Simulating Synthesis

The essential difference between experiment (synthesis) and atomistic simulation is the ability of the simulator to be able to manipulate the structure with total atomistic control. Conversely, the experimentalist has less control and is generally limited to being able to manipulate only the reagents and synthetic conditions of manufacture. As shown later, attempts to simulate synthesis to generate atomistic models with sufficient structural detail and complexity to be of value to experimenters have been successful. However, this does come at a cost in that atomistic modelling and simulation looses, in part, potentially one of its most important attributes — total atomistic control. 

In this second section of this chapter we explore simulation methods, which can loosely be described as simulating synthesis including simulated annealing, atom deposition and simulated crystallisation. 

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It should be noted that the above strategy, although first employed In the delineation of protein antigenic sites. Is applicable, with appropriate adaptations, to the precise delineation and chemical synthesis of other types of protein binding sites. The Introduction of the concept of surface-simulation synthesis ( 4, ) has provided a methodology by which In principle any type of protein binding site can be mimicked synthetically after careful chemical characterization. 

Figure 4. Photograph of a lysozyme model showing the relative positions of the residues constituting antigenic sites 1 and 2. The side chains of the residues in the sites are outlined, those making up site 1 are speckled areas, while those constituting site 2 are shown as dotted areas to avoid confusion. The preferred direction of site 1 (at least by surface-simulation synthesis) is Arg-125 to Lys-13. Site 2 also had a preferred direction (Trp-62 to Asp-87) ...

Gorshenev, V.N., Bibikov, S.B. and Spector, V.N., Simulation, synthesis and investigation of microwave absorbing composite materials, Synthetic Metals, 1997, 86(1-3), 2255-2256. 

For a given pair of electrode reactions of known thermodynamic and kinetic characteristics, electrochemical engineering procedures must provide a reactor design in which these reactions can occur with high material and energy efficiencies. Simultaneously, appropriate provisions have to be made for the input of reactants and outflow of products and for the addition (or removal) of electric and thermal energy. The emphasis here is on the complete system and the inter-related surface reactions and transport processes. System analysis and design of electrochemical reactors require elaborate computer-implemented process simulation, synthesis, and optimization. 

C. A warm trap (100°C) and cold trap (0°C) were used to collect light wax and the water plus oil samples, respectively, by condensing from the vapor phase that was continuously withdrawn from the reactor vapor space. CO and H2 mass flow controllers were used to provide a simulated synthesis gas of the desired composition. After the catalysts was activated with CO, syngas was introduced into the CSTR with a stirrer speed of 750 rpm. Reaction conditions were 1.2 Mpa, H2/CO = 0.67, 230°C for potassium promoted catalyst and 270°C for beryllium promoted catalyst. 

Sayle DC, Feng XD, Ding Y et al (2007) Simulating synthesis ceria nanosphere self-assembly into nanorods and framework arcMtectuies. J Am Chem Soc 129(25) 7924—7935... 

Process simulation, synthesis of distillation trains and heat-exchanger networks... 

A. Debreil, C. Berthet, A.A. Jerraya "Symbolic computation of hierarchical and interconnected FSM s", in VHDL for simulation, synthesis and formal proof of hardware (ed.J. Mermet), Kluwer, 1992... 

VHDL FOR SIMULATION, SYNTHESIS AND FORMAL PROOFS OF HARDWARE, J. 

It is difficult to construct atomistic models for a nanomaterial using conventional methods of simulation, such as symmetry operators, because of the hierarchical levels of structural complexity. Experimentally, such nanostructures evolved during synthesis and therefore perhaps the easiest way to generate full atomistic models is to simulate synthesis . We explore such endeavours in the second section of this chapter. 

On the other hand, if the models comprising all hierarchical levels of structural complexity are generated by simulating synthesis rather than generating each component by-hand using symmetry operators, one loses ultimate control over the atomistic structure instead, similar to experiments, control over the microstructures and architectures may only be achieved indirectly by controlling, for example, temperature, pressure and methods of (self-) assembly. 

Fig. 9,2. The antigenic sites of hen egg white lysozyme and the corresponding synthetic peptides used in the method of surface simulation synthesis (from Atassi and Lee, 1978b).

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