The role of mutation rate variation and genetic diversity in the architecture of human disease

Background We have investigated the role that the mutation rate and the structure of genetic variation at a locus play in determining whether a gene is involved in disease. We predict that the mutation rate and its genetic diversity should be higher in genes associated with disease, unless all genes that could cause disease have already been identified. Results Consistent with our predictions we find that genes associated with Mendelian and complex disease are substantially longer than non-disease genes. However, we find that both Mendelian and complex disease genes are found in regions of the genome with relatively low mutation rates, as inferred from intron divergence between humans and chimpanzees, and they are predicted to have similar rates of non-synonymous mutation as other genes. Finally, we find that disease genes are in regions of significantly elevated genetic diversity, even when variation in the rate of mutation is controlled for. The effect is small nevertheless. Conclusions Our results suggest that gene length contributes to whether a gene is associated with disease. However, the mutation rate and the genetic architecture of the locus appear to play only a minor role in determining whether a gene is associated with disease

Structurally perturbed chiral Bragg reflectors for elliptically polarized light

The structure of an inorganic chiral medium represented as a stack of identical form-birefringent layers that twist steadily with increasing thickness is perturbed by realigning a fraction of each layer to a fixed direction. Experimental results show that the resulting chiral-birefringent composite medium exhibits Bragg resonance with elliptically polarized light, and simulations indicate that Bragg reflectors can be designed for any polarization including linear. © 2005 Optical Society of America

Tan(beta) enhanced Yukawa couplings for supersymmetric Higgs singlets at one loop

Extensions of the MSSM generically feature gauge singlet Higgs bosons. These singlet Higgs bosons have tan(beta)-enhanced Yukawa couplings to down-type quarks and leptons at the one-loop level. We present an effective Lagrangian incorporating these Yukawa couplings and use it to study their effect on singlet Higgs boson phenomenology within both the mnSSM and NMSSM. It is found that the loop-induced couplings represent an appreciable effect for the singlet pseudoscalar in particular, and may dominate its decay modes in some regions of parameter space.Comment: Submitted for the SUSY07 proceedings, 4 pages, 5 figure

Blending of nanoscale and microscale in uniform large-area sculptured thin-film architectures

The combination of large thickness ($>3$ $\mu$m), large--area uniformity (75 mm diameter), high growth rate (up to 0.4 $\mu$m/min) in assemblies of complex--shaped nanowires on lithographically defined patterns has been achieved for the first time. The nanoscale and the microscale have thus been blended together in sculptured thin films with transverse architectures. SiO$_x$ ($x\approx 2$) nanowires were grown by electron--beam evaporation onto silicon substrates both with and without photoresist lines (1--D arrays) and checkerboard (2--D arrays) patterns. Atomic self--shadowing due to oblique--angle deposition enables the nanowires to grow continuously, to change direction abruptly, and to maintain constant cross--sectional diameter. The selective growth of nanowire assemblies on the top surfaces of both 1--D and 2--D arrays can be understood and predicted using simple geometrical shadowing equations.Comment: 17 pages, 9 figure

Scalable design of tailored soft pulses for coherent control

We present a scalable scheme to design optimized soft pulses and pulse sequences for coherent control of interacting quantum many-body systems. The scheme is based on the cluster expansion and the time dependent perturbation theory implemented numerically. This approach offers a dramatic advantage in numerical efficiency, and it is also more convenient than the commonly used Magnus expansion, especially when dealing with higher order terms. We illustrate the scheme by designing 2nd-order pi-pulses and a 6th-order 8-pulse refocusing sequence for a chain of qubits with nearest-neighbor couplings. We also discuss the performance of soft-pulse refocusing sequences in suppressing decoherence due to low-frequency environment.Comment: 4 pages, 2 tables. (modified first table, references added, minor text changes

The Mersey Estuary : sediment geochemistry

This report describes a study of the geochemistry of the Mersey estuary carried out between April 2000 and December 2002. The study was the first in a new programme of surveys of the geochemistry of major British estuaries aimed at enhancing our knowledge and understanding of the distribution of contaminants in estuarine sediments. The report first summarises the physical setting, historical development, geology, hydrography and bathymetry of the Mersey estuary and its catchment. Details of the sampling and analytical programmes are then given followed by a discussion of the sedimentology and geochemistry. The chemistry of the water column and suspended particulate matter have not been studied, the chief concern being with the geochemistry of the surface and near-surface sediments of the Mersey estuary and an examination of their likely sources and present state of contamination

Thin-Film Metamaterials called Sculptured Thin Films

Morphology and performance are conjointed attributes of metamaterials, of which sculptured thin films (STFs) are examples. STFs are assemblies of nanowires that can be fabricated from many different materials, typically via physical vapor deposition onto rotating substrates. The curvilinear--nanowire morphology of STFs is determined by the substrate motions during fabrication. The optical properties, especially, can be tailored by varying the morphology of STFs. In many cases prototype devices have been fabricated for various optical, thermal, chemical, and biological applications.Comment: to be published in Proc. ICTP School on Metamaterials (Augsut 2009, Sibiu, Romania

Theory and design of Inx_{x}Ga1−x_{1-x}As1−y_{1-y}Biy_{y} mid-infrared semiconductor lasers: type-I quantum wells for emission beyond 3 μ\mum on InP substrates

We present a theoretical analysis and optimisation of the properties and performance of mid-infrared semiconductor lasers based on the dilute bismide alloy In$_{x}$Ga$_{1-x}$As$_{1-y}$Bi$_{y}$, grown on conventional (001) InP substrates. The ability to independently vary the epitaxial strain and emission wavelength in this quaternary alloy provides significant scope for band structure engineering. Our calculations demonstrate that structures based on compressively strained In$_{x}$Ga$_{1-x}$As$_{1-y}$Bi$_{y}$ quantum wells (QWs) can readily achieve emission wavelengths in the 3 -- 5 $\mu$m range, and that these QWs have large type-I band offsets. As such, these structures have the potential to overcome a number of limitations commonly associated with this application-rich but technologically challenging wavelength range. By considering structures having (i) fixed QW thickness and variable strain, and (ii) fixed strain and variable QW thickness, we quantify key trends in the properties and performance as functions of the alloy composition, structural properties, and emission wavelength, and on this basis identify routes towards the realisation of optimised devices for practical applications. Our analysis suggests that simple laser structures -- incorporating In$_{x}$Ga$_{1-x}$As$_{1-y}$Bi$_{y}$ QWs and unstrained ternary In$_{0.53}$Ga$_{0.47}$As barriers -- which are compatible with established epitaxial growth, provide a route to realising InP-based mid-infrared diode lasers.Comment: Submitted versio