Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study

PubMed Central

Chikenji, George; Fujitsuka, Yoshimi; Takada, Shoji

2006-01-01

Predicting protein tertiary structure by folding-like simulations is one of the most stringent tests of how much we understand the principle of protein folding. Currently, the most successful method for folding-based structure prediction is the fragment assembly (FA) method. Here, we address why the FA method is so successful and its lesson for the folding problem. To do so, using the FA method, we designed a structure prediction test of “chimera proteins.” In the chimera proteins, local structural preference is specific to the target sequences, whereas nonlocal interactions are only sequence-independent compaction forces. We find that these chimera proteins can find the native folds of the intact sequences with high probability indicating dominant roles of the local interactions. We further explore roles of local structural preference by exact calculation of the HP lattice model of proteins. From these results, we suggest principles of protein folding: For small proteins, compact structures that are fully compatible with local structural preference are few, one of which is the native fold. These local biases shape up the funnel-like energy landscape. PMID:16488978

Development of Lightweight, Compact, Structurally-Integrated Acoustic Liners for Broadband Low-Frequency Noise Mitigation

NASA Astrophysics Data System (ADS)

Chambers, Andrew T.

Airborne noise with a low dominant frequency content (< 500 Hz) has detrimental effects in many applications, but is as yet beyond the scope of conventional acoustic noise mitigation techniques using liners, foams or claddings owing to mass and volume considerations. Its low evanescence contributes significantly to environmental noise pollution, and unwanted structural vibrations causing diminished efficiency, comfort, payload integrity and mission capabilities. An alternative approach using liner configurations with realistic mass and volume constraints having innovative 'folded' core geometries is investigated to ascertain its low-frequency noise absorption characteristics. In contrast to mass-driven approaches, the folded core approach relies on tailoring interactions between acoustic resonances to tune the liner's impedance to suit the dominant low-frequency content of the source. This allows to keep non-structural mass-addition to a minimum, while retaining an overall thickness comparable to conventional liners for these low-frequency liner designs. The relative acoustic performance of various candidate folded core designs is evaluated by means of a new composite metric termed the Low-Frequency Performance (LFP) factor, which is educed from the absorption coefficient spectrum obtained using Zwikker-Kosten Transmission Line (ZKTL) theory-based numerical studies. An LFP-based software tool is developed to determine optimal 3D cavity packing for a prescribed liner volume and target frequency range. ZKTL-based parametric studies on core dimensions and face sheet porosity are utilized for detailed design of test articles. Experimental verification of absorption coefficient spectra conducted using 3D printed test articles in a normal incidence acoustic impedance tube yield good correlation with simulations. More than 100 Hz of continuous bandwidth with an absorption coefficient greater than 0.6 is shown to be possible in the 300 to 400 Hz range with a 38.1-mm (1.5-inch) thick liner. Further, the influence of face sheet type, Mach number, and sound pressure level on the attenuation across folded core liners is evaluated using grazing flow impedance tube tests. Up to 20 dB of attenuation is observed in the targeted frequency range in these tests indicating potential for performance retention in an operational scenario. With current additive and hybrid manufacturing techniques attaining critical commercial maturity, lightweight and compact acoustic liners employing folded cores could provide a promising practical solution to mitigate low-frequency airborne noise, especially in aerospace applications.

Hydrophobic folding units derived from dissimilar monomer structures and their interactions.

PubMed

Tsai, C J; Nussinov, R

1997-01-01

We have designed an automated procedure to cut a protein into compact hydrophobic folding units. The hydrophobic units are large enough to contain tertiary non-local interactions, reflecting potential nucleation sites during protein folding. The quality of a hydrophobic folding unit is evaluated by four criteria. The first two correspond to visual characterization of a structural domain, namely, compactness and extent of isolation. We use the definition of Zehfus and Rose (Zehfus MH, Rose GD, 1986, Biochemistry 25:35-340) to calculate the compactness of a cut protein unit. The isolation of a unit is based on the solvent accessible surface area (ASA) originally buried in the interior and exposed to the solvent after cutting. The third quantity is the hydrophobicity, equivalent to the fraction of the buried non-polar ASA with respect to the total non-polar ASA. The last criterion in the evaluation of a folding unit is the number of segments it includes. To conform with the rationale of obtaining hydrophobic units, which may relate to early folding events, the hydrophobic interactions are implicitly and explicitly applied in their generation and assessment. We follow Holm and Sander (Holm L, Sander C, 1994, Proteins 19:256-268) to reduce the multiple cutting-point problem to a one-dimensional search for all reasonable trial cuts. However, as here we focus on the hydrophobic cores, the contact matrix used to obtain the first non-trivial eigenvector contains only hydrophobic contracts, rather than all, hydrophobic and hydrophilic, interactions. This dataset of hydrophobic folding units, derived from structurally dissimilar single chain monomers, is particularly useful for investigations of the mechanism of protein folding. For cases where there are kinetic data, the one or more hydrophobic folding units generated for a protein correlate with the two or with the three-state folding process observed. We carry out extensive amino acid sequence order independent structural comparisons to generate a structurally non-redundant set of hydrophobic folding units for fold recognition and for statistical purposes.

Syntectonic fluid flux during rift faulting: Record from the MIS core, Victoria Land Basin, Antarctica

NASA Astrophysics Data System (ADS)

Millan, C.; Wilson, T. J.; Paulsen, T. S.

2009-12-01

The McMurdo Ice Shelf project successfully recovered 1285 m of Neogene sedimentary core from the Victoria Land Basin, a large rift basin within the West Antarctic Rift System (WARS) of Antarctica. The core contains 1475 natural fractures that were logged as faults, veins and clastic dikes, associated with the southern extension of the Neogene-active? Terror Rift fault zone. Veins constitute about 625 of this population. Most veins are filled with calcite, although zeolites and minor chlorite are common towards the bottom of the core. In the lower ~300 m of the core, veins contain opening-mode fiber fills and are wavy to tightly folded due to vertical shortening. Folded, opening-mode folded veins are filled by calcite fibers that grew normal to vein walls, indicating the host sediment was cohesive enough to fracture but was not fully lithified and accommodated vein buckling during compaction. Fold hinges are fractured and wedging of vein segments is marked by overlapping tips separated by zones with strong chlorite and clay fabrics, suggesting shearing during further vertical contraction of the host rock. Calcite veins are commonly strongly twinned. Cathodoluminescence microscopy shows minor changes in color and intensity and minimal concentric or sectoral zoning, suggesting relatively rapid crystallization of fluids of similar chemistry. However, stable isotope analyses reveal large variations in values, with carbon values ranging from -21.91 to -7.15 (VPBD) and oxygen values ranging from -5.35 to -11.97 (VPBD). Further detailed investigation of the fracture fills using cathodoluminescence and electron microscopy combined with isotopic analysis of carbon and oxygen will document the generations of the filling material in more detail and will constrain the sources and evolution of the fluids. There has clearly been significant structural control on fluid pathways during lithification, compaction and diagenesis of strata deforming within the Terror Rift zone.

Aromatic residues engineered into the beta-turn nucleation site of ubiquitin lead to a complex folding landscape, non-native side-chain interactions, and kinetic traps.

PubMed

Rea, Anita M; Simpson, Emma R; Meldrum, Jill K; Williams, Huw E L; Searle, Mark S

2008-12-02

The fast folding of small proteins is likely to be the product of evolutionary pressures that balance the search for native-like contacts in the transition state with the minimum number of stable non-native interactions that could lead to partially folded states prone to aggregation and amyloid formation. We have investigated the effects of non-native interactions on the folding landscape of yeast ubiquitin by introducing aromatic substitutions into the beta-turn region of the N-terminal beta-hairpin, using both the native G-bulged type I turn sequence (TXTGK) as well as an engineered 2:2 XNGK type I' turn sequence. The N-terminal beta-hairpin is a recognized folding nucleation site in ubiquitin. The folding kinetics for wt-Ub (TLTGK) and the type I' turn mutant (TNGK) reveal only a weakly populated intermediate, however, substitution with X = Phe or Trp in either context results in a high propensity to form a stable compact intermediate where the initial U-->I collapse is visible as a distinct kinetic phase. The introduction of Trp into either of the two host turn sequences results in either complex multiphase kinetics with the possibility of parallel folding pathways, or formation of a highly compact I-state stabilized by non-native interactions that must unfold before refolding. Sequence substitutions with aromatic residues within a localized beta-turn capable of forming non-native hydrophobic contacts in both the native state and partially folded states has the undesirable consequence that folding is frustrated by the formation of stable compact intermediates that evolutionary pressures at the sequence level may have largely eliminated.

On the polymer physics origins of protein folding thermodynamics.

PubMed

Taylor, Mark P; Paul, Wolfgang; Binder, Kurt

2016-11-07

A remarkable feature of the spontaneous folding of many small proteins is the striking similarity in the thermodynamics of the folding process. This process is characterized by simple two-state thermodynamics with large and compensating changes in entropy and enthalpy and a funnel-like free energy landscape with a free-energy barrier that varies linearly with temperature. One might attribute the commonality of this two-state folding behavior to features particular to these proteins (e.g., chain length, hydrophobic/hydrophilic balance, attributes of the native state) or one might suspect that this similarity in behavior has a more general polymer-physics origin. Here we show that this behavior is also typical for flexible homopolymer chains with sufficiently short range interactions. Two-state behavior arises from the presence of a low entropy ground (folded) state separated from a set of high entropy disordered (unfolded) states by a free energy barrier. This homopolymer model exhibits a funneled free energy landscape that reveals a complex underlying dynamics involving competition between folding and non-folding pathways. Despite the presence of multiple pathways, this simple physics model gives the robust result of two-state thermodynamics for both the cases of folding from a basin of expanded coil states and from a basin of compact globule states.

On the polymer physics origins of protein folding thermodynamics

NASA Astrophysics Data System (ADS)

Taylor, Mark P.; Paul, Wolfgang; Binder, Kurt

2016-11-01

A remarkable feature of the spontaneous folding of many small proteins is the striking similarity in the thermodynamics of the folding process. This process is characterized by simple two-state thermodynamics with large and compensating changes in entropy and enthalpy and a funnel-like free energy landscape with a free-energy barrier that varies linearly with temperature. One might attribute the commonality of this two-state folding behavior to features particular to these proteins (e.g., chain length, hydrophobic/hydrophilic balance, attributes of the native state) or one might suspect that this similarity in behavior has a more general polymer-physics origin. Here we show that this behavior is also typical for flexible homopolymer chains with sufficiently short range interactions. Two-state behavior arises from the presence of a low entropy ground (folded) state separated from a set of high entropy disordered (unfolded) states by a free energy barrier. This homopolymer model exhibits a funneled free energy landscape that reveals a complex underlying dynamics involving competition between folding and non-folding pathways. Despite the presence of multiple pathways, this simple physics model gives the robust result of two-state thermodynamics for both the cases of folding from a basin of expanded coil states and from a basin of compact globule states.

Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops

PubMed Central

Paslawski, Wojciech; Lillelund, Ove K.; Kristensen, Julie Veje; Schafer, Nicholas P.; Baker, Rosanna P.; Urban, Sinisa; Otzen, Daniel E.

2015-01-01

Despite the ubiquity of helical membrane proteins in nature and their pharmacological importance, the mechanisms guiding their folding remain unclear. We performed kinetic folding and unfolding experiments on 69 mutants (engineered every 2–3 residues throughout the 178-residue transmembrane domain) of GlpG, a membrane-embedded rhomboid protease from Escherichia coli. The only clustering of significantly positive ϕ-values occurs at the cytosolic termini of transmembrane helices 1 and 2, which we identify as a compact nucleus. The three loops flanking these helices show a preponderance of negative ϕ-values, which are sometimes taken to be indicative of nonnative interactions in the transition state. Mutations in transmembrane helices 3–6 yielded predominantly ϕ-values near zero, indicating that this part of the protein has denatured-state–level structure in the transition state. We propose that loops 1–3 undergo conformational rearrangements to position the folding nucleus correctly, which then drives folding of the rest of the domain. A compact N-terminal nucleus is consistent with the vectorial nature of cotranslational membrane insertion found in vivo. The origin of the interactions in the transition state that lead to a large number of negative ϕ-values remains to be elucidated. PMID:26056273

Compactness of viral genomes: effect of disperse and localized random mutations

NASA Astrophysics Data System (ADS)

Lošdorfer Božič, Anže; Micheletti, Cristian; Podgornik, Rudolf; Tubiana, Luca

2018-02-01

Genomes of single-stranded RNA viruses have evolved to optimize several concurrent properties. One of them is the architecture of their genomic folds, which must not only feature precise structural elements at specific positions, but also allow for overall spatial compactness. The latter was shown to be disrupted by random synonymous mutations, a disruption which can consequently negatively affect genome encapsidation. In this study, we use three mutation schemes with different degrees of locality to mutate the genomes of phage MS2 and Brome Mosaic virus in order to understand the observed sensitivity of the global compactness of their folds. We find that mutating local stretches of their genomes’ sequence or structure is less disruptive to their compactness compared to inducing randomly-distributed mutations. Our findings are indicative of a mechanism for the conservation of compactness acting on a global scale of the genomes, and have several implications for understanding the interplay between local and global architecture of viral RNA genomes.

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy

PubMed Central

Soranno, Andrea; Buchli, Brigitte; Nettels, Daniel; Cheng, Ryan R.; Müller-Späth, Sonja; Pfeil, Shawn H.; Hoffmann, Armin; Lipman, Everett A.; Makarov, Dmitrii E.; Schuler, Benjamin

2012-01-01

Internal friction, which reflects the “roughness” of the energy landscape, plays an important role for proteins by modulating the dynamics of their folding and other conformational changes. However, the experimental quantification of internal friction and its contribution to folding dynamics has remained challenging. Here we use the combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and microfluidic mixing to determine the reconfiguration times of unfolded proteins and investigate the mechanisms of internal friction contributing to their dynamics. Using concepts from polymer dynamics, we determine internal friction with three complementary, largely independent, and consistent approaches as an additive contribution to the reconfiguration time of the unfolded state. We find that the magnitude of internal friction correlates with the compactness of the unfolded protein: its contribution dominates the reconfiguration time of approximately 100 ns of the compact unfolded state of a small cold shock protein under native conditions, but decreases for more expanded chains, and approaches zero both at high denaturant concentrations and in intrinsically disordered proteins that are expanded due to intramolecular charge repulsion. Our results suggest that internal friction in the unfolded state will be particularly relevant for the kinetics of proteins that fold in the microsecond range or faster. The low internal friction in expanded intrinsically disordered proteins may have implications for the dynamics of their interactions with cellular binding partners. PMID:22492978

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy.

PubMed

Soranno, Andrea; Buchli, Brigitte; Nettels, Daniel; Cheng, Ryan R; Müller-Späth, Sonja; Pfeil, Shawn H; Hoffmann, Armin; Lipman, Everett A; Makarov, Dmitrii E; Schuler, Benjamin

2012-10-30

Internal friction, which reflects the "roughness" of the energy landscape, plays an important role for proteins by modulating the dynamics of their folding and other conformational changes. However, the experimental quantification of internal friction and its contribution to folding dynamics has remained challenging. Here we use the combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and microfluidic mixing to determine the reconfiguration times of unfolded proteins and investigate the mechanisms of internal friction contributing to their dynamics. Using concepts from polymer dynamics, we determine internal friction with three complementary, largely independent, and consistent approaches as an additive contribution to the reconfiguration time of the unfolded state. We find that the magnitude of internal friction correlates with the compactness of the unfolded protein: its contribution dominates the reconfiguration time of approximately 100 ns of the compact unfolded state of a small cold shock protein under native conditions, but decreases for more expanded chains, and approaches zero both at high denaturant concentrations and in intrinsically disordered proteins that are expanded due to intramolecular charge repulsion. Our results suggest that internal friction in the unfolded state will be particularly relevant for the kinetics of proteins that fold in the microsecond range or faster. The low internal friction in expanded intrinsically disordered proteins may have implications for the dynamics of their interactions with cellular binding partners.

Folding of human telomerase RNA pseudoknot using ion-jump and temperature-quench simulations.

PubMed

Biyun, Shi; Cho, Samuel S; Thirumalai, D

2011-12-21

Globally RNA folding occurs in multiple stages involving chain compaction and subsequent rearrangement by a number of parallel routes to the folded state. However, the sequence-dependent details of the folding pathways and the link between collapse and folding are poorly understood. To obtain a comprehensive picture of the thermodynamics and folding kinetics we used molecular simulations of coarse-grained model of a pseudoknot found in the conserved core domain of the human telomerase (hTR) by varying both temperature (T) and ion concentration (C). The phase diagram in the [T,C] plane shows that the boundary separating the folded and unfolded state for the finite 47-nucleotide system is relatively sharp, implying that from a thermodynamic perspective hTR behaves as an apparent two-state system. However, the folding kinetics following single C-jump or T-quench is complicated, involving multiple channels to the native state. Although globally folding kinetics triggered by T-quench and C-jump are similar, the kinetics of chain compaction are vastly different, which reflects the role of initial conditions in directing folding and collapse. Remarkably, even after substantial reduction in the overall size of hTR, the ensemble of compact conformations are far from being nativelike, suggesting that the search for the folded state occurs among the ensemble of low-energy fluidlike globules. The rate of unfolding, which occurs in a single step, is faster upon C-decrease compared to a jump in temperature. To identify "hidden" states that are visited during the folding process we performed simulations by periodically interrupting the approach to the folded state by lowering C. These simulations show that hTR reaches the folded state through a small number of connected clusters that are repeatedly visited during the pulse sequence in which the folding or unfolding is interrupted. The results from interrupted folding simulations, which are in accord with non-equilibrium single-molecule folding of a large ribozyme, show that multiple probes are needed to reveal the invisible states that are sampled by RNA as it folds. Although we have illustrated the complexity of RNA folding using hTR as a case study, general arguments and qualitative comparisons to time-resolved scattering experiments on Azoarcus group I ribozyme and single-molecule non-equilibrium periodic ion-jump experiments establish the generality of our findings. © 2011 American Chemical Society

Two-step crystal growth mechanism during crystallization of an undercooled Ni50Al50 alloy

NASA Astrophysics Data System (ADS)

An, Simin; Li, Jiahao; Li, Yang; Li, Shunning; Wang, Qi; Liu, Baixin

2016-08-01

Crystallization processes are always accompanied by the emergence of multiple intermediate states, of which the structures and transition dynamics are far from clarity, since it is difficult to experimentally observe the microscopic pathway. To insight the structural evolution and the crystallization dynamics, we perform large-scale molecular dynamics simulations to investigate the time-dependent crystallization behavior of the NiAl intermetallic upon rapid solidification. The simulation results reveal that the crystallization process occurs via a two-step growth mechanism, involving the formation of initial non-equilibrium long range order (NLRO) regions and of the subsequent equilibrium long range order (ELRO) regions. The formation of the NLRO regions makes the grains rather inhomogeneous, while the rearrangement of the NLRO regions into the ELRO regions makes the grains more ordered and compact. This two-step growth mechanism is actually controlled by the evolution of the coordination polyhedra, which are characterized predominantly by the transformation from five-fold symmetry to four-fold and six-fold symmetry. From liquids to NLRO and further to ELRO, the five-fold symmetry of these polyhedra gradually fades, and finally vanishes when B2 structure is distributed throughout the grain bulk. The energy decrease along the pathway further implies the reliability of the proposed crystallization processes.

The folding pathways and thermodynamics of semiflexible polymers

NASA Astrophysics Data System (ADS)

Wu, Jing; Cheng, Chenqian; Liu, Gaoyuan; Zhang, Ping; Chen, Tao

2018-05-01

Inspired by the protein folding and DNA packing, we have systematically studied the thermodynamic and kinetic behaviors of single semiflexible homopolymers by Langevin dynamics simulations. In line with experiments, a rich variety of folding products, such as rod-like bundles, hairpins, toroids, and a mixture of them, are observed in the complete diagram of states. Moreover, knotted structures with a significant population are found in a certain range of bending stiffness in thermal equilibrium. As the solvent quality becomes poorer, the population of the intermediate occurring in the folding process increases, which leads to a severe chevron rollover for the folding arm. However, the population of the intermediates in the unfolding process is very low, insufficient to induce unfolding arm rollover. The total types of folding pathways from the coil state to the toroidal state for a semiflexible polymer chain remain unchanged by varying the solvent quality or temperature, whereas the kinetic partitioning into different folding events can be tuned significantly. In the process of knotting, three types of mechanisms, namely, plugging, slipknotting, and sliding, are discovered. Along the folding evolution, a semiflexible homopolymer chain can knot at any stage of folding upon leaving the extended coil state, and the probability to find a knot increases with chain compactness. In addition, we find rich types of knotted topologies during the folding of a semiflexible homopolymer chain. This study should be helpful in gaining insight into the general principles of biopolymer folding.

Sequence Determinants of Compaction in Intrinsically Disordered Proteins

PubMed Central

Marsh, Joseph A.; Forman-Kay, Julie D.

2010-01-01

Abstract Intrinsically disordered proteins (IDPs), which lack folded structure and are disordered under nondenaturing conditions, have been shown to perform important functions in a large number of cellular processes. These proteins have interesting structural properties that deviate from the random-coil-like behavior exhibited by chemically denatured proteins. In particular, IDPs are often observed to exhibit significant compaction. In this study, we have analyzed the hydrodynamic radii of a number of IDPs to investigate the sequence determinants of this compaction. Net charge and proline content are observed to be strongly correlated with increased hydrodynamic radii, suggesting that these are the dominant contributors to compaction. Hydrophobicity and secondary structure, on the other hand, appear to have negligible effects on compaction, which implies that the determinants of structure in folded and intrinsically disordered proteins are profoundly different. Finally, we observe that polyhistidine tags seem to increase IDP compaction, which suggests that these tags have significant perturbing effects and thus should be removed before any structural characterizations of IDPs. Using the relationships observed in this analysis, we have developed a sequence-based predictor of hydrodynamic radius for IDPs that shows substantial improvement over a simple model based upon chain length alone. PMID:20483348

A new class of compact high sensitive tiltmeter based on the UNISA folded pendulum mechanical architecture

NASA Astrophysics Data System (ADS)

Barone, Fabrizio; Giordano, Gerardo

2018-02-01

We present the Extended Folded Pendulum Model (EFPM), a model developed for a quantitative description of the dynamical behavior of a folded pendulum generically oriented in space. This model, based on the Tait-Bryan angular reference system, highlights the relationship between the folded pendulum orientation in the gravitational field and its natural resonance frequency. Tis model validated by tests performed with a monolithic UNISA Folded Pendulum, highlights a new technique of implementation of folded pendulum based tiltmeters.

The role of protein homochirality in shaping the energy landscape of folding

PubMed Central

Nanda, Vikas; Andrianarijaona, Aina; Narayanan, Chitra

2007-01-01

The homochirality, or isotacticity, of the natural amino acids facilitates the formation of regular secondary structures such as α-helices and β-sheets. However, many examples exist in nature where novel polypeptide topologies use both l- and d-amino acids. In this study, we explore how stereochemistry of the polypeptide backbone influences basic properties such as compactness and the size of fold space by simulating both lattice and all-atom polypeptide chains. We formulate a rectangular lattice chain model in both two and three dimensions, where monomers are chiral, having the effect of restricting local conformation. Syndiotactic chains with alternating chirality of adjacent monomers have a very large ensemble of accessible conformations characterized predominantly by extended structures. Isotactic chains on the other hand, have far fewer possible conformations and a significant fraction of these are compact. Syndiotactic chains are often unable to access maximally compact states available to their isotactic counterparts of the same length. Similar features are observed in all-atom models of isotactic versus syndiotactic polyalanine. Our results suggest that protein isotacticity has evolved to increase the enthalpy of chain collapse by facilitating compact helical states and to reduce the entropic cost of folding by restricting the size of the unfolded ensemble of competing states. PMID:17600146

A compact Acousto-Optic Lens for 2D and 3D femtosecond based 2-photon microscopy.

PubMed

Kirkby, Paul A; Srinivas Nadella, K M Naga; Silver, R Angus

2010-06-21

We describe a high speed 3D Acousto-Optic Lens Microscope (AOLM) for femtosecond 2-photon imaging. By optimizing the design of the 4 AO Deflectors (AODs) and by deriving new control algorithms, we have developed a compact spherical AOL with a low temporal dispersion that enables 2-photon imaging at 10-fold lower power than previously reported. We show that the AOLM can perform high speed 2D raster-scan imaging (>150 Hz) without scan rate dependent astigmatism. It can deflect and focus a laser beam in a 3D random access sequence at 30 kHz and has an extended focusing range (>137 mum; 40X 0.8NA objective). These features are likely to make the AOLM a useful tool for studying fast physiological processes distributed in 3D space.

Exploring the Universe of Protein Structures beyond the Protein Data Bank

PubMed Central

Cossio, Pilar; Trovato, Antonio; Pietrucci, Fabio; Seno, Flavio; Maritan, Amos; Laio, Alessandro

2010-01-01

It is currently believed that the atlas of existing protein structures is faithfully represented in the Protein Data Bank. However, whether this atlas covers the full universe of all possible protein structures is still a highly debated issue. By using a sophisticated numerical approach, we performed an exhaustive exploration of the conformational space of a 60 amino acid polypeptide chain described with an accurate all-atom interaction potential. We generated a database of around 30,000 compact folds with at least of secondary structure corresponding to local minima of the potential energy. This ensemble plausibly represents the universe of protein folds of similar length; indeed, all the known folds are represented in the set with good accuracy. However, we discover that the known folds form a rather small subset, which cannot be reproduced by choosing random structures in the database. Rather, natural and possible folds differ by the contact order, on average significantly smaller in the former. This suggests the presence of an evolutionary bias, possibly related to kinetic accessibility, towards structures with shorter loops between contacting residues. Beside their conceptual relevance, the new structures open a range of practical applications such as the development of accurate structure prediction strategies, the optimization of force fields, and the identification and design of novel folds. PMID:21079678

How interfaces affect hydrophobically driven polymer folding.

PubMed

Jamadagni, Sumanth N; Godawat, Rahul; Dordick, Jonathan S; Garde, Shekhar

2009-04-02

Studies of folding-unfolding of hydrophobic polymers in water provide an excellent starting point to probe manybody hydrophobic interactions in the context of realistic self-assembly processes. Such studies in bulk water have highlighted the similarities between thermodynamics of polymer collapse and of protein folding, and emphasized the role of hydration-water structure, density, and fluctuations-in the folding kinetics. Hydrophobic polymers are interfacially active-that is, they prefer locations at aqueous interfaces relative to bulk water-consistent with their low solubility. How does the presence of a hydrophobic solid surface or an essentially hydrophobic vapor-water interface affect the structural, thermodynamic, and kinetic aspects of polymer folding? Using extensive molecular dynamics simulations, we show that the large hydrophobic driving force for polymer collapse in bulk water is reduced at a solid alkane-water interface and further reduced at a vapor-water interface. As a result, at the solid-water interface, folded structures are marginally stable, whereas the vapor-liquid interface unfolds polymers completely. Structural sampling is also significantly affected by the interface. For example, at the solid-water interface, polymer conformations are quasi-2- dimensional, with folded states being pancake-like structures. At the vapor-water interface, the hydrophobic polymer is significantly excluded from the water phase and freely samples a broad range of compact to extended structures. Interestingly, although the driving force for folding is considerably lower, kinetics of folding are faster at both interfaces, highlighting the role of enhanced water fluctuations and dynamics at a hydrophobic interface.

The role of atomic level steric effects and attractive forces in protein folding.

PubMed

Lammert, Heiko; Wolynes, Peter G; Onuchic, José N

2012-02-01

Protein folding into tertiary structures is controlled by an interplay of attractive contact interactions and steric effects. We investigate the balance between these contributions using structure-based models using an all-atom representation of the structure combined with a coarse-grained contact potential. Tertiary contact interactions between atoms are collected into a single broad attractive well between the C(β) atoms between each residue pair in a native contact. Through the width of these contact potentials we control their tolerance for deviations from the ideal structure and the spatial range of attractive interactions. In the compact native state dominant packing constraints limit the effects of a coarse-grained contact potential. During folding, however, the broad attractive potentials allow an early collapse that starts before the native local structure is completely adopted. As a consequence the folding transition is broadened and the free energy barrier is decreased. Eventually two-state folding behavior is lost completely for systems with very broad attractive potentials. The stabilization of native-like residue interactions in non-perfect geometries early in the folding process frequently leads to structural traps. Global mirror images are a notable example. These traps are penalized by the details of the repulsive interactions only after further collapse. Successful folding to the native state requires simultaneous guidance from both attractive and repulsive interactions. Copyright © 2011 Wiley Periodicals, Inc.

Statistical thermodynamics of protein folding: Comparison of a mean-field theory with Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Hao, Ming-Hong; Scheraga, Harold A.

1995-01-01

A comparative study of protein folding with an analytical theory and computer simulations, respectively, is reported. The theory is based on an improved mean-field formalism which, in addition to the usual mean-field approximations, takes into account the distributions of energies in the subsets of conformational states. Sequence-specific properties of proteins are parametrized in the theory by two sets of variables, one for the energetics of mean-field interactions and one for the distribution of energies. Simulations are carried out on model polypeptides with different sequences, with different chain lengths, and with different interaction potentials, ranging from strong biases towards certain local chain states (bond angles and torsional angles) to complete absence of local conformational preferences. Theoretical analysis of the simulation results for the model polypeptides reveals three different types of behavior in the folding transition from the statistical coiled state to the compact globular state; these include a cooperative two-state transition, a continuous folding, and a glasslike transition. It is found that, with the fitted theoretical parameters which are specific for each polypeptide under a different potential, the mean-field theory can describe the thermodynamic properties and folding behavior of the different polypeptides accurately. By comparing the theoretical descriptions with simulation results, we verify the basic assumptions of the theory and, thereby, obtain new insights about the folding transitions of proteins. It is found that the cooperativity of the first-order folding transition of the model polypeptides is determined mainly by long-range interactions, in particular the dipolar orientation; the local interactions (e.g., bond-angle and torsion-angle potentials) have only marginal effect on the cooperative characteristic of the folding, but have a large impact on the difference in energy between the folded lowest-energy structure and the unfolded conformations of a protein.

Accommodating Thickness in Origami-Based Deployable Arrays

NASA Technical Reports Server (NTRS)

Zirbel, Shannon A.; Magleby, Spencer P.; Howell, Larry L.; Lang, Robert J.; Thomson, Mark W.; Sigel, Deborah A.; Walkemeyer, Phillip E.; Trease, Brian P.

2013-01-01

The purpose of this work is to create deployment systems with a large ratio of stowed-to-deployed diameter. Deployment from a compact form to a final flat state can be achieved through origami-inspired folding of panels. There are many models capable of this motion when folded in a material with negligible thickness; however, when the application requires the folding of thick, rigid panels, attention must be paid to the effect of material thickness not only on the final folded state, but also during the folding motion (i.e., the panels must not be required to flex to attain the final folded form). The objective is to develop new methods for deployment from a compact folded form to a large circular array (or other final form). This paper describes a mathematical model for modifying the pattern to accommodate material thickness in the context of the design, modeling, and testing of a deployable system inspired by an origami six-sided flasher model. The model is demonstrated in hardware as a 1/20th scale prototype of a deployable solar array for space applications. The resulting prototype has a ratio of stowed-to-deployed diameter of 9.2 (or 1.25 m deployed outer diameter to 0.136 m stowed outer diameter).

Compaction history of Upper Cretaceous shale (Al-Khod Formation) and its relationship to plate margin tectonics, Arabian Plate, Sultanate of Oman

NASA Astrophysics Data System (ADS)

AL-Sarmi, Musaab; Mattern, Frank; Scharf, Andreas; Pracejus, Bernhard; Al-Mamari, Amira; Al-Hinaai, Al-Shima

2017-04-01

Conglomerates of the late Cretaceous Al-Khod Formation have been intruded by older shale of the same formation along faults, which were opened/widened by extension, thus, resulting in shale dike formation. Following intrusion the shale was behaving plastically as its fissility follows the contact contours of the conglomeratic host rock and as stoped sandstone blocks are floating within the shale. Vertical calcite veins were ptygmatically folded with subhorizontal fold axial planes. All these aspects show that the shale contained a high water content in the beginning. The ptygmatically folded calcite veins display vertical shortening amounts of 40 % corresponding to 35 % to 45 % of water loss during compaction. Incalculable numbers of calcite veins of different orientations and thicknesses within the conglomerate along the shale contact indicate that the fluid was expelled from the shale into the conglomerate host rock under high pressure (overpressure?). Shale dyke formation took place after the late Cretaceous obduction of the Semail Ophiolite, before the deposition of early Tertiary carbonate rocks, and during the latest Cretaceous doming of the Saih Hatat area which was caused by deformation and slab breakoff, likely associated with gravitational collapse and elastic rebound. Shale intrusion was followed by deposition of 100 to 200 m thick sediments of the upper part of Al-Khod Formation, leading to compaction and water loss. The shale retained much of its water during the uppermost Cretaceous-late Paleocene stratigraphic hiatus as this interval is marked by erosion and a reduction of overburden, which was probably due to the elastic rebound. Folding of calcite veins together with a high amount of water loss was a consequence of compaction caused by the overburden of 1000 m thick shallow marine limestones which were deposited from the Eocene to Oligocene.

A compact acousto-optic lens for 2D and 3D femtosecond based 2-photon microscopy

PubMed Central

Kirkby, Paul A.; Naga Srinivas, N.K.M.; Silver, R. Angus

2010-01-01

We describe a high speed 3D Acousto-Optic Lens Microscope (AOLM) for femtosecond 2-photon imaging. By optimizing the design of the 4 AO Deflectors (AODs) and by deriving new control algorithms, we have developed a compact spherical AOL with a low temporal dispersion that enables 2-photon imaging at 10-fold lower power than previously reported. We show that the AOLM can perform high speed 2D raster-scan imaging (>150 Hz) without scan rate dependent astigmatism. It can deflect and focus a laser beam in a 3D random access sequence at 30 kHz and has an extended focusing range (>137 μm; 40X 0.8NA objective). These features are likely to make the AOLM a useful tool for studying fast physiological processes distributed in 3D space PMID:20588506

Foldability of a Natural De Novo Evolved Protein.

PubMed

Bungard, Dixie; Copple, Jacob S; Yan, Jing; Chhun, Jimmy J; Kumirov, Vlad K; Foy, Scott G; Masel, Joanna; Wysocki, Vicki H; Cordes, Matthew H J

2017-11-07

The de novo evolution of protein-coding genes from noncoding DNA is emerging as a source of molecular innovation in biology. Studies of random sequence libraries, however, suggest that young de novo proteins will not fold into compact, specific structures typical of native globular proteins. Here we show that Bsc4, a functional, natural de novo protein encoded by a gene that evolved recently from noncoding DNA in the yeast S. cerevisiae, folds to a partially specific three-dimensional structure. Bsc4 forms soluble, compact oligomers with high β sheet content and a hydrophobic core, and undergoes cooperative, reversible denaturation. Bsc4 lacks a specific quaternary state, however, existing instead as a continuous distribution of oligomer sizes, and binds dyes indicative of amyloid oligomers or molten globules. The combination of native-like and non-native-like properties suggests a rudimentary fold that could potentially act as a functional intermediate in the emergence of new folded proteins de novo. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin.

PubMed

Yang, A S; Honig, B

1994-04-15

A recently developed approach to calculate the pH dependence of protein stability from three-dimensional structure information is applied to the analysis of acid denaturation of sperm whale apomyoglobin. The finite difference Poisson-Boltzmann method is used to calculate pKa values and these are used to obtain titration curves for the folded protein as well as for compact intermediates. The total electrostatic free energy change involved in apomyoglobin unfolding is then evaluated. Calculations are carried out of the unfolding free energy of the native (N) and the compact intermediate (I) of apomyoglobin relative to the unfolded state (U) over a range of pH at various ionic strengths. The contributions from key ionizable groups to the unfolding process are discussed. For the acid-induced partial unfolding of apomyoglobin near pH 5, the transition from N to I is found to be driven by three histidines that are exposed when the B, C, D and E helices unfold. Similarly, the unfolding of the compact intermediate I consisting of the A, G and H helices is driven primarily by a few carboxylic acids with low pKa values in the compact state. This picture is in contrast to the view which attributes acid denaturation to electrostatic repulsion resulting from the build up of positive charge. In fact, charge-charge interactions in myoglobin are found to be attractive at all pH values where the protein unfolds. pH-dependent changes in these interactions contribute to acid denaturation but other electrostatic effects, such as hydrogen bonding and solvation, are important as well. The effect of increasing ionic strength on unfolding is attributed to the decrease of attractive charge-charge interactions which destabilize the N state relative to I, but stabilize the I state relative to U by reducing the pKa shifts of a few critical carboxylic acids. The I state is found to be more stable than U at neutral pH thus accounting for its presence as an intermediate on the protein folding pathway. Our results have implications for the origins of compact intermediates or "molten globule" states.

Structure, function and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding.

NASA Astrophysics Data System (ADS)

Samiotakis, Antonios; Dhar, Apratim; Ebbinghaus, Simon; Nienhaus, Lea; Homouz, Dirar; Gruebele, Martin; Cheung, Margaret

2010-10-01

We combine experiment and computer simulation to show how macromolecular crowding dramatically affects the structure, function and folding landscape of phosphoglycerate kinase (PGK). Fluorescence labeling shows that compact states of yeast PGK are populated as the amount of crowding agents (Ficoll 70) increases. Coarse-grained molecular simulations reveal three compact ensembles: C (crystal structure), CC (collapsed crystal) and Sph (spherical compact). With an adjustment for viscosity, crowded wild type PGK and fluorescent PGK are about 15 times or more active in 200 mg/ml Ficoll than in aqueous solution. Our results suggest a new solution to the classic problem of how the ADP and diphosphoglycerate binding sites of PGK come together to make ATP: rather than undergoing a hinge motion, the ADP and substrate sites are already located in proximity under crowded conditions that mimic the in vivo conditions under which the enzyme actually operates.

Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c.

PubMed

Fazelinia, Hossein; Xu, Ming; Cheng, Hong; Roder, Heinrich

2014-01-15

Many proteins undergo a sharp decrease in chain dimensions during early stages of folding, prior to the rate-limiting step in folding. However, it remains unclear whether compact states are the result of specific folding events or a general hydrophobic collapse of the poly peptide chain driven by the change in solvent conditions. To address this fundamental question, we extended the temporal resolution of NMR-detected H/D exchange labeling experiments into the microsecond regime by adopting a microfluidics approach. By observing the competition between H/D exchange and folding as a function of labeling pH, coupled with direct measurement of exchange rates in the unfolded state, we were able to monitor hydrogen-bond formation for over 50 individual backbone NH groups within the initial 140 microseconds of folding of horse cytochrome c. Clusters of solvent-shielded amide protons were observed in two α-helical segments in the C-terminal half of the protein, while the N-terminal helix remained largely unstructured, suggesting that proximity in the primary structure is a major factor in promoting helix formation and association at early stages of folding, while the entropically more costly long-range contacts between the N- and C-terminal helices are established only during later stages. Our findings clearly indicate that the initial chain condensation in cytochrome c is driven by specific interactions among a subset of α-helical segments rather than a general hydrophobic collapse.

Force-Induced Unfolding of Fibronectin in the Extracellular Matrix of Living Cells

PubMed Central

Smith, Michael L; Gourdon, Delphine; Little, William C; Kubow, Kristopher E; Eguiluz, R. Andresen; Luna-Morris, Sheila; Vogel, Viola

2007-01-01

Whether mechanically unfolded fibronectin (Fn) is present within native extracellular matrix fibrils is controversial. Fn extensibility under the influence of cell traction forces has been proposed to originate either from the force-induced lengthening of an initially compact, folded quaternary structure as is found in solution (quaternary structure model, where the dimeric arms of Fn cross each other), or from the force-induced unfolding of type III modules (unfolding model). Clarification of this issue is central to our understanding of the structural arrangement of Fn within fibrils, the mechanism of fibrillogenesis, and whether cryptic sites, which are exposed by partial protein unfolding, can be exposed by cell-derived force. In order to differentiate between these two models, two fluorescence resonance energy transfer schemes to label plasma Fn were applied, with sensitivity to either compact-to-extended conformation (arm separation) without loss of secondary structure or compact-to-unfolded conformation. Fluorescence resonance energy transfer studies revealed that a significant fraction of fibrillar Fn within a three-dimensional human fibroblast matrix is partially unfolded. Complete relaxation of Fn fibrils led to a refolding of Fn. The compactly folded quaternary structure with crossed Fn arms, however, was never detected within extracellular matrix fibrils. We conclude that the resting state of Fn fibrils does not contain Fn molecules with crossed-over arms, and that the several-fold extensibility of Fn fibrils involves the unfolding of type III modules. This could imply that Fn might play a significant role in mechanotransduction processes. PMID:17914904

The Intermodal Bike: multi-modal integration of cycling mobility through product and process innovations in bicycle design.

PubMed

Tosi, Francesca; Belli, Alessandro; Rinaldi, Alessandra; Tucci, Grazia

2012-01-01

The paper presents the early results of the UE-FP7 project "The Intermodal Bike". The research aim is to provide a super-compactable, super-lightweight folding bicycle as a realistic solution to graft the cycling mode onto the root of the public or private transportation systems. The folding bikes now on the international market reach weighs between 12-15 kg, with a variable footprint but occupying -when compacted- an average volume of about 100 liters. To encourage the use of this vehicle and to extend it to a larger number of users with different characteristics, the research project has set its goal in increasing as possible compactness and light weight, creating a bicycle with a volume when compacted of 20 liters (reduction factor =5), with a shape of 48 × 36 × 12 cm and a weight of 5 kg. max., ensuring stability and improving vehicle usability and efficiency, during the ride and in the phase of bike folding. To achieve this goal ergonomic and usability tests have been carried out. The tests allowed to find a posture that would ensure efficiency and comfort in the ride to as many users as possible. Parallel tests were made on the vehicle usability in the urban transport system and intermodal. The need for light weight has required special studies on the optimization of the vehicle's architecture and research on super-lightweight materials.

Kinetic studies of the folding of heterodimeric monellin: evidence for switching between alternative parallel pathways.

PubMed

Aghera, Nilesh; Udgaonkar, Jayant B

2012-07-13

Determining whether or not a protein uses multiple pathways to fold is an important goal in protein folding studies. When multiple pathways are present, defined by transition states that differ in their compactness and structure but not significantly in energy, they may manifest themselves by causing the dependence on denaturant concentration of the logarithm of the observed rate constant of folding to have an upward curvature. In this study, the folding mechanism of heterodimeric monellin [double-chain monellin (dcMN)] has been studied over a range of protein and guanidine hydrochloride (GdnHCl) concentrations, using the intrinsic tryptophan fluorescence of the protein as the probe for the folding reaction. Refolding is shown to occur in multiple kinetic phases. In the first stage of refolding, which is silent to any change in intrinsic fluorescence, the two chains of monellin bind to one another to form an encounter complex. Interrupted folding experiments show that the initial encounter complex folds to native dcMN via two folding routes. A productive folding intermediate population is identified on one route but not on both of these routes. Two intermediate subpopulations appear to form in a fast kinetic phase, and native dcMN forms in a slow kinetic phase. The chevron arms for both the fast and slow phases of refolding are shown to have upward curvatures, suggesting that at least two pathways each defined by a different intermediate are operational during these kinetic phases of structure formation. Refolding switches from one pathway to the other as the GdnHCl concentration is increased. Copyright © 2012 Elsevier Ltd. All rights reserved.

Multiposition Seat

NASA Technical Reports Server (NTRS)

Macconochie, Ian O.

1994-01-01

Back of seat pivots about either of two axes: one axis for folding back to form bed and second, higher axis for folding forward to form compact ottoman, even when seat thickly padded. Long and short links used to adjust back of seat to variety of positions. Multiposition seat designed for use in spacecraft also adapted to airplanes and land vehicles.

Mechanical monolithic compact sensors for real-time linear and angular broadband low frequency monitoring and control of spacecrafts and satellites

NASA Astrophysics Data System (ADS)

Barone, F.; Giordano, G.

