Direct observation of hierarchical protein dynamics

One of the fundamental challenges of physical biology is to understand the relationship between protein dynamics and function. At physiological temperatures, functional motions arise from the complex interplay of thermal motions of proteins and their environments. Here, we determine the hierarchy in the protein conformational energy landscape that underlies these motions, based on a series of temperature-dependent magic-angle spinning multinuclear nuclear-magnetic-resonance relaxation measurements in a hydrated nanocrystalline protein. The results support strong coupling between protein and solvent dynamics above 160 kelvin, with fast solvent motions, slow protein side-chain motions, and fast protein backbone motions being activated consecutively. Low activation energy, small-amplitude local motions dominate at low temperatures, with larger-amplitude, anisotropic, and functionally relevant motions involving entire peptide units becoming dominant at temperatures above 220 kelvin

Fundamental Oscillation Periods of the Interlayer Exchange Coupling beyond the RKKY Approximation

A general method for obtaining the oscillation periods of the interlayer exchange coupling is presented. It is shown that it is possible for the coupling to oscillate with additional periods beyond the ones predicted by the RKKY theory. The relation between the oscillation periods and the spacer Fermi surface is clarified, showing that non-RKKY periods do not bear a direct correspondence with the Fermi surface. The interesting case of a FCC(110) structure is investigated, unmistakably proving the existence and relevance of non-RKKY oscillations. The general conditions for the occurrence of non-RKKY oscillations are also presented.Comment: 34 pages, 10 figures ; to appear in J. Phys.: Condens. Mat

ac Losses in a Finite Z Stack Using an Anisotropic Homogeneous-Medium Approximation

A finite stack of thin superconducting tapes, all carrying a fixed current I, can be approximated by an anisotropic superconducting bar with critical current density Jc=Ic/2aD, where Ic is the critical current of each tape, 2a is the tape width, and D is the tape-to-tape periodicity. The current density J must obey the constraint \int J dx = I/D, where the tapes lie parallel to the x axis and are stacked along the z axis. We suppose that Jc is independent of field (Bean approximation) and look for a solution to the critical state for arbitrary height 2b of the stack. For c<|x|<a we have J=Jc, and for |x|<c the critical state requires that Bz=0. We show that this implies \partial J/\partial x=0 in the central region. Setting c as a constant (independent of z) results in field profiles remarkably close to the desired one (Bz=0 for |x|<c) as long as the aspect ratio b/a is not too small. We evaluate various criteria for choosing c, and we show that the calculated hysteretic losses depend only weakly on how c is chosen. We argue that for small D/a the anisotropic homogeneous-medium approximation gives a reasonably accurate estimate of the ac losses in a finite Z stack. The results for a Z stack can be used to calculate the transport losses in a pancake coil wound with superconducting tape.Comment: 21 pages, 17 figures, accepted by Supercond. Sci. Techno

New possibilities for research on reef fish across the continental shelf of South Africa

[From introduction] Subtidal research presents numerous challenges that restrict the ability to answer fundamental ecological questions related to reef systems. These challenges are closely associated with traditional monitoring methods and include depth restrictions (e.g. safe diving depths for underwater visual census), habitat destruction (e.g. trawling), mortality of target species (e.g. controlled angling and fish traps), and high operating costs (e.g. remotely operated vehicles and large research vessels. Whereas many of these challenges do not apply or are avoidable in the shallow subtidal environment, the difficulties grow as one attempts to sample deeper benthic habitats. This situation has resulted in a paucity of knowledge on the structure and ecology of deep water reef habitats around the coast of South Africa and in most marine areas around the world. Furthermore, the inability to effectively survey deep water benthic environments has limited the capacity of researchers to investigate connectivity between shallow and deep water habitats in a standardised and comparable fashio

Application of realistic effective interactions to the structure of the Zr isotopes

We calculate the low-lying spectra of the zirconium isotopes Z=40 with neutron numbers from N=52 to N=60 using the 1p1/20g9/2 proton and 2s1d0g7/20h11/2 neutron sub-shells to define the model space. Effective proton-proton, neutron--neutron and proton-neutron interactions have been derived using 88Sr as closed core and employing perturbative many-body techniques. The starting point is the nucleon-nucleon potential derived from modern meson exchange models. The comprehensive shell-model calculation performed in this work provides a qualitative reproduction of essential properties such as the sub-shell closures in 96Zr and 98Zr.Comment: To appear in Phys Rev C, june 2000, 8 figs, Revtex latex styl

New possibilities for research on reef fish across the continental shelf of South Africa

[From introduction] Subtidal research presents numerous challenges that restrict the ability to answer fundamental ecological questions related to reef systems. These challenges are closely associated with traditional monitoring methods and include depth restrictions (e.g. safe diving depths for underwater visual census), habitat destruction (e.g. trawling), mortality of target species (e.g. controlled angling and fish traps), and high operating costs (e.g. remotely operated vehicles and large research vessels. Whereas many of these challenges do not apply or are avoidable in the shallow subtidal environment, the difficulties grow as one attempts to sample deeper benthic habitats. This situation has resulted in a paucity of knowledge on the structure and ecology of deep water reef habitats around the coast of South Africa and in most marine areas around the world. Furthermore, the inability to effectively survey deep water benthic environments has limited the capacity of researchers to investigate connectivity between shallow and deep water habitats in a standardised and comparable fashion

O(12) limit and complete classification of symmetry schemes in proton-neutron interacting boson model

It is shown that the proton-neutron interacting boson model (pnIBM) admits new symmetry limits with O(12) algebra which break F-spin but preserves the quantum number M_F. The generators of O(12) are derived and the quantum number `v' of O(12) for a given boson number N is determined by identifying the corresponding quasi-spin algebra. The O(12) algebra generates two symmetry schemes and for both of them, complete classification of the basis states and typical spectra are given. With the O(12) algebra identified, complete classification of pnIBM symmetry limits with good M_F is established.Comment: 22 pages, 1 figur

Fermi Surface Properties of Low Concentration Cex_{x}La1−x_{1-x}B6_{6}: dHvA

The de Haas-van Alphen effect is used to study angular dependent extremal areas of the Fermi Surfaces (FS) and effective masses of Ce$_{x}$La$_{1-x}$B$_{6}$ alloys for $x$ between 0 and 0.05. The FS of these alloys was previously observed to be spin polarized at low Ce concentration ($x$ = 0.05). This work gives the details of the initial development of the topology and spin polarization of the FS from that of unpolarized metallic LaB$_{6}$ to that of spin polarized heavy Fermion CeB$_{6}$ .Comment: 7 pages, 9 figures, submitted to PR

Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages

There is increasing evidence that strain variation in Mycobacterium tuberculosis complex (MTBC) might influence the outcome of tuberculosis infection and disease. To assess genotype-phenotype associations, phylogenetically robust molecular markers and appropriate genotyping tools are required. Most current genotyping methods for MTBC are based on mobile or repetitive DNA elements. Because these elements are prone to convergent evolution, the corresponding genotyping techniques are suboptimal for phylogenetic studies and strain classification. By contrast, single nucleotide polymorphisms (SNP) are ideal markers for classifying MTBC into phylogenetic lineages, as they exhibit very low degrees of homoplasy. In this study, we developed two complementary SNP-based genotyping methods to classify strains into the six main human-associated lineages of MTBC, the 'Beijing' sublineage, and the clade comprising Mycobacterium bovis and Mycobacterium caprae. Phylogenetically informative SNPs were obtained from 22 MTBC whole-genome sequences. The first assay, referred to as MOL-PCR, is a ligation-dependent PCR with signal detection by fluorescent microspheres and a Luminex flow cytometer, which simultaneously interrogates eight SNPs. The second assay is based on six individual TaqMan real-time PCR assays for singleplex SNP-typing. We compared MOL-PCR and TaqMan results in two panels of clinical MTBC isolates. Both methods agreed fully when assigning 36 well-characterized strains into the main phylogenetic lineages. The sensitivity in allele-calling was 98.6% and 98.8% for MOL-PCR and TaqMan, respectively. Typing of an additional panel of 78 unknown clinical isolates revealed 99.2% and 100% sensitivity in allele-calling, respectively, and 100% agreement in lineage assignment between both methods. While MOL-PCR and TaqMan are both highly sensitive and specific, MOL-PCR is ideal for classification of isolates with no previous information, whereas TaqMan is faster for confirmation. Furthermore, both methods are rapid, flexible and comparably inexpensive