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  1. Book ; Online: Next Generation Agriculture: Understanding Plant Life for Food, Health and Energy

    De Martinis, Domenico / Benvenuto, Eugenio / Colonna, Nicola / Llorente, Briardo / Rybicki, Edward

    2020  

    Keywords Science: general issues ; Botany & plant sciences ; climate change ; agriculture ; bioproducts ; food ; biofuel ; bioeconomy ; artificial intelligence ; molecular farming
    Size 1 electronic resource (247 pages)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021230872
    ISBN 9782889660629 ; 2889660621
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Koopmans Spectral Functionals in Periodic Boundary Conditions.

    Colonna, Nicola / De Gennaro, Riccardo / Linscott, Edward / Marzari, Nicola

    Journal of chemical theory and computation

    2022  Volume 18, Issue 9, Page(s) 5435–5448

    Abstract: Koopmans spectral functionals aim to describe simultaneously ground-state properties and charged excitations of atoms, molecules, nanostructures, and periodic crystals. This is achieved by augmenting standard density functionals with simple but ... ...

    Abstract Koopmans spectral functionals aim to describe simultaneously ground-state properties and charged excitations of atoms, molecules, nanostructures, and periodic crystals. This is achieved by augmenting standard density functionals with simple but physically motivated orbital-density-dependent corrections. These corrections act on a set of localized orbitals that, in periodic systems, resemble maximally localized Wannier functions. At variance with the original, direct supercell implementation (
    Language English
    Publishing date 2022-08-04
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.2c00161
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Molecular Composition and Biological Activity of a Novel Acetonitrile-Water Extract of Lens Culinaris Medik in Murine Native Cells and Cell Lines Exposed to Different Chemotherapeutics Using Mass Spectrometry.

    Di Turi, Annamaria / Antonacci, Marina / Dibenedetto, Jacopo Raffaele / Maqoud, Fatima / Leonetti, Francesco / Centoducati, Gerardo / Colonna, Nicola / Tricarico, Domenico

    Cells

    2023  Volume 12, Issue 4

    Abstract: We evaluated the effects of a new extract (70% acetonitrile, 2E0217022196DIPFARMTDA) of Lens culinaris Medik (Terre di Altamura SRL, Altamura BA) to prevent cytotoxic damage from cisplatin, staurosporine, irinotecan, doxorubicin, and the glucocorticoid ... ...

    Abstract We evaluated the effects of a new extract (70% acetonitrile, 2E0217022196DIPFARMTDA) of Lens culinaris Medik (Terre di Altamura SRL, Altamura BA) to prevent cytotoxic damage from cisplatin, staurosporine, irinotecan, doxorubicin, and the glucocorticoid dexamethasone. The acetonitrile-water extract (range 0.1-5 mg/mL) was obtained by extracting 10 g of lentil flour with 50 milliliters of the acetonitrile-water extraction mixture in a 70:30 ratio, first for 3 h and then overnight in a shaker at room temperature. The next day, the extract was filtered and passed through a Rotavapor to obtain only the aqueous component and eliminate that with acetonitrile, and then freeze-dried to finally have the powdered extract. In vitro experiments showed that the extract prevented the cytotoxic damage induced by cisplatin, irinotecan, and doxorubicin on HEK293 and SHSY5Y cell lines after 24-96 h. In murine osteoblasts after 24-72 h of incubation time, the extract was cytoprotective against all chemicals. The extract was effective against dexamethasone, leading to synergic cell proliferation in all cell types. In bone marrow cells, the extract is cytoprotective after 72 h against doxorubicin, staurosporine, and dexamethasone. Instead, on muscle fibers, the extract has a synergic effect with chemotherapeutics, increasing cytotoxicity induced by doxorubicin and staurosporine. LC-MS attested to the existence of several phenolic structures in the extract. The most abundant families of compounds were flavonoids (25.7%) and mellitic acid (18%). Thus, the development of this extract could be implemented in the area of research related to the chemoprevention of damage to renal, neuronal, bone marrow cells, and osteoblasts by chemotherapeutics; moreover, it could be used as a reinforcer of cytotoxic action of chemotherapeutics on muscle fibers.
    MeSH term(s) Humans ; Animals ; Mice ; Lens Plant/chemistry ; Lens Plant/metabolism ; Water/metabolism ; Irinotecan ; Cisplatin/metabolism ; HEK293 Cells ; Staurosporine ; Mass Spectrometry ; Acetonitriles/metabolism ; Doxorubicin ; Dexamethasone
    Chemical Substances Water (059QF0KO0R) ; Irinotecan (7673326042) ; Cisplatin (Q20Q21Q62J) ; Staurosporine (H88EPA0A3N) ; Acetonitriles ; Doxorubicin (80168379AG) ; Dexamethasone (7S5I7G3JQL)
    Language English
    Publishing date 2023-02-10
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells12040575
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: koopmans: An Open-Source Package for Accurately and Efficiently Predicting Spectral Properties with Koopmans Functionals.

