A Hyperstable Miniprotein: Additive Effects of D- and L-Ala Substitutions

The effects of alanine substitutions in each helical segment of the structure, and Gly to D-Ala mutations at sites where glycines have positive phi angles in the Trp-cage miniprotein are reported. The effects of the stabilizing mutation were additive, yielding a 20-residue construct (Tm = 83^o^C). Gly to L-Ala substitutions were uniformly destabilizing ([DELTA][DELTA]G~F~ > 11 kJ/mol): the preference for a D-Ala can be as large as 16 kJ/mol. Glycine to D-Ala mutations are validated as a strategy for the design of hyperstable miniprotein scaffolds suitable for stereospecific pharmacophore display

Infrared properties of SiC particles

We present basic laboratory infrared data on a large number of SiC particulate samples, which should be of great value for the interpretation of the 11.3 micron feature observed in the spectra of carbon-rich stars. The laboratory spectra show a wide variety of the SiC phonon features in the 10-13 micron wavelength range, both in peak wavelength and band shape. The main parameters determining the band profile are morphological factors as grain size and shape and, in many cases, impurities in the material. We discovered the interesting fact that free charge carriers, generated e.g. by nitrogen doping, are a very common characteristics of many SiC particle samples. These free charge carriers produce very strong plasmon absorption in the near and middle infrared, which may also heavily influence the 10-13 micron feature profile via plasmon-phonon coupling. We also found that there is no systematic dependence of the band profile on the crystal type (alpha- vs. beta-SiC). This is proven both experimentally and by theoretical calculations based on a study of the SiC phonon frequencies. Further, we give optical constants of amorphous SiC. We discuss the implications of the new laboratory results for the interpretation of the spectra of carbon stars.Comment: 17 pages, 12 figures. To appear in A&

Role of multiorbital effects in the magnetic phase diagram of iron-pnictides

We elucidate the pivotal role of the bandstructure's orbital content in deciding the type of commensurate magnetic order stabilized within the itinerant scenario of iron-pnictides. Recent experimental findings in the tetragonal magnetic phase attest to the existence of the so-called charge and spin ordered density wave over the spin-vortex crystal phase, the latter of which tends to be favored in simplified band models of itinerant magnetism. Here we show that employing a multiorbital itinerant Landau approach based on realistic bandstructures can account for the experimentally observed magnetic phase, and thus shed light on the importance of the orbital content in deciding the magnetic order. In addition, we remark that the presence of a hole pocket centered at the Brillouin zone's ${\rm M}$-point favors a magnetic stripe rather than a tetragonal magnetic phase. For inferring the symmetry properties of the different magnetic phases, we formulate our theory in terms of magnetic order parameters transforming according to irreducible representations of the ensuing D$_{\rm 4h}$ point group. The latter method not only provides transparent understanding of the symmetry breaking schemes but also reveals that the leading instabilities always belong to the $\{A_{1g},B_{1g}\}$ subset of irreducible representations, independent of their C$_2$ or C$_4$ nature.Comment: 11 pages, 6 figure

Phase transition in a spring-block model of surface fracture

A simple and robust spring-block model obeying threshold dynamics is introduced to study surface fracture of an overlayer subject to stress induced by adhesion to a substrate. We find a novel phase transition in the crack morphology and fragment-size statistics when the strain and the substrate coupling are varied. Across the transition, the cracks display in succession short-range, power-law and long-range correlations. The study of stress release prior to cracking yields useful information on the cracking process.Comment: RevTeX, 4 pages, 4 Postscript figures included using epsfi

Bounding the dimensions of rational cohomology groups

Let $k$ be an algebraically closed field of characteristic $p > 0$, and let $G$ be a simple simply-connected algebraic group over $k$ that is defined and split over the prime field $\mathbb{F}_p$. In this paper we investigate situations where the dimension of a rational cohomology group for $G$ can be bounded by a constant times the dimension of the coefficient module. We then demonstrate how our results can be applied to obtain effective bounds on the first cohomology of the symmetric group. We also show how, for finite Chevalley groups, our methods permit significant improvements over previous estimates for the dimensions of second cohomology groups.Comment: 13 page

Self-contained Kondo effect in single molecules

Kondo coupling of f and conduction electrons is a common feature of f-electron intermetallics. Similar effects should occur in carbon ring systems(metallocenes). Evidence for Kondo coupling in Ce(C8H8)2 (cerocene) and the ytterbocene Cp*2Yb(bipy) is reported from magnetic susceptibility and L_III-edge x-ray absorption spectroscopy. These well-defined systems provide a new way to study the Kondo effect on the nanoscale, should generate insight into the Anderson Lattice problem, and indicate the importance of this often-ignored contribution to bonding in organometallics.Comment: 4 pages, 5 figures (eps

Stellar activity as noise in exoplanet detection I. Methods and application to solar-like stars and activity cycles

The detection of exoplanets using any method is prone to confusion due to the intrinsic variability of the host star. We investigate the effect of cool starspots on the detectability of the exoplanets around solar-like stars using the radial velocity method. For investigating this activity-caused "jitter" we calculate synthetic spectra using radiative transfer, known stellar atomic and molecular lines, different surface spot configurations, and an added planetary signal. Here, the methods are described in detail, tested and compared to previously published studies. The methods are also applied to investigate the activity jitter in old and young solar-like stars, and over a solar-like activity cycles. We find that the mean full jitter amplitude obtained from the spot surfaces mimicking the solar activity varies during the cycle approximately between 1 m/s and 9 m/s. With a realistic observing frequency a Neptune mass planet on a one year orbit can be reliably recovered. On the other hand, the recovery of an Earth mass planet on a similar orbit is not feasible with high significance. The methods developed in this study have a great potential for doing statistical studies of planet detectability, and also for investigating the effect of stellar activity on recovered planetary parameters.Comment: Accepted to MNRA

Large-scale electronic structure theory for simulating nanostructure process

Fundamental theories and practical methods for large-scale electronic structure calculations are given, in which the computational cost is proportional to the system size. Accuracy controlling methods for microscopic freedoms are focused on two practical solver methods, Krylov-subspace method and generalized-Wannier-state method. A general theory called the 'multi-solver' scheme is also formulated, as a hybrid between different solver methods. Practical examples are carried out in several insulating and metallic systems with 10^3-10^5 atoms. All the theories provide general guiding principles of constructing an optimal calculation for simulating nanostructure processes, since a nanostructured system consists of several competitive regions, such as bulk and surface regions, and the simulation is designed to reproduce the competition with an optimal computational cost.Comment: 19 pages, 6 figures. To appear in J. Phys. Cond. Matt. A preprint PDF file in better graphics is available at http://fujimac.t.u-tokyo.ac.jp/lses/index_e.htm