Decoupled motion

However, a complete set of molecular energy levels needed for calculation of the partition function (Eq. (1.16)) is not available in most cases. The arising problem can be simplified through the approximation that the different types of motion such as vibration, rotation, and electronic excitations are on a different timescale and therefore are unaffected by each other and can be treated as decoupled motions. This leads to a separation of Q into factors that correspond to separate partition functions for electronic excitations, translation, vibration, external molecular rotation, and hindered and free internal rotation ... 

For the fragments OH and H from H2O, the internal motion of OH is not only rotation and vibration, but also electronic motion. In addition, rotational and electronic motions are coupled in OH with the coupling being intermediate between Hund s cases a and b. Although the other product is an atom, the spin of the electron of the H-atom has to be coupled to the partner product OH. This is why in most cases, (l6) does not describe the asymptotic motion of the products correctly. Instead, linear combinations of such wavefunctions have to be used in the general case. Nevertheless we first discuss the simplified case of decoupled motion. 

FIEXIMF.5PACEER DECOUPLES MOTIONS (X MAIN AND SOX CHAIN... 

For model A, the interfaces decouple from the bulk dynamics and their motion is driven entirely by the local curvature, and the surface tension plays only a background, but still an important, role. From this model A... 

We find it convenient to reverse the historical ordering and to stait with (neatly) exact nonrelativistic vibration-rotation Hamiltonians for triatomic molecules. From the point of view of molecular spectroscopy, the optimal Hamiltonian is that which maximally decouples from each other vibrational and rotational motions (as well different vibrational modes from one another). It is obtained by employing a molecule-bound frame that takes over the rotations of the complete molecule as much as possible. Ideally, the only remaining motion observable in this system would be displacements of the nuclei with respect to one another, that is, molecular vibrations. It is well known, however, that such a program can be realized only approximately by introducing the Eckart conditions [38]. 

It was stated above that the Schrodinger equation cannot be solved exactly for any molecular systems. However, it is possible to solve the equation exactly for the simplest molecular species, Hj (and isotopically equivalent species such as ITD" ), when the motion of the electrons is decoupled from the motion of the nuclei in accordance with the Bom-Oppenheimer approximation. The masses of the nuclei are much greater than the masses of the electrons (the resting mass of the lightest nucleus, the proton, is 1836 times heavier than the resting mass of the electron). This means that the electrons can adjust almost instantaneously to any changes in the positions of the nuclei. The electronic wavefunction thus depends only on the positions of the nuclei and not on their momenta. Under the Bom-Oppenheimer approximation the total wavefunction for the molecule can be written in the following form ... 

This algorithm alternates between the electronic structure problem and the nuclear motion It turns out that to generate an accurate nuclear trajectory using this decoupled algoritlun th electrons must be fuUy relaxed to the ground state at each iteration, in contrast to Ihe Car-Pairinello approach, where some error is tolerated. This need for very accurate basis se coefficients means that the minimum in the space of the coefficients must be located ver accurately, which can be computationally very expensive. However, conjugate gradient rninimisation is found to be an effective way to find this minimum, especially if informatioi from previous steps is incorporated [Payne et cd. 1992]. This reduces the number of minimi sation steps required to locate accurately the best set of basis set coefficients. 

The first finite element schemes for differential viscoelastic models that yielded numerically stable results for non-zero Weissenberg numbers appeared less than two decades ago. These schemes were later improved and shown that for some benchmark viscoelastic problems, such as flow through a two-dimensional section with an abrupt contraction (usually a width reduction of four to one), they can generate simulations that were qualitatively comparable with the experimental evidence. A notable example was the coupled scheme developed by Marchal and Crochet (1987) for the solution of Maxwell and Oldroyd constitutive equations. To achieve stability they used element subdivision for the stress approximations and applied inconsistent streamline upwinding to the stress terms in the discretized equations. In another attempt, Luo and Tanner (1989) developed a typical decoupled scheme that started with the solution of the constitutive equation for a fixed-flow field (e.g. obtained by initially assuming non-elastic fluid behaviour). The extra stress found at this step was subsequently inserted into the equation of motion as a pseudo-body force and the flow field was updated. These authors also used inconsistent streamline upwinding to maintain the stability of the scheme. 

In Chapter 4 the development of axisymmetric models in which the radial and axial components of flow field variables remain constant in the circumferential direction is discussed. In situations where deviation from such a perfect symmetry is small it may still be possible to decouple components of the equation of motion and analyse the flow regime as a combination of one- and two-dimensional systems. To provide an illustrative example for this type of approximation, in this section we consider the modelling of the flow field inside a cone-and-plate viscometer. 

MODELS BASED ON DECOUPLED FLOW EQUATIONS 163 Componeot of the equation of motion in the predominant, i.e. 6 direction... 

