Embedding method

Luft J H 1961 Improvements in epoxy resin embedding methods J. Biophys. Biochem. Cytol. 9 409-14... 

In this chapter, we will review some basic features of embedding methods, with a particular emphasis on some QM/MM techniques. We will discuss the basic theory, and some practical aspects of how to perform QM/MM calculations on biological... 

Roos N. Freeze-substitution and other low temperature embedding methods, in Electron Microscopy in Biology—A Practical Approach (Harris JR, ed.), IRL Press, Oxford, UK, 1991, pp. 39-58. 

Reymond O, Pickett-Heaps J. A routine flat embedding method for electron microscopy of microorganisms allowing selection and precisely oriented sectioning of single cells by light microscopy. J Microsc 1983 130 79-84. 

Sawada H, Esaki M. A simple flat embedding method for the correlative light and electron microscopic immunocytochemistry. J Electron Microsc 1998 47 535-537. 

The electrostatic embedding method is included in numerous quantum chemistry packages and although quantum chemical computations using this technique are straightforward, some difficulties in its application in the context of QM/MM approaches are encountered (27,34). The main problems are associated with the derivation of forces in a periodic environment which has to be employed to ensure that the system reflects the bulk of a liquid. 

Investigation of the mechanism of nitrate reduction by Desulfovibrio desulfuricans nitrate reductase at various levels of theory has confirmed the utility of the orbital-free embedding method in the description of enzymatic processes.379... 

Kojima Y, Yoon SY, Kayama T (1988b) A study of production of CTMP from hardwood Part 3 Characterization of pulps produced by CTMP O-i process J Jpn Tappi 42 953-962 Lange PW (1954) The distribution of lignin in the cell wall of normal and reaction wood from spruce and a few hardwoods Sven Papperstidn 57 525-532 Luft JH (1961) Improvements in epoxy resin embedding method J Biophys Biochem Cytol 9 409-414... 

The overwhelming majority of the theoretical studies were performed on cluster models of the catalytic site, hi spite of the fact that the role of space confinement and the secondary interactions with the framework atoms is well-known, there are only a few electronic structure calculations on lattice models involving hydrocarbons, using either periodic DFT calculations, or embedding methods. In this brief account of the subject we attempt to overview some of the recent computational results of the literature and present some new data obtained from ab initio DFT pseudopotential plane wave calculations on Cl - C4 alkanes in the chabazite framework. 

Two-way embedded methods. These involve embedding of molecules or parts of molecules modelled using QM into a system of molecules modelled using MM, e.g. using QM to model a substrate, and MM to model the enzyme and solvent. 

Two-way embedded methods. These involve the running of simulations in which an atomistic region (e.g. a membrane protein) is embedded within a CG model (e.g. a lipid membrane). 

In ref. 172 a new embedded pair of explicit Runge-Kutta-Nystrom (RKN) methods adapted to the numerical solution of general perturbed oscillators is produced. This pair is based on the methods developed by Franco.These methods can be used for general problems. It is proved that the embedded methods have algebraic order 4 and 3. 

G. Avdelas and T. E. Simos, Embedded methods for the numerical solution of the Schrodinger equation, Comput. Math. Appl., 1996, 31, 85-102. 

The large unit cells required to represent zeolites in periodic DFT calculations have motivated many quantum chemistry cluster studies of zeolites. A complication in these studies is that long-range electrostatic contributions from the zeolite framework and steric constraints from the zeolite pore shape are often significant.259 This complication can be overcome by using embedding methods in which quantum chemistry calculations are coupled with classical force fields,260 but the fact that periodic DFT calculations have now become computationally accessible for these systems suggests that these calculations will widely supplant cluster approaches in the future. 

Within the quasi-steady-state approximation, the most popular method is the embedding method involving the successive solving of a series of direct problems and corrections of the TE working surface until a desired shape of the WP is assured [45, 46, 50, 51]. Several methods of TE correction have been proposed they have a lot in common and can be presented in the following generalized form ... 

KEYWORDS oxide glass, embedded method, DV-Xa, silicate Corresponding author, e-mail ykowada sci.hyogo-u.ac.jp... 

In Refs. 244 and 248 the possibility to control friction has been discussed in model systems described by differential equations. Usually, in realistic systems, time series of dynamical variables rather than governing equations are experimentally available. In this case the time-delay embedding method [258] can be applied in order to transform a scalar time series into a trajectory in phase space. This procedure allows one to find the desired unstable periodic orbits and to calculate variations of parameters required to control friction. 

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