2017-09-01

In this paper we describe the characteristics and performances of a monolithic sensor designed for low frequency motion measurement of spacecrafts and satellites, whose mechanics is based on the UNISA Folded Pendulum. The latter, developed for ground-based applications, exhibits unique features (compactness, lightness, scalability, low resonance frequency and high quality factor), consequence of the action of the gravitational force on its inertial mass. In this paper we introduce and discuss the general methodology used to extend the application of ground-based folded pendulums to space, also in total absence of gravity, still keeping all their peculiar features and characteristics.

A new broadband square law detector. [microwave radiometers

NASA Technical Reports Server (NTRS)

Reid, M. S.; Gardner, R. A.; Stelzried, C. T.

1975-01-01

A broadband constant law detector was developed for precision power measurements, radio metric measurements, and other applications. It has a wide dynamic range and an accurate square law response. Other desirable characteristics, which are all included in a single compact unit, are: (1) high-level dc output with immunity to ground loop problems; (2) fast response times; (3) ability to insert known time constants; and (4) good thermal stability. The detector and its performance are described in detail. The detector can be operated in a programmable system with a ten-fold increase in accuracy. The use and performance of the detector in a noise-adding radiometer system is also discussed.

Cytology of DNA Replication Reveals Dynamic Plasticity of Large-Scale Chromatin Fibers.

PubMed

Deng, Xiang; Zhironkina, Oxana A; Cherepanynets, Varvara D; Strelkova, Olga S; Kireev, Igor I; Belmont, Andrew S

2016-09-26

In higher eukaryotic interphase nuclei, the 100- to >1,000-fold linear compaction of chromatin is difficult to reconcile with its function as a template for transcription, replication, and repair. It is challenging to imagine how DNA and RNA polymerases with their associated molecular machinery would move along the DNA template without transient decondensation of observed large-scale chromatin "chromonema" fibers [1]. Transcription or "replication factory" models [2], in which polymerases remain fixed while DNA is reeled through, are similarly difficult to conceptualize without transient decondensation of these chromonema fibers. Here, we show how a dynamic plasticity of chromatin folding within large-scale chromatin fibers allows DNA replication to take place without significant changes in the global large-scale chromatin compaction or shape of these large-scale chromatin fibers. Time-lapse imaging of lac-operator-tagged chromosome regions shows no major change in the overall compaction of these chromosome regions during their DNA replication. Improved pulse-chase labeling of endogenous interphase chromosomes yields a model in which the global compaction and shape of large-Mbp chromatin domains remains largely invariant during DNA replication, with DNA within these domains undergoing significant movements and redistribution as they move into and then out of adjacent replication foci. In contrast to hierarchical folding models, this dynamic plasticity of large-scale chromatin organization explains how localized changes in DNA topology allow DNA replication to take place without an accompanying global unfolding of large-scale chromatin fibers while suggesting a possible mechanism for maintaining epigenetic programming of large-scale chromatin domains throughout DNA replication. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tectonic insight based on anisotropy of magnetic susceptibility and compaction studies in the Sierras Australes thrust and fold belt (southwest Gondwana boundary, Argentina)

NASA Astrophysics Data System (ADS)

Arzadún, Guadalupe; Tomezzoli, Renata N.; Cesaretti, Nora N.

2016-04-01

The Sierras Australes fold and thrust belt (Buenos Aires Province, Argentina) was in the southwestern Gondwanaland margin during the Paleozoic. The Tunas Formation (Permian) is exposed along the eastern part of it and continues eastward beneath the Claromecó Basin. Anisotropy of magnetic susceptibility (AMS) and compaction studies are described and compared with previous paleomagnetic studies with the aim of determining direction and magnitude of the main stresses acting during the sedimentation of the Tunas Formation. The anisotropy ellipsoids are triaxial with oblate or prolate shapes, reflecting different stages of layer parallel shortening during the evolution of the basin. Kmax axes trend NW-SE, parallel to the fold axes, while Kmin move from a horizontal (base) to a vertical orientation at the top of the succession, showing a change from a tectonic to almost a sedimentary fabric. The magnitude of anisotropy and compaction degree decreases toward the top of the succession. The AMS results are consistent with the outcrop structural observations and the compaction and paleomagnetic data. Regional pattern indicates a compression from the SW along this part of Gondwana, with a migration of the orogenic front and attenuation toward the NE in the foreland basin during the Upper Paleozoic. This deformation, locally assigned to the San Rafael noncollisional orogenic phase, is the result of the latitudinal movements toward the Equator of Gondwana (southern plates) and Laurentia (northern plates) during the Permian. This movement is the result of a rearrangement of the microplates that collided with Gondwana during the Late Devonian, to configure Pangea during the Triassic.

Jigsaw model of the origin of life

NASA Astrophysics Data System (ADS)

McGowan, John F.

2002-02-01

It is suggested that life originated in a three-step process referred to as the jigsaw model. RNA, proteins, or similar organic molecules polymerized in a dehydrated carbon-rich environment, on surfaces in a carbon-rich environment, or in another environment where polymerization occurs. These polymers subsequently entered an aqueous environment where they folded into compact structures. It is argued that the folding of randomly generated polymers such as RNA or proteins in water tends to partition the folded polymer into domains with hydrophobic cores and matching shapes to minimize energy. In the aqueous environment hydrolysis or other reactions fragmented the compact structures into two or more matching molecules, occasionally producing simple living systems, also knows as autocatalytic sets of molecules. It is argued that the hydrolysis of folded polymers such as RNA or proteins is not random. The hydrophobic cores of the domains are rarely bisected due to the energy requirements in water. Hydrolysis preferentially fragments the folded polymers into pieces with complementary structures and chemical affinities. Thus the probability of producing a system of matched, interacting molecules in prebiotic chemistry is much higher than usually estimated. Environments where this process may occur are identified. For example, the jigsaw model suggests life may have originated at a seep or carbonaceous fluids beneath the ocean. The polymerization occurred beneath the sea floor. The folding and fragmentation occurred in the ocean. The implications of this hypothesis for seeking life or prebiotic chemistry in the Solar System are explored.

Time dependence of triplet-singlet excitation transfer from compact poly rA to bound dye at 77 K.

PubMed Central

Pearlstein, R M; Van Nostrand, F; Nairn, J A

1979-01-01

The nonexponential phosphorescence decay of a highly folded form of poly-riboadenylic acid (poly rA) with noncovalently bound dye is explained by a novel application of a well-known theory of electronic excitation transfer based on the Förster mechanism. This theory, originally used to describe singlet-singlet energy transfer from donor molecules to an acceptor in a solution, is here applied to the transfer of triplet excitation from the adenine (in poly rA) to the singlet manifold of either of the bound dyes, ethidium bromide or proflavine. New experimental data are presented that allow straight-forward theoretical interpretation. These data fit the form predicted by the theory, U(t) exp(-Bt1/2), where U(t) is the decay of the poly rA phosphorescence in the absence of dye, for a range of relative concentrations of either dye. The self-consistency of these theoretical fits is demonstrated by the proportionality of B to the square root of the Förster triplet-singlet overlap integrals for transfer from poly rA to each of the dyes, as demanded by the theory. From these self-consistent values of B, the theory enables one to deduce the mean packing density of nucleotides in this folded poly rA, which we estimate to be approximately 1 nm-3. We conclude that some variations of the method described here may be useful for deducing packing densities of nucleotides in other compact nucleic acid structures. PMID:262411

GroEL actively stimulates folding of the endogenous substrate protein PepQ.

PubMed

Weaver, Jeremy; Jiang, Mengqiu; Roth, Andrew; Puchalla, Jason; Zhang, Junjie; Rye, Hays S

2017-06-30

Many essential proteins cannot fold without help from chaperonins, like the GroELS system of Escherichia coli. How chaperonins accelerate protein folding remains controversial. Here we test key predictions of both passive and active models of GroELS-stimulated folding, using the endogenous E. coli metalloprotease PepQ. While GroELS increases the folding rate of PepQ by over 15-fold, we demonstrate that slow spontaneous folding of PepQ is not caused by aggregation. Fluorescence measurements suggest that, when folding inside the GroEL-GroES cavity, PepQ populates conformations not observed during spontaneous folding in free solution. Using cryo-electron microscopy, we show that the GroEL C-termini make physical contact with the PepQ folding intermediate and help retain it deep within the GroEL cavity, resulting in reduced compactness of the PepQ monomer. Our findings strongly support an active model of chaperonin-mediated protein folding, where partial unfolding of misfolded intermediates plays a key role.

Folding and Hydrodynamics of a DNA i-Motif from the c-MYC Promoter Determined by Fluorescent Cytidine Analogs

PubMed Central

Reilly, Samantha M.; Lyons, Daniel F.; Wingate, Sara E.; Wright, Robert T.; Correia, John J.; Jameson, David M.; Wadkins, Randy M.

2014-01-01

The four-stranded i-motif (iM) conformation of cytosine-rich DNA has importance to a wide variety of biochemical systems that range from their use in nanomaterials to potential roles in oncogene regulation. The iM structure is formed at slightly acidic pH, where hemiprotonation of cytosine results in a stable C-C+ basepair. Here, we performed fundamental studies to examine iM formation from a C-rich strand from the promoter of the human c-MYC gene. We used a number of biophysical techniques to characterize both the hydrodynamic properties and folding kinetics of a folded iM. Our hydrodynamic studies using fluorescence anisotropy decay and analytical ultracentrifugation show that the iM structure has a compact size in solution and displays the rigidity of a double strand. By studying the rates of circular dichroism spectral changes and quenching of fluorescent cytidine analogs, we also established a mechanism for the folding of a random coil oligo into the iM. In the course of determining this folding pathway, we established that the fluorescent dC analogs tC° and PdC can be used to monitor individual residues of an iM structure and to determine the pKa of an iM. We established that the C-C+ hydrogen bonding of certain bases initiates the folding of the iM structure. We also showed that substitutions in the loop regions of iMs give a distinctly different kinetic signature during folding compared with bases that are intercalated. Our data reveal that the iM passes through a distinct intermediate form between the unfolded and folded forms. Taken together, our results lay the foundation for using fluorescent dC analogs to follow structural changes during iM formation. Our technique may also be useful for examining folding and structural changes in more complex iMs. PMID:25296324

Disruption of Higher-Order Folding by Core Histone Acetylation Dramatically Enhances Transcription of Nucleosomal Arrays by RNA Polymerase III

PubMed Central

Tse, Christin; Sera, Takashi; Wolffe, Alan P.; Hansen, Jeffrey C.

1998-01-01

We have examined the effects of core histone acetylation on the transcriptional activity and higher-order folding of defined 12-mer nucleosomal arrays. Purified HeLa core histone octamers containing an average of 2, 6, or 12 acetates per octamer (8, 23, or 46% maximal site occupancy, respectively) were assembled onto a DNA template consisting of 12 tandem repeats of a 208-bp Lytechinus 5S rRNA gene fragment. Reconstituted nucleosomal arrays were transcribed in a Xenopus oocyte nuclear extract and analyzed by analytical hydrodynamic and electrophoretic approaches to determine the extent of array compaction. Results indicated that in buffer containing 5 mM free Mg2+ and 50 mM KCl, high levels of acetylation (12 acetates/octamer) completely inhibited higher-order folding and concurrently led to a 15-fold enhancement of transcription by RNA polymerase III. The molecular mechanisms underlying the acetylation effects on chromatin condensation were investigated by analyzing the ability of differentially acetylated nucleosomal arrays to fold and oligomerize. In MgCl2-containing buffer the folding of 12-mer nucleosomal arrays containing an average of two or six acetates per histone octamer was indistinguishable, while a level of 12 acetates per octamer completely disrupted the ability of nucleosomal arrays to form higher-order folded structures at all ionic conditions tested. In contrast, there was a linear relationship between the extent of histone octamer acetylation and the extent of disruption of Mg2+-dependent oligomerization. These results have yielded new insight into the molecular basis of acetylation effects on both transcription and higher-order compaction of nucleosomal arrays. PMID:9671473

Mesoscale Modeling of Chromatin Folding

NASA Astrophysics Data System (ADS)

Schlick, Tamar

2009-03-01

Eukaryotic chromatin is the fundamental protein/nucleic acid unit that stores the genetic material. Understanding how chromatin fibers fold and unfold in physiological conditions is important for interpreting fundamental biological processes like DNA replication and transcription regulation. Using a mesoscopic model of oligonucleosome chains and tailored sampling protocols, we elucidate the energetics of oligonucleosome folding/unfolding and the role of each histone tail, linker histones, and divalent ions in regulating chromatin structure. The resulting compact topologies reconcile features of the zigzag model with straight linker DNAs with the solenoid model with bent linker DNAs for optimal fiber organization and reveal dynamic and energetic aspects involved.

An XMM-Newton and NuSTAR Study of IGR J18214-1318: A Non-pulsating High-mass X-Ray Binary with a Neutron Star

NASA Astrophysics Data System (ADS)

Fornasini, Francesca M.; Tomsick, John A.; Bachetti, Matteo; Krivonos, Roman A.; Fürst, Felix; Natalucci, Lorenzo; Pottschmidt, Katja; Wilms, Jörn

2017-05-01

IGR J18214-1318, a Galactic source discovered by the International Gamma-Ray Astrophysics Laboratory, is a high-mass X-ray binary (HMXB) with a supergiant O-type stellar donor. We report on the XMM-Newton and NuSTAR observations that were undertaken to determine the nature of the compact object in this system. This source exhibits high levels of aperiodic variability, but no periodic pulsations are detected with a 90% confidence upper limit of 2% fractional rms between 0.00003-88 Hz, a frequency range that includes the typical pulse periods of neutron stars (NSs) in HMXBs (0.1-103 s). Although the lack of pulsations prevents us from definitively identifying the compact object in IGR J18214-1318, the presence of an exponential cutoff with e-folding energy ≲ 30 {keV} in its 0.3-79 keV spectrum strongly suggests that the compact object is an NS. The X-ray spectrum also shows a Fe Kα emission line and a soft excess, which can be accounted for by either a partial-covering absorber with {N}{{H}}≈ {10}23 cm-2, which could be due to the inhomogeneous supergiant wind, or a blackbody component with {kT}={1.74}-0.05+0.04 keV and {R}{BB}≈ 0.3 km, which may originate from NS hot spots. Although neither explanation for the soft excess can be excluded, the former is more consistent with the properties observed in other supergiant HMXBs. We compare IGR J18214-1318 to other HMXBs that lack pulsations or have long pulsation periods beyond the range covered by our observations.

Active Transcription of rRNA Operons Condenses the Nucleoid in Escherichia coli: Examining the Effect of Transcription on Nucleoid Structure in the Absence of Transertion | Center for Cancer Research

Cancer.gov

In Escherichia coli the genome must be compacted ∼1,000-fold to be contained in a cellular structure termed the nucleoid. It is proposed that the structure of the nucleoid is determined by a balance of multiple compaction forces and one major expansion force. The latter is mediated by transertion, a coupling of transcription, translation, and translocation of nascent membrane

Time dependence of triplet--singlet excitation transfer from compact poly rA to bound dye at 77 k

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pearlstein, R.M.; Nostrand, F.V.; Nairn, J.A.

1979-04-01

The nonexponential phosphorescence decay of a highly folded form of polyriboadenylic acid (poly rA) with noncovalently bound dye is explained by a novel application of a well-known theory of electronic excitation transfer based on the Forster mechanism. This theory, originally used to describe singlet-singlet energy transfer from donor molecules to an acceptor in a solution, is here applied to the transfer of triplet excitation from the adenine (in poly rA) to the singlet manifold of either of the bound dyes, ethidium bromide or proflavine. New experimental data are presented that allow straight-forward theoretical interpretation. These data fit the form predictedmore » by the theory, U(t)exp(-Bt/sup 1/2/), where U(t) is the decay of the poly rA phosphorescence in the absence of dye, for a range of relative concentrations of either dye. The self-consistency of these theoretical fits is demonstrated by the proportionality of B to the square root of the Forster triplet-singlet overlap integrals for transfer from poly rA to each of the dyes, as demanded by the theory. From these self-consistent values of B, the theory enables one to deduce the mean packing density of nucleotides in this folded poly rA, which we estimate to be approx. 1 nm/sup -3/. We conclude that some variation of the method described here may be useful for deducing packing densities of nucleotides in other compact nucleic acid structures.« less

Probing the cytochrome c' folding landscape.

PubMed

Pletneva, Ekaterina V; Zhao, Ziqing; Kimura, Tetsunari; Petrova, Krastina V; Gray, Harry B; Winkler, Jay R

2007-11-01

The folding kinetics of R. palustris cytochrome c' (cyt c') have been monitored by heme absorption and native Trp72 fluorescence at pH 5. The Trp72 fluorescence burst signal suggests early compaction of the polypeptide ensemble. Analysis of heme transient absorption spectra reveals deviations from two-state behavior, including a prominent slow phase that is accelerated by the prolyl isomerase cyclophilin. A nonnative proline configuration (Pro21) likely interferes with the formation of the helical bundle surrounding the heme.

Principles of Chromosome Architecture Revealed by Hi-C.

PubMed

Eagen, Kyle P

2018-06-01

Chromosomes are folded and compacted in interphase nuclei, but the molecular basis of this folding is poorly understood. Chromosome conformation capture methods, such as Hi-C, combine chemical crosslinking of chromatin with fragmentation, DNA ligation, and high-throughput DNA sequencing to detect neighboring loci genome-wide. Hi-C has revealed the segregation of chromatin into active and inactive compartments and the folding of DNA into self-associating domains and loops. Depletion of CTCF, cohesin, or cohesin-associated proteins was recently shown to affect the majority of domains and loops in a manner that is consistent with a model of DNA folding through extrusion of chromatin loops. Compartmentation was not dependent on CTCF or cohesin. Hi-C contact maps represent the superimposition of CTCF/cohesin-dependent and -independent folding states. Copyright © 2018 Elsevier Ltd. All rights reserved.

Persistence length changes dramatically as RNA folds.

PubMed

Caliskan, G; Hyeon, C; Perez-Salas, U; Briber, R M; Woodson, S A; Thirumalai, D

2005-12-31

We determine the persistence length l(p) for a bacterial group I ribozyme as a function of concentration of monovalent and divalent cations by fitting the distance distribution functions P(r) obtained from small angle x-ray scattering intensity data to the asymptotic form of the calculated P(WLC)(r) for a wormlike chain. The l(p) values change dramatically over a narrow range of Mg(2+) concentration from approximately 21 Angstroms in the unfolded state (U) to approximately 10 Angstroms in the compact (I(C)) and native states. Variations in l(p) with increasing Na(+) concentration are more gradual. In accord with the predictions of polyelectrolyte theory we find l(p) alpha 1/kappa(2) where kappa is the inverse Debye-screening length.

Study of foldable elastic tubes for large space structure applications, phase 3

NASA Technical Reports Server (NTRS)

Jones, I. W.; Mitchell, S. O.

1981-01-01

A bi-convex foldable elastic tube, suitable for use in self deploying space structures, was subjected to a series of buckling tests to deterine initial buckling loads, collapse loads, and the buckling mode. The tube is cylindrical with a cross-section that is lenticular-like with flared edges. It is capable of being flattened in the center and folded compactly, storing up strain energy in the process. Upon removal of constraint, it springs back to its original straight configuration, releasing the stored strain energy. The tests showed that this type of tube has good resistance to buckling, with the initial buckling loads all falling within or above the range of those for comparable circular cylindrical tubes.

Polyimide/Carbon Nanotube Composite Films for Electrostatic Charge Mitigation

NASA Technical Reports Server (NTRS)

Smith, Joseph G., Jr.; Delozier, Donavon M.; Connell, John W.; Watson, Kent A.

2004-01-01

Low color, space environmentally durable polymeric films with sufficient electrical conductivity to mitigate electrostatic charge (ESC) build-up have potential applications on large, deployable, ultra-light weight Gossamer spacecraft as thin film membranes on antennas, solar sails, thermal/optical coatings, multi-layer insulation blankets, etc.. The challenge has been to develop a method to impart robust electrical conductivity into these materials without increasing solar absorptivity (alpha ) or decreasing optical transparency or film flexibility. Since these spacecraft will require significant compaction prior to launch, the film portion of the spacecraft will require folding. The state-of-the-art clear, conductive coating (e.g. indium-tin-oxide, ITO) is brittle and cannot tolerate folding. In this report, doping a polymer with single-walled carbon nanotubes (SWNTs) using two different methods afforded materials with good flexibility and surface conductivities in the range sufficient for ESC mitigation. A coating method afforded materials with minimal effects on the mechanical, optical, and thermo-optical properties as compared to dispersal of SWNTs in the matrix. The chemistry and physical properties of these nanocomposites are discussed.

The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis

PubMed Central

Beck, Kirsten; Vannini, Alessandro; Cramer, Patrick; Lipps, Georg

2010-01-01

The plasmid pRN1 encodes for a multifunctional replication protein with primase, DNA polymerase and helicase activity. The minimal region required for primase activity encompasses amino-acid residues 40–370. While the N-terminal part of that minimal region (residues 47–247) folds into the prim/pol domain and bears the active site, the structure and function of the C-terminal part (residues 248–370) is unknown. Here we show that the C-terminal part of the minimal region folds into a compact domain with six helices and is stabilized by a disulfide bond. Three helices superimpose well with the C-terminal domain of the primase of the bacterial broad host range plasmid RSF1010. Structure-based site-directed mutagenesis shows that the C-terminal helix of the helix bundle domain is required for primase activity although it is distant to the active site in the crystallized conformation. Furthermore, we identified mutants of the C-terminal domain, which are defective in template binding, dinucleotide formation and conformation change prior to DNA extension. PMID:20511586

An Optically Pumped Far-Infrared Folded Mirror-Less Cavity

NASA Astrophysics Data System (ADS)

Liu, Chuang; Wang, Dashuai; Zhang, Peng; Qu, Yanchen

2017-12-01

A compact and efficient mirror-less cavity is presented for an optically pumped 192-μm far-infrared laser. With a gold-coated mirror and 30°-inclined anti-reflection coated Ge plate serving as highly reflective mirrors, a folded mirror-less CH3F cavity is achieved. Maximum energy of 0.72 mJ is obtained with the pump energy of 600 mJ, which gives an energy increment of 75% in comparison with the previous 1.85-m mirror-less system. The beam divergence angle of the FIR radiation from this folded mirror-less cavity is measured to be 14.2 mrad.

Compaction of fibrin clots reveals the antifibrinolytic effect of factor XIII.

PubMed

Rijken, D C; Abdul, S; Malfliet, J J M C; Leebeek, F W G; Uitte de Willige, S

2016-07-01

Essentials Factor XIIIa inhibits fibrinolysis by forming fibrin-fibrin and fibrin-inhibitor cross-links. Conflicting studies about magnitude and mechanisms of inhibition have been reported. Factor XIIIa most strongly inhibits lysis of mechanically compacted or retracted plasma clots. Cross-links of α2-antiplasmin to fibrin prevent the inhibitor from being expelled from the clot. Background Although insights into the underlying mechanisms of the effect of factor XIII on fibrinolysis have improved considerably in the last few decades, in particular with the discovery that activated FXIII (FXIIIa) cross-links α2 -antiplasmin to fibrin, the topic remains a matter of debate. Objective To elucidate the mechanisms of the antifibrinolytic effect of FXIII. Methods and Results Platelet-poor plasma clot lysis, induced by the addition of tissue-type plasminogen activator, was measured in the presence or absence of a specific FXIIIa inhibitor. Both in a turbidity assay and in a fluorescence assay, the FXIIIa inhibitor had only a small inhibitory effect: 1.6-fold less tissue-type plasminogen activator was required for 50% clot lysis in the presence of the FXIIIa inhibitor. However, when the plasma clot was compacted by centrifugation, the FXIIIa inhibitor had a strong inhibitory effect, with 7.7-fold less tissue-type plasminogen activator being required for 50% clot lysis in the presence of the FXIIIa inhibitor. In both experiments, the effects of the FXIIIa inhibitor were entirely dependent on the cross-linking of α2 -antiplasmin to fibrin. The FXIIIa inhibitor reduced the amount of α2 -antiplasmin present in the compacted clots from approximately 30% to < 4%. The results were confirmed with experiments in which compaction was achieved by platelet-mediated clot retraction. Conclusions Compaction or retraction of fibrin clots reveals the strong antifibrinolytic effect of FXIII. This is explained by the cross-linking of α2 -antiplasmin to fibrin by FXIIIa, which prevents the plasmin inhibitor from being fully expelled from the clot during compaction/retraction. © 2016 The Authors. Journal of Thrombosis and Haemostasis published by Wiley Periodicals, Inc. on behalf of International Society on Thrombosis and Haemostasis.

Asymmetric hindwing foldings in rove beetles.

PubMed

Saito, Kazuya; Yamamoto, Shuhei; Maruyama, Munetoshi; Okabe, Yoji

2014-11-18

Foldable wings of insects are the ultimate deployable structures and have attracted the interest of aerospace engineering scientists as well as entomologists. Rove beetles are known to fold their wings in the most sophisticated ways that have right-left asymmetric patterns. However, the specific folding process and the reason for this asymmetry remain unclear. This study reveals how these asymmetric patterns emerge as a result of the folding process of rove beetles. A high-speed camera was used to reveal the details of the wing-folding movement. The results show that these characteristic asymmetrical patterns emerge as a result of simultaneous folding of overlapped wings. The revealed folding mechanisms can achieve not only highly compact wing storage but also immediate deployment. In addition, the right and left crease patterns are interchangeable, and thus each wing internalizes two crease patterns and can be folded in two different ways. This two-way folding gives freedom of choice for the folding direction to a rove beetle. The use of asymmetric patterns and the capability of two-way folding are unique features not found in artificial structures. These features have great potential to extend the design possibilities for all deployable structures, from space structures to articles of daily use.

Folded optics with birefringent reflective polarizers

NASA Astrophysics Data System (ADS)

Wong, Timothy L.; Yun, Zhisheng; Ambur, Gregg; Etter, Jo

2017-06-01

Polymeric, birefringent reflective polarizers have been used to produce compact, mid-field-of-view eyepieces and wide field-of-view optics for virtual reality (VR) head-mounted displays using the "pancake" lens configuration. Multiple configurations for pancake lens systems are discussed as are their advantages and disadvantages relative to refractive systems. Polarization control is an important consideration and the polarizing effects of different components are discussed. Designs for mid-FOV and wide FOV are presented and additional benefits of using folded optics for virtual reality systems are explored.

A prototype fully polarimetric 160-GHz bistatic ISAR compact radar range

NASA Astrophysics Data System (ADS)

Beaudoin, C. J.; Horgan, T.; DeMartinis, G.; Coulombe, M. J.; Goyette, T.; Gatesman, A. J.; Nixon, William E.

2017-05-01

We present a prototype bistatic compact radar range operating at 160 GHz and capable of collecting fullypolarimetric radar cross-section and electromagnetic scattering measurements in a true far-field facility. The bistatic ISAR system incorporates two 90-inch focal length, 27-inch-diameter diamond-turned mirrors fed by 160 GHz transmit and receive horns to establish the compact range. The prototype radar range with its modest sized quiet zone serves as a precursor to a fully developed compact radar range incorporating a larger quiet zone capable of collecting X-band bistatic RCS data and 3D imagery using 1/16th scale objects. The millimeter-wave transmitter provides 20 GHz of swept bandwidth in the single linear (Horizontal/Vertical) polarization while the millimeter-wave receiver, that is sensitive to linear Horizontal and Vertical polarization, possesses a 7 dB noise figure. We present the design of the compact radar range and report on test results collected to validate the system's performance.

Preparation of bulk superhard B-C-N nanocomposite compact

DOEpatents

Zhao, Yusheng [Los Alamos, NM; He, Duanwei [Sichuan, CN

2011-05-10

Bulk, superhard, B--C--N nanocomposite compacts were prepared by ball milling a mixture of graphite and hexagonal boron nitride, encapsulating the ball-milled mixture at a pressure in a range of from about 15 GPa to about 25 GPa, and sintering the pressurized encapsulated ball-milled mixture at a temperature in a range of from about 1800-2500 K. The product bulk, superhard, nanocomposite compacts were well sintered compacts with nanocrystalline grains of at least one high-pressure phase of B--C--N surrounded by amorphous diamond-like carbon grain boundaries. The bulk compacts had a measured Vicker's hardness in a range of from about 41 GPa to about 68 GPa.

Ultrathin zoom telescopic objective.

PubMed

Li, Lei; Wang, Di; Liu, Chao; Wang, Qiong-Hua

2016-08-08

We report an ultrathin zoom telescopic objective that can achieve continuous zoom change and has reduced compact volume. The objective consists of an annular folded lens and three electrowetting liquid lenses. The annular folded lens undertakes the main part of the focal power of the lens system. Due to a multiple-fold design, the optical path is folded in a lens with the thickness of ~1.98mm. The electrowetting liquid lenses constitute a zoom part. Based on the proposed objective, an ultrathin zoom telescopic camera is demonstrated. We analyze the properties of the proposed objective. The aperture of the proposed objective is ~15mm. The total length of the system is ~18mm with a tunable focal length ~48mm to ~65mm. Compared with the conventional zoom telescopic objective, the total length has been largely reduced.

3D wide field-of-view Gabor-domain optical coherence microscopy advancing real-time in-vivo imaging and metrology

NASA Astrophysics Data System (ADS)

Canavesi, Cristina; Cogliati, Andrea; Hayes, Adam; Tankam, Patrice; Santhanam, Anand; Rolland, Jannick P.

2017-02-01

Real-time volumetric high-definition wide-field-of-view in-vivo cellular imaging requires micron-scale resolution in 3D. Compactness of the handheld device and distortion-free images with cellular resolution are also critically required for onsite use in clinical applications. By integrating a custom liquid lens-based microscope and a dual-axis MEMS scanner in a compact handheld probe, Gabor-domain optical coherence microscopy (GD-OCM) breaks the lateral resolution limit of optical coherence tomography through depth, overcoming the tradeoff between numerical aperture and depth of focus, enabling advances in biotechnology. Furthermore, distortion-free imaging with no post-processing is achieved with a compact, lightweight handheld MEMS scanner that obtained a 12-fold reduction in volume and 17-fold reduction in weight over a previous dual-mirror galvanometer-based scanner. Approaching the holy grail of medical imaging - noninvasive real-time imaging with histologic resolution - GD-OCM demonstrates invariant resolution of 2 μm throughout a volume of 1 x 1 x 0.6 mm3, acquired and visualized in less than 2 minutes with parallel processing on graphics processing units. Results on the metrology of manufactured materials and imaging of human tissue with GD-OCM are presented.

Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS.

PubMed

Devine, Paul W A; Fisher, Henry C; Calabrese, Antonio N; Whelan, Fiona; Higazi, Daniel R; Potts, Jennifer R; Lowe, David C; Radford, Sheena E; Ashcroft, Alison E

2017-09-01

Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein's size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds. Graphical Abstract ᅟ.

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

PubMed Central

Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro; Piana, Stefano

2009-01-01

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins. Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For the Trp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap. Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at of 4.4 Å from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the and chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data. PMID:19662155

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

PubMed

Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro; Piana, Stefano

2009-08-01

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

Polar nephelometer for atmospheric particulate studies

NASA Technical Reports Server (NTRS)

Hansen, M. Z.; Evans, W. H.

1980-01-01

A polar nephelometer for use in studying atmospheric aerosols was developed. The nephelometer detects molecular scatter from air and measures scattering from very clean air using pure molecular scattering for calibration. A compact system using a folded light path with an air cooled argon laser for the light source was designed. A small, sensitive detector unit permits easy angular rotation for changing the scattering angle. A narrow detector field of view of + or - 1/4 degree of scattering along with a single wavelength of incident light is used to minimize uncertainties in the scattering theory. The system is automated for data acquisition of the scattering matrix elements over an angular range from 2 degrees to 178 degrees of scattering. Both laser output and detector sensitivity are monitored to normalize the measured light scattering.

Modulation of frustration in folding by sequence permutation.

PubMed

Nobrega, R Paul; Arora, Karunesh; Kathuria, Sagar V; Graceffa, Rita; Barrea, Raul A; Guo, Liang; Chakravarthy, Srinivas; Bilsel, Osman; Irving, Thomas C; Brooks, Charles L; Matthews, C Robert

2014-07-22

Folding of globular proteins can be envisioned as the contraction of a random coil unfolded state toward the native state on an energy surface rough with local minima trapping frustrated species. These substructures impede productive folding and can serve as nucleation sites for aggregation reactions. However, little is known about the relationship between frustration and its underlying sequence determinants. Chemotaxis response regulator Y (CheY), a 129-amino acid bacterial protein, has been shown previously to populate an off-pathway kinetic trap in the microsecond time range. The frustration has been ascribed to premature docking of the N- and C-terminal subdomains or, alternatively, to the formation of an unproductive local-in-sequence cluster of branched aliphatic side chains, isoleucine, leucine, and valine (ILV). The roles of the subdomains and ILV clusters in frustration were tested by altering the sequence connectivity using circular permutations. Surprisingly, the stability and buried surface area of the intermediate could be increased or decreased depending on the location of the termini. Comparison with the results of small-angle X-ray-scattering experiments and simulations points to the accelerated formation of a more compact, on-pathway species for the more stable intermediate. The effect of chain connectivity in modulating the structures and stabilities of the early kinetic traps in CheY is better understood in terms of the ILV cluster model. However, the subdomain model captures the requirement for an intact N-terminal domain to access the native conformation. Chain entropy and aliphatic-rich sequences play crucial roles in biasing the early events leading to frustration in the folding of CheY.

Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy.

PubMed

Eichmann, Cédric; Preissler, Steffen; Riek, Roland; Deuerling, Elke

2010-05-18

The folding of proteins in living cells may start during their synthesis when the polypeptides emerge gradually at the ribosomal exit tunnel. However, our current understanding of cotranslational folding processes at the atomic level is limited. We employed NMR spectroscopy to monitor the conformation of the SH3 domain from alpha-spectrin at sequential stages of elongation via in vivo ribosome-arrested (15)N,(13)C-labeled nascent polypeptides. These nascent chains exposed either the entire SH3 domain or C-terminally truncated segments thereof, thus providing snapshots of the translation process. We show that nascent SH3 polypeptides remain unstructured during elongation but fold into a compact, native-like beta-sheet assembly when the entire sequence information is available. Moreover, the ribosome neither imposes major conformational constraints nor significantly interacts with exposed unfolded nascent SH3 domain moieties. Our data provide evidence for a domainwise folding of the SH3 domain on ribosomes without significant population of folding intermediates. The domain follows a thermodynamically favorable pathway in which sequential folding units are stabilized, thus avoiding kinetic traps during the process of cotranslational folding.

Application of graphics processing units to search pipelines for gravitational waves from coalescing binaries of compact objects

NASA Astrophysics Data System (ADS)

Chung, Shin Kee; Wen, Linqing; Blair, David; Cannon, Kipp; Datta, Amitava

2010-07-01

We report a novel application of a graphics processing unit (GPU) for the purpose of accelerating the search pipelines for gravitational waves from coalescing binaries of compact objects. A speed-up of 16-fold in total has been achieved with an NVIDIA GeForce 8800 Ultra GPU card compared with one core of a 2.5 GHz Intel Q9300 central processing unit (CPU). We show that substantial improvements are possible and discuss the reduction in CPU count required for the detection of inspiral sources afforded by the use of GPUs.

Solution structure of an ATP-binding RNA aptamer reveals a novel fold.

PubMed Central

Dieckmann, T; Suzuki, E; Nakamura, G K; Feigon, J

1996-01-01

In vitro selection has been used to isolate several RNA aptamers that bind specifically to biological cofactors. A well-characterized example in the ATP-binding RNA aptamer family, which contains a conserved 11-base loop opposite a bulged G and flanked by regions of double-stranded RNA. The nucleotides in the consensus sequence provide a binding pocket for ATP (or AMP), which binds with a Kd in the micromolar range. Here we present the three-dimensional solution structure of a 36-nucleotide ATP-binding RNA aptamer complexed with AMP, determined from NMR-derived distance and dihedral angle restraints. The conserved loop and bulged G form a novel compact, folded structure around the AMP. The backbone tracing of the loop nucleotides can be described by a Greek zeta (zeta). Consecutive loop nucleotides G, A, A form a U-turn at the bottom of the zeta, and interact with the AMP to form a structure similar to a GNRA tetraloop, with AMP standing in for the final A. Two asymmetric G. G base pairs close the stems flanking the internal loop. Mutated aptamers support the existence of the tertiary interactions within the consensus nucleotides and with the AMP found in the calculated structures. PMID:8756406

Magnetic Actuation of Self-Assembled DNA Hinges

NASA Astrophysics Data System (ADS)

Lauback, S.; Mattioli, K.; Armstrong, M.; Miller, C.; Pease, C.; Castro, C.; Sooryakumar, R.

DNA nanotechnology offers a broad range of applications spanning from the creation of nanoscale devices, motors and nanoparticle templates to the development of precise drug delivery systems. Central to advancing this technology is the ability to actuate or reconfigure structures in real time, which is currently achieved primarily by DNA strand displacement yielding slow actuation times (about 1-10min). Here we exploit superparamagnetic beads to magnetically actuate DNA structures which also provides a system to measure forces associated with molecular interactions. DNA nanodevices are folded using DNA origami, whereby a long single-stranded DNA is folded into a precise compact geometry using hundreds of short oligonucleotides. Our DNA nanodevice is a nanohinge from which rod shaped DNA nanostructures are polymerized into micron-scale filaments forming handles for actuation. By functionalizing one arm of the hinge and the filament ends, the hinge can be attached to a surface while still allowing an arm to rotate and the filaments can be labeled with magnetic beads enabling the hinge to be actuated almost instantaneously by external magnetic fields. These results lay the groundwork to establish real-time manipulation and direct force application of DNA constructs.

Effects of compaction pressure and particle shape on the porosity and compression mechanical properties of sintered Ti6Al4V powder compacts for hard tissue implantation.

PubMed

Güden, Mustafa; Celik, Emrah; Hizal, Alpay; Altindiş, Mustafa; Cetiner, Sinan

2008-05-01

Sintered Ti6Al4V powder compacts potentially to be used in implant applications were prepared using commercially available spherical and angular powders (100-200 mum) within the porosity range of 34-54%. Cylindrical green powder compacts were cold compacted at various pressures and then sintered at 1200 degrees C for 2 h. The final percent porosity and mean pore sizes were determined as functions of the applied compaction pressure and powder type. The mechanical properties were investigated through compression testing. Results have shown that yield strength of the powder compacts of 40-42% porosity was comparable with that of human cortical bone. As compared with previously investigated Ti powder compacts, Ti6Al4V powder compacts showed higher strength at similar porosity range. Microscopic observations on the failed compact samples revealed that failure occurred primarily by the separation of interparticle bond regions in the planes 45 degrees to the loading axis. Copyright 2007 Wiley Periodicals, Inc.

Folded path LWIR system for SWAP constrained platforms

NASA Astrophysics Data System (ADS)

Fleet, Erin F.; Wilson, Michael L.; Linne von Berg, Dale; Giallorenzi, Thomas; Mathieu, Barry

2014-06-01

Folded path reflection and catadioptric optics are of growing interest, especially in the long wave infrared (LWIR), due to continuing demands for reductions in imaging system size, weight and power (SWAP). We present the optical design and laboratory data for a 50 mm focal length low f/# folded-path compact LWIR imaging system. The optical design uses 4 concentric aspheric mirrors, each of which is described by annular aspheric functions well suited to the folded path design space. The 4 mirrors are diamond turned onto two thin air-spaced aluminum plates which can be manually focused onto the uncooled LWIR microbolometer array detector. Stray light analysis will be presented to show how specialized internal baffling can be used to reduce stray light propagation through the folded path optical train. The system achieves near diffraction limited performance across the FOV with a 15 mm long optical train and a 5 mm back focal distance. The completed system is small enough to reside within a 3 inch diameter ball gimbal.

Design and implementation of the ESL compact range underhung bridge crane

NASA Technical Reports Server (NTRS)

Shamansky, H. T.; Dominek, A. K.; Burnside, W. D.

1987-01-01

As the indoor compact range technology has continued to increase, the need to handle larger and heavier targets has also increased. This need for target lifting and handling prompted the feasibility study of the use of an underhung bridge crane to be installed in the ESL (ElectroScience Laboratory, Ohio State University) compact range. This report documents both the design of the underhung bridge crane that was installed and the implementation of the design in the actual installation of the crane.

16 CFR Appendix F2 to Part 305 - Compact Clothes Washers

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 1 2014-01-01 2014-01-01 false Compact Clothes Washers F2 Appendix F2 to... LABELING RULEâ) Pt. 305, App. F2 Appendix F2 to Part 305—Compact Clothes Washers Range Information “Compact” includes all household clothes washers with a tub capacity of less than 1.6 cu. ft. Capacity Range of...

Principles of protein folding--a perspective from simple exact models.

PubMed Central

Dill, K. A.; Bromberg, S.; Yue, K.; Fiebig, K. M.; Yee, D. P.; Thomas, P. D.; Chan, H. S.

1995-01-01

General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics--fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which at least one monomer type is solvent-averse. PMID:7613459

Recovery of severely compacted soils in the Mojave Desert, California, USA

USGS Publications Warehouse

Webb, R.H.

2002-01-01

Often as a result of large-scale military maneuvers in the past, many soils in the Mojave Desert are highly vulnerable to soil compaction, particularly when wet. Previous studies indicate that natural recovery of severely compacted desert soils is extremely slow, and some researchers have suggested that subsurface compaction may not recover. Poorly sorted soils, particularly those with a loamy sand texture, are most vulnerable to soil compaction, and these soils are the most common in alluvial fans of the Mojave Desert. Recovery of compacted soil is expected to vary as a function of precipitation amounts, wetting-and-drying cycles, freeze-thaw cycles, and bioturbation, particularly root growth. Compaction recovery, as estimated using penetration depth and bulk density, was measured at 19 sites with 32 site-time combinations, including the former World War II Army sites of Camps Ibis, Granite, Iron Mountain, Clipper, and Essex. Although compaction at these sites was caused by a wide variety of forces, ranging from human trampling to tank traffic, the data do not allow segregation of differences in recovery rates for different compaction forces. The recovery rate appears to be logarithmic, with the highest rate of change occurring in the first few decades following abandonment. Some higher-elevation sites have completely recovered from soil compaction after 70 years. Using a linear model of recovery, the full recovery time ranges from 92 to 100 years; using a logarithmic model, which asymptotically approaches full recovery, the time required for 85% recovery ranges from 105-124 years.

GroEL stimulates protein folding through forced unfolding

PubMed Central

Lin, Zong; Madan, Damian; Rye, Hays S

2013-01-01

Many proteins cannot fold without the assistance of chaperonin machines like GroEL and GroES. The nature of this assistance, however, remains poorly understood. Here we demonstrate that unfolding of a substrate protein by GroEL enhances protein folding. We first show that capture of a protein on the open ring of a GroEL–ADP–GroES complex, GroEL’s physiological acceptor state for non-native proteins in vivo, leaves the substrate protein in an unexpectedly compact state. Subsequent binding of ATP to the same GroEL ring causes rapid, forced unfolding of the substrate protein. Notably, the fraction of the substrate protein that commits to the native state following GroES binding and protein release into the GroEL–GroES cavity is proportional to the extent of substrate-protein unfolding. Forced protein unfolding is thus a central component of the multilayered stimulatory mechanism used by GroEL to drive protein folding. PMID:18311152

Free-energy landscape of a hyperstable RNA tetraloop.

PubMed

Miner, Jacob C; Chen, Alan A; García, Angel E

2016-06-14

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.

Plasmonic waveguide with folded stubs for highly confined terahertz propagation and concentration.

