Ry/034

Permeation of Organometallic Compounds through Phospholipid Membranes

von 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

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.

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