Self-organized nanoscale pattern formation on vicinal Si(111) surfaces via a two-stage faceting transition

Journal ArticleWe demonstrate a self-organized pattern formation on vicinal Si(111) surfaces that are miscut toward the [211] direction. All the patterns, consisting of a periodic array of alternating (7 X 7) reconstructed terraces and step-bunched facets, have the same periodicity and facet structure, independent of the miscut angle, while the width of the facets increases linearly with miscut angle. We attribute such unique pattern formation to a surface faceting transition that involves two transition stages: the first stage forms a stress-domain structure defining the universal periodicity; the second stage forms the low-energy facets controlling the facet width

Resonant Charge Transfer In Symmetric Alkali-ion Alkali-atom Collisions

Resonant charge transfer in alkali-ion alkali-atom collisions is investigated by using the molecular-orbital expansion method incorporating the use of electron translation factors. Molecular wave functions and eigen energies are obtained by the pseudopotential method. Molecular properties, Re, De, and e, obtained in the present calculation are in good accord with other recent theoretical results, as well as spectroscopic measurements. Three-state close-coupling calculations reproduce the positions of the maxima and minima in the oscillatory structure seen experimentally in the resonant-charge-transfer cross sections for the Li2 + and Cs2 + systems. The magnitude of the total cross sections and their velocity dependence are in agreement with experimental measurements. © 1986 The American Physical Society

Pattern formation via a two-step faceting transition on vicinal Si(111) surfaces

Journal ArticleWe demonstrate a self-organized pattern formation on vicinal Si(l 11) surfaces that are miscut toward the [211] direction. All the patterns, consisting of a periodic array of alternating (7x7) reconstructed terraces and step-bunched facets, have the same periodicity and facet structure, independent of the miscut angle; while the width of the facets increases linearly with miscut angle. We attribute such unique pattern formation to a surface faceting transition that involves two transition steps: the first step forms a stress-domain structure defining the universal periodicity; the second step forms the low-energy facets controlling the facet width

GPU-based Iterative Cone Beam CT Reconstruction Using Tight Frame Regularization

X-ray imaging dose from serial cone-beam CT (CBCT) scans raises a clinical concern in most image guided radiation therapy procedures. It is the goal of this paper to develop a fast GPU-based algorithm to reconstruct high quality CBCT images from undersampled and noisy projection data so as to lower the imaging dose. For this purpose, we have developed an iterative tight frame (TF) based CBCT reconstruction algorithm. A condition that a real CBCT image has a sparse representation under a TF basis is imposed in the iteration process as regularization to the solution. To speed up the computation, a multi-grid method is employed. Our GPU implementation has achieved high computational efficiency and a CBCT image of resolution 512\times512\times70 can be reconstructed in ~5 min. We have tested our algorithm on a digital NCAT phantom and a physical Catphan phantom. It is found that our TF-based algorithm is able to reconstrct CBCT in the context of undersampling and low mAs levels. We have also quantitatively analyzed the reconstructed CBCT image quality in terms of modulation-transfer-function and contrast-to-noise ratio under various scanning conditions. The results confirm the high CBCT image quality obtained from our TF algorithm. Moreover, our algorithm has also been validated in a real clinical context using a head-and-neck patient case. Comparisons of the developed TF algorithm and the current state-of-the-art TV algorithm have also been made in various cases studied in terms of reconstructed image quality and computation efficiency.Comment: 24 pages, 8 figures, accepted by Phys. Med. Bio

Deciphering the genetic basis for polyketide variation among mycobacteria producing mycolactones.

BACKGROUND: Mycolactones are immunosuppressive and cytotoxic polyketides, comprising five naturally occurring structural variants (named A/B, C, D, E and F), produced by different species of very closely related mycobacteria including the human pathogen, Mycobacterium ulcerans. In M. ulcerans strain Agy99, mycolactone A/B is produced by three highly homologous type I polyketide megasynthases (PKS), whose genes (mlsA1: 51 kb, mlsA2: 7.2 kb and mlsB: 42 kb) are found on a 174 kb plasmid, known as pMUM001. RESULTS: We report here comparative genomic analysis of pMUM001, the complete DNA sequence of a 190 kb megaplasmid (pMUM002) from Mycobacterium liflandii 128FXT and partial sequence of two additional pMUM replicons, combined with liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis. These data reveal how PKS module and domain differences affecting MlsB correlate with the production of mycolactones E and F. For mycolactone E these differences from MlsB in M. ulcerans Agy99 include replacement of the AT domain of the loading module (acetate to propionate) and the absence of an entire extension module. For mycolactone F there is also a reduction of one extension module but also a swap of ketoreductase domains that explains the characteristic stereochemistry of the two terminal side-chain hydroxyls, an arrangement unique to mycolactone F CONCLUSION: The mycolactone PKS locus on pMUM002 revealed the same large, three-gene structure and extraordinary pattern of near-identical PKS domain sequence repetition as observed in pMUM001 with greater than 98.5% nucleotide identity among domains of the same function. Intra- and inter-strain comparisons suggest that the extreme sequence homogeneity seen among the mls PKS genes is caused by frequent recombination-mediated domain replacement. This work has shed light on the evolution of mycolactone biosynthesis among an unusual group of mycobacteria and highlights the potential of the mls locus to become a toolbox for combinatorial PKS biochemistry.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

GPU-based Low Dose CT Reconstruction via Edge-preserving Total Variation Regularization

