Role of structural saturation and geometry in the luminescence of silicon-based nanostructured materials

The structural saturation and stability, the energy gap, and the density of states of a series of small, silicon-based clusters have been studied by means of the PM3 and some ab initio (HF/6-31G* and 6-311++G**, CIS/6-31G* and MP2/6-31G*) calculations. It is shown that in order to maintain a stable nanometric and tetrahedral silicon crystallite and remove the gap states, the saturation atom or species such as H, F, Cl, OH, O, or N is necessary, and that both the cluster size and the surface species affect the energetic distribution of the density of states. This research suggests that the visible luminescence in the silicon-based nanostructured material essentially arises from the nanometric and crystalline silicon domains but is affected and protected by the surface species, and we have thus linked most of the proposed mechanisms of luminescence for the porous silicon, e.g., the quantum confinement effect due to the cluster size and the effect of Si-based surface complexes.

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. Recent analyses have suggested that the genomes of chimpanzee and human have been particularly enriched for this form of genetic variation. Here, we set out to assess the extent of structural variation in the gorilla lineage by generating 10-fold genomic sequence coverage from a western lowland gorilla and integrating these data into a physical and cytogenetic framework of structural variation. We discovered and validated over 7665 structural changes within the gorilla lineage, including sequence resolution of inversions, deletions, duplications, and mobile element insertions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet convergent patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human genomes.

The effect of mutations in the DRY motif on the constitutive activity and structural instability of the histamine H(2) receptor.

In previous studies we showed that the wild-type histamine H(2) receptor stably expressed in Chinese hamster ovary cells is constitutively active. Because constitutive activity of the H(2) receptor is already found at low expression levels (300 fmol/mg protein) this receptor is a relatively unique member of the G-protein-coupled receptor (GPCR) family and a useful tool for studying GPCR activation. In this study the role of the highly conserved DRY motif in activation of the H(2) receptor was investigated. Mutation of the aspartate 115 residue in this motif resulted in H(2) receptors with high constitutive activity, increased agonist affinity, and increased signaling properties. In addition, the mutant receptors were shown to be highly structurally instable. Mutation of the arginine 116 residue in the DRY motif resulted also in a highly structurally instable receptor; expression of the receptor could only be detected after stabilization with either an agonist or inverse agonist. Moreover, the agonist affinity at the Arg-116 mutant receptors was increased, whereas the signal transduction properties of these receptors were decreased. We conclude that the Arg-116 mutant receptors can adopt an active conformation but have a decreased ability to couple to or activate the G(s)-protein. This study examines the pivotal role of the aspartate and arginine residues of the DRY motif in GPCR function. Disruption of receptor stabilizing constraints by mutation in the DRY motif leads to the formation of active GPCR conformations, but concomitantly to GPCR instability.

Agricultural productivity and structural transformation. Evidence from Brazil

We study the effects of the adoption of new agricultural technologies on structural transformation. To guide empirical work, we present a simple model where the effect of agriculturalproductivity on industrial development depends on the factor bias of technical change. We testthe predictions of the model by studying the introduction of genetically engineered soybeanseeds in Brazil, which had heterogeneous effects on agricultural productivity across areas withdifferent soil and weather characteristics. We find that technical change in soy production wasstrongly labor saving and lead to industrial growth, as predicted by the model.

Silicon quantum dots embedded in a SiO2 matrix: From structural study to carrier transport properties

We study the details of electronic transport related to the atomistic structure of silicon quantum dots embedded in a silicon dioxide matrix using ab initio calculations of the density of states. Several structural and composition features of quantum dots (QDs), such as diameter and amorphization level, are studied and correlated with transport under transfer Hamiltonian formalism. The current is strongly dependent on the QD density of states and on the conduction gap, both dependent on the dot diameter. In particular, as size increases, the available states inside the QD increase, while the QD band gap decreases due to relaxation of quantum confinement. Both effects contribute to increasing the current with the dot size. Besides, valence band offset between the band edges of the QD and the silica, and conduction band offset in a minor grade, increases with the QD diameter up to the theoretical value corresponding to planar heterostructures, thus decreasing the tunneling transmission probability and hence the total current. We discuss the influence of these parameters on electron and hole transport, evidencing a correlation between the electron (hole) barrier value and the electron (hole) current, and obtaining a general enhancement of the electron (hole) transport for larger (smaller) QD. Finally, we show that crystalline and amorphous structures exhibit enhanced probability of hole and electron current, respectively.

CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature.

The main goal of CleanEx is to provide access to public gene expression data via unique gene names. A second objective is to represent heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-data set comparisons. A consistent and up-to-date gene nomenclature is achieved by associating each single experiment with a permanent target identifier consisting of a physical description of the targeted RNA population or the hybridization reagent used. These targets are then mapped at regular intervals to the growing and evolving catalogues of human genes and genes from model organisms. The completely automatic mapping procedure relies partly on external genome information resources such as UniGene and RefSeq. The central part of CleanEx is a weekly built gene index containing cross-references to all public expression data already incorporated into the system. In addition, the expression target database of CleanEx provides gene mapping and quality control information for various types of experimental resource, such as cDNA clones or Affymetrix probe sets. The web-based query interfaces offer access to individual entries via text string searches or quantitative expression criteria. CleanEx is accessible at: http://www.cleanex.isb-sib.ch/.

Structural variation and its effect on expression.

Structural variation, whether it is caused by copy number variants or present in a balanced form, such as reciprocal translocations and inversions, can have a profound and dramatic effect on the expression of genes mapping within and close to the rearrangement, as well as affecting others genome wide. These effects can be caused by altering the copy number of one or more genes or regulatory elements (dosage effect) or from physical disruption of links between regulatory elements and their associated gene or genes, resulting in perturbation of expression. Similarly, large-scale structural variants can result in genome-wide expression changes by altering the positions that chromosomes occupy within the nucleus, potentially disrupting not only local cis interactions, but also trans interactions that occur throughout the genome. Structural variation is, therefore, a significant factor in the study of gene expression and is discussed here in more detail.

Holism and structural realism

We first introduce structural realism as a position in the metaphysics of science, pointing out the way in which this position replaces intrinsic properties with relations so that it amounts to a holistic in contrast to an atomistic metaphysics. We argue in favour of a moderate version of structural realism that puts objects and relations on the same ontological footing and assess the general philosophical arguments for this position. The second section shows how structural realism gains support from quantum physics. The third section explains how structural realism can be applied to the metaphysics of space-time.

Synthetic Fabric to Improve Structural Capacity in Asphalt Overlays, HR-516, 1984

Iowa's first field application of synthetic engineering fabrics was on research project HR-158, "Prevention of Reflective Cracking in Asphalt Overlays". This research placed in September 1971 used three different engineering fabrics. A final report concluding generally favorable performance was distributed in May 1977. There have been a number of Iowa engineering fabric installations since that initial project.

Ferromagnetic shape memory alloys: structural and thermal properties

The most extensively studied Heusler alloys are those based on the Ni-Mn-Ga system. However, to overcome the high cost of Gallium and the usually low martensitic transformation temperature, the search for Ga-free alloys has been recently attempted, particularly, by introducing In, Sn or Sb. In this work, two alloys (Mn50Ni35.5In14.5 and Ni50Mn35In15) have been obtained by melt spinning. We outline their structural and thermal behaviour. Mn50Ni35.5In14.5 alloy has the transformation above room temperature whereas Ni50Mn35In15 does not have this transformation in the temperature range here analyzed

Thermally-Induced Structural Transformations on Polymorphous Silicon

Polymorphous Si is a nanostructured form of hydrogenated amorphous Si that contains a small fraction of Si nanocrystals or clusters. Its thermally induced transformations such as relaxation, dehydrogenation, and crystallization have been studied by calorimetry and evolved gas analysis as a complementary technique. The observed behavior has been compared to that of conventional hydrogenated amorphous Si and amorphous Si nanoparticles. In the temperature range of our experiments (650700 C), crystallization takes place at almost the same temperature in polymorphous and in amorphous Si. In contrast, dehydrogenation processes reflect the presence of different hydrogen states. The calorimetry and evolved gas analysis thermograms clearly show that polymorphous Si shares hydrogen states of both amorphous Si and Si nanoparticles. Finally, the total energy of the main SiH group present in polymorphous Si has been quantified

Holism and structural realism

We first introduce structural realism as a position in the metaphysics of science, pointing out the way in which this position replaces intrinsic properties with relations so that it amounts to a holistic in contrast to an atomistic metaphysics. We argue in favour of a moderate version of structural realism that puts objects and relations on the same ontological footing and assess the general philosophical arguments for this position. The second section shows how structural realism gains support from quantum physics. The third section explains how structural realism can be applied to the metaphysics of space-time.

