29,663 research outputs found
Structure-function relations in phosphorylcholine-binding mouse myeloma proteins
The binding site interactions between the phosphorylcholine (phosphocholine)-binding mouse myeloma proteins TEPC 15, W3207, McPC 603, MOPC 167, and MOPC 511 and the isotopically substituted hapten phosphoryl-[methyl-13C]choline have been investigated using 13C and 31P nuclear magnetic resonance (NMR) spectroscopy. Each protein exhibits a unique NMR pattern, but extensive similarities in chemical shift parameters upon binding of hapten to immunoglobulin suggest a significant degree of conservation of important hapten-binding site interactions. Moreover, independent binding studies, in conjunction with the NMR data, allow construction of a simple model of the binding sites of these antibodies, analyzed in terms of the relative strength of interaction between hapten and two main subsites. The NMR evidence supports the view that the heavy chains of these proteins dominate in interacting with bound phosphorylcholine; the various subspecificities of these proteins for phosphorylcholine analogues can be accounted for by amino acid changes in the hypervariable regions of the heavy chains
A projection method for statics and dynamics of lattice spin systems
A method based on Monte Carlo sampling of the probability flows projected
onto the subspace of one or more slow variables is proposed for investigation
of dynamic and static properties of lattice spin systems. We illustrate the
method by applying it, with projection onto the order-parameter subspace, to
the three-dimensional 3-state Potts model in equilibrium and to metastable
decay in a three-dimensional 3-state kinetic Potts model.Comment: 4 pages, 3 figures, RevTex, final version to appear in Phys. Rev.
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The effect of parallel static and microwave electric fields on excited hydrogen atoms
Motivated by recent experiments we analyse the classical dynamics of a
hydrogen atom in parallel static and microwave electric fields. Using an
appropriate representation and averaging approximations we show that resonant
ionisation is controlled by a separatrix, and provide necessary conditions for
a dynamical resonance to affect the ionisation probability.
The position of the dynamical resonance is computed using a high-order
perturbation series, and estimate its radius of convergence. We show that the
position of the dynamical resonance does not coincide precisely with the
ionisation maxima, and that the field switch-on time can dramatically affect
the ionisation signal which, for long switch times, reflects the shape of an
incipient homoclinic. Similarly, the resonance ionisation time can reflect the
time-scale of the separatrix motion, which is therefore longer than
conventional static field Stark ionisation. We explain why these effects should
be observed in the quantum dynamics.
PACs: 32.80.Rm, 33.40.+f, 34.10.+x, 05.45.Ac, 05.45.MtComment: 47 pages, 20 figure
Outer-Sphere Effects on Reduction Potentials of Copper Sites in Proteins: The Curious Case of High Potential Type 2 C112D/M121E Pseudomonas aeruginosa Azurin
Redox and spectroscopic (electronic absorption, multifrequency electron paramagnetic resonance (EPR), and X-ray absorption) properties together with X-ray crystal structures are reported for the type 2 Cu^(II) C112D/M121E variant of Pseudomonas aeruginosa azurin. The results suggest that Cu^(II) is constrained from interaction with the proximal glutamate; this structural frustration implies a “rack” mechanism for the 290 mV (vs NHE) reduction potential measured at neutral pH. At high pH (~9), hydrogen bonding in the outer coordination sphere is perturbed to allow axial glutamate ligation to Cu^(II), with a decrease in potential to 119 mV. These results highlight the role played by outer-sphere interactions, and the structural constraints they impose, in determining the redox behavior of transition metal protein cofactors
Magnetization switching in nanoscale ferromagnetic grains: simulations with heterogeneous nucleation
We present results obtained with various types of heterogeneous nucleation in
a kinetic Ising model of magnetization switching in single-domain ferromagnetic
nanoparticles. We investigate the effect of the presence of the system boundary
and make comparison with simulations on periodic lattices. We also study
systems with bulk disorder and compare how two different types of disorder
influence the switching behavior.Comment: 3 pages, 4 Postscript figure
Direct and indirect selection on flowering time, water-use efficiency (WUE, δ (13)C), and WUE plasticity to drought in Arabidopsis thaliana.
Flowering time and water-use efficiency (WUE) are two ecological traits that are important for plant drought response. To understand the evolutionary significance of natural genetic variation in flowering time, WUE, and WUE plasticity to drought in Arabidopsis thaliana, we addressed the following questions: (1) How are ecophysiological traits genetically correlated within and between different soil moisture environments? (2) Does terminal drought select for early flowering and drought escape? (3) Is WUE plasticity to drought adaptive and/or costly? We measured a suite of ecophysiological and reproductive traits on 234 spring flowering accessions of A. thaliana grown in well-watered and season-ending soil drying treatments, and quantified patterns of genetic variation, correlation, and selection within each treatment. WUE and flowering time were consistently positively genetically correlated. WUE was correlated with WUE plasticity, but the direction changed between treatments. Selection generally favored early flowering and low WUE, with drought favoring earlier flowering significantly more than well-watered conditions. Selection for lower WUE was marginally stronger under drought. There were no net fitness costs of WUE plasticity. WUE plasticity (per se) was globally neutral, but locally favored under drought. Strong genetic correlation between WUE and flowering time may facilitate the evolution of drought escape, or constrain independent evolution of these traits. Terminal drought favored drought escape in these spring flowering accessions of A. thaliana. WUE plasticity may be favored over completely fixed development in environments with periodic drought
Extreme Long-time Dynamic Monte Carlo Simulations
We study the extreme long-time behavior of the metastable phase of the
three-dimensional Ising model with Glauber dynamics in an applied magnetic
field and at a temperature below the critical temperature. For these
simulations we use the advanced simulation method of projective dynamics. The
algorithm is described in detail, together with its application to the escape
from the metastable state. Our results for the field dependence of the
metastable lifetime are in good agreement with theoretical expectations and
span more than fifty decades in time.Comment: 13 pages with embedded eps figures. Int. J. Mod. Phys. C, in pres
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