Coupled cluster benchmarks of water monomers and dimers extracted from DFT liquid water: the importance of monomer deformations

To understand the performance of popular density-functional theory (DFT) exchange-correlation (xc) functionals in simulations of liquid water, water monomers and dimers were extracted from a PBE simulation of liquid water and examined with coupled cluster with single and double excitations plus a perturbative correction for connected triples [CCSD(T)]. CCSD(T) reveals that most of the dimers are unbound compared to two gas phase equilibrium water monomers, largely because monomers within the liquid have distorted geometries. Of the three xc functionals tested, PBE and BLYP systematically underestimate the cost of the monomer deformations and consequently predict too large dissociation energies between monomers within the dimers. This is in marked contrast to how these functionals perform for an equilibrium water dimer and other small water clusters in the gas phase, which only have moderately deformed monomers. PBE0 reproduces the CCSD(T) monomer deformation energies very well and consequently the dimer dissociation energies much more accurately than PBE and BLYP. Although this study is limited to water monomers and dimers, the results reported here may provide an explanation for the overstructured radial distribution functions routinely observed in BLYP and PBE simulations of liquid water and are of relevance to water in other phases and to other associated molecular liquids.Comment: 10 pages, 8 figures, Submitted to Journal of Chemical Physics, Related information can be found in http://www.fhi-berlin.mpg.de/th

Gas-Liquid Nucleation in Two Dimensional System

We study the nucleation of the liquid phase from a supersaturated vapor in two dimensions (2D). Using different Monte Carlo simulation methods, we calculate the free energy barrier for nucleation, the line tension and also investigate the size and shape of the critical nucleus. The study is carried out at an intermediate level of supersaturation(away from the spinodal limit). In 2D, a large cut-off in the truncation of the Lennard-Jones (LJ) potential is required to obtain converged results, whereas low cut-off (say, $2.5\sigma$ is generally sufficient in three dimensional studies, where $\sigma$ is the LJ diameter) leads to a substantial error in the values of line tension, nucleation barrier and characteristics of the critical cluster. It is found that in 2D, the classical nucleation theory (CNT) fails to provide a reliable estimate of the free energy barrier. It underestimates the barrier by as much as 70% at the saturation-ratio S=1.1 (defined as S=P/PC, where PC is the coexistence pressure at reduced temperature $T^{\star}= 0.427$). Interestingly, CNT has been found to overestimate the nucleation free energy barrier in three dimensional (3D)systems near the triple point. In fact, the agreement with CNT is worse in 2D than in 3D. Moreover, the existing theoretical estimate of the line tension overestimates the value significantly.Comment: 24 pages, 8 figure

Ab initio theory and modeling of water

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice I{\it h} at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner

SNP discovery in proso millet (\u3ci\u3ePanicum miliaceum\u3c/i\u3e L.) using lowpass genome sequencing

Domesticated ~10,000 years ago in northern China, Proso millet (Panicum miliaceum L.) is a climate-resilient and human health-promoting cereal crop. The genome size of this self-pollinated allotetraploid is 923 Mb. Proso millet seeds are an important part of the human diet in many countries. In the USA, its use is restricted to the birdseed and pet food market. Proso millet is witnessing gradual demand in the global human health and wellness food market owing to its health-promoting properties such as low glycemic index and gluten-free. The breeding efforts for developing improved proso millet cultivars are hindered by the dearth of genomic resources available to researchers. The publication of the reference genome and availability of costeffective NGS methodologies could lead to the identification of high-quality genetic variants, which can be incorporated into breeding pipelines. Here, we report the identification of single-nucleotide polymorphisms (SNPs) by low-pass (1x) genome sequencing of 85 diverse proso millet accessions from 23 different countries. The 2 x 150 bp Illumina paired-end reads generated after sequencing were aligned to the proso millet reference genome. The resulting sequence alignment information was used to call SNPs. We obtained 972,863 bi-allelic SNPs after quality filtering of the raw SNPs. These SNPs were used to assess the population structure and phylogenetic relationships among the accessions. Most of the accessions were found to be highly inbred with heterozygosity ranging between .05 and .20. Principal component analysis (PCA) showed that PC1 (principal component) and PC2 explained 19% of the variability in the population. PCA also clustered all the genotypes into three groups. A neighbor-joining tree clustered the genotypes into four distinct groups exhibiting diverse representation within the population. The SNPs identified in our study could be used for molecular breeding and genetics research (e.g., genetic and association mapping, and population genetics) in proso millet after proper validation

Noncovalent Interactions by QMC: Speedup by One-Particle Basis-Set Size Reduction

While it is empirically accepted that the fixed-node diffusion Monte-Carlo (FN-DMC) depends only weakly on the size of the one-particle basis sets used to expand its guiding functions, limits of this observation are not settled yet. Our recent work indicates that under the FN error cancellation conditions, augmented triple zeta basis sets are sufficient to achieve a benchmark level of 0.1 kcal/mol in a number of small noncovalent complexes. Here we report on a possibility of truncation of the one-particle basis sets used in FN-DMC guiding functions that has no visible effect on the accuracy of the production FN-DMC energy differences. The proposed scheme leads to no significant increase in the local energy variance, indicating that the total CPU cost of large-scale benchmark noncovalent interaction energy FN-DMC calculations may be reduced.Comment: ACS book chapter, accepte