Hydro-Surface Preparation and Coating for Painted Structural Steel, TR-407, 1999

Cities and counties in Iowa have more than 8,890 steel bridges, most of which are painted with red lead paint. The Iowa Department of Transportation (Iowa DOT) maintains less than 35 bridges coated with red lead paint, including seven of the large border bridges over the Mississippi and Missouri Rivers. Because of the federal and state regulations for bridge painting, many governmental agencies have opted not to repaint, or otherwise maintain, lead paint coatings. Consequently, the paint condition on many of these bridges is poor, and some bridges are experiencing severe rusting of structural members. This research project was developed with two objectives: 1) to evaluate the effectiveness of preparing the structural steel surface of a bridge with high pressure water jetting instead of abrasive blasting and 2) to coat the structural steel surface with a moisture-cured polyurethane paint under different surface preparation conditions.

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.

Studies of the structural basis of protein thermostability have produced a confusing picture. Small sets of proteins have been analyzed from a variety of thermophilic species, suggesting different structural features as responsible for protein thermostability. Taking advantage of the recent advances in structural genomics, we have compiled a relatively large protein structure dataset, which was constructed very carefully and selectively; that is, the dataset contains only experimentally determined structures of proteins from one specific organism, the hyperthermophilic bacterium Thermotoga maritima, and those of close homologs from mesophilic bacteria. In contrast to the conclusions of previous studies, our analyses show that oligomerization order, hydrogen bonds, and secondary structure play minor roles in adaptation to hyperthermophily in bacteria. On the other hand, the data exhibit very significant increases in the density of salt-bridges and in compactness for proteins from T.maritima. The latter effect can be measured by contact order or solvent accessibility, and network analysis shows a specific increase in highly connected residues in this thermophile. These features account for changes in 96% of the protein pairs studied. Our results provide a clear picture of protein thermostability in one species, and a framework for future studies of thermal adaptation.

Development of LRFD Procedures for Bridge Pile Foundations in Iowa, Volume I: An Electronic Database for PIle LOad Tests (PILOT), TR-573, 2011

For well over 100 years, the Working Stress Design (WSD) approach has been the traditional basis for geotechnical design with regard to settlements or failure conditions. However, considerable effort has been put forth over the past couple of decades in relation to the adoption of the Load and Resistance Factor Design (LRFD) approach into geotechnical design. With the goal of producing engineered designs with consistent levels of reliability, the Federal Highway Administration (FHWA) issued a policy memorandum on June 28, 2000, requiring all new bridges initiated after October 1, 2007, to be designed according to the LRFD approach. Likewise, regionally calibrated LRFD resistance factors were permitted by the American Association of State Highway and Transportation Officials (AASHTO) to improve the economy of bridge foundation elements. Thus, projects TR-573, TR-583 and TR-584 were undertaken by a research team at Iowa State University’s Bridge Engineering Center with the goal of developing resistance factors for pile design using available pile static load test data. To accomplish this goal, the available data were first analyzed for reliability and then placed in a newly designed relational database management system termed PIle LOad Tests (PILOT), to which this first volume of the final report for project TR-573 is dedicated. PILOT is an amalgamated, electronic source of information consisting of both static and dynamic data for pile load tests conducted in the State of Iowa. The database, which includes historical data on pile load tests dating back to 1966, is intended for use in the establishment of LRFD resistance factors for design and construction control of driven pile foundations in Iowa. Although a considerable amount of geotechnical and pile load test data is available in literature as well as in various State Department of Transportation files, PILOT is one of the first regional databases to be exclusively used in the development of LRFD resistance factors for the design and construction control of driven pile foundations. Currently providing an electronically organized assimilation of geotechnical and pile load test data for 274 piles of various types (e.g., steel H-shaped, timber, pipe, Monotube, and concrete), PILOT (http://srg.cce.iastate.edu/lrfd/) is on par with such familiar national databases used in the calibration of LRFD resistance factors for pile foundations as the FHWA’s Deep Foundation Load Test Database. By narrowing geographical boundaries while maintaining a high number of pile load tests, PILOT exemplifies a model for effective regional LRFD calibration procedures.