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Permeation of Organometallic Compounds through Phospholipid Membranes

von Dr. Raycho Yonchev

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[1.] Ry/Fragment 034 01 - Diskussion
Zuletzt bearbeitet: 2016-04-10 12:24:59 WiseWoman
Accelrys Inc. - Forcefield-Based Simulations 1998, Fragment, Gesichtet, Ry, SMWFragment, Schutzlevel sysop, Verschleierung

Typus
Verschleierung
Bearbeiter
Klgn
Gesichtet
Yes.png
Untersuchte Arbeit:
Seite: 34, Zeilen: 1 ff. (entire page)
Quelle: Accelrys Inc. - Forcefield-Based Simulations 1998
Seite(n): 3, 4, 192, Zeilen: 3:4ff; 4:1-3; 192:18-22
II.1. Molecular dynamics simulations

Typical use of molecular dynamics (MD) include:

- Searching the conformational space of alternative amino acid side chains in site-specific mutation studies.

- Identifying likely conformational states for highly flexible polymers or for flexible regions of macromolecules such as protein loops.

- Producing sets of 3D structures consistent with distance and torsion constraints deduced from NMR experiments (simulated annealing).

- Calculating free energies of binding, including solvation and entropy effects.

- Probing the locations, conformations, and motions of molecules on catalyst surfaces.

- Running diffusion calculations.

In addition, simulation engines can be routinely used for:

- Calculating normal modes of vibration and vibrational frequencies.

- Analyzing intra molecular and inter molecular interactions in terms of residue-residue or molecule-molecule interactions, energy per residue, or interactions within a radius.

- Calculating diffusion coefficients of small molecules in a polymer matrix.

- Calculating thermal expansion coefficients of amorphous polymers.

- Calculating the radial distribution of liquids and amorphous polymers.

- Performing rigid-body comparisons between minimized conformations of the same or similar structures or between simulated and experimentally observed structures.

At its simplest, molecular dynamics solves Newton’s equation of motion:

\mathrm{F}_i(t)=m_i \, \mathrm{a}_i (t)=m_i \, \frac{\partial ^{2}\mathrm{r}_i}{\partial t_i^{2}} (2.1)

where Fi is the force, mi is the mass and ai is the acceleration of atom i.

Molecular dynamics

Typical uses of molecular dynamics include:

  • Searching the conformational space of alternative amino acid sidechains in site-specific mutation studies.
  • Identifying likely conformational states for highly flexible polymers or for flexible regions of macromolecules such as protein loops.
  • Producing sets of 3D structures consistent with distance and torsion constraints deduced from NMR experiments (simulated annealing).
  • Calculating free energies of binding, including solvation and entropy effects.
  • Probing the locations, conformations, and motions of molecules on catalyst surfaces.
  • Running diffusion calculations.

Other forcefield-based calculations

In addition, simulation engines can be routinely used for:

  • Calculating normal modes of vibration and vibrational frequencies.
  • Analyzing intramolecular and intermolecular interactions in terms of residue-residue or molecule-molecule interactions, energy per residue, or interactions within a radius.
  • Calculating diffusion coefficients of small molecules in a polymer matrix.
  • Calculating thermal expansion coefficients of amorphous polymers.
  • Calculating the radial distribution of liquids and amorphous polymers.

[page 4]

  • Performing rigid-body rms comparisons between minimized conformations of the same or similar structures or between simulated and experimentally observed structures.

[page 192]

At its simplest, molecular dynamics solves Newton's familiar equation of motion:

\mathbf{F}_i(t)=m_i \mathbf{a}_i (t) Eq. 83

where Fi is the force, mi is the mass, and ai is the acceleration of atom i.

Anmerkungen

No source is given.

Sichter
(Klgn), WiseWoman


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