Some thoughts on the use of InSAR data to constrain models of surface deformation: Noise structure and data downsampling

Repeat-pass Interferometric Synthetic Aperture Radar (InSAR) provides spatially dense maps of surface deformation with potentially tens of millions of data points. Here we estimate the actual covariance structure of noise in InSAR data. We compare the results for several independent interferograms with a large ensemble of GPS observations of tropospheric delay and discuss how the common approaches used during processing of InSAR data affects the inferred covariance structure. Motivated by computational concerns associated with numerical modeling of deformation sources, we then combine the data-covariance information with the inherent resolution of an assumed source model to develop an efficient algorithm for spatially variable data resampling (or averaging). We illustrate these technical developments with two earthquake scenarios at different ends of the earthquake magnitude spectrum. For the larger events, our goal is to invert for the coseismic fault slip distribution. For smaller events, we infer the hypocenter location and moment. We compare the results of inversions using several different resampling algorithms, and we assess the importance of using the full noise covariance matrix

Locations of selected small earthquakes in the Zagros mountains

Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 6 (2005): Q03001, doi:10.1029/2004GC000849.The Zagros mountains of southern Iran are marked by a zone of high seismicity and accommodate a significant portion of the convergence between Arabia and Eurasia. Due to the lack of dense local seismic or geodetic networks, the inferred kinematics of the collision in Iran is mainly based on catalogs of teleseismically determined earthquake locations. We surveyed all M w > 4.5 earthquakes in the Harvard Centroid Moment Tensor (HCMT) and International Seismological Centre (ISC) catalogs that occurred in the Zagros mountains during the period 1992–2002 and that were spanned by Interferometric Synthetic Aperture Radar (InSAR) images from the ERS 1 and 2 satellites. We invert the observed deformation for the best fitting point source, single fault plane, and distributed fault slip for four earthquakes and one unexplained deformation event. We find that we can precisely locate earthquakes that are too small to be well-located by either the HCMT or ISC catalogs, allowing us to tie specific earthquakes to active geologic structures.ERS 1 and 2 data were acquired through an ESA category-1 proposal. R. Lohman is partially supported by a NASA New Investigator Program grant award to M. Simons

Some thoughts on the use of InSAR data to constrain models of surface deformation : noise structure and data downsampling

Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 6 (2005): Q01007, doi:10.1029/2004GC000841.Repeat-pass Interferometric Synthetic Aperture Radar (InSAR) provides spatially dense maps of surface deformation with potentially tens of millions of data points. Here we estimate the actual covariance structure of noise in InSAR data. We compare the results for several independent interferograms with a large ensemble of GPS observations of tropospheric delay and discuss how the common approaches used during processing of InSAR data affects the inferred covariance structure. Motivated by computational concerns associated with numerical modeling of deformation sources, we then combine the data-covariance information with the inherent resolution of an assumed source model to develop an efficient algorithm for spatially variable data resampling (or averaging). We illustrate these technical developments with two earthquake scenarios at different ends of the earthquake magnitude spectrum. For the larger events, our goal is to invert for the coseismic fault slip distribution. For smaller events, we infer the hypocenter location and moment. We compare the results of inversions using several different resampling algorithms, and we assess the importance of using the full noise covariance matrix.R. Lohman is partially supported by a NASA New Investigator Program grant award to M. Simons

Helicase activity on DNA as a propagating front

We develop a propagating front analysis, in terms of a local probability of zipping, for the helicase activity of opening up a double stranded DNA (dsDNA). In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front separates the zipped and unzipped phases of a dsDNA and a drive acts locally around the front. Bounds from variational analysis and numerical estimates for the speed of a helicase are obtained. Different types of helicase behaviours can be distinguished by the nature of the drive.Comment: 5 pages, 5 eps figures; replaced by the published versio

Velocity and processivity of helicase unwinding of double-stranded nucleic acids

Helicases are molecular motors which unwind double-stranded nucleic acids (dsNA) in cells. Many helicases move with directional bias on single-stranded (ss) nucleic acids, and couple their directional translocation to strand separation. A model of the coupling between translocation and unwinding uses an interaction potential to represent passive and active helicase mechanisms. A passive helicase must wait for thermal fluctuations to open dsNA base pairs before it can advance and inhibit NA closing. An active helicase directly destabilizes dsNA base pairs, accelerating the opening rate. Here we extend this model to include helicase unbinding from the nucleic-acid strand. The helicase processivity depends on the form of the interaction potential. A passive helicase has a mean attachment time which does not change between ss translocation and ds unwinding, while an active helicase in general shows a decrease in attachment time during unwinding relative to ss translocation. In addition, we describe how helicase unwinding velocity and processivity vary if the base-pair binding free energy is changed.Comment: To appear in special issue on molecular motors, Journal of Physics - Condensed Matte

Relationships among seismic velocity, metamorphism, and seismic and aseismic fault slip in the Salton Sea Geothermal Field region

Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Solid Earth 120 (2015): 2600–2615, doi:10.1002/2014JB011579.The Salton Sea Geothermal Field is one of the most geothermally and seismically active areas in California and presents an opportunity to study the effect of high-temperature metamorphism on the properties of seismogenic faults. The area includes numerous active tectonic faults that have recently been imaged with active source seismic reflection and refraction. We utilize the active source surveys, along with the abundant microseismicity data from a dense borehole seismic network, to image the 3-D variations in seismic velocity in the upper 5 km of the crust. There are strong velocity variations, up to ~30%, that correlate spatially with the distribution of shallow heat flow patterns. The combination of hydrothermal circulation and high-temperature contact metamorphism has significantly altered the shallow sandstone sedimentary layers within the geothermal field to denser, more feldspathic, rock with higher P wave velocity, as is seen in the numerous exploration wells within the field. This alteration appears to have a first-order effect on the frictional stability of shallow faults. In 2005, a large earthquake swarm and deformation event occurred. Analysis of interferometric synthetic aperture radar data and earthquake relocations indicates that the shallow aseismic fault creep that occurred in 2005 was localized on the Kalin fault system that lies just outside the region of high-temperature metamorphism. In contrast, the earthquake swarm, which includes all of the M > 4 earthquakes to have occurred within the Salton Sea Geothermal Field in the last 15 years, ruptured the Main Central Fault (MCF) system that is localized in the heart of the geothermal anomaly. The background microseismicity induced by the geothermal operations is also concentrated in the high-temperature regions in the vicinity of operational wells. However, while this microseismicity occurs over a few kilometer scale region, much of it is clustered in earthquake swarms that last from hours to a few days and are localized near the MCF system.This work was funded by USGS NEHRP proposal G10AP00101 and NSF proposal 0943906.2015-10-2

Expression and Site-Directed Mutagenesis of Type III Polyketide Synthases

Natural products are a well-established source of drugs, and evolution has yielded polyketides such as leinamycin and iso-migrastatin that have demonstrated anti-tumor activity. Polyketides are large metabolites with a high degree of chemical variability and are commonly produced by soil bacteria. Polyketide synthases (PKS) exist as three different archetypes, and the reaction mechanisms of ketosynthases from all archetypes is not understood. Type III PKSs exist as an independently functioning ketosynthase (KS), which primarily use coenzyme A (CoA), with some exceptions, for the biosynthesis of polyketides. We elected to focus our studies on ketosynthases, because they are responsible for forming the carbon-carbon bonds seen in polyketides. To study these Type III PKS KS, we expressed Streptomyces coelicolor germicidin synthase (Gcs) and tetrahydroxynaphthlene synthase (THNS) in E. coli and mutant versions where the catalytic active cysteine was changed to a serine or glutamine. In previous studies, serine slowed the overall progress of the reaction, and glutamine abolished carbon-carbon bond formation but promoted malonyl-CoA decarboxylation. We verified our mutations using a third party organization’s fluorescent sequencing by dye termination services, as well as confirmed that an acceptable level of expression of our protein is occurring in our BL21 cell lines using SDS-PAGE and Fast Protein Liquid Chromatography (FPLC). Now that we have successfully expressed and mutated our protein, we can move forward and use substrate mimics in conjunction with our mutants to further understand the catalytic mechanism of ketosynthases

Proposal for a Performance Dashboard for the Monitoringof Water and Sewage Service Companies (WaSCs)

The water and sewage industry provides an essential service to the community, but it is characterized by natural monopoly tendencies of service suppliers. In this framework, it is very important to assist regulators with a small set of critical indicators (performance dashboard) for the evaluation and monitoring of the service provided by Water and Sewage Companies (WaSCs). The paper originates from the analysis of situation of Piemonte (Italy), where each regional and local body adopts a proprietary Performance Measurement System (PMS). In order to improve the coordination of information flow and to support the definition of common service standards, a methodology to merge existing PMSs and define a unique shared reference system is proposed. The Kaplan and Norton's Balanced Scorecard (BSC) is adopted as the reference model of this approach. BSC is widely recognized to be an exhaustive and balanced framework in describing the performances of an organization and ensures that all the operational aspects of WaSCs are adequately monitored. The output of the proposed procedure is a general performance dashboard for the monitoring of WaSCs. The dashboard is shown and some remarks about indicators properties are developed. In particular, this analysis highlights some common pitfalls originated by a ‘rushed' aggregation of several performance indicators. Description is supported by several example

Forecasting the cost of processing multi-join queries via hashing for main-memory databases (Extended version)

Database management systems (DBMSs) carefully optimize complex multi-join queries to avoid expensive disk I/O. As servers today feature tens or hundreds of gigabytes of RAM, a significant fraction of many analytic databases becomes memory-resident. Even after careful tuning for an in-memory environment, a linear disk I/O model such as the one implemented in PostgreSQL may make query response time predictions that are up to 2X slower than the optimal multi-join query plan over memory-resident data. This paper introduces a memory I/O cost model to identify good evaluation strategies for complex query plans with multiple hash-based equi-joins over memory-resident data. The proposed cost model is carefully validated for accuracy using three different systems, including an Amazon EC2 instance, to control for hardware-specific differences. Prior work in parallel query evaluation has advocated right-deep and bushy trees for multi-join queries due to their greater parallelization and pipelining potential. A surprising finding is that the conventional wisdom from shared-nothing disk-based systems does not directly apply to the modern shared-everything memory hierarchy. As corroborated by our model, the performance gap between the optimal left-deep and right-deep query plan can grow to about 10X as the number of joins in the query increases.Comment: 15 pages, 8 figures, extended version of the paper to appear in SoCC'1

Four problems with global carbon markets: a critical review

This article offers a critique of global carbon markets and trading, with a special focus on the Clean Development Mechanism of the Kyoto Protocol. It explores problems with the use of tradable permits to address climate change revolving around four areas: homogeneity, justice, gaming, and information. Homogeneity problems arise from the non-linear nature of climate change and sensitivity of emissions, which complicate attempts to calculate carbon offsets. Justice problems involve issues of dependency and the concentration of wealth among the rich, meaning carbon trading often counteracts attempts to reduce poverty. Gaming problems include pressures to promote high-volume, least-cost projects and the consequences of emissions leakage. Information problems encompass transaction costs related to carbon trading and market participation and the comparatively weak institutional capacity of project evaluators