). The composition of the total aerosols was characterized using the Particle Analysis by Laser Mass Spectrometry (PALMS) and Wideband Integrated Bioaerosol Sensor (WIBS) instruments, and aerosol size distributions were measured by a laser aerosol spectrometer (LAS). The dominant total particle compositions present during FIN-03 were composed of sulfates, organic compounds, and nitrates, as well as particles derived from biomass burning. Mineral-dust-containing particles were ubiquitous throughout and represented 67 % of supermicron particles. Total WIBS fluorescing particle concentrations for particles with diameters of > 0.5 µm were 0.04 ± 0.02 cm−3 (0.1 cm−3 highest; 0.02 cm−3 lowest), typical of the warm season in this region and representing ≈ 9 % of all particles in this size range as a campaign average. The primary focus of FIN-03 was the measurement of INP concentrations via immersion freezing at temperatures > −33 °C. Additionally, some measurements were made in the deposition nucleation regime at these same temperatures, representing one of the first efforts to include both mechanisms within a field campaign. INP concentrations via immersion freezing agreed within factors ranging from nearly 1 to 5 times on average between matched (time and temperature) measurements, and disagreements only rarely exceeded 1 order of magnitude for sampling times coordinated to within 3 h. Comparisons were restricted to temperatures lower than −15 °C due to the limits of detection related to sample volumes and very low INP concentrations. Outliers of up to 2 orders of magnitude occurred between −25 and −18 °C; a better agreement was seen at higher and lower temperatures. Although the 5–10 factor agreement of INP measurements found in FIN-03 aligned with the results of the FIN-02 laboratory comparison phase, giving confidence in progress of this measurement field, this level of agreement still equates to temperature uncertainties of 3.5 to 5 °C that may not be sufficient for numerical cloud modeling applications that utilize INP information. INP activity in the immersion-freezing mode was generally found to be an order of magnitude or more, making it more efficient than in the deposition regime at 95 %–99 % water relative humidity, although this limited data set should be augmented in future efforts. To contextualize the study results, an assessment was made of the composition of INPs during the late-summer to early-fall period of this study inferred through comparison to existing ice nucleation parameterizations and through measurement of the influence of thermal and organic carbon digestion treatments on immersion-freezing ice nucleation activity. Consistent with other studies in continental regions, biological INPs dominated at temperatures of > −20 °C and sometimes colder, while arable dust-like or other organic-influenced INPs were inferred to dominate below −20 °C.
54 ENVIRONMENTAL SCIENCES↗
The diffusion approximation. An application to radiative transfer in clouds
It is shown how the radiative transfer equation reduces to the diffusion equation. To keep the mathematics as simple as possible, the approximation is applied to a cylindrical cloud of radius R and height h. The diffusion equation separates in cylindrical coordinates and, in a sample calculation, the solution is evaluated for a range of cloud radii with cloud heights of 0.5 km and 1.0 km. The simplicity of the method and the speed with which solutions are obtained give it potential as a tool with which to study the effects of finite-sized clouds on the albedo of the earth-atmosphere system.
Arduini, R. F.↗
Potential applications of digital, visible, and infrared data from geostationary environmental satellites
An hourly, digital data base from the Visible/Infrared Spin-Scan Radiometer (VISSR) instrument on the GOES-1 and SMS-2 geostationary satellites is described. Several examples of developmental applications of these quantitative digital data are presented. These include a review of recent attempts to develop products that are of use to meteorologists who provide services to aviation, agriculture, forestry, hydrology, oceanography, and climatology. The sample products include high resolution thermal gradients of land and ocean surfaces, thermal change analyses, fruit frost/freeze application, cloud-top altitude analysis, analysis of hurricane characteristics, and analyses of solar insolation.
Miller, D. B.↗