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Abstract The Sc2.0 global consortium to design and construct a synthetic genome based on theSaccharomyces cerevisiaegenome commenced in 2006, comprising 16 synthetic chromosomes and a new-to-nature tRNA neochromosome. In this paper we describe assembly and debugging of the 902,994-bp syntheticSaccharomyces cerevisiaechromosomesynXVIof the Sc2.0 project. Application of the CRISPR D-BUGS protocol identified defective loci, which were modified to improve sporulation and recover wild-type like growth when grown on glycerol as a sole carbon source when grown at 37˚C. LoxPsym sites inserted downstream of dubious open reading frames impacted the 5’ UTR of genes required for optimal growth and were identified as a systematic cause of defective growth. Based on lessons learned from analysis of Sc2.0 defects andsynXVI, anin-silicoredesign of thesynXVIchromosome was performed, which can be used as a blueprint for future synthetic yeast genome designs. Thein-silicoredesign ofsynXVIincludes reduced PCR tag frequency, modified chunk and megachunk termini, and adjustments to allocation of loxPsym sites and TAA stop codons to dubious ORFs. This redesign provides a roadmap into applications of Sc2.0 strategies in non-yeast organisms. 

One of the most promising avenues to perform numerical evolutions in theories beyond general relativity is the approach, a proposal in which new “driver” equations are added to the evolution equations in a way that allows for stable numerical evolutions. In this direction, we extend the numerical relativity code p to evolve a “fixed” version of scalar Gauss-Bonnet theory in the decoupling limit, a phenomenologically interesting theory that allows for hairy black hole solutions in vacuum. We focus on isolated black hole systems both with and without linear and angular momentum, and propose a new driver equation to improve the recovery of such stationary solutions. We demonstrate the effectiveness of the latter by numerically evolving black holes that undergo spontaneous scalarization using different driver equations. Finally, we evaluate the accuracy of the obtained solutions by comparing with the original unaltered theory. Published by the American Physical Society2024 

SpECTRE is an open-source code for multi-scale, multi-physics problems in astrophysics and gravitational physics. In the future, we hope that it can be applied to problems across discipline boundaries in fluid dynamics, geoscience, plasma physics, nuclear physics, and engineering. It runs at petascale and is designed for future exascale computers. SpECTRE is being developed in support of our collaborative Simulating eXtreme Spacetimes (SXS) research program into the multi-messenger astrophysics of neutron star mergers, core-collapse supernovae, and gamma-ray bursts. 

Abstract Binary black holes are the most abundant source of gravitational-wave observations. Gravitational-wave observatories in the next decade will require tremendous increases in the accuracy of numerical waveforms modeling binary black holes, compared to today’s state of the art. One approach to achieving the required accuracy is using spectral-type methods that scale to many processors. Using theSpECTREnumerical-relativity (NR) code, we present the first simulations of a binary black hole inspiral, merger, and ringdown using discontinuous Galerkin (DG) methods. The efficiency of DG methods allows us to evolve the binary through ∼ 18 orbits at reasonable computational cost. We then useSpECTRE’s Cauchy Characteristic Evolution (CCE) code to extract the gravitational waves at future null infinity. The open-source nature ofSpECTREmeans this is the first time a spectral-type method for simulating binary black hole evolutions is available to the entire NR community.