Frequency-dependent energy diffusion, heat

We shall calculate here the coefficient of thermal conductivity and thermal diffusivity for myoglobin. We then need to calculate for each mode of myoglobin the heat capacity with Eq. (15) and to estimate the frequency-dependent energy diffusion coefficient, D(go). We are assuming that the heat capacity, calculated per unit volume of protein, is a function only of its vibrational energy. To estimate the volume of myoglobin, we assume for simplicity that the protein is a sphere with radius 17 A [111]. 

In the second part of the chapter, we have examined the spread of vibrational energy through coordinate space in systems that are large on the molecular scale—in particular, clusters of hundreds of water molecules and proteins—and computed thermal transport coefficients for these systems. The coefficient of thermal conductivity is given by the product of the heat capacity per unit volume and the energy diffusion coefficient summed over all vibrational modes. For the water clusters, the frequency-dependent energy diffusion coefficient was... 

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. 

Extended nonequilibrium thermodynamics is not based on the local equilibrium hypothesis, and uses the conserved variables and nonconserved dissipative fluxes as the independent variables to establish evolution equations for the dissipative fluxes satisfying the second law of thermodynamics. For conservation laws in hydrodynamic systems, the independent variables are the mass density, p, velocity, v, and specific internal energy, u, while the nonconserved variables are the heat flux, shear and bulk viscous pressure, diffusion flux, and electrical flux. For the generalized entropy with the properties of additivity and convex function considered, extended nonequilibrium thermodynamics formulations provide a more complete formulation of transport and rate processes beyond local equilibrium. The formulations can relate microscopic phenomena to a macroscopic thermodynamic interpretation by deriving the generalized transport laws expressed in terms of the generalized frequency and wave-vector-dependent transport coefficients. 

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