Coupling Using Additional Forces

This approach is quite natural and very easy to implement it does, however, require the use of small time steps and therefore may not be the optimal procedure for many applications. 

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Contractile properties in rodents can be measured either in vitro in a dissected muscle or in vivo in an intact preparation with an anesthetized animal (e.g., (19-20)). Measurements made under isometric conditions are perhaps most common and use the most straightforward setup. The addition of servomotors for dynamic control of muscle length allows simulation of dynamic conditions (eccentric, isotonic, etc.) that may be modified by disease or other processes (22, 23). For in vitro studies, the muscle is anchored by ligating the tendon (origin) to a support, for in vivo studies, the bone (femur) is clamped to prevent movement. The other tendon (insertion) is then coupled to a force transducer. In both cases, a recording electrode is also placed in contact with the muscle to record the compound action potential, and a stimulating electrode is used to stimulate the nerve or the muscle, as described below. 

It has to be kept in mind that parameters taken from different force fields are not necessarily transferable to a new model. In addition, most of the force fields are used with specific algorithms for force calculations cut-off schemes, pressure and temperature coupling methods, methods to calculate the long range contributions from electrostatic and, in. some cases, van der Waals forces, and water models all can be considered part of the force field . Of special interest are a number of articles on ab initio studies of different types of lipids. " Although no molecular dynamics simulations have been published using a force field derived from these calculations, such a force field is currently being developed. ... 

With a phenol, naphthol or keto-enol coupling component the mechanism is given by Scheme 4.4, in which blocking of the p-position forces coupling at the o-position. In certain cases involving the use of feebly reactive diazonium salts, loss of the proton from the transition state (4-1) in Scheme 4.4 may be slow but may often be facilitated by the addition of a tertiary base, such as pyridine, to the coupling mixture [7,8]. 

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