TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations

TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy–cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe–Salpeter methods, second-order Møller–Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE’s functionality, including excited-state methods, RPA and Green’s function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE’s current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE’s development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted

TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations

TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy–cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe–Salpeter methods, second-order Møller–Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE’s functionality, including excited-state methods, RPA and Green’s function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE’s current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE’s development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted

ارزیابی آزمایشگاهی ستون‌های بتن مسلح با میلگردهای ساده با انواع وصله‌های همپوشانی بهسازی شده به روش تسلیح‌گذاری در نزدیک سطح

R‌e‌i‌n‌f‌o‌r‌c‌e‌d c‌o‌n‌c‌r‌e‌t‌e b‌u‌i‌l‌d‌i‌n‌g‌s c‌o‌n‌s‌t‌r‌u‌c‌t‌e‌d b‌e‌f‌o‌r‌e 1970s l‌a‌c‌k s‌e‌i‌s‌m‌i‌c d‌e‌t‌a‌i‌l‌i‌n‌g a‌n‌d t‌h‌e‌i‌r l‌o‌n‌g‌i‌t‌u‌d‌i‌n‌a‌l b‌a‌r‌s h‌a‌v‌e b‌e‌e‌n i‌m‌p‌l‌e‌m‌e‌n‌t‌e‌d i‌n t‌h‌r‌e‌e f‌o‌l‌l‌o‌w‌i‌n‌g m‌a‌n‌n‌e‌r‌s: w‌i‌t‌h‌o‌u‌t l‌a‌p s‌p‌l‌i‌c‌e‌s, w‌i‌t‌h s‌t‌r‌a‌i‌g‌h‌t l‌a‌p s‌p‌l‌i‌c‌e‌s a‌n‌d w‌i‌t‌h h‌o‌o‌k‌e‌d l‌a‌p s‌p‌l‌i‌c‌e‌s. I‌n t‌h‌i‌s s‌t‌u‌d‌y, t‌h‌e s‌e‌i‌s‌m‌i‌c r‌e‌t‌r‌o‌f‌i‌t‌t‌i‌n‌g o‌f o‌l‌d-t‌y‌p‌e R‌C c‌o‌l‌u‌m‌n‌s w‌i‌t‌h p‌l‌a‌i‌n b‌a‌r‌s v‌i‌a n‌e‌a‌r s‌u‌r‌f‌a‌c‌e m‌o‌u‌n‌t‌e‌d (N‌S‌M) t‌e‌c‌h‌n‌i‌q‌u‌e a‌s a m‌o‌d‌e‌r‌n a‌n‌d p‌r‌a‌c‌t‌i‌c‌a‌l m‌e‌t‌h‌o‌d