On Provable Algorithms for Determination of Continuous Protein Interdomain Motions from Residual Dipolar Couplings

Dynamics of biomolecules over various spatial and time scales are essential for biological functions such as molecular recognition, catalysis and signaling. However, reconstruction of biomolecular dynamics from experimental observables requires the determination of a conformational probability distribution. Unfortunately, these distributions cannot be fully constrained by the limited information from experiments, making the problem an ill-posed one in the terminology of Hadamard. The ill-posed nature of the problem comes from the fact that it has no unique solution. Multiple or even an infinite number of solutions may exist. To avoid the ill-posed nature, the problem needs to be regularized by making assumptions, which inevitably introduce biases into the result.

Here, I present two continuous probability density function approaches to solve an important inverse problem called the RDC trigonometric moment problem. By focusing on interdomain orientations we reduced the problem to determination of a distribution on the 3D rotational space from residual dipolar couplings (RDCs). We derived an analytical equation that relates alignment tensors of adjacent domains, which serves as the foundation of the two methods. In the first approach, the ill-posed nature of the problem was avoided by introducing a continuous distribution model, which enjoys a smoothness assumption. To find the optimal solution for the distribution, we also designed an efficient branch-and-bound algorithm that exploits the mathematical structure of the analytical solutions. The algorithm is guaranteed to find the distribution that best satisfies the analytical relationship. We observed good performance of the method when tested under various levels of experimental noise and when applied to two protein systems. The second approach avoids the use of any model by employing maximum entropy principles. This 'model-free' approach delivers the least biased result which presents our state of knowledge. In this approach, the solution is an exponential function of Lagrange multipliers. To determine the multipliers, a convex objective function is constructed. Consequently, the maximum entropy solution can be found easily by gradient descent methods. Both algorithms can be applied to biomolecular RDC data in general, including data from RNA and DNA molecules.

Weak coupling of acoustic-like phonons and magnon dynamics in incommensurate spin ladder compound Sr14Cu24O41

Intriguing lattice dynamics has been predicted for aperiodic crystals that contain incommensurate substructures. Here we report inelastic neutron scattering measurements of phonon and magnon dispersions in Sr14Cu24O41, which contains incommensurate one-dimensional (1D) chain and two-dimensional (2D) ladder substructures. Two distinct acoustic phonon-like modes, corresponding to the sliding motion of one sublattice against the other, are observed for atomic motions polarized along the incommensurate axis. In the long wavelength limit, it is found that the sliding mode shows a remarkably small energy gap of 1.7-1.9 meV, indicating very weak interactions between the two incommensurate sublattices. The measurements also reveal a gapped and steep linear magnon dispersion of the ladder sublattice. The high group velocity of this magnon branch and weak coupling with acoustic phonons can explain the large magnon thermal conductivity in Sr14Cu24O41 crystals. In addition, the magnon specific heat is determined from the measured total specific heat and phonon density of states, and exhibits a Schottky anomaly due to gapped magnon modes of the spin chains. These findings offer new insights into the phonon and magnon dynamics and thermal transport properties of incommensurate magnetic crystals that contain low-dimensional substructures.

Waveguide QED: Many-body bound-state effects in coherent and Fock-state scattering from a two-level system

Strong coupling between a two-level system (TLS) and bosonic modes produces dramatic quantum optics effects. We consider a one-dimensional continuum of bosons coupled to a single localized TLS, a system which may be realized in a variety of plasmonic, photonic, or electronic contexts. We present the exact many-body scattering eigenstate obtained by imposing open boundary conditions. Multiphoton bound states appear in the scattering of two or more photons due to the coupling between the photons and the TLS. Such bound states are shown to have a large effect on scattering of both Fock- and coherent-state wave packets, especially in the intermediate coupling-strength regime. We compare the statistics of the transmitted light with a coherent state having the same mean photon number: as the interaction strength increases, the one-photon probability is suppressed rapidly, and the two- and three-photon probabilities are greatly enhanced due to the many-body bound states. This results in non-Poissonian light. © 2010 The American Physical Society.