PubMed

Ye, Longfang; Xiao, Yifan; Liu, Na; Song, Zhengyong; Zhang, Wei; Liu, Qing Huo

2017-01-23

We proposed a novel planar terahertz (THz) plasmonic waveguide with folded stub arrays to achieve excellent terahertz propagation performance with tight field confinement and compact size based on the concept of spoof surface plasmon polaritons (spoof SPPs). It is found that the waveguide propagation characteristics can be directly manipulated by increasing the length of the folded stubs without increasing its lateral dimension, which exhibits much lower asymptotic frequency of the dispersion relation and even tighter terahertz field confinement than conventional plasmonic waveguides with rectangular stub arrays. Based on this waveguiding scheme, a terahertz concentrator with gradual step-length folded stubs is proposed to achieve high terahertz field enhancement, and an enhancement factor greater than 20 is demonstrated. This work offers a new perspective on very confined terahertz propagation and concentration, which may have promising potential applications in various integrated terahertz plasmonic circuits and devices, terahertz sensing and terahertz nonlinear optics.

Transmembrane Segments Form Tertiary Hairpins in the Folding Vestibule of the Ribosome.

PubMed Central

Tu, LiWei; Khanna, Pooja; Deutsch, Carol

2013-01-01

Folding of membrane proteins begins in the ribosome as the peptide is elongated. During this process, the nascent peptide navigates along 100 Å of tunnel from the peptidyltransferase center to the exit port. Proximal to the exit port is a ‘folding vestibule’ that permits the nascent peptide to compact and explore conformational space for potential tertiary folding partners. The latter occurs for cytosolic subdomains, but has not yet been shown for transmembrane segments. We now demonstrate, using an accessibility assay and an improved, intramolecular crosslinking assay, that the helical transmembrane S3b-S4 hairpin (‘paddle’) of a voltage-gated potassium (Kv) channel, a critical region of the Kv voltage sensor, forms in the vestibule. S3-S4 hairpin interactions are detected at an early stage of Kv biogenesis. Moreover, this vestibule hairpin is consistent with a closed-state conformation of the Kv channel in the plasma membrane. PMID:24055377

Peptide folding in the presence of interacting protein crowders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bille, Anna, E-mail: anna.bille@thep.lu.se; Irbäck, Anders, E-mail: anders@thep.lu.se; Mohanty, Sandipan, E-mail: s.mohanty@fz-juelich.de

2016-05-07

Using Monte Carlo methods, we explore and compare the effects of two protein crowders, BPTI and GB1, on the folding thermodynamics of two peptides, the compact helical trp-cage and the β-hairpin-forming GB1m3. The thermally highly stable crowder proteins are modeled using a fixed backbone and rotatable side-chains, whereas the peptides are free to fold and unfold. In the simulations, the crowder proteins tend to distort the trp-cage fold, while having a stabilizing effect on GB1m3. The extent of the effects on a given peptide depends on the crowder type. Due to a sticky patch on its surface, BPTI causes largermore » changes than GB1 in the melting properties of the peptides. The observed effects on the peptides stem largely from attractive and specific interactions with the crowder surfaces, and differ from those seen in reference simulations with purely steric crowder particles.« less

Geometry and controls on the development of igneous sill-related forced folds: 2D seismic reflection case study from offshore Southern Australia

NASA Astrophysics Data System (ADS)

Jackson, Christopher; Schofield, Nick; Magee, Craig; Golenkov, Bogdan

2017-04-01

Emplacement of magma in the shallow subsurface can result in the development of dome-shaped folds at the Earth's surface. These so-called 'forced folds' have been described in the field and in subsurface datasets, although the exact geometry of the folds and the nature of their relationship to underlying sills remains unclear and, in some cases, controversial. As a result, the utility of these features in tracking the subsurface movement of magma, and predicting the potential size and location of potentially hazardous volcanic eruptions, is uncertain. Here we use high-quality, 2D seismic reflection and borehole data from the Ceduna sub-basin, offshore southern Australia to describe the structure and infer the evolution of igneous sill-related forced folds in the Bight Basin Igneous Complex (BBIC). We mapped 33 igneous sills, which were emplaced 200-1500 m below the palaeo-seabed in an Upper Cretaceous, coal-bearing, predominantly coastal-plain succession. The intrusions, which are expressed as packages of high-amplitude reflections, are 32-250 m thick and 7-19 km in diameter. They are overlain by dome-shaped folds, which are up to 17 km wide and display up to 210 m of relief. The edges of these folds coincide with the margins of the underlying sills and the folds display the greatest relief where the underlying sills are thickest; the folds are therefore interpreted as forced folds that formed in response to emplacement of magma in the shallow subsurface. The folds are onlapped by Lutetian (middle Eocene) strata, indicating they formed and the intrusions were emplaced during the latest Ypresian (c. 48 Ma). We demonstrate that fold amplitude is typically less than sill thickness even for sills with very large diameter-to-depth ratios, suggesting that pure elastic bending (forced folding) of the overburden is not the only process accommodating magma emplacement, and that supra-sill compaction may be important even at relatively shallow depths. Based on the observation that the sills intruded a shallowly-buried succession, the discrepancy between fold amplitude and sill thickness may reflect loss of host rock volume by fluidisation and pore fluid expulsion from poorly-lithified, water-rich beds. This study indicates that host rock composition, emplacement depth and deformation mechanisms are important controls on the style of deformation that occurs during intrusive igneous activity, and that forced fold amplitude may not always reflect the thickness of an underlying igneous intrusion. In addition, the results of this study suggest that physical and numerical models need to model more complex host rock stratigraphies and rheologies if they wish to capture the full range of deformation mechanisms that occur during magma emplacement in the Earth's shallow subsurface.

An echelle spectrograph for middle ultraviolet solar spectroscopy from rockets.

PubMed

Tousey, R; Purcell, J D; Garrett, D L

1967-03-01

An echelle grating spectrograph is ideal for use in a rocket when high resolution is required becaus itoccupies a minimum of space. The instrument described covers the range 4000-2000 A with a resolution of 0.03 A. It was designed to fit into the solar biaxial pointing-control section of an Aerobee-150 rocket. The characteristics of the spectrograph are illustrated with laboratory spectra of iron and carbon are sources and with solar spectra obtained during rocket flights in 1961 and 1964. Problems encountered in analyzing the spectra are discussed. The most difficult design problem was the elimination of stray light when used with the sun. Of the several methods investigated, the most effective was a predispersing system in the form of a zero-dispersion double monochromator. This was made compact by folding the beam four times.

TOPICAL REVIEW: Protein stability and enzyme activity at extreme biological temperatures

NASA Astrophysics Data System (ADS)

Feller, Georges

2010-08-01

Psychrophilic microorganisms thrive in permanently cold environments, even at subzero temperatures. To maintain metabolic rates compatible with sustained life, they have improved the dynamics of their protein structures, thereby enabling appropriate molecular motions required for biological activity at low temperatures. As a consequence of this structural flexibility, psychrophilic proteins are unstable and heat-labile. In the upper range of biological temperatures, thermophiles and hyperthermophiles grow at temperatures > 100 °C and synthesize ultra-stable proteins. However, thermophilic enzymes are nearly inactive at room temperature as a result of their compactness and rigidity. At the molecular level, both types of extremophilic proteins have adapted the same structural factors, but in opposite directions, to address either activity at low temperatures or stability in hot environments. A model based on folding funnels is proposed accounting for the stability-activity relationships in extremophilic proteins.

Submicron cubic boron nitride as hard as diamond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Guoduan; Kou, Zili, E-mail: kouzili@scu.edu.cn, E-mail: yanxz@hpstar.ac.cn; Lei, Li

Here, we report the sintering of aggregated submicron cubic boron nitride (sm-cBN) at a pressure of 8 GPa. The sintered cBN compacts exhibit hardness values comparable to that of single crystal diamond, fracture toughness about 5-fold that of cBN single crystal, in combination with a high oxidization temperature. Thus, another way has been demonstrated to improve the mechanical properties of cBN besides reducing the grain size to nano scale. In contrast to other ultrahard compacts with similar hardness, the sm-cBN aggregates are better placed for potential industrial application, as their relative low pressure manufacturing perhaps be easier and cheaper.

Acrylonitrile Quenching of Trp Phosphorescence in Proteins: A Probe of the Internal Flexibility of the Globular Fold

PubMed Central

Strambini, Giovanni B.; Gonnelli, Margherita

2010-01-01

Quenching of Trp phosphorescence in proteins by diffusion of solutes of various molecular sizes unveils the frequency-amplitude of structural fluctuations. To cover the sizes gap between O2 and acrylamide, we examined the potential of acrylonitrile to probe conformational flexibility of proteins. The distance dependence of the through-space acrylonitrile quenching rate was determined in a glass at 77 K, with the indole analog 2-(3-indoyl) ethyl phenyl ketone. Intensity and decay kinetics data were fitted to a rate, k(r) = k0 exp[−(r − r0)/re], with an attenuation length re = 0.03 nm and a contact rate k0 = 3.6 × 1010 s−1. At ambient temperature, the bimolecular quenching rate constant (kq) was determined for a series of proteins, appositely selected to test the importance of factors such as the degree of Trp burial and structural rigidity. Relative to kq = 1.9 × 109 M−1s−1 for free Trp in water, in proteins kq ranged from 6.5 × 106 M−1s−1 for superficial sites to 1.3 × 102 M−1s−1 for deep cores. The short-range nature of the interaction and the direct correlation between kq and structural flexibility attest that in the microsecond-second timescale of phosphorescence acrylonitrile readily penetrates even compact protein cores and exhibits significant sensitivity to variations in dynamical structure of the globular fold. PMID:20682273

Origins of structure in globular proteins.

PubMed Central

Chan, H S; Dill, K A

1990-01-01

The principal forces of protein folding--hydrophobicity and conformational entropy--are nonspecific. A long-standing puzzle has, therefore, been: What forces drive the formation of the specific internal architectures in globular proteins? We find that any self-avoiding flexible polymer molecule will develop large amounts of secondary structure, helices and parallel and antiparallel sheets, as it is driven to increasing compactness by any force of attraction among the chain monomers. Thus structure formation arises from the severity of steric constraints in compact polymers. This steric principle of organization can account for why short helices are stable in globular proteins, why there are parallel and anti-parallel sheets in proteins, and why weakly unfolded proteins have some secondary structure. On this basis, it should be possible to construct copolymers, not necessarily using amino acids, that can collapse to maximum compactness in incompatible solvents and that should then have structural organization resembling that of proteins. Images PMID:2385597

Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin

PubMed Central

Bandaria, Jigar N.; Qin, Peiwu; Berk, Veysel; Chu, Steven; Yildiz, Ahmet

2016-01-01

SUMMARY Telomeres, repetitive DNA sequences at chromosome ends, are shielded against the DNA damage response (DDR) by the shelterin complex. To understand how shelterin protects telomere ends, we investigated the structural organization of telomeric chromatin in human cells using super-resolution microscopy. We found that telomeres form compact globular structures through a complex network of interactions between shelterin subunits and telomeric DNA, and not by DNA methylation, histone deacetylation or histone trimethylation at telomeres and subtelomeric regions. Mutations that abrogate shelterin assembly or removal of individual subunits from telomeres cause up to a 10-fold increase in telomere volume. Decompacted telomeres become more accessible to telomere-associated proteins and accumulate DDR signals. Recompaction of telomeric chromatin using an orthogonal method displaces DDR signals from telomeres. These results reveal the chromatin remodeling activity of shelterin and demonstrate that shelterin-mediated compaction of telomeric chromatin provides robust protection of chromosome ends against the DDR machinery. PMID:26871633

Magnesium-dependent association and folding of oligonucleosomes reconstituted with ubiquitinated H2A.

PubMed

Jason, L J; Moore, S C; Ausio, J; Lindsey, G

2001-05-04

The MgCl2-induced folding of defined 12-mer nucleosomal arrays, in which ubiquitinated histone H2A (uH2A) replaced H2A, was analyzed by quantitative agarose gel electrophoresis and analytical centrifugation. Both types of analysis showed that uH2A arrays attained a degree of compaction similar to that of control arrays in 2 mM MgCl2. These results indicate that attachment of ubiquitin to H2A has little effect on the ability of nucleosomal arrays to form higher order folded structures in the ionic conditions tested. In contrast, uH2A arrays were found to oligomerize at lower MgCl2 concentrations than control nucleosomal arrays, suggesting that histone ubiquitination may play a role in nucleosomal fiber association.

Advanced freeform optics enabling ultra-compact VR headsets

NASA Astrophysics Data System (ADS)

Benitez, Pablo; Miñano, Juan C.; Zamora, Pablo; Grabovičkić, Dejan; Buljan, Marina; Narasimhan, Bharathwaj; Gorospe, Jorge; López, Jesús; Nikolić, Milena; Sánchez, Eduardo; Lastres, Carmen; Mohedano, Ruben

2017-06-01

We present novel advanced optical designs with a dramatically smaller display to eye distance, excellent image quality and a large field of view (FOV). This enables headsets to be much more compact, typically occupying about a fourth of the volume of a conventional headset with the same FOV. The design strategy of these optics is based on a multichannel approach, which reduces the distance from the eye to the display and the display size itself. Unlike conventional microlens arrays, which are also multichannel devices, our designs use freeform optical surfaces to produce excellent imaging quality in the entire field of view, even when operating at very oblique incidences. We present two families of compact solutions that use different types of lenslets: (1) refractive designs, whose lenslets are composed typically of two refractive surfaces each; and (2) light-folding designs that use prism-like three-surface lenslets, in which rays undergo refraction, reflection, total internal reflection and refraction again. The number of lenslets is not fixed, so different configurations may arise, adaptable for flat or curved displays with different aspect ratios. In the refractive designs the distance between the optics and the display decreases with the number of lenslets, allowing for displaying a light-field when the lenslet becomes significantly small than the eye pupil. On the other hand, the correlation between number of lenslets and the optics to display distance is broken in light-folding designs, since their geometry permits achieving a very short display to eye distance with even a small number of lenslets.

Compact CFB: The next generation CFB boiler

DOE Office of Scientific and Technical Information (OSTI.GOV)

Utt, J.

1996-12-31

The next generation of compact circulating fluidized bed (CFB) boilers is described in outline form. The following topics are discussed: compact CFB = pyroflow + compact separator; compact CFB; compact separator is a breakthrough design; advantages of CFB; new design with substantial development history; KUHMO: successful demo unit; KUHMO: good performance over load range with low emissions; KOKKOLA: first commercial unit and emissions; KOKKOLA: first commercial unit and emissions; compact CFB installations; next generation CFB boiler; grid nozzle upgrades; cast segmented vortex finders; vortex finder installation; ceramic anchors; pre-cast vertical bullnose; refractory upgrades; and wet gunning.

Deformation Rates From Climate Cycles in Marine Synorogenic Turbidites, Jaca Basin, Spanish Pyrenees

NASA Astrophysics Data System (ADS)

Anastasio, D. J.; Kodama, K. P.; Pares, J. M.; Hinnov, L. A.

2007-12-01

Synsedimentary structures provide a link between depositional and deformational processes in orogenic belts. Marine growth strata offer great promise in determining precise long-term deformation rates such as uplift, shortening, fault-slip, and folding rates. Magnetostratigraphy and cyclostratigraphy of the Eocene Arguis Fm., a delta slope deposit and the overlying delta plain Belsue-Atares Fm. monitors the varying pace of deformation at Pico del Aguila, a transverse decollement fold in the south Pyrenean foothills. Anhysteretic remanent magnetization (ARM) data show hierarchical cyclicity at all predicted Milankovitch frequencies. ARM is a proxy for fine-grained detrital magnetite concentration. The age distorting effects of pre-lithification compaction on bed thickness and on the rock and paleomagnetic data series were removed using empirical calibration of anisotropy of anhysteretic remanence magnetization to volume loss from laboratory compaction experiments. The decompacted ARM depth domain was converted to time using an improved magnetostratigraphy within the growth section. Tuning filtered ARM data series to the precession index according to the LA2004 orbital model refined the magnetostratigraphic time scale. The precession-tuned growth strata mapped with precision GPS record variable folding rates at 100skyr timescales for 7 Myr and55° of limb tilt. Folding rates accelerate twice to ~30°/Myr and are punctuated by more gradual decelerations to 0-3°/Myr. Submarine folding rates at Pico del Aguila are attributed to episodic thrusting in the fold core along a roof ramp fault and along the basal decollement. Formation-scale deposition in the Paleogene wedge-top basin responded to tectonic forcing, however, clastic facies patterns in the prodeltaic and slope environments reflect regional uplift controlling sediment supply, sea level variations controlling delta front position and climate forcing (e.g. monsoon strength and frequency, pedogenesis) of runoff variability and ecology in intermountain watersheds. Lithologic parameters sensitive to sea level, such as bed thickness and grain size variations in the turbidite section record strong obliquity and eccentricity modulation, whereas, the ARM derived magnetite concentrations record terrestrial watershed sensitive processes such as aridity and windiness operating at precessional time scales.

Discovery of Compact Quiescent Galaxies at Intermediate Redshifts in DEEP2

NASA Astrophysics Data System (ADS)

Blancato, Kirsten; Chilingarian, Igor; Damjanov, Ivana; Moran, Sean; Katkov, Ivan

2015-01-01

Compact quiescent galaxies in the redshift range 0.6 < z < 1.1 are the missing link needed to complete the evolutionary histories of these objects from the high redshift z ≥ 2 Universe to the local z ~ 0 Universe. We identify the first intermediate redshift compact quiescent galaxies by searching a sample of 1,089 objects in the DEEP2 Redshift Survey that have multi-band photometry, spectral fitting, and readily available structural parameters. We find 27 compact quiescent candidates between z = 0.6 and z = 1.1 where each candidate galaxy has archival Hubble Space Telescope (HST) imaging and is visually confirmed to be early-type. The candidates have half-light radii ranging from 0.83 < Re,c < 7.14 kpc (median Re,c = 1.77 kpc) and virial masses ranging from 2.2E10 < Mdyn < 5.6E11 Msun (median Mdyn = 7.7E10 Msun). Of our 27 compact quiescent candidates, 13 are truly compact with sizes at most half of the size of their z ~ 0 counterparts of the same mass. In addition to their structural properties bridging the gap between their high and low redshift counterparts, our sample of intermediate redshift quiescent galaxies span a large range of ages but is drawn from two distinct epochs of galaxy formation: formation at z > 2 which suggests these objects may be the relics of the observed high redshift compact galaxies and formation at z ≤ 2 which suggests there is an additional population of more recently formed massive compact galaxies. This work is supported in part by the NSF REU and DOD ASSURE programs under NSF grant no. 1262851 and by the Smithsonian Institution.

Preliminary results of post-irradiation examination of the AGR-1 TRISO fuel compacts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paul Demkowicz; John Hunn; Robert Morris

2012-10-01

Five irradiated fuel compacts from the AGR-1 experiment have been examined in detail in order to assess in-pile fission product release behavior. Compacts were electrolytically deconsolidated and analyzed using the leach-burn-leach technique to measure fission product inventory in the compact matrix and identify any particles with a defective SiC layer. Loose particles were then gamma counted to measure the fission product inventory. One particle with a defective SiC layer was found in the five compacts examined. The fractional release of Ag 110m from the particles was significant. The total fraction of silver released from all the particles within a compactmore » ranged from 0-0.63 and individual particles within a single compact often exhibited a very wide range of silver release. The average fractional release of Eu-154 from all particles in a compact was 2.4×10-4—1.3×10-2, which is indicative of release through intact coatings. The fractional Cs-134 inventory in the compact matrix was <2×10-5 when all coatings remained intact, indicating good cesium retention. Approximately 1% of the palladium inventory was found in the compact matrix for two of the compacts, indicating significant release through intact coatings.« less

Folding and faulting of an elastic continuum

NASA Astrophysics Data System (ADS)

Bigoni, Davide; Gourgiotis, Panos A.

2016-03-01

Folding is a process in which bending is localized at sharp edges separated by almost undeformed elements. This process is rarely encountered in Nature, although some exceptions can be found in unusual layered rock formations (called `chevrons') and seashell patterns (for instance Lopha cristagalli). In mechanics, the bending of a three-dimensional elastic solid is common (for example, in bulk wave propagation), but folding is usually not achieved. In this article, the route leading to folding is shown for an elastic solid obeying the couple-stress theory with an extreme anisotropy. This result is obtained with a perturbation technique, which involves the derivation of new two-dimensional Green's functions for applied concentrated force and moment. While the former perturbation reveals folding, the latter shows that a material in an extreme anisotropic state is also prone to a faulting instability, in which a displacement step of finite size emerges. Another failure mechanism, namely the formation of dilation/compaction bands, is also highlighted. Finally, a geophysical application to the mechanics of chevron formation shows how the proposed approach may explain the formation of natural structures.

Folding and faulting of an elastic continuum

PubMed Central

Gourgiotis, Panos A.

2016-01-01

Folding is a process in which bending is localized at sharp edges separated by almost undeformed elements. This process is rarely encountered in Nature, although some exceptions can be found in unusual layered rock formations (called ‘chevrons’) and seashell patterns (for instance Lopha cristagalli). In mechanics, the bending of a three-dimensional elastic solid is common (for example, in bulk wave propagation), but folding is usually not achieved. In this article, the route leading to folding is shown for an elastic solid obeying the couple-stress theory with an extreme anisotropy. This result is obtained with a perturbation technique, which involves the derivation of new two-dimensional Green's functions for applied concentrated force and moment. While the former perturbation reveals folding, the latter shows that a material in an extreme anisotropic state is also prone to a faulting instability, in which a displacement step of finite size emerges. Another failure mechanism, namely the formation of dilation/compaction bands, is also highlighted. Finally, a geophysical application to the mechanics of chevron formation shows how the proposed approach may explain the formation of natural structures. PMID:27118925

Protein denaturation in vacuo: intrinsic unfolding pathways associated with the native tertiary structure of lysozyme

NASA Astrophysics Data System (ADS)

Arteca, Gustavo A.; Tapia, O.

Using computer-simulated molecular dynamics, we study the effect of sequence mutation on the unfolding mechanism of a native fold. The system considered is the native fold of hen egg-white lysozyme, exposed to centrifugal unfolding in vacuo. This unfolding bias elicits configurational transitions that imitate the behaviour of anhydrous proteins diffusing after electrospraying from neutral-pH solutions. By changing the sequences threaded onto the native fold of lysozyme, we probe the role of disulfide bridges and the effect of a global mutation. We find that the initial denaturing steps share common characteristics for the tested sequences. Recurrent features are: (i) the presence of dumbbell conformers with significant residual secondary structure, (ii) the ubiquitous formation of hairpins and two-stranded β-sheets regardless of disulfide bridges, and (iii) an unfolding pattern where the reduction in folding complexity is highly correlated with the decrease in chain compactness. These findings appear to be intrinsic to the shape of the native fold, suggesting that similar unfolding pathways may be accessible to many protein sequences.

Ultrathin thermoresponsive self-folding 3D graphene

PubMed Central

Xu, Weinan; Qin, Zhao; Chen, Chun-Teh; Kwag, Hye Rin; Ma, Qinli; Sarkar, Anjishnu; Buehler, Markus J.; Gracias, David H.

2017-01-01

Graphene and other two-dimensional materials have unique physical and chemical properties of broad relevance. It has been suggested that the transformation of these atomically planar materials to three-dimensional (3D) geometries by bending, wrinkling, or folding could significantly alter their properties and lead to novel structures and devices with compact form factors, but strategies to enable this shape change remain limited. We report a benign thermally responsive method to fold and unfold monolayer graphene into predesigned, ordered 3D structures. The methodology involves the surface functionalization of monolayer graphene using ultrathin noncovalently bonded mussel-inspired polydopamine and thermoresponsive poly(N-isopropylacrylamide) brushes. The functionalized graphene is micropatterned and self-folds into ordered 3D structures with reversible deformation under a full control by temperature. The structures are characterized using spectroscopy and microscopy, and self-folding is rationalized using a multiscale molecular dynamics model. Our work demonstrates the potential to design and fabricate ordered 3D graphene structures with predictable shape and dynamics. We highlight applicability by encapsulating live cells and creating nonlinear resistor and creased transistor devices. PMID:28989963

Transition Pathway and Its Free-Energy Profile: A Protocol for Protein Folding Simulations

PubMed Central

Lee, In-Ho; Kim, Seung-Yeon; Lee, Jooyoung

2013-01-01

We propose a protocol that provides a systematic definition of reaction coordinate and related free-energy profile as the function of temperature for the protein-folding simulation. First, using action-derived molecular dynamics (ADMD), we investigate the dynamic folding pathway model of a protein between a fixed extended conformation and a compact conformation. We choose the pathway model to be the reaction coordinate, and the folding and unfolding processes are characterized by the ADMD step index, in contrast to the common a priori reaction coordinate as used in conventional studies. Second, we calculate free-energy profile as the function of temperature, by employing the replica-exchange molecular dynamics (REMD) method. The current method provides efficient exploration of conformational space and proper characterization of protein folding/unfolding dynamics from/to an arbitrary extended conformation. We demonstrate that combination of the two simulation methods, ADMD and REMD, provides understanding on molecular conformational changes in proteins. The protocol is tested on a small protein, penta-peptide of met-enkephalin. For the neuropeptide met-enkephalin system, folded, extended, and intermediate sates are well-defined through the free-energy profile over the reaction coordinate. Results are consistent with those in the literature. PMID:23917881

Planar near-field scanning for compact range bistatic radar cross-section measurement. Thesis Final Report

NASA Technical Reports Server (NTRS)

Tuhela-Reuning, S. R.; Walton, E. K.

1991-01-01

The design, construction, and testing of a low cost, planar scanning system to be used in a compact range environment for bistatic radar cross-section (bistatic RCS) measurement data are discussed. This scanning system is similar to structures used for measuring near-field antenna patterns. A synthetic aperture technique is used for plane wave reception. System testing entailed comparison of measured and theoretical bistatic RCS of a sphere and a right circular cylinder. Bistatic scattering analysis of the ogival target support, target and pedestal interactions, and compact range room was necessary to determine measurement validity.

Mitotic chromosome compaction via active loop extrusion

NASA Astrophysics Data System (ADS)

Goloborodko, Anton; Imakaev, Maxim; Marko, John; Mirny, Leonid; MIT-Northwestern Team

During cell division, two copies of each chromosome are segregated from each other and compacted more than hundred-fold into the canonical X-shaped structures. According to earlier microscopic observations and the recent Hi-C study, chromosomes are compacted into arrays of consecutive loops of ~100 kilobases. Mechanisms that lead to formation of such loop arrays are largely unknown. Here we propose that, during cell division, chromosomes can be compacted by enzymes that extrude loops on chromatin fibers. First, we use computer simulations and analytical modeling to show that a system of loop-extruding enzymes on a chromatin fiber self-organizes into an array of consecutive dynamic loops. Second, we model the process of loop extrusion in 3D and show that, coupled with the topo II strand-passing activity, it leads to robust compaction and segregation of sister chromatids. This mechanism of chromosomal condensation and segregation does not require additional proteins or specific DNA markup and is robust against variations in the number and properties of such loop extruding enzymes. Work at NU was supported by the NSF through Grants DMR-1206868 and MCB-1022117, and by the NIH through Grants GM105847 and CA193419. Work at MIT was supported by the NIH through Grants GM114190 R01HG003143.

Robust control of electrostatic torsional micromirrors using adaptive sliding-mode control

NASA Astrophysics Data System (ADS)

Sane, Harshad S.; Yazdi, Navid; Mastrangelo, Carlos H.

2005-01-01

This paper presents high-resolution control of torsional electrostatic micromirrors beyond their inherent pull-in instability using robust sliding-mode control (SMC). The objectives of this paper are two-fold - firstly, to demonstrate the applicability of SMC for MEMS devices; secondly - to present a modified SMC algorithm that yields improved control accuracy. SMC enables compact realization of a robust controller tolerant of device characteristic variations and nonlinearities. Robustness of the control loop is demonstrated through extensive simulations and measurements on MEMS with a wide range in their characteristics. Control of two-axis gimbaled micromirrors beyond their pull-in instability with overall 10-bit pointing accuracy is confirmed experimentally. In addition, this paper presents an analysis of the sources of errors in discrete-time implementation of the control algorithm. To minimize these errors, we present an adaptive version of the SMC algorithm that yields substantial performance improvement without considerably increasing implementation complexity.

Compact, flexible, frequency agile parametric wavelength converter

DOEpatents

Velsko, Stephan P.; Yang, Steven T.

2002-01-01

This improved Frequency Agile Optical Parametric Oscillator provides near on-axis pumping of a single QPMC with a tilted periodically poled grating to overcome the necessity to find a particular crystal that will permit collinear birefringence in order to obtain a desired tuning range. A tilted grating design and the elongation of the transverse profile of the pump beam in the angle tuning plane of the FA-OPO reduces the rate of change of the overlap between the pumped volume in the crystal and the resonated and non-resonated wave mode volumes as the pump beam angle is changed. A folded mirror set relays the pivot point for beam steering from a beam deflector to the center of the FA-OPO crystal. This reduces the footprint of the device by as much as a factor of two over that obtained when using the refractive telescope design.

Compact quantum dot-antibody conjugates for FRET immunoassays with subnanomolar detection limits.

PubMed

Mattera, Lucia; Bhuckory, Shashi; Wegner, K David; Qiu, Xue; Agnese, Fabio; Lincheneau, Christophe; Senden, Tim; Djurado, David; Charbonnière, Loïc J; Hildebrandt, Niko; Reiss, Peter

2016-06-07

A novel two-step approach for quantum dot (QD) functionalization and bioconjugation is presented, which yields ultra-compact, stable, and highly luminescent antibody-QD conjugates suitable for use in FRET immunoassays. Hydrophobic InPZnS/ZnSe/ZnS (emission wavelength: 530 nm), CdSe/ZnS (605 nm), and CdSeTe/ZnS (705 nm) QDs were surface functionalized with zwitterionic penicillamine, enabling aqueous phase transfer under conservation of the photoluminescence properties. Post-functionalization with a heterobifunctional crosslinker, containing a lipoic acid group and a maleimide function, enabled the subsequent coupling to sulfhydryl groups of proteins. This was demonstrated by QD conjugation with fragmented antibodies (F(ab)). The obtained F(ab)-QD conjugates range among the smallest antibody-functionalized nanoprobes ever reported, with a hydrodynamic diameter <13 nm, PL quantum yield up to 66% at 705 nm, and colloidal stability of several months in various buffers. They were applied as FRET acceptors in homogeneous, time-gated immunoassays using Tb-antibodies as FRET donors, both coupled by an immunological sandwich complex between the two antibodies and a PSA (prostate specific antigen) biomarker. The advantages of the compact surface coating for FRET could be demonstrated by an 6.2 and 2.5 fold improvement of the limit of detection (LOD) for PSA compared to commercially available hydrophilic QDs emitting at 605 and 705 nm, respectively. While the commercial QDs contain identical inorganic cores responsible for their fluorescence, they are coated with a comparably thick amphiphilic polymer layer leading to much larger hydrodynamic diameters (>26 nm without biomolecules). The LODs of 0.8 and 3.7 ng mL(-1) obtained in 50 μL serum samples are below the clinical cut-off level of PSA (4 ng mL(-1)) and demonstrate their direct applicability in clinical diagnostics.

Multilayer DNA Origami Packed on a Square Lattice

PubMed Central

Ke, Yonggang; Douglas, Shawn M.; Liu, Minghui; Sharma, Jaswinder; Cheng, Anchi; Leung, Albert; Liu, Yan; Shih, William M.; Yan, Hao

2009-01-01

Molecular self-assembly using DNA as a structural building block has proven to be an efficient route to the construction of nanoscale objects and arrays of increasing complexity. Using the remarkable “scaffolded DNA origami” strategy, Rothemund demonstrated that a long single-stranded DNA from a viral genome (M13) can be folded into a variety of custom two-dimensional (2D) shapes using hundreds of short synthetic DNA molecules as staple strands. More recently, we generalized a strategy to build custom-shaped, three-dimensional (3D) objects formed as pleated layers of helices constrained to a honeycomb lattice, with precisely controlled dimensions ranging from 10 to 100 nm. Here we describe a more compact design for 3D origami, with layers of helices packed on a square lattice, that can be folded successfully into structures of designed dimensions in a one-step annealing process, despite the increased density of DNA helices. A square lattice provides a more natural framework for designing rectangular structures, the option for a more densely packed architecture, and the ability to create surfaces that are more flat than is possible with the honeycomb lattice. Thus enabling the design and construction of custom 3D shapes from helices packed on a square lattice provides a general foundational advance for increasing the versatility and scope of DNA nanotechnology. PMID:19807088

Free-energy landscape of a hyperstable RNA tetraloop

PubMed Central

Miner, Jacob C.; Chen, Alan A.; García, Angel E.

2016-01-01

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif. PMID:27233937

Measuring internal friction of an ultrafast-folding protein.

PubMed

Cellmer, Troy; Henry, Eric R; Hofrichter, James; Eaton, William A

2008-11-25

Nanosecond laser T-jump was used to measure the viscosity dependence of the folding kinetics of the villin subdomain under conditions where the viscogen has no effect on its equilibrium properties. The dependence of the unfolding/refolding relaxation time on solvent viscosity indicates a major contribution to the dynamics from internal friction. The internal friction increases with increasing temperature, suggesting a shift in the transition state along the reaction coordinate toward the native state with more compact structures, and therefore, a smaller diffusion coefficient due to increased landscape roughness. Fitting the data with an Ising-like model yields a relatively small position dependence for the diffusion coefficient. This finding is consistent with the excellent correlation found between experimental and calculated folding rates based on free energy barrier heights using the same diffusion coefficient for every protein.

Compact range for variable-zone measurements

DOEpatents

Burnside, Walter D.; Rudduck, Roger C.; Yu, Jiunn S.

1988-08-02

A compact range for testing antennas or radar targets includes a source for directing energy along a feedline toward a parabolic reflector. The reflected wave is a spherical wave with a radius dependent on the distance of the source from the focal point of the reflector.

Compact range for variable-zone measurements

DOEpatents

Burnside, Walter D.; Rudduck, Roger C.; Yu, Jiunn S.

1988-01-01

A compact range for testing antennas or radar targets includes a source for directing energy along a feedline toward a parabolic reflector. The reflected wave is a spherical wave with a radius dependent on the distance of the source from the focal point of the reflector.

Role of Tryptophan Side Chain Dynamics on the Trp-Cage Mini-Protein Folding Studied by Molecular Dynamics Simulations

PubMed Central

Kannan, Srinivasaraghavan; Zacharias, Martin

2014-01-01

The 20 residue Trp-cage mini-protein is one of smallest proteins that adopt a stable folded structure containing also well-defined secondary structure elements. The hydrophobic core is arranged around a single central Trp residue. Despite several experimental and simulation studies the detailed folding mechanism of the Trp-cage protein is still not completely understood. Starting from fully extended as well as from partially folded Trp-cage structures a series of molecular dynamics simulations in explicit solvent and using four different force fields was performed. All simulations resulted in rapid collapse of the protein to on average relatively compact states. The simulations indicate a significant dependence of the speed of folding to near-native states on the side chain rotamer state of the central Trp residue. Whereas the majority of intermediate start structures with the central Trp side chain in a near-native rotameric state folded successfully within less than 100 ns only a fraction of start structures reached near-native folded states with an initially non-native Trp side chain rotamer state. Weak restraining of the Trp side chain dihedral angles to the state in the folded protein resulted in significant acceleration of the folding both starting from fully extended or intermediate conformations. The results indicate that the side chain conformation of the central Trp residue can create a significant barrier for controlling transitions to a near native folded structure. Similar mechanisms might be of importance for the folding of other protein structures. PMID:24563686

Compact range for variable-zone measurements

DOEpatents

Burnside, W.D.; Rudduck, R.C.; Yu, J.S.

1987-02-27

A compact range for testing antennas or radar targets includes a source for directing energy along a feedline toward a parabolic reflector. The reflected wave is a spherical wave with a radius dependent on the distance of the source from the focal point of the reflector. 2 figs.

Structures of D14 and D14L in the strigolactone and karrikin signaling pathways.

PubMed

Kagiyama, Megumi; Hirano, Yoshinori; Mori, Tomoyuki; Kim, Sun-Yong; Kyozuka, Junko; Seto, Yoshiya; Yamaguchi, Shinjiro; Hakoshima, Toshio

2013-02-01

Strigolactones (SLs) are plant hormones that inhibit shoot branching. DWARF14 (D14) inhibits rice tillering and is an SL receptor candidate in the branching inhibition pathway, whereas the close homologue DWARF14-LIKE (D14L) participates in the signaling pathway of karrikins (KARs), which are derived from burnt vegetation as smoke stimulants of seed germination. We provide the first evidence for direct binding of the bioactive SL analogue GR24 to D14. Isothermal titration calorimetry measurements show a D14-GR24 binding affinity in the sub-micromolar range. Similarly, bioactive KAR1 directly binds D14L in the micromolar range. The crystal structure of rice D14 shows a compact α-/β-fold hydrolase domain forming a deep ligand-binding pocket capable of accommodating GR24. Insertion of four α-helices between β6 strand and αD helix forms the helical cap of the pocket, although the pocket is open to the solvent. The pocket contains the conserved catalytic triad Ser-His-Asp aligned with the oxyanion hole, suggesting hydrolase activity. Although these structural characteristics are conserved in D14L, the D14L pocket is smaller than that of D14. The KAR-insensitive mutation kai2-1 is located at the prominent long β6-αD1 loop, which is characteristic in D14 and D14L, but not in related α-/β-fold hydrolases. © 2013 The Authors Genes to Cells © 2013 by the Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

Cell Adhesion Molecule L1 in Folded (Horseshoe) and Extended Conformations

PubMed Central

Schürmann, Gregor; Haspel, Jeffrey; Grumet, Martin; Erickson, Harold P.

2001-01-01

We have investigated the structure of the cell adhesion molecule L1 by electron microscopy. We were particularly interested in the conformation of the four N-terminal immunoglobulin domains, because x-ray diffraction showed that these domains are bent into a horseshoe shape in the related molecules hemolin and axonin-1. Surprisingly, rotary-shadowed specimens showed the molecules to be elongated, with no indication of the horseshoe shape. However, sedimentation data suggested that these domains of L1 were folded into a compact shape in solution; therefore, this prompted us to look at the molecules by an alternative technique, negative stain. The negative stain images showed a compact shape consistent with the expected horseshoe conformation. We speculate that in rotary shadowing the contact with the mica caused a distortion of the protein, weakening the bonds forming the horseshoe and permitting the molecule to extend. We have thus confirmed that the L1 molecule is primarily in the horseshoe conformation in solution, and we have visualized for the first time its opening into an extended conformation. Our study resolves conflicting interpretations from previous electron microscopy studies of L1. PMID:11408583

Equations of state for neutron stars and core-collapse supernovae

NASA Astrophysics Data System (ADS)

Oertel, Micaela; Providência, Constança

2018-04-01

Modelling compact stars is a complex task which depends on many ingredients, among others the properties of dense matter. In this contribution models for the equation of state (EoS) of dense matter will be discussed, relevant for the description of core-collapse supernovae, compact stars and compact star mergers. Such EoS models have to cover large ranges in baryon number density, temperature and isospin asymmetry. The characteristics of matter change dramatically within these ranges, from a mixture of nucleons, nuclei, and electrons to uniform, strongly interacting matter containing nucleons, and possibly other particles such as hyperons or quarks. Some implications for compact star astrophysics will be highlighted, too.

Towards next generation time-domain diffuse optics devices

NASA Astrophysics Data System (ADS)

Dalla Mora, Alberto; Contini, Davide; Arridge, Simon R.; Martelli, Fabrizio; Tosi, Alberto; Boso, Gianluca; Farina, Andrea; Durduran, Turgut; Martinenghi, Edoardo; Torricelli, Alessandro; Pifferi, Antonio

2015-03-01

Diffuse Optics is growing in terms of applications ranging from e.g. oximetry, to mammography, molecular imaging, quality assessment of food and pharmaceuticals, wood optics, physics of random media. Time-domain (TD) approaches, although appealing in terms of quantitation and depth sensibility, are presently limited to large fiber-based systems, with limited number of source-detector pairs. We present a miniaturized TD source-detector probe embedding integrated laser sources and single-photon detectors. Some electronics are still external (e.g. power supply, pulse generators, timing electronics), yet full integration on-board using already proven technologies is feasible. The novel devices were successfully validated on heterogeneous phantoms showing performances comparable to large state-of-the-art TD rack-based systems. With an investigation based on simulations we provide numerical evidence that the possibility to stack many TD compact source-detector pairs in a dense, null source-detector distance arrangement could yield on the brain cortex about 1 decade higher contrast as compared to a continuous wave (CW) approach. Further, a 3-fold increase in the maximum depth (down to 6 cm) is estimated, opening accessibility to new organs such as the lung or the heart. Finally, these new technologies show the way towards compact and wearable TD probes with orders of magnitude reduction in size and cost, for a widespread use of TD devices in real life.

Characterization of DNA condensates induced by poly(ethylene oxide) and polylysine.

PubMed Central

Laemmli, U K

1975-01-01

High-molecular-weight DNA is known to collapse into very compact particles in a salt solution containing polymers like poly(ethylene oxide) [(EO)n] or polyacrylate. The biological relevance of this phenomenon is suggested by our recent finding that high concentrations of the highly acidic internal peptides found in the mature T4 bacteriophage head, as well as poly(glutamic acid) and poly(aspartic acid), can collapse DNA in a similar manner. The structure of DNAs collapsed by various methods has been studied with electron microscope. We find (EO)n collapses T4 or T7 bacteriophage DNA into compact particles only slightly larger than the size of the T4 and T7 head, respectively. In contrast, polylysine collapses DNA into different types of structures. Double-stranded DNA collapsed with (EO)n is cut by the single-strand specific Neurospora crassa endonuclease (EC 3.1.4.21) into small fragments. Extensive digestion only occurs above the critical concentration of polymer required for DNA collapse, demonstrating the (EO)n-collapsed DNA contains enzyme-vulnerable regions (probably at each fold), which are preferentially attacked. The size of the DNA fragments produced by limit-digestion with the nuclease ranges between 200 and 400 base pairs when DNA is collapsed by (EO)n. Only fragments of DNA which are larger than 600 base pairs are cut by the endonuclease in (EO)n-containing solution. Images PMID:1060108

Holographic duals of 3d S-fold CFTs

NASA Astrophysics Data System (ADS)

Assel, Benjamin; Tomasiello, Alessandro

2018-06-01

We construct non-geometric AdS4 solutions of IIB string theory where the fields in overlapping patches are glued by elements of the S-duality group. We obtain them by suitable quotients of compact and non-compact geometric solutions. The quotient procedure suggests CFT duals as quiver theories with links involving the so-called T [U( N)] theory. We test the validity of the non-geometric solutions (and of our proposed holographic duality) by computing the three-sphere partition function Z of the CFTs. A first class of solutions is obtained by an S-duality quotient of Janus-type non-compact solutions and is dual to 3d N=4 SCFTs; for these we manage to compute Z of the dual CFT at finite N, and it agrees perfectly with the supergravity result in the large N limit. A second class has five-branes, it is obtained by a Möbius-like S-quotient of ordinary compact solutions and is dual to 3d N=3 SCFTs. For these, Z agrees with the supergravity result if one chooses the limit carefully so that the effect of the fivebranes does not backreact on the entire geometry. Other limits suggest the existence of IIA duals.

