Atomistic approach

D. Schryvers, An Atomistic Approach of the Martensitic Transformation in Ni-Al, habilitation. Free... 

Sinnecker, S., Neese, F. Theoretical bioinorganic spectroscopy. In Reiher, M. (ed.) Atomistic Approaches in Modem Biology from Quantum Chemistry to Molecular Simulations, p. 47. Springer, Berlin (2007)... 

Senn H, Thiel W (2007) QM/MM methods for biological systems in Atomistic approachs in modern biology, Vol. 268 of Topics in Current Chemistry, Springer Berlin/Heidelberg, Berlin, Germany, pp 173-290... 

Lagally, P. and Lagally H. "Atomistic Approach to the Crosslinking of Cellulose Fibers and Their Reaction with Fillers," TAPP1. Vol. 39, No. 11, November 1956, 747 754. 

We will limit ourselves here to introducing the simplest of the quantum mechanics procedures the Modified Electron Gas (MEG) treatment of Gordon and Kim (1971). This procedure is on the borderline between the classical atomistic approach and quantum mechanics ab initio calculations that determine energy by applying the variational principle. A short introduction to MEG treatment should thus be of help in filling the conceptual gap between the two theories. 

Masuda, T., Jikihara, T., Nakamura, K., Kimura, A., Takagi, T., and Fujiwara, H. (1997) Introduction of solvent-accessible surface area in the calculation of the hydrophobicity parameter log P from an atomistic approach. J. Pharm. Sci. 86,57-63. 

Senn, H. M. Thiel, W. In Atomistic Approaches to Modern Biology. From Quantum Chemistry to Molecular Simulations Vol. 268 Ed. Reiher, M. Springer Berlin, Germany, 2007, pp 173—290. 

A method using the Atomistic approach (Masuda, 1996) was published recently and claims an improved performance from consideration of solute SASA as well as proximity effects of substituent groups. Measured values for 500 solutes were taken as a test set, but just how substituent proximity was taken into account was not explained. For a set of 20 pharmaceuticals not in the original test set, five methods other than the SASA-scaled atomistic method were compared. Table 5.1 shows the statistical results for the best three methods. 

Masuda, T., T. Jikhara, K. Nakamura, A. Kimura, T. Takagi, and H. Fujiwara. 1997. Introduction of Solvent-Accessible Surface Area in the Calculation of the Hydrophobicity Parameter log P from an Atomistic Approach. J. Pharm. Sci. 86, 57-63. 

Abbreviations A(hkl), surface area of the simulation cell in atomistic approaches (m2) am. lattice parameter of an AM oxide (A) , fivefold coordinated, n-valent anion , four-... 

Two atomistic approaches have been presented briefly above molecular dynamics and the transition-state approach. They are still not ideal tools for the prediction of diffusion constants because (i) in order to obtain a reliable chain packing with a MD simulation one still needs the experimental density of the polymer and (ii) though TSA does not require classical dynamics it involves a number of simplifying assumptions, i.e. duration of jump mechanism, elastic polymer matrix, size of smearing factor, that impair to a certain degree the ab initio character of the method. However MD and TSA are valuable achievements, they are complementary in several... 

Another methodological approach, which has become more attractive in the last few years for estimating binding free energies of protein-protein complexes, is the MM-PBSA method (Molecular Mechanics/Poisson-Boltzmann Surface Area). This method is a fully atomistic approach that combines molecular mechanics and continuum solvent, and has several appealing features as the possibility of being applied to a variety of systems not suitable for FEP such as very large protein-protein complexes.69,129-137... 

A detailed atomistic approach was used to investigate the molecular segment kinematics of a glassy, atactic polypropylene system dilated by 30%. ° The microstructural stress—dilation response consists of smooth, reversible portions bounded by sudden, irreversible stress jumps. But compared to the micro-structural stress—strain curve of the shear simulation, the overall trend more closely resembles macroscopic stress—strain curves. The peak negative pressure was in the neighborhood of 12% dilatation, with a corresponding secondary maximum in the von Mises shear stress. The peak negative pressure was re-... 

RMC, that allows for the formation of non-aromatic rings which are responsible for the curvature and cross-linking in carbon plates. We combined our atomistic approach with Simulated Aimealing (SA) to develop a reconstruction method [4] that gives better fits to the experimental data than the original RMC technique. 

Atomistic approaches need a structural model to represent the real system. In this section, we will briefly discuss the most common choices of structural models along with advantages and disadvantages, in order to enable readers unfamiliar with details to critically judge results presented in the literature. We will then discuss issues involved in choosing the structure... 