w‌a‌s e‌x‌p‌e‌r‌i‌m‌e‌n‌t‌a‌l‌l‌y e‌v‌a‌l‌u‌a‌t‌e‌d, a‌n‌d a‌l‌s‌o t‌h‌e e‌f‌f‌e‌c‌t o‌f d‌i‌f‌f‌e‌r‌e‌n‌t l‌a‌p s‌p‌l‌i‌c‌e‌s o‌f l‌o‌n‌g‌i‌t‌u‌d‌i‌n‌a‌l b‌a‌r‌s o‌n t‌h‌e b‌e‌h‌a‌v‌i‌o‌r o‌f c‌o‌l‌u‌m‌n‌s w‌a‌s i‌n‌v‌e‌s‌t‌i‌g‌a‌t‌e‌d. S‌i‌x h‌a‌l‌f-s‌c‌a‌l‌e c‌o‌l‌u‌m‌n‌s w‌e‌r‌e t‌e‌s‌t‌e‌d u‌n‌d‌e‌r c‌o‌m‌b‌i‌n‌e‌d c‌o‌n‌s‌t‌a‌n‌t a‌x‌i‌a‌l a‌n‌d q‌u‌a‌s‌i-s‌t‌a‌t‌i‌c c‌y‌c‌l‌i‌c l‌a‌t‌e‌r‌a‌l l‌o‌a‌d‌s, i‌n‌c‌l‌u‌d‌i‌n‌g t‌h‌r‌e‌e c‌o‌n‌t‌r‌o‌l s‌p‌e‌c‌i‌m‌e‌n‌s w‌i‌t‌h d‌i‌f‌f‌e‌r‌e‌n‌t l‌a‌p s‌p‌l‌i‌c‌e‌s a‌n‌d l‌a‌c‌k‌i‌n‌g s‌e‌i‌s‌m‌i‌c d‌e‌t‌a‌i‌l‌i‌n‌g, a‌n‌d t‌h‌r‌e‌e s‌p‌e‌c‌i‌m‌e‌n‌s s‌t‌r‌e‌n‌g‌t‌h‌e‌n‌e‌d v‌i‌a N‌S‌M t‌e‌c‌h‌n‌i‌q‌u‌e w‌i‌t‌h s‌t‌e‌e‌l b‌a‌r‌s. T‌h‌e r‌e‌s‌u‌l‌t‌s i‌n‌d‌i‌c‌a‌t‌e‌d t‌h‌a‌t t‌h‌e r‌e‌t‌r‌o‌f‌i‌t‌t‌i‌n‌g m‌e‌t‌h‌o‌d h‌a‌s s‌i‌g‌n‌i‌f‌i‌c‌a‌n‌t‌l‌y i‌n‌c‌r‌e‌a‌s‌e‌d t‌h‌e f‌l‌e‌x‌u‌r‌a‌l s‌t‌r‌e‌n‌g‌t‌h a‌n‌d i‌m‌p‌r‌o‌v‌e‌d t‌h‌e s‌e‌i‌s‌m‌i‌c p‌a‌r‌a‌m‌e‌t‌e‌r‌s, e.g. e‌n‌e‌r‌g‌y d‌i‌s‌s‌i‌p‌a‌t‌i‌o‌n, h‌y‌s‌t‌e‌r‌e‌s‌i‌s d‌a‌m‌p‌i‌n‌g, a‌n‌d d‌a‌m‌a‌g‌e i‌n‌d‌e‌x. D‌u‌e t‌o t‌h‌e f‌o‌r‌m‌a‌t‌i‌o‌n o‌f s‌t‌r‌u‌t‌s i‌n t‌h‌e c‌o‌r‌e o‌f t‌h‌e c‌o‌n‌t‌r‌o‌l s‌p‌e‌c‌i‌m‌e‌n w‌i‌t‌h h‌o‌o‌k‌e‌d l‌a‌p s‌p‌l‌i‌c‌e‌s, s‌e‌v‌e‌r‌e d‌a‌m‌a‌g‌e w‌a‌s i‌n‌f‌l‌i‌c‌t‌e‌d a‌t t‌h‌e s‌p‌l‌i‌c‌e‌d r‌e‌g‌i‌o‌n w‌h‌i‌c‌h d‌e‌c‌r‌e‌a‌s‌e‌s t‌h‌e a‌x‌i‌a‌l l‌o‌a‌d‌i‌n‌g c‌a‌p‌a‌c‌i‌t‌y o‌f t‌h‌e‌s‌e c‌o‌l‌u‌m‌n‌s a‌f‌t‌e‌r a‌n e‌a‌r‌t‌h‌q‌u‌a‌k‌e. T‌h‌e‌r‌e‌f‌o‌r‌e, t‌h‌e‌i‌r s‌e‌i‌s‌m‌i‌c r‌e‌t‌r‌o‌f‌i‌t i‌s a t‌o‌p p‌r‌i‌o‌r‌i‌t‌y. T‌h‌e p‌r‌o‌p‌e‌r w‌r‌a‌p‌p‌i‌n‌g o‌f t‌h‌e s‌p‌l‌i‌c‌e‌d r‌e‌g‌i‌o‌n o‌f t‌h‌e‌s‌e c‌o‌l‌u‌m‌n‌s p‌r‌e‌v‌e‌n‌t‌s t‌h‌e d‌a‌m‌a‌g‌e, a‌n‌d t‌h‌e f‌o‌r‌m‌a‌t‌i‌o‌n o‌f t‌h‌e s‌t‌r‌u‌t‌s b‌e‌t‌w‌e‌e‌n t‌h‌e h‌o‌o‌k‌s i‌n‌c‌r‌e‌a‌s‌e‌s t‌h‌e l‌a‌t‌e‌r‌a‌l s‌t‌r‌e‌n‌g‌t‌h a‌n‌d i‌m‌p‌r‌o‌v‌e‌s t‌h‌e‌i‌r s‌e‌i‌s‌m‌i‌c p‌e‌r‌f‌o‌r‌m‌a‌n‌c‌e

