Computer simulations aggregation

Brown W D and Ball R C 1985 Computer simulation of chemically limited aggregation J. Phys. A Math. Gen. 18 L517-21... 

S. C. Ke, L. J. DeLucas, J. G. Harrison. Computer simulation of protein crystal growth using aggregates as the growth unit. J Phy D 57 1064, 1998. 

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. 

Patapoff, T. W., Mrsny, R. J., and Lee, W. A., The application of size exclusion chromatography and computer simulation to study the thermodynamic and kinetic parameters for short-lived dissociable protein aggregates, Anal. Bio-chem., 212, 71, 1993. 

A computer simulation carried out by C. Kuhn (2001) was able to confirm certain critical phases in the first steps of Kuhn s theory, such as the formation of aggregates (collector strand and hairpin strand). In this simulation, the process of the development of a simple genetic apparatus took place in three stages ... 

Corresponding approaches were developed in all the research methods theoretical, computer simulation, and, moreover, experimental. Thus, copolymers were synthesized in vitro, which form non-aggregating structures of the type hydrophobic core-hydrophilic shell. The structure of such copolymers is similar in this respect to that of protein macromolecules [125-127]. 

The term D is called the fractal index and represents the packing change with distance from the centre of the floe. Computer simulation and experiments allow the value of D to be related to the mechanism of aggregation. Typical values are for ... 

Theories or computer simulations used to calculate the potential of mean force W(r) are typically based on numerous simplifying assumptions and approximations (de Kruif, 1999 Bratko et al., 2002 Prausnitz, 2003 de Kruif and Tuinier, 2005 Home et al., 2007 Jonsson et al., 2007). Therefore they can provide only a qualitative or, at best, semi-quantitative description of the potential of mean force. Such calculations are nevertheless useful because they can serve as a guide for trends in the factors determining the interactions of both biopolymers and colloidal particles. Thus, an increase in the absolute value of the calculated negative depth of W(r) may be attributed to a predominant type of molecular feature favouring aggregation or self-association. To assist with such a theoretical analysis, expressions for some of the mean force potentials will be presented here in the discussion of specific kinds of interactions occurring between pairs of colloidal particles covered by biopolymers in food colloids. 

Computer simulations combined with experiments have also shown that one can deduce from the fractal dimension the nature of nucleation and growth of particles and what chemical and physical mechanisms control the formation of particle aggregates. We consider this briefly before proceeding to other topics. 

These computer simulations permit the number density of primary particles within the aggregate to be evaluated, important information for relating the properties of the aggregate to its composition. As might be expected, however, it is difficult to know a priori what model to use for a particular system. However, this technique does allow some interesting a posteriori interpretations of known structures to be made. Another closely related problem that has been... 

One of the major difficulties in developing theories of the rheology of coagulated or flocculated dispersions is that the microstructures of the aggregates are nonequilibrium structures under shear. Understandably, the rheology of such dispersions is history dependent, as we have seen above, and requires computer simulations and nonequilibrium statistical mechanics for proper study. 

In the case of diffusion-controlled A + B —> 0 reaction distinctive spatial distributions of reactants observed in computer simulations (e.g., [21]) are qualitatively the same as were presented earlier in Figs 1.20 and 1.21. Quite similar aggregation of similar particles into loose clusters occurs in agreement with a distinctive block-structure characterized by the diffusion length Id = f Dt shown in Fig. 2.8. When the reaction is controlled by the particle diffusion, these clusters (domains) are less pronounced since diffusion is known to smooth nonuniform particle distribution created in a course of reaction. 

In this Chapter the kinetics of the Frenkel defect accumulation under permanent particle source (irradiation) is discussed with special emphasis on many-particle effects. Defect accumulation is restricted by their diffusion and annihilation, A + B — 0, if the relative distance between dissimilar particles is less than some critical distance 7 0. The formalism of many-point particle densities based on Kirkwood s superposition approximation, other analytical approaches and finally, computer simulations are analyzed in detail. Pattern formation and particle self-organization, as well as the dependence of the saturation concentration after a prolonged irradiation upon spatial dimension (d= 1,2,3), defect mobility and the initial correlation within geminate pairs are analyzed. Special attention is paid to the conditions of aggregate formation caused by the elastic attraction of particles (defects). 

It is believed that, using this model and the methods of sequence design suitable for computer simulations, one can construct copolymers capable of forming nonaggregating heteropolymer globules, with the ultimate objective of learning how to manipulate the polymer chemistry and system conditions in order to preclude the aggregation processes. 

Recent studies showed that amphiphilic properties have to be taken into account for most water-soluble monomer units when their behavior in water solutions is considered. The amphiphilic properties of monomer units lead to an anisotropic shape of the polymer structures formed under appropriate conditions, which is confirmed both by computer simulation and experimental investigations. The concept of amphiphilicity applied to the monomer units leads to a new classification based on the interfacial and partitioning properties of the monomers. The classification in question opens a broad prospective for predicting properties of polymer systems with developed interfaces (i.e., micelles, polymer globules, fine dispersions of polymer aggregates). The relation between the standard free energy of adsorption and partition makes it possible to estimate semiquantitatively the distribution between the bulk and the interface of monomers and monomer units in complex polymer systems. 

Figure 1. Computer simulation of the formation of clay tactoid by a process of aggregation of lCr particles. Ration length to thickness 9/1. In the three topmost diagrams each rectangle endorses a portion of the tactoid shown enlarged below, df is represented by the thickness of the line enclosing the sheets in contact. Adapted from ref. 6. N.B. With respect to the next section, the molar fraction xi consists of the water in the interlamellar space and in the closed spaces within the tactoid. The molar fraction xb is in a 10 A thick layer on the external contour of the tactoid.

The atomic density of the hex phase is about 20% higher than that of the 1 x 1 phase. As could be demonstrated by scanning tunneling microscopy (STM) (49), during the CO-induced hex — 1 x 1 transformation, these additional atoms are squeezed out from the surface layer, on top of which they are aggregating to new small I x 1 patches, a result which could also be successfully modeled by computer simulations (50). 

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