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Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel

Article Abstract:

The permeation properties of the open and inactive states of a homology model of HERG are studied to examine the role of the S6-P linker in this inactivation mechanism. Structural results of molecular dynamics simulation on the HERG model, followed by free energy, structural, and continuum electrostatics calculations reveal that, in the inactive state, the S5-P linkers move closer to the channel axis, possibly causing a steric hindrance to permeating [K.sup.+] ions.

Permeability

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When is a molecule properly solvated by a continuum model or in a cluster ansatz? A first-principles simulations of alanine hydration

Article Abstract:

The first-principles molecular dynamics simulations of the alanine hydration was carried out to test the validity of the cluster ansatz approach and the continuum model approach. Sufficient convergence of the cluster ansatz approach is observed for either of the two solvent shells around the polar groups and one solvent shell around the apolar groups or two solvent shells around the polar groups surrounded by a dielectric continuum.

Electric properties, Alanine, Mechanical properties, Structure, Dielectric measurements, Dielectric measurement

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On the relationship between Fickian diffusivities at the continuum and molecular levels

Article Abstract:

A general description of the relationship between Fickian diffusivities at the continuum and molecular levels of description is presented. An algorithm is provided to be implemented in a molecular dynamics simulation with which one can generate Fickian diffusivities under the same se of criteria as used in the derivation of the continuum equations.

Continuum mechanics, Classical mechanics

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