Linear response theory, vibrational modes

At T 0 the sharp lines corresponding to the harmonic modes are broadened by anharmonic effects until, at high temperature, the simple relationship between vibrational density of states and dynamical matrix is lost. In this regime, and especially for large aggregates, MD is the most suitable tool to compute the vibrational spectrum. Standard linear response theory within classical statistical mechanics shows that the spectrum f(co) is given by the Fourier transform of the velocity-velocity autocorrelation function... 

We turn first to computation of thermal transport coefficients, which provides a description of heat flow in the linear response regime. We compute the coefficient of thermal conductivity, from which we obtain the thermal diffusivity that appears in Fourier s heat law. Starting with the kinetic theory of gases, the main focus of the computation of the thermal conductivity is the frequency-dependent energy diffusion coefficient, or mode diffusivity. In previous woik, we computed this quantity by propagating wave packets filtered to contain only vibrational modes around a particular mode frequency [26]. This approach has the advantage that one can place the wave packets in a particular region of interest, for instance the core of the protein to avoid surface effects. Another approach, which we apply in this chapter, is via the heat current operator [27], and this method is detailed in Section 11.2. 

An important achievement of the early theories was the derivation of the exact quantum mechanical expression for the ET rate in the Fermi Golden Rule limit in the linear response regime by Kubo and Toyozawa [4b], Levich and co-workers [20a] and by Ovchinnikov and Ovchinnikova [21], in terms of the dielectric spectral density of the solvent and intramolecular vibrational modes of donor and acceptor complexes. The solvent model was improved to take into account time and space correlation of the polarization fluctuations [20,21]. The importance of high-frequency intramolecular vibrations was fully recognized by Dogonadze and Kuznetsov [22], Efrima and Bixon [23], and by Jortner and co-workers [24,25] and Ulstrup [26]. It was shown that the main role of quantum modes is to effectively reduce the activation energy and thus to increase the reaction rate in the inverted... 

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