Scalable Electron Correlation Methods. 5. Parallel Perturbative Triples Correction for Explicitly Correlated Local Coupled Cluster with Pair Natural Orbitals

A well-parallelized perturbative triples correction implementation for the pair natural orbital based coupled cluster method PNO-LCCSD­(T)-F12 is presented. A composite approach is adopted in addressing the coupling due to off-diagonal Fock matrix elements, in which the local triples amplitudes are iteratively solved using small domains of triples natural orbitals, and a semicanonical (T0) domain correction with larger domains is applied to reduce the domain errors. This treatment adds only about 20% to the computational cost of (T0) calculations with large domains, and the errors due to the use of small domains in the iterations are very small. In addition, a two-step triple list selection method is applied: First, an initial triple list is generated using LCCSD-F12 pair energy criteria, and the (T0) triples energies are computed using small domains. Second, this list is reduced by neglecting triples with small energy contributions, and the final calculation with large domains is only carried out for the reduced list. The cost of the (T) calculation scales asymptotically linear with the molecular size and shows excellent parallelization efficiency up to hundreds of CPU cores. The convergence of the (T) contribution to the relative energies of large molecular systems is carefully tested, and for most of the cases the results obtained with our default thresholds agree within ∼0.5 kcal mol^–1 with those computed with very tight thresholds. For all tested molecular systems where canonical calculations are still feasible, the PNO-LCCSD­(T)-F12 relative energies also agree within 0.5 kcal mol^–1 with the canonical CCSD­(T)-F12 results using the same F12 treatment. The (T) calculation generally takes 3–5 times the cost of the preceding PNO-LCCSD-F12 calculation, primarily due to the large number of triples required in obtaining accurate relative energies. We find that for large molecular systems the triple selection criteria used in previous local triples methods are insufficient, and a much larger number of triples are required than it was assumed so far. Still, using a commodity computer cluster, the PNO-LCCSD­(T)-F12 calculation of molecules with ∼100 atoms using augmented triple-ζ basis sets can be carried out in a few hours of elapsed time

Scalable Electron Correlation Methods. 4. Parallel Explicitly Correlated Local Coupled Cluster with Pair Natural Orbitals (PNO-LCCSD-F12)

We present an efficient explicitly correlated pair natural orbital local coupled cluster (PNO-LCCSD-F12) method. The method is an extension of our previously reported PNO-LCCSD approach (Schwilk et al., J. Chem. Theory Comput. 2017, 13, 3650−3675). Near linear scaling with the molecular size is achieved by using pair, domain, and projection approximations, local density fitting and local resolution of the identity, and by exploiting the sparsity of the local molecular orbitals as well as of the projected atomic orbitals. The effect of the various domain approximations is tested for a wide range of chemical reactions and intermolecular interactions. In accordance with previous findings, it is demonstrated that the F12 terms significantly reduce the domain errors. The convergence of the reaction and interaction energies with respect to the parameters that determine the domain sizes and pair approximations is extensively tested. The results obtained with our default thresholds agree within a few tenths of a kcal mol^–1 with the ones computed with very tight options. For cases where canonical calculations are still feasible, the relative energies of local and canonical calculations agree within similar error bounds. The PNO-LCCSD-F12 method needs only 25–40% more computer time than a corresponding PNO-LCCSD calculation while greatly improving the accuracy. Our program is well parallelized and capable of computing accurate correlation energies for molecules with more than 150 atoms using augmented triple-ζ basis sets and more than 5000 basis functions. Using several nodes of a small computer cluster, such calculations can be carried out within a few hours

Lignin-Containing Cellulose Nanofibril-Reinforced Polyvinyl Alcohol Hydrogels

Two lignin-containing cellulose nanofibril (LCNF) samples, produced from two unbleached kraft pulps with very different lignin contents, were used to produce reinforced polyvinyl alcohol (PVA) hydrogels. The effects of LCNF loading (0.25–2 wt %) and lignin content on the rheological and mechanical properties of the reinforced hydrogels were investigated. The 2 wt % LCNF-reinforced PVA hydrogels exhibited up to a 17-fold increase in storage modulus and a 4-fold increase in specific Young’s modulus over that of pure PVA hydrogel. Both the mechanical and rheological properties of LCNF-reinforced PVA hydrogels can be tuned by varying LCNF loading and LCNF lignin content. During LCNF production, lignin reduced cellulose depolymerization, resulting in LCNF with high aspect ratios that promoted entanglement and physical bridging of the hydrogel network. Free lignin particles generated during LCNF production acted as multifunctional nanospacers that increased porosity of the hydrogels. Because LCNFs were produced from unbleached chemical pulps, which have high yields and do not require bleaching, this study provides a more sustainable approach to utilize lignocelluloses to produce biomass-based hydrogels than by methods using commercial bleached pulps

Scandium-Substituted Na₃Zr₂(SiO₄)₂(PO₄) Prepared by a Solution-Assisted Solid-State Reaction Method as Sodium-Ion Conductors

