Slow modes

Most properties of linear polymers are controlled by two different factors. The chemical constitution of tire monomers detennines tire interaction strengtli between tire chains, tire interactions of tire polymer witli host molecules or witli interfaces. The monomer stmcture also detennines tire possible local confonnations of tire polymer chain. This relationship between the molecular stmcture and any interaction witli surrounding molecules is similar to tliat found for low-molecular-weight compounds. The second important parameter tliat controls polymer properties is tire molecular weight. Contrary to tire situation for low-molecular-weight compounds, it plays a fimdamental role in polymer behaviour. It detennines tire slow-mode dynamics and tire viscosity of polymers in solutions and in tire melt. These properties are of utmost importance in polymer rheology and condition tlieir processability. The mechanical properties, solubility and miscibility of different polymers also depend on tlieir molecular weights. 

The essential slow modes of a protein during a simulation accounting for most of its conformational variability can often be described by only a few principal components. Comparison of PGA with NMA for a 200 ps simulation of bovine pancreatic trypsic inhibitor showed that the variation in the first principal components was twice as high as expected from normal mode analy-si.s ([Hayward et al. 1994]). The so-called essential dynamics analysis method ([Amadei et al. 1993]) is a related method and will not be discussed here. 

For example, the SHAKE algorithm [17] freezes out particular motions, such as bond stretching, using holonomic constraints. One of the differences between SHAKE and the present approach is that in SHAKE we have to know in advance the identity of the fast modes. No such restriction is imposed in the present investigation. Another related algorithm is the Backward Euler approach [18], in which a Langevin equation is solved and the slow modes are constantly cooled down. However, the Backward Euler scheme employs an initial value solver of the differential equation and therefore the increase in step size is limited. 

The first chapter, on Conformational Dynamics, includes discussion of several rather recent computational approaches to treat the dominant slow modes of molecular dynamical systems. In the first paper, SCHULTEN and his group review the new field of steered molecular dynamics (SMD), in which large external forces are applied in order to be able to study unbinding of ligands and conformation changes on time scales accessible to MD... 

For small wavevectors the test particle density is a nearly conserved variable and will vary slowly in time. The correlation function in the memory term in the above equation involves evolution, where this slow mode is projected... 

In order for the averaged momentum p to point along the slow manifold (i.e., for the components of momentum in the fast manifold to average to zero), one has to choose the averaging time r so as to be several times longer than the period of the fast modes but shorter than those of the slow modes. 

C. The Effective Hamiltonians of the Slow Mode in Different Representations... 

E. Narrowing of the Lineshapes by Pure Damping of the Slow Mode... 

Figure 1. Main anharmonicities of the fast mode. F, fast mode S, slow mode (intrinsic anharmonic Morse potential) B, bending mode.

On the other hand, one has to take into account the influence of the surrounding which must induce an irreversible evolution of the H-bond system when its fast mode is excited the fast mode may be directly damped by the medium that is the direct relaxation mechanism. It may be also damped through the slow mode to which it is anharmonically coupled, that is the indirect relaxation mechanism. A schematical illustration of these two damping mechanism is given in Fig. 2. Of course, the role played by damping must be more important for H bonds in condensed phase. 

The cornerstone of the strong anharmonic coupling theory relies on the assumption of a modulation of the fast mode frequency by the intermonomer distance. This behavior is correlated by many experimental observations, and it is undoubtly one of the main mechanisms that take place in a hydrogen bond. Because the intermonomer distance is, in the quantum model, represented by the dimensionless position coordinate Q of the slow mode, the effective angular frequency of the fast mode may be written [52,53]... 

Now, recall that for weak hydrogen bonds the high-frequency mode is much faster than the slow mode because 0 m 20 00. As a consequence, the quantum adiabatic approximation may be assumed to be verified when the anharmonic coupling parameter aG is not too strong. Thus, neglecting the diabatic part of the Hamiltonian (22) and using Eqs. (18) to (20), one obtains... 

Passing to the Boson operators by aid of Table II, and after neglecting the zero-point-energy of the fast mode, we obtain a quantum representation we shall name I, in which the effective Hamiltonians of the slow mode corresponding respectively to the ground and first excited states of the fast mode are... 

The eigenvalue equation of the representation of the effective Hamiltonian operators (28) in the base of the number occupation operator of the slow mode is characterized by the equation... 

If we want to remove the driven term in the potential of the slow mode, when k = 0 (ground state of the fast mode), it is suitable to perform the following phase transformation ... 

The effective Hamiltonian /7 °f, related to the ground states 0 ) and [0]) of the fast and bending modes, is the Hamiltonian of a quantum harmonic oscillator characterizing the slow mode ... 

Similarly, the effective Hamiltonian holds for a double excitation of the bending mode, but involves the nondriven Hamiltonian of the slow mode (92). Within the sub-base (89c), it may be written... 

Several studies of Fermi resonances in the absence of H bond have been made [76-80]. We shall account for this situation by simply ignoring the anharmonic coupling between the fast and slow modes (a = 0). The theory then describes the coupling between the fast mode and a bending mode through the potential Htf, with both of these modes being damped in the same way. Because aG = 0, the slow mode does not play any role, so that the total Hamiltonian does not refer to it ... 

There are two kinds of damping that are considered within the strong anharmonic coupling theory the direct and the indirect. In the direct mechanism the excited state of the high-frequency mode relaxes directly toward the medium, whereas in the indirect mechanism it relaxes toward the slow mode to which it is anharmonically coupled, which relaxes in turn toward the medium. 

It may be shown [8] that both semiclassical [83,84], and full quantum mechanical approaches [7,32,33,58,87] of anharmonic coupling have in common the assumption that the angular frequency of the fast mode depends linearly on the slow mode coordinate and thus may be written... 

In the full quantum mechanical approach [8], one uses Eq. (22) and considers both the slow and fast mode obeying quantum mechanics. Then, one obtains within the adiabatic approximation the starting equations involving effective Hamiltonians characterizing the slow mode that are at the basis of all principal quantum approaches of the spectral density of weak H bonds [7,24,25,32,33,58, 61,87,91]. It has been shown recently [57] that, for weak H bonds and within direct damping, the theoretical lineshape avoiding the adiabatic approximation, obtained directly from Hamiltonian (22), is the same as that obtained from the RR spectral density (involving adiabatic approximation). 

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