Compact Conformations of Human Protein Disulfide Isomerase

PubMed Central

Cui, Lei; Ding, Xiang; Niu, Lili; Yang, Fuquan; Wang, Chao; Wang, Chih-chen; Lou, Jizhong

2014-01-01

Protein disulfide isomerase (PDI) composed of four thioredoxin-like domains a, b, b', and a', is a key enzyme catalyzing oxidative protein folding in the endoplasmic reticulum. Large scale molecular dynamics simulations starting from the crystal structures of human PDI (hPDI) in the oxidized and reduced states were performed. The results indicate that hPDI adopts more compact conformations in solution than in the crystal structures, which are stabilized primarily by inter-domain interactions, including the salt bridges between domains a and b' observed for the first time. A prominent feature of the compact conformations is that the two catalytic domains a and a' can locate close enough for intra-molecular electron transfer, which was confirmed by the characterization of an intermediate with a disulfide between the two domains. Mutations, which disrupt the inter-domain interactions, lead to decreased reductase activity of hPDI. Our molecular dynamics simulations and biochemical experiments reveal the intrinsic conformational dynamics of hPDI and its biological impact. PMID:25084354

GEOS-2 C-band radar system project. Spectral analysis as related to C-band radar data analysis

NASA Technical Reports Server (NTRS)

1972-01-01

Work performed on spectral analysis of data from the C-band radars tracking GEOS-2 and on the development of a data compaction method for the GEOS-2 C-band radar data is described. The purposes of the spectral analysis study were to determine the optimum data recording and sampling rates for C-band radar data and to determine the optimum method of filtering and smoothing the data. The optimum data recording and sampling rate is defined as the rate which includes an optimum compromise between serial correlation and the effects of frequency folding. The goal in development of a data compaction method was to reduce to a minimum the amount of data stored, while maintaining all of the statistical information content of the non-compacted data. A digital computer program for computing estimates of the power spectral density function of sampled data was used to perform the spectral analysis study.

Predicting Achievable Fundamental Frequency Ranges in Vocalization Across Species

PubMed Central

Titze, Ingo; Riede, Tobias; Mau, Ted

2016-01-01

Vocal folds are used as sound sources in various species, but it is unknown how vocal fold morphologies are optimized for different acoustic objectives. Here we identify two main variables affecting range of vocal fold vibration frequency, namely vocal fold elongation and tissue fiber stress. A simple vibrating string model is used to predict fundamental frequency ranges across species of different vocal fold sizes. While average fundamental frequency is predominantly determined by vocal fold length (larynx size), range of fundamental frequency is facilitated by (1) laryngeal muscles that control elongation and by (2) nonlinearity in tissue fiber tension. One adaptation that would increase fundamental frequency range is greater freedom in joint rotation or gliding of two cartilages (thyroid and cricoid), so that vocal fold length change is maximized. Alternatively, tissue layers can develop to bear a disproportionate fiber tension (i.e., a ligament with high density collagen fibers), increasing the fundamental frequency range and thereby vocal versatility. The range of fundamental frequency across species is thus not simply one-dimensional, but can be conceptualized as the dependent variable in a multi-dimensional morphospace. In humans, this could allow for variations that could be clinically important for voice therapy and vocal fold repair. Alternative solutions could also have importance in vocal training for singing and other highly-skilled vocalizations. PMID:27309543

Fission Product Inventory and Burnup Evaluation of the AGR-2 Irradiation by Gamma Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harp, Jason Michael; Stempien, John Dennis; Demkowicz, Paul Andrew

Gamma spectrometry has been used to evaluate the burnup and fission product inventory of different components from the US Advanced Gas Reactor Fuel Development and Qualification Program's second TRISO-coated particle fuel irradiation test (AGR-2). TRISO fuel in this irradiation included both uranium carbide / uranium oxide (UCO) kernels and uranium oxide (UO 2) kernels. Four of the 6 capsules contained fuel from the US Advanced Gas Reactor program, and only those capsules will be discussed in this work. The inventories of gamma-emitting fission products from the fuel compacts, graphite compact holders, graphite spacers and test capsule shell were evaluated. Thesemore » data were used to measure the fractional release of fission products such as Cs-137, Cs-134, Eu-154, Ce-144, and Ag-110m from the compacts. The fraction of Ag-110m retained in the compacts ranged from 1.8% to full retention. Additionally, the activities of the radioactive cesium isotopes (Cs-134 and Cs-137) have been used to evaluate the burnup of all US TRISO fuel compacts in the irradiation. The experimental burnup evaluations compare favorably with burnups predicted from physics simulations. Predicted burnups for UCO compacts range from 7.26 to 13.15 % fission per initial metal atom (FIMA) and 9.01 to 10.69 % FIMA for UO 2 compacts. Measured burnup ranged from 7.3 to 13.1 % FIMA for UCO compacts and 8.5 to 10.6 % FIMA for UO 2 compacts. Results from gamma emission computed tomography performed on compacts and graphite holders that reveal the distribution of different fission products in a component will also be discussed. Gamma tomography of graphite holders was also used to locate the position of TRISO fuel particles suspected of having silicon carbide layer failures that lead to in-pile cesium release.« less

Fission Product Inventory and Burnup Evaluation of the AGR-2 Irradiation by Gamma Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harp, Jason M.; Demkowicz, Paul A.; Stempien, John D.

Gamma spectrometry has been used to evaluate the burnup and fission product inventory of different components from the US Advanced Gas Reactor Fuel Development and Qualification Program's second TRISO-coated particle fuel irradiation test (AGR-2). TRISO fuel in this irradiation included both uranium carbide / uranium oxide (UCO) kernels and uranium oxide (UO2) kernels. Four of the 6 capsules contained fuel from the US Advanced Gas Reactor program, and only those capsules will be discussed in this work. The inventories of gamma-emitting fission products from the fuel compacts, graphite compact holders, graphite spacers and test capsule shell were evaluated. These datamore » were used to measure the fractional release of fission products such as Cs-137, Cs-134, Eu-154, Ce-144, and Ag-110m from the compacts. The fraction of Ag-110m retained in the compacts ranged from 1.8% to full retention. Additionally, the activities of the radioactive cesium isotopes (Cs-134 and Cs-137) have been used to evaluate the burnup of all US TRISO fuel compacts in the irradiation. The experimental burnup evaluations compare favorably with burnups predicted from physics simulations. Predicted burnups for UCO compacts range from 7.26 to 13.15 % fission per initial metal atom (FIMA) and 9.01 to 10.69 % FIMA for UO2 compacts. Measured burnup ranged from 7.3 to 13.1 % FIMA for UCO compacts and 8.5 to 10.6 % FIMA for UO2 compacts. Results from gamma emission computed tomography performed on compacts and graphite holders that reveal the distribution of different fission products in a component will also be discussed. Gamma tomography of graphite holders was also used to locate the position of TRISO fuel particles suspected of having silicon carbide layer failures that lead to in-pile cesium release.« less

A molecular mechanism of chaperone-client recognition

PubMed Central

He, Lichun; Sharpe, Timothy; Mazur, Adam; Hiller, Sebastian

2016-01-01

Molecular chaperones are essential in aiding client proteins to fold into their native structure and in maintaining cellular protein homeostasis. However, mechanistic aspects of chaperone function are still not well understood at the atomic level. We use nuclear magnetic resonance spectroscopy to elucidate the mechanism underlying client recognition by the adenosine triphosphate-independent chaperone Spy at the atomic level and derive a structural model for the chaperone-client complex. Spy interacts with its partially folded client Im7 by selective recognition of flexible, locally frustrated regions in a dynamic fashion. The interaction with Spy destabilizes a partially folded client but spatially compacts an unfolded client conformational ensemble. By increasing client backbone dynamics, the chaperone facilitates the search for the native structure. A comparison of the interaction of Im7 with two other chaperones suggests that the underlying principle of recognizing frustrated segments is of a fundamental nature. PMID:28138538

Investigation of hindwing folding in ladybird beetles by artificial elytron transplantation and microcomputed tomography.

PubMed

Saito, Kazuya; Nomura, Shuhei; Yamamoto, Shuhei; Niiyama, Ryuma; Okabe, Yoji

2017-05-30

Ladybird beetles are high-mobility insects and explore broad areas by switching between walking and flying. Their excellent wing transformation systems enabling this lifestyle are expected to provide large potential for engineering applications. However, the mechanism behind the folding of their hindwings remains unclear. The reason is that ladybird beetles close the elytra ahead of wing folding, preventing the observation of detailed processes occurring under the elytra. In the present study, artificial transparent elytra were transplanted on living ladybird beetles, thereby enabling us to observe the detailed wing-folding processes. The result revealed that in addition to the abdominal movements mentioned in previous studies, the edge and ventral surface of the elytra, as well as characteristic shaped veins, play important roles in wing folding. The structures of the wing frames enabling this folding process and detailed 3D shape of the hindwing were investigated using microcomputed tomography. The results showed that the tape spring-like elastic frame plays an important role in the wing transformation mechanism. Compared with other beetles, hindwings in ladybird beetles are characterized by two seemingly incompatible properties: ( i ) the wing rigidity with relatively thick veins and ( ii ) the compactness in stored shapes with complex crease patterns. The detailed wing-folding process revealed in this study is expected to facilitate understanding of the naturally optimized system in this excellent deployable structure.

Investigation of hindwing folding in ladybird beetles by artificial elytron transplantation and microcomputed tomography

PubMed Central

Nomura, Shuhei; Yamamoto, Shuhei; Niiyama, Ryuma; Okabe, Yoji

2017-01-01

Ladybird beetles are high-mobility insects and explore broad areas by switching between walking and flying. Their excellent wing transformation systems enabling this lifestyle are expected to provide large potential for engineering applications. However, the mechanism behind the folding of their hindwings remains unclear. The reason is that ladybird beetles close the elytra ahead of wing folding, preventing the observation of detailed processes occurring under the elytra. In the present study, artificial transparent elytra were transplanted on living ladybird beetles, thereby enabling us to observe the detailed wing-folding processes. The result revealed that in addition to the abdominal movements mentioned in previous studies, the edge and ventral surface of the elytra, as well as characteristic shaped veins, play important roles in wing folding. The structures of the wing frames enabling this folding process and detailed 3D shape of the hindwing were investigated using microcomputed tomography. The results showed that the tape spring-like elastic frame plays an important role in the wing transformation mechanism. Compared with other beetles, hindwings in ladybird beetles are characterized by two seemingly incompatible properties: (i) the wing rigidity with relatively thick veins and (ii) the compactness in stored shapes with complex crease patterns. The detailed wing-folding process revealed in this study is expected to facilitate understanding of the naturally optimized system in this excellent deployable structure. PMID:28507159

Folding dynamics of linear emulsion polymers into 3D architectures

NASA Astrophysics Data System (ADS)

McMullen, Angus; Bargteil, Dylan; Brujic, Jasna

Colloidal polymers have been limited to inflexible, solid colloids. Here we show that the fluidity of emulsion droplets allows for the self-assembly of flexible droplet chains, which can subsequently be folded into 3D structures via secondary interactions. We achieve this using DNA-guided interactions, to initially form the chain, and then program its folding pathways. When two emulsion droplets labeled with complementary DNA meet, the balance of hybridization energy and droplet deformation yields an equilibrium patch size. Therefore, the concentration of DNA on the surface determines the number of droplet-droplet bonds in the assembly. We find that 96 % of bound droplets successfully self-assemble into chains. Droplet binding is a stochastic process, following a Poisson distribution of lengths. Since the fluid droplets can rearrange, we compare the dynamics of emulsion chains to that of polymers. We also trigger secondary interactions along the chain, causing the formation of specific loops or compact clusters. This approach will allow us to fold our emulsion polymers into a wide array of soft structures, giving us a powerful biomimetic colloidal system to investigate protein folding on the mesoscopic scale. This work was supported by the NSF MRSEC Program (DMR-0820341).

RF Metamaterials for Foliage Penetration (FOPEN) Application

DTIC Science & Technology

2013-02-01

from LM TRACER program to develop those prototypes. Fig. 29 is an OSU prototype (#1, 7x7 array) fabricated and tested inside the ESL compact range...Fig. 29 shows the Prototype #1 under testing inside the ESL compact range. Figure 29 -Prototype #1 (7x7 Single-pol. Array) 3.2.3.1.2

Wide range stress intensity factor expressions for ASTM E 399 standard fracture toughness specimens

NASA Technical Reports Server (NTRS)

Srawley, J. E.

1976-01-01

For each of the two types of specimens, bend and compact, described previously for plane strain fracture toughness of materials, E 399, a polynominal expression is given for calculation of the stress intensity factor, K, from the applied force, P, and the specimen dimensions. It is explicitly stated, however, that these expressions should not be used outside the range of relative crack length, a/W, from 0.45 to 0.55. While this range is sufficient for the purpose of E 399, the same specimen types are often used for other purposes over a much wider range of a/W; for example, in the study of fatigue crack growth. Expressions are presented which are at least as accurate as those in E 399-74, and which cover much wider ranges of a/W: for the three-point bend specimen from 0 to 1; and for the compact specimen from 0.2 to 1. The range has to be restricted for the compact specimen because of the proximity of the loading pin holes to the crackline, which causes the stress intensity factor to be sensitive to small variations in dimensions when a/W is small. This is a penalty inherently associated with the compactness of the specimen.

Site preparation treatments and nutrient loss following complete harvest csing the Nicholson-Koch mobile chipper

Treesearch

R. Gordon; James H. Miller; C. Brewer

1981-01-01

Site disturbance, vegetation control, and nutrient loss were assessed following complete biomass harvesting of a pine plantation by the Nicholson-Koch mobile chipper. Thirty-two percent of the soil area was significantly compacted to a 10 cm depth. Litter zone material showed a two-fold increase due to chips lost during harvest. Herbicide treatments (Tordon 10K and...

Relative costs of transporting low-level waste according to four postulated regional-management cases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilmot, E.L.; Shirley, C.G.

1982-01-01

Results presented in this paper show that almost any compact binding states into cooperating regions for disposal of LLW will reduce nationwide transportation costs markedly. As a corollary, the reduction of costs may reflect a two- to four-fold reduction of transportation distances with consequent reduction of risk to the public since risk generally decreases directly as transport distances decrease.

Milli-Biology

DTIC Science & Technology

2011-10-30

techniques can produce nanostructured programmable objects. The length scale of the driving physics limits the size scale of objects in DNA origami ...been working on developing a more compact design for 3D origami , with layers of helices packed on a square lattice, that can be folded successfully...version of the CADnano DNA origami CAD software to support square lattice designs. Achieving a simple and standardized way to create designs with the

Compact silicon photonic wavelength-tunable laser diode with ultra-wide wavelength tuning range

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kita, Tomohiro, E-mail: tkita@ecei.tohoku.ac.jp; Tang, Rui; Yamada, Hirohito

2015-03-16

We present a wavelength-tunable laser diode with a 99-nm-wide wavelength tuning range. It has a compact wavelength-tunable filter with high wavelength selectivity fabricated using silicon photonics technology. The silicon photonic wavelength-tunable filter with wide wavelength tuning range was realized using two ring resonators and an asymmetric Mach-Zehnder interferometer. The wavelength-tunable laser diode fabricated by butt-joining a silicon photonic filter and semiconductor optical amplifier shows stable single-mode operation over a wide wavelength range.

76 FR 52640 - Determination Under the Textile and Apparel Commercial Availability Provision of the Dominican...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-23

... (``CITA'') has determined that an acceptable substitute for certain compacted, plied, ring spun cotton... to remove or restrict (``Request'') certain compacted, plied, ring spun cotton yarns, currently on... Spun Cotton Yarns Compacted, plied, ring spun cotton yarns, with yarn counts in the range from 42 to...

Physics of protein folding

NASA Astrophysics Data System (ADS)

Finkelstein, A. V.; Galzitskaya, O. V.

2004-04-01

Protein physics is grounded on three fundamental experimental facts: protein, this long heteropolymer, has a well defined compact three-dimensional structure; this structure can spontaneously arise from the unfolded protein chain in appropriate environment; and this structure is separated from the unfolded state of the chain by the “all-or-none” phase transition, which ensures robustness of protein structure and therefore of its action. The aim of this review is to consider modern understanding of physical principles of self-organization of protein structures and to overview such important features of this process, as finding out the unique protein structure among zillions alternatives, nucleation of the folding process and metastable folding intermediates. Towards this end we will consider the main experimental facts and simple, mostly phenomenological theoretical models. We will concentrate on relatively small (single-domain) water-soluble globular proteins (whose structure and especially folding are much better studied and understood than those of large or membrane and fibrous proteins) and consider kinetic and structural aspects of transition of initially unfolded protein chains into their final solid (“native”) 3D structures.

Assessing the Potential of Folded Globular Polyproteins As Hydrogel Building Blocks

PubMed Central

2016-01-01

The native states of proteins generally have stable well-defined folded structures endowing these biomolecules with specific functionality and molecular recognition abilities. Here we explore the potential of using folded globular polyproteins as building blocks for hydrogels. Photochemically cross-linked hydrogels were produced from polyproteins containing either five domains of I27 ((I27)5), protein L ((pL)5), or a 1:1 blend of these proteins. SAXS analysis showed that (I27)5 exists as a single rod-like structure, while (pL)5 shows signatures of self-aggregation in solution. SANS measurements showed that both polyprotein hydrogels have a similar nanoscopic structure, with protein L hydrogels being formed from smaller and more compact clusters. The polyprotein hydrogels showed small energy dissipation in a load/unload cycle, which significantly increased when the hydrogels were formed in the unfolded state. This study demonstrates the use of folded proteins as building blocks in hydrogels, and highlights the potential versatility that can be offered in tuning the mechanical, structural, and functional properties of polyproteins. PMID:28006103

Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water

PubMed Central

Juraszek, Jarek; Bolhuis, Peter G.

2008-01-01

We report rate constant calculations and a reaction coordinate analysis of the rate-limiting folding and unfolding process of the Trp-cage mini-protein in explicit solvent using transition interface sampling. Previous transition path sampling simulations revealed that in this (un)folding process the protein maintains its compact configuration, while a (de)increase of secondary structure is observed. The calculated folding rate agrees reasonably with experiment, while the unfolding rate is 10 times higher. We discuss possible origins for this mismatch. We recomputed the rates with the forward flux sampling method, and found a discrepancy of four orders of magnitude, probably caused by the method's higher sensitivity to the choice of order parameter with respect to transition interface sampling. Finally, we used the previously computed transition path-sampling ensemble to screen combinations of many order parameters for the best model of the reaction coordinate by employing likelihood maximization. We found that a combination of the root mean-square deviation of the helix and of the entire protein was, of the set of tried order parameters, the one that best describes the reaction coordination. PMID:18676648

Temporary Seismic Installation in Eastern Bangladesh: Microseismicity and Structure of an On-Land Accretionary Prism

NASA Astrophysics Data System (ADS)

Foster, A. E.; Almeida, R. V.; Akhter, S. H.; Hubbard, J.; Bhattacharya, R.; Shing, U. M.; Hosain, A.; Bulbul, M. A.

2016-12-01

Eastern Bangladesh is underlain by a fold and thrust belt accumulating 13-17 mm/yr of plate convergence on a locked, shallowly dipping décollement (Steckler et al., 2016). We have installed a network of short-period and broadband instruments in this region to better assess microseismicity and investigate the structure of the fold belt. Stations will remain in place for 1-2 years and will complement the temporary stations installed by the University of Dhaka and the Lamont-Doherty Earth Observatory. Thirteen Lennartz 1-Hz instruments and three Trillium Compact 120-s instruments were installed in the Sylhet area in June 2016. Station spacing is between 15-30 km. Installations ranged from shallow vaults to above-ground locations on solid foundations, as required by local conditions. One focus of this deployment is to locate microseismicity. Neither large numbers nor magnitudes of earthquakes are expected in this area, but improved locations may help define active areas of the convergence as well as illuminate the interactions between the Dauki fault (responsible for uplift of the Shillong Plateau), the Sylhet anticline, and the rest of the Indo-Burman Ranges. Nine additional short-period instruments and three additional broadband instruments will be installed in the Chittagong area in September 2016. The southern-most stations are located over the Andaman subduction zone, thought to be associated with a large subduction earthquake in 1762 (Steckler et al., 1998). Thus, the full deployment will span the transition from an on-land accretionary prism to an area considered a classic subduction zone. Combined, the northern and southern parts of the network should provide good locations for events within the Tripura area (India) as well. We present initial estimates of station quality and the potential for an earthquake catalogue. We plan to obtain earthquake locations and focal mechanisms, when possible, as the data is collected. We will apply ambient noise tomography methods to investigate the structure of the fold belt. These applications and others may contribute to unanswered questions in the area, such as the location of the frontal-most deformation associated with the fold and thrust belt and the geometry of the basal décollement at depth, and allow better characterization of the risk to nearby populations.

New Evidence for a Black Hole in the Compact Binary Cygnus X-3

NASA Technical Reports Server (NTRS)

Shrader, Chris R.; Titarchuk, Lev; Shaposhnikov, Nikolai

2010-01-01

The bright and highly variable X-ray and radio source known as Cygnus X-3 was among the first X-ray sources discovered, yet it remains in many ways an enigma. Its known to consist of a massive. Wolf-Rayet primary in an extremely tight orbit with a compact object. Yet one of the most basic of pa.ranietern the mass of the compact object - is not known. Nor is it even clear whether its is a neutron star or a black hole. In this Paper we present our analysis of the broad-band high-energy continua covering a substantial range in luminosity and spectral morphology. We apply these results to a recently identified scaling relationship which has been demonstrated to provide reliable estimates of the compact object mass in a number of accretion powered binaries. This analysis leads us to conclude that the compact object in Cygnus X-3 has a mass greater than 4.2 solar mass thus clearly indicative of a black hole and as such resolving a longstanding issue. The full range of uncertainty in our analysis and from using a. range of recently published distance estimates constrains the compact object mass to lie between 4.2 solar mass and 14.4 solar mass. Our favored estimate, based on a 9.0 kpc distance estimate is approx. l0 solar mass, with the. error margin of 3.2 solar masses. This result may thus pose challenges to shared-envelope evolutionary models of compact binaries. as well as establishing Cygnus X-3 as the first confirmed accretion-powered galactic gamma: ray source.

Micromechanical study of mitotic chromosome structure

NASA Astrophysics Data System (ADS)

Marko, John

2011-03-01

Our group has developed micromanipulation techniques for study of the highly compacted mitotic form of chromosome found in eukaryote cells during cell division. Each metaphase chromosome contains two duplicate centimeter-long DNA molecules, folded up by proteins into cylindrical structures several microns in length. Native chromosomes display linear and reversible stretching behavior over a wide range of extensions (up to 5x native length for amphibian chromosomes), described by a Young modulus of about 300 Pa. Studies using DNA-cutting and protein-cutting enzymes have revealed that metaphase chromosomes behave as a network of chromatin fibers held together by protein-based isolated crosslinks. Our results are not consistent with the more classical model of loops of chromatin attached to a protein-based structural organizer or ``scaffold". In short, our experiments indicate that metaphase chromosomes can be considered to be ``gels" of chromatin; the stretching modulus of a whole chromosome is consistent with stretching of the chromatin fibers contained within it. Experiments using topoisomerases suggest that topological constraints may play an appreciable role in confining chromatin in the metaphase chromosome. Finally, recent experiments on human chromosomes will be reviewed, including results of experiments where chromosome-folding proteins are specifically depleted using siRNA methods. Supported by NSF-MCB-1022117, DMR-0715099, PHY-0852130, DMR-0520513, NCI 1U54CA143869-01 (NU-PS-OC), and the American Heart Association.

Development and Modeling of a Novel Self-Assembly Process for Polymer and Polymeric Composite Nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sumpter, Bobby G.; Carrillo, Jan-Michael Y.; Ahn, Suk-Kyun

Extensive computational simulations and experiments have been used to investigate the structure, dynamics and resulting photophysical properties of a number para-phenylenevinylene (PPV) based polymers and oligomers. These studies have shown how the morphology and structure are controlled to a large extent by the nature of the solute-solvent interactions in the initial solution phase preparation. A good solvent such as dichloromethane generates non-compact structures with more of a defect-extended chain like morphology while a bad solvent such as toluene leads to compact organized and folded structures with rod-like morphologies. Secondary structural organization is induced by using the solution phase structures tomore » generate solvent-free single molecule nanoparticles. These nanoparticles are very compact and rod shaped, consisting of near-cofacial ordering of the conjugated PPV chain backbones between folds located at tetrahedral defects (sp3 C-C bonds). The resulting photophysical properties exhibit a significant enhancement in the photoluminescence quantum yield, lifetime, and stability. In addition, the single molecule nanoparticles have Gaussian-like emission spectra with discrete center frequencies that are correlated to a conjugation length, allowing the design of nanoparticles which luminesces at a particular frequency. We followed a similar approach and applied a comparable methodology in our recent work on polythiophenes in order to study the effect of polymer architecture on nanoscale assembly. Unlike linear chains of comparable size, we observed aggregation of the bottlebrush architecture of poly(norbornene)-g-poly(3-hexylthiophene) (PNB-g-P3HT) after the freeze-drying and dissolution processes. The behavior can be attributed to a significant enhancement in the number of π-π interactions between grafted P3HT side chains.« less

Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model.

PubMed

Jacobs, Donald J; Livesay, Dennis R; Hules, Jeremy; Tasayco, Maria Luisa

2006-05-05

Numerous quantitative stability/flexibility relationships, within Escherichia coli thioredoxin (Trx) and its fragments are determined using a minimal distance constraint model (DCM). A one-dimensional free energy landscape as a function of global flexibility reveals Trx to fold in a low-barrier two-state process, with a voluminous transition state. Near the folding transition temperature, the native free energy basin is markedly skewed to allow partial unfolded forms. Under native conditions the skewed shape is lost, and the protein forms a compact structure with some flexibility. Predictions on ten Trx fragments are generally consistent with experimental observations that they are disordered, and that complementary fragments reconstitute. A hierarchical unfolding pathway is uncovered using an exhaustive computational procedure of breaking interfacial cross-linking hydrogen bonds that span over a series of fragment dissociations. The unfolding pathway leads to a stable core structure (residues 22-90), predicted to act as a kinetic trap. Direct connection between degree of rigidity within molecular structure and non-additivity of free energy is demonstrated using a thermodynamic cycle involving fragments and their hierarchical unfolding pathway. Additionally, the model provides insight about molecular cooperativity within Trx in its native state, and about intermediate states populating the folding/unfolding pathways. Native state cooperativity correlation plots highlight several flexibly correlated regions, giving insight into the catalytic mechanism that facilitates access to the active site disulfide bond. Residual native cooperativity correlations are present in the core substructure, suggesting that Trx can function when it is partly unfolded. This natively disordered kinetic trap, interpreted as a molten globule, has a wide temperature range of metastability, and it is identified as the "slow intermediate state" observed in kinetic experiments. These computational results are found to be in overall agreement with a large array of experimental data.

Observations of compact radio nuclei in Cygnus A, Centaurus A, and other extended radio sources

NASA Technical Reports Server (NTRS)

Kellermann, K. I.; Clark, B. G.; Niell, A. E.; Shaffer, D. B.

1975-01-01

Observations of Cygnus A show a compact radio core 2 milliarcsec in extent oriented in the same direction as the extended components. Other large double- or multiple-component sources, including Centaurus A, have also been found to contain compact radio nuclei with angular sizes in the range 1-10 milliarcsec.

A Tracking Analysis of Compact Students within Level 1 of Their Higher Education Programmes

ERIC Educational Resources Information Center

Wakely, Katrina; Saunders, Danny

2004-01-01

This article presents a tracking analysis of level 1 undergraduates who entered the University of Glamorgan through the Compact schools initiative. The Compact initiative aims to widen access to higher education by encouraging young people from disadvantaged backgrounds to attend a range of preparatory activities and by offering lower entry…

Portable Dental System

NASA Technical Reports Server (NTRS)

1980-01-01

Portable dental system provides dental care in isolated communities. System includes a patient's chair and a dentist's stool, an X-ray machine and a power unit, all of which fold into compact packages. A large yellow "pumpkin" is a collapsible compressed air tank. Portable system has been used successfully in South America in out of the way communities with this back-packable system, and in American nursing homes. This product is no longer manufactured.

Protein-like Nanoparticles Based on Orthogonal Self-Assembly of Chimeric Peptides.

PubMed

Jiang, Linhai; Xu, Dawei; Namitz, Kevin E; Cosgrove, Michael S; Lund, Reidar; Dong, He

2016-10-01

A novel two-component self-assembling chimeric peptide is designed where two orthogonal protein folding motifs are linked side by side with precisely defined position relative to one another. The self-assembly is driven by a combination of symmetry controlled molecular packing, intermolecular interactions, and geometric constraint to limit the assembly into compact dodecameric protein nanoparticles. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides.

PubMed

Islam, S M Ashiqul; Sajed, Tanvir; Kearney, Christopher Michel; Baker, Erich J

2015-07-05

Numerous organisms have evolved a wide range of toxic peptides for self-defense and predation. Their effective interstitial and macro-environmental use requires energetic and structural stability. One successful group of these peptides includes a tri-disulfide domain arrangement that offers toxicity and high stability. Sequential tri-disulfide connectivity variants create highly compact disulfide folds capable of withstanding a variety of environmental stresses. Their combination of toxicity and stability make these peptides remarkably valuable for their potential as bio-insecticides, antimicrobial peptides and peptide drug candidates. However, the wide sequence variation, sources and modalities of group members impose serious limitations on our ability to rapidly identify potential members. As a result, there is a need for automated high-throughput member classification approaches that leverage their demonstrated tertiary and functional homology. We developed an SVM-based model to predict sequential tri-disulfide peptide (STP) toxins from peptide sequences. One optimized model, called PredSTP, predicted STPs from training set with sensitivity, specificity, precision, accuracy and a Matthews correlation coefficient of 94.86%, 94.11%, 84.31%, 94.30% and 0.86, respectively, using 200 fold cross validation. The same model outperforms existing prediction approaches in three independent out of sample testsets derived from PDB. PredSTP can accurately identify a wide range of cystine stabilized peptide toxins directly from sequences in a species-agnostic fashion. The ability to rapidly filter sequences for potential bioactive peptides can greatly compress the time between peptide identification and testing structural and functional properties for possible antimicrobial and insecticidal candidates. A web interface is freely available to predict STP toxins from http://crick.ecs.baylor.edu/.

Exploration of the relationship between topology and designability of conformations

NASA Astrophysics Data System (ADS)

Leelananda, Sumudu P.; Towfic, Fadi; Jernigan, Robert L.; Kloczkowski, Andrzej

2011-06-01

Protein structures are evolutionarily more conserved than sequences, and sequences with very low sequence identity frequently share the same fold. This leads to the concept of protein designability. Some folds are more designable and lots of sequences can assume that fold. Elucidating the relationship between protein sequence and the three-dimensional (3D) structure that the sequence folds into is an important problem in computational structural biology. Lattice models have been utilized in numerous studies to model protein folds and predict the designability of certain folds. In this study, all possible compact conformations within a set of two-dimensional and 3D lattice spaces are explored. Complementary interaction graphs are then generated for each conformation and are described using a set of graph features. The full HP sequence space for each lattice model is generated and contact energies are calculated by threading each sequence onto all the possible conformations. Unique conformation giving minimum energy is identified for each sequence and the number of sequences folding to each conformation (designability) is obtained. Machine learning algorithms are used to predict the designability of each conformation. We find that the highly designable structures can be distinguished from other non-designable conformations based on certain graphical geometric features of the interactions. This finding confirms the fact that the topology of a conformation is an important determinant of the extent of its designability and suggests that the interactions themselves are important for determining the designability.

Folding associated with extensional faulting: Sheep Range detachment, southern Nevada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guth, P.L.

1985-01-01

The Sheep Range detachment is a major Miocene extensional fault system of the Great Basin. Its major faults have a scoop shape, with straight, N-S traces extending 15-30 km and then abruptly turning to strike E-W. Tertiary deformation involved simultaneous normal faulting, sedimentation, landsliding, and strike-slip faulting. Folds occur in two settings: landslide blocks and drag along major faults. Folds occur in landslide blocks and beneath them. Most folds within landslide blocks are tight anticlines, with limbs dipping 40-60 degrees. Brecciation of the folds and landslide blocks suggests brittle deformation. Near Quijinump Canyon in the Sheep Range, at least threemore » landslide blocks (up to 500 by 1500 m) slid into a small Tertiary basin. Tertiary limestone beneath the Paleozoic blocks was isoclinally folded. Westward dips reveal drag folds along major normal faults, as regional dips are consistently to the east. The Chowderhead anticline is the largest drag fold, along an extensional fault that offsets Ordovician units 8 km. East-dipping Ordovician and Silurian rocks in the Desert Range form the hanging wall. East-dipping Cambrian and Ordovician units in the East Desert Range form the foot wall and east limb of the anticline. Caught along the fault plane, the anticline's west-dipping west limb contains mostly Cambrian units.« less

Evaluation of the Grafted Fascia in the Vocal Fold of Dogs: A Histologic Study.

PubMed

Carvalho, Eduardo G B; Pauna, Henrique F; Machado, Almiro J; Nicola, Ester M D; Altemani, Albina M A M; Crespo, Agrício N

2017-09-01

There is no consensus on the ideal graft for medialization surgery of the vocal folds in the literature. One of the most favorable proposals is the use of autologous fascia, which seems limited by the lack of information regarding the integration of grafted tissue. Our study aims to evaluate the degree of fully engrafted fascia integration in the vocal fold lamina propria of dogs. Fourteen adult mongrel dogs that underwent intravenous general anesthesia were selected and kept under spontaneous ventilation. A fascia lata fragment of 4 cm 2 was obtained from the right leg of each dog. The dogs underwent laryngoscopy; a 3 mm incision was made in the vocal process, next to the vestibular process, and the fascia was grafted into the right vocal fold. The left vocal fold was used as a control. The animals were divided into two groups: group A, evaluated after 2 months of the procedure, and group B, evaluated after 6 months of the procedure. Histologic analysis was made semiquantitatively regarding the presence of inflammatory reaction, fibrosis, and neovascularization. Our final studied group comprised 12 dogs. Microscopic examination of the larynx revealed the absence of any detectable inflammation in the incision site. The lamina propria of the grafted vocal fold showed identifiable compact, thick, and eosinophilic collagen bands. The surrounding tissue showed thin collagen bands with some organization, similar to the contralateral vocal fold. The grafted fascia integrates into the vocal fold lamina propria and seems not to cause inflammatory reaction response. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Protein unfolding under isometric tension-what force can integrins generate, and can it unfold FNIII domains?

PubMed

Erickson, Harold P

2017-02-01

Extracellular matrix fibrils of fibronectin (FN) are highly elastic, and are typically stretched three to four times their relaxed length. The mechanism of stretching has been controversial, in particular whether it involves tension-induced unfolding of FNIII domains. Recent studies have found that ∼5pN is the threshold isometric force for unfolding various protein domains. FNIII domains should therefore not be unfolded until the tension approaches 5pN. Integrins have been reported to generate forces ranging from 1 to >50pN, but I argue that studies reporting 1-2pN are the most convincing. This is not enough to unfold FNIII domains. Even if domains were unfolded, 2pN would only extend the worm-like-chain to about twice the length of the folded domain. Overall I conclude that stretching FN matrix fibrils involves primarily the compact to extended conformational change of FN dimers, with minimal contribution from unfolding FNIII domains. Copyright © 2016 Elsevier Ltd. All rights reserved.

Modulation of Correlated Segment Fluctuations in IDPs upon Complex Formation as an Allosteric Regulatory Mechanism.

PubMed

Beier, Andreas; Schwarz, Thomas C; Kurzbach, Dennis; Platzer, Gerald; Tribuzio, Francesca; Konrat, Robert

2018-05-05

Molecular recognition of and by intrinsically disordered proteins (IDPs) is an intriguing and still largely elusive phenomenon. Typically, protein recognition involving IDPs requires either folding upon binding or, alternatively, the formation of "fuzzy complexes." Here we show via correlation analyses of paramagnetic relaxation enhancement data unprecedented and striking alterations of the concerted fluctuations within the conformational ensemble of IDPs upon ligand binding. We study the binding of α-synuclein to calmodulin, a ubiquitous calcium-binding protein, and the binding of the extracellular matrix IDP osteopontin to heparin, a mimic of the extracellular matrix ligand hyaluronic acid. In both cases, binding leads to reduction of correlated long-range motions in these two IDPs and thus indicates a loosening of structural compaction upon binding. Most importantly, however, the simultaneous presence of correlated and anti-correlated fluctuations in IDPs suggests the prevalence of "energetic frustration" and provides an explanation for the puzzling observation of disordered allostery in IDPs. Copyright © 2018. Published by Elsevier Ltd.

Double-stranded DNA organization in bacteriophage heads: an alternative toroid-based model.

PubMed Central

Hud, N V

1995-01-01

Studies of the organization of double-stranded DNA within bacteriophage heads during the past four decades have produced a wealth of data. However, despite the presentation of numerous models, the true organization of DNA within phage heads remains unresolved. The observations of toroidal DNA structures in electron micrographs of phage lysates have long been cited as support for the organization of DNA in a spool-like fashion. This particular model, like all other models, has not been found to be consistent will all available data. Recently we proposed that DNA within toroidal condensates produced in vitro is organized in a manner significantly different from that suggested by the spool model. This new toroid model has allowed the development of an alternative model for DNA organization within bacteriophage heads that is consistent with a wide range of biophysical data. Here we propose that bacteriophage DNA is packaged in a toroid that is folded into a highly compact structure. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 PMID:8534805

GPU-accelerated low-latency real-time searches for gravitational waves from compact binary coalescence

NASA Astrophysics Data System (ADS)

Liu, Yuan; Du, Zhihui; Chung, Shin Kee; Hooper, Shaun; Blair, David; Wen, Linqing

2012-12-01

We present a graphics processing unit (GPU)-accelerated time-domain low-latency algorithm to search for gravitational waves (GWs) from coalescing binaries of compact objects based on the summed parallel infinite impulse response (SPIIR) filtering technique. The aim is to facilitate fast detection of GWs with a minimum delay to allow prompt electromagnetic follow-up observations. To maximize the GPU acceleration, we apply an efficient batched parallel computing model that significantly reduces the number of synchronizations in SPIIR and optimizes the usage of the memory and hardware resource. Our code is tested on the CUDA ‘Fermi’ architecture in a GTX 480 graphics card and its performance is compared with a single core of Intel Core i7 920 (2.67 GHz). A 58-fold speedup is achieved while giving results in close agreement with the CPU implementation. Our result indicates that it is possible to conduct a full search for GWs from compact binary coalescence in real time with only one desktop computer equipped with a Fermi GPU card for the initial LIGO detectors which in the past required more than 100 CPUs.

Load and inflation pressure effects on soil compaction of forwarder tires

Treesearch

Tim McDonald; Tom Way; Bjorn Lofgren; Fernando Seixas; Mats Landstrom

1996-01-01

A standard forwarder tire (600/55-26.5) was tested to determine its range of soil compaction with various inflation pressures and dynamic loads. Past research has shown that compaction of heavier equipment can be somewhat mitigated by operating with lower inflation pressures. Results indicated a significant effect of both load and inflation pressure on bulk density,...

From the endoplasmic reticulum to the plasma membrane: mechanisms of CFTR folding and trafficking.

PubMed

Farinha, Carlos M; Canato, Sara

2017-01-01

CFTR biogenesis starts with its co-translational insertion into the membrane of endoplasmic reticulum and folding of the cytosolic domains, towards the acquisition of a fully folded compact native structure. Efficiency of this process is assessed by the ER quality control system that allows the exit of folded proteins but targets unfolded/misfolded CFTR to degradation. If allowed to leave the ER, CFTR is modified at the Golgi and reaches the post-Golgi compartments to be delivered to the plasma membrane where it functions as a cAMP- and phosphorylation-regulated chloride/bicarbonate channel. CFTR residence at the membrane is a balance of membrane delivery, endocytosis, and recycling. Several adaptors, motor, and scaffold proteins contribute to the regulation of CFTR stability and are involved in continuously assessing its structure through peripheral quality control systems. Regulation of CFTR biogenesis and traffic (and its dysregulation by mutations, such as the most common F508del) determine its overall activity and thus contribute to the fine modulation of chloride secretion and hydration of epithelial surfaces. This review covers old and recent knowledge on CFTR folding and trafficking from its synthesis to the regulation of its stability at the plasma membrane and highlights how several of these steps can be modulated to promote the rescue of mutant CFTR.

Analysis of Technology for Compact Coherent Lidar

NASA Technical Reports Server (NTRS)

Amzajerdian, Farzin

1997-01-01

In view of the recent advances in the area of solid state and semiconductor lasers has created new possibilities for the development of compact and reliable coherent lidars for a wide range of applications. These applications include: Automated Rendezvous and Capture, wind shear and clear air turbulence detection, aircraft wake vortex detection, and automobile collision avoidance. The work performed by the UAH personnel under this Delivery Order, concentrated on design and analyses of a compact coherent lidar system capable of measuring range and velocity of hard targets, and providing air mass velocity data. The following is the scope of this work. a. Investigate various laser sources and optical signal detection configurations in support of a compact and lightweight coherent laser radar to be developed for precision range and velocity measurements of hard and fuzzy targets. Through interaction with MSFC engineers, the most suitable laser source and signal detection technique that can provide a reliable compact and lightweight laser radar design will be selected. b. Analyze and specify the coherent laser radar system configuration and assist with its optical and electronic design efforts. Develop a system design including its optical layout design. Specify all optical components and provide the general requirements of the electronic subsystems including laser beam modulator and demodulator drivers, detector electronic interface, and the signal processor. c. Perform a thorough performance analysis to predict the system measurement range and accuracy. This analysis will utilize various coherent laser radar sensitivity formulations and different target models.

Fine tuning of process parameters for improving briquette production from palm kernel shell gasification waste.

PubMed

Bazargan, Alireza; Rough, Sarah L; McKay, Gordon

2018-04-01

Palm kernel shell biochars (PKSB) ejected as residues from a gasifier have been used for solid fuel briquette production. With this approach, palm kernel shells can be used for energy production twice: first, by producing rich syngas during gasification; second, by compacting the leftover residues from gasification into high calorific value briquettes. Herein, the process parameters for the manufacture of PKSB biomass briquettes via compaction are optimized. Two possible optimum process scenarios are considered. In the first, the compaction speed is increased from 0.5 to 10 mm/s, the compaction pressure is decreased from 80 Pa to 40 MPa, the retention time is reduced from 10 s to zero, and the starch binder content of the briquette is halved from 0.1 to 0.05 kg/kg. With these adjustments, the briquette production rate increases by more than 20-fold; hence capital and operational costs can be reduced and the service life of compaction equipment can be increased. The resulting product satisfactorily passes tensile (compressive) crushing strength and impact resistance tests. The second scenario involves reducing the starch weight content to 0.03 kg/kg, while reducing the compaction pressure to a value no lower than 60 MPa. Overall, in both cases, the PKSB biomass briquettes show excellent potential as a solid fuel with calorific values on par with good-quality coal. CHNS: carbon, hydrogen, nitrogen, sulfur; FFB: fresh fruit bunch(es); HHV: higher heating value [J/kg]; LHV: lower heating value [J/kg]; PKS: palm kernel shell(s); PKSB: palm kernel shell biochar(s); POME: palm oil mill effluent; RDF: refuse-derived fuel; TGA: thermogravimetric analysis.

Adapted to Roar: Functional Morphology of Tiger and Lion Vocal Folds

PubMed Central

Klemuk, Sarah A.; Riede, Tobias; Walsh, Edward J.; Titze, Ingo R.

2011-01-01

Vocal production requires active control of the respiratory system, larynx and vocal tract. Vocal sounds in mammals are produced by flow-induced vocal fold oscillation, which requires vocal fold tissue that can sustain the mechanical stress during phonation. Our understanding of the relationship between morphology and vocal function of vocal folds is very limited. Here we tested the hypothesis that vocal fold morphology and viscoelastic properties allow a prediction of fundamental frequency range of sounds that can be produced, and minimal lung pressure necessary to initiate phonation. We tested the hypothesis in lions and tigers who are well-known for producing low frequency and very loud roaring sounds that expose vocal folds to large stresses. In histological sections, we found that the Panthera vocal fold lamina propria consists of a lateral region with adipocytes embedded in a network of collagen and elastin fibers and hyaluronan. There is also a medial region that contains only fibrous proteins and hyaluronan but no fat cells. Young's moduli range between 10 and 2000 kPa for strains up to 60%. Shear moduli ranged between 0.1 and 2 kPa and differed between layers. Biomechanical and morphological data were used to make predictions of fundamental frequency and subglottal pressure ranges. Such predictions agreed well with measurements from natural phonation and phonation of excised larynges, respectively. We assume that fat shapes Panthera vocal folds into an advantageous geometry for phonation and it protects vocal folds. Its primary function is probably not to increase vocal fold mass as suggested previously. The large square-shaped Panthera vocal fold eases phonation onset and thereby extends the dynamic range of the voice. PMID:22073246

DNA compaction into new DNA vectors based on cyclodextrin polymer: surface enhanced Raman spectroscopy characterization.