    Linscott, Edward B / Colonna, Nicola / De Gennaro, Riccardo / Nguyen, Ngoc Linh / Borghi, Giovanni / Ferretti, Andrea / Dabo, Ismaila / Marzari, Nicola

    Journal of chemical theory and computation

    2023  Volume 19, Issue 20, Page(s) 7097–7111

    Abstract: Over the past decade we have developed Koopmans functionals, a computationally efficient approach for predicting spectral properties with an orbital-density-dependent functional framework. These functionals impose a generalized piecewise linearity ... ...

    Abstract Over the past decade we have developed Koopmans functionals, a computationally efficient approach for predicting spectral properties with an orbital-density-dependent functional framework. These functionals impose a generalized piecewise linearity condition to the entire electronic manifold, ensuring that orbital energies match the corresponding electron removal/addition energy differences (in contrast to semilocal DFT, where a mismatch between the two lies at the heart of the band gap problem and, more generally, the unreliability of Kohn-Sham orbital energies). This strategy has proven to be very powerful, yielding molecular orbital energies and solid-state band structures with comparable accuracy to many-body perturbation theory but at greatly reduced computational cost while preserving a functional formulation. This paper reviews the theory of Koopmans functionals, discusses the algorithms necessary for their implementation, and introduces koopmans, an open-source package that contains all of the code and workflows needed to perform Koopmans functional calculations and obtain reliable spectral properties of molecules and materials.
    Language English
    Publishing date 2023-08-23
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.3c00652
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Book ; Online: Koopmans spectral functionals in periodic-boundary conditions

    Colonna, Nicola / De Gennaro, Riccardo / Linscott, Edward / Marzari, Nicola

    2022  

    Abstract: Koopmans spectral functionals aim to describe simultaneously ground state properties and charged excitations of atoms, molecules, nanostructures and periodic crystals. This is achieved by augmenting standard density functionals with simple but physically ...

    Abstract Koopmans spectral functionals aim to describe simultaneously ground state properties and charged excitations of atoms, molecules, nanostructures and periodic crystals. This is achieved by augmenting standard density functionals with simple but physically motivated orbital-density-dependent corrections. These corrections act on a set of localized orbitals that, in periodic systems, resemble maximally localized Wannier functions. At variance with the original, direct supercell implementation [Phys. Rev. X 8, 021051 (2018)], we discuss here i) the complex but efficient formalism required for a periodic-boundary code using explicit Brillouin zone sampling, and ii) the calculation of the screened Koopmans corrections with density-functional perturbation theory. In addition to delivering improved scaling with system size, the present development makes the calculation of band structures with Koopmans functionals straightforward. The implementation in the open-source Quantum ESPRESSO distribution and the application to prototypical insulating and semiconducting systems are presented and discussed.
    Keywords Condensed Matter - Materials Science ; Physics - Computational Physics
    Subject code 541
    Publishing date 2022-02-16
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Gas Transport across Carbon Nitride Nanopores: A Comparison of van der Waals Functionals against the Random-Phase Approximation

    Vahdat, Mohammad Tohidi / Campi, Davide / Colonna, Nicola / Marzari, Nicola / Agrawal, Kumar Varoon

    Journal of physical chemistry. 2021 Aug. 18, v. 125, no. 34

    2021  

    Abstract: C₂N is an ordered two-dimensional carbon nitride with a high density (1.7 × 10¹⁴ cm–²) of 3.1 Å-sized nanopores, making it promising for high-flux gas sieving for energy-efficient He and H₂ purification. Herein, we discuss the accurate calculation of ... ...