As possible electrolyte materials for all-solid-state Na-ion batteries (NIBs), scandium-substituted Na₃Zr₂­(SiO₄)₂(PO₄) in the structure of NASICONs (Na superionic conductors) has received hardly any attention so far, although among all the trivalent cations, Sc³⁺ might be the most suitable substitution ion for Na₃Zr₂(SiO₄)₂(PO₄) because the ionic radius of Sc³⁺ (74.5 pm) is the closest to that of Zr⁴⁺ (72.0 pm). In this study, a solution-assisted solid-state reaction (SASSR) method is described, and a series of scandium-substituted Na₃Zr₂(SiO₄)₂(PO₄) with the formula of Na_3+<i>x</i>Sc_<i>x</i>Zr_2‑<i>x</i>(SiO₄)₂(PO₄) (NSZSP<i>x</i>, 0 ≤ <i>x</i> ≤ 0.6) have been prepared. This synthesis route can be applied for powder preparation on a large scale and at low cost. With increasing degrees of scandium substitution, the total conductivity of the samples also increases. An optimum total Na-ion conductivity of 4.0 × 10^–3 S cm^–1 at 25 °C is achieved by Na_3.4Sc_0.4Zr_1.6­(SiO₄)₂(PO₄) (NSZSP0.4), which is the best value of all reported polycrystalline Na-ion conductors. The possible reasons for such high conductivity are discussed

Whole-genome variance components linkage analysis using single-nucleotide polymorphisms versus microsatellites on quantitative traits of derived phenotypes from factor analysis of electroencephalogram waves-1

<p><b>Copyright information:</b></p><p>Taken from "Whole-genome variance components linkage analysis using single-nucleotide polymorphisms versus microsatellites on quantitative traits of derived phenotypes from factor analysis of electroencephalogram waves"</p><p></p><p>BMC Genetics 2005;6(Suppl 1):S15-S15.</p><p>Published online 30 Dec 2005</p><p>PMCID:PMC1866785.</p><p></p

The Association of Adiponectin Gene Promoter Variations with Non-Small Cell Lung Cancer in a Han Chinese Population

<div><p>Recently, in vitro studies have demonstrated that adiponectin has antiangiogenic and tumor growth-limiting properties. Additionally, serum adiponectin levels have been associated with the risk of several cancers; specifically, serum adiponectin was significantly lower in lung cancer patients with advanced-stage disease. In this study, we examined the association of adiponectin gene promoter variations associated with adiponectin gene expression and plasma levels in non-small cell lung cancer (NSCLC) in a Han Chinese population. A total of 319 patients with NSCLC and 489 healthy individuals were recruited to evaluate the association of four adiponectin gene promoter single-nucleotide polymorphisms (SNPs) (SNP-12140G>A, SNP-11426A>G, SNP-11391G>A and SNP-11377C>G) with NSCLS risk. Additionally, we constructed haplotypes of these four SNPs and evaluated the association of these haplotypes with NSCLS risk. Our results showed that among these four SNPs, only SNP-12140G>A was associated with NSCLC risk(P<0.05). The haplotype analysis showed that no haplotype was associated with NSCLC after performing a Bonferroni correction (P>0.05). Additionally, an association analysis of the four SNPs stratified into pathologic stages I+II and III+IV showed that these SNPs did not exhibit significant differences between pathologic stages I+II and III+IV. Moreover, we did not observe any differences in allele and genotype frequency for these SNPs between adenocarcinoma and squamous cell carcinoma. Our results indicated that the G allele of SNP-12140may be a risk factor for NSCLC (OR = 1.516; 95% CI: 1.098–2.094) in this Han Chinese population.</p></div

Different inheritance models analysis of the SNP-11377C>G in adiponectin gene promoter between NSCLC and control groups.

<p>Different inheritance models analysis of the SNP-11377C>G in adiponectin gene promoter between NSCLC and control groups.</p

Whole-genome variance components linkage analysis using single-nucleotide polymorphisms versus microsatellites on quantitative traits of derived phenotypes from factor analysis of electroencephalogram waves-0

<p><b>Copyright information:</b></p><p>Taken from "Whole-genome variance components linkage analysis using single-nucleotide polymorphisms versus microsatellites on quantitative traits of derived phenotypes from factor analysis of electroencephalogram waves"</p><p></p><p>BMC Genetics 2005;6(Suppl 1):S15-S15.</p><p>Published online 30 Dec 2005</p><p>PMCID:PMC1866785.</p><p></p

Association analysis of the adiponectin promoter SNP-12140G>A, SNP-11426A>G, SNP-11377C>G between adenocarcinoma (AC) and squamous cell carcinoma (SCC).

<p>Association analysis of the adiponectin promoter SNP-12140G>A, SNP-11426A>G, SNP-11377C>G between adenocarcinoma (AC) and squamous cell carcinoma (SCC).</p

Comparison of genotypic and allelic distribution of SNP-12140G>A, SNP-11426A>G, SNP-11377C>G between pathologic stages I+II and III+IV.

<p>Comparison of genotypic and allelic distribution of SNP-12140G>A, SNP-11426A>G, SNP-11377C>G between pathologic stages I+II and III+IV.</p