PubMed

Burckbuchler, V; Wintgens, V; Lecomte, S; Percot, A; Leborgne, C; Danos, O; Kichler, A; Amiel, C

2006-04-05

The ability of DNA to bind polycation yielding polyplexes is widely used in nonviral gene delivery. The aim of the present study was to evaluate the DNA compaction with a new DNA vector using Raman spectroscopy. The polyplexes result from an association of a beta-cyclodextrin polymer (polybeta-CD), an amphiphilic cationic connector (DC-Chol or adamantane derivative Ada2), and DNA. The charge of the polymeric vector is effectively controlled by simple addition of cationic connector in the medium. We used surface enhanced Raman spectroscopy (SERS) to characterize this ternary complex, monitoring the accessibility of adenyl residues to silver colloids. The first experiments were performed using model systems based on polyA (polyadenosine monophosphate) well characterized by SERS. This model was then extended to plasmid DNA to study polybeta-CD/Ada2/DNA and polybeta-CD/DC-Chol/DNA polyplexes. The SERS spectra show a decrease of signal intensity when the vector/DNA charge ratio (Z+/-) increases. At the highest ratio (Z+/- = 10) the signal is 6-fold and 3-fold less intense than the DNA reference signal for Ada2 and DC-Chol polyplexes, respectively. Thus adenyl residues have a reduced accessibility as DNA is bound to the vector. Moreover, the SERS intensity variations are in agreement with gel electrophoresis and zeta potential experiments on the same systems. The overall study clearly demonstrates that the cationic charges neutralizing the negative charges of DNA result in the formation of stable polyplexes. In vitro transfection efficiency of those DNA vectors are also presented and compared to the classical DC-Chol lipoplexes (DC-Chol/DNA). The results show an increase of the transfection efficiency 2-fold higher with our vector based on polybeta-CD. Copyright 2005 Wiley Periodicals, Inc.

Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions.

PubMed

Strulson, Christopher A; Yennawar, Neela H; Rambo, Robert P; Bevilacqua, Philip C

2013-11-19

In an effort to relate RNA folding to function under cellular-like conditions, we monitored the self-cleavage reaction of the human hepatitis delta virus-like CPEB3 ribozyme in the background of physiological ionic concentrations and various crowding and cosolute agents. We found that at physiological free Mg(2+) concentrations (∼0.1-0.5 mM), both crowders and cosolutes stimulate the rate of self-cleavage, up to ∼6-fold, but that in 10 mM Mg(2+) (conditions widely used for in vitro ribozyme studies) these same additives have virtually no effect on the self-cleavage rate. We further observe a dependence of the self-cleavage rate on crowder size, wherein the level of rate stimulation is diminished for crowders larger than the size of the unfolded RNA. Monitoring effects of crowding and cosolute agents on rates in biological amounts of urea revealed additive-promoted increases at both low and high Mg(2+) concentrations, with a maximal stimulation of more than 10-fold and a rescue of the rate to its urea-free values. Small-angle X-ray scattering experiments reveal a structural basis for this stimulation in that higher-molecular weight crowding agents favor a more compact form of the ribozyme in 0.5 mM Mg(2+) that is essentially equivalent to the form under standard ribozyme conditions of 10 mM Mg(2+) without a crowder. This finding suggests that at least a portion of the rate enhancement arises from favoring the native RNA tertiary structure. We conclude that cellular-like crowding supports ribozyme reactivity by favoring a compact form of the ribozyme, but only under physiological ionic and cosolute conditions.

Hydraulic conductivity of compacted zeolites.

PubMed

Oren, A Hakan; Ozdamar, Tuğçe

2013-06-01

Hydraulic conductivities of compacted zeolites were investigated as a function of compaction water content and zeolite particle size. Initially, the compaction characteristics of zeolites were determined. The compaction test results showed that maximum dry unit weight (γ(dmax)) of fine zeolite was greater than that of granular zeolites. The γ(dmax) of compacted zeolites was between 1.01 and 1.17 Mg m(-3) and optimum water content (w(opt)) was between 38% and 53%. Regardless of zeolite particle size, compacted zeolites had low γ(dmax) and high w(opt) when compared with compacted natural soils. Then, hydraulic conductivity tests were run on compacted zeolites. The hydraulic conductivity values were within the range of 2.0 × 10(-3) cm s(-1) to 1.1 × 10(-7) cm s(-1). Hydraulic conductivity of all compacted zeolites decreased almost 50 times as the water content increased. It is noteworthy that hydraulic conductivity of compacted zeolite was strongly dependent on the zeolite particle size. The hydraulic conductivity decreased almost three orders of magnitude up to 39% fine content; then, it remained almost unchanged beyond 39%. Only one report was found in the literature on the hydraulic conductivity of compacted zeolite, which is in agreement with the findings of this study.

Annular folded electrowetting liquid lens.

PubMed

Li, Lei; Liu, Chao; Ren, Hongwen; Deng, Huan; Wang, Qiong-Hua

2015-05-01

We report an annular folded electrowetting liquid lens. The front surface of the lens is coated with a circular reflection film, while the back surface of the lens is coated with a ring-shaped reflection film. This approach allows the lens to get optical power from the liquid-liquid interface three times so that the optical power is tripled. An analysis of the properties of the annular folded electrowetting liquid lens is presented along with the design, fabrication, and testing of a prototype. Our results show that the optical power of the proposed liquid lens can be enhanced from ∼20.1 to ∼50.2  m(-1) in comparison with that of the conventional liquid lens (aperture ∼3.9  mm). It can reduce the operating voltage by ∼10  V to reach the same diopter as a conventional liquid lens. Our liquid lens has the advantages of compact structure, light weight, and improved optical resolution.

Crystal structure of group II intron domain 1 reveals a template for RNA assembly

DOE PAGES

Zhao, Chen; Rajashankar, Kanagalaghatta R.; Marcia, Marco; ...

2015-10-26

Although the importance of large noncoding RNAs is increasingly appreciated, our understanding of their structures and architectural dynamics remains limited. In particular, we know little about RNA folding intermediates and how they facilitate the productive assembly of RNA tertiary structures. In this paper, we report the crystal structure of an obligate intermediate that is required during the earliest stages of group II intron folding. Composed of domain 1 from the Oceanobacillus iheyensis group II intron (266 nucleotides), this intermediate retains native-like features but adopts a compact conformation in which the active site cleft is closed. Transition between this closed andmore » the open (native) conformation is achieved through discrete rotations of hinge motifs in two regions of the molecule. Finally, the open state is then stabilized by sequential docking of downstream intron domains, suggesting a 'first come, first folded' strategy that may represent a generalizable pathway for assembly of large RNA and ribonucleoprotein structures.« less

A wavelet-based approach for a continuous analysis of phonovibrograms.

PubMed

Unger, Jakob; Meyer, Tobias; Doellinger, Michael; Hecker, Dietmar J; Schick, Bernhard; Lohscheller, Joerg

2012-01-01

Recently, endoscopic high-speed laryngoscopy has been established for commercial use and constitutes a state-of-the-art technique to examine vocal fold dynamics. Despite overcoming many limitations of commonly applied stroboscopy it has not gained widespread clinical application, yet. A major drawback is a missing methodology of extracting valuable features to support visual assessment or computer-aided diagnosis. In this paper a compact and descriptive feature set is presented. The feature extraction routines are based on two-dimensional color graphs called phonovibrograms (PVG). These graphs contain the full spatio-temporal pattern of vocal fold dynamics and are therefore suited to derive features that comprehensively describe the vibration pattern of vocal folds. Within our approach, clinically relevant features such as glottal closure type, symmetry and periodicity are quantified in a set of 10 descriptive features. The suitability for classification tasks is shown using a clinical data set comprising 50 healthy and 50 paralytic subjects. A classification accuracy of 93.2% has been achieved.

The Number Density of Quiescent Compact Galaxies at Intermediate Redshift

NASA Astrophysics Data System (ADS)

Damjanov, Ivana; Hwang, Ho Seong; Geller, Margaret J.; Chilingarian, Igor

2014-09-01

Massive compact systems at 0.2 < z < 0.6 are the missing link between the predominantly compact population of massive quiescent galaxies at high redshift and their analogs and relics in the local volume. The evolution in number density of these extreme objects over cosmic time is the crucial constraining factor for the models of massive galaxy assembly. We select a large sample of ~200 intermediate-redshift massive compacts from the Baryon Oscillation Spectroscopic Survey (BOSS) spectroscopy by identifying point-like Sloan Digital Sky Survey photometric sources with spectroscopic signatures of evolved redshifted galaxies. A subset of our targets have publicly available high-resolution ground-based images that we use to augment the dynamical and stellar population properties of these systems by their structural parameters. We confirm that all BOSS compact candidates are as compact as their high-redshift massive counterparts and less than half the size of similarly massive systems at z ~ 0. We use the completeness-corrected numbers of BOSS compacts to compute lower limits on their number densities in narrow redshift bins spanning the range of our sample. The abundance of extremely dense quiescent galaxies at 0.2 < z < 0.6 is in excellent agreement with the number densities of these systems at high redshift. Our lower limits support the models of massive galaxy assembly through a series of minor mergers over the redshift range 0 < z < 2.

Compact Ocean Models Enable Onboard AUV Autonomy and Decentralized Adaptive Sampling

DTIC Science & Technology

2014-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Compact Ocean Models Enable Onboard AUV Autonomy and...transmitted onboard an AUV . 3. Develop algorithms for adaptive planning of AUV surveys. 4. Demonstrate use of compact ocean models onboard a long...range AUV during a field deployment. Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of

Recovery of compacted soils in Mojave Desert ghost towns.

USGS Publications Warehouse

Webb, R.H.; Steiger, J.W.; Wilshire, H.G.

1986-01-01

Residual compaction of soils was measured at seven sites in five Mojave Desert ghost towns. Soils in these Death Valley National Monument townsites were compacted by vehicles, animals, and human trampling, and the townsites had been completely abandoned and the buildings removed for 64 to 75 yr. Recovery times extrapolated using a linear recovery model ranged from 80 to 140 yr and averaged 100 yr. The recovery times were related to elevation, suggesting freeze-thaw loosening as an important factor in ameliorating soil compaction in the Mojave Desert. -from Authors

Using RNA nanoparticles with thermostable motifs and fluorogenic modules for real-time detection of RNA folding and turnover in prokaryotic and eukaryotic cells.

PubMed

Zhang, Hui; Pi, Fengmei; Shu, Dan; Vieweger, Mario; Guo, Peixuan

2015-01-01

RNA nanotechnology is an emerging field at the interface of biochemistry and nanomaterials that shows immense promise for applications in nanomedicines, therapeutics and nanotechnology. Noncoding RNAs, such as siRNA, miRNA, ribozymes, and riboswitches, play important roles in the regulation of cellular processes. They carry out highly specific functions on a compact and efficient footprint. The properties of specificity and small size make them excellent modules in the construction of multifaceted RNA nanoparticles for targeted delivery and therapy. Biological activity of RNA molecules, however, relies on their proper folding. Therefore their thermodynamic and biochemical stability in the cellular environment is critical. Consequently, it is essential to assess global fold and intracellular lifetime of multifaceted RNA nanoparticles to optimize their therapeutic effectiveness. Here, we describe a method to express and assemble stable RNA nanoparticles in cells, and to assess the folding and turnover rate of RNA nanoparticles in vitro as well as in vivo in real time using a thermostable core motif derived from pRNA of bacteriophage Phi29 DNA packaging motor and fluorogenic RNA modules.

A partially folded structure of amyloid-beta(1-40) in an aqueous environment.

PubMed

Vivekanandan, Subramanian; Brender, Jeffrey R; Lee, Shirley Y; Ramamoorthy, Ayyalusamy

2011-07-29

Aggregation of the Aβ(1-40) peptide is linked to the development of extracellular plaques characteristic of Alzheimer's disease. While previous studies commonly show the Aβ(1-40) is largely unstructured in solution, we show that Aβ(1-40) can adopt a compact, partially folded structure. In this structure (PDB ID: 2LFM), the central hydrophobic region of the peptide forms a 3(10) helix from H13 to D23 and the N- and C-termini collapse against the helix due to the clustering of hydrophobic residues. Helical intermediates have been predicted to be crucial on-pathway intermediates in amyloid fibrillogenesis, and the structure presented here presents a new target for investigation of early events in Aβ(1-40) fibrillogenesis. Copyright © 2011 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kong, Leopold; Giang, Erick; Nieusma, Travis

Hepatitis C virus (HCV), a Hepacivirus, is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV envelope glycoproteins E1 and E2 mediate fusion and entry into host cells and are the primary targets of the humoral immune response. The crystal structure of the E2 core bound to broadly neutralizing antibody AR3C at 2.65 angstroms reveals a compact architecture composed of a central immunoglobulin-fold β sandwich flanked by two additional protein layers. The CD81 receptor binding site was identified by electron microscopy and site-directed mutagenesis and overlaps with the AR3C epitope. The x-ray and electron microscopy E2 structuresmore » differ markedly from predictions of an extended, three-domain, class II fusion protein fold and therefore provide valuable information for HCV drug and vaccine design.« less

Radiation and Scattering Compact Antenna Laboratory (RASCAL) Capabilities Brochure

DTIC Science & Technology

2016-09-06

Array Measurements Integrated Measurement of Subsystems with Digital Backends RADIATION AND SCATTERING COMPACT ANTENNA LABORATORY...hardware gating to eliminate sources of error within the range itself. Processing is also available for multi-arm spiral antennas for the generation

A macromolecular crowding study of RNA folding and activity: polymer pore size matters! (Conference Presentation)

NASA Astrophysics Data System (ADS)

Börner, Richard; Fiorini, Erica; Paudel, Bishnu; Rueda, David; Sigel, Roland K. O.

2016-03-01

Catalytic RNAs, like the group IIB intron ribozyme of S. cerevesiae, require a high magnesium(II) concentration to show folding and function in vitro [1]. In contrast, in vivo conditions are characterized by a highly crowded cellular environment and much lower ion concentration. Molecular crowding agents are a widespread tool to mimic cellular crowding [2]. However, particular physical/chemical properties explaining the crowders influence are mostly not understood. In this study, we gain new insights on how polymer properties like viscosity, pore size etc. influence the activity and folding of a large RNA. We combined bulk activity assays and single-molecule Förster Resonance Energy Transfer experiments, screening the PEG volume fraction (%) and molecular weight (MW). Our results revealed that upon the influence of crowding agents, a compaction of the underlying structure depends on the PEG % and the presence of different PEG MW and % unveiled an optimal pore size in terms of catalytic activity. In summary, an increasing density of the crowding environment shifts the RNA towards the most compact state, but the ribozyme is only active if the crowders network matches its size [4]. We interpret the most compact state as necessary, but not sufficient, to keep the ribozyme active. Financial support from the European Research Council (MIRNA N° 259092, to RKOS), the Swiss National Fund (SNF), and the Forschungskredit Grant of the University of Zürich (FK-14-096 and 15-092 to RB) are gratefully acknowledged. [1] Swisher J.F., Su L.J., Brenowitz M., Anderson V.E., Pyle A.M., J. Mol. Bio., 315, 297-310 (2002). [2] Kilburn D., Roh J.H., Guo L., Briber R.M., Woodson S.A., JACS, 132, 8690-6 (2010). [3] Steiner M., Karunatilaka K.S., Sigel R.K.O., Rueda D., Proc. Natl. Acad. Sci. U.S.A.,105, 13853-8 (2008). [4] aBörner R, Fiorini E, Sigel R.K.O., Chimia, 69, 207-212 (2015).; bFiorini E., Paudel B., Börner R., Rueda D., Sigel R.K.O., submitted. [5] König S.L.B., Hadzic M., Fiorini E., Börner R., Kowerko D., Blanckenhorn W.U., Sigel R.K.O., PLoS ONE, 8, e84157 (2013).

Synchrotron radiation circular dichroism spectroscopy study of recombinant T β4 folding

NASA Astrophysics Data System (ADS)

Huang, Yung-Chin; Chu, Hsueh-Liang; Chen, Peng-Jen; Chang, Chia-Ching

Thymosin beta 4 (T β4) is a 43-amino acid small peptide, has been demonstrated that it can promote cardiac repair, wound repair, tissue protection, and involve in the proliferation of blood cell precursor stem cells of bone marrow. Moreover, T β4 has been identified as a multifunction intrinsically disordered protein, which is lacking the stable tertiary structure. Owing to the small size and disordered character, the T β4 protein degrades rapidly and the storage condition is critical. Therefore, it is not easy to reveal its folding mechanism of native T β4. However, recombinant T β4 protein (rT β4), which fused with a 5-kDa peptide in its amino-terminal, is stable and possesses identical function of T β4. Therefore, rT β4 can be used to study its folding mechanism. By using over-critical folding process, stable folding intermediates of rT β4 can be obtained. Structure analysis of folding intermediates by synchrotron radiation circular dichroism (SRCD) and fluorescence spectroscopies indicate that rT β4 is a random coli major protein and its hydrophobic region becomes compact gradually. Moreover, the rT β4 folding is a two state transition. Thermal denaturation analysis indicates that rT β4 lacks stable tertiary structure. These results indicated that rT β4, similar to T β4, is an intrinsically disordered protein. Research is supported by MOST, Taiwan. MOST 103-2112-M-009-011-MY3. Corresponding author: Chia-Ching Chang; ccchang01@faculty.nctu.edu.tw.

Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions

PubMed Central

Li, Mai Suan; Hu, Chin-Kun; Klimov, Dmitri K.; Thirumalai, D.

2006-01-01

Mechanical folding trajectories for polyproteins starting from initially stretched conformations generated by single-molecule atomic force microscopy experiments [Fernandez, J. M. & Li, H. (2004) Science 303, 1674–1678] show that refolding, monitored by the end-to-end distance, occurs in distinct multiple stages. To clarify the molecular nature of folding starting from stretched conformations, we have probed the folding dynamics, upon force quench, for the single I27 domain from the muscle protein titin by using a Cα-Go model. Upon temperature quench, collapse and folding of I27 are synchronous. In contrast, refolding from stretched initial structures not only increases the folding and collapse time scales but also decouples the two kinetic processes. The increase in the folding times is associated primarily with the stretched state to compact random coil transition. Surprisingly, force quench does not alter the nature of the refolding kinetics, but merely increases the height of the free-energy folding barrier. Force quench refolding times scale as \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}{\\tau}_{F}\\approx {\\tau}_{F}^{0}{\\mathrm{exp}}(f_{q}{\\Delta}x_{f}/k_{{\\mathrm{B}}}T)\\end{equation*}\\end{document}, where Δxf ≈ 0.6 nm is the location of the average transition state along the reaction coordinate given by end-to-end distance. We predict that τF and the folding mechanism can be dramatically altered by the initial and/or final values of force. The implications of our results for design and analysis of experiments are discussed. PMID:16373511

Effect of deformations on the compactness of odd-Z superheavy nuclei formed in cold and hot fusion reactions

NASA Astrophysics Data System (ADS)

Kaur, Gurjit; Sandhu, Kirandeep; Sharma, Manoj K.

2018-03-01

Using the extended fragmentation theory, the compactness of hot and cold fusion reactions is analyzed for odd-Z nuclei ranging Z = 105- 117. The calculations for the present work are carried out at T = 0MeV and ℓ = 0 ħ, as the temperature and angular momentum effects remain silent while addressing the orientation degree of freedom (i.e. compact angle configuration). In the hot fusion, 48Ca (spherical) + actinide (prolate) reaction, the non-equatorial compact (nec) shape is obtained for Z = 113 nucleus. On the other hand, Z > 113 nuclei favor equatorial compact (ec) configuration. The distribution of barrier height (VB) illustrate that the ec-shape is obtained when the magnitude of quadrupole deformation of the nucleus is higher than the hexadecupole deformation. In other words, negligible or small -ve β4-deformations support ec configurations. On the other hand, large (+ve) magnitude of the β4-deformation suggests that the configuration appears for compact angle θc < 90 °, leading to nec structure. Similar deformation effects are observed for Bi-induced reactions, in which not belly-to-belly compact (nbbc) configurations are seen at θc = 42 °. In addition to the effect of β2 and β4-deformations, the exclusive role of octupole deformations (β3) is also analyzed. The β3-deformations do not follow the reflection symmetry as that of β2 and β4, leading to the possible occurrence of compact configuration within 0° to 180° angular range.

Laser Resonator

NASA Technical Reports Server (NTRS)

Harper, L. L. (Inventor)

1983-01-01

An optical resonator cavity configuration has a unitary mirror with oppositely directed convex and concave reflective surfaces disposed into one fold and concertedly reversing both ends of a beam propagating from a laser rod disposed between two total internal reflection prisms. The optical components are rigidly positioned with perpendicularly crossed virtual rooflines by a compact optical bed. The rooflines of the internal reflection prisms, are arranged perpendicularly to the axis of the laser beam and to the optical axes of the optical resonator components.

Generalized Alvarez lens for correction of laser aberrations

DOE Office of Scientific and Technical Information (OSTI.GOV)

LaFortune, K N

2004-12-02

The Alvarez lens (US Patent No. 3,305,294 [1]) is a compact aberration corrector. The original design emphasized in the patent consists of a pair of adjacent optical elements that provide a variable focus. A lens system with a variable effective focal length is nothing new. Such systems are widely used in cameras, for example. It is the compactness and simplicity of operation that is the key advantage of the Alvarez lens. All of the complexity is folded into the design and fabrication of the optical elements. As mentioned in the Alvarez patent [1] and elaborated upon in Palusinski et al.more » [2], if one is willing to fold even more complexity into the optical elements, it is possible to correct higher-order aberrations as well. There is no theoretical limit to the number or degree of wavefront distortions that can be corrected. The only limitation is that there must be a fixed relative magnitude of the aberrations. Independent correction of each component of the higher-order aberrations can not be performed without additional elements and degrees of freedom [3]. Under some circumstances, coupling may be observed between different aberrations. This can be mitigated with the appropriate choice of design parameters. New methods are available today that increase the practicality of making higher-order aberration correctors [4,5,6].« less

Deformation bands, early markers of tectonic activity in front of a fold-and-thrust belt: Example from the Tremp-Graus basin, southern Pyrenees, Spain

NASA Astrophysics Data System (ADS)

Robert, Romain; Robion, Philippe; Souloumiac, Pauline; David, Christian; Saillet, Elodie

2018-05-01

Strain localization in a porous calcarenite facies of the Aren formation in the Tremp basin was studied. This Maastrichtian syn-tectonic formation exposed in front of the Boixols thrust, in the Central South Pyrenean Zone, hosts bedding perpendicular deformation bands. These bands are organized in two major band sets, striking East-West and N-020 respectively. Both populations formed during early deformation stages linked to the growth of the fold and thrust. A magnetic fabric study (Anisotropy of Magnetic Susceptibility, AMS) was carried out to constrain the shortening direction responsible for the deformation bands development during the upper Cretaceous-Paleocene N-S contraction in the region, which allowed us to define populations of Pure Compaction Bands (PCB) and Shear Enhanced Compaction Bands (SECB) regarding their orientations compared to the shortening direction. Both sets are formed by cataclastic deformation, but more intense in the case of SECBs, which are also thinner than PCBs. The initial pore space is both mechanically reduced and chemically filled by several cementation phases. We propose a geomechanical model based on the regional context of layer parallel shortening, thrusting and strike-slip tectonics considering the burial history of the formation, in order to explain the development of both types of bands at remarkably shallow depths.

Ultrathin triple-band polarization-insensitive wide-angle compact metamaterial absorber

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shang, Shuai; Yang, Shizhong; Tao, Lu

2016-07-15

In this study, the design, realization, and characterization of an ultrathin triple-band polarization-insensitive wide-angle metamaterial absorber are reported. The metamaterial absorber comprises a periodic array of modified six-fold symmetric snowflake-shaped resonators with strip spiral line load, which is printed on a dielectric substrate backed by a metal ground plane. It is shown that the absorber exhibits three distinct near-unity absorption peaks, which are distributed across C, X, Ku bands, respectively. Owing to the six-fold symmetry, the absorber is insensitive to the polarization of the incident radiation. In addition, the absorber shows excellent absorption performance over wide oblique incident angles formore » both transverse electric and transverse magnetic polarizations. Simulated surface current and field distributions at the three absorption peaks are demonstrated to understand the absorption mechanism. Particularly, the absorption modes come from the fundamental and high-order dipole resonances. Furthermore, the experimental verification of the designed absorber is conducted, and the measured results are in reasonable agreement with the simulated ones. The proposed ultrathin (∼0.018λ{sub 0}, λ{sub 0} corresponding to the lowest peak absorption frequency) compact (0.168λ{sub 0}×0.168λ{sub 0} corresponding to the area of a unit cell) absorber enables potential applications such as stealth technology, electromagnetic interference and spectrum identification.« less

Fabrication of metallic glass structures

DOEpatents

Cline, Carl F.

1986-01-01

Amorphous metal powders or ribbons are fabricated into solid shapes of appreciable thickness by the application of compaction energy. The temperature regime wherein the amorphous metal deforms by viscous flow is measured. The metal powders or ribbons are compacted within the temperature range.

Bistatic image processing for a 32 x 19 inch model aircraft using scattered fields obtained in the OSU-ESL compact range

NASA Technical Reports Server (NTRS)

Lee, T-H.; Burnside, W. D.

1992-01-01

Inverse Synthetic Aperture Radar (ISAR) images for a 32 in long and 19 in wide model aircraft are documented. Both backscattered and bistatic scattered fields of this model aircraft were measured in the OSU-ESL compact range to obtain these images. The scattered fields of the target were measured for frequencies from 2 to 18 GHz with a 10 MHz increment and for full 360 deg azimuth rotation angles with a 0.2 deg step. For the bistatic scattering measurement, the compact range was used as the transmitting antenna; while, a broad band AEL double ridge horn was used as the receiving antenna. Bistatic angles of 90 deg and 135 deg were measured. Due to the size of the chamber and target, the receiving antenna was in the near field of the target; nevertheless, the image processing algorithm was valid for this case.

Soil compaction effects on water status of ponderosa pine assessed through 13C/12C composition.

PubMed

Gomez, G Armando; Singer, Michael J; Powers, Robert F; Horwath, William R

2002-05-01

Soil compaction is a side effect of forest reestablishment practices resulting from use of heavy equipment and site preparation. Soil compaction often alters soil properties resulting in changes in plant-available water. The use of pressure chamber methods to assess plant water stress has two drawbacks: (1) the measurements are not integrative; and (2) the method is difficult to apply extensively to establish seasonal soil water status. We evaluated leaf carbon isotopic composition (delta13C) as a means of assessing effects of soil compaction on water status and growth of young ponderosa pine (Pinus ponderosa var. ponderosa Dougl. ex Laws) stands across a range of soil textures. Leaf delta13C in cellulose and whole foliar tissue were highly correlated. Leaf delta13C in both whole tissue and cellulose (holocellulose) was up to 1.0 per thousand lower in trees growing in non-compacted (NC) loam or clay soils than in compacted (SC) loam or clay soils. Soil compaction had the opposite effect on leaf delta13C in trees growing on sandy loam soil, indicating that compaction increased water availability in this soil type. Tree growth response to compaction also varied with soil texture, with no effect, a negative effect and a positive effect as a result of compaction of loam, clay and sandy loam soils, respectively. There was a significant correlation between 13C signature and tree growth along the range of soil textures. Leaf delta13C trends were correlated with midday stem water potentials. We conclude that leaf delta13C can be used to measure retrospective water status and to assess the impact of site preparation on tree growth. The advantage of the leaf delta13C approach is that it provides an integrative assessment of past water status in different aged leaves.

Development of Discrete Compaction Bands in Two Porous Sandstones

NASA Astrophysics Data System (ADS)

Tembe, S.; Baud, P.; Wong, T.

2003-12-01

Compaction band formation has been documented by recent field and laboratory studies as a localized failure mode occurring in porous sandstones. The coupling of compaction and localization may significantly alter the stress field and strain partitioning, and act as barriers within reservoirs. Two end-members of this failure mode that develop subperpendicular to the maximum principal stress have been identified: numerous discrete compaction bands with a thickness of only several grains, or a few diffuse bands that are significantly thicker. Much of what is known about discrete compaction bands derives from laboratory experiments performed on the relatively homogeneous Bentheim sandstone with 23% porosity. In this study we observe similar compaction localization behavior in the Diemelstadt sandstone, that has an initial porosity of 24.4% and a modal composition of 68% quartz, 26% feldspar, 4% oxides, and 2% micas. CT scans of the Diemelstadt sandstone indicate bedding corresponding to low porosity laminae. Saturated samples cored perpendicular to bedding were deformed at room temperature under drained conditions at a constant pore pressure of 10 MPa and a confining pressure range of 20-175 MPa. Acoustic emission activity and pore volume change were recorded continuously. Samples were deformed to axial strains of 1-4% and recovered from the triaxial cell for microstructural analysis. The mechanical data map the transition in failure mode from brittle faulting to compactive cataclastic flow. The brittle regime occurred at effective pressures up to 40 MPa, associated with failure by conjugate shear bands. At an effective pressure range of 60-175 MPa strain hardening and shear-enhanced compaction were accompanied by the development of discrete compaction bands, that was manifested by episodic surges of acoustic emission. Preliminary microstructural observations of the failed samples suggest that bedding influenced the band orientations which varies between 75-90\\deg relative to the maximum principle stress. Our study demonstrates that despite their different mineralogy, failure modes and development of the compaction localization are similar in the Diemelstadt and Benthiem sandstones.

Fold assessment for comparative protein structure modeling.

PubMed

Melo, Francisco; Sali, Andrej

2007-11-01

Accurate and automated assessment of both geometrical errors and incompleteness of comparative protein structure models is necessary for an adequate use of the models. Here, we describe a composite score for discriminating between models with the correct and incorrect fold. To find an accurate composite score, we designed and applied a genetic algorithm method that searched for a most informative subset of 21 input model features as well as their optimized nonlinear transformation into the composite score. The 21 input features included various statistical potential scores, stereochemistry quality descriptors, sequence alignment scores, geometrical descriptors, and measures of protein packing. The optimized composite score was found to depend on (1) a statistical potential z-score for residue accessibilities and distances, (2) model compactness, and (3) percentage sequence identity of the alignment used to build the model. The accuracy of the composite score was compared with the accuracy of assessment by single and combined features as well as by other commonly used assessment methods. The testing set was representative of models produced by automated comparative modeling on a genomic scale. The composite score performed better than any other tested score in terms of the maximum correct classification rate (i.e., 3.3% false positives and 2.5% false negatives) as well as the sensitivity and specificity across the whole range of thresholds. The composite score was implemented in our program MODELLER-8 and was used to assess models in the MODBASE database that contains comparative models for domains in approximately 1.3 million protein sequences.

Small-Angle Neutron Scattering Reveals pH-Dependent Conformational Changes in Trichoderma reesei Cellobiohydrolase I: Implications for Enzymatic Activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pingali, Sai Venkatesh; O'Neill, Hugh Michael; McGaughey, Joseph

2011-01-01

Cellobiohydrolase I (Cel7A) of the fungus Trichoderma reesei (now classified as an anamorph of Hypocrea jecorina) hydrolyzes crystalline cellulose to soluble sugars, making it of key interest for producing fermentable sugars from biomass for biofuel production. The activity of the enzyme is pH-dependent, with its highest activity occurring at pH 4 5. To probe the response of the solution structure of Cel7A to changes in pH, we measured small angle neutron scattering of it in a series of solutions having pH values of 7.0, 6.0, 5.3, and 4.2. As the pH decreases from 7.0 to 5.3, the enzyme structure remainsmore » well defined, possessing a spatial differentiation between the cellulose binding domain and the catalytic core that only changes subtly. At pH 4.2, the solution conformation of the enzyme changes to a structure that is intermediate between a properly folded enzyme and a denatured, unfolded state, yet the secondary structure of the enzyme is essentially unaltered. The results indicate that at the pH of optimal activity, the catalytic core of the enzyme adopts a structure in which the compact packing typical of a fully folded polypeptide chain is disrupted and suggest that the increased range of structures afforded by this disordered state plays an important role in the increased activity of Cel7A through conformational selection.« less

2D stepping drive for hyperspectral systems

NASA Astrophysics Data System (ADS)

Endrödy, Csaba; Mehner, Hannes; Grewe, Adrian; Sinzinger, Stefan; Hoffmann, Martin

2015-07-01

We present the design, fabrication and characterization of a compact 2D stepping microdrive for pinhole array positioning. The miniaturized solution enables a highly integrated compact hyperspectral imaging system. Based on the geometry of the pinhole array, an inch-worm drive with electrostatic actuators was designed resulting in a compact (1 cm2) positioning system featuring a step size of about 15 µm in a 170 µm displacement range. The high payload (20 mg) as required for the pinhole array and the compact system design exceed the known electrostatic inch-worm-based microdrives.

Underwater explosive compaction-sintering of tungsten-copper coating on a copper surface

NASA Astrophysics Data System (ADS)

Chen, Xiang; Li, Xiaojie; Yan, Honghao; Wang, Xiaohong; Chen, Saiwei

2018-01-01

This study investigated underwater explosive compaction-sintering for coating a high-density tungsten-copper composite on a copper surface. First, 50% W-50% Cu tungsten-copper composite powder was prepared by mechanical alloying. The composite powder was pre-compacted and sintered by hydrogen. Underwater explosive compaction was carried out. Finally, a high-density tungsten-copper coating was obtained by diffusion sintering of the specimen after explosive compaction. A simulation of the underwater explosive compaction process showed that the peak value of the pressure in the coating was between 3.0 and 4.8 GPa. The hardness values of the tungsten-copper layer and the copper substrate were in the range of 87-133 and 49 HV, respectively. The bonding strength between the coating and the substrate was approximately 100-105 MPa.

Towards endoscopic ultrafast laser microsurgery of vocal folds

NASA Astrophysics Data System (ADS)

Hoy, Christopher L.; Everett, W. Neil; Yildirim, Murat; Kobler, James; Zeitels, Steven M.; Ben-Yakar, Adela

2012-03-01

Vocal fold scarring is a predominant cause of voice disorders yet lacks a reliable treatment method. The injection of soft biomaterials to improve mechanical compliance of the vocal folds has emerged as a promising treatment. Here, we study the use of precise femtosecond laser microsurgery to ablate subsurface voids, with a goal of eventually creating a plane in dense subepithelial scar tissue into which biomaterials can be injected for their improved localization. Specifically, we demonstrate the ablation of small subepithelial voids in porcine vocal fold tissue up to 120 µm below the surface such that larger voids in the active area of vocal fold mucosa (~3×10 mm2) can eventually be ablated in about 3 min. We use sub-µJ, 776-nm pulses from a compact femtosecond fiber laser system operating at a 500-kHz repetition rate. The use of relatively high repetition rates, with a small number of overlapping pulses, is critical to achieving ablation in a very short time while still avoiding significant heat deposition. Additionally, we use the same laser for nonlinear optical imaging to provide visual feedback of tissue structure and to confirm successful ablation. The ablation parameters, including pulse duration, pulse energy, spot size, and scanning speed, are comparable to the specifications in our recently developed miniaturized femtosecond laser surgery probes, illustrating the feasibility of developing an ultrafast laser surgical instrument.

Entropic and Electrostatic Effects on the Folding Free Energy of a Surface-Attached Biomolecule: An Experimental and Theoretical Study

PubMed Central

Watkins, Herschel M.; Vallée-Bélisle, Alexis; Ricci, Francesco; Makarov, Dmitrii E.; Plaxco, Kevin W.

2012-01-01

Surface-tethered biomolecules play key roles in many biological processes and biotechnologies. However, while the physical consequences of such surface attachment have seen significant theoretical study, to date this issue has seen relatively little experimental investigation. In response we present here a quantitative experimental and theoretical study of the extent to which attachment to a charged –but otherwise apparently inert– surface alters the folding free energy of a simple biomolecule. Specifically, we have measured the folding free energy of a DNA stem loop both in solution and when site-specifically attached to a negatively charged, hydroxyl-alkane-coated gold surface. We find that, whereas surface attachment is destabilizing at low ionic strength it becomes stabilizing at ionic strengths above ~130 mM. This behavior presumably reflects two competing mechanisms: excluded volume effects, which stabilize the folded conformation by reducing the entropy of the unfolded state, and electrostatics, which, at lower ionic strengths, destabilizes the more compact folded state via repulsion from the negatively charged surface. To test this hypothesis we have employed existing theories of the electrostatics of surface-bound polyelectrolytes and the entropy of surface-bound polymers to model both effects. Despite lacking any fitted parameters, these theoretical models quantitatively fit our experimental results, suggesting that, for this system, current knowledge of both surface electrostatics and excluded volume effects is reasonably complete and accurate. PMID:22239220

The Histone Database: an integrated resource for histones and histone fold-containing proteins

PubMed Central

Mariño-Ramírez, Leonardo; Levine, Kevin M.; Morales, Mario; Zhang, Suiyuan; Moreland, R. Travis; Baxevanis, Andreas D.; Landsman, David

2011-01-01

Eukaryotic chromatin is composed of DNA and protein components—core histones—that act to compactly pack the DNA into nucleosomes, the fundamental building blocks of chromatin. These nucleosomes are connected to adjacent nucleosomes by linker histones. Nucleosomes are highly dynamic and, through various core histone post-translational modifications and incorporation of diverse histone variants, can serve as epigenetic marks to control processes such as gene expression and recombination. The Histone Sequence Database is a curated collection of sequences and structures of histones and non-histone proteins containing histone folds, assembled from major public databases. Here, we report a substantial increase in the number of sequences and taxonomic coverage for histone and histone fold-containing proteins available in the database. Additionally, the database now contains an expanded dataset that includes archaeal histone sequences. The database also provides comprehensive multiple sequence alignments for each of the four core histones (H2A, H2B, H3 and H4), the linker histones (H1/H5) and the archaeal histones. The database also includes current information on solved histone fold-containing structures. The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins. Database URL: The Histone Sequence Database is freely available and can be accessed at http://research.nhgri.nih.gov/histones/. PMID:22025671

Data precision of X-ray fluorescence (XRF) scanning of discrete samples with the ITRAX XRF core-scanner exemplified on loess-paleosol samples

NASA Astrophysics Data System (ADS)

Profe, Jörn; Ohlendorf, Christian

2017-04-01

XRF-scanning is the state-of-the-art technique for geochemical analyses in marine and lacustrine sedimentology for more than a decade. However, little attention has been paid to data precision and technical limitations so far. Using homogenized, dried and powdered samples (certified geochemical reference standards and samples from a lithologically-contrasting loess-paleosol sequence) minimizes many adverse effects that influence the XRF-signal when analyzing wet sediment cores. This allows the investigation of data precision under ideal conditions and documents a new application of the XRF core-scanner technology at the same time. Reliable interpretations of XRF results require data precision evaluation of single elements as a function of X-ray tube, measurement time, sample compaction and quality of peak fitting. Ten-fold measurement of each sample constitutes data precision. Data precision of XRF measurements theoretically obeys Poisson statistics. Fe and Ca exhibit largest deviations from Poisson statistics. The same elements show the least mean relative standard deviations in the range from 0.5% to 1%. This represents the technical limit of data precision achievable by the installed detector. Measurement times ≥ 30 s reveal mean relative standard deviations below 4% for most elements. The quality of peak fitting is only relevant for elements with overlapping fluorescence lines such as Ba, Ti and Mn or for elements with low concentrations such as Y, for example. Differences in sample compaction are marginal and do not change mean relative standard deviation considerably. Data precision is in the range reported for geochemical reference standards measured by conventional techniques. Therefore, XRF scanning of discrete samples provide a cost- and time-efficient alternative to conventional multi-element analyses. As best trade-off between economical operation and data quality, we recommend a measurement time of 30 s resulting in a total scan time of 30 minutes for 30 samples.

The KMOS3D Survey: Rotating Compact Star-forming Galaxies and the Decomposition of Integrated Line Widths

NASA Astrophysics Data System (ADS)

Wisnioski, E.; Mendel, J. T.; Förster Schreiber, N. M.; Genzel, R.; Wilman, D.; Wuyts, S.; Belli, S.; Beifiori, A.; Bender, R.; Brammer, G.; Chan, J.; Davies, R. I.; Davies, R. L.; Fabricius, M.; Fossati, M.; Galametz, A.; Lang, P.; Lutz, D.; Nelson, E. J.; Momcheva, I.; Rosario, D.; Saglia, R.; Tacconi, L. J.; Tadaki, K.; Übler, H.; van Dokkum, P. G.

2018-03-01

Using integral field spectroscopy, we investigate the kinematic properties of 35 massive centrally dense and compact star-forming galaxies (SFGs; {log}{\\overline{M}}* [{M}ȯ ]=11.1, {log}({{{Σ }}}1{kpc}[{M}ȯ {kpc}}-2])> 9.5, {log}({M}* /{r}e1.5[{M}ȯ {kpc}}-1.5])> 10.3) at z ∼ 0.7–3.7 within the KMOS3D survey. We spatially resolve 23 compact SFGs and find that the majority are dominated by rotational motions with velocities ranging from 95 to 500 km s‑1. The range of rotation velocities is reflected in a similar range of integrated Hα line widths, 75–400 km s‑1, consistent with the kinematic properties of mass-matched extended galaxies from the full KMOS3D sample. The fraction of compact SFGs that are classified as “rotation-dominated” or “disklike” also mirrors the fractions of the full KMOS3D sample. We show that integrated line-of-sight gas velocity dispersions from KMOS3D are best approximated by a linear combination of their rotation and turbulent velocities with a lesser but still significant contribution from galactic-scale winds. The Hα exponential disk sizes of compact SFGs are, on average, 2.5 ± 0.2 kpc, 1–2× the continuum sizes, in agreement with previous work. The compact SFGs have a 1.4× higher active galactic nucleus (AGN) incidence than the full KMOS3D sample at fixed stellar mass with an average AGN fraction of 76%. Given their high and centrally concentrated stellar masses, as well as stellar-to-dynamical mass ratios close to unity, the compact SFGs are likely to have low molecular gas fractions and to quench on a short timescale unless replenished with inflowing gas. The rotation in these compact systems suggests that their direct descendants are rotating passive galaxies. Based on observations obtained at the Very Large Telescope (VLT) of the European Southern Observatory (ESO), Paranal, Chile (ESO program IDs 092A-0091, 093.A-0079, 094.A-0217, 095.A-0047, 096.A-0025, 097.A-0028, and 098.A-0045).

A compact time-of-flight mass spectrometer for ion source characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, L., E-mail: l.chen03@gmail.com; Wan, X.; Jin, D. Z.

2015-03-15

A compact time-of-flight mass spectrometer with overall dimension of about 413 × 250 × 414 mm based on orthogonal injection and angle reflection has been developed for ion source characterization. Configuration and principle of the time-of-flight mass spectrometer are introduced in this paper. The mass resolution is optimized to be about 1690 (FWHM), and the ion energy detection range is tested to be between about 3 and 163 eV with the help of electron impact ion source. High mass resolution and compact configuration make this spectrometer useful to provide a valuable diagnostic for ion spectra fundamental research and study themore » mass to charge composition of plasma with wide range of parameters.« less

Scalar field configurations supported by charged compact reflecting stars in a curved spacetime

NASA Astrophysics Data System (ADS)

Peng, Yan

2018-05-01

We study the system of static scalar fields coupled to charged compact reflecting stars through both analytical and numerical methods. We enclose the star in a box and our solutions are related to cases without box boundaries when putting the box far away from the star. We provide bottom and upper bounds for the radius of the scalar hairy compact reflecting star. We obtain numerical scalar hairy star solutions satisfying boundary conditions and find that the radius of the hairy star in a box is continuous in a range, which is very different from cases without box boundaries where the radius is discrete in the range. We also examine effects of the star charge and mass on the largest radius.

