Fandom

VroniPlag Wiki

Ry/039

< Ry

31.358Seiten in
diesem Wiki
Seite hinzufügen
Diskussion0 Share

Störung durch Adblocker erkannt!


Wikia ist eine gebührenfreie Seite, die sich durch Werbung finanziert. Benutzer, die Adblocker einsetzen, haben eine modifizierte Ansicht der Seite.

Wikia ist nicht verfügbar, wenn du weitere Modifikationen in dem Adblocker-Programm gemacht hast. Wenn du sie entfernst, dann wird die Seite ohne Probleme geladen.

Permeation of Organometallic Compounds through Phospholipid Membranes

von Dr. Raycho Yonchev

vorherige Seite | zur Übersichtsseite | folgende Seite
Statistik und Sichtungsnachweis dieser Seite findet sich am Artikelende
[1.] Ry/Fragment 039 01 - Diskussion
Zuletzt bearbeitet: 2016-03-04 20:31:14 WiseWoman
Anézo 2003, Fragment, Gesichtet, Ry, SMWFragment, Schutzlevel sysop, Verschleierung

Typus
Verschleierung
Bearbeiter
Klgn
Gesichtet
Yes.png
Untersuchte Arbeit:
Seite: 39, Zeilen: 1-22
Quelle: Anézo 2003
Seite(n): 62, 56, 57, Zeilen: 62: 2 ff; 56:28-29; 57: 1-4
[This introduces the problem of combining the right conditions and parameters in order to] obtain a correct bilayer model system, such simulation conditions being indeed an integral part of the model.

II.2.2 Force fields

The choice of interatomic force fields and related parameters is of crucial importance for the simulation of a biomolecular system. The ability of a model membrane to reproduce realistic static and dynamic features depends strongly on the balance between attractive and repulsive forces, which directly results from the force field employed. A force field is indeed required to compute the potential energy of the system as a function of the instantaneous atomic coordinates. Various force fields have been developed to simulate proteins and nucleic acids; no special force fields have however been designed for the modeling of lipid bilayers. With the exception of charges, which are often derived from ab initio quantum chemical calculations on lipid fragments, the parameters in the potential functions are thus usually taken from pre-existing force fields for proteins or nucleic acids. The most popular force fields used in membrane simulation studies are the AMBER [46], the CHARMM [47], and the GROMOS [48] force fields. One of these force fields is often applied in combination with the OPLS (Optimized Potentials for Liquid Simulations) [49] parameter set for the computation of the non-bonded interactions.

All necessary information for system description is contained in the potential V, which is derived from the force field. The force field can be defined as set of equations (potential functions) and parameters, which characterize interactions into the system. Both components are interdependent.


46. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765.

47. Brooks, B. R.; R. E. Bruccoleri; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comp. Chem. 1983, 4, 187.

48. Gunsteren, W. F. v.; Berendsen, H. J. C. Groningen Molecular Simulation (GROMOS) Library Manual; Biomos: Groningen, The Netherlands, 1987.

49. Schlenkrich, M.; Brickman, J.; Jr., A. D. M.; Karplus, M. An Empirical Potential Energy Function for Phopholipids: Criteria for Parameter Optimization and Applications. In Biological Membranes: A Molecular Perspective from Computation and Experiment; Jr., K. M. M., Roux, B., Eds.; Birhдuser [sic]: Boston, 1996.

[page 62]

This introduces the problem of combining the right conditions and parameters in order to obtain a correct bilayer model system, such simulation conditions being indeed an integral part of the model.

3.2.2.1 Force fields

The choice of interatomic force fields and related parameters is of crucial importance for the simulation of a biomolecular system. The ability of a model membrane to reproduce realistic static and dynamic features depends strongly on the balance between attractive and repulsive forces, which directly results from the force field employed. A force field is indeed required to compute the potential energy of the system as a function of the instantaneous atomic coordinates. Various force fields have been developed to simulate proteins and nucleic acids; no special force fields have however been designed for the modeling of lipid bilayers [44]. With the exception of charges, which are often derived from ab initio quantum chemical calculations on lipid fragments, the parameters in the potential functions are thus usually taken from pre-existing force fields for proteins or nucleic acids. The most popular force fields used in membrane simulation studies are the AMBER [86], the CHARMM [87], and the GROMOS [88] force fields. One of these force fields is often applied in combination with the OPLS (Optimized Potentials for Liquid Simulations) parameter set [89] for the computation of the non-bonded interactions. [...]

[page 56]

[...] All the information necessary to describe the system simulated is contained in the interaction potential V, which is a function of the underlying force field. A force field can be

[page 57]

defined as a set of equations (potential functions) on the one hand, and parameters on the other hand, characterizing the strength of the various interactions within the system. Both components – potential functions and parameters used in these functions – are however interdependent and are combined to form a consistent set.


[44] M. Wiese. Computer Simulation of Phospholipids and Drug-Phospholipid Interactions. In: Drug-Membrane Interactions. J. K. Seydel and M. Wiese (Eds.), Wiley- VCH Verlag GmbH, Weinheim, 2002.

[86] S. J.Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. Weiner. J. Am. Chem. Soc., 106:765–784, 1984.

[87] B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. J. Comput. Chem., 4:187–217, 1983.

[88] W. F. van Gunsteren and H. J. C. Berendsen. Groningen Molecular Simulation (GROMOS) Library manual. Biomos, Nijenborgh 4, 9747 AG Groningen, The Netherlands, 1987.

[89] W. Jorgensen and J. Tirado-Rives. J. Am. Chem. Soc., 110:1666–1671, 1988.

[90] M. Schlenkrich, J. Brickmann, A. D. MacKerell Jr., and M. Karplus. An Empirical Potential Energy Function for Phospholipids: Criteria for Parameter Optimization and Applications. In: Biological Membranes: A Molecular Perspective from Computation and Experiment. K. M. Merz Jr. and B. Roux (Eds.), Birhäuser, Boston, 1996.

Anmerkungen

No source is given.

The Russian letter д instead of ä is found twice in the thesis. This happens when copy & pasting with a Cyrillic keyboard.

Reference 49. in Ry is reference [90] in the source, not [89].

Sichter
(Klgn), WiseWoman

[2.] Ry/Fragment 039 23 - Diskussion
Zuletzt bearbeitet: 2016-04-10 13:11:43 WiseWoman
Accelrys Inc. - Forcefield-Based Simulations 1998, Fragment, Gesichtet, Ry, SMWFragment, Schutzlevel sysop, Verschleierung

Typus
Verschleierung
Bearbeiter
Klgn
Gesichtet
Yes.png
Untersuchte Arbeit:
Seite: 39, Zeilen: 23-26
Quelle: Accelrys Inc. - Forcefield-Based Simulations 1998
Seite(n): 54, Zeilen: 13-16
AMBER Force Field

The AMBER energy expression contains a minimal number of terms. No cross terms are included. The functional forms of the energy terms used by AMBER are given in Equation (2.6).

Standard AMBER forcefield

The AMBER energy expression contains a minimal number of terms. No cross terms are included. The functional forms of the energy terms used by AMBER are given in Eq. 19.

Anmerkungen

No source is given. The text continues on the next page with Ry/Fragment 040 01.

Sichter
(Klgn), WiseWoman


vorherige Seite | zur Übersichtsseite | folgende Seite
Letzte Bearbeitung dieser Seite: durch Benutzer:WiseWoman, Zeitstempel: 20160304203206

Auch bei Fandom

Zufälliges Wiki