Sign Learning Kink based Quantum Monte Carlo Applied to Multiple Large Systems H\u3csub\u3e2\u3c/sub\u3eO, N\u3csub\u3e2\u3c/sub\u3e, F\u3csub\u3e2\u3c/sub\u3e

A Sign Learning Kink (SiLK) based Quantum Monte Carlo (QMC) method is used to calculate the ground state energies for H2O, N2 and F2 molecules. This method has two stages. The first (learning stage) reduces the minus sign problem by optimizing the states which are used in the second (QMC stage). I test the method in Single, Double excitations (SD), Single, Double, and Triple excitations (SDT), and Full Configuration Interaction (FCI) vector spaces. I also perform exact diagonalization in those vector spaces as a benchmark. In each vector space and for each molecule, I perform SiLK QMC for different bond lengths demonstrating that the SiLK QMC is applicable to many systems

Sign learning kink-based (SiLK) quantum Monte Carlo for molecular systems

The Sign Learning Kink (SiLK) based Quantum Monte Carlo (QMC) method is used to calculate the ab initio ground state energies for multiple geometries of the H$_{2}$O, N$_2$, and F$_2$ molecules. The method is based on Feynman's path integral formulation of quantum mechanics and has two stages. The first stage is called the learning stage and reduces the well-known QMC minus sign problem by optimizing the linear combinations of Slater determinants which are used in the second stage, a conventional QMC simulation. The method is tested using different vector spaces and compared to the results of other quantum chemical methods and to exact diagonalization. Our findings demonstrate that the SiLK method is accurate and reduces or eliminates the minus sign problem.Comment: 20 pages, 9 figures, to appear in the Journal of Chemical Physic

An integrated global chemomics and system biology approach to analyze the mechanisms of the traditional Chinese medicinal preparation Eriobotrya japonica – Fritillaria usuriensis dropping pills for pulmonary diseases

The quality of each herb and CBPP extract, and the targets and pathway predicted by PharmMapper and KEGG. (DOC 4286 kb

Chemical composition and source apportionment of PM _2.5 in urban areas of Xiangtan, central south China

Xiangtan, South China, is characterized by year-round high relative humidity and very low wind speeds. To assess levels of PM2.5, daily samples were collected from 2016 to 2017 at two urban sites. The mass concentrations of PM2.5 were in the range of 30⁻217 µg/m3, with the highest concentrations in winter and the lowest in spring. Major water-soluble ions (WSIIs) and total carbon (TC) accounted for 58⁻59% and 21⁻24% of the PM2.5 mass, respectively. Secondary inorganic ions (SO42−, NO3−, and NH4+) dominated the WSIIs and accounted for 73% and 74% at the two sites. The concentrations of K, Fe, Al, Sb, Ca, Zn, Mg, Pb, Ba, As, and Mn in the PM2.5 at the two sites were higher than 40 ng/m3, and decreased in the order of winter > autumn > spring. Enrichment factor analysis indicates that Co, Cu, Zn, As, Se, Cd, Sb, Tl, and Pb mainly originates from anthropogenic sources. Source apportionment analysis showed that secondary inorganic aerosols, vehicle exhaust, coal combustion and secondary aerosols, fugitive dust, industrial emissions, steel industry are the major sources of PM2.5, contributing 25⁻27%, 21⁻22%, 19⁻21%, 16⁻18%, 6⁻9%, and 8⁻9% to PM2.5 mass

Mechanism Assay of Honeysuckle for Heat-Clearing Based on Metabolites and Metabolomics

Nonsteroidal anti-inflammatory drugs (NSAIDs), such as cyclooxygenase (Cox)-1/2 inhibitor, have emerged as potent antipyretics and analgesics. However, few herbs with Cox-1/2 inhibitory activity are commonly used for heat-clearing in China. Although these are known to have antipyretic activity, there is a lack of molecular data supporting their activity. Using the traditional Chinese medicine herb honeysuckle (Hon) as an example, we explored key antipyretic active compounds and their mechanisms of action by assessing their metabolites and metabolomics. Mitogen-activated protein kinase (MAPK) 3 and protein kinase B (AKT) 1 were suggested as key targets regulated primarily by chlorogenic acid (CA) and swertiamarin (SWE). CA and SWE synergistically inhibited the production of interleukin (IL)-1 and IL-6, alleviated generation of prostaglandin E2, and played an antipyretic role equivalent to honeysuckle extract at the same dose contents within 3 h. Collectively, these findings indicated that lipopolysaccharide-induced fever can be countered by CA with SWE synergistically, allowing the substitution of a crude extract of complex composition with active compounds. Our findings demonstrated that, unlike the traditional NSAIDs, the Hon extract showed a remote and indirect mechanism for alleviating fever that depended on the phosphatidylinositol-3-kinase–AKT and MAPK pathways by regulating the principal mediator of inflammation