Ozone Measurements with the US EPA UV-DIAL: Preliminary Results

NASA Technical Reports Server (NTRS)

Moosmueller, H.; Diebel, D.; Bundy, D. H.; Bristow, M. P.; Alvarez, R. J., II; Kovalev, V. A.; Edmonds, C. M.; Turner, R. M.; Mcelroy, J. L.

1992-01-01

A compact airborne down-looking lidar system was developed at the Environmental Protection Agency in Las Vegas. This differential absorption lidar (DIAL) was designed to simultaneously measure range-resolved concentrations of ozone (O3) and sulfur dioxide (SO2) in the lower troposphere, together with an indication of the aerosol distribution. The five laser wavelengths (i.e., lambda(sub 1) = 277 nm, lambda(sub 2) = 292 nm, lambda(sub 3) = 313 nm, lambda(sub4) = 319 nm, lambda(sub 5) = 369 nm) were generated via Raman conversion of a focused KrF excimer laser. The system is currently installed in a truck-based mobile laboratory. For the ground testing, an opening in the truck floor together with a folding mirror under the truck makes a horizontal, or upwardly inclined direction of measurement possible. Initial ground testing has been performed in the vicinity of a Desert Research Institute (DRI) ambient air monitoring site, located at Cottonwood Cove approximately 85 km south east of Las Vegas, Nevada. At this site O3 and SO2 concentrations are continuously monitored with an average accuracy better than +/- 10 percent. A temporary ozone measurement station with identical accuracy was set up at a distance to get a second point of comparison for the range-resolved DIAL measurements.

Fatigue crack growth in 7475-T651 aluminum alloy plate in hard vacuum and water vapor. M.S. Thesis - George Washington Univ.

NASA Technical Reports Server (NTRS)

Dicus, D. L.

1981-01-01

Compact specimens of 25 mm thick aluminum alloy plate were subjected to constant amplitude fatigue testing at a load ratio of 0.2. Crack growth rates were determined at frequencies of 1 Hz and 10 Hz in hard vacuum and laboratory air, and in mixtures of water vapor and nitrogen at water vapor partial pressures ranging from 94 Pa to 3.8 kPa. A significant effect of water vapor on fatigue crack growth rates was observed at the lowest water vapor pressure tested. Crack rates changed little for pressures up to 1.03 kPa, but abruptly accelerated at higher pressures. At low stress intensity factor ranges, cracking rates at the lowest and highest water vapor pressure tested were, respectively, two and five times higher than rates in vacuum. Although a frequency was observed in laboratory air, cracking rates in water vapor and vacuum are insensitive to a ten-fold change in frequency. Surfaces of specimens tested in water vapor and vacuum exhibited different amounts of residual deformation. Reduced deformation on the fracture surfaces of the specimens tested in water vapor suggests embrittlement of the plastic zone ahead of the crack tip as a result of environmental interaction.

Compact, singular G 2-holonomy manifolds and M/heterotic/F-theory duality

NASA Astrophysics Data System (ADS)

Braun, Andreas P.; Schäfer-Nameki, Sakura

2018-04-01

We study the duality between M-theory on compact holonomy G 2-manifolds and the heterotic string on Calabi-Yau three-folds. The duality is studied for K3-fibered G 2-manifolds, called twisted connected sums, which lend themselves to an application of fiber-wise M-theory/Heterotic Duality. For a large class of such G 2-manifolds we are able to identify the dual heterotic as well as F-theory realizations. First we establish this chain of dualities for smooth G 2-manifolds. This has a natural generalization to situations with non-abelian gauge groups, which correspond to singular G 2-manifolds, where each of the K3-fibers degenerates. We argue for their existence through the chain of dualities, supported by non-trivial checks of the spectra. The corresponding 4d gauge groups can be both Higgsable and non-Higgsable, and we provide several explicit examples of the general construction.

The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling.

PubMed

Su, Ting; Cheng, Jingdong; Sohmen, Daniel; Hedman, Rickard; Berninghausen, Otto; von Heijne, Gunnar; Wilson, Daniel N; Beckmann, Roland

2017-05-30

Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 Å cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two α-helices connected by an α-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50-55 Å of the exit tunnel. The structure reveals how α-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome.

Structural and Functional Characterization of the Recombinant Death Domain from Death-Associated Protein Kinase

PubMed Central

Dioletis, Evangelos; Dingley, Andrew J.; Driscoll, Paul C.

2013-01-01

Death-associated protein kinase (DAPk) is a calcium/calmodulin-regulated Ser/Thr-protein kinase that functions at an important point of integration for cell death signaling pathways. DAPk has a structurally unique multi-domain architecture, including a C-terminally positioned death domain (DD) that is a positive regulator of DAPk activity. In this study, recombinant DAPk-DD was observed to aggregate readily and could not be prepared in sufficient yield for structural analysis. However, DAPk-DD could be obtained as a soluble protein in the form of a translational fusion protein with the B1 domain of streptococcal protein G. In contrast to other DDs that adopt the canonical six amphipathic α-helices arranged in a compact fold, the DAPk-DD was found to possess surprisingly low regular secondary structure content and an absence of a stable globular fold, as determined by circular dichroism (CD), NMR spectroscopy and a temperature-dependent fluorescence assay. Furthermore, we measured the in vitro interaction between extracellular-regulated kinase-2 (ERK2) and various recombinant DAPk-DD constructs. Despite the low level of structural order, the recombinant DAPk-DD retained the ability to interact with ERK2 in a 1∶1 ratio with a K d in the low micromolar range. Only the full-length DAPk-DD could bind ERK2, indicating that the apparent ‘D-motif’ located in the putative sixth helix of DAPk-DD is not sufficient for ERK2 recognition. CD analysis revealed that binding of DAPk-DD to ERK2 is not accompanied by a significant change in secondary structure. Taken together our data argue that the DAPk-DD, when expressed in isolation, does not adopt a classical DD fold, yet in this state retains the capacity to interact with at least one of its binding partners. The lack of a stable globular structure for the DAPk-DD may reflect either that its folding would be supported by interactions absent in our experimental set-up, or a limitation in the structural bioinformatics assignment of the three-dimensional structure. PMID:23922916

Structural and functional characterization of the recombinant death domain from death-associated protein kinase.

PubMed

Dioletis, Evangelos; Dingley, Andrew J; Driscoll, Paul C

2013-01-01

Death-associated protein kinase (DAPk) is a calcium/calmodulin-regulated Ser/Thr-protein kinase that functions at an important point of integration for cell death signaling pathways. DAPk has a structurally unique multi-domain architecture, including a C-terminally positioned death domain (DD) that is a positive regulator of DAPk activity. In this study, recombinant DAPk-DD was observed to aggregate readily and could not be prepared in sufficient yield for structural analysis. However, DAPk-DD could be obtained as a soluble protein in the form of a translational fusion protein with the B1 domain of streptococcal protein G. In contrast to other DDs that adopt the canonical six amphipathic α-helices arranged in a compact fold, the DAPk-DD was found to possess surprisingly low regular secondary structure content and an absence of a stable globular fold, as determined by circular dichroism (CD), NMR spectroscopy and a temperature-dependent fluorescence assay. Furthermore, we measured the in vitro interaction between extracellular-regulated kinase-2 (ERK2) and various recombinant DAPk-DD constructs. Despite the low level of structural order, the recombinant DAPk-DD retained the ability to interact with ERK2 in a 1∶1 ratio with a K d in the low micromolar range. Only the full-length DAPk-DD could bind ERK2, indicating that the apparent 'D-motif' located in the putative sixth helix of DAPk-DD is not sufficient for ERK2 recognition. CD analysis revealed that binding of DAPk-DD to ERK2 is not accompanied by a significant change in secondary structure. Taken together our data argue that the DAPk-DD, when expressed in isolation, does not adopt a classical DD fold, yet in this state retains the capacity to interact with at least one of its binding partners. The lack of a stable globular structure for the DAPk-DD may reflect either that its folding would be supported by interactions absent in our experimental set-up, or a limitation in the structural bioinformatics assignment of the three-dimensional structure.

Vertical surface displacements along a part of the Newport-Inglewood zone of folds and faults, Los Angeles and Orange counties, California

USGS Publications Warehouse

Castle, Robert O.; Buchanan-Banks, Jane M.

1989-01-01

During the past half century, the onshore section of the Newport- Inglewood zone of folds and faults between the Dominguez oil field and Corona del Mar (fig. 1) has been repeatedly leveled to geodetic standards. These essentially fortuitous surveys are unrelated to either the tectonic framework or the urbanization of the Los Angeles basin, but were established instead because the Newport-Inglewood zone southward from the Long Beach area is roughly coincident with the coastline--and, hence, is roughly coincident with a naturally defined leveling route. Although these have been several relevelings athwart this zone north of the long Beach area, notably in the Baldwin Hills area (Castle and Yerkes, 1976), about 25 km to the northwest, the survey density, in both space and time, diminishes markedly northward. Thus, the results of the indicated relevelings along the Los Angeles-Orange County coast have permitted the relatively detailed appraisal of historic vertical surface movements described in this report. The Newport-Inglewood zone of folds and faults forms the surface expression of a major crustal boundary separating the Peninsular Ranges province on the east from the Continental Borderland province on the west (Castle and others, 1984, p. 8-9, pl. 1). Transcurrent fault movement along this boundary has produced not only continuing seismic activity, for which this zone is justly famous, but also folds and other structural features within the sedimentary veneer that have entrapped the petroleum deposits for which the Newport-Inglewood zone is even more famous. Although the northeast boundary of the exceptionally prolific Wilmington oil field is roughly coincident with the southeast edge of the Newport-Inglewood zone, we have deliberately excluded this area from consideration--in other than a peripheral way--simply because compaction-induced subsidence centering on the Wilmington field is viewed as a singularly spectacular example of this phenomenon and, hence, has been the subject of a series of detailed investigation (Harris and Harlow, 1947; Gilluly and Grant, 1949; Hudson, 1956; Miller, 1966; Poland and Davis, 1969; Allen and Mayuga, 1970; Castle and Yerkes, 1976).

Low-cost compact MEMS scanning ladar system for robotic applications

NASA Astrophysics Data System (ADS)

Moss, Robert; Yuan, Ping; Bai, Xiaogang; Quesada, Emilio; Sudharsanan, Rengarajan; Stann, Barry L.; Dammann, John F.; Giza, Mark M.; Lawler, William B.

2012-06-01

Future robots and autonomous vehicles require compact low-cost Laser Detection and Ranging (LADAR) systems for autonomous navigation. Army Research Laboratory (ARL) had recently demonstrated a brass-board short-range eye-safe MEMS scanning LADAR system for robotic applications. Boeing Spectrolab is doing a tech-transfer (CRADA) of this system and has built a compact MEMS scanning LADAR system with additional improvements in receiver sensitivity, laser system, and data processing system. Improved system sensitivity, low-cost, miniaturization, and low power consumption are the main goals for the commercialization of this LADAR system. The receiver sensitivity has been improved by 2x using large-area InGaAs PIN detectors with low-noise amplifiers. The FPGA code has been updated to extend the range to 50 meters and detect up to 3 targets per pixel. Range accuracy has been improved through the implementation of an optical T-Zero input line. A compact commercially available erbium fiber laser operating at 1550 nm wavelength is used as a transmitter, thus reducing the size of the LADAR system considerably from the ARL brassboard system. The computer interface has been consolidated to allow image data and configuration data (configuration settings and system status) to pass through a single Ethernet port. In this presentation we will discuss the system architecture and future improvements to receiver sensitivity using avalanche photodiodes.

Shock-induced compaction of nanoparticle layers into nanostructured coating

NASA Astrophysics Data System (ADS)

Mayer, Alexander E.; Ebel, Andrei A.

2017-10-01

A new process of shock wave consolidation of nanoparticles into a nanocrystalline coating is theoretically considered. In the proposed scheme, the nanoparticle layers, which are attached to the substrate surface by adhesion, are compacted by plane ultra-short shock waves coming from the substrate. The initial adhesion is self-arisen at any contact between the nanoparticles without a pre-compression. The absence of the nanoparticle ejections due to the shock wave action is connected with the strong adhesive forces, which allow nanoparticles to be attached to each other and to substrate while they are being compacted; this should be valid for small enough nanoparticles. Severe plastic deformation of the nanoparticles and the increased temperature due to collapse of voids between them facilitate their compaction into the monolithic nanocrystalline layer. We consider the examples of Cu and Ni nanoparticles on Al substrate using molecular dynamic simulations. We show the efficiency of the action of multiple shock waves with the duration in the range 2-20 ps and the amplitude in the range 4-12 GPa for sequential layerwise compaction of nanoparticles. A series of shock waves can be created by a repetitive powerful pulsed laser irradiation of the opposite surface of the substrate. The method offers the challenge for the formation of nanostructured coatings of various compositions. The thickness of the compacted nanocrystalline coating can be locally varied and controlled by the number of acting pulses.

Detection-dependent kinetics as a probe of folding landscape microstructure.

PubMed

Yang, Wei Yuan; Gruebele, Martin

2004-06-30

The folding landscapes of polypeptides and proteins exhibit a hierarchy of local minima. The causes range from proline isomerization all the way down to microstructure in the free energy caused by residual frustration inherent in even the best 20 amino acid design. The corresponding time scales range from hours to submicroseconds. The smallest microstructures are difficult to detect. We have measured the folding/unfolding kinetics of the engineered trpzip2 peptide at different tryptophan fluorescence wavelengths, each yielding a different rate. Wavelength-dependent folding kinetics on 0.1-2 mus time scales show that different microstructures with a range of solvent exposure and local dynamics are populated. We estimate a lower limit for the roughness of the free energy surface based on the range of rates observed.

Bellow seal and anchor

DOEpatents

Mansure, Arthur J.

2001-01-01

An annular seal is made of a collapsible bellows. The bellows can function as an anchor or a seal and is easily set into position using relative component movement. The bellows folds can be slanted and their outer sealing edges can have different profiles to meet expected conditions. The bellows is expanded for insertion to reduce its outer dimension and sets by compaction as a result of relative movement. The bellows can be straight or tapered and is settable with a minimal axial force.

Optically-programmable nonlinear photonic component for dielectric-loaded plasmonic circuitry.

PubMed

Krasavin, Alexey V; Randhawa, Sukanya; Bouillard, Jean-Sebastien; Renger, Jan; Quidant, Romain; Zayats, Anatoly V

2011-12-05

We demonstrate both experimentally and numerically a compact and efficient, optically tuneable plasmonic component utilizing a surface plasmon polariton ring resonator with nonlinearity based on trans-cis isomerization in a polymer material. We observe more than 3-fold change between high and low transmission states of the device at milliwatt control powers (∼100 W/cm² by intensity), with the performance limited by switching speed of the material. Such plasmonic components can be employed in optically programmable and reconfigurable integrated photonic circuitry.

Water-level altitudes 2012 and water-level changes in the Chicot, Evangeline, and Jasper aquifers and compaction 1973-2011 in the Chicot and Evangeline aquifers, Houston-Galveston region, Texas

USGS Publications Warehouse

Kasmarek, Mark C.; Johnson, Michaela R.; Ramage, Jason K.

2012-01-01

Compaction of subsurface sediments (mostly in the clay layers) composing the Chicot and Evangeline aquifers was recorded continuously at 13 borehole extensometers at 11 sites. For the period of record beginning in 1973 (or later) and ending in December 2011, cumulative compaction data collected from the 13 extensometers ranged from 0.102 ft at the Texas City–Moses Lake site to 3.621 ft at the Addicks site. The rate of compaction varies from site to site because of differences in groundwater withdrawals near each site and differences among sites in the clay-to-sand ratio in the subsurface sediments. Therefore, it is not possible to extrapolate or infer a rate of compaction for adjacent areas on the basis of the rate of compaction measured at a nearby extensometer.

Correlating particle hardness with powder compaction performance.

PubMed

Cao, Xiaoping; Morganti, Mikayla; Hancock, Bruno C; Masterson, Victoria M

2010-10-01

Assessing particle mechanical properties of pharmaceutical materials quickly and with little material can be very important to early stages of pharmaceutical research. In this study, a wide range of pharmaceutical materials were studied using atomic force microscopy (AFM) nanoindentation. A significant amount of particle hardness and elastic modulus data were provided. Moreover, powder compact mechanical properties of these materials were investigated in order to build correlation between the particle hardness and powder compaction performance. It was found that the materials with very low or high particle hardness most likely exhibit poor compaction performance while the materials with medium particle hardness usually have good compaction behavior. Additionally, the results from this study enriched Hiestand's special case concept on particle hardness and powder compaction performance. This study suggests that the use of AFM nanoindentation can help to screen mechanical properties of pharmaceutical materials at early development stages of pharmaceutical research.

The origin and development of plains-type folds during the cretaceous in Central and western Kansas

USGS Publications Warehouse

Merriam, D.F.; Forster, A.

2000-01-01

Kansas is part of the Central Stable Region of North America. Structural movement on this part of the craton has been mainly the result of tectonism in nearby areas. Response to the outside tectonic forces, transmitted through the rigid Precambrian basement, has been vertical adjustment. Differential movement along an indigenous fault/fracture pattern in the basement created displaced blocks over which the later sediments were draped by differential compaction. After initial formation of this structural regimen in late Mississippian-early Pennsylvanian time, continued movement of the basement blocks gave rise to the plains-type folds so prevalent in the U.S. Midcontinent. The incremental movement continues through the late Paleozoic, Mesozoic, and Tertiary until today. This paper demonstrates the Cretaceous development of some of these structures in central and western Kansas.

Electrotransfection of Polyamine Folded DNA Origami Structures.

PubMed

Chopra, Aradhana; Krishnan, Swati; Simmel, Friedrich C

2016-10-12

DNA origami structures are artificial molecular nanostructures in which DNA double helices are forced into a closely packed configuration by a multitude of DNA strand crossovers. We show that three different types of origami structures (a flat sheet, a hollow tube, and a compact origami block) can be formed in magnesium-free buffer solutions containing low (<1 mM) concentrations of the condensing agent spermidine. Much like in DNA condensation, the amount of spermidine required for origami folding is proportional to the DNA concentration. At excessive amounts, the structures aggregate and precipitate. In contrast to origami structures formed in conventional buffers, the resulting structures are stable in the presence of high electric field pulses, such as those commonly used for electrotransfection experiments. We demonstrate that spermidine-stabilized structures are stable in cell lysate and can be delivered into mammalian cells via electroporation.

Multi-resonant wideband energy harvester based on a folded asymmetric M-shaped cantilever

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Meng; Mao, Haiyang; Li, Zhigang

2015-07-15

This article reports a compact wideband piezoelectric vibration energy harvester consisting of three proof masses and an asymmetric M-shaped cantilever. The M-shaped beam comprises a main beam and two folded and dimension varied auxiliary beams interconnected through the proof mass at the end of the main cantilever. Such an arrangement constitutes a three degree-of-freedom vibrating body, which can tune the resonant frequencies of its first three orders close enough to obtain a utility wide bandwidth. The finite element simulation results and the experimental results are well matched. The operation bandwidth comprises three adjacent voltage peaks on account of the frequencymore » interval shortening mechanism. The result shows that the proposed piezoelectric energy harvester could be efficient and adaptive in practical vibration circumstance based on multiple resonant modes.« less

Compact quantum dot-antibody conjugates for FRET immunoassays with subnanomolar detection limits

NASA Astrophysics Data System (ADS)

Mattera, Lucia; Bhuckory, Shashi; Wegner, K. David; Qiu, Xue; Agnese, Fabio; Lincheneau, Christophe; Senden, Tim; Djurado, David; Charbonnière, Loïc J.; Hildebrandt, Niko; Reiss, Peter

2016-05-01

A novel two-step approach for quantum dot (QD) functionalization and bioconjugation is presented, which yields ultra-compact, stable, and highly luminescent antibody-QD conjugates suitable for use in FRET immunoassays. Hydrophobic InPZnS/ZnSe/ZnS (emission wavelength: 530 nm), CdSe/ZnS (605 nm), and CdSeTe/ZnS (705 nm) QDs were surface functionalized with zwitterionic penicillamine, enabling aqueous phase transfer under conservation of the photoluminescence properties. Post-functionalization with a heterobifunctional crosslinker, containing a lipoic acid group and a maleimide function, enabled the subsequent coupling to sulfhydryl groups of proteins. This was demonstrated by QD conjugation with fragmented antibodies (F(ab)). The obtained F(ab)-QD conjugates range among the smallest antibody-functionalized nanoprobes ever reported, with a hydrodynamic diameter <13 nm, PL quantum yield up to 66% at 705 nm, and colloidal stability of several months in various buffers. They were applied as FRET acceptors in homogeneous, time-gated immunoassays using Tb-antibodies as FRET donors, both coupled by an immunological sandwich complex between the two antibodies and a PSA (prostate specific antigen) biomarker. The advantages of the compact surface coating for FRET could be demonstrated by an 6.2 and 2.5 fold improvement of the limit of detection (LOD) for PSA compared to commercially available hydrophilic QDs emitting at 605 and 705 nm, respectively. While the commercial QDs contain identical inorganic cores responsible for their fluorescence, they are coated with a comparably thick amphiphilic polymer layer leading to much larger hydrodynamic diameters (>26 nm without biomolecules). The LODs of 0.8 and 3.7 ng mL-1 obtained in 50 μL serum samples are below the clinical cut-off level of PSA (4 ng mL-1) and demonstrate their direct applicability in clinical diagnostics.A novel two-step approach for quantum dot (QD) functionalization and bioconjugation is presented, which yields ultra-compact, stable, and highly luminescent antibody-QD conjugates suitable for use in FRET immunoassays. Hydrophobic InPZnS/ZnSe/ZnS (emission wavelength: 530 nm), CdSe/ZnS (605 nm), and CdSeTe/ZnS (705 nm) QDs were surface functionalized with zwitterionic penicillamine, enabling aqueous phase transfer under conservation of the photoluminescence properties. Post-functionalization with a heterobifunctional crosslinker, containing a lipoic acid group and a maleimide function, enabled the subsequent coupling to sulfhydryl groups of proteins. This was demonstrated by QD conjugation with fragmented antibodies (F(ab)). The obtained F(ab)-QD conjugates range among the smallest antibody-functionalized nanoprobes ever reported, with a hydrodynamic diameter <13 nm, PL quantum yield up to 66% at 705 nm, and colloidal stability of several months in various buffers. They were applied as FRET acceptors in homogeneous, time-gated immunoassays using Tb-antibodies as FRET donors, both coupled by an immunological sandwich complex between the two antibodies and a PSA (prostate specific antigen) biomarker. The advantages of the compact surface coating for FRET could be demonstrated by an 6.2 and 2.5 fold improvement of the limit of detection (LOD) for PSA compared to commercially available hydrophilic QDs emitting at 605 and 705 nm, respectively. While the commercial QDs contain identical inorganic cores responsible for their fluorescence, they are coated with a comparably thick amphiphilic polymer layer leading to much larger hydrodynamic diameters (>26 nm without biomolecules). The LODs of 0.8 and 3.7 ng mL-1 obtained in 50 μL serum samples are below the clinical cut-off level of PSA (4 ng mL-1) and demonstrate their direct applicability in clinical diagnostics. Electronic supplementary information (ESI) available: SI-1: UV-vis/PL spectra; SI-2: TEM images; SI-3: DLS; SI-4: gel electrophoresis; SI-5: FTIR spectra; SI-6: overlap between QD absorption spectra and area-normalized Tb emission; SI-7: photographs of the samples; and optical characterization of QD-F(ab) conjugates (Table S1). See DOI: 10.1039/c6nr03261c

Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field

PubMed Central

Buck, Patrick M.; Bystroff, Christopher

2015-01-01

Protein folding is a hierarchical process where structure forms locally first, then globally. Some short sequence segments initiate folding through strong structural preferences that are independent of their three-dimensional context in proteins. We have constructed a knowledge-based force field in which the energy functions are conditional on local sequence patterns, as expressed in the hidden Markov model for local structure (HMMSTR). Carbon-alpha force field (CALF) builds sequence specific statistical potentials based on database frequencies for α-carbon virtual bond opening and dihedral angles, pairwise contacts and hydrogen bond donor-acceptor pairs, and simulates folding via Brownian dynamics. We introduce hydrogen bond donor and acceptor potentials as α-carbon probability fields that are conditional on the predicted local sequence. Constant temperature simulations were carried out using 27 peptides selected as putative folding initiation sites, each 12 residues in length, representing several different local structure motifs. Each 0.6 μs trajectory was clustered based on structure. Simulation convergence or representativeness was assessed by subdividing trajectories and comparing clusters. For 21 of the 27 sequences, the largest cluster made up more than half of the total trajectory. Of these 21 sequences, 14 had cluster centers that were at most 2.6 Å root mean square deviation (RMSD) from their native structure in the corresponding full-length protein. To assess the adequacy of the energy function on nonlocal interactions, 11 full length native structures were relaxed using Brownian dynamics simulations. Equilibrated structures deviated from their native states but retained their overall topology and compactness. A simple potential that folds proteins locally and stabilizes proteins globally may enable a more realistic understanding of hierarchical folding pathways. PMID:19137613

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

NASA Astrophysics Data System (ADS)

Henke, Paul S.; Mak, Chi H.

2014-08-01

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping.

PubMed

Henke, Paul S; Mak, Chi H

2014-08-14

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg(2+) that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis.

PubMed

Yamagami, Ryota; Bingaman, Jamie L; Frankel, Erica A; Bevilacqua, Philip C

2018-06-01

Most RNA folding studies have been performed under non-physiological conditions of high concentrations (≥10 mM) of Mg 2+ free , while actual cellular concentrations of Mg 2+ free are only ~1 mM in a background of greater than 50 mM Mg 2+ total . To uncover cellular behavior of RNA, we devised cytoplasm mimic systems that include biological concentrations of amino acids, which weakly chelate Mg 2+ . Amino acid-chelated Mg 2+ (aaCM) of ~15 mM dramatically increases RNA folding and prevents RNA degradation. Furthermore, aaCM enhance self-cleavage of several different ribozymes, up to 100,000-fold at Mg 2+ free of just 0.5 mM, indirectly through RNA compaction. Other metabolites that weakly chelate magnesium offer similar beneficial effects, which implies chelated magnesium may enhance RNA function in the cell in the same way. Overall, these results indicate that the states of Mg 2+ should not be limited to free and bound only, as weakly bound Mg 2+ strongly promotes RNA function under cellular conditions.

Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme

DOE PAGES

Lee, Hui-Ting; Kilburn, D.; Behrouzi, R.; ...

2014-12-05

The native structure of the Azoarcus group I ribozyme is stabilized by the cooperative formation of tertiary interactions between double helical domains. Thus, even single mutations that break this network of tertiary interactions reduce ribozyme activity in physiological Mg2+ concentrations. Here, we report that molecular crowding comparable to that in the cell compensates for destabilizing mutations in the Azoarcus ribozyme. Small angle X-ray scattering, native polyacrylamide gel electrophoresis and activity assays were used to compare folding free energies in dilute and crowded solutions containing 18% PEG1000. Crowder molecules allowed the wild-type and mutant ribozymes to fold at similarly low Mg2+more » concentrations and stabilized the active structure of the mutant ribozymes under physiological conditions. This compensation helps explains why ribozyme mutations are often less deleterious in the cell than in the test tube. Nevertheless, crowding did not rescue the high fraction of folded but less active structures formed by double and triple mutants. We conclude that crowding broadens the fitness landscape by stabilizing compact RNA structures without improving the specificity of self-assembly.« less

Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Hui-Ting; Kilburn, D.; Behrouzi, R.

The native structure of the Azoarcus group I ribozyme is stabilized by the cooperative formation of tertiary interactions between double helical domains. Thus, even single mutations that break this network of tertiary interactions reduce ribozyme activity in physiological Mg2+ concentrations. Here, we report that molecular crowding comparable to that in the cell compensates for destabilizing mutations in the Azoarcus ribozyme. Small angle X-ray scattering, native polyacrylamide gel electrophoresis and activity assays were used to compare folding free energies in dilute and crowded solutions containing 18% PEG1000. Crowder molecules allowed the wild-type and mutant ribozymes to fold at similarly low Mg2+more » concentrations and stabilized the active structure of the mutant ribozymes under physiological conditions. This compensation helps explains why ribozyme mutations are often less deleterious in the cell than in the test tube. Nevertheless, crowding did not rescue the high fraction of folded but less active structures formed by double and triple mutants. We conclude that crowding broadens the fitness landscape by stabilizing compact RNA structures without improving the specificity of self-assembly.« less

Efficient production of a folded and functional, highly disulfide-bonded beta-helix antifreeze protein in bacteria.

PubMed

Bar, Maya; Bar-Ziv, Roy; Scherf, Tali; Fass, Deborah

2006-08-01

The Tenebrio molitor thermal hysteresis protein has a cysteine content of 19%. This 84-residue protein folds as a compact beta-helix, with eight disulfide bonds buried in its core. Exposed on one face of the protein is an array of threonine residues, which constitutes the ice-binding face. Previous protocols for expression of this protein in recombinant expression systems resulted in inclusion bodies or soluble but largely inactive material. A long and laborious refolding procedure was performed to increase the fraction of active protein and isolate it from inactive fractions. We present a new protocol for production of fully folded and active T. molitor thermal hysteresis protein in bacteria, without the need for in vitro refolding. The protein coding sequence was fused to those of various carrier proteins and expressed at low temperature in a bacterial strain specially suited for production of disulfide-bonded proteins. The product, after a simple and robust purification procedure, was analyzed spectroscopically and functionally and was found to compare favorably to previously published data on refolded protein and protein obtained from its native source.

Laser diode stack beam shaping for efficient and compact long-range laser illuminator design

NASA Astrophysics Data System (ADS)

Lutz, Y.; Poyet, J. M.

2014-04-01

Laser diode stacks are interesting laser sources for active imaging illuminators. They allow the accumulation of large amounts of energy in multi-pulse mode, which is best suited for long-range image recording. Even when the laser diode stacks are equipped with fast-axis collimation (FAC) and slow-axis collimation (SAC) micro-lenses, their beam parameter products BPP are not compatible with direct use in highly efficient and compact illuminators. This is particularly true when narrow divergences are required such as for long-range applications. A solution to overcome these difficulties is to enhance the poor slow-axis BPP by virtually restacking the laser diode stack. We present a beam shaping and homogenization method that is low-cost and efficient and has low alignment sensitivity. After conducting simulations, we have realized and characterized the illuminator. A compact long-range laser illuminator has been set up with a divergence of 3.5×2.6 mrad and a global efficiency of 81%. Here, a projection lens with a clear aperture of 62 mm and a focal length of 571 mm was used.

Adjusting the Ion Permeability of Polyelectrolyte Multilayers through Layer-by-Layer Assembly under a High Gravity Field.

PubMed

Jiang, Chao; Luo, Caijun; Liu, Xiaolin; Shao, Lei; Dong, Youqing; Zhang, Yingwei; Shi, Feng

2015-05-27

The layer-by-layer (LbL) assembled multilayer has been widely used as good barrier film or capsule due to the advantages of its flexible tailoring of film permeability and compactness. Although many specific systems have been proposed for film design, developing a versatile strategy to control film compactness remains a challenge. We introduced the simple mechanical energy of a high gravity field to the LbL assembly process to tailor the multilayer permeability through adjusting film compactness. By taking poly(diallyldimethylammonium chloride) (PDDA) and poly{1-4[4-(3-carboxy-4-hydroxyphenylazo)benzenesulfonamido]-1,2-ethanediyl sodium salt} (PAzo) as a model system, we investigated the LbL assembly process under a high gravity field. The results showed that the high gravity field introduced effectively accelerated the multilayer deposition process by 20-fold compared with conventional dipping assembly; the adsorption rate was positively dependent on the rotating speed of the high gravity equipment and the concentration of the building block solutions. More interestingly, the film compactness of the PDDA/PAzo multilayer prepared under the high gravity field increased remarkably with the growing rotational speed of the high gravity equipment, as demonstrated through comparisons of surface morphology, cyclic voltammetry curves, and photoisomerization kinetics of PDDA/PAzo multilayers fabricated through the conventional dipping method and through LbL assembly under a high gravity field, respectively. In this way, we have introduced a simple and versatile external form of mechanical energy into the LbL assembling process to improve film compactness, which should be useful for further applications in controlled ion permeability, anticorrosion, and drug loading.

A compact LWIR hyperspectral system employing a microbolometer array and a variable gap Fabry-Perot interferometer employed as a Fourier transform spectrometer

NASA Astrophysics Data System (ADS)

Lucey, Paul G.; Hinrichs, John L.; Akagi, Jason

2012-06-01

A prototype long wave infrared Fourier transform spectral imaging system using a wedged Fabry-Perot interferometer and a microbolometer array was designed and built. The instrument can be used at both short (cm) and long standoff ranges (infinity focus). Signal to noise ratios are in the several hundred range for 30 C targets. The sensor is compact, fitting in a volume about 12 x12 x 4 inches.

Kinematics and strain distribution of a thrust-related fold system in the Lewis thrust plate, northwestern Montana (U.S.A.)

NASA Astrophysics Data System (ADS)

Yin, An; Oertel, Gerhard

1993-06-01

In order to understand interactions between motion along thrusts and the associated style of deformation and strain distribution in their hangingwalls, geologic mapping and strain measurements were conducted in an excellently exposed thrust-related fold system in the Lewis thrust plate, northwestern Montana. This system consists of: (1) an E-directed basal thrust (the Gunsight thrust) that has a flat-ramp geometry and a slip of about 3.6 km; (2) an E-verging asymmetric anticline with its nearly vertical forelimb truncated by the basal thrust from below; (3) a 4-km wide fold belt, the frontal fold complex, that lies directly in front of the E-verging anticline; (4) a W-directed bedding-parallel fault (the Mount Thompson fault) that bounds the top of the frontal fold belt and separates it from the undeformed to broadly folded strata above; and (5) regionally developed, W-dipping spaced cleavage. Although the overall geometry of the thrust-related fold system differs from any previously documented fault-related folds, the E-verging anticline itself resembles geometrically a Rich-type fault-bend fold. The observed initial cut-off and fold interlimb angles of this anticline, however, cannot be explained by cross-section balancing models for the development of either a fault-bend fold or a fault propagation fold. Possible origins for the E-verging anticline include (1) the fold initiated as an open fault-bend fold and tightened only later during its emplacement along the basal thrust and (2) the fold started as either a fault-bend or a fault-propagation fold, but simultaneous or subsequent volume change incompatible with any balanced cross-section models altered its shape. Strain in the thrust-related fold system was determined by the preferred orientation of mica and chlorite grains. The direction and magnitude of the post-compaction strain varies from place to place. Strains in the foreclimb of the hangingwall anticline imply bedding-parallel thinning at some localities and thickening at others. This inhomogeneity may be caused by the development of thrusts and folds. Strain in the backlimb of the hangingwall anticline implies bedding-parallel stretching in the thrust transport direction. This could be the effect of bending as the E-verging anticline was tightened and transported across the basal thrust ramp. Strain measured next to the Gunsight thrust again indicates locally varying shortening and extension in the transport direction, perhaps in response to inhomogeneous friction on the fault or else to a history of alternating strain hardening and softening in the basal thrust zone.

Ultrasonic real-time in-die monitoring of the tablet compaction process-a proof of concept study.

PubMed

Stephens, James D; Kowalczyk, Brian R; Hancock, Bruno C; Kaul, Goldi; Cetinkaya, Cetin

2013-02-14

The mechanical properties of a drug tablet can affect its performance (e.g., dissolution profile and its physical robustness. An ultrasonic system for real-time in-die tablet mechanical property monitoring during compaction has been demonstrated. The reported set-up is a proof of concept compaction monitoring system which includes an ultrasonic transducer mounted inside the upper punch of the compaction apparatus. This upper punch is utilized to acquire ultrasonic pressure wave phase velocity waveforms and extract the time-of-flight of pressure waves travelling within the compact at a number of compaction force levels during compaction. The reflection coefficients for the waves reflecting from punch tip-powder bed interface are extracted from the acquired waveforms. The reflection coefficient decreases with an increase in compaction force, indicating solidification. The data acquisition methods give an average apparent Young's moduli in the range of 8-20 GPa extracted during the compaction and release/decompression phases in real-time. A monitoring system employing such methods is capable of determining material properties and the integrity of the tablet during compaction. As compared to the millisecond time-scale dwell time of a typical commercial compaction press, the micro-second pulse duration and ToF of an acoustic pulse are sufficiently fast for real-time monitoring. Copyright © 2012 Elsevier B.V. All rights reserved.

Ultrafast optical ranging using microresonator soliton frequency combs

NASA Astrophysics Data System (ADS)

Trocha, P.; Karpov, M.; Ganin, D.; Pfeiffer, M. H. P.; Kordts, A.; Wolf, S.; Krockenberger, J.; Marin-Palomo, P.; Weimann, C.; Randel, S.; Freude, W.; Kippenberg, T. J.; Koos, C.

2018-02-01

Light detection and ranging is widely used in science and industry. Over the past decade, optical frequency combs were shown to offer advantages in optical ranging, enabling fast distance acquisition with high accuracy. Driven by emerging high-volume applications such as industrial sensing, drone navigation, or autonomous driving, there is now a growing demand for compact ranging systems. Here, we show that soliton Kerr comb generation in integrated silicon nitride microresonators provides a route to high-performance chip-scale ranging systems. We demonstrate dual-comb distance measurements with Allan deviations down to 12 nanometers at averaging times of 13 microseconds along with ultrafast ranging at acquisition rates of 100 megahertz, allowing for in-flight sampling of gun projectiles moving at 150 meters per second. Combining integrated soliton-comb ranging systems with chip-scale nanophotonic phased arrays could enable compact ultrafast ranging systems for emerging mass applications.

An analysis of nuclear fuel burnup in the AGR-1 TRISO fuel experiment using gamma spectrometry, mass spectrometry, and computational simulation techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harp, Jason M.; Demkowicz, Paul A.; Winston, Philip L.

AGR 1 was the first in a series of experiments designed to test US TRISO fuel under high temperature gas-cooled reactor irradiation conditions. This experiment was irradiated in the Advanced Test Reactor (ATR) at Idaho National Laboratory (INL) and is currently undergoing post irradiation examination (PIE) at INL and Oak Ridge National Laboratory. One component of the AGR 1 PIE is the experimental evaluation of the burnup of the fuel by two separate techniques. Gamma spectrometry was used to non destructively evaluate the burnup of all 72 of the TRISO fuel compacts that comprised the AGR 1 experiment. Two methodsmore » for evaluating burnup by gamma spectrometry were developed, one based on the Cs 137 activity and the other based on the ratio of Cs 134 and Cs 137 activities. Burnup values determined from both methods compared well with the values predicted from simulations. The highest measured burnup was 20.1% FIMA for the direct method and 20.0% FIMA for the ratio method (compared to 19.56% FIMA from simulations). An advantage of the ratio method is that the burnup of the cylindrical fuel compacts can determined in small (2.5 mm) axial increments and an axial burnup profile can be produced. Destructive chemical analysis by inductively coupled mass spectrometry (ICP MS) was then performed on selected compacts that were representative of the expected range of fuel burnups in the experiment to compare with the burnup values determined by gamma spectrometry. The compacts analyzed by mass spectrometry had a burnup range of 19.3% FIMA to 10.7% FIMA. The mass spectrometry evaluation of burnup for the four compacts agreed well with the gamma spectrometry burnup evaluations and the expected burnup from simulation. For all four compacts analyzed by mass spectrometry, the maximum range in the three experimentally determined values and the predicted value was 6% or less. Furthermore, the results confirm the accuracy of the nondestructive burnup evaluation from gamma spectrometry for TRISO fuel compacts across a burnup range of approximately 10 to 20% FIMA and also validate the approach used in the physics simulation of the AGR 1 experiment.« less

An analysis of nuclear fuel burnup in the AGR-1 TRISO fuel experiment using gamma spectrometry, mass spectrometry, and computational simulation techniques

DOE PAGES

Harp, Jason M.; Demkowicz, Paul A.; Winston, Philip L.; ...

2014-09-03

AGR 1 was the first in a series of experiments designed to test US TRISO fuel under high temperature gas-cooled reactor irradiation conditions. This experiment was irradiated in the Advanced Test Reactor (ATR) at Idaho National Laboratory (INL) and is currently undergoing post irradiation examination (PIE) at INL and Oak Ridge National Laboratory. One component of the AGR 1 PIE is the experimental evaluation of the burnup of the fuel by two separate techniques. Gamma spectrometry was used to non destructively evaluate the burnup of all 72 of the TRISO fuel compacts that comprised the AGR 1 experiment. Two methodsmore » for evaluating burnup by gamma spectrometry were developed, one based on the Cs 137 activity and the other based on the ratio of Cs 134 and Cs 137 activities. Burnup values determined from both methods compared well with the values predicted from simulations. The highest measured burnup was 20.1% FIMA for the direct method and 20.0% FIMA for the ratio method (compared to 19.56% FIMA from simulations). An advantage of the ratio method is that the burnup of the cylindrical fuel compacts can determined in small (2.5 mm) axial increments and an axial burnup profile can be produced. Destructive chemical analysis by inductively coupled mass spectrometry (ICP MS) was then performed on selected compacts that were representative of the expected range of fuel burnups in the experiment to compare with the burnup values determined by gamma spectrometry. The compacts analyzed by mass spectrometry had a burnup range of 19.3% FIMA to 10.7% FIMA. The mass spectrometry evaluation of burnup for the four compacts agreed well with the gamma spectrometry burnup evaluations and the expected burnup from simulation. For all four compacts analyzed by mass spectrometry, the maximum range in the three experimentally determined values and the predicted value was 6% or less. Furthermore, the results confirm the accuracy of the nondestructive burnup evaluation from gamma spectrometry for TRISO fuel compacts across a burnup range of approximately 10 to 20% FIMA and also validate the approach used in the physics simulation of the AGR 1 experiment.« less

A compact, rugged, high repetition rate CO2 laser incorporating catalyst

NASA Technical Reports Server (NTRS)

Schwarzenberger, P. M.; Matzangou, X.

1990-01-01

The principal design features and operating characteristics of a high repetition rate CO2 laser are outlined. The laser is a compact, rugged unit, completely sealed and incorporating an unheated solid catalyst. Stable operation has been successfully demonstrated over a temperature range of -35 C to 65 C.

The contribution of twins conceived by assisted reproduction technology to the very preterm birth rate: a population-based study.

PubMed

Tul, Natasa; Lucovnik, Miha; Verdenik, Ivan; Druskovic, Mirjam; Novak, Ziva; Blickstein, Isaac

2013-12-01

To assess the contribution of ART twins to the very preterm birth rate in Slovenia. In this retrospective population-based study we stratified by plurality and gestational age (<32 weeks vs >32 week) all deliveries >24 weeks in women who conceived by ART. We counted the frequencies of all ART liveborn twins among all liveborn infants and among all liveborn twins and frequencies in the subgroup of very preterm births. During the period 1987-2010, there were 13,293 twins (2.73%, range 1.93-3.62%, a nearly 2-fold increase from 1987 to 2010), 6939 infants born after ART (1.42%, range 0.03-2.62%, an 87-fold increase from 1987 to 2010), including 2317 (33.4%, range 14.28-44.83%, a 3-fold increase from 1987 to 2010) twins (0.47% of all deliveries). A total of 425 twin infants (0.99%, range: 1.07-1.2%, insignificant increase) were born at <32 weeks' gestation, including 261 after ART (61.4%, range 20-100%, 5-fold increase). Twins after ART born at <32 weeks comprised 0.05% of all births (range 0.004-0.11%) and increased 27-fold from 1987 to 2010. The incidence of twins after ART born at <32 weeks increased 27-fold from 1987 to 2010 and has not reduced from its peak incidence over the last decade. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Compact FEL-driven inverse compton scattering gamma-ray source

DOE PAGES

Placidi, M.; Di Mitri, Simone; Pellegrini, C.; ...