LB Films of Polymeric Amphiphile. Since the first successful deposition of a polymeric LB film (61), there have been a large number of studies examining different stmctural parameters on the transferabiHty and stabiHty of the polymeric LB films (4). One interesting idea for polymers for LB films is the use of a spacer group (mosdy hydrophilic) to decouple the motion of the polymer from that of the Hpid membrane (62,63). Monolayers from a poljmier (10) having hydrophilic phosphate groups and a tetraethylene oxide spacer were used to link a glycerol diether to the polymer chain (63). 

The Q and ft) dependence of neutron scattering structure factors contains infonnation on the geometry, amplitudes, and time scales of all the motions in which the scatterers participate that are resolved by the instrument. Motions that are slow relative to the time scale of the measurement give rise to a 8-function elastic peak at ft) = 0, whereas diffusive motions lead to quasielastic broadening of the central peak and vibrational motions attenuate the intensity of the spectrum. It is useful to express the structure factors in a form that permits the contributions from vibrational and diffusive motions to be isolated. Assuming that vibrational and diffusive motions are decoupled, we can write the measured structure factor as... 

Having demonstrated that our simulation reproduces the neutron data reasonably well, we may critically evaluate the models used to interpret the data. For the models to be analytically tractable, it is generally assumed that the center-of-mass and internal motions are decoupled so that the total intermediate scattering function can be written as a product of the expression for the center-of-mass motion and that for the internal motions. We have confirmed the validity of the decoupling assumption over a wide range of Q (data not shown). In the next two sections we take a closer look at our simulation to see to what extent the dynamics is consistent with models used to describe the dynamics. We discuss the motion of the center of mass in the next section and the internal dynamics of the hydrocarbon chains in Section IV.F. 

This e qnession for the propagators is still exact, as long as, the principal sub-manifold h and its complement sub-manifold h arc complete, and the characteristics of the propagator is reflected in the construction of these submanifolds (47,48). It should be noted that a different (asymmetric) metric for the superoperator space, Eq. (2.5), could be invoked so that another decoupling of the equations of motion is obtained (62,63,82-84). Such a metric will not be explored here, but it just shows the versatility of the propagator methods. 

The theory behind body-fixed representations and the associated angular momentum function expansions of the wavefunction (or wave packet) in terms of bases parameterized by the relevant constants of the motion and approximate constants of the motion is highly technical. Some pertinent results will simply be stated. The two good constants of the motion are total angular momentum, J, and parity, p = +1 or 1. An approximate constant of the motion is K, the body-fixed projection of total angular momentum on the body-fixed axis. For simplicity, we will restrict attention to the helicity-decoupled or centrifugal sudden (CS) approximation in which K can be assumed to be a constant of the motion. In terms of aU its components, and the iteration number k, the real wave packet is taken to be [21]... 

Because the degrees of freedom decouple in the linear approximation, it is easy to describe the dynamics in detail. There is the motion across a harmonic barrier in one degree of freedom and N — 1 harmonic oscillators. Phase-space plots of the dynamics are shown in Fig. 1. The transition from the reactant region at q <0 to the product region at q >0 is determined solely by the dynamics in (pi,qi), which in the traditional language of reaction dynamics is called the reactive mode. 

Figure 1 Schematic representation of the 13C (or 15N) spin-lattice relaxation times (7"i), spin-spin relaxation (T2), and H spin-lattice relaxation time in the rotating frame (Tlp) for the liquid-like and solid-like domains, as a function of the correlation times of local motions. 13C (or 15N) NMR signals from the solid-like domains undergoing incoherent fluctuation motions with the correlation times of 10 4-10 5 s (indicated by the grey colour) could be lost due to failure of attempted peak-narrowing due to interference of frequency with proton decoupling or magic angle spinning.

The 140-residue protein AS is able to form amyloid fibrils and as such is the main component of protein inclusions involved in Parkinson s disease. Full-length 13C/15N-labelled AS fibrils and AS reverse-labelled for two of the most abundant amino acids, K and V, were examined by homonuclear and heteronuclear 2D and 3D NMR.147 Two different types of fibrils display chemical shift differences of up to 13 ppm in the l5N dimension and up to 5 ppm for the backbone and side-chain 13C chemical shifts. Selection of regions with different mobility indicates the existence of monomers in the sample and allows the identification of mobile segments of the protein within the fibril in the presence of monomeric protein. At least 35 C-terminal residues are mobile and lack a defined secondary structure, whereas the N terminus is rigid starting from residue 22. In addition, temperature-dependent sensitivity enhancement is also noted for the AS fibrils due to both the CP efficiency and motional interference with proton decoupling.148... 

The 15N spectral peaks of fully hydrated [15N]Gly-bR, obtained via cross-polarization, are suppressed at 293 K due to interference with the proton decoupling frequency, and also because of short values of T2 in the loops.208 The motion of the TM a-helices in bR is strongly affected by the freezing of excess water at low temperatures. It is shown that motions in the 10-j-is correlation regime may be functionally important for the photocycle of bR, and protein-lipid interactions are motionally coupled in this dynamic regime. 

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