The Sign Learning Kink (SiLK) based Quantum Monte Carlo for Molecular Systems

Purpose The Sign Learning Kink (SiLK) based Quantum Monte Carlo (QMC) method is based on Feynman\u27s path integral formulation of quantum mechanics, and can reduce the minus sign problem when calculating energies in atomic and molecular systems. The code requires as input the one and two electron integrals, which usually are computed using the NWChem package. Example input files are distributed with this package. The code also requires an parameter file, specifying run-time parameters such as input/output directories, or specific code parameters. For all example inputs a corresponding parameter file is distributed as well. Systems The code has been tuned for cluster systems supporting MPI and Fortran 90 compilers. Contents This package contains the source code and sample data. Acknowledgments This code was developed by Xiaoyao Ma ([email protected]) and Frank Löffler ([email protected]) with the assistance of Randall Hall ([email protected]), Karol Kowalski ([email protected]), Mark Jarrell ([email protected]), and Juana Moreno ([email protected]

Glycyrrhetinic acid binds to the conserved P-loop region and interferes with the interaction of RAS-effector proteins

Members of the RAS proto-oncogene superfamily are indispensable molecular switches that play critical roles in cell proliferation, differentiation, and cell survival. Recent studies have attempted to prevent the interaction of RAS/GTP with RAS guanine nucleotide exchange factors (GEFs), impair RAS-effector interactions, and suppress RAS localization to prevent oncogenic signalling. The present study aimed to investigate the effect of the natural triterpenoic acid inhibitor glycyrrhetinic acid, which is isolated from the roots of Glycyrrhiza plant species, on RAS stability. We found that glycyrrhetinic acid may bind to the P-loop of RAS and alter its stability. Based on our biochemical tests and structural analysis results, glycyrrhetinic acid induced a conformational change in RAS. Meanwhile, glycyrrhetinic acid abolishes the function of RAS by interfering with the effector protein RAF kinase activation and RAS/MAPK signalling. KEY WORDS: Glycyrrhetinic acid, RAS, Allosteric inhibitor, RAS/MAPK signallin

Qingfei Xiaoyan Wan, a traditional Chinese medicine formula, ameliorates Pseudomonas aeruginosa–induced acute lung inflammation by regulation of PI3K/AKT and Ras/MAPK pathways

Gram-negative pathogen–induced nosocomial infections and resistance are a most serious menace to global public health. Qingfei Xiaoyan Wan (QF), a traditional Chinese medicine (TCM) formula, has been used clinically in China for the treatment of upper respiratory tract infections, acute or chronic bronchitis and pulmonary infection. In this study, the effects of QF on Pseudomonas aeruginosa–induced acute pneumonia in mice were evaluated. The mechanisms by which four typical anti-inflammatory ingredients from QF, arctigenin (ATG), cholic acid (CLA), chlorogenic acid (CGA) and sinapic acid (SPA), regulate anti-inflammatory signaling pathways and related targets were investigated using molecular biology and molecular docking techniques. The results showed that pretreatment with QF significantly inhibits the release of cytokines (TNF-α and IL-6) and chemokines (IL-8 and RANTES), reduces leukocytes recruitment into inflamed tissues and ameliorates pulmonary edema and necrosis. In addition, ATG was identified as the primary anti-inflammatory agent with action on the PI3K/AKT and Ras/MAPK pathways. CLA and CGA enhanced the actions of ATG and exhibited synergistic NF-κB inactivation effects possibly via the Ras/MAPK signaling pathway. Moreover, CLA is speculated to target FGFR and MEK firstly. Overall, QF regulated the PI3K/AKT and Ras/MAPK pathways to inhibit pathogenic bacterial infections effectively