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  1. AU="Andreas M. Köster"
  2. AU="Diana Karolina Maniak"
  3. AU="Cahuana-Hurtado, Lucero"
  4. AU="Ebert, Christoph"
  5. AU="Köhler, Matthias"
  6. AU=Fitzgerald Amelia Lucy AU=Fitzgerald Amelia Lucy
  7. AU="Yang, Charles"
  8. AU="Fraser, Alice j"
  9. AU=MacKenzie James A
  10. AU=Guettari Moez AU=Guettari Moez
  11. AU=McLeod Carolyn
  12. AU="Patel P.M"
  13. AU="Patel N.M"
  14. AU="Naganawa, Mika"
  15. AU="Viecelli, Claudio"
  16. AU=Valls Joan
  17. AU="Yang, Qizhang"
  18. AU=Wilt Timothy J
  19. AU="Dene R. Littler" AU="Dene R. Littler"
  20. AU="Petrenko, Andrei"
  21. AU=Valentino Kristin
  22. AU=Swash M
  23. AU="Adedipe, Ifeoluwa"
  24. AU=Shen Hongcheng
  25. AU="Padhy, Biswajit"
  26. AU="Kruglikov, Alibek"
  27. AU="Tasu, Jean Pierre"
  28. AU="Floate, Kevin D"
  29. AU="Mark Rijpkema"
  30. AU="Gjeloshi, Klodian"
  31. AU="Lucie Beaudoin"

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Suchoptionen

  1. Artikel ; Online: Development of Barostats for Finite Systems Born-Oppenheimer Molecular Dynamics Simulations

    Gabriel Ulises Gamboa / Patrizia Calaminici / Andreas M. Köster

    Journal of the Mexican Chemical Society, Vol 56, Iss 3, Pp 279-

    2012  Band 286

    Abstract: Se presenta un nuevo método para controlar la presión en simulaciones de dinámica molecular de primeros principios. La metodología del Lagrangiano extendido es aplicada para la generación de las ecuaciones de movimiento y el volumen del sistema se ... ...

    Abstract Se presenta un nuevo método para controlar la presión en simulaciones de dinámica molecular de primeros principios. La metodología del Lagrangiano extendido es aplicada para la generación de las ecuaciones de movimiento y el volumen del sistema se obtiene de un procedimiento puramente geométrico, el cual es económico en términos de costo computacional. La implementación de los algoritmos discutidos se llevó a cabo en el programa deMon2k, donde existe una maquinaria robusta para cálculos de teoría de funcionales de la densidad auxiliar. La metodología aquí descrita amplía nuestro esfuerzo en cálculos de propiedades más allá de la aproximación del gas ideal con base en cálculos de estructura electrónica de primeros principios.
    Schlagwörter Chemistry ; QD1-999 ; Science ; Q
    Sprache Spanisch
    Erscheinungsdatum 2012-01-01T00:00:00Z
    Verlag Sociedad Química de México
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review

    Aurélien de la Lande / Aurelio Alvarez-Ibarra / Karim Hasnaoui / Fabien Cailliez / Xiaojing Wu / Tzonka Mineva / Jérôme Cuny / Patrizia Calaminici / Luis López-Sosa / Gerald Geudtner / Isabelle Navizet / Cristina Garcia Iriepa / Dennis R. Salahub / Andreas M. Köster

    Molecules, Vol 24, Iss 9, p

    2019  Band 1653

    Abstract: deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ... ...

    Abstract deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born−Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.
    Schlagwörter QM/MM simulations ; DFT ; electron and nuclear dynamics ; Organic chemistry ; QD241-441
    Thema/Rubrik (Code) 541
    Sprache Englisch
    Erscheinungsdatum 2019-04-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: QM/MM Calculations with deMon2k

    Dennis R. Salahub / Sergei Yu. Noskov / Bogdan Lev / Rui Zhang / Van Ngo / Annick Goursot / Patrizia Calaminici / Andreas M. Köster / Aurelio Alvarez-Ibarra / Daniel Mejía-Rodríguez / Jan Řezáč / Fabien Cailliez / Aurélien de la Lande

    Molecules, Vol 20, Iss 3, Pp 4780-

    2015  Band 4812

    Abstract: The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) ... ...

    Abstract The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes.
    Schlagwörter Quantum Mechanical/Molecular Mechanical ; QM/MM ; density functional theory ; deMon2k software ; biomolecular modeling ; auxiliary DFT ; double asymptotic expansion ; constrained DFT ; Organic chemistry ; QD241-441 ; Chemistry ; QD1-999 ; Science ; Q
    Thema/Rubrik (Code) 541
    Sprache Englisch
    Erscheinungsdatum 2015-03-01T00:00:00Z
    Verlag Multidisciplinary Digital Publishing Institute
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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