    Abstract C₂N is an ordered two-dimensional carbon nitride with a high density (1.7 × 10¹⁴ cm–²) of 3.1 Å-sized nanopores, making it promising for high-flux gas sieving for energy-efficient He and H₂ purification. Herein, we discuss the accurate calculation of potential energy surfaces for He, H₂, N₂, and CO₂ across C₂N nanopores, to characterize the gas-sieving potential of C₂N. We compare the potential energy surface derived from density-functional theory calculations using five commonly used van der Waals (vdW) approximations. While all five functionals point that the C₂N nanopore yields He/N₂ and H₂/N₂ selectivities over 1000, adsorption energies and energy barriers vary remarkably depending on the approximation chosen. To make progress, we compare the calculations against the results from the adiabatic connection fluctuation dissipation theory, with random-phase approximation, known to be accurate in capturing vdW interactions. The comparison indicates that the interaction energy is less accurate with vdW density functional theory. On the other hand, more empirical corrections work reasonably well, a finding that we also confirm for another carbon nitride lattice, poly(triazine imide). Overall, we recommend these for screening carbon nitride materials for gas separation, but also comparing functionals with higher-order approaches when dealing with different materials.
    Keywords adsorption ; carbon dioxide ; carbon nitride ; density functional theory ; energy efficiency ; nanopores ; potential energy ; triazines ; van der Waals forces
    Language English
    Dates of publication 2021-0818
    Size p. 18896-18904.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1932-7455
    DOI 10.1021/acs.jpcc.1c03822
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Counteractions of a Novel Hydroalcoholic Extract from Lens Culinaria against the Dexamethasone-Induced Osteoblast Loss of Native Murine Cells.

    Antonacci, Marina / Dibenedetto, Jacopo Raffaele / Maqoud, Fatima / Centoducati, Gerardo / Colonna, Nicola / Leonetti, Francesco / Tricarico, Domenico

    Cells

    2022  Volume 11, Issue 19

    Abstract: The cytoprotective effects of a novel hydroalcoholic extract (0.01-5 mg/mL) from Lens culinaria (Terre di Altamura Srl) were investigated within murine native skeletal muscle fibers, bone marrow cells, and osteoblasts, and in cell lines treated with the ... ...

    Abstract The cytoprotective effects of a novel hydroalcoholic extract (0.01-5 mg/mL) from Lens culinaria (Terre di Altamura Srl) were investigated within murine native skeletal muscle fibers, bone marrow cells, and osteoblasts, and in cell lines treated with the apoptotic agent staurosporine (2.14 × 10
    MeSH term(s) Animals ; Antimitotic Agents/metabolism ; Antimitotic Agents/pharmacology ; Cisplatin/metabolism ; Cisplatin/pharmacology ; Dexamethasone/pharmacology ; Doxorubicin/pharmacology ; Ethanol/pharmacology ; Flavonoids/pharmacology ; Gentian Violet/metabolism ; Gentian Violet/pharmacology ; HEK293 Cells ; Humans ; Immunosuppressive Agents/pharmacology ; Irinotecan/pharmacology ; Mice ; Osteoblasts/metabolism ; Reactive Oxygen Species/metabolism ; Salicylates/metabolism ; Salicylates/pharmacology ; Staurosporine/pharmacology ; Topoisomerase I Inhibitors/metabolism ; Topoisomerase I Inhibitors/pharmacology ; Water/metabolism
    Chemical Substances Antimitotic Agents ; Flavonoids ; Immunosuppressive Agents ; Reactive Oxygen Species ; Salicylates ; Topoisomerase I Inhibitors ; Water (059QF0KO0R) ; Ethanol (3K9958V90M) ; Irinotecan (7673326042) ; Dexamethasone (7S5I7G3JQL) ; Doxorubicin (80168379AG) ; Staurosporine (H88EPA0A3N) ; Gentian Violet (J4Z741D6O5) ; Cisplatin (Q20Q21Q62J)
    Language English
    Publishing date 2022-09-20
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells11192936
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Koopmans-Compliant Functionals and Potentials and Their Application to the GW100 Test Set.

