Folding of Cu, Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis

Cu,Zn superoxide dismutase (SOD1) has been implicated in the familial form of the neurodegenerative disease Amyotrophic Lateral Sclerosis (ALS). It has been suggested that mutant mediated SOD1 misfolding/aggregation is an integral part of the pathology of ALS. We study the folding thermodynamics and kinetics of SOD1 using a hybrid molecular dynamics approach. We reproduce the experimentally observed SOD1 folding thermodynamics and find that the residues which contribute the most to SOD1 thermal stability are also crucial for apparent two-state folding kinetics. Surprisingly, we find that these residues are located on the surface of the protein and not in the hydrophobic core. Mutations in some of the identified residues are found in patients with the disease. We argue that the identified residues may play an important role in aggregation. To further characterize the folding of SOD1, we study the role of cysteine residues in folding and find that non-native disulfide bond formation may significantly alter SOD1 folding dynamics and aggregation propensity.Comment: 16 pages, 5 figure

Optical Conductivity in a Simple Model of Pseudogap State in Two-Dimensional System

We present calculation of optical conductivity in a simple model of electronic spectrum of two-dimensional system with "hot patches" on the Fermi surface, leading to non Fermi-liquid renormalization of the spectral density (pseudogap) on these patches. It is shown that this model qualitatively reproduces basic anomalies of optical experiments in the pseudogap state of copper oxides.Comment: 12 pages, 6 figures, RevTeX 3.0, Postscript figures attache

Metastability of Asymptotically Well-Behaved Potential Games

One of the main criticisms to game theory concerns the assumption of full rationality. Logit dynamics is a decentralized algorithm in which a level of irrationality (a.k.a. "noise") is introduced in players' behavior. In this context, the solution concept of interest becomes the logit equilibrium, as opposed to Nash equilibria. Logit equilibria are distributions over strategy profiles that possess several nice properties, including existence and uniqueness. However, there are games in which their computation may take time exponential in the number of players. We therefore look at an approximate version of logit equilibria, called metastable distributions, introduced by Auletta et al. [SODA 2012]. These are distributions that remain stable (i.e., players do not go too far from it) for a super-polynomial number of steps (rather than forever, as for logit equilibria). The hope is that these distributions exist and can be reached quickly by logit dynamics. We identify a class of potential games, called asymptotically well-behaved, for which the behavior of the logit dynamics is not chaotic as the number of players increases so to guarantee meaningful asymptotic results. We prove that any such game admits distributions which are metastable no matter the level of noise present in the system, and the starting profile of the dynamics. These distributions can be quickly reached if the rationality level is not too big when compared to the inverse of the maximum difference in potential. Our proofs build on results which may be of independent interest, including some spectral characterizations of the transition matrix defined by logit dynamics for generic games and the relationship of several convergence measures for Markov chains

Three realizations of quantum affine algebra Uq(A2(2))U_q(A_2^{(2)})

In this article we establish explicit isomorphisms between three realizations of quantum twisted affine algebra $U_q(A_2^{(2)})$: the Drinfeld ("current") realization, the Chevalley realization and the so-called $RLL$ realization, investigated by Faddeev, Reshetikhin and Takhtajan.Comment: 15 page

Ginzburg-Landau Expansion in a Toy Model of Superconductor with Pseudogap

We propose a toy model of electronic spectrum of two-dimensional system with ``hot-patches'' on the Fermi surface, which leads to essential renormalization of spectral density (pseudogap). Within this model we derive Ginzburg-Landau expansion for both s-wave and d-wave Cooper pairing and analyze the influence of pseudogap formation on the basic properties of superconductors.Comment: 14 pages, 14 figures, RevTeX 3.0, Postscript figures attached, some changes in the explanation of the model, published in JETP 115, No.2, (1999

Models of the Pseudogap State of Two-Dimensional Systems

We analyze a number of ``nearly exactly'' solvable models of electronic spectrum of two-dimensional systems with well-developed fluctuations of short range order of ``dielectric'' (e.g. antiferromagnetic) or ``superconducting'' type, which lead to the formation of anisotropic pseudogap state on certain parts of the Fermi surface. We formulate a recurrence procedure to calculate one-electron Green's function which takes into account all Feynman diagrams in perturbation series and is based upon the approximate Ansatz for higher-order terms in this series. Detailed results for spectral densities and density of states are presented. We also discuss some important points concerning the justification of our Ansatz for higher-order contributions.Comment: 22 pages, 15 figures, RevTeX 3.0, Postscript figures attache

Modeling two-dimensional structure at the core-mantle boundary

Recent studies of SKS waveform modeling emphasize the strong variation of seismic properties at the core-mantle boundary (CMB) and the need for two-dimensional and three-dimensional waveform modeling capabilities. In particular, the bifurcation of SKS into SP _dKS and SKP _dS near 110° shows strong regional variations. The first of these phases has a P wave diffraction along the bottom of the mantle near the source, while the latter phase occurs at the receiver end. Generalized ray theory proves effective in generating theoretical seismograms in this type of problem because each of these diffractions is associated with a particular transmission coefficient: T_(sp) which transmits shear waves into primary waves when crossing the CMB and T_(sp) which transmits the primary waves back into shear waves at the receiver end. Each region can then be isolated and have its separate fine structure, sharp or gradational. Two classes of boundaries are explored: the CMB as a simple, sharp interface and the CMB with a very low velocity transition layer (10% slower than reference models). The two diffractions produced by these structures have diagnostic arrival times and wave shapes and when combined with the geometric SKS produce distinct waveform characteristics not easily generated by other means. Since the ray paths associated with these three phases are virtually identical in the mantle and only differ along a short sample of CMB and in the one-dimensional fluid core, we can isolate the small localized CMB region sampled. Thus the waveform character of the extended SKS in the range of 105° to 120° becomes an excellent CMB probe which we demonstrate on a small sample of observations from the Fiji-Tonga region as recorded in North America

Manifestation of impurity induced s_{+-} -> s_{++} transition: multiband model for dynamical response functions

We investigate effects of disorder on the density of states, the single particle response function and optical conductivity in multiband superconductors with s_{+-} symmetry of the order parameter, where s_{+-} -> s_{++} transition may take place. In the vicinity of the transition the superconductive gapless regime is realized. It manifests itself in anomalies in the above mentioned properties. As a result, intrinsically phase-insensitive experimental methods like ARPES, tunneling and terahertz spectroscopy may be used for revealing of information about the underlying order parameter symmetry.Comment: 14 pages, 6 figure