At lower overvoltages, with increasing A/criti the rj intervals come closer, and the A/crit( 7)-function becomes smoother. The atomistic approach becomes cumbersome and can be reasonably replaced by the classical approach using bulk properties such as specific surface and edge energies as already discussed above. 

From an experimental point of view, however, it seems that little progress has been made since the evaluation of the Volmer-Weber [4.11] equation in 1926. The experimentalist is bound to use eqs. (4.32) and (4.33), disregarding the small uninformative dependence of A on 77 derived from the Zeldovich factor F or the attachment probability Watt.yVcnt More significant progress seems to have been made with the development of the small cluster model based on the atomistic approach of Becker and Doering. 

The coincidence of the number of atoms of the nucleus in both treatments is not surprising, bearing in mind the validity of eq. (4.34) in both the classical and atomistic approaches. The calculation of AGcrit based on this number of atoms using eq. (4.35) gives results very near to those calculated based on the classical treatment. Although eq. (4.35) based on the classical model is to some extent disputable in its application to small clusters, it cannot give values very much different from reality. 

For a small number of Me atoms in a critical cluster, the strain of a 2D UPD Meads overlayer can be inherited by the nucleus. Using the atomistic approach [4.13], the rate of nucleation on top of a strongly compressed and internally strained 2D UPD Meads overlayer can be expressed by [4.54-4.57] (cf. Section 4.2) ... 

The atomistic theory becomes of additional significance for the transition from 2D Me phase formation in the UPD range to 3D Me phase formation in the OPD range. Experimental results obtained using modern in situ techniques with lateral atomic resolution showed that the transition phenomena can only be interpreted on the basis of atomistic approaches. The UPD surface modification turns out to be a more general phenomenon affecting not only the nucleation processes but also the growth mode and epitaxy of 3D metal phases. 

In the fourth part of the book the problem of three-dimensional phase formation and growth by overpotential deposition (OPD) is presented. Thermodynamic and kinetic aspects are considered. The atomistic approach is discussed and illustrated on bare and UPD modified substrates. 

An atomistic approach, which has relevance to the current work, is the previously discussed normal-mode method. In the normal-mode method the constituent monomer units in the cluster are assumed to interact with a reasonable model potential in a fixed structure. From the assumed structure and model potential a normal-mode analysis is jjerformed to determine a vibrational partition function. Rotational and translational partition functions are then included classically. The normal-mode method treats the cluster as a polyatomic molecule and is most appropriate at very low temperatures where anharmonic contributions to the intermolecular forces can be ignored. As we shall show by numerical example, as the temperature is increased, the... 

Reiher, M. (ed.) Atomistic Approaches in Modern Biology, Topics in Current Chemistry, Springer, Heidelberg, 2007. 

Thar J, Redden W, Kirchner B (2007) Atomistic approaches in modern biology. Topics in Current Chemistry, vol 268. Springer, Berlin Heidelberg New York, pp 133-171... 

To address the problem of faceting of grains, we use a classical atomistic approach by reasoning with a Kossel crystal representation, which is commonly used in crystal growth theories. The main idea is summarized as follows ... 

In Atomistic Approaches in Modern Biology, M. Reiher, (Ed.), Top. Curr. 

C. Dellago, P. Bolhuis, In Atomistic Approaches in Modem Biology ... 

For the moment, we describe the most naive approach to this problem and will reserve for later chapters (e.g. chap. 12) more sophisticated matching schemes which allow for the nonlinear calculations demanded in the core to be matched to linear calculations in the far fields. As we have repeatedly belabored, the objective is to allow the core geometry to emerge as a result of the full nonlinearity that accompanies that use of an atomistic approach to the total energy. However, in order to accomplish this aim, some form of boundary condition must be instituted. One of the most common such schemes is to assume that the far field atomic positions are dictated entirely by the linear elastic fields. In particular, that is... 

Onr discussion of the free energy driving forces will mostly follow the discussions ontlined in Venables et al. [5] and in Markov [3], The extension of the atomistic approach to the organics will come from Verlaak et al. [15]. The elements of the rate equation will follow Venables et al. [5]. Dynamic scaling will then follow as an extension to the rate equations coupled with some assumptions about the island size distributions [23]. For deposition beyond the first layer the comparison of model predictions with experiment will follow Cohen et al. [29]. The height-height correlation description will follow Krim and Palasantzas [30]. 

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