SHAKE method

These various techniques were recently applied to molecular simulations [11, 20]. Both of these articles used the rotation matrix formulation, together with either the explicit reduction-based integrator or the SHAKE method to preserve orthogonality directly. In numerical experiments with realistic model problems, both of these symplectic schemes were shown to exhibit vastly superior long term stability and accuracy (measured in terms of energy error) compared to quaternionic schemes. 

The SHAKE method for bond constraints reduces the number of degrees of freedom during the initial stages of simulations it is good for minimizing solvent bath overhead. 

Stirring andBlendingMethods. Like shaking methods, these are very depeadeat oa procedural and equipment details, but they are simple to use and are widely employed for comparative purposes. 

The mixed solvent ether-acetone-hexane-heptane (2 1.1 1) proved to be an excellent solvent system for the residue analysis of all three compounds with the shaking method. Soxhlet extraction with chloroform, gave quite... 

In order to obtain pure cultures, the crude culture which contained Chromatium species was serially diluted in this modified medium as suggested by van Niel ( 1). This was repeated several times to ensure the purity of the culture. The agar shake method was not used as the large photosynthetic bacteria fail to grow in agar shake tubes ( 1). In pure culture the Chromatium species did not grow as well as in the mixed culture situation. The culture was not as dense or as rich in colour as the crude cultures. 

This method was used officially by the International Association of Leather Trades Chemists before the shaking method was introduced (1907), and is still often used in practice, especially by manufacturers of extracts. 

Flow methods have also been widely used to measure rapid reaction rates in solution. They are forms of mix and shake methods that initiate reactions and that are concerned with fast mixing of the reactant and subsequently with rapid measurements of solution concentration changes (Robinson, 1986). 

Many works [5] have illustrated that there is a linear relationship between R values and log P. R values also can be used to measure the Upophilicities of chemical substances. In general, the chromatographic method is an excellent alternative to the traditional flask-shaking method for lipophilicity determination. It avoids the difficulties that one may encounter in the flask-shaking method. It is simple and rapid and requires only minute amounts of substances (which need not necessarily be very pure) it does not need quantitative analysis the nature of the organic modifier does not affect the measurement of the lipophilic character, as the R value is not affected by the organic modifier. 

Fig. 1. Preparation of 0-palmitoyl mannan-anchored vesicles. Liposomes were prepared by hand-shaking method and coating of liposomes with these hydrophobized polysaccharides (OPM) was performed by incubation of aqueous soiutions of polysaccharide derivatives with preformed liposomal dispersion...

Fig. 2. AFM image of OPM-coated and-uncoated iiposomes (a) Piain iiposomes, and (b) OPM-coated iiposomes. Liposomes were prepared by hand-shaking method and a drop of iiposomai formuiation was transferred to a mica sheet. Each image shows the sphericai shape determined from the AFM observation. AFM image of the iiposomes indicated that piain iiposomes have iower size compared to OPM-coated iiposomes...

Filter paper degrading cellulase activity was measured by the author s (39) shaking method using 2 sheets of Toyo filter paper No. 2, 10 mm. X 10 mm. at 40°C., pH 5.0. Complete degradation was shown by + + ++. 

The principle of the classical cold shaking method is based on LSE. This sample method consists in shaking the sample in a solvent at atmospheric pressure and room temperature and is of interest because it gives results similar those of the Soxhlet method. It requires large volumes of organic solvent (200 ml of acetone) and long extraction times (several hours) and includes a distribution step with water and dichloromethane. 

ISO 11246 recommends using this method for the extraction of a wide variety of herbicides. A study carried out on soils using the shaking method with acetate ethyl obtained recoveries of 85% for diazinon and 88% for chlorpyriphos (Table 23.7). 

The SHAKE method has been extended by Tobias and Brooks [Tobias and Brooks 1988] to enable constraints to be applied to arbitrary internal coordinates. This enables the torsion angle of a rotatable bond to be constrained to a particular value during a molecular dynamics simulation, which is particularly useful when used in conjunction with methods for calculating free energies (see Section 11.7)... 

Changes in temperature of, say, 5°C, have little effect on a partition coefficient. When log P is above 4, the shaking method has little reliability and recourse must be made to chromatography, or to calculation from Rekker s fragmental constants (see below). 

In some cases semi-implicit methods can be developed which may only require the solution of a low-dimensional nonlinear system at each step. In Chap. 4, we discuss constrained systems for which implicit methods are needed and, in the case of the SHAKE method, for which the nonlinear system that must be solved at each step is of dimension equal to the number of constraints imposed. This is an example of a semi-implicit method. 

An alternative, simpler, and probably more robust, procedure is simply to fix the value of A(q) by constraining q to its mechanical equilibrium value [189] in which case no fast averaging whatsoever needs to be performed. This approach relies on the use of the SHAKE method of constrained molecular dynamics (see the following section). 

The projected symplectic constrained method (4.20)-(4.24) is only first order accurate. We forego providing a detailed proof of this fact, but note that it could be demonstrated using standard methods [164]. Note that (4.20)-(4.24) reduces to the symplectic Euler method in the absence of constraints, and the projection of the momenta would not alter this fact. There are several constraint-preserving, second-order alternatives which generalize the Stormer-Verlet scheme. One of these is the SHAKE method [322]. The original derivation of the SHAKE method began from the position-only, two-step form of the Stormer rule for q = F(q)... 

To determine whether the inherent silver and silver coated thread samples would show antimicrobial activity when subjected to soaking wet conditions, the dynamic shake method, ASTM E2149, was performed. The log reduction results after 1 hour and 24 hours incubation at 37 "C (Table 3) show that under soaking wet conditions the inherent silver and silver coated thread samples do exhibit a reduction in bacterial growth. The untreated control samples show an increase in bacterial growth. From these results it would appear the antibacterial activity of inherent silver and silver coated thread samples require soaking wet conditions to exhibit dieir antibacterial properties. As with the AATCC 100 method, the carbonised bamboo sample showed no antimicrobial activity. 

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