Atomism Atomists

Based on interactive forces and boundary conditions, atomistic modeling predicts the positions of atoms. Atomistic modeling techniques can be classified into three main categories, namely the MD, MC and Ab initio approaches. Other atomistic modeling techniques such as TBMD, LD, DFT, Morse potential function model, and modified Morse potential function model were also applied as discussed in last section. 

The fundamental entity in atomistic or molecular simulations is the atom or the molecule and is based on the fundamentals of statistical mechanics. The detailed electronic structure is no longer present, thus preventing the treatment of electron transfer, bond breaking and bond making processes. The system is instead described by the forces that act upon the atoms or molecule. This significantly lowers the CPU cost on a per atom basis, thus allowing the simulation of 10 10 atoms. Atomistic simulation can be... 

Since and depend only on die valence charge densities, they can be detennined once the valence pseudo- wavefiinctions are known. Because the pseudo-wavefiinctions are nodeless, the resulting pseudopotential is well defined despite the last temi in equation Al.3.78. Once the pseudopotential has been constructed from the atom, it can be transferred to the condensed matter system of interest. For example, the ionic pseudopotential defined by equation Al.3.78 from an atomistic calculation can be transferred to condensed matter phases without any significant loss of accuracy. 

Atomistically detailed models account for all atoms. The force field contains additive contributions specified in tenns of bond lengtlis, bond angles, torsional angles and possible crosstenns. It also includes non-bonded contributions as tire sum of van der Waals interactions, often described by Lennard-Jones potentials, and Coulomb interactions. Atomistic simulations are successfully used to predict tire transport properties of small molecules in glassy polymers, to calculate elastic moduli and to study plastic defonnation and local motion in quasi-static simulations [fy7, ( ]. The atomistic models are also useful to interiDret scattering data [fyl] and NMR measurements [70] in tenns of local order. 

Molecular dynamics simulations ([McCammon and Harvey 1987]) propagate an atomistic system by iteratively solving Newton s equation of motion for each atomic particle. Due to computational constraints, simulations can only be extended to a typical time scale of 1 ns currently, and conformational transitions such as protein domains movements are unlikely to be observed. 

II of the actual atoms (or at least the non-hydrogen atoms) in the core system are lented explicitly. Atomistic simulations can provide very detailed information about haviour of the system, but as we have discussed this typically limits a simulation to nosecond timescale. Many processes of interest occur over a longer timescale. In the if processes which occur on a macroscopic timescale (i.e. of the order of seconds) rather simple models may often be applicable. Between these two extremes are imena that occur on an intermediate scale (of the order of microseconds). This is the... 

Empirical energy functions can fulfill the demands required by computational studies of biochemical and biophysical systems. The mathematical equations in empirical energy functions include relatively simple terms to describe the physical interactions that dictate the structure and dynamic properties of biological molecules. In addition, empirical force fields use atomistic models, in which atoms are the smallest particles in the system rather than the electrons and nuclei used in quantum mechanics. These two simplifications allow for the computational speed required to perform the required number of energy calculations on biomolecules in their environments to be attained, and, more important, via the use of properly optimized parameters in the mathematical models the required chemical accuracy can be achieved. The use of empirical energy functions was initially applied to small organic molecules, where it was referred to as molecular mechanics [4], and more recently to biological systems [2,3]. 

Although the folding of short proteins has been simulated at the atomic level of detail [159,160], a simplified protein representation is often applied. Simplifications include using one or a few interaction centers per residue [161] as well as a lattice representation of a protein [162]. Some methods are hierarchical in that they begin with a simplified lattice representation and end up with an atomistic detailed molecular dynamics simulation [163]. 

Fig. 2.32. Atomistic view of interaction processes between incident high-energy electrons and electrons of an individual atom.

Very recently, people who engage in computer simulation of crystals that contain dislocations have begun attempts to bridge the continuum/atomistic divide, now that extremely powerful computers have become available. It is now possible to model a variety of aspects of dislocation mechanics in terms of the atomic structure of the lattice around dislocations, instead of simply treating them as lines with macroscopic properties (Schiotz et al. 1998, Gumbsch 1998). What this amounts to is linking computational methods across different length scales (Bulatov et al. 1996). We will return to this briefly in Chapter 12. 

