Computer simulation definitions

Finally, in this Introduction, it is worthwhile to reproduce one of the several current definitions, in the Oxford English Dictionary, of the word simulate To imitate the conditions or behaviour of (a situation or process) by means of a model, especially for the purpose of study or training specifically, to produce a computer model of (a process) . The Dictionary quotes this early (1958) passage from a text on high-speed data processing A computer can simulate a warehouse, a factory, an oil refinery, or a river system, and if due regard is paid to detail the imitation can be very exact . Clearly, in 1958 the scientific uses of computer simulation were not yet thought worthy of mention, or perhaps the authors did not know about them. 

To illustrate the relationship between the microscopic structure and experimentally accessible information, we compute pseudo-experimental solvation-force curves F h)/R [see Eq. (22)] as they would be determined in SEA experiments from computer-simulation data for T z [see Eqs. (93), (94), (97)]. Numerical values indicated by an asterisk are given in the customary dimensionless (i.e., reduced) units (see [33,75,78] for definitions in various model systems). Results are correlated with the microscopic structure of a thin film confined between plane parallel substrates separated by a distance = h. Here the focus is specifically on a simple fluid in which the interaction between a pair of film molecules is governed by the Lennard-Jones (12,6) potential [33,58,59,77,79-84]. A confined simple fluid serves as a suitable model for approximately spherical OMCTS molecules confined... 

None of the methods currently used to study molecular dynamics can span the whole time range of motions of interest, from picoseconds to seconds and minutes. However, the structural resolution of a method is of equal importance. A method has to not only provide information about the existence of motions with definite velocities but also to identify what structural element is moving and what is the mechanism of motion. Computer simulation of molecular dynamics has proved to be a very important tool for the development of theories concerning times and mechanisms of motions in proteins. In this approach, the initial coordinates and forces on each atom are input into the calculations, and classical equations of motions are solved by numerical means. The lengthy duration of the calculation procedure, even with powerful modem computers, does not permit the time interval investigated to be extended beyond hundreds of picoseconds. In addition, there are strong... 

Chronopotentiometry, galvanostatic transients, 1411 as analytical technique, 1411 activation overpotential, 1411 Clavilier, and single crystals, 1095 Cluster formation energy of, 1304 and Frumkin isotherm, 1197 Cobalt-nickel plating, 1375 Cold combustion, definition, 1041 Cole-Cole plot, impedance, 1129, 1135 Colloidal particles, 880, 882 and differential capacity, 880 Complex impedance, 1135 Computer simulation, 1160 of adsorption processes, 965 and overall reaction, 1259 and rate determining step, 1260... 

Can observe surface terrain at 1-2-mn definition occasionally atomic resolution, in solution. AFM particularly useful in observation of biosurfaccs Can be programmed to recognize patterns of behavior characteristic of certain mechanism sequences. Computer simulation is vital in, e.g., impedance spectroscopy... 

Table 8.1 describes the steps of the methodology in more detail. The procedure starts with the Problem definition production rate, chemistry, product specifications, safety, health and environmental constraints, physical properties, available technologies. Then, a first evaluation of feasibility is performed by an equilibrium design. This is based on a thermodynamic analysis that includes simultaneous chemical and physical equilibrium (CPE). The investigation can be done directly by computer simulation, or in a more systematic way by building a residue curve map (RCM), as explained in the Appendix A. This step will identify additional thermodynamic experiments necessary to consolidate the design decisions, mainly phase-equilibrium measurements. Limitations set by chemical equilibrium or by thermodynamic boundaries should be analyzed here. 

In the last IS years, various potentials for water have been used in computer simulation experiments a recent review on this topic is available in ref. 20, and a comparative analysis in ref. 21. We shall report some experimental results from which two possible definitions of the hydrogen bond must be inferred. 

Hydrogen-Bond Energetic Definition The hydrogen bond is intact if the energy V is less than a threshold value HB> otherwise the bond is broken. TTie probability p V) that the interaction energy between two water molecules is F, as obtained from computer simulation, is shown at various temperatures in Fig. 1. The hydrogen bond is related to the presence of a maximum in the attractive part of the interaction. 

Using a weak definition of the bond, a greater number of hydrogen bonds than the natural is obtained, and the quantity tends to the number of nearest neighbors of a molecule. This is only sli tly dependent on temperature." Statistical data have been reported recently" for the H-bond network obtained at 2S°C using various different potentials and a weak definition of the bond = —2.25 kcal/mol). The values obtained from computer simulation data with different potentials are listed in Table I. 

The soundest energetic definition seems to be that of assuming HB — 3.5 kcal/mol this value corresponds to the temperature-invariant point exhibited by p(V) (see Fig. 1). However, the dependence of Mjjb on temperature turns out to be more or less marked according to whether the definition is stronger or weaker. As a consequence pg cannot be derived straightforwardly from the computer simulation alone, even if this turns out to be useful as a checking tool. Furthermore, in our opinion, a theory for dynamics should be comprehensive and coherent, able to account for the thermodynamic and structural properties of water. 

Using the values obtained for Pg, and p, we can calculate Pb T) from Eq. (5.2). The resulting Pb(T) values are shown in Fig. 5 together with the values calculated using the computer simulation data ( hb) Yamamoto et al. These authors used in their experiment an attractive cutoff potential R = 4.4 A) and an energetic definition with Kjjb = 3.5 kcal/mol. The Pb(T) values obtained by Angell are also drawn in Fig. 5. 

---