    Colonna, Nicola / Nguyen, Ngoc Linh / Ferretti, Andrea / Marzari, Nicola

    Journal of chemical theory and computation

    2019  Volume 15, Issue 3, Page(s) 1905–1914

    Abstract: Koopmans-compliant (KC) functionals have been shown to provide accurate spectral properties through a generalized condition of piecewise linearity of the total energy as a function of the fractional addition/removal of an electron to/from any orbital. We ...

    Abstract Koopmans-compliant (KC) functionals have been shown to provide accurate spectral properties through a generalized condition of piecewise linearity of the total energy as a function of the fractional addition/removal of an electron to/from any orbital. We analyze the performance of different KC functionals on a large and standardized set of 100 molecules, the GW100 test set, comparing vertical ionization potentials (taken as opposite of the orbital energies) to those obtained from accurate quantum chemistry methods, and to experimental results. We find excellent agreement, with a mean absolute error of 0.20 eV for the KIPZ functional on the first ionization potential, which is state-of-the-art for both density functional theory (DFT)-based calculations and many-body perturbation theory. We highlight similarities and differences between KC functionals and other electronic-structure approaches, such as dielectric-dependent hybrid functionals and Green's function methods, both from a theoretical and from a practical point of view, arguing that KC potentials can be considered as local and orbital-dependent approximations to the electronic self-energy, already including approximate vertex corrections.
    Language English
    Publishing date 2019-02-07
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.8b00976
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online: Bloch's theorem in orbital-density-dependent functionals

    De Gennaro, Riccardo / Colonna, Nicola / Linscott, Edward / Marzari, Nicola

    Band structures from Koopmans spectral functionals

    2021  

    Abstract: Koopmans-compliant functionals provide an orbital-density-dependent framework for an accurate evaluation of spectral properties; they are obtained by imposing a generalized piecewise-linearity condition on the total energy of the system with respect to ... ...

    Abstract Koopmans-compliant functionals provide an orbital-density-dependent framework for an accurate evaluation of spectral properties; they are obtained by imposing a generalized piecewise-linearity condition on the total energy of the system with respect to the occupation of any orbital. In crystalline materials, due to the orbital-density-dependent nature of the functionals, minimization of the total energy to a ground state provides a set of minimizing variational orbitals that are localized and thus break the periodicity of the underlying lattice. Despite this, we show that Bloch symmetry can be preserved and it is possible to describe the electronic states with a band-structure picture, thanks to the Wannier-like character of the variational orbitals. We also present a method to unfold and interpolate the electronic bands from supercell ($\Gamma$-point) calculations, which enables us to calculate full band structures with Koopmans-compliant functionals. The results obtained for a set of benchmark semiconductors and insulators show very good agreement with state-of-the-art many-body perturbation theory and experiments, underscoring the reliability of these spectral functionals in predicting band structures.

    Comment: 34 pages, 4 figures
    Keywords Condensed Matter - Materials Science ; Physics - Computational Physics
    Subject code 541
    Publishing date 2021-11-18
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  10. Article: Editorial: Next Generation Agriculture: Understanding Plant Life for Food, Health and Energy.

    De Martinis, Domenico / Rybicki, Edward P / Colonna, Nicola / Benvenuto, Eugenio / Llorente, Briardo

    Frontiers in plant science

    2020  Volume 11, Page(s) 1238

    Keywords covid19
    Language English
    Publishing date 2020-08-12
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2711035-7
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2020.01238
    Database MEDical Literature Analysis and Retrieval System OnLINE

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