Computer simulation boundaries

D. Beglov and B. Roux. Finite representation of an infinite bulk system Solvent boundary potential for computer simulations. J. Chem. Phys., 100 9050-9063, 1994. 

Electric field measurement at the boundary of a metal container filled with charged material. Examples include pipelines and storage vessels. The electric field can be used to calculate charge density (3-5.1). Eield meters can also be lowered into containers such as silos to determine the local fields and polarities. Quantitative interpretation of the reading requires correction for field intensification and is sometimes accomplished using computer simulations. 

Time available It takes some time to set up a simulation case. After a basic configuration has run successfully, it is easy and quick to do additional computer simulations with different boundary conditions. Experiments, on the other hand, are generally time-consuming. 

Both extreme models of surface heterogeneity presented above can be readily used in computer simulation studies. Application of the patch wise model is amazingly simple, if one recalls that adsorption on each patch occurs independently of adsorption on any other patch and that boundary effects are neglected in this model. For simplicity let us assume here the so-called two-dimensional model of adsorption, which is based on the assumption that the adsorbed layer forms an individual thermodynamic phase, being in thermal equilibrium with the bulk uniform gas. In such a case, adsorption on a uniform surface (a single patch) can be represented as... 

Computer simulations of bulk liquids are usually performed by employing periodic boundary conditions in all three directions of space, in order to eliminate artificial surface effects due to the small number of molecules. Most simulations of interfaces employ parallel planar interfaces. In such simulations, periodic boundary conditions in three dimensions can still be used. The two phases of interest occupy different parts of the simulation cell and two equivalent interfaces are formed. The simulation cell consists of an infinite stack of alternating phases. Care needs to be taken that the two phases are thick enough to allow the neglect of interaction between an interface and its images. An alternative is to use periodic boundary conditions in two dimensions only. The first approach allows the use of readily available programs for three-dimensional lattice sums if, for typical systems, the distance between equivalent interfaces is at least equal to three to five times the width of the cell parallel to the interfaces. The second approach prevents possible interactions between interfaces and their periodic images. 

Boundary Conditions although CA are a.ssumed to live on infinitely large lattices, computer simulations must necessarily be run on finite sets. For a one dimensional lattice with N cells, it is common to use periodic boundary conditions, in which ctn + i is identified with ai. Alternatively, all cells to the left and right of a finite block of N cells may be arbitrarily defined to possess value 0 for all time, so that their dynamics remains uncoupled with that taking place within the block. Similarly, in two dimensions, it is usual to have the dynamics take place on a torus, in which o m+i = <7, 2 and = cTi,j- As we will see later it turns one... 

Besides crystalline order and structure, the chain conformation and segment orientation of polymer molecules in the vicinity of the surface are also expected to be modified due to the specific interaction and boundary condition at the surface between polymers and air (Fig. 1 a). According to detailed computer simulations [127, 128], the chain conformation at the free polymer surface is disturbed over a distance corresponding approximately to the radius of gyration of one chain. The chain segments in the outermost layers are expected to be oriented parallel to the surface and chain ends will be enriched at the surface. Experiments on the chain conformation in this region are not available, but might be feasible with evanescent wave techniques described previously. Surface structure on a micrometer scale is observed with IR-ATR techniques [129],... 

The structures of phases such as the chiral nematic, the blue phases and the twist grain boundary phases are known to result from the presence of chiral interactions between the constituent molecules [3]. It should be possible, therefore, to explore the properties of such phases with computer simulations by introducing chirality into the pair potential and this can be achieved in two quite different ways. In one a point chiral interaction is added to the Gay-Berne potential in essentially the same manner as electrostatic interactions have been included (see Sect. 7). In the other, quite different approach a chiral molecule is created by linking together two or more Gay-Berne particles as in the formation of biaxial molecules (see Sect. 10). Here we shall consider the phases formed by chiral Gay-Berne systems produced using both strategies. 

In the previous sections, we have seen how computer simulations have contributed to our understanding of the microscopic structure of liquid crystals. By applying periodic boundary conditions preferably at constant pressure, a bulk fluid can be simulated free from any surface interactions. However, the surface properties of liquid crystals are significant in technological applications such as electro-optic displays. Liquid crystals also show a number of interesting features at surfaces which are not seen in the bulk phase and are of fundamental interest. In this final section, we describe recent simulations designed to study the interfacial properties of liquid crystals at various types of interface. First, however, it is appropriate to introduce some necessary terminology. 

The present author has performed computer simulations to examine the transition of pressure distributions and shear response from a hydrodynamic to boundary lubrication. Figure 4(a) shows an example of a smooth elastic sphere in contact with a rigid plane, the EHL pressure calculated at a very low rolling speed coincides perfectly with the... 

The favourable properties which mark out vesicles as protocell models were confirmed by computer simulation (Pohorill and Wilson, 1995). These researchers studied the molecular dynamics of simple membrane/water boundary layers the bilayer surface fluctuated in time and space. The model membrane consisted of glycerine-1-monooleate defects were present which allowed ion transport to occur, whereby negative ions passed through the bilayer more easily than positive ions. The membrane-water boundary layer should be particularly suited to reactions which are accelerated by heterogeneous catalysis. Thus, the authors believe that these vesicles fulfil almost all the conditions required for the first protocells on earth ... 

Figure 8.40. Computer-simulated IDFs gi (u) of ID two-phase structure formed by the iterated stochastic structure formation process. tt is the thickness of the transition layer at the phase boundary. o> is the standard deviation of a Gaussian crystallite thickness distribution... 

The determination of the character and location of phase transitions has been an active area of research from the early days of computer simulation, all the way back to the 1953 Metropolis et al. [59] MC paper. Within a two-phase coexistence region, small systems simulated under periodic boundary conditions show regions of apparent thermodynamic instability [60] simulations in the presence of an explicit interface eliminate this at some cost in system size and equilibration time. The determination of precise coexistence boundaries was usually done indirectly, through the... 

Let us discuss the four main types of boundary conditions reflecting, absorbing, periodic, and the so-called natural boundary conditions that are much more widely used than others, especially for computer simulations. 

Fig. 36 Computer simulation of a regular triangular superlattice of a Coulomb alloy Ai-x x with X = 1/4. A piece of triangular superlattice is shown together with a piece of rectangular lattice where the domain boundaries are marked. Reprinted with permission from [278]. Copyright American Physical Society...

Atomistic computer simulations are a statistical mechanical tool to sample configurations from the phase space of the physical system of interest. The system is uniquely treated by specifying the interactions between the particles (which are usually described as being pointlike), the masses of all the particles, and the boundary conditions. The interactions are calculated either on-the-fly by an electronic structure calculation (see Section 2.2.3) or from potential functions, which have been parametrized before the simulation by fitting to the results of electronic structure calculations or a set of experimental data. In the first case, one frequently speaks of AIMD (see Section 2.2.3), although the motion of the nuclei is still treated classically. 

In Figure 1 we compare our numerical solutions with the molecular dynamics computer simulations of Thompson, et al. (7). In this comparison we use liquid and vapor densities obtained from the simulation studies. In the next section we obtain the required boundary values by approximate evaluation of vapor-liquid equilibrium for a small system. 

Fig. 3.8 (b) Computer simulation image of same Ir surface. In this simple simulated image, no image brightness variation is considered. Thus the boundary is less clearly seen. Brightness variations can be incorporated into the simulation. For alloys, different colors can be used for different chemical species. 

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