Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion

One benefit of a computational Grid is the ability to run high‐performance applications over distributed resources simply and securely. We demonstrated this benefit with an experiment in which we studied the protein‐folding process with the CHARMM molecular simulation package over a Grid managed by Legion, a Grid operating system. High‐performance applications can take advantage of Grid resources if the Grid operating system provides both low‐level functionality as well as high‐level services. We describe the nature of services provided by Legion for high‐performance applications. Our experiences indicate that human factors continue to play a crucial role in the configuration of Grid resources, underlying resources can be problematic, Grid services must tolerate underlying problems or inform the user, and high‐level services must continue to evolve to meet user requirements. Our experiment not only helped a scientist perform an important study, but also showed the viability of an integrated approach such as Legion's for managing a Grid. Copyright © 2004 John Wiley & Sons, Ltd.     

Relating Cost Growth from the Initial Estimate to Design Fee for Transportation Projects

Intuitively, there should be a relationship between the size of the design fee for a transportation project and the quality of the resulting design. This study sought that relationship by looking at the fee expressed as a percentage of the construction cost and the final construction cost growth from the engineer’s initial estimate of the construction cost at the time the design contract was awarded. The research team analyzed 31 projects from the Oklahoma Turnpike Authority with a total construction value of $90 million. The projects were divided into road and bridge projects. Based on the results of the analysis, it seems that as the design fee decreases, the absolute percentage of construction cost growth from the engineer’s early estimate increases. The relationship is strongest for bridge projects, which tend to be more technically complex to design than roadway projects. This confirms for U.S. projects the result of an earlier study in Saudi Arabia. This paper concludes that the design fee should be viewed as an investment at a point in time where the ability to impact the project is the highest and can accrue the benefit of reduced cost growth.     

Integrating motivational, social, and contextual work design features: A meta-analytic summary and theoretical extension of the work design literature.

The authors developed and meta-analytically examined hypotheses designed to test and extend work design theory by integrating motivational, social, and work context characteristics. Results from a summary of 259 studies and 219,625 participants showed that 14 work characteristics explained, on average, 43% of the variance in the 19 worker attitudes and behaviors examined. For example, motivational characteristics explained 25% of the variance in subjective performance, 2% in turnover perceptions, 34% in job satisfaction, 24% in organizational commitment, and 26% in role perception outcomes. Beyond motivational characteristics, social characteristics explained incremental variances of 9% of the variance in subjective performance, 24% in turnover intentions, 17% in job satisfaction, 40% in organizational commitment, and 18% in role perception outcomes. Finally, beyond both motivational and social characteristics, work context characteristics explained incremental variances of 4% in job satisfaction and 16% in stress. The results of this study suggest numerous opportunities for the continued development of work design theory and practice. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Mesh refinement and iterative solution methods for finite element computations

Global and element residuals are introduced to determine a posteriori, computable, error bounds for finite element computations on a given mesh. The element residuals provide a criterion for determining where a finite element mesh requires refinement. This indicator is implemented in an algorithm in a finite element research program. There it is utilized to automatically refine the mesh for sample two-point problems exhibiting boundary layer and interior layer solutions. Results for both linear and nonlinear problems are presented. An important aspect of this investigation concerns the use of adaptive refinement in conjunction with iterative methods for system solution. As the mesh is being enriched through the refinement process, the solution on a given mesh provides an accurate starting iterate for the next mesh, and so on. A wide range of iterative methods are examined in a feasibility study and strategies for interweaving refinement and iteration are compared.     

Clear cell neoplasms of the urinary tract and male reproductive system

Herein is a review of clear cell neoplasms of selected sites in the urinary tract and male reproductive system, including the kidney, the urinary bladder, testis, epididymis, and prostate. Clear cell cytoplasmic alteration in neoplasms at these sites is a relatively common light microscopic finding. Examples of such neoplasms with clear cell change include the clear cell type of renal cell carcinoma, clear cell adenocarcinoma of urethra and bladder, the classic type of seminoma, papillary cystadenoma of the epididymis, and well-differentiated adenocarcinoma of the prostate. Of importance, numerous non-neoplastic benign entities may also manifest cleared cytoplasm and therefore are presented in the differential in this review. Indeed, knowledge of the neoplastic and non-neoplastic entities displaying clear cell change at each anatomic site should enable the surgical pathologist to approach the differential diagnosis of these conditions in a more logical and rigorous fashion.     

Using structural analysis of social behavior to assess critical but elusive family processes: A new solution to an old problem.

Describes how the 2nd author's (see record 1975-02991-001) structural analysis of social behavior (SASB) offers a new approach to the old problem of how to measure the complex and elusive concepts that are critical to family theory and therapy. SASB includes a theoretical model and an assessment methodology that can be applied to disturbed family relationships and interaction patterns. It also provides operational definitions and measures of distressed family processes that have been linked to major psychopathology, such as double binds and pseudomutuality. The conceptual framework of SASB is compatible with family systems and psychodynamic theories, and it applies to a range of healthy and distressed family functioning. SASB's promise for family assessment is illustrated, and an overview of the SASB model and methods is presented. Several central concepts from selected theories of the schizophrenic's family are operationalized. (44 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Bubbles in Liquid Helium Containing Electrons in Excited States

When an electron enters liquid helium, it forces open a cavity within the liquid. We calculate the size and shape of these electron bubbles for different quantum states of the electron, and determine the negative pressure at which the different bubbles explode.     

Particle conservation in the hot‐carrier solar cell

In conventional p–n junction solar cells, carrier multiplication by impact ionisation, is negligible, owing to the low temperature of the electron–hole pairs. This leads to particle conservation between the net number of absorbed photons and the number of electron–hole pairs withdrawn from the cell. In hot‐carrier solar cells, in which electrons are at a high temperature by assuming suppression of electron–phonon scattering, such particle conservation leads to peculiar results. Numerical calculations show that entire current–voltage characteristics with meaningful values of temperature and chemical potential do not exist. If the energy at which electron–hole pairs are extracted is smaller than the average energy of absorbed photons, the temperature of the electrons and holes becomes much larger than the tem perature of the sun. When the extraction energy is larger than the average energy of the absorbed photons, an entire current–voltage curve cannot always be obtained. It follows that impact ionisation and Auger recombination cannot be neglected when the thermal energy of the electron–hole pairs is comparable to the bandgap of the absorber. Accounting for these processes results in current–voltage characteristics that are well behaved. Copyright © 2005 John Wiley & Sons, Ltd.     

Influence of topography and specimen preparation on backscattered electron images of bone

Backscattered electron (BSE) images of bone exhibit graylevel contrast between adjacent lamellae. Mathematical models suggest that interlamellar contrast in BSE images is an artifact due to topographic irregularities. However, little experimental evidence has been published to support these models, and it is not clear whether submicron topographical features will alter BSE graylevels. The goal of this study was to determine the effects of topography on BSE image mean graylevels and graylevel histogram widths using conventional specimen preparation techniques. White-light interferometry and quantitative BSE imaging were used to investigate the relationship between the BSE signal and specimen roughness. Backscattered electron image graylevel histogram widths correlated highly with surface roughness in rough preparations of homogeneous materials. The relationship between BSE histogram width and surface roughness was specimen dependent. Specimen topography coincided with the lamellar patterns within the bone tissue. Diamond micromilling reduced average surface roughness when compared with manual polishing techniques but did not significantly affect BSE graylevel histogram width. The study suggests that topography is a confounding factor in quantitative BSE analysis of bone. However, there is little quantitative difference between low-to-moderate magnification BSE images of bone specimens prepared by conventional polishing or diamond micromilling.