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Typical vibration modes of aircraft braking systems are discussed in this paper. Special attention is given to squeal vibrations of carbon brakes. From flight tests, a wide range of response amplitudes are analyzed to determine the nature of the motion. Fourier analysis indicates the presence of a high amplitude limit cycle which seems to be initiated by a transient chaotic region. A singular system approach based on a time delay embedding confirms this finding. Time delay analysis makes it possible to contruct model equations via which intrinsic dynamics of the system can be recovered, and opens up the possibility of preventing large amplitude vibration by controlling the chaotic motion.

The coupling between Librational motions and rotational isomeric jumps in polymers is investigated. Librations originate from bond stretching, bond angle distortion, and small-amplitude fluctuations in the bond dihedral angles. Molecular dynamics trajectories for a polymer chain of 100 bonds in vacuo are used for assessing the contribution of librations to the dynamic behavior of chains. Each trajectory is resolved into two sets of components, low and high frequency, representing bond rotameric transitions and librations, respectively. Librational motions are observed to be strongly correlated with the rotational jumps of bonds between isomeric states. In fact, the passage from an isomeric state to another is accompanied by an enhancement in librational motions. Examination of the contribution of Librations to the local relaxation behavior of polymers indicates that librations affect the mechanism of motion via two opposing effects. On the one hand, they provide an additional degree of freedom which causes a faster relaxation of the conformational correlation functions associated with the bond dihedral angles. On the other hand, the orientational correlation functions associated with the spatial reorientation of backbone bonds exhibit a slower time decay due to the compensating effect of librational motions. In fact, librational motions are not random but highly directed such that they collectively preserve local chain direction and help in accommodating the local reorientations induced by isomeric jumps, which would otherwise result in larger displacements of chain segments. Finally, it is shown that replacing the librations of a trajectory with random, uncorrelated fluctuations leads to an overestimation of the relaxation rate of configurational correlations.

A single-parameter harmonic Hamiltonian based on local packing density and contact topology is proposed for studying residue fluctuations in native proteins. The internal energy obeys an equipartition law, and free energy changes result from entropy fluctuations only. Frequency--wave-number maps show communication between residues involved in slow and fast modes. Fast modes are strongly localized, resulting from the geometric irregularity of the structure. Comparison with experiments shows that slow and fast modes are associated, respectively, with function and stability. Specifically, domain motions and folding cores of HIV-1 protease are accurately identified.

Human transferrin (hTF) binds and delivers Fe+3 to cells; lowered pH within the endosome (5.6) is implicated in the controlled release of bound ions [1]. Although the kinetics of the process is well studied, detailed molecular mechanisms at work are unknown. Bacterial transferrin, also known as ferric binding protein(FBP), is involved in scavenging iron from hTf [2]. These host/pathogen iron uptake proteins are thought to be distantly related through divergent evolution from an anion binding function; FBP displays similarity to one of the iron binding lobes of hTf in structural fold and highly conserved set of iron-coordinating residues.Perturbation response scanning (PRS) takes advantage of the differences between ligand-bound/unbound conformations to decipher residues having a direct effect on binding mechanisms [3]. PRS on apo and holo forms of FBP implicates D52, a charged residue located ca. 30 A from the bound ion, as playing a crucial role in ion release. Using pKa calculations [4] we find D52 is the most sensitive to subtle pH variations in the physiological range. The effect of protonation and D52A mutation in both the apo and holo forms was investigated via a series of molecular dynamics simulations. Only in the protonated and D52A holo FBP is an hinge motion triggering opening of the iron binding site observed. Our results lend clues as to how a single residue may be utilized for pH regulation of protein binding modes in iron transport proteins such as FBP and hTf.1.Steere et al., Biochim. Biophys. Acta, 1820, 326 (2012)2.Noinaj et al., Nature, 483, 53 (2012)3.Atilgan and Atilgan, PLoS Comput Biol 5, e1000544 (2009)4.Kantardjiev and Atanasov, Nucl. Acids Res., 37, W422 (2009)5.Parker-Siburt et al., Biochim. Biophys. Acta, 1820, 326 (2012)