Community Code Verification Exercise for Simulating Sequences of Earthquakes and Aseismic Slip (SEAS)

Numerical simulations of sequences of earthquakes and aseismic slip (SEAS) have made great progress over past decades to address important questions in earthquake physics. However, significant challenges in SEAS modeling remain in resolving multiscale interactions between earthquake nucleation, dynamic rupture, and aseismic slip, and understanding physical factors controlling observables such as seismicity and ground deformation. The increasing complexity of SEAS modeling calls for extensive efforts to verify codes and advance these simulations with rigor, reproducibility, and broadened impact. In 2018, we initiated a community code‐verification exercise for SEAS simulations, supported by the Southern California Earthquake Center. Here, we report the findings from our first two benchmark problems (BP1 and BP2), designed to verify different computational methods in solving a mathematically well‐defined, basic faulting problem. We consider a 2D antiplane problem, with a 1D planar vertical strike‐slip fault obeying rate‐and‐state friction, embedded in a 2D homogeneous, linear elastic half‐space. Sequences of quasi‐dynamic earthquakes with periodic occurrences (BP1) or bimodal sizes (BP2) and their interactions with aseismic slip are simulated. The comparison of results from 11 groups using different numerical methods show excellent agreements in long‐term and coseismic fault behavior. In BP1, we found that truncated domain boundaries influence interseismic stressing, earthquake recurrence, and coseismic rupture, and that model agreement is only achieved with sufficiently large domain sizes. In BP2, we found that complexity of fault behavior depends on how well physical length scales related to spontaneous nucleation and rupture propagation are resolved. Poor numerical resolution can result in artificial complexity, impacting simulation results that are of potential interest for characterizing seismic hazard such as earthquake size distributions, moment release, and recurrence times. These results inform the development of more advanced SEAS models, contributing to our further understanding of earthquake system dynamics

Community Code Verification Exercise for Simulating Sequences of Earthquakes and Aseismic Slip (SEAS)

Numerical simulations of sequences of earthquakes and aseismic slip (SEAS) have made great progress over past decades to address important questions in earthquake physics. However, significant challenges in SEAS modeling remain in resolving multiscale interactions between earthquake nucleation, dynamic rupture, and aseismic slip, and understanding physical factors controlling observables such as seismicity and ground deformation. The increasing complexity of SEAS modeling calls for extensive efforts to verify codes and advance these simulations with rigor, reproducibility, and broadened impact. In 2018, we initiated a community code‐verification exercise for SEAS simulations, supported by the Southern California Earthquake Center. Here, we report the findings from our first two benchmark problems (BP1 and BP2), designed to verify different computational methods in solving a mathematically well‐defined, basic faulting problem. We consider a 2D antiplane problem, with a 1D planar vertical strike‐slip fault obeying rate‐and‐state friction, embedded in a 2D homogeneous, linear elastic half‐space. Sequences of quasi‐dynamic earthquakes with periodic occurrences (BP1) or bimodal sizes (BP2) and their interactions with aseismic slip are simulated. The comparison of results from 11 groups using different numerical methods show excellent agreements in long‐term and coseismic fault behavior. In BP1, we found that truncated domain boundaries influence interseismic stressing, earthquake recurrence, and coseismic rupture, and that model agreement is only achieved with sufficiently large domain sizes. In BP2, we found that complexity of fault behavior depends on how well physical length scales related to spontaneous nucleation and rupture propagation are resolved. Poor numerical resolution can result in artificial complexity, impacting simulation results that are of potential interest for characterizing seismic hazard such as earthquake size distributions, moment release, and recurrence times. These results inform the development of more advanced SEAS models, contributing to our further understanding of earthquake system dynamics

Supplementary material for 3D Acoustic-Elastic Coupling with Gravity: The Dynamics of the 2018 Palu, Sulawesi Earthquake and Tsunami

This repository contains the supplementary files for our SC21 submission: "3D Acoustic-Elastic Coupling with Gravity: The Dynamics of the 2018 Palu, Sulawesi Earthquake and Tsunami". It contains the input data for all simulations. For more details, please refer to the included README.md files. The directory "seissol-sc21-revision-source-code" contains the version of SeisSol that we used

SFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs)

Abstract New technologies enabling genome-wide interrogation have led to a large and rapidly growing number of autism spectrum disorder (ASD) candidate genes. Although encouraging, the volume and complexity of these data make it challenging for scientists, particularly non-geneticists, to comprehensively evaluate available evidence for individual genes. Described here is the Gene Scoring module within SFARI Gene 2.0 (https://gene.sfari.org/autdb/GS_Home.do), a platform developed to enable systematic community driven assessment of genetic evidence for individual genes with regard to ASD

HIV-1 subtypes and recombinants in Northern Tanzania: distribution of viral quasispecies.

This study analyzed the distribution and prevalence of HIV-1 subtypes, multiplicity of HIV-1 infection, and frequency of inter-subtype recombination among HIV-1-infected female bar and hotel workers in Moshi, Kilimanjaro Region, Tanzania, from 2004 to 2007. The HIV-1 viral sequences spanning the V1-C5 region of HIV-1 env gp120 were analyzed from 50 subjects by single genome amplification and sequencing (SGA/S) technique. A total of 1740 sequences were amplified and sequenced from the HIV-1 proviral DNA template. The median env sequences analyzed per subject per two time points was 38 (IQR 28-50) over one year of HIV infection. In a subset of 14 subjects, a total of 239 sequences were obtained from HIV-1 RNA template at the baseline visit. The most prevalent HIV-1 subtypes were A1 (56%) and C (30%), while HIV-1 subtype D and inter-subtype recombinant viruses were found in 6% and 8% of subjects respectively. Transmission of multiple HIV-1 variants was evident in 27% of the subjects infected with pure HIV-1 subtypes A1, C, or D. The HIV-1 inter-subtype recombinants were found in 8% including HIV-1 C/A, D/A, and complex mosaic recombinants. Multiple viral variants were found in two subjects infected with inter-subtype recombinants. One subject harbored quasispecies of both pure HIV-1 A1 and C/A recombinant. The other subject was infected with two complex mosaic inter-subtype recombinant variants belonging to subtype D. HIV-1 multiple infections and ongoing recombination contribute significantly to the genetic diversity of circulating HIV-1 in Tanzania and have important implications for vaccine design and the development of therapeutic strategies

A genome-wide linkage and association scan reveals novel loci for autism

Although autism is a highly heritable neurodevelopmental disorder, attempts to identify specific susceptibility genes have thus far met with limited success 1. Genome-wide association studies (GWAS) using half a million or more markers, particularly those with very large sample sizes achieved through meta-analysis, have shown great success in mapping genes for other complex genetic traits (http://www.genome.gov/26525384). Consequently, we initiated a linkage and association mapping study using half a million genome-wide SNPs in a common set of 1,031 multiplex autism families (1,553 affected offspring). We identified regions of suggestive and significant linkage on chromosomes 6q27 and 20p13, respectively. Initial analysis did not yield genome-wide significant associations; however, genotyping of top hits in additional families revealed a SNP on chromosome 5p15 (between SEMA5A and TAS2R1) that was significantly associated with autism (P = 2 × 10(−7)). We also demonstrated that expression of SEMA5A is reduced in brains from autistic patients, further implicating SEMA5A as an autism susceptibility gene. The linkage regions reported here provide targets for rare variation screening while the discovery of a single novel association demonstrates the action of common variants