The simplest atomistic model for the formation of a crystal in continuous space requires the definition of some effective attractive potential between any two atoms, which is defined independently of the other atoms in the cluster or crystal. The most frequently studied potential is the Lennard-Jones potential... 

Since some earlier work based on anisotropic elasticity theory had not been successful in describing the observed mechanical behaviour of NiAl (for an overview see [11]), several studies have addressed dislocation processes on the atomic length scale [6, 7, 8]. Their findings are encouraging for the use of atomistic methods, since they could explain several of the experimental observations. Nevertheless, most of the quantitative data they obtained are somewhat suspicious. For example, the Peierls stresses of the (100) and (111) dislocations are rather similar [6] and far too low to explain the measured yield stresses in hard oriented crystals. 

The precursor of such atomistic studies is a description of atomic interactions or, generally, knowledge of the dependence of the total energy of the system on the positions of the atoms. In principle, this is available in ab-initio total energy calculations based on the loc density functional theory (see, for example, Pettifor and Cottrell 1992). However, for extended defects, such as dislocations and interfaces, such calculations are only feasible when the number of atoms included into the calculation is well below one hundred. Hence, only very special cases can be treated in this framework and, indeed, the bulk of the dislocation and interfacial... 

The elucidation of the factors determining the relative stability of alternative crystalline structures of a substance would be of the greatest significance in the development of the theory of the solid state. Why, for example, do some of the alkali halides crystallize with the sodium chloride structure and some with the cesium chloride structure Why does titanium dioxide under different conditions assume the different structures of rutile, brookite and anatase Why does aluminum fluosilicate, AljSiCV F2, crystallize with the structure of topaz and not with some other structure These questions are answered formally by the statement that in each case the structure with the minimum free energy is stable. This answer, however, is not satisfying what is desired in our atomistic and quantum theoretical era is the explanation of this minimum free energy in terms of atoms or ions and their properties. 

Chemical vapor deposition may be defined as the deposition of a solid on a heated surface from a chemical reaction in the vapor phase. It belongs to the class of vapor-transfer processes which is atomistic in nature, that is the deposition species are atoms or molecules or a combination ofthese. Beside CVD, they include various physical-vapor-deposition processes (PVD) such as evaporation, sputtering, molecular-beam epitaxy, and ion plating. 

It is our experience that to the first question, the most common student response is something akin to Because my teacher told me so . One is tempted to say that it is a pity that the scientific belief of so mat r students is sourced from an authority, rather than from empirical evidence - except that when chemists are asked question (ii), they find it not at all easy to answer. There is, after all, no single defining experiment that conclusively proves the claim, even though it was the phenomenon of Brownian motion that finally seems to have clinched the day for the atomists 150 or so years ago. Of course, from atomic forced microscopy (AFM), we see pictures of gold atoms being manipulated one by one - but the output from AFM is itself the result of application of interpretive models. 

In summary, for Leukipp and Demokrit, the empty space between the atoms was a key assumption in their model, because, if particles were closely packed, they could not move and substances could not be mixed. When asking students to philosophise about the nature of matter, we indeed find parallels to the ancient Greek thinking, both to the so-called atomists and to the continuous ideas of Aristotle and others. For example, Leukipp s and Demokrit s explanation for the specific weight of substances corresponds to one student conception younger students especially tend to explain differences in the specific weight (but also hardness of substances) with differences in the closeness of particles (Fig. 10.6). They seldom take into account that the particles could have a different weight themselves. 

The rapid rise in computer power over the last ten years has opened up new possibilities for modelling complex chemical systems. One of the most important areas of chemical modelling has involved the use of classical force fields which represent molecules by atomistic potentials. Typically, a molecule is represented by a series of simple potential functions situated on each atom that can describe the non-bonded interaction energy between separate atomic sites. A further set of atom-based potentials can then be used to describe the intramolecular interactions within the molecule. Together, the potential functions comprise a force field for the molecule of interest. 

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