High radiation dose in CT scans increases a lifetime risk of cancer and has become a major clinical concern. Recently, iterative reconstruction algorithms with Total Variation (TV) regularization have been developed to reconstruct CT images from highly undersampled data acquired at low mAs levels in order to reduce the imaging dose. Nonetheless, TV regularization may lead to over-smoothed images and lost edge information. To solve this problem, in this work we develop an iterative CT reconstruction algorithm with edge-preserving TV regularization to reconstruct CT images from highly undersampled data obtained at low mAs levels. The CT image is reconstructed by minimizing an energy consisting of an edge-preserving TV norm and a data fidelity term posed by the x-ray projections. The edge-preserving TV term is proposed to preferentially perform smoothing only on non-edge part of the image in order to avoid over-smoothing, which is realized by introducing a penalty weight to the original total variation norm. Our iterative algorithm is implemented on GPU to improve its speed. We test our reconstruction algorithm on a digital NCAT phantom, a physical chest phantom, and a Catphan phantom. Reconstruction results from a conventional FBP algorithm and a TV regularization method without edge preserving penalty are also presented for comparison purpose. The experimental results illustrate that both TV-based algorithm and our edge-preserving TV algorithm outperform the conventional FBP algorithm in suppressing the streaking artifacts and image noise under the low dose context. Our edge-preserving algorithm is superior to the TV-based algorithm in that it can preserve more information of fine structures and therefore maintain acceptable spatial resolution.Comment: 21 pages, 6 figures, 2 table

GPU-based fast Monte Carlo simulation for radiotherapy dose calculation

Monte Carlo (MC) simulation is commonly considered to be the most accurate dose calculation method in radiotherapy. However, its efficiency still requires improvement for many routine clinical applications. In this paper, we present our recent progress towards the development a GPU-based MC dose calculation package, gDPM v2.0. It utilizes the parallel computation ability of a GPU to achieve high efficiency, while maintaining the same particle transport physics as in the original DPM code and hence the same level of simulation accuracy. In GPU computing, divergence of execution paths between threads can considerably reduce the efficiency. Since photons and electrons undergo different physics and hence attain different execution paths, we use a simulation scheme where photon transport and electron transport are separated to partially relieve the thread divergence issue. High performance random number generator and hardware linear interpolation are also utilized. We have also developed various components to handle fluence map and linac geometry, so that gDPM can be used to compute dose distributions for realistic IMRT or VMAT treatment plans. Our gDPM package is tested for its accuracy and efficiency in both phantoms and realistic patient cases. In all cases, the average relative uncertainties are less than 1%. A statistical t-test is performed and the dose difference between the CPU and the GPU results is found not statistically significant in over 96% of the high dose region and over 97% of the entire region. Speed up factors of 69.1 ~ 87.2 have been observed using an NVIDIA Tesla C2050 GPU card against a 2.27GHz Intel Xeon CPU processor. For realistic IMRT and VMAT plans, MC dose calculation can be completed with less than 1% standard deviation in 36.1~39.6 sec using gDPM.Comment: 18 pages, 5 figures, and 3 table

Exploratory genome-wide analyses of cortical inhibition, facilitation, and plasticity in late-life depression

Late-life depression (LLD) is a heterogenous mood disorder influenced by genetic factors. Cortical physiological processes such as cortical inhibition, facilitation, and plasticity may be markers of illness that are more strongly associated with genetic factors than the clinical phenotype. Thus, exploring the relationship between genetic factors and these physiological processes may help to characterize the biological mechanisms underlying LLD and improve diagnosis and treatment selection. Transcranial magnetic stimulation (TMS) combined with electromyography was used to measure short interval intracortical inhibition (SICI), cortical silent period (CSP), intracortical facilitation (ICF), and paired associative stimulation (PAS) in 79 participants with LLD. We used exploratory genome-wide association and gene-based analyses to assess for genetic correlations of these TMS measures. MARK4 (which encodes microtubule affinity-regulating kinase 4) and PPP1R37 (which encodes protein phosphatase 1 regulatory subunit 37) showed genome-wide significant association with SICI. EGFLAM (which encodes EGF-like fibronectin type III and laminin G domain) showed genome-wide significant association with CSP. No genes met genome-wide significant association with ICF or PAS. We observed genetic influences on cortical inhibition in older adults with LLD. Replication with larger sample sizes, exploration of clinical phenotype subgroups, and functional analysis of relevant genotypes is warranted to better characterize genetic influences on cortical physiology in LLD. This work is needed to determine whether cortical inhibition may serve as a biomarker to improve diagnostic precision and guide treatment selection in LLD

Orbital effects of a monochromatic plane gravitational wave with ultra-low frequency incident on a gravitationally bound two-body system

We analytically compute the long-term orbital variations of a test particle orbiting a central body acted upon by an incident monochromatic plane gravitational wave. We assume that the characteristic size of the perturbed two-body system is much smaller than the wavelength of the wave. Moreover, we also suppose that the wave's frequency is much smaller than the particle's orbital one. We make neither a priori assumptions about the direction of the wavevector nor on the orbital geometry of the planet. We find that, while the semi-major axis is left unaffected, the eccentricity, the inclination, the longitude of the ascending node, the longitude of pericenter and the mean anomaly undergo non-vanishing long-term changes. They are not secular trends because of the slow modulation introduced by the tidal matrix coefficients and by the orbital elements themselves. They could be useful to indepenedently constrain the ultra-low frequency waves which may have been indirectly detected in the BICEP2 experiment. Our calculation holds, in general, for any gravitationally bound two-body system whose characteristic frequency is much larger than the frequency of the external wave. It is also valid for a generic perturbation of tidal type with constant coefficients over timescales of the order of the orbital period of the perturbed particle.Comment: LaTex2e, 24 pages, no figures, no tables. Changes suggested by the referees include