Explicit goal representation

Tarek et al. [388] studied a system with some similarities to the work of Bocker et al. described earlier—a monolayer of n-tetradecyltrimethylammonium bromide. They also used explicit representations of the water molecules in a slab orientation, with the mono-layer on either side, in a molecular dynamics simulation. Their goal was to model more disordered, liquid states, so they chose two larger molecular areas, 0.45 and 0.67 nm molecule Density profiles normal to the interface were calculated and compared to neutron reflectivity data, with good agreement reported. The hydrocarbon chains were seen as highly disordered, and the diffusion was seen at both areas, with a factor of about 2.5 increase from the smaller molecular area to the larger area. They report no evidence of a tendency for the chains to aggregate into ordered islands, so perhaps this work can be seen as a realistic computer simulation depiction of a monolayer in an LE state. 

Plan Representation in SECS. The SECS Simulation and Evaluation of Chemical Synthesis program explicitly represents its plans(2) as a list structure of goal instructions with logical connectives. A goal instruction can specify one of the following ... 

At the other end of the spectrum, our goal might be a set of differential equations that describe the behavior of each of the components and their interactions. These would likely attract anyone who aspired to reduce chemical phenomena to mechanics, whether classical (in Butlerov s time) or quantum (in our own). Butlerov explicitly rejected Gerhardt s option while expressing considerable doubt about when, if ever, the second option would be attainable. As it happened, the subsequent history of chemical structure has seen the development of a number of intermediate representations. 

In many cases explicit solvent models are more useful than implicit models. Examples include simulations in which a detailed picture of solvent structure is one of the goals and cases for which there is evidence that a particular structural feature of the solvent is playing a key role (e.g., a specific water-macromolecule hydrogen bond), although explicit representation of some water molecules combined with implicit solvation may suffice. MD simulations used to study kinetic, or time-dependence, properties of macromolecular processes, comprise another important example. 

In contrast, there will be many cases where continuum solvent models are less useful. These include situations where one of the goals of the simulation is to obtain a detailed picture of solvent structure, or where there is evidence that a particular structural feature of the solvent is playing a key role (for example, a specific water-macromolecule hydrogen bond). In these situations, however, explicit representation of some water combined with implicit solvation may suffice. Another example is when molecular dynamics simulations are used to study kinetic, or time-dependent phenomena. The absence of the frictional effects of solvent will lead to overestimation of rates. In addition, more subtle time-dependent effects arising from the solvent will be missing from continuum models. Continuum solvent models are in effect frilly adiabatic, in the sense that for any instantaneous macromolecular conformation, the solvent is taken to be completely relaxed. For electrostatic effects, this implies instantaneous dielectric and ionic double layer relaxation rates, and for the hydrophobic effect, instantaneous structural rearrangement. An exception would be dielectric models that involve a frequency-dependent dielectric. Nevertheless, continuum solvent models should be used with caution in studying the time dependence of macromolecular processes. 

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