Semi system

Ai, X., "Numerical Analyses of Elastohydrodynamically Lubricated Line and Point Contacts with Rough Surfaces by Using Semi-System and Multi-Grid Methods, Ph.D. Thesis, Northwestern University, 1993. 

Organic polymers have traditionally been named on the basis of the monomer used, a hypothetical monomer or a semi-system-atic structure. Alternatively, they may be named in the same way as organic compounds, i.e., on the basis of a structure as drawn. The former method, often called source-based nomenclature or monomer-based nomenclature, sometimes results in ambiguity and multiple names for a single material. The latter method, termed structure-based nomenclature, generates a sometimes cumbersome unique name for a given polymer, independent of its source. Within their limitations, both types of names are acceptable and well-documented. The use of stereochemical descriptors with both types of polymer nomenclature has been published. ... 

Using a batch reactor, a constant concentration of sulfuric acid can be maintained by adding concentrated sulfuric acid as the reaction progresses, i.e., semi-batch operation. Good temperature control of such systems can be maintained, as we shall discuss later. 

The calculation of the time evolution operator in multidimensional systems is a fomiidable task and some results will be discussed in this section. An alternative approach is the calculation of semi-classical dynamics as demonstrated, among others, by Heller [86, 87 and 88], Marcus [89, 90], Taylor [91, 92], Metiu [93, 94] and coworkers (see also [83] as well as the review by Miller [95] for more general aspects of semiclassical dynamics). This method basically consists of replacing the 5-fimction distribution in the true classical calculation by a Gaussian distribution in coordinate space. It allows for a simulation of the vibrational... 

The behaviour of the BZ system ean be modelled semi-quantitatively by the oregonator model [15] ... 

The flux-flux expression and its extensions have been used to calculate reaction probabilities for several important reactions, including H2+02 H + H2O, by explicit calculation of the action of G in a grid representation with absorbmg potentials. The main power of the flux-flux fomuila over the long mn will be the natural way in which approximations and semi-classical expressions can be inserted into it to treat larger systems. 

In this paper, we discuss semi-implicit/implicit integration methods for highly oscillatory Hamiltonian systems. Such systems arise, for example, in molecular dynamics [1] and in the finite dimensional truncation of Hamiltonian partial differential equations. Classical discretization methods, such as the Verlet method [19], require step-sizes k smaller than the period e of the fast oscillations. Then these methods find pointwise accurate approximate solutions. But the time-step restriction implies an enormous computational burden. Furthermore, in many cases the high-frequency responses are of little or no interest. Consequently, various researchers have considered the use of scini-implicit/implicit methods, e.g. [6, 11, 9, 16, 18, 12, 13, 8, 17, 3]. 

Fig. 1. A semi-implicit integrator the implicit scheme is applied only to the fast system.

The quantum mechanical techniques discussed so far are typically appUed to moderate-sized molecules (up to about 100 atoms for ab-initio or DFT and up to 500 for semi-empirical MO techniques). However, what about very large systems, such as enzymes or DNA, for which we need to treat tens of thousand of atoms. There are two possible solutions to this problem, depending on the application. 

For many applications, especially studies on enzyme reaction mechanisms, we do not need to treat the entire system quantum mechanically. It is often sufficient to treat the center of interest (e.g., the active site and the reacting molecules) quantum mechanically. The rest of the molecule can be treated using classical molecular mechanics (MM see Section 7.2). The quantum mechanical technique can be ab-initio, DFT or semi-empirical. Many such techniques have been proposed and have been reviewed and classified by Thiel and co-workers [50] Two effects of the MM environment must be incorporated into the quantum mechanical system. 

A textbook describing the theory associated with calculation s of Ih e electronic structure of molecti lar system s. While the book focuses on ab ini/rci calculation s, much of the in formation is also relevant to semi-empirical methods. The sections on the Hartree-fock an d Con figuration ItUeracTion s tn elh ods, in particular, apply to HyperChem. fhe self-paced exercisesare useful for the beginning computational chemist. 

WFth all semi-empirical methods, IlyperChem can also perform psendo-RIfF calculations for open -shell systems. For a doublet stale, all electrons except one are paired. The electron is formally divided into isvo "half electron s" with paired spins. Each halfelec-... 

Not all Iterative semi-empirical or ah iniiio calculations converge for all cases. For SCF calculation s of electronic stnictiire. system s with a small energy gap between the highest occupied orbital and the lowest unoccupied orbital may not converge or may converge slowly. (They are generally poorly described by the Ilartree-Foch method.)... 

For small molecules, the accuracy of solutions to the Schrtidinger equation competes with the accuracy of experimental results. However, these accurate a i initw calculations require enormous com putation an d are on ly suitable for the molecular system s with small or medium size. Ah initio calculations for very large molecules are beyond the realm of current computers, so HyperChern also supports sern i-em p irical quantum meclian ics m eth ods. Sem i-em pirical approximate solutions are appropriate and allow extensive cliem ical exploration, Th e in accuracy of the approxirn ation s made in semi-empirical methods is offset to a degree by recourse to experimental data in defining the parameters of the method. 

Each of these tools has advantages and limitations. Ab initio methods involve intensive computation and therefore tend to be limited, for practical reasons of computer time, to smaller atoms, molecules, radicals, and ions. Their CPU time needs usually vary with basis set size (M) as at least M correlated methods require time proportional to at least M because they involve transformation of the atomic-orbital-based two-electron integrals to the molecular orbital basis. As computers continue to advance in power and memory size, and as theoretical methods and algorithms continue to improve, ab initio techniques will be applied to larger and more complex species. When dealing with systems in which qualitatively new electronic environments and/or new bonding types arise, or excited electronic states that are unusual, ab initio methods are essential. Semi-empirical or empirical methods would be of little use on systems whose electronic properties have not been included in the data base used to construct the parameters of such models. 

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