Twisted Split Fermions

The observed flavor structure of the standard model arises naturally in "split fermion" models which localize fermions at different places in an extra dimension. It has, until now, been assumed that the bulk masses for such fermions can be chosen to be flavor diagonal simultaneously at every point in the extra dimension, with all the flavor violation coming from the Yukawa couplings to the Higgs. We consider the more natural possibility in which the bulk masses cannot be simultaneously diagonalized, that is, that they are twisted in flavor space. We show that, in general, this does not disturb the natural generation of hierarchies in the flavor parameters. Moreover, it is conceivable that all the flavor mixing and CP-violation in the standard model may come only from twisting, with the five-dimensional Yukawa couplings taken to be universal.Comment: 15 pages, 1 figur

Dispersion interactions from a local polarizability model

A local approximation for dynamic polarizability leads to a nonlocal functional for the long-range dispersion interaction energy via an imaginary-frequency integral. We analyze several local polarizability approximations and argue that the form underlying the construction of our recent van der Waals functional [O. A. Vydrov and T. Van Voorhis, Phys. Rev. Lett. 103, 063004 (2009)] is particularly well physically justified. Using this improved formula, we compute dynamic dipole polarizabilities and van der Waals C_6 coefficients for a set of atoms and molecules. Good agreement with the benchmark values is obtained in most cases

Bremsstrahlung in Alpha-Decay

We present the first fully quantum mechanical calculation of photon radiation accompanying charged particle decay from a barrier resonance. The soft-photon limit agrees with the classical results, but differences appear at next-to-leading-order. Under the conditions of alpha-decay of heavy nuclei, the main contribution to the photon emission stems from Coulomb acceleration and may be computed analytically. We find only a small contribution from the tunneling wave function under the barrier.Comment: 12 pages, 2 Postscript figure

Supersymmetry on a Spatial Lattice

We construct a variety of supersymmetric gauge theories on a spatial lattice, including N=4 supersymmetric Yang-Mills theory in 3+1 dimensions. Exact lattice supersymmetry greatly reduces or eliminates the need for fine tuning to arrive at the desired continuum limit in these examples.Comment: Version 3: Text brought in line with published version (extended discussion of orbifolding

Two-dimensional N=(2,2) super Yang-Mills theory on computer

We carry out preliminary numerical study of Sugino's lattice formulation \cite{Sugino:2004qd,Sugino:2004qdf} of the two-dimensional $\mathcal{N}=(2,2)$ super Yang-Mills theory (2d $\mathcal{N}=(2,2)$ SYM) with the gauge group \SU(2). The effect of dynamical fermions is included by re-weighting a quenched ensemble by the pfaffian factor. It appears that the complex phase of the pfaffian due to lattice artifacts and flat directions of the classical potential are not problematic in Monte Carlo simulation. Various one-point supersymmetric Ward-Takahashi (WT) identities are examined for lattice spacings up to $a=0.5/g$ with the fixed physical lattice size $L=4.0/g$, where $g$ denotes the gauge coupling constant in two dimensions. WT identities implied by an exact fermionic symmetry of the formulation are confirmed in fair accuracy and, for most of these identities, the quantum effect of dynamical fermions is clearly observed. For WT identities expected only in the continuum limit, the results seem to be consistent with the behavior expected from supersymmetry, although we do not see clear distintion from the quenched simulation. We measure also the expectation values of renormalized gauge-invariant bi-linear operators of scalar fields.Comment: 24 pages, 10 figures, the distribution of the complex phase of the pffafian is also measured, the final version to appear in JHE

High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier.

Nucleosomes represent mechanical and energetic barriers that RNA Polymerase II (Pol II) must overcome during transcription. A high-resolution description of the barrier topography, its modulation by epigenetic modifications, and their effects on Pol II nucleosome crossing dynamics, is still missing. Here, we obtain topographic and transcriptional (Pol II residence time) maps of canonical, H2A.Z, and monoubiquitinated H2B (uH2B) nucleosomes at near base-pair resolution and accuracy. Pol II crossing dynamics are complex, displaying pauses at specific loci, backtracking, and nucleosome hopping between wrapped states. While H2A.Z widens the barrier, uH2B heightens it, and both modifications greatly lengthen Pol II crossing time. Using the dwell times of Pol II at each nucleosomal position we extract the energetics of the barrier. The orthogonal barrier modifications of H2A.Z and uH2B, and their effects on Pol II dynamics rationalize their observed enrichment in +1 nucleosomes and suggest a mechanism for selective control of gene expression

Unravelling quantum carpets: a travelling wave approach

Quantum carpets are generic spacetime patterns formed in the probability distributions P(x,t) of one-dimensional quantum particles, first discovered in 1995. For the case of an infinite square well potential, these patterns are shown to have a detailed quantitative explanation in terms of a travelling-wave decomposition of P(x,t). Each wave directly yields the time-averaged structure of P(x,t) along the (quantised)spacetime direction in which the wave propagates. The decomposition leads to new predictions of locations, widths depths and shapes of carpet structures, and results are also applicable to light diffracted by a periodic grating and to the quantum rotator. A simple connection between the waves and the Wigner function of the initial state of the particle is demonstrated, and some results for more general potentials are given.Comment: Latex, 26 pages + 6 figures, submitted to J. Phys. A (connections with prior literature clarified

A reduced subduction graph and higher multiplicity in S_n transformation coefficients

Transformation coefficients between {\it standard} bases for irreducible representations of the symmetric group $S_n$ and {\it split} bases adapted to the $S_{n_1} \times S_{n_2} \subset S_n$ subgroup ($n_1 +n_2 = n$) are considered. We first provide a \emph{selection rule} and an \emph{identity rule} for the subduction coefficients which allow to decrease the number of unknowns and equations arising from the linear method by Pan and Chen. Then, using the {\it reduced subduction graph} approach, we may look at higher multiplicity instances. As a significant example, an orthonormalized solution for the first multiplicity-three case, which occurs in the decomposition of the irreducible representation $[4,3,2,1]$ of $S_{10}$ into $[3,2,1] \otimes [3,1]$ of $S_6 \times S_4$, is presented and discussed.Comment: 12 pages, 1 figure, iopart class, Revisited version (several typographical errors have been corrected). Accepted for publication in J. Phys. A: Math. Ge

Spider silk-bone sialoprotein fusion proteins for bone tissue engineering

The remarkable mechanical characteristics of the spider silk protein major ampullate spidroin protein suggest this polymer as a promising biomaterial to consider for the fabrication of scaffolds for bone regeneration. Herein, a new functionalized spider silk-bone sialoprotein fusion protein was designed, cloned, expressed, purified and the osteogenic activity studied. Bone sialoprotein (BSP) is a multidomain protein with the ability to induce cell attachment and differentiation and the deposition of calcium phosphates (CaP). Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) was used to assess the secondary structure of the fusion protein. In vitro mineralization studies demonstrated that this new fusion protein with BSP retained the ability to induce the deposition of CaP. Studies in vitro indicated that human mesenchymal stem cells had significant improvement towards osteogenic outcomes when cultivated in the presence of the new fusion protein vs. silk alone. The present work demonstrates the potential of this new fusion protein for future applications in bone regenerationPhD grant SFRH/BD/28603/2006; Chimera project, PTDC/EBB-EBI/109093/2008; NIH, P41 EB002520, EB003210 and DE017207.Foundation for Science and Technolog