Dynamics and Transport in Random Antiferromagnetic Spin Chains

We present the first results on the low-frequency dynamical and transport properties of random antiferromagnetic spin chains at low temperature ($T$). We obtain the momentum and frequency dependent dynamic structure factor in the Random Singlet (RS) phases of both spin-1/2 and spin-1 chains, as well as in the Random Dimer phase of spin-1/2 chains. We also show that the RS phases are unusual `spin-metals' with divergent low-frequency conductivity at T=0, and follow the spin conductivity through `metal-insulator' transitions tuned by the strength of dimerization or Ising anisotropy in the spin-1/2 case, and by the strength of disorder in the spin-1 case.Comment: 4 pages (two-column format). Presentation substantially revised to accomodate new result

A Left-handed β Helix Revealed by the Crystal Structure of a Carbonic Anhydrase from the Archaeon Methanosarcina thermophila

A carbonic anhydrase from the thermophilic archaeon Methanosarcina thermophila that exhibits no significant sequence similarity to known carbonic anhydrases has recently been characterized. Here we present the structure of this enzyme, which adopts a left-handed parallel β-helix fold. This fold is of particular interest since it contains only left-handed crossover connections between the parallel β-strands, which so far have been observed very infrequently. The active form of the enzyme is a trimer with three zinc-containing active sites, each located at the interface between two monomers. While the arrangement of active site groups differs between this enzyme and the carbonic anhydrases from higher vertebrates, there are structural similarities in the zinc coordination environment, suggestive of convergent evolution dictated by the chemical requirements for catalysis of the same reaction. Based on sequence similarities, the structure of this enzyme is the prototype of a new class of carbonic anhydrases with representatives in all three phylogenetic domains of life

Molybdenum-cofactor-containing enzymes: structure and mechanism

Molybdenum-containing enzymes catalyze basic metabolic reactions in the nitrogen, sulfur, and carbon cycles. With the exception of the nitrogenase cofactor, molybdenum is incorporated into proteins as the molybdenum cofactor that contains a mononuclear molybdenum atom coordinated to the sulfur atoms of a pterin derivative named molybdopterin. Certain microorganisms can also utilize tungsten in a similar fashion. Molybdenum-cofactor-containing enzymes catalyze the transfer of an oxygen atom, ultimately derived from or incorporated into water, to or from a substrate in a two-electron redox reaction. On the basis of sequence alignments and spectroscopic properties, four families of molybdenum-cofactor-containing enzymes have been identified. The available crystallographic structures for members of these families are discussed within the framework of the active site structure and catalytic mechanisms of molybdenum-cofactor-containing enzymes. Although the function of the molybdopterin ligand has not yet been conclusively established, interactions of this ligand with the coordinated metal are sensitive to the oxidation state, indicating that the molybdopterin may be directly involved in the enzymatic mechanism

Superconductor-to-Normal Phase Transition in a Vortex Glass Model: Numerical Evidence for a New Percolation Universality Class

The three-dimensional strongly screened vortex-glass model is studied numerically using methods from combinatorial optimization. We focus on the effect of disorder strength on the ground state and found the existence of a disorder-driven normal-to-superconducting phase transition. The transition turns out to be a geometrical phase transition with percolating vortex loops in the ground state configuration. We determine the critical exponents and provide evidence for a new universality class of correlated percolation.Comment: 11 pages LaTeX using IOPART.cls, 11 eps-figures include

A crystallographic view of the molybdenum cofactor

The molybdenum cofactor (Moco) has been found to be associated with a diverse set of redox enzymes and contains a mononuclear molybdenum or tungsten ion co-ordinated by the dithiolene sulfurs of one or two molybdopterin {a pterin [2-amino-4(1H)-pteridinone] derivative} ligands. The remaining co-ordination sites on the metal are occupied by non-protein oxygen or sulfur species and, occasionally, amino acid side chains. The molybdopterin ligand can exhibit oxidation-state-dependent changes in structure and metal co-ordination, and may also interact with other redox groups in the enzyme. These observations suggest that the molybdopterin may participate in the various electron-transfer reactions associated with the catalytic mechanism of Moco containing enzymes

Spin-filter effect of the europium chalcogenides: An exactly solved many-body model

