Molecular dynamics time-domain analysis

One of the main attractions of normal mode analysis is that the results are easily visualized. One can sort the modes in tenns of their contributions to the total MSF and concentrate on only those with the largest contributions. Each individual mode can be visualized as a collective motion that is certainly easier to interpret than the welter of information generated by a molecular dynamics trajectory. Figure 4 shows the first two normal modes of human lysozyme analyzed for their dynamic domains and hinge axes, showing how clean the results can sometimes be. However, recent analytical tools for molecular dynamics trajectories, such as the principal component analysis or essential dynamics method [25,62-64], promise also to provide equally clean, and perhaps more realistic, visualizations. That said, molecular dynamics is also limited in that many of the functional motions in biological molecules occur in time scales well beyond what is currently possible to simulate. 

The result of a molecular dynamics simulation is a time dependent wavefunction (quantum dynamics) or a swarm of trajectories in a phase space (classical dynamics). To analyze what are the processes taking the place during photodissoeiation one can directly look at these. This analysis is, however, impractical for systems with a high dimensionality. We can calculate either (juantities in the time domain or in the energy domain, fn the time domain survival probabilities can be measured by pump-probe experiments [44], in the energy domain the distribution of the hydrogen kinetic energy can be experimentally obtained [8]. 

The kind of NMR data required (e.g. signal amplitudes, relaxation information or chemical shift information with limited spectral resolution) plays a significant role in defining the design criteria for both hardware and software components. In common practice, in low-resolution NMR the concern is with the analysis of the NMR signal in the time domain (FID) and the characterisation of the physical structure of the bulk sample. The global characterisation of the sample in terms of molecular dynamics is key to successful use of low-field NMR. Relaxation information should provide rapid, reliable quantitative information for improved process control. The relaxation behaviour can provide extremely useful information on various aspects of mobile phases, e.g. moisture determination. 

In order to monitor the real-time dynamics of gas molecules interacting with surface, time-resolved study is required. It is generally known that the time domains for the gas adsorption/desorption on surface are within pico-second regime while the molecular vibration on surface is within femto-second regime. To accommodate this time-requirement as well as chemical analysis on surface, a type of pump and probe experiment is required, which makes use of synchronization between a laser pulse and a synchrotron radiation pulse of AP-XPS endstation. For example, the carrier dynamics and reaction mechanism of photocatalysts under AP conditions can be an ideal system to look at with this time-resolved experimental set-up. At present, the synchronization technique has been well developed as shown in a block diagram (Fig. 9.24). This time-resolved set-up can be further refined and adapted into advanced system when the free electron X-ray source is available. 

A traditional working tool in structural chemistry has been symmetry analysis, including that of achirality which is a special case of symmetry. Symmetry point groups and space groups have been used as reference configurations which either exist or not in the structure under study. This traditional approach fails to capture the richness of shapes and structures, both static and dynamic, which is found in the molecular and supramolecular domains. Most of these are not symmetric. At most they are approximately symmetric, either permanently or temporarily if the time-resolution of observation is sufficiently narrow. 

This chapter presents an ab initio description of the nature and dynamics of photoexcited states in semiconductor QDs, in the energy and time domains. By combining the bulk and molecular viewpoints, the analysis elucidates the controversies and provides a unified atomistic picture of the excited state processes. These ab initio methods are used to study excited state composition, evolution and relaxation, as well as electron phonon dephasing, all with an eye towards the incorporation of QDs in solar cells. For further reading on the work featured in this chapter see publications by the Prezhdo group. ... 

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