# Ry/036

## < Ry

32.141Seiten in
diesem Wiki
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
 Zuletzt bearbeitet: 2016-04-10 12:35:49 WiseWoman Accelrys Inc. - Forcefield-Based Simulations 1998, Fragment, Gesichtet, Ry, SMWFragment, Schutzlevel sysop, Verschleierung

 Typus Verschleierung Bearbeiter Klgn Gesichtet
Untersuchte Arbeit:
Seite: 36, Zeilen: 1-6
Quelle: Accelrys Inc. - Forcefield-Based Simulations 1998
Seite(n): 195, Zeilen: 15ff
Verlet Leap-Frog algorithm requires r(t), v(tt/2), and a(t), which are (respectively) the position, velocity, and acceleration at times t, tt/2, and t, and compute:

$v \left ( t + \frac{\Delta t}{2} \right ) = v \left ( t - \frac{\Delta t}{2} \right ) + \Delta t \, \mathrm{a} (t)$ (2.3)

$\mathrm{r} (t + \Delta t) = \mathrm{r}(t) + \Delta t v \left ( t + \frac{\Delta t}{2} \right )$ (2.4)

$\mathrm{a} (t + \Delta t) = \frac{\mathrm{f}(t+\Delta t)}{m}$ (2.5)

where f(t + Δt) is evaluated from -dV/dr at r(t + Δt).

The leapfrog algorithm

The Verlet leapfrog algorithm is as follows:

Given r(t), v(tt/2), and a(t), which are (respectively) the position, velocity, and acceleration at times t, tt/2, and t, compute:

where f(t + Δt) is evaluated from -dV/dr at r(t + Δt).

 Anmerkungen No source is given. Sichter (Klgn), WiseWoman

 Zuletzt bearbeitet: 2016-04-10 12:29:58 WiseWoman Anézo 2003, Fragment, Gesichtet, Ry, SMWFragment, Schutzlevel sysop, Verschleierung

 Typus Verschleierung Bearbeiter Klgn Gesichtet
Untersuchte Arbeit:
Seite: 36, Zeilen: 7-20
Quelle: Anézo 2003
Seite(n): 56, 60, Zeilen: 56:21-23; 60:8-19
If the corresponding velocities are not known, they are obtained from a Maxwell – Boltzmann distribution and are scaled (or rerandomized) until kinetic and potential energies are in equipartition and the desired temperature is reached.

II.2. Molecular dynamics studies of lipid bilayers

II.2.1 Review

MD simulations provide a powerful tool to analyze biomolecular systems from an atomic perspective with a level of detail missing in any other approach. This technique has been widely used in studies of proteins and nucleic acids, but has been less applied to the analysis of biological membranes for several reasons. Biomembranes are indeed very complex in terms of both structural and dynamic properties. Unlike proteins or nucleic acids, which have well-defined three-dimensional structures, membrane components derive a large majority of their properties and functions from their fluid nature. The fluid character of the physiologically relevant fluid crystalline phase makes experimental studies particularly difficult and only limited atomic-level data from X-ray or neutron [diffraction have been for long accessible, compared with the amount of data available on proteins and nucleic acids.]

[page 56]

If the corresponding velocities are not available, they are typically obtained from a Maxwell-Boltzmann distribution and are scaled (or rerandomized) until kinetic and potential energies are in equipartition and the target temperature is reached.

[page 60]

3.2 Molecular dynamics studies of lipid bilayers

3.2.1 Review

MD simulations provide a powerful tool to analyze biomolecular systems from an atomic perspective with a level of detail missing in any other approach. This technique has been widely used in studies of proteins and nucleic acids, but has been less applied to the analysis of biological membranes for several reasons. Biomembranes are indeed very complex in terms of both structural and dynamic properties. Unlike proteins or nucleic acids which have well-defined three-dimensional structures, membrane components derive a large majority of their properties and functions from their fluid nature. The fluid character of the physiologically relevant fluid crystalline phase makes experimental studies particularly difficult and only limited atomic-level data from X-ray or neutron diffraction have been for long accessible, compared with the amount of data available on proteins and nucleic acids.

 Anmerkungen No source is given. Sichter (Klgn), WiseWoman

vorherige Seite | zur Übersichtsseite | folgende Seite
Letzte Bearbeitung dieser Seite: durch Benutzer:WiseWoman, Zeitstempel: 20160410123256