A model Hamiltonian is introduced which considers the main features of the experimental spin filter situation as s-f interaction, planar geometry and the strong external electric field. The proposed many-body model can be solved analytically and exactly using Green functions. The spin polarization of the field-emitted electrons is expressed in terms of spin-flip probabilities, which on their part are put down to the exactly known dynamic quantities of the system. The calculated electron spin polarization shows remarkable dependencies on the electron velocity perpendicular to the emitting plane and the strength of s-f coupling. Experimentally observed polarization values of about 90% are well understood within the framework of the proposed model.Comment: accepted (Physical Review B); 10 pages, 11 figures; http://orion.physik.hu-berlin.de

Ground state properties of fluxlines in a disordered environment

A new numerical method to calculate exact ground states of multi-fluxline systems with quenched disorder is presented, which is based on the minimum cost flow algorithm from combinatorial optimization. We discuss several models that can be studied with this method including their specific implementations, physically relevant observables and results: 1) the N-line model with N fluxlines (or directed polymers) in a d-dimensional environment with point and/or columnar disorder and hard or soft core repulsion; 2) the vortex glass model for a disordered superconductor in the strong screening limit and 3) the Sine-Gordon model with random pase shifts in the strong coupling limit.Comment: 4 pages RevTeX, 3 eps-figures include

Dynamics and transport in random quantum systems governed by strong-randomness fixed points

We present results on the low-frequency dynamical and transport properties of random quantum systems whose low temperature ($T$), low-energy behavior is controlled by strong disorder fixed points. We obtain the momentum and frequency dependent dynamic structure factor in the Random Singlet (RS) phases of both spin-1/2 and spin-1 random antiferromagnetic chains, as well as in the Random Dimer (RD) and Ising Antiferromagnetic (IAF) phases of spin-1/2 random antiferromagnetic chains. We show that the RS phases are unusual `spin metals' with divergent low-frequency spin conductivity at T=0, and we also follow the conductivity through novel `metal-insulator' transitions tuned by the strength of dimerization or Ising anisotropy in the spin-1/2 case, and by the strength of disorder in the spin-1 case. We work out the average spin and energy autocorrelations in the one-dimensional random transverse field Ising model in the vicinity of its quantum critical point. All of the above calculations are valid in the frequency dominated regime \omega \agt T, and rely on previously available renormalization group schemes that describe these systems in terms of the properties of certain strong-disorder fixed point theories. In addition, we obtain some information about the behavior of the dynamic structure factor and dynamical conductivity in the opposite `hydrodynamic' regime $\omega < T$ for the special case of spin-1/2 chains close to the planar limit (the quantum x-y model) by analyzing the corresponding quantities in an equivalent model of spinless fermions with weak repulsive interactions and particle-hole symmetric disorder.Comment: Long version (with many additional results) of Phys. Rev. Lett. {\bf 84}, 3434 (2000) (available as cond-mat/9904290); two-column format, 33 pages and 8 figure

Single molecule analysis reveals monomeric XPA bends DNA and undergoes episodic linear diffusion during damage search

Nucleotide excision repair (NER) removes a wide range of DNA lesions, including UV-induced photoproducts and bulky base adducts. XPA is an essential protein in eukaryotic NER, although reports about its stoichiometry and role in damage recognition are controversial. Here, by PeakForce Tapping atomic force microscopy, we show that human XPA binds and bends DNA by similar to 60 degrees as a monomer. Furthermore, we observe XPA specificity for the helix-distorting base adduct N-(2'-deoxyguanosin-8-yl)-2-acetylaminofluorene over non-damaged dsDNA. Moreover, single molecule fluorescence microscopy reveals that DNA-bound XPA exhibits multiple modes of linear diffusion between paused phases. The presence of DNA damage increases the frequency of pausing. Truncated XPA, lacking the intrinsically disordered N- and C-termini, loses specificity for DNA lesions and shows less pausing on damaged DNA. Our data are consistent with a working model in which monomeric XPA bends DNA, displays episodic phases of linear diffusion along DNA, and pauses in response to DNA damage. It is not fully understood how XPA interacts with a DNA lesion during nucleotide excision repair. Here, the authors use single molecule analysis to study XPA-DNA interactions, including the DNA bend angle, protein stoichiometry, and diffusive properties during damage search