The genome sequence of a metallic wood-boring beetle, Agrilus cyanescens (Ratzeburg, 1837).

We present a genome assembly from an individual female Agrilus cyanescens (metallic wood-boring beetle; Arthropoda; Insecta; Coleoptera; Buprestidae). The genome sequence is 292.3 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.91 kilobases in length.

The genome sequence of the Early Thorn, Selenia dentaria (Fabricius, 1775).

We present a genome assembly from an individual male Selenia dentaria (the Early Thorn; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 1,030.8 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.41 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,390 protein coding genes.

The genome sequence of the brimstone moth, Opisthograptis luteolata (Linnaeus, 1758).

We present a genome assembly from an individual male Opisthograptis luteolata (the brimstone moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 363 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.7 kilobases in length.

The genome sequence of the black arches, Lymantria monacha (Linnaeus, 1758).

We present a genome assembly from an individual male Lymantria monacha (the black arches; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 916 megabases in span. The majority of the assembly (99.99%) is scaffolded into 28 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome was also assembled, and is 15.6 kilobases in length.

Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations.

The growing interest in the complexity of biological interactions is continuously driving the need to increase system size in biophysical simulations, requiring not only powerful and advanced hardware but adaptable software that can accommodate a large number of atoms interacting through complex forcefields. To address this, we developed and implemented strategies in the GENESIS molecular dynamics package designed for large numbers of processors. Long-range electrostatic interactions were parallelized by minimizing the number of processes involved in communication. A novel algorithm was implemented for nonbonded interactions to increase single instruction multiple data (SIMD) performance, reducing memory usage for ultra large systems. Memory usage for neighbor searches in real-space nonbonded interactions was reduced by approximately 80%, leading to significant speedup. Using experimental data describing physical 3D chromatin interactions, we constructed the first atomistic model of an entire gene locus (GATA4). Taken together, these developments enabled the first billion-atom simulation of an intact biomolecular complex, achieving scaling to 65,000 processes (130,000 processor cores) with 1 ns/day performance. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.