Continuum boundary conditions

In continuum boundary conditions the protein or other macromolecule is treated as a macroscopic body surrounded by a featureless continuum representing the solvent. The internal forces of the protein are described by using the standard force field including the Coulombic interactions in Eq. (6), whereas the forces due to the presence of the continuum solvent are described by solvation tenns derived from macroscopic electrostatics and fluid dynamics. 

If the simulated system uses periodic boundary conditions, the logical long-range interaction includes a lattice sum over all particles with all their images. Apart from some obvious and resolvable corrections for self-energy and for image interaction between excluded pairs, the question has been raised if one really wishes to enhance the effect of the artificial boundary conditions by including lattice sums. The effect of the periodic conditions should at least be evaluated by simulation with different box sizes or by continuum corrections, if applicable (see below). 

Wood, R.H. Continuum electrostatics in a computational universe with finite cut-off radii and periodic boundary conditions Correction to computed free energies of ionic solvation. J. Chem. Phys. 103 (1995) 6177-6187. 

Clearly then, the continuum approach as outlined above is faulty. Furthermore, since our erroneous result depends only on the non-slip boundary condition for V together with the Navier-Stokes equation (4.3), one or... 

At Che opposite limit, where Che density Is high enough for mean free paths to be short con ared with pore diameters, the problem can be treated by continuum mechanics. In the simplest ease of a straight tube of circular cross-section, the fluid velocity field can easily be obtained by Integrating Che Nsvler-Stokes equations If an appropriate boundary condition at Che... 

It is sometimes desirable to include the effect of the rest of the system, outside of the QM and MM regions. One way to do this is using periodic boundary conditions, as is done in liquid-state simulations. Some researchers have defined a potential that is intended to reproduce the effect of the bulk solvent. This solvent potential may be defined just for this type of calculation, or it may be a continuum solvation model as described in the next chapter. For solids, a set of point charges, called a Madelung potential, is often used. 

The partial wave basis functions with which the radial dipole matrix elements fLv constructed (see Appendix A) are S-matrix normalized continuum functions obeying incoming wave boundary conditions. 

Hunenberger, P. H., McCammon, J. A. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions a continuum... 

If the Brownian particles were macroscopic in size, the solvent could be treated as a viscous continuum, and the particles would couple to the continuum solvent through appropriate boundary conditions. Then the two-particle friction may be calculated by solving the Navier-Stokes equations in the presence of the two fixed particles. The simplest approximation for hydrodynamic interactions is through the Oseen tensor [54],... 

This establishes the natural relation between the modulus and the minimum nonzero eigenvalue of the force constant matrix. The precise form of this relationship, i.e., the values of the constants, depends upon the geometry of the body, both through the boundary conditions on the continuum and through the structure of the force constant matrix, which indirectly determines m... 

Molecular calculations provide approaches to supramolecular structure and to the dynamics of self-assembly by extending atomic-molecular physics. Alternatively, the tools of finite element analysis can be used to approach the simulation of self-assembled film properties. The voxel4 size in finite element analysis needs be small compared to significant variation in structure-property relationships for self-assembled structures, this implies use of voxels of nanometer dimensions. However, the continuum constitutive relationships utilized for macroscopic-system calculations will be difficult to extend at this scale because nanostructure properties are expected to differ from microstructural properties. In addition, in structures with a high density of boundaries (such as thin multilayer films), poorly understood boundary conditions may contribute to inaccuracies. 

In subcooled impact, the initial droplet temperature is lower than the saturated temperature of the liquid of the droplet, thus the transient heat transfer inside the droplet needs to be considered. Since the thickness of the vapor layer may be comparable with the mean free path of the gas molecules in the subcooled impact, the kinetic slip treatment of the boundary condition needs to be applied at the liquid-vapor and vapor-solid interface to modify the continuum system. 

The vapor-layer model developed in Section IV.A.2 is based on the continuum assumption of the vapor flow. This assumption, however, needs to be modified by considering the kinetic slip at the boundary when the Knudsen number of the vapor is larger than 0.01 (Bird, 1976). With the assumption that the thickness of the vapor layer is much smaller than the radius of the droplet, the reduced continuity and momentum equations for incompressible vapor flows in the symmetrical coordinates ( ,2) are given as Eqs. (43) and (47). When the Knudsen number of the vapor flow is between 0.01 and 0.1, the flow is in the slip regime. In this regime, the flow can still be considered as a continuum at several mean free paths distance from the boundary, but an effective slip velocity needs to be used to describe the molecular interaction between the gas molecules and the boundary. Based on the simple kinetic analysis of vapor molecules near the interface (Harvie and Fletcher, 2001c), the boundary conditions of the vapor flow at the solid surface can be given by... 

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