Puzzle Hi-C: An accurate scaffolding software.

High-quality, chromosome-scale genomes are essential for genomic analyses. Analyses, including 3D genomics, epigenetics, and comparative genomics rely on a high-quality genome assembly, which is often accomplished with the assistance of Hi-C data. Curation of genomes reveal that current Hi-C-assisted scaffolding algorithms either generate ordering and orientation errors or fail to assemble high-quality chromosome-level scaffolds.

Diffusion Monte Carlo method for barrier heights of multiple proton exchanges and complexation energies in small water, ammonia, and hydrogen fluoride clusters.

Proton exchange reactions are of key importance in many processes in water. However, it is nontrivial to achieve reliable barrier heights for multiple proton exchanges and complexation energies in hydrogen-bonded systems theoretically. Performance of the fixed-node diffusion quantum Monte Carlo (FN-DMC) with the single-Slater-Jastrow trial wavefunction on total energies, barrier heights of multiple proton exchanges, and complexation energies of small water, ammonia, and hydrogen fluoride clusters is investigated in this study.

Diffusion quantum Monte Carlo study on magnesium clusters as large as nanoparticles.

Nanoscale magnesium clusters are important potential hydrogen storage materials, and density functional theory (DFT) is mainly used for their theoretical investigation. The results of the coupled-cluster theory at the singles and doubles level with a perturbative treatment of triples [CCSD(T)] were employed previously to choose proper exchange-correlation (XC) functionals in DFT calculations for magnesium clusters, but it is too expensive to be applied to Mgn with n > 7. The diffusion Monte Carlo (DMC) method is employed in this work to study magnesium clusters up to nanosize.

Spectral behavior of light waves on scattering from a semi-soft-boundary medium with spectral dependence.

The far-zone behavior of polychromatic light waves on scattering from an isotropic semi-soft-boundary medium with spectral dependence is considered, and both spectral shifts and spectral switches of the scattered field have been discussed. It is shown that the spectral behavior of the far-zone scattered field is influenced by the structural function width of the dielectric susceptibility of the scattering medium. In particular, the structural function width of the dielectric susceptibility of the scattering medium plays an important role in the direction at which the spectral switch occurs.