On the Electric Charge of Monopoles at Finite Temperature

We calculate the electric charge at finite temperature $T$ for non-Abelian monopoles in spontaneously broken gauge theories with a CP violating $\theta$-term. A careful treatment of dyon's gauge degrees of freedom shows that Witten formula for the dyon charge at $T=0$, $Q = e(n - \theta/2\pi)$, remains valid at $T \ne 0$.Comment: 13 pages, latex file, no figure

Parity (and time-reversal) anomaly in a semiconductor

The physics of a parity anomaly, potentially observable in a narrow-gap semiconductor, is revisited. Fradkin, Dagotto, and Boyanovsky have suggested that a Hall current of anomalous parity can be induced by a Peierls distortion on a domain wall. I argue that a perturbation inducing the parity anomaly must break the time reversal symmetry, which rules out the Peierls distortion as a potential cause. I list all possible perturbations that can generate the anomaly.Comment: 11 pages, 1 figure. Sign errors fixe

Effective action and density functional theory

The effective action for the charge density and the photon field is proposed as a generalization of the density functional. A simple definition is given for the density functional, as the functional Legendre transform of the generator functional of connected Green functions for the density and the photon field, offering systematic approximation schemes. The leading order of the perturbation expansion reproduces the Hartree-Fock equation. A renormalization group motivated method is introduced to turn on the Coulomb interaction gradually and to find corrections to the Hartree-Fock and the Kohn-Sham schemes.Comment: New references and a numerical algorithm added, to appear in Phys. Rev. B. 30 pages, no figure

Effective field theory

I give a brief review of effective field theory, disscussing the contribution of Feza G\"ursey in particular and focusing on the literature I am most familiar with.Comment: 17 pages, no figs, macros appended, plain te

Molecular adaptation to high pressure in cytochrome P450 1A and aryl hydrocarbon receptor systems of the deep-sea fish Coryphaenoides armatus.

Limited knowledge of the molecular evolution of deep-sea fish proteomes so far suggests that a few widespread residue substitutions in cytosolic proteins binding hydrophilic ligands contribute to resistance to the effects of high hydrostatic pressure (HP). Structure-function studies with additional protein systems, including membrane bound proteins, are essential to provide a more general picture of adaptation in these extremophiles. We explored molecular features of HP adaptation in proteins binding hydrophobic ligands, either in lipid bilayers (cytochrome P450 1A - CYP1A) or in the cytosol (the aryl hydrocarbon receptor - AHR), and their partners P450 oxidoreductase (POR) and AHR nuclear translocator (ARNT), respectively. Cloning studies identified the full-length coding sequence of AHR, CYP1A and POR, and a partial sequence of ARNT from Coryphaenoides armatus, an abyssal gadiform fish thriving down to 5000m depth. Inferred protein sequences were aligned with many non-deep-sea homologs to identify unique amino acid substitutions of possible relevance in HP adaptation. Positionally unique substitutions of various physicochemical properties were found in all four proteins, usually at sites of strong-to-absolute residue conservation. Some were in domains deemed important for protein-protein interaction or ligand binding. In addition, some involved removal or addition of beta-branched residues; local modifications of beta-branched residue patterns could be important to HP adaptation. In silico predictions further suggested that some unique substitutions might substantially modulate the flexibility of the polypeptide segment in which they are found. Repetitive motifs unique to the abyssal fish AHR were predicted to be rich in glycosylation sites, suggesting that post-translational changes could be involved in adaptation as well. Recombinant CYP1A and AHR showed functional properties (spectral characteristics, catalytic activity and ligand binding) that demonstrate proper folding at 1atm, indicating that they could be used as deep-sea fish protein models to further evaluate protein function under pressure

Molecular adaptation to high pressure in cytochrome P450 1A and aryl hydrocarbon receptor systems of the deep-sea fish <i>Coryphaenoides armatus</i>

Limited knowledge of the molecular evolution of deep-sea fish proteomes so far suggests that a few widespread residue substitutions in cytosolic proteins binding hydrophilic ligands contribute to resistance to the effects of high hydrostatic pressure (HP). Structure-function studies with additional protein systems, including membrane bound proteins, are essential to provide a more general picture of adaptation in these extremophiles. We explored molecular features of HP adaptation in proteins binding hydrophobic ligands, either in lipid bilayers (cytochrome P450 1A - CYP1A) or in the cytosol (the aryl hydrocarbon receptor - AHR), and their partners P450 oxidoreductase (POR) and AHR nuclear translocator (ARNT), respectively. Cloning studies identified the full-length coding sequence of AHR, CYP1A and POR, and a partial sequence of ARNT from Coryphaenoides armatus, an abyssal gadiform fish thriving down to 5000 m depth. Inferred protein sequences were aligned with many non-deep-sea homologs to identify unique amino acid substitutions of possible relevance in HP adaptation. Positionally unique substitutions of various physicochemical properties were found in all four proteins, usually at sites of strong-to-absolute residue conservation. Some were in domains deemed important for protein-protein interaction or ligand binding. In addition, some involved removal or addition of beta-branched residues; local modifications of beta-branched residue patterns could be important to HP adaptation. In silico predictions further suggested that some unique substitutions might substantially modulate the flexibility of the polypeptide segment in which they are found. Repetitive motifs unique to the abyssal fish AHR were predicted to be rich in glycosylation sites, suggesting that post-translational changes could be involved in adaptation as well. Recombinant CYP1A and AHR showed functional properties (spectral characteristics, catalytic activity and ligand binding) that demonstrate proper folding at 1 atm, indicating that they could be used as deep-sea fish protein models to further evaluate protein function under pressure. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone"