D. Van Neck

Starting from integrable su(2) (quasi-)spin Richardson–Gaudin (RG) XXZ models we derive several properties of integrable spin models coupled to a bosonic mode. We focus on the Dicke–Jaynes–Cummings–Gaudin models and the two-channel (p + ip)-wave pairing Hamiltonian. The pseudo-deformation of the underlying su(2) algebra is here introduced as a way to obtain these models in the contraction limit of different RG models. This allows for the construction of the full set of conserved charges, the Bethe ansatz state, and the resulting RG equations. For these models an alternative and simpler set of quadratic equations can be found in terms of the eigenvalues of the conserved charges. Furthermore, the recently proposed eigenvalue-based determinant expressions for the overlaps and form factors of local operators are extended to these models, linking the results previously presented for the Dicke–Jaynes–Cummings–Gaudin models with the general results for RG XXZ models.

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Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3N(a) x 3N(a) matrix with N-a the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each.

Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible - but not necessarily optimized - geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian.

In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.