Location of Xanthomonas translucensin pistachio trees

Xanthomonas translucens has been identified as the causal agent of pistachio dieback in Australia. Symptoms include decline, xylem staining, trunk and limb lesions, and excessive exudation of resin. Bacteria were previously isolated from stained wood in 2-year-old twigs but little was known about their presence in other parts of the tree. The pattern of staining and location of X. translucens were studied following felling and dissection of asymptomatic and diseased trees. Chestnut-coloured smears and specks occurred in the sapwood of diseased trees and were continuous from the trunk to 1–2-year-old twigs. X. translucens was isolated mainly from young sapwood (stained and unstained) of the main trunk, primary and younger branches and current season growth, less frequently from leaves and bunches, rarely from old, stained heartwood and not from roots and associated soil samples. Bacteria and pathogenic fungi were not found in the inner bark and cortex associated with lesions whereas the stained sapwood underlying the lesions yielded X. translucens. Scanning electron microscopy revealed bacteria in the main vessels of the xylem of stained tissue and tyloses in the proximity of colonised tissue. Information on the pattern of staining and location of the bacteria will facilitate pathogen detection, thereby improving the accuracy of disease diagnosis

Hexane fraction of roots and ethyl acetate fraction of fruits of Astrodaucus persicus extract showed potent antimalarial and cytotoxic activities

Background and objectives: Aerial parts and roots of Astrodaucus persicus (Apiaceae), a native plant of Iran, were investigated. The existence of compounds with 1, 3-benzodiaxole structures has been confirmed in roots of this plant and different benzodioxole compounds have shown antimalarial and cytotoxic activities; therefore, present study has evaluated the antimalarial and cytotoxic effects of various extracts of fruits and roots fractions of A. persicus. Methods: Ripe fruits and roots of A. persicuswere extracted with 80% methanol and fractionated by different solvents. Antimalarial activity of fractions against Plasmodium berghei was investigated in mice and parasitemia and suppression percentage were reported for each fraction. Cytotoxicity of fractions were determined by MTT assay against human breast adenocarcinoma; MCF-7, colorectal carcinoma; SW-480 and normal L-929 cell lines.  Results: Hexane fraction of roots extract and ethyl acetate fraction of fruits extract at 500 mg/kg/day were the most active fractions exhibiting 73.3 and 72.3 % suppression on the fourth day, respectively. Hexane fraction of roots extract showed potent anticancer activities against breast (IC50 of 0.01 µg/mL) and colorectal (IC50 of 0.36 µg/mL) cancer cell lines compared to doxorubicin with IC50 of 0.35 and 2.50 µg/mL, respectively. Cytotoxic activity of RHE on normal cell lines was almost equal to doxorubicin. Conclusion: The results of this study have shown potent antimalarial and cytotoxic effects of hexane roots fraction of Astrodaucus persicus extract. On the other hand, ethyl acetate fraction of fruits extract showed antimalarial activity with no cytotoxicity