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. Here, we offer the software Puzzle Hi-C, which uses Hi-C reads to accurately assign contigs or scaffolds to chromosomes. Puzzle Hi-C uses the triangle region instead of the square region to count interactions in a Hi-C heatmap. This strategy dramatically diminishes scaffolding interference caused by long-range interactions. This software also introduces a dynamic, triangle window strategy during assembly. Initially small, the window expands with interactions to produce more effective clustering. Puzzle Hi-C outperforms available scaffolding tools.

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. Effects of basis sets and those of locality approximation (LA), T-move approximation (T-move), and determinant localization approximation (DLA) schemes in dealing with the nonlocal part of pseudopotentials on FN-DMC results are evaluated. According to our results, diffuse basis functions are important in achieving reliable barrier heights and complexation energies with FN-DMC, although the cardinal number of the basis set is more important than diffuse basis functions on total energies of these systems. Our results also show that the time step bias with DLA and LA is smaller than T-move; however, the time step bias of DMC energies with respect to time steps using the T-move is roughly linear up to 0.06 a.u., while this is not the case with LA and DLA. Barrier heights and complexation energies with FN-DMC using these three schemes are always within chemical accuracy. Taking into account the fact that T-move and DLA are typically more stable than LA, FN-DMC calculations with the T-move or DLA scheme and basis sets containing diffuse basis functions are suggested for barrier heights of multiple proton exchanges and complexation energies of hydrogen-bonded clusters.

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. The error of atomization energies with DMC using single-determinant-Jastrow (SDJ) trial wavefunctions has been shown to be somewhat larger than that of CCSD(T) for many molecules. However, cohesive energies with DMC using SDJ for Mgn with n ≤ 7 are in excellent agreement with those of CCSD(T) using the aug-cc-pVQZ basis set, with a difference of less than 1 kcal/mol. DMC results are employed to investigate the performance of different XC functionals on magnesium clusters. Our results indicate that the PBE0 functional is the best XC functional for determining the lowest-energy isomer when compared with DMC results, while the RPBE functional is the best XC functional for calculating cohesive energies per atom of these magnesium clusters with a mean absolute error of 0.5 kcal/mol. These XC functionals are expected to provide reasonable results for even larger magnesium clusters.

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. These results may have potential applications in areas such as the inverse scattering problem.