2017-02-28

Many research and applications areas require photon sources capable of producing gamma-ray beams in the multi-MeV energy range with reasonably high fluxes and compact footprints. Besides industrial, nuclear physics and security applications, a considerable interest comes from the possibility to assess the state of conservation of cultural assets like statues, columns etc., via visualization and analysis techniques using high energy photon beams. Computed Tomography scans, widely adopted in medicine at lower photon energies, presently provide high quality three-dimensional imaging in industry and museums. We explore the feasibility of a compact source of quasi-monochromatic, multi-MeV gamma-rays based on Inverse Compton Scatteringmore » (ICS) from a high intensity ultra-violet (UV) beam generated in a free-electron laser by the electron beam itself. This scheme introduces a stronger relationship between the energy of the scattered photons and that of the electron beam, resulting in a device much more compact than a classic ICS for a given scattered energy. As a result, the same electron beam is used to produce gamma-rays in the 10–20 MeV range and UV radiation in the 10–15 eV range, in a ~4 × 22 m 2 footprint system.« less

Compact LWIR sensors using spatial interferometric technology (Conference Presentation)

NASA Astrophysics Data System (ADS)

Bingham, Adam L.; Lucey, Paul G.; Knobbe, Edward T.

2017-05-01

Recent developments in reducing the cost and mass of hyperspectral sensors have enabled more widespread use for short range compositional imaging applications. HSI in the long wave infrared (LWIR) is of interest because it is sensitive to spectral phenomena not accessible to other wavelengths, and because of its inherent thermal imaging capability. At Spectrum Photonics we have pursued compact LWIR hyperspectral sensors both using microbolometer arrays and compact cryogenic detector cameras. Our microbolometer-based systems are principally aimed at short standoff applications, currently weigh 10-15 lbs and feature sizes approximately 20x20x10 cm, with sensitivity in the 1-2 microflick range, and imaging times on the order of 30 seconds. Our systems that employ cryogenic arrays are aimed at medium standoff ranges such as nadir looking missions from UAVs. Recent work with cooled sensors has focused on Strained Layer Superlattice (SLS) technology, as these detector arrays are undergoing rapid improvements, and have some advantages compared to HgCdTe detectors in terms of calibration stability. These sensors include full on-board processing sensor stabilization so are somewhat larger than the microbolometer systems, but could be adapted to much more compact form factors. We will review our recent progress in both these application areas.

Compact FEL-driven inverse compton scattering gamma-ray source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Placidi, M.; Di Mitri, Simone; Pellegrini, C.

Many research and applications areas require photon sources capable of producing gamma-ray beams in the multi-MeV energy range with reasonably high fluxes and compact footprints. Besides industrial, nuclear physics and security applications, a considerable interest comes from the possibility to assess the state of conservation of cultural assets like statues, columns etc., via visualization and analysis techniques using high energy photon beams. Computed Tomography scans, widely adopted in medicine at lower photon energies, presently provide high quality three-dimensional imaging in industry and museums. We explore the feasibility of a compact source of quasi-monochromatic, multi-MeV gamma-rays based on Inverse Compton Scatteringmore » (ICS) from a high intensity ultra-violet (UV) beam generated in a free-electron laser by the electron beam itself. This scheme introduces a stronger relationship between the energy of the scattered photons and that of the electron beam, resulting in a device much more compact than a classic ICS for a given scattered energy. As a result, the same electron beam is used to produce gamma-rays in the 10–20 MeV range and UV radiation in the 10–15 eV range, in a ~4 × 22 m 2 footprint system.« less

Fracture toughness testing of Linde 1092 reactor vessel welds in the transition range using Charpy-sized specimens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pavinich, W.A.; Yoon, K.K.; Hour, K.Y.

1999-10-01

The present reference toughness method for predicting the change in fracture toughness can provide over estimates of these values because of uncertainties in initial RT{sub NDT} and shift correlations. It would be preferable to directly measure fracture toughness. However, until recently, no standard method was available to characterize fracture toughness in the transition range. ASTM E08 has developed a draft standard that shows promise for providing lower bound transition range fracture toughness using the master curve approach. This method has been successfully implemented using 1T compact fracture specimens. Combustion Engineering reactor vessel surveillance programs do not have compact fracture specimens.more » Therefore, the CE Owners Group developed a program to validate the master curve method for Charpy-sized and reconstituted Charpy-sized specimens for future application on irradiated specimens. This method was validated for Linde 1092 welds using unirradiated Charpy-sized and reconstituted Charpy-sized specimens by comparison of results with those from compact fracture specimens.« less

County-Level Population Economic Status and Medicare Imaging Resource Consumption.

PubMed

Rosenkrantz, Andrew B; Hughes, Danny R; Prabhakar, Anand M; Duszak, Richard

2017-06-01

The aim of this study was to assess relationships between county-level variation in Medicare beneficiary imaging resource consumption and measures of population economic status. The 2013 CMS Geographic Variation Public Use File was used to identify county-level per capita Medicare fee-for-service imaging utilization and nationally standardized costs to the Medicare program. The County Health Rankings public data set was used to identify county-level measures of population economic status. Regional variation was assessed, and multivariate regressions were performed. Imaging events per 1,000 Medicare beneficiaries varied 1.8-fold (range, 2,723-4,843) at the state level and 5.3-fold (range, 1,228-6,455) at the county level. Per capita nationally standardized imaging costs to Medicare varied 4.2-fold (range, $84-$353) at the state level and 14.1-fold (range, $33-$471) at the county level. Within individual states, county-level utilization varied on average 2.0-fold (range, 1.1- to 3.1-fold), and costs varied 2.8-fold (range, 1.1- to 6.4-fold). For both large urban populations and small rural states, Medicare imaging resource consumption was heterogeneously variable at the county level. Adjusting for county-level gender, ethnicity, rural status, and population density, countywide unemployment rates showed strong independent positive associations with Medicare imaging events (β = 26.96) and costs (β = 4.37), whereas uninsured rates showed strong independent positive associations with Medicare imaging costs (β = 2.68). Medicare imaging utilization and costs both vary far more at the county than at the state level. Unfavorable measures of county-level population economic status in the non-Medicare population are independently associated with greater Medicare imaging resource consumption. Future efforts to optimize Medicare imaging use should consider the influence of local indigenous socioeconomic factors outside the scope of traditional beneficiary-focused policy initiatives. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

The Influence of fold and fracture development on reservoir behavior of the Lisburne Group of northern Alaska

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wesley K. Wallace; Catherine L. Hanks; Jerry Jensen: Michael T. Whalen

2004-07-01

The Carboniferous Lisburne Group is a major carbonate reservoir unit in northern Alaska. The Lisburne is folded and thrust faulted where it is exposed throughout the Brooks Range, but is relatively undeformed in areas of current production in the subsurface of the North Slope. The objectives of this study were to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of folds and their truncation by thrust faults. (2) The influence of folding on fracture patterns. (3) The influence of deformation on fluid flow. (4) Lithostratigraphy and its influence on folding, faulting, fracturing,more » and reservoir characteristics. Symmetrical detachment folds characterize the Lisburne in the northeastern Brooks Range. In contrast, Lisburne in the main axis of the Brooks Range is deformed into imbricate thrust sheets with asymmetrical hangingwall anticlines and footwall synclines. The Continental Divide thrust front separates these different structural styles in the Lisburne and also marks the southern boundary of the northeastern Brooks Range. Field studies were conducted for this project during 1999 to 2001 in various locations in the northeastern Brooks Range and in the vicinity of Porcupine Lake, immediately south of the Continental Divide thrust front. Results are summarized below for the four main subject areas of the study.« less

COMPACT NON-CONTACT TOTAL EMISSION DETECTION FOR IN-VIVO MULTI-PHOTON EXCITATION MICROSCOPY

PubMed Central

Glancy, Brian; Karamzadeh, Nader S.; Gandjbakhche, Amir H.; Redford, Glen; Kilborn, Karl; Knutson, Jay R.; Balaban, Robert S.

2014-01-01

Summary We describe a compact, non-contact design for a Total Emission Detection (c-TED) system for intra-vital multi-photon imaging. To conform to a standard upright two-photon microscope design, this system uses a parabolic mirror surrounding a standard microscope objective in concert with an optical path that does not interfere with normal microscope operation. The non-contact design of this device allows for maximal light collection without disrupting the physiology of the specimen being examined. Tests were conducted on exposed tissues in live animals to examine the emission collection enhancement of the c-TED device compared to heavily optimized objective-based emission collection. The best light collection enhancement was seen from murine fat (5×-2× gains as a function of depth), while murine skeletal muscle and rat kidney showed gains of over two and just under two-fold near the surface, respectively. Gains decreased with imaging depth (particularly in the kidney). Zebrafish imaging on a reflective substrate showed close to a two-fold gain throughout the entire volume of an intact embryo (approximately 150 μm deep). Direct measurement of bleaching rates confirmed that the lower laser powers (enabled by greater light collection efficiency) yielded reduced photobleaching in vivo. The potential benefits of increased light collection in terms of speed of imaging and reduced photo-damage, as well as the applicability of this device to other multi-photon imaging methods is discussed. PMID:24251437

Photometric Calibration and Image Stitching for a Large Field of View Multi-Camera System

PubMed Central

Lu, Yu; Wang, Keyi; Fan, Gongshu

2016-01-01

A new compact large field of view (FOV) multi-camera system is introduced. The camera is based on seven tiny complementary metal-oxide-semiconductor sensor modules covering over 160° × 160° FOV. Although image stitching has been studied extensively, sensor and lens differences have not been considered in previous multi-camera devices. In this study, we have calibrated the photometric characteristics of the multi-camera device. Lenses were not mounted on the sensor in the process of radiometric response calibration to eliminate the influence of the focusing effect of uniform light from an integrating sphere. Linearity range of the radiometric response, non-linearity response characteristics, sensitivity, and dark current of the camera response function are presented. The R, G, and B channels have different responses for the same illuminance. Vignetting artifact patterns have been tested. The actual luminance of the object is retrieved by sensor calibration results, and is used to blend images to make panoramas reflect the objective luminance more objectively. This compensates for the limitation of stitching images that are more realistic only through the smoothing method. The dynamic range limitation of can be resolved by using multiple cameras that cover a large field of view instead of a single image sensor with a wide-angle lens. The dynamic range is expanded by 48-fold in this system. We can obtain seven images in one shot with this multi-camera system, at 13 frames per second. PMID:27077857

Origin of intraformational folds in the Jurassic Todilto Limestone, Ambrosia Lake uranium mining district, McKinley and Valencia counties, New Mexico

USGS Publications Warehouse

Green, M.W.

1982-01-01

The Todilto Limestone of Middle Jurassic age in the Ambrosia Lake uranium mining district of McKinley and Valencia Counties, New Mexico, is the host formation for numerous small- to medium-sized uranium deposits in joints, shear zones, and fractures within small- to large-scale intraformational folds. The folds probably were formed as a result of differential sediment loading when eolian sand dunes of the overlying Summerville Formation of Middle Jurassic age migrated over soft, chemically precipitated, lime muds of the Todilto shortly after their deposition in a regressive, mixed fresh and saline lacustrine or marine environment of deposition. Encroachment of Summerville eolian dunes over soft Todilto lime muds was apparently a local phenomenon and was restricted to postulated beltlike zones which trended radially across the Todilto coastline toward the receding body of water. Intraformational folding is believed to be confined to the pathways of individual eolian dunes or clusters of dunes within the dune belts. During the process of sediment loading by migrating sand dunes, layers of Todilto lime mud were differentially compacted, contorted, and dewatered, producing both small- and large-scale plastic deformation structures, including convolute laminations, mounds, rolls, folds, and small anticlines and synclines. With continued compaction and dewatering, the mud, in localized areas, reached a point of desaturation at which sediment plasticity was lost. Prolonged loading by overlying dune sands thus caused faulting, shearing, fracturing, and jointing of contorted limestone beds. These areas or zones of deformation within the limestone became the preferred sites of epigenetic uranium mineralization because of the induced transmissivity created by sediment rupture. Along most of the prograding Todilto coastline, adjacent to the eolian dune belts, both interdune and coastal sabkha environments dominated during Todilto-Summerville time. Sediments in coastal areas consisted mainly of clay, silt, sandy silt, and very fine-grained sand, which was apparently derived from the winnowing of the finer grained fraction of sediment from adjacent dune fields during periods of eolian activity. Most of the sabkha sediments were probably carried in airborne suspension to the low-lying, ground-water-saturated coastal areas, where they were deposited as relatively uniform blanket-like layers. Deposition of sabkha deposits was apparently slow and uniform over most of the Todilto coastal areas and crested only small-scale deformation features in underlying Todilto rocks. Large-scale deformation features and uranium deposits are both notably absent in the Todilto where it is overlain by finer textured sabkha deposits in the Summerville.

Three-dimensional simulations of nanopowder compaction processes by granular dynamics method.

PubMed

Boltachev, G Sh; Lukyashin, K E; Shitov, V A; Volkov, N B

2013-07-01

In order to describe and to study the processes of cold compaction within the discrete element method a three-dimensional model of nanosized powder is developed. The elastic forces of repulsion, the tangential forces of "friction" (Cattaneo-Mindlin), and the dispersion forces of attraction (van der Waals-Hamaker), as well as the formation and destruction of hard bonds between the individual particles are taken into account. The monosized powders with the size of particles in the range 10-40 nm are simulated. The simulation results are compared to the experimental data of the alumina nanopowders compaction. It is shown that the model allows us to reproduce experimental data reliably and, in particular, describes the size effect in the compaction processes. A number of different external loading conditions is used in order to perform the theoretical and experimental researches. The uniaxial compaction (the closed-die compaction), the biaxial (radial) compaction, and the isotropic compaction (the cold isostatic pressing) are studied. The real and computed results are in a good agreement with each other. They reveal a weak sensitivity of the oxide nanopowders to the loading condition (compaction geometry). The application of the continuum theory of the plastically hardening porous body, which is usually used for the description of powders, is discussed.

Three-dimensional simulations of nanopowder compaction processes by granular dynamics method

NASA Astrophysics Data System (ADS)

Boltachev, G. Sh.; Lukyashin, K. E.; Shitov, V. A.; Volkov, N. B.

2013-07-01

In order to describe and to study the processes of cold compaction within the discrete element method a three-dimensional model of nanosized powder is developed. The elastic forces of repulsion, the tangential forces of “friction” (Cattaneo-Mindlin), and the dispersion forces of attraction (van der Waals-Hamaker), as well as the formation and destruction of hard bonds between the individual particles are taken into account. The monosized powders with the size of particles in the range 10-40 nm are simulated. The simulation results are compared to the experimental data of the alumina nanopowders compaction. It is shown that the model allows us to reproduce experimental data reliably and, in particular, describes the size effect in the compaction processes. A number of different external loading conditions is used in order to perform the theoretical and experimental researches. The uniaxial compaction (the closed-die compaction), the biaxial (radial) compaction, and the isotropic compaction (the cold isostatic pressing) are studied. The real and computed results are in a good agreement with each other. They reveal a weak sensitivity of the oxide nanopowders to the loading condition (compaction geometry). The application of the continuum theory of the plastically hardening porous body, which is usually used for the description of powders, is discussed.

Variation in practice and resource utilization associated with the diagnosis and management of appendicitis at freestanding children's hospitals: implications for value-based comparative analysis.

PubMed

Rice-Townsend, Samuel; Barnes, Jeff N; Hall, Matthew; Baxter, Jessica L; Rangel, Shawn J

2014-06-01

To characterize the scope and magnitude of practice variation associated with the diagnosis and treatment of appendicitis at freestanding children's hospitals. Variation in care has been associated with poor outcomes and is believed to be a key driver of excess health care spending. Retrospective cohort study of 13,328 patients treated with appendicitis at 34 children's hospitals (9/2010-9/2011). Patients were divided into complicated and uncomplicated cohorts and examined for interhospital variation in the use of diagnostic imaging (computed tomography or ultrasonography), laboratory tests, parenteral nutrition (PN), peripherally inserted central catheters (PICC), and hospital cost. The number and distribution of statistical outliers were calculated for all measures. Significant variation was found for all measures, including a 3.5-fold difference in preoperative imaging (aggregate rate: 49.0%, range across hospitals: 21.2%-73.5%, P < 0.001) and a 5-fold difference in preoperative laboratory utilization (aggregate median: 2 tests/encounter, range: 1-5 tests/encounter, P < 0.001). For patients with complicated appendicitis, we characterized a 12-fold difference in postoperative imaging (aggregate rate: 19.4%, range: 4.9%-61.6%, P < 0.001), a 48-fold difference in PICC lines (aggregate rate: 18.9%, range: 1.7%-81.8%, P < 0.001), and a 100-fold difference in PN utilization (aggregate rate: 9.3%, range: 0.4%-42.0%, P < 0.001). Median hospital cost differed 4-fold for patients with uncomplicated disease (aggregate median: $6804, range: $4200-$16,796, P < 0.001) and 4.6-fold for patients with complicated disease (aggregate median: $13,138, range: $5419-$24,779, P < 0.001). Statistical outliers on the basis of high and low utilization were identified for all measures. Significant variation exists in practice, resource utilization, and treatment-related cost associated with the management of appendicitis at freestanding children's hospitals. Value-based measures are needed for benchmarking and to prioritize collaborative quality improvement efforts.

All complete intersection Calabi-Yau four-folds

NASA Astrophysics Data System (ADS)

Gray, James; Haupt, Alexander S.; Lukas, Andre

2013-07-01

We present an exhaustive, constructive, classification of the Calabi-Yau four-folds which can be described as complete intersections in products of projective spaces. A comprehensive list of 921,497 configuration matrices which represent all topologically distinct types of complete intersection Calabi-Yau four-folds is provided and can be downloaded from http://www-thphys.physics.ox.ac.uk/projects/CalabiYau/Cicy4folds/index.html. The manifolds have non-negative Euler characteristics in the range 0 ≤ χ ≤ 2610. This data set will be of use in a wide range of physical and mathematical applications. Nearly all of these four-folds are elliptically fibered and are thus of interest for F-theory model building.

Mutational Analysis of the Stability of the H2A and H2B Histone Monomers

PubMed Central

Stump, Matthew R.; Gloss, Lisa M.

2008-01-01

The eukaryotic histone heterodimer H2A-H2B folds through an obligatory dimeric intermediate that forms in a nearly diffusion-limited association reaction in the stopped-flow dead time. It is unclear whether there is partial folding of the isolated monomers before association. To address the possible contributions of structure in the monomers to the rapid association, we characterized H2A and H2B monomers in the absence of their heterodimeric partner. By far-UV circular dichroism, the H2A and H2B monomers are 15% and 31% helical, respectively—significantly less than observed in X-ray crystal structures. Acrylamide quenching of the intrinsic Tyr fluorescence was indicative of tertiary structure. The H2A and H2B monomers exhibit free energies of unfolding of 2.5 and 2.9 kcal mol−1, respectively; at 10 μM, the sum of the stability of the monomers is ~60% of the stability of the native dimer. The helical content, stability and m values indicate that H2B has a more stable, compact structure than H2A. The monomer m values are larger than expected for the extended histone fold motif, suggesting that the monomers adopt an overly-collapsed structure. Stopped-flow refolding—initiated from urea-denatured monomers or the partially folded monomers populated at low denaturant concentrations—yielded essentially identical rates, indicating that monomer folding is productive in the rapid association and folding of the heterodimer. A series of Ala and Gly mutations were introduced into H2A and H2B to probe the importance of helix propensity on the structure and stability of the monomers. The mutational studies show that the central α-helix of the histone fold, which makes extensive inter-monomer contacts, is structured in H2B but only partially folded in H2A. PMID:18976667

Matrix Extension Study: Validation of the Compact Dry EC Method for Enumeration of Escherichia coli and non-E. coli Coliform Bacteria in Selected Foods.

PubMed

Mizuochi, Shingo; Nelson, Maria; Baylis, Chris; Green, Becky; Jewell, Keith; Monadjemi, Farinaz; Chen, Yi; Salfinger, Yvonne; Fernandez, Maria Cristina

2016-01-01

The Compact Dry "Nissui" EC method, originally certified by the AOAC Research Institute Performance Test Method(SM) program for enumeration of Escherichia coli and non-E. coli coliforms in raw meat products (Performance Tested Method(SM) 110402), has undergone an evaluation to extend the method's claim to cooked chicken, prewashed bagged shredded iceberg lettuce, frozen cod filets, instant nonfat dry milk powder, and pasteurized milk (2% fat). Compact Dry EC is a ready-to-use dry media sheet containing a cold-soluble gelling agent, selective agents, and a chromogenic medium, which are rehydrated by adding 1 mL diluted sample. E. coli form blue/blue-purple colonies, whereas other coliform bacteria form red/pink colonies. Users can obtain an E. coli count (blue/blue-purple colonies only) and a total coliform count (red/pink plus blue/blue-purple colonies) after 24 ± 2 h of incubation at 37 ± 1°C. The matrix extension study was organized by Campden BRI (formerly Campden and Chorleywood Food Research Association Technology, Ltd), Chipping Campden, United Kingdom. Method comparison data for cooked chicken, prewashed bagged shredded iceberg lettuce, frozen cod filets, and instant nonfat dry milk powder were collected in a single-laboratory evaluation by Campden BRI. A multilaboratory study was conducted on pasteurized milk (2% fat), with 13 laboratories participating. The Compact Dry EC method was compared to ISO 16649-2:2001 "Microbiology of food and animal feeding stuffs-Horizontal method for the enumeration of beta-glucuronidase-positive Escherichia coli-Part 2: Colony-count technique at 44 degrees C using 5-bromo-4-chloro-3-indolyl beta-D-glucuronide" and to ISO 4832:2006 "Microbiology of food and animal feeding stuffs-Horizontal method for the enumeration of coliforms-Colony-count technique," the current standards at the time of this study. Each matrix was evaluated separately for E. coli and non-E. coli coliforms at each contamination level (including an uncontaminated level). In the single-laboratory evaluation (cooked chicken, prewashed bagged shredded iceberg lettuce, frozen cod filets, and instant nonfat dry milk powder), colony counts were logarithmically transformed, and then the data were analyzed at each level for sr, RSDr, and mean difference between methods with 95% confidence intervals (CIs). A CI outside a range of -0.5 to 0.5 on the log10 mean difference between methods was used as the criterion to establish a significant statistical difference. In the multilaboratory study on pasteurized milk, after logarithmic transformation, the data were analyzed for sR and RSDR in addition to sr, RSDr, and mean difference with 95% CIs. Regression analysis was performed on all matrixes and reported as r(2). In the single-laboratory evaluation, statistical differences were indicated between the Compact Dry EC and ISO 16649-2 methods for the enumeration of E. coli in two of five contamination levels tested for lettuce, and in the low contamination level for cooked chicken. For the cooked chicken and lettuce at the low level, only a few colonies were recovered for each method, and thus not a true indication of the methods' performance. For the high contamination level of lettuce, counts varied within the sets of five replicates more than 10-fold for each method, which may have contributed to the significant difference. Statistical differences were also indicated between the Compact Dry EC and ISO 4832 methods for the enumeration of coliforms in two of five contamination levels tested for lettuce, two of five contamination levels of milk powder, and in the low contamination level for frozen fish. For the lowest levels of frozen fish and milk powder, only a few colonies were recovered for each method. For the lettuce and the other level of milk powder, counts varied within the sets of five replicates more than 10-fold for each method, which may have contributed to the significant differences indicated in the those contamination levels. In most cases, mean differences between the Compact Dry EC and International Organization of Standardization (ISO) methods were well below 0.5 log10, and the CIs were within the acceptance criterion (-0.5 to 0.5). The sr and RSDr values were similar for both methods, and r(2) values were >0.92 for all comparisons. In the multilaboratory study, no statistical differences were indicated between the methods. The sr, RSDr, sR, and RSDr values were similar for each method and even slightly smaller in most cases for the Compact Dry EC. The r(2) value was 0.97 in comparison to ISO 16649-2, and 0.99 in comparison to ISO 4832. The Compact Dry EC offers comparable results to the ISO standard plating methods in a space saving, easy-to-use format.

Everything you ever wanted to know about the ultraviolet spectra of star-forming galaxies but were afraid to ask

NASA Technical Reports Server (NTRS)

Kinney, A. L.; Bohlin, R.; Calzetti, D.; Panagia, N.; Wyse, R.

1993-01-01

We present ultraviolet spectra of 143 star-forming galaxies of different morphological types and activity classes including S0, Sa, Sb, Sc, Sd, irregular, starburst, blue compact, blue compact dwarf, Liner, and Seyfert 2 galaxies. These IUE spectra cover the wavelength range from 1200 to 3200 A and are taken in a large aperture (10 x 20 inch). The ultraviolet spectral energy distributions are shown for a subset of the galaxies, ordered by spectral index, and separated by type for normal galaxies, Liners, starburst galaxies, blue compact (BCG) and blue compact dwarf (BCDG) galaxies, and Seyfert 2 galaxies. The ultraviolet spectra of Liners are, for the most part, indistinguishable from the spectra of normal galaxies. Starburst galaxies have a large range of ultraviolet slope, from blue to red. The star-forming galaxies which are the bluest in the optical (BCG and BCDG), also have the 'bluest' average ultraviolet slope of beta = -1.75 +/- 0.63. Seyfert 2 galaxies are the only galaxies in the sample that consistently have detectable UV emission lines.

From Sequence and Forces to Structure, Function and Evolution of Intrinsically Disordered Proteins

PubMed Central

Forman-Kay, Julie D.; Mittag, Tanja

2015-01-01

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales and compactness is shaping a unified understanding of structure-dynamics-disorder/function relationships. On the 20th anniversary of this journal, Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional and evolutionary properties. PMID:24010708

From sequence and forces to structure, function, and evolution of intrinsically disordered proteins.

PubMed

Forman-Kay, Julie D; Mittag, Tanja

2013-09-03

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics, and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales, and compactness are shaping a unified understanding of structure-dynamics-disorder/function relationships. In the 20(th) anniversary of Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional, and evolutionary properties. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sandstone and shale compaction curves derived from sonic and gamma ray logs in offshore wells, North Slope, Alaska; parameters for basin modeling

USGS Publications Warehouse

Rowan, Elisabeth L.; Hayba, Daniel O.; Nelson, Philip H.; Burns, W. Matthew; Houseknecht, David W.

2003-01-01

Representative compaction curves for the principle lithologies are essential input for reliable models of basin history. Compaction curves influence estimates of maximum burial and erosion. Different compaction curves may produce significantly different thermal histories. Default compaction curves provided by basin modeling packages may or may not be a good proxy for the compaction properties in a given area. Compaction curves in the published literature span a wide range, even within one lithology, e.g., sandstone (see Panel 3). An abundance of geophysical well data for the North Slope, from both government and private sources, provides us with an unusually good opportunity to develop compaction curves for the Cretaceous-Tertiary Brookian sandstones, siltstones, and shales. We examined the sonic and gamma ray logs from 19 offshore wells (see map), where significant erosion is least likely to have occurred. Our data are primarily from the Cretaceous-Tertiary Brookian sequence and are less complete for older sequences. For each well, the fraction of shale (Vsh) at a given depth was estimated from the gamma ray log, and porosity was computed from sonic travel time. By compositing porosities for the near-pure sand (Vsh99%)from many individual wells we obtained data over sufficient depth intervals to define sandstone and shale 'master' compaction curves. A siltstone curve was defined using the sonic-derived porosities for Vsh values of 50%. These compaction curves generally match most of the sonic porosities with an error of 5% or less. Onshore, the curves are used to estimate the depth of maximum burial at the end of Brookian sedimentation. The depth of sonic-derived porosity profiles is adjusted to give the best match with the 'master' compaction curves. The amount of the depth adjustment is the erosion estimate. Using our compaction curves, erosion estimates on the North Slope range from zero in much of the offshore, to as much as 1500 ft along the coast, and to more than 10,000 ft in the foothills (Panel 3). Compaction curves provide an alternative to vitrinite reflectance for estimating erosion. Vitrinite reflectance data are often very sparse in contrast to well log data and are subject to inconsistencies when measurements are made by different labs. The phenomenon of 'recycling' can also make the reflectance values of dispersed vitrinite problematic for quantifying erosion. Recycling is suspected in dispersed vitrinite in North Slope rocks, particularly in the younger, Cretaceous-Tertiary section. The compaction curves defined here are being integrated into our burial history and thermal models to determine the timing of source rock maturation. An example on Panel 3 shows the results of calculating the maturity of the Shublik Fm. at the Tulaga well using two different sets of shale and siltstone compaction curves. Finally, accurate compaction curves improve a model's ability to realistically simulate the pressure regime during burial, including overpressures.

PREPARATION OF UO$sub 2$ FOR NUCLEAR REACTOR FUEL PELLETS

DOEpatents

Googin, J.M.

1962-06-01

A method is given for preparing high-density UO/sub 2/ compacts. An aqueous uranyl fluoride solution is contacted with an aqueous ammonium hydroxide solution at an ammonium to-uranium ratio of 25: 1 to 30:1 to form a precipitate. The precipitate is separated from the- mother liquor, dried, and contacted with steam at a uniform temperature within the range of 400 to 650 deg C to produce U/ sub 3/O/sub 8/. The U/sub 3/O/sub 8/ is red uced to UO/sub 2/ with hydrogen at a uniform temperature within the range of 550 to 600 deg C. The UO/sub 2/ is then compressed into compacts and sintered. High-density compacts are fabricated to close tolerances without use of a binder and without machining or grinding. (AEC)

Mode 1 crack surface displacements for a round compact specimen subject to a couple and force

NASA Technical Reports Server (NTRS)

Gross, B.

1979-01-01

Mode I displacement coefficients along the crack surface are presented for a radially cracked round compact specimen, treated as a plane elastostatic problem, subjected to two types of loading; a uniform tensile stress and a nominal bending stress distribution across the net section. By superposition the resultant displacement coefficient or the corresponding influence coefficient can be obtained for any practical load location. Load line displacements are presented for A/D ratios ranging from 0.40 to 0.95, where A is the crack length measured from the crack mouth to the crack tip and D is the specimen diameter. Through a linear extrapolation procedure crack mouth displacements are also obtained. Experimental evidence shows that the results are valid over the range of A/D ratios analyzed for a practical pin loaded round compact specimen.

Modeling of porosity loss during compaction and cementation of sandstones

NASA Astrophysics Data System (ADS)

Lemée, Claire; Guéguen, Yves

1996-10-01

Irreversible inelastic processes are responsible for mechanical and chemical compaction of sedimentary rocks at the time of burying. Our purpose is to describe the inelastic response of the rock at large time scales. In order to do this, we build a model that describes how porosity progressively decreases at depth. We use a previous geometrical model for the compaction process of a sandstone by grain interpenetration that is restricted to the case of mass conservation. In addition, we introduce a compaction equilibrium concept. Solid grains can support stresses up to a critical effective stress, σc, before plastic flow occurs. This critical stress depends on temperature and is derived from the pressure-solution deformation law. Pressure solution is the plastic deformation mechanism implemented during compaction. Our model predicts a porosity destruction at a depth of about 3 km. This model has the property to define a range of compaction curves. We investigate the sensitivity of the model to the main input parameters: liquid film thickness, grain size, temperature gradient, and activation energy.

FACT, Mega-ROSA, SOLAROSA

NASA Technical Reports Server (NTRS)

Spence, Brian; White, Steve; Schmid, Kevin; Douglas Mark

2012-01-01

The Flexible Array Concentrator Technology (FACT) is a lightweight, high-performance reflective concentrator blanket assembly that can be used on flexible solar array blankets. The FACT concentrator replaces every other row of solar cells on a solar array blanket, significantly reducing the cost of the array. The modular design is highly scalable for the array system designer, and exhibits compact stowage, good off-pointing acceptance, and mass/cost savings. The assembly s relatively low concentration ratio, accompanied by a large radiative area, provides for a low cell operating temperature, and eliminates many of the thermal problems inherent in high-concentration-ratio designs. Unlike other reflector technologies, the FACT concentrator modules function on both z-fold and rolled flexible solar array blankets, as well as rigid array systems. Mega-ROSA (Mega Roll-Out Solar Array) is a new, highly modularized and extremely scalable version of ROSA that provides immense power level range capability from 100 kW to several MW in size. Mega-ROSA will enable extremely high-power spacecraft and SEP-powered missions, including space-tug and largescale planetary science and lunar/asteroid exploration missions. Mega-ROSA's inherent broad power scalability is achieved while retaining ROSA s solar array performance metrics and missionenabling features for lightweight, compact stowage volume and affordability. This innovation will enable future ultra-high-power missions through lowcost (25 to 50% cost savings, depending on PV and blanket technology), lightweight, high specific power (greater than 200 to 400 Watts per kilogram BOL (beginning-of-life) at the wing level depending on PV and blanket technology), compact stowage volume (greater than 50 kilowatts per cubic meter for very large arrays), high reliability, platform simplicity (low failure modes), high deployed strength/stiffness when scaled to huge sizes, and high-voltage operation capability. Mega-ROSA is adaptable to all photovoltaic and concentrator flexible blanket technologies, and can readily accommodate standard multijunction and emerging ultra-lightweight IMM (inverted metamorphic) photovoltaic flexible blanket assemblies, as well as ENTECHs Stretched Lens Array (SLA) and DSSs (Deployable Space Systems) FACT, which allows for cost reduction at the array level.

Investigating the Effect of Compaction Characteristics on the Erodibility of Cohesive Soils Using the JET Method

NASA Astrophysics Data System (ADS)

Asghari Tabrizi, A.; LaRocque, L. A.; Chaudhry, M.; Imran, J.

2013-12-01

Several flood disasters occur every year all over the world, mostly due to levee and dam failure which result in human fatalities as well as devastating economic damages. To model and predict earthen embankment failures for the preparation of emergency action plans and risk assessments, the soil erodibility by flowing water is an essential parameter. The determination of erodibility becomes even more complicated for cohesive soils because of the large number of parameters controlling their erosion behavior (e.g. clay content, plasticity, compaction effort, compaction water content) and the difficulty of estimating these parameters. In this study the effect of the compaction energy and compaction water content on the erodibility of a sandy loam soil was assessed. Soil samples were prepared in a standard diameter compaction mold, 101.6 mm, for three levels of compaction effort and water content (i.e. low, medium, and high) with two replications for each case (18 tests total) and examined using the jet erosion test (JET). Observations from qualitative and statistical analyses of the data are: 1) a wide range of erodibility, from very erodible to very resistant, was produced by changes in the compaction characteristics; 2) for a given compaction energy, the erosion resistance based on the detachment rate coefficient kd tends to become minimum near the optimum compaction water content. On the dry side of optimum compaction water content, kd decreases with steep gradients by increasing the water content, while it increases with a flatter gradient on the wet side; 3) At a given water content, the soil erosion resistance increases with compaction efforts; 4) compaction water content influences soil erosibility more than compaction energy, especially on the dry side of the optimum compaction water content; and 5) for a given compaction effort, the critical shear stress increases with water content up to an optimum water content and then it decreases which is in consistent with the kd trends.

Impact of High-Temperature, High-Pressure Synthesis Conditions on the Formation of the Grain Structure and Strength Properties of Intermetallic Ni3Al

NASA Astrophysics Data System (ADS)

Ovcharenko, V. E.; Ivanov, K. V.; Boyangin, E. N.; Krylova, T. A.; Pshenichnikov, A. P.

2018-01-01

The impact of the preliminary load on 3Ni+Al powder mixture and the impact of the duration of the delay in application of compacting pressure to synthesis product under the conditions of continuous heating of the mixture up to its self-ignition on the grain size and strength properties of the synthesized Ni3Al intermetallide material have been studied. The grain structure of the intermetallide synthesized under pressure was studied by means of metallography, transmission electron microscopy and EBSD analysis, with the dependence of ultimate tensile strength on the grain size in the synthesized intermetallide having been investigated at room temperature and at temperatures up to 1000°C. It is shown that an increase in the pressure preliminarily applied to the initial mixture compact results in reduced grain size of the final intermetallide, whereas an increase in pre-compaction time makes the grain size increased. A decrease in the grain size increases the ultimate tensile strength of the intermetallide. The maximum value of the ultimate tensile strength in the observed anomalous temperature dependence of this strength exhibits a shift by 200°C toward higher temperatures, and the ultimate strength of the synthesized intermetallide at 1000°C increases roughly two-fold.

Validation of a Compact Isokinetic Total Water Content Probe for Wind Tunnel Characterization at NASA Glenn Icing Research Tunnel and at NRC Ice Crystal Tunnel

NASA Technical Reports Server (NTRS)

Davison, Craig R.; Landreville, Charles; Ratvasky, Thomas P.

2017-01-01

A new compact isokinetic probe to measure total water content in a wind tunnel environment has been developed. The probe has been previously tested under altitude conditions. This paper presents a comprehensive validation of the probe under a range of liquid water conditions at sea level in the NASA Glenn Icing Research Tunnel and with ice crystals at sea level at the NRC wind tunnel. The compact isokinetic probe is compared to tunnel calibrations and other probes.

Compact Submillimeter-Wave Receivers Made with Semiconductor Nano-Fabrication Technologies

NASA Technical Reports Server (NTRS)

Jung, C.; Thomas, B.; Lee, C.; Peralta, A.; Chattopadhyay, G.; Gill, J.; Cooper, K.; Mehdi, I.

2011-01-01

Advanced semiconductor nanofabrication techniques are utilized to design, fabricate and demonstrate a super-compact, low-mass (<10 grams) submillimeter-wave heterodyne front-end. RF elements such as waveguides and channels are fabricated in a silicon wafer substrate using deep-reactive ion etching (DRIE). Etched patterns with sidewalls angles controlled with 1 deg precision are reported, while maintaining a surface roughness of better than 20 nm rms for the etched structures. This approach is being developed to build compact 2-D imaging arrays in the THz frequency range.

Experimental Measurement and Numerical Modeling of the Effective Thermal Conductivity of TRISO Fuel Compacts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Folsom, Charles; Xing, Changhu; Jensen, Colby

2015-03-01

Accurate modeling capability of thermal conductivity of tristructural-isotropic (TRISO) fuel compacts is important to fuel performance modeling and safety of Generation IV reactors. To date, the effective thermal conductivity (ETC) of tristructural-isotropic (TRISO) fuel compacts has not been measured directly. The composite fuel is a complicated structure comprised of layered particles in a graphite matrix. In this work, finite element modeling is used to validate an analytic ETC model for application to the composite fuel material for particle-volume fractions up to 40%. The effect of each individual layer of a TRISO particle is analyzed showing that the overall ETC ofmore » the compact is most sensitive to the outer layer constituent. In conjunction with the modeling results, the thermal conductivity of matrix-graphite compacts and the ETC of surrogate TRISO fuel compacts have been successfully measured using a previously developed measurement system. The ETC of the surrogate fuel compacts varies between 50 and 30 W m -1 K -1 over a temperature range of 50-600°C. As a result of the numerical modeling and experimental measurements of the fuel compacts, a new model and approach for analyzing the effect of compact constituent materials on ETC is proposed that can estimate the fuel compact ETC with approximately 15-20% more accuracy than the old method. Using the ETC model with measured thermal conductivity of the graphite matrix-only material indicate that, in the composite form, the matrix material has a much greater thermal conductivity, which is attributed to the high anisotropy of graphite thermal conductivity. Therefore, simpler measurements of individual TRISO compact constituents combined with an analytic ETC model, will not provide accurate predictions of overall ETC of the compacts emphasizing the need for measurements of composite, surrogate compacts.« less

Monolithically, widely tunable quantum cascade lasers based on a heterogeneous active region design.

PubMed

Zhou, Wenjia; Bandyopadhyay, Neelanjan; Wu, Donghai; McClintock, Ryan; Razeghi, Manijeh

2016-06-08

Quantum cascade lasers (QCLs) have become important laser sources for accessing the mid-infrared (mid-IR) spectral range, achieving watt-level continuous wave operation in a compact package at room temperature. However, up to now, wavelength tuning, which is desirable for most applications, has relied on external cavity feedback or exhibited a limited monolithic tuning range. Here we demonstrate a widely tunable QCL source over the 6.2 to 9.1 μm wavelength range with a single emitting aperture by integrating an eight-laser sampled grating distributed feedback laser array with an on-chip beam combiner. The laser gain medium is based on a five-core heterogeneous QCL wafer. A compact tunable laser system was built to drive the individual lasers within the array and produce any desired wavelength within the available spectral range. A rapid, broadband spectral measurement (520 cm(-1)) of methane using the tunable laser source shows excellent agreement to a measurement made using a standard low-speed infrared spectrometer. This monolithic, widely tunable laser technology is compact, with no moving parts, and will open new opportunities for MIR spectroscopy and chemical sensing.

Monolithically, widely tunable quantum cascade lasers based on a heterogeneous active region design

PubMed Central

Zhou, Wenjia; Bandyopadhyay, Neelanjan; Wu, Donghai; McClintock, Ryan; Razeghi, Manijeh

2016-01-01

Quantum cascade lasers (QCLs) have become important laser sources for accessing the mid-infrared (mid-IR) spectral range, achieving watt-level continuous wave operation in a compact package at room temperature. However, up to now, wavelength tuning, which is desirable for most applications, has relied on external cavity feedback or exhibited a limited monolithic tuning range. Here we demonstrate a widely tunable QCL source over the 6.2 to 9.1 μm wavelength range with a single emitting aperture by integrating an eight-laser sampled grating distributed feedback laser array with an on-chip beam combiner. The laser gain medium is based on a five-core heterogeneous QCL wafer. A compact tunable laser system was built to drive the individual lasers within the array and produce any desired wavelength within the available spectral range. A rapid, broadband spectral measurement (520 cm−1) of methane using the tunable laser source shows excellent agreement to a measurement made using a standard low-speed infrared spectrometer. This monolithic, widely tunable laser technology is compact, with no moving parts, and will open new opportunities for MIR spectroscopy and chemical sensing. PMID:27270634

Investigation of guided wave propagation and attenuation in pipe buried in sand

NASA Astrophysics Data System (ADS)

Leinov, Eli; Lowe, Michael J. S.; Cawley, Peter

2015-07-01

Long-range guided wave testing is a well-established method for detection of corrosion defects in pipelines. The method is currently used routinely for above ground pipelines in a variety of industries, e.g. petrochemical and energy. When the method is applied to pipes buried in soil, test ranges tend to be significantly compromised and unpredictable due to attenuation of the guided wave resulting from energy leakage into the embedding soil. The attenuation characteristics of guided wave propagation in an 8 in. pipe buried in sand are investigated using a laboratory full-scale experimental rig and model predictions. We report measurements of attenuation of the T(0,1) and L(0,2) guided wave modes over a range of sand conditions, including loose, compacted, mechanically compacted, water saturated and drained. Attenuation values are found to be in the range of 1.65-5.5 dB/m and 0.98-3.2 dB/m for the torsional and longitudinal modes, respectively, over the frequency of 11-34 kHz. The application of overburden pressure modifies the compaction of the sand and increases the attenuation. Mechanical compaction of the sand yields similar attenuation values to those obtained with applied overburden pressure. The attenuation decreases in the fully water-saturated sand, and increases in drained sand to values comparable with those obtained for compacted sand. Attenuation measurements are compared with Disperse software model predictions and confirm that the attenuation phenomenon in buried pipes is essentially governed by the bulk shear velocity in the sand. The attenuation behaviour of the torsional guided wave mode is found not to be captured by a uniform soil model; comparison with predictions obtained with the Disperse software suggest that this is likely to be due to a layer of sand adhering to the surface of the pipe.

Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

PubMed Central

Wang, Yong; Chu, Xiakun; Longhi, Sonia; Roche, Philippe; Han, Wei; Wang, Erkang; Wang, Jin

2013-01-01

Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as molecular recognition elements (MoREs). They fold into ordered structures upon binding to their partner molecules. Currently, there is still a lack of in-depth understanding of how coupled binding and folding occurs in MoREs. Here, we quantified the unbound ensembles of the α-MoRE within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein. We developed a multiscaled approach by combining a physics-based and an atomic hybrid model to decipher the mechanism by which the α-MoRE interacts with the X domain of the measles virus phosphoprotein. Our multiscaled approach led to remarkable qualitative and quantitative agreements between the theoretical predictions and experimental results (e.g., chemical shifts). We found that the free α-MoRE rapidly interconverts between multiple discrete partially helical conformations and the unfolded state, in accordance with the experimental observations. We quantified the underlying global folding–binding landscape. This leads to a synergistic mechanism in which the recognition event proceeds via (minor) conformational selection, followed by (major) induced folding. We also provided evidence that the α-MoRE is a compact molten globule-like IDP and behaves as a downhill folder in the induced folding process. We further provided a theoretical explanation for the inherent connections between “downhill folding,” “molten globule,” and “intrinsic disorder” in IDP-related systems. Particularly, we proposed that binding and unbinding of IDPs proceed in a stepwise way through a “kinetic divide-and-conquer” strategy that confers them high specificity without high affinity. PMID:24043820

Minichaperone (GroEL191-345) mediated folding of MalZ proceeds by binding and release of native and functional intermediates.

PubMed

Jain, Neha; Knowles, Timothy J; Lund, Peter A; Chaudhuri, Tapan K

2018-06-02

The isolated apical domain of GroEL consisting of residues 191-345 (known as "minichaperone") binds and assists the folding of a wide variety of client proteins without GroES and ATP, but the mechanism of its action is still unknown. In order to probe into the matter, we have examined minichaperone-mediated folding of a large aggregation prone protein Maltodextrin-glucosidase (MalZ). The key objective was to identify whether MalZ exists free in solution, or remains bound to, or cycling on and off the minichaperone during the refolding process. When GroES was introduced during refolding process, production of the native MalZ was inhibited. We also observed the same findings with a trap mutant of GroEL, which stably captures a predominantly non-native MalZ released from minichaperone during refolding process, but does not release it. Tryptophan and ANS fluorescence measurements indicated that refolded MalZ has the same structure as the native MalZ, but that its structure when bound to minichaperone is different. Surface plasmon resonance measurements provide an estimate for the equilibrium dissociation constant KD for the MalZ-minichaperone complex of 0.21 ± 0.04 μM, which are significantly higher than for most GroEL clients. This showed that minichaperone interacts loosely with MalZ to allow the protein to change its conformation and fold while bound during the refolding process. These observations suggest that the minichaperone works by carrying out repeated cycles of binding aggregation-prone protein MalZ in a relatively compact conformation and in a partially folded but active state, and releasing them to attempt to fold in solution. Copyright © 2018 Elsevier B.V. All rights reserved.

Void-Free Lid for Food Packaging

NASA Technical Reports Server (NTRS)

Watson, C. D.; Farris, W. P.

1986-01-01

Flexible cover eliminates air pockets in sealed container. Universal food-package lid formed from flexible plastic. Partially folded, lid unfolded by depressing center portion. Height of flat portion of lid above flange thereby reduced. Pressure of food against central oval depression pops it out, forming dome that provides finger grip for mixing contents with water or opening lid. Therefore food stays fresh, allows compact stacking of partially filled containers, and resists crushing. Originally developed for packaging dehydrated food for use in human consumption on Space Shuttle missions. Other uses include home canning and commercial food packaging.

Orogenic remagnetizations and paleomagnetic analysis of fault propagation folds in Lower Carboniferous carbonates, Northern Rockies, NW Montana and SW Alberta

NASA Astrophysics Data System (ADS)

Zechmeister, M. S.; O'Brien, V. J.; Elmore, R. D.; Evans, M. A.

2006-12-01

Results from paleomagnetic analysis of Lower Carboniferous carbonates in the Sawtooth Range, northwestern Montana and the Livingstone range in Southwestern Alberta are presented. Paleomagnetic cores were collected from both limbs of four fault propagation folds, one at Swift Dam in MT as well as one along Green Creek and two along Oldman River in Alberta. The Swift Dam Fold is in the Madison Group and contains a widespread characteristic remanent magnetization (ChRM) that resides in magnetite with southerly declinations and moderately steep up inclinations. A tilt test reveals a synfolding ChRM, and the paleopole suggests remanence acquisition in the Cretaceous to Early Tertiary. This result contrasts with results from another fold in MT, the Teton anticline, which is a buckle fold where a similar ChRM is pretilting. The reason for the differences in the fold test results are under investigation. The ChRM is not thermoviscous in origin based on a comparison of unblocking temperature with the low burial temperatures and is interpreted as a chemical remanent magnetization (CRM). Preliminary data from the folds in Livingstone Range suggest a similar ChRM in the organic rich lithologies of the Livingstone, Banff and Mount Head formations. Tilt test results for the fault propagation folds in Alberta will be presented as well as a discussion on the origin of orogenic remagnetizations.

Conformational State Distributions and Catalytically Relevant Dynamics of a Hinge-Bending Enzyme Studied by Single-Molecule FRET and a Coarse-Grained Simulation

PubMed Central

Gabba, Matteo; Poblete, Simón; Rosenkranz, Tobias; Katranidis, Alexandros; Kempe, Daryan; Züchner, Tina; Winkler, Roland G.; Gompper, Gerhard; Fitter, Jörg

2014-01-01

Over the last few decades, a view has emerged showing that multidomain enzymes are biological machines evolved to harness stochastic kicks of solvent particles into highly directional functional motions. These intrinsic motions are structurally encoded, and Nature makes use of them to catalyze chemical reactions by means of ligand-induced conformational changes and states redistribution. Such mechanisms align reactive groups for efficient chemistry and stabilize conformers most proficient for catalysis. By combining single-molecule Förster resonance energy transfer measurements with normal mode analysis and coarse-grained mesoscopic simulations, we obtained results for a hinge-bending enzyme, namely phosphoglycerate kinase (PGK), which support and extend these ideas. From single-molecule Förster resonance energy transfer, we obtained insight into the distribution of conformational states and the dynamical properties of the domains. The simulations allowed for the characterization of interdomain motions of a compact state of PGK. The data show that PGK is intrinsically a highly dynamic system sampling a wealth of conformations on timescales ranging from nanoseconds to milliseconds and above. Functional motions encoded in the fold are performed by the PGK domains already in its ligand-free form, and substrate binding is not required to enable them. Compared to other multidomain proteins, these motions are rather fast and presumably not rate-limiting in the enzymatic reaction. Ligand binding slightly readjusts the orientation of the domains and feasibly locks the protein motions along a preferential direction. In addition, the functionally relevant compact state is stabilized by the substrates, and acts as a prestate to reach active conformations by means of Brownian motions. PMID:25418172

Uniform GTD solution for the diffraction by metallic tapes on panelled compact-range reflectors

NASA Technical Reports Server (NTRS)

Somers, G. A.; Pathak, P. H.

1992-01-01

Metallic tape is commonly used to cover the interpanel gaps which occur in paneled compact-range reflectors. It is therefore of interest to study the effect of the scattering by the tape on the field in the target zone of the range. An analytical solution is presented for the target zone fields scattered by 2D metallic tapes. It is formulated by the generalized scattering matrix technique in conjunction with the Wiener-Hopf procedure. An extension to treat 3D tapes can be accomplished using the 2D solution via the equivalent current concept. The analytical solution is compared with a reference moment method solution to confirm the accuracy of the former.

Compact Analyzer/Controller For Oxygen-Enrichment System

NASA Technical Reports Server (NTRS)

Puster, Richard L.; Singh, Jag J.; Sprinkle, Danny R.

1990-01-01

System controls hypersonic air-breathing engine tests. Compact analyzer/controller developed, built, and tested in small-scale wind tunnel prototype of the 8' HTT (High-Temperature Tunnel). Monitors level of oxygen and controls addition of liquid oxygen to enrich atmosphere for combustion. Ensures meaningful ground tests of hypersonic engines in range of speeds from mach 4 to mach 7.

Gas breakthrough and emission through unsaturated compacted clay in landfill final cover

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ng, C.W.W.; Chen, Z.K.; Coo, J.L.

Highlights: • Explore feasibility of unsaturated clay as a gas barrier in landfill cover. • Gas breakthrough pressure increases with clay thickness and degree of saturation. • Gas emission rate decreases with clay thickness and degree of saturation. • A 0.6 m-thick clay layer may be sufficient to meet gas emission rate limit. - Abstract: Determination of gas transport parameters in compacted clay plays a vital role for evaluating the effectiveness of soil barriers. The gas breakthrough pressure has been widely studied for saturated swelling clay buffer commonly used in high-level radioactive waste disposal facility where the generated gas pressuremore » is very high (in the order of MPa). However, compacted clay in landfill cover is usually unsaturated and the generated landfill gas pressure is normally low (typically less than 10 kPa). Furthermore, effects of clay thickness and degree of saturation on gas breakthrough and emission rate in the context of unsaturated landfill cover has not been quantitatively investigated in previous studies. The feasibility of using unsaturated compacted clay as gas barrier in landfill covers is thus worthwhile to be explored over a wide range of landfill gas pressures under various degrees of saturation and clay thicknesses. In this study, to evaluate the effectiveness of unsaturated compacted clay to minimize gas emission, one-dimensional soil column tests were carried out on unsaturated compacted clay to determine gas breakthrough pressures at ultimate limit state (high pressure range) and gas emission rates at serviceability limit state (low pressure range). Various degrees of saturation and thicknesses of unsaturated clay sample were considered. Moreover, numerical simulations were carried out using a coupled gas–water flow finite element program (CODE-BRIGHT) to better understand the experimental results by extending the clay thickness and varying the degree of saturation to a broader range that is typical at different climate conditions. The results of experimental study and numerical simulation reveal that as the degree of saturation and thickness of clay increase, the gas breakthrough pressure increases but the gas emission rate decreases significantly. Under a gas pressure of 10 kPa (the upper bound limit of typical landfill gas pressure), a 0.6 m or thicker compacted clay is able to prevent gas breakthrough at degree of saturation of 60% or above (in humid regions). Furthermore, to meet the limit of gas emission rate set by the Australian guideline, a 0.6 m-thick clay layer may be sufficient even at low degree of saturation (i.e., 10% like in arid regions)« less

In vivo cross-sectional imaging of the phonating larynx using long-range Doppler optical coherence tomography

NASA Astrophysics Data System (ADS)

Coughlan, Carolyn A.; Chou, Li-Dek; Jing, Joseph C.; Chen, Jason J.; Rangarajan, Swathi; Chang, Theodore H.; Sharma, Giriraj K.; Cho, Kyoungrai; Lee, Donghoon; Goddard, Julie A.; Chen, Zhongping; Wong, Brian J. F.

2016-03-01

Diagnosis and treatment of vocal fold lesions has been a long-evolving science for the otolaryngologist. Contemporary practice requires biopsy of a glottal lesion in the operating room under general anesthesia for diagnosis. Current in-office technology is limited to visualizing the surface of the vocal folds with fiber-optic or rigid endoscopy and using stroboscopic or high-speed video to infer information about submucosal processes. Previous efforts using optical coherence tomography (OCT) have been limited by small working distances and imaging ranges. Here we report the first full field, high-speed, and long-range OCT images of awake patients’ vocal folds as well as cross-sectional video and Doppler analysis of their vocal fold motions during phonation. These vertical-cavity surface-emitting laser source (VCSEL) OCT images offer depth resolved, high-resolution, high-speed, and panoramic images of both the true and false vocal folds. This technology has the potential to revolutionize in-office imaging of the larynx.

Force generation by titin folding.

PubMed

Mártonfalvi, Zsolt; Bianco, Pasquale; Naftz, Katalin; Ferenczy, György G; Kellermayer, Miklós

2017-07-01

Titin is a giant protein that provides elasticity to muscle. As the sarcomere is stretched, titin extends hierarchically according to the mechanics of its segments. Whether titin's globular domains unfold during this process and how such unfolded domains might contribute to muscle contractility are strongly debated. To explore the force-dependent folding mechanisms, here we manipulated skeletal-muscle titin molecules with high-resolution optical tweezers. In force-clamp mode, after quenching the force (<10 pN), extension fluctuated without resolvable discrete events. In position-clamp experiments, the time-dependent force trace contained rapid fluctuations and a gradual increase of average force, indicating that titin can develop force via dynamic transitions between its structural states en route to the native conformation. In 4 M urea, which destabilizes H-bonds hence the consolidated native domain structure, the net force increase disappeared but the fluctuations persisted. Thus, whereas net force generation is caused by the ensemble folding of the elastically-coupled domains, force fluctuations arise due to a dynamic equilibrium between unfolded and molten-globule states. Monte-Carlo simulations incorporating a compact molten-globule intermediate in the folding landscape recovered all features of our nanomechanics results. The ensemble molten-globule dynamics delivers significant added contractility that may assist sarcomere mechanics, and it may reduce the dissipative energy loss associated with titin unfolding/refolding during muscle contraction/relaxation cycles. © 2017 The Protein Society.

Differential conformational modulations of MreB folding upon interactions with GroEL/ES and TRiC chaperonin components

PubMed Central

Moparthi, Satish Babu; Carlsson, Uno; Vincentelli, Renaud; Jonsson, Bengt-Harald; Hammarström, Per; Wenger, Jérôme

2016-01-01

Here, we study and compare the mechanisms of action of the GroEL/GroES and the TRiC chaperonin systems on MreB client protein variants extracted from E. coli. MreB is a homologue to actin in prokaryotes. Single-molecule fluorescence correlation spectroscopy (FCS) and time-resolved fluorescence polarization anisotropy report the binding interaction of folding MreB with GroEL, GroES and TRiC. Fluorescence resonance energy transfer (FRET) measurements on MreB variants quantified molecular distance changes occurring during conformational rearrangements within folding MreB bound to chaperonins. We observed that the MreB structure is rearranged by a binding-induced expansion mechanism in TRiC, GroEL and GroES. These results are quantitatively comparable to the structural rearrangements found during the interaction of β-actin with GroEL and TRiC, indicating that the mechanism of chaperonins is conserved during evolution. The chaperonin-bound MreB is also significantly compacted after addition of AMP-PNP for both the GroEL/ES and TRiC systems. Most importantly, our results showed that GroES may act as an unfoldase by inducing a dramatic initial expansion of MreB (even more than for GroEL) implicating a role for MreB folding, allowing us to suggest a delivery mechanism for GroES to GroEL in prokaryotes. PMID:27328749

The topomer-sampling model of protein folding

PubMed Central

Debe, Derek A.; Carlson, Matt J.; Goddard, William A.

1999-01-01

Clearly, a protein cannot sample all of its conformations (e.g., ≈3100 ≈ 1048 for a 100 residue protein) on an in vivo folding timescale (<1 s). To investigate how the conformational dynamics of a protein can accommodate subsecond folding time scales, we introduce the concept of the native topomer, which is the set of all structures similar to the native structure (obtainable from the native structure through local backbone coordinate transformations that do not disrupt the covalent bonding of the peptide backbone). We have developed a computational procedure for estimating the number of distinct topomers required to span all conformations (compact and semicompact) for a polypeptide of a given length. For 100 residues, we find ≈3 × 107 distinct topomers. Based on the distance calculated between different topomers, we estimate that a 100-residue polypeptide diffusively samples one topomer every ≈3 ns. Hence, a 100-residue protein can find its native topomer by random sampling in just ≈100 ms. These results suggest that subsecond folding of modest-sized, single-domain proteins can be accomplished by a two-stage process of (i) topomer diffusion: random, diffusive sampling of the 3 × 107 distinct topomers to find the native topomer (≈0.1 s), followed by (ii) intratopomer ordering: nonrandom, local conformational rearrangements within the native topomer to settle into the precise native state. PMID:10077555

Formation of the bulge of Iapetus through long-wavelength folding of the lithosphere

NASA Astrophysics Data System (ADS)

Kay, Jonathan P.; Dombard, Andrew J.

2018-03-01

Previous models that attempted to explain the formation of the pronounced oblate shape of Iapetus suggested that it was a preserved rotational bulge. These models found that heating was provided by short-lived radioactive isotopes that decayed rapidly and allowed the excess flattening of the lithosphere to be locked in by a thickening lithosphere, but placed severe timing constraints on the formation of Iapetus and its bulge. Here, we show that finite element simulations with an elastic-viscous-plastic rheology indicate it is possible to form the bulge through long-wavelength folding of the lithosphere of Iapetus during an epoch of contraction combined with a latitudinal surface temperature gradient. In contrast to models of a frozen rotational bulge, heat generated by long-lived radioactive isotopes warms the interior, which causes porosity loss and forces Iapetus to compact by ∼10%. Our simulations are most successful when there is a 30 K temperature difference between the pole and the equator. Tectonic growth of the bulge is not sensitive to the time scale over which the moon contracts, and lithospheric thickness primarily controls whether a fold can form, not fold wavelength. In addition, long term simulations show that when no stress is applied, the mechanical lithosphere is strong enough to support the bulge, with negligible relaxation over billion year time scales.

Water-level altitudes 2010 and water-level changes in the Chicot, Evangeline, and Jasper aquifers and compaction 1973-2009 in the Chicot and Evangeline aquifers, Houston-Galveston region, Texas

USGS Publications Warehouse

Kasmarek, Mark C.; Johnson, Michaela R.; Ramage, Jason K.

2010-01-01

Most of the subsidence in the Houston-Galveston region has occurred as a direct result of groundwater withdrawals for municipal supply, industrial use, and irrigation that depressured and dewatered the Chicot and Evangeline aquifers causing compaction of the clay layers of the aquifer sediments. This report, prepared by the U.S. Geological Survey, in cooperation with the Harris-Galveston Subsidence District, City of Houston, Fort Bend Subsidence District, and Lone Star Groundwater Conservation District, is one in an annual series of reports depicting water-level altitudes and water-level changes in the Chicot, Evangeline, and Jasper aquifers and compaction in the Chicot and Evangeline aquifers in the Houston-Galveston region. The report contains maps showing 2010 water-level altitudes for the Chicot, Evangeline, and Jasper aquifers, respectively; maps showing 1-year (2009-10) water-level-altitude changes for each aquifer; maps showing 5-year (2005-10) water-level-altitude changes for each aquifer; maps showing long-term (1990-2010 and 1977-2010) water-level-altitude changes for the Chicot and Evangeline aquifers; a map showing long-term (2000-10) water-level-altitude change for the Jasper aquifer; a map showing locations of borehole extensometer sites; and graphs showing measured compaction of subsurface material at the extensometers from 1973, or later, through 2009. Tables listing the data used to construct each aquifer-data map and the compaction graphs are included. Water levels in the Chicot, Evangeline, and Jasper aquifers were measured during December 2009-March 2010. In 2010, water-level-altitude contours for the Chicot aquifer ranged from 200 feet below National Geodetic Vertical Datum of 1929 or North American Vertical Datum of 1988 (hereinafter, datum) in a small area in southwestern Harris County to 200 feet above datum in central to southwestern Montgomery County. Water-level-altitude changes in the Chicot aquifer ranged from a 49-foot decline to a 67-foot rise (2009-10), from a 25-foot decline to a 35-foot rise (2005-10), from a 40-foot decline to an 80-foot rise (1990-2010), and from a 140-foot decline to a 200-foot rise (1977-2010). In 2010, water-level-altitude contours for the Evangeline aquifer ranged from 300 feet below datum in north-central Harris County to 200 feet above datum at the boundary of Waller, Montgomery, and Grimes Counties. Water-level-altitude changes in the Evangeline aquifer ranged from a 58-foot decline to a 69-foot rise (2009-10), from an 80-foot decline to an 80-foot rise (2005-10), from a 200-foot decline to a 220-foot rise (1990-2010), and from a 320-foot decline to a 220-foot rise (1977-2010). In 2010, water-level-altitude contours for the Jasper aquifer ranged from 200 feet below datum in south-central Montgomery County to 250 feet above datum in eastern-central Grimes County. Water-level-altitude changes in the Jasper aquifer ranged from a 39-foot decline to a 39-foot rise (2009-10), from a 110-foot decline to no change (2005-10), and from a 180-foot decline to no change (2000-10). Compaction of subsurface materials (mostly in the clay layers) composing the Chicot and Evangeline aquifers was recorded continuously at 13 borehole extensometers at 11 sites. For the period of record beginning in 1973, or later, and ending in December 2009, cumulative clay compaction data measured by 12 extensometers ranged from 0.088 foot at the Texas City-Moses Lake site to 3.559 foot at the Addicks site. The rate of compaction varies from site to site because of differences in groundwater withdrawals near each site and differences among sites in the clay-to-sand ratio in the subsurface materials. Therefore, it is not possible to extrapolate or infer a rate of clay compaction for an area based on the rate of compaction measured at a nearby extensometer.

Water-level altitudes 2011 and water-level changes in the Chicot, Evangeline, and Jasper aquifers and compaction 1973-2010 in the Chicot and Evangeline aquifers, Houston-Galveston region, Texas

USGS Publications Warehouse

Johnson, Michaela R.; Ramage, Jason K.; Kasmarek, Mark C.

2011-01-01

Most of the subsidence in the Houston–Galveston region has occurred as a direct result of groundwater withdrawals for municipal supply, industrial use, and irrigation that depressured and dewatered the Chicot and Evangeline aquifers causing compaction of the clay layers of the aquifer sediments. This report, prepared by the U.S. Geological Survey, in cooperation with the Harris–Galveston Subsidence District, City of Houston, Fort Bend Subsidence District, and Lone Star Groundwater Conservation District, is one in an annual series of reports depicting water-level altitudes and water-level changes in the Chicot, Evangeline, and Jasper aquifers and compaction in the Chicot and Evangeline aquifers in the Houston–Galveston region. The report contains maps showing 2011 water-level altitudes for the Chicot, Evangeline, and Jasper aquifers; maps showing 1-year (2010–11) water-level-altitude changes for each aquifer; maps showing 5-year (2006–11) water-level-altitude changes for each aquifer; maps showing long-term (1990–2011 and 1977–2011) water-level-altitude changes for the Chicot and Evangeline aquifers; a map showing long-term (2000–11) water-level-altitude change for the Jasper aquifer; a map showing locations of borehole extensometer sites; and graphs showing measured compaction of subsurface material at the extensometers from 1973, or later, through 2010. Tables listing the data used to construct each aquifer-data map and the compaction graphs are included.Water levels in the Chicot, Evangeline, and Jasper aquifers were measured during December 2010–February 2011. In 2011, water-level-altitude contours for the Chicot aquifer ranged from 200 feet below North American Vertical Datum of 1988 (hereinafter, datum) in a small area in southwestern Harris County to 200 feet above datum in central to southwestern Montgomery County. Water-level-altitude changes in the Chicot aquifer ranged from a 40-foot decline to a 33-foot rise (2010–11), from a 10-foot decline to an 80-foot rise (2006–11), from a 140-foot decline to a 100-foot rise (1990–2011), and from a 120-foot decline to a 200-foot rise (1977–2011). In 2011, water-level-altitude contours for the Evangeline aquifer ranged from 300 feet below datum in north-central Harris County to 200 feet above datum at the boundary of Waller, Montgomery, and Grimes Counties. Water-level-altitude changes in the Evangeline aquifer ranged from a 43-foot decline to a 73-foot rise (2010–11), from a 40-foot decline to a 160-foot rise (2006–11), from a 200-foot decline to a 240-foot rise (1990–2011), and from a 340-foot decline to a 260-foot rise (1977–2011). In 2011, water-level-altitude contours for the Jasper aquifer ranged from 200 feet below datum in south-central Montgomery County to 250 feet above datum in east-central Grimes County. Water-level-altitude changes in the Jasper aquifer ranged from a 45-foot decline to a 29-foot rise (2010–11), from a 90-foot decline to a 10-foot rise (2006–11), and from a 190-foot decline to no change (2000–11). Compaction of subsurface materials (mostly in the clay layers) composing the Chicot and Evangeline aquifers was recorded continuously at 13 borehole extensometers at 11 sites. For the period of record beginning in 1973, or later, and ending in December 2010, cumulative clay compaction data measured by 12 extensometers ranged from 0.100 foot at the Texas City–Moses Lake site to 3.544 foot at the Addicks site. The rate of compaction varies from site to site because of differences in groundwater withdrawals near each site and differences among sites in the clay-to-sand ratio in the subsurface materials. Therefore, it is not possible to extrapolate or infer a rate of clay compaction for an area based on the rate of compaction measured at a nearby extensometer.

Human Protein-disulfide Isomerase Is a Redox-regulated Chaperone Activated by Oxidation of Domain a′*

PubMed Central

Wang, Chao; Yu, Jiang; Huo, Lin; Wang, Lei; Feng, Wei; Wang, Chih-chen

2012-01-01

Protein-disulfide isomerase (PDI), with domains arranged as abb′xa′c, is a key enzyme and chaperone localized in the endoplasmic reticulum (ER) catalyzing oxidative folding and preventing misfolding/aggregation of proteins. It has been controversial whether the chaperone activity of PDI is redox-regulated, and the molecular basis is unclear. Here, we show that both the chaperone activity and the overall conformation of human PDI are redox-regulated. We further demonstrate that the conformational changes are triggered by the active site of domain a′, and the minimum redox-regulated cassette is located in b′xa′. The structure of the reduced bb′xa′ reveals for the first time that domain a′ packs tightly with both domain b′ and linker x to form one compact structural module. Oxidation of domain a′ releases the compact conformation and exposes the shielded hydrophobic areas to facilitate its high chaperone activity. Thus, the study unequivocally provides mechanistic insights into the redox-regulated chaperone activity of human PDI. PMID:22090031

The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling

PubMed Central

Su, Ting; Cheng, Jingdong; Sohmen, Daniel; Hedman, Rickard; Berninghausen, Otto; von Heijne, Gunnar; Wilson, Daniel N; Beckmann, Roland

2017-01-01

Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 Å cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two α-helices connected by an α-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50–55 Å of the exit tunnel. The structure reveals how α-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome. DOI: http://dx.doi.org/10.7554/eLife.25642.001 PMID:28556777

In vitro activity of doripenem and other carbapenems against contemporary Gram-negative pathogens isolated from hospitalised patients in the Asia-Pacific region: results of the COMPACT Asia-Pacific Study.

PubMed

Christiansen, K J; Ip, M; Ker, H B; Mendoza, M; Hsu, L; Kiratisin, P; Chongthaleong, A; Redjeki, I S; Quintana, A; Flamm, R; Garcia, J; Cassettari, M; Cooper, D; Okolo, P; Morrissey, I

2010-12-01

The Comparative Activity of Carbapenems Testing (COMPACT) Study was designed to determine the in vitro potency of doripenem compared with imipenem and meropenem against a large number of contemporary Gram-negative pathogens from more than 100 centres across Europe and the Asia-Pacific region and to assess the reliability of Etest methodology for doripenem minimum inhibitory concentration (MIC) determination against these pathogens. Data from eight countries within the Asia-Pacific region, which collected 1612 bacterial isolates, are presented here. Etest methodology was found to be a reliable method for MIC determination. Doripenem showed in vitro activity similar to or better than meropenem and at least four-fold better than imipenem against Enterobacteriaceae. Against Pseudomonas aeruginosa, doripenem was also the most active of the three carbapenems in vitro. However, in vitro results do not necessarily correlate with clinical outcome. Copyright © 2010 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Future GOES-R global ground receivers

NASA Astrophysics Data System (ADS)

Dafesh, P. A.; Grayver, E.

2006-08-01

The Aerospace Corporation has developed an end-to-end testbed to demonstrate a wide range of modern modulation and coding alternatives for future broadcast by the GOES-R Global Rebroadcast (GRB) system. In particular, this paper describes the development of a compact, low cost, flexible GRB digital receiver that was designed, implemented, fabricated, and tested as part of the development. This receiver demonstrates a 10-fold increase in data rate compared to the rate achievable by the current GOES generation, without a major impact on either cost or size. The digital receiver is integrated on a single PCI card with an FPGA device, and analog-to-digital converters. It supports a wide range of modulations (including 8-PSK and 16-QAM) and turbo coding. With appropriate FPGA firmware and software changes, it can also be configured to receive the current (legacy) GOES signals. The receiver has been validated by sending large image files over a high-fidelity satellite channel emulator, including a space-qualified power amplifier and a white noise source. The receiver is a key component of a future GOES-R weather receiver system (also called user terminal) that includes the antenna, low-noise amplifier, downconverter, filters, digital receiver, and receiver system software. This work describes this receiver proof of concept and its application to providing a very credible estimate of the impact of using modern modulation and coding techniques in the future GOES-R system.

Magnetic field induced quantum dot brightening in liquid crystal synergized magnetic and semiconducting nanoparticle composite assemblies

DOE PAGES

Amaral, Jose Jussi; Wan, Jacky; Rodarte, Andrea L.; ...

2014-10-22

The design and development of multifunctional composite materials from artificial nano-constituents is one of the most compelling current research areas. This drive to improve over nature and produce ‘meta-materials’ has met with some success, but results have proven limited with regards to both the demonstration of synergistic functionalities and in the ability to manipulate the material properties post-fabrication and in situ. Here, magnetic nanoparticles (MNPs) and semiconducting quantum dots (QDs) are co-assembled in a nematic liquid crystalline (LC) matrix, forming composite structures in which the emission intensity of the quantum dots is systematically and reversibly controlled with a small appliedmore » magnetic field (<100 mT). This magnetic field-driven brightening, ranging between a two- to three-fold peak intensity increase, is a truly cooperative effect: the LC phase transition creates the co-assemblies, the clustering of the MNPs produces LC re-orientation at atypical low external field, and this re-arrangement produces compaction of the clusters, resulting in the detection of increased QD emission. These results demonstrate a synergistic, reversible, and an all-optical process to detect magnetic fields and additionally, as the clusters are self-assembled in a fluid medium, they offer the possibility for these sensors to be used in broad ranging fluid-based applications.« less

Effect of particle size on in-die and out-of-die compaction behavior of ranitidine hydrochloride polymorphs.

PubMed

Khomane, Kailas S; Bansal, Arvind K

2013-09-01

The present study investigates the effect of particle size on compaction behavior of forms I and II of ranitidine hydrochloride. Compaction studies were performed using three particle size ranges [450-600 (A), 300-400 (B), and 150-180 (C) μm] of both the forms, using a fully instrumented rotary tableting machine. Compaction data were analyzed for out-of-die compressibility, tabletability, and compactibility profiles and in-die Heckel and Kawakita analysis. Tabletability of the studied size fractions followed the order; IB > IA > > IIC > IIB > IIA at all the compaction pressures. In both the polymorphs, decrease in particle size improved the tabletability. Form I showed greater tabletability over form II at a given compaction pressure and sized fraction. Compressibility plot and Heckel and Kawakita analysis revealed greater compressibility and deformation behavior of form II over form I at a given compaction pressure and sized fraction. Decrease in particle size increased the compressibility and plastic deformation of both the forms. For a given polymorph, improved tabletability of smaller sized particles was attributed to their increased compressibility. However, IA and IB, despite poor compressibility and deformation, showed increased tabletability over IIA, IIB, and IIC by virtue of their greater compactibility. Microtensile testing also revealed higher nominal fracture strength of form I particles over form II, thus, supporting greater compactibility of form I. Taken as a whole, though particle size exhibited a trend on tabletability of individual forms, better compactibility of form I over form II has an overwhelming impact on tabletability.

Range-Gated Metrology: An Ultra-Compact Sensor for Dimensional Stabilization

NASA Technical Reports Server (NTRS)

Lay, Oliver P.; Dubovitsky, Serge; Shaddock, Daniel A.; Ware, Brent; Woodruff, Christopher S.

2008-01-01

Point-to-point laser metrology systems can be used to stabilize large structures at the nanometer levels required for precision optical systems. Existing sensors are large and intrusive, however, with optical heads that consist of several optical elements and require multiple optical fiber connections. The use of point-to-point laser metrology has therefore been limited to applications where only a few gauges are needed and there is sufficient space to accommodate them. Range-Gated Metrology is a signal processing technique that preserves nanometer-level or better performance while enabling: (1) a greatly simplified optical head - a single fiber optic collimator - that can be made very compact, and (2) a single optical fiber connection that is readily multiplexed. This combination of features means that it will be straightforward and cost-effective to embed tens or hundreds of compact metrology gauges to stabilize a large structure. In this paper we describe the concept behind Range-Gated Metrology, demonstrate the performance in a laboratory environment, and give examples of how such a sensor system might be deployed.

[Studies on sintering of dental porcelain. (Part 1) Binary system sintering of alumina and low fusing frit (author's transl)].

PubMed

Kuwayama, N; Kon, M

1981-04-01

Dental porcelains were made from frit and glass powder with electro fused alumina powder addition in the range from 20 to 60 wt% using sintering method at the temperature from 500 degree C to 1 000 degree C, and the effects of alumina content and firing temperature on firing processes of sintered composite were investigated. Shrinkage curves of the powder compacts varied with kind of frit and content of alumina. Particulary, powder compact with alumina addition in the range from 50 to 55% was found to have a remarkable influence for extention of firing temperature range. The densification of the powder compacts was considered to be accelerated by the dissolution of a small a mount of alumina particle into the frit and glass above 900 degree C. Expansion coefficient value of sintered composite of alumina and Pyrex glass powder gradually increased with increase of alumina content. Inversely, expansion coefficient of soda-lime-silica glass showed the minimum value at 40 wt% alumina content and then had a tendency of slight increases with increase of alumina content.

Design of a compact CMOS-compatible photonic antenna by topological optimization.

PubMed

Pita, Julián L; Aldaya, Ivan; Dainese, Paulo; Hernandez-Figueroa, Hugo E; Gabrielli, Lucas H

2018-02-05

Photonic antennas are critical in applications such as spectroscopy, photovoltaics, optical communications, holography, and sensors. In most of those applications, metallic antennas have been employed due to their reduced sizes. Nevertheless, compact metallic antennas suffer from high dissipative loss, wavelength-dependent radiation pattern, and they are difficult to integrate with CMOS technology. All-dielectric antennas have been proposed to overcome those disadvantages because, in contrast to metallic ones, they are CMOS-compatible, easier to integrate with typical silicon waveguides, and they generally present a broader wavelength range of operation. These advantages are achieved, however, at the expense of larger footprints that prevent dense integration and their use in massive phased arrays. In order to overcome this drawback, we employ topological optimization to design an all-dielectric compact antenna with vertical emission over a broad wavelength range. The fabricated device has a footprint of 1.78 µm × 1.78 µm and shows a shift in the direction of its main radiation lobe of only 4° over wavelengths ranging from 1470 nm to 1550 nm and a coupling efficiency bandwidth broader than 150 nm.

Self-catalyzed growth of S layers via an amorphous-to-crystalline transition limited by folding kinetics.

PubMed

Chung, Sungwook; Shin, Seong-Ho; Bertozzi, Carolyn R; De Yoreo, James J

2010-09-21

The importance of nonclassical, multistage crystallization pathways is increasingly evident from theoretical studies on colloidal systems and experimental investigations of proteins and biomineral phases. Although theoretical predictions suggest that proteins follow these pathways as a result of fluctuations that create unstable dense-liquid states, microscopic studies indicate these states are long-lived. Using in situ atomic force microscopy to follow 2D assembly of S-layer proteins on supported lipid bilayers, we have obtained a molecular-scale picture of multistage protein crystallization that reveals the importance of conformational transformations in directing the pathway of assembly. We find that monomers with an extended conformation first form a mobile adsorbed phase, from which they condense into amorphous clusters. These clusters undergo a phase transition through S-layer folding into crystalline clusters composed of compact tetramers. Growth then proceeds by formation of new tetramers exclusively at cluster edges, implying tetramer formation is autocatalytic. Analysis of the growth kinetics leads to a quantitative model in which tetramer creation is rate limiting. However, the estimated barrier is much smaller than expected for folding of isolated S-layer proteins, suggesting an energetic rationale for this multistage pathway.

Effects of aspartic acid and potassium chloride on arginine kinase from shrimp.

PubMed

Tang, Hong-min; Yang, Yin-ye; Zhang, Song-fu

2006-12-15

The aspartic acid (Asp)-induced unfolding and the salt-induced folding of arginine kinase (AK) were studied in terms of enzyme activity, intrinsic fluorescence emission spectra, 1-anilino-8-naphthalenesulfonate (ANS) fluorescence spectra and far-UV circular dichroism (CD) spectra. The results showed that Asp caused inactivation and unfolding of AK with no aggregation during AK denaturation. The unfolding of the whole molecule and the inactivation of AK in different Asp concentrations were compared. Much lower Asp concentration was required to induce inactivation than to produce significant conformational changes of the enzyme molecule. However, with further addition of Asp, the molar ellipticity at 222 and 208 nm, the wavelength shift and the emission intensity of ANS hardly changed. Asp denatured AK was reactivated by dilution. In addition, potassium chloride (KCl) induced the molten globule state with a compact structure after AK was denatured with 7.5 mM Asp. These results collectively elucidate the osmotic effect of Asp anions for the molten globule formed during unfolding process. They also suggest that the effect of Asp differed from that of other denaturants such as guanidine hydrochloride or urea during AK folding. The molten globule state indicates that intermediates exist during AK folding.

Strain localization and elastic-plastic coupling during deformation of porous sandstone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dewers, Thomas A.; Issen, Kathleen A.; Holcomb, David J.

Results of axisymmetric compression tests on weak, porous Castlegate Sandstone (Cretaceous, Utah, USA), covering a range of dilational and compactional behaviors, are examined for localization behavior. Assuming isotropy, bulk and shear moduli evolve as increasing functions of mean stress and Mises equivalent shear stress respectively, and as decreasing functions of work-conjugate plastic strains. Acoustic emissions events located during testing show onset of localization and permit calculation of observed shear and low-angle compaction localization zones, or bands, as localization commences. Total strain measured experimentally partitions into: A) elastic strain with constant moduli, B) elastic strain due to stress dependence of moduli,more » C) elastic strain due to moduli degradation with increasing plastic strain, and D) plastic strain. The third term is the elastic-plastic coupling strain, and though often ignored, contributes significantly to pre-failure total strain for brittle and transitional tests. Constitutive parameters and localization predictions derived from experiments are compared to theoretical predictions. In the brittle regime, predictions of band angles (angle between band normal and maximum compression) demonstrate good agreement with observed shear band angles. Compaction localization was observed in the transitional regime in between shear localization and spatially pervasive compaction, over a small range of mean stresses. In contrast with predictions however, detailed acoustic emissions analyses in this regime show low angle, compaction-dominated but shear-enhanced, localization.« less

Mode I crack surface displacements for a round compact specimen subject to a couple and force

NASA Technical Reports Server (NTRS)

Gross, B.

1979-01-01

Mode I displacement coefficients along the crack surface are presented for a radially cracked round compact specimen, treated as a plane elastostatic problem, subjected to two types of loading; a uniform tensile stress and a nominal bending stress distribution across the net section. By superposition the resultant displacement coefficient or the corresponding influence coefficient can be obtained for any practical load location. Load line displacements are presented for A/D ratios ranging from 0.40 to 0.95, where A is the crack length measured from the crack mouth to the crack tip and D is the specimen diameter. Through a linear extrapolation procedure crack mouth displacements are also obtained. Experimental evidence shows that the results of this study are valid over the range of A/D ratios analyzed for a practical pin loaded round compact specimen.

Forces Driving Chaperone Action

PubMed Central

Koldewey, Philipp; Stull, Frederick; Horowitz, Scott; Martin, Raoul; Bardwell, James C. A.

2016-01-01

SUMMARY It is still unclear what molecular forces drive chaperone-mediated protein folding. Here, we obtain a detailed mechanistic understanding of the forces that dictate the four key steps of chaperone-client interaction: initial binding, complex stabilization, folding, and release. Contrary to the common belief that chaperones recognize unfolding intermediates by their hydrophobic nature, we discover that the model chaperone Spy uses long-range electrostatic interactions to rapidly bind to its unfolded client protein Im7. Short-range hydrophobic interactions follow, which serve to stabilize the complex. Hydrophobic collapse of the client protein then drives its folding. By burying hydrophobic residues in its core, the client’s affinity to Spy decreases, which causes client release. By allowing the client to fold itself, Spy circumvents the need for client-specific folding instructions. This mechanism might help explain how chaperones can facilitate the folding of various unrelated proteins. PMID:27293188

Deglaciation events in part of the Manchester South 7.5' quadrangle south-central New Hampshire

USGS Publications Warehouse

Stone, Byron D.

1971-01-01

The study-area lies in south-central New Hampshire, and is bordered on the west by the Merrimack River, the principal north-south drainage route of central New Hampshire. The classical two tills of New England outcrop in the area. In a unique exposure of the sandy upper till, a loose ablation unit overlies a compact basal unit. Both upper till facies overlie a sheared section of dense, olive-gray lower till. Outwash sequences mapped in the study-area are progressively younger to the north, indicating backwastage of the Wisconsinan ice sheet. Primary structures in proglacial Lake Merrimack sediments include contorted bedding, buckled laminae, and folds. A large slumped section in lake sediments exhibits three distinct deformation zones, characterized by brittle, ductile, and unconsolidated deformation. Cross-cutting relationships establish four fold generations and a deformation sequence in the slumped section. Slip in each fold generation was along nearly parallel slip-lines, as deduced from analyses of fold rotation senses. The primary and slump deformation features contrast sharply with the intense style of deformation of lake beds below till at an apparent ice readvance cut. The deduced drag fold slip-line agrees with till fabric point maxima and dip-slip on one group of thrust faults. A southerly movement of readvancing ice is inferred.The study-area was deglaciated about 13,000 years ago, according to a proposed deglaciation model for New Hampshire. The model is based on Nye's theoretical glacier surface gradient, and evidence for active retreat of the Wisconsinan ice sheet.

Compact high reliability fiber coupled laser diodes for avionics and related applications

NASA Astrophysics Data System (ADS)

Daniel, David R.; Richards, Gordon S.; Janssen, Adrian P.; Turley, Stephen E. H.; Stockton, Thomas E.

1993-04-01

This paper describes a newly developed compact high reliability fiber coupled laser diode which is capable of providing enhanced performance under extreme environmental conditions including a very wide operating temperature range. Careful choice of package materials to minimize thermal and mechanical stress, used with proven manufacturing methods, has resulted in highly stable coupling of the optical fiber pigtail to a high performance MOCVD-grown Multi-Quantum Well laser chip. Electro-optical characteristics over temperature are described together with a demonstration of device stability over a range of environmental conditions. Real time device lifetime data is also presented.

Shock compaction of molybdenum powder

NASA Technical Reports Server (NTRS)

Ahrens, T. J.; Kostka, D.; Vreeland, T., Jr.; Schwarz, R. B.; Kasiraj, P.

1983-01-01

Shock recovery experiments which were carried out in the 9 to 12 GPa range on 1.4 distension Mo and appear adequate to compact to full density ( 45 (SIGMA)m) powders were examined. The stress levels, however, are below those calculated to be from 100 to approx. 22 GPa which a frictional heating model predicts are required to consolidate approx. 10 to 50 (SIGMA)m particles. The model predicts that powders that have a distension of m=1.6 shock pressures of 14 to 72 GPa are required to consolidate Mo powders in the 50 to 10 (SIGMA)m range.

A Study of Production of Miscibility Gap Alloys with Controlled Structures

NASA Technical Reports Server (NTRS)

Parr, R. A.; Johnston, M. H.; Burka, J. A.; Davis, J. H.; Lee, J. A.

1983-01-01

Composite materials were directionally solidified using a new technique to align the constituents longitudinally along the length of the specimen. In some instances a tin coating was applied and diffused into the sample to form a high transition temperature superconducting phase. The superconducting properties were measured and compared with the properties obtained for powder composites and re-directionally solidified powder compacts. The samples which were compacted and redirectionally solidified showed the highest transition temperature and wildest transition range. This indicates that both steps, powder compaction and resolidification, determine the final superconducting properties of the material.

Equilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics.

PubMed

Singh, Richa; Bansal, Rohit; Rathore, Anurag Singh; Goel, Gaurav

2017-04-25

Earliest events in the aggregation process, such as single molecule reconfiguration, are extremely important and the most difficult to characterize in experiments. To this end, we have used well-tempered bias exchange metadynamics simulations to determine the equilibrium ensembles of an insulin molecule under amyloidogenic conditions of low pH and high temperature. A bin-based clustering method that uses statistics accumulated in bias exchange metadynamics trajectories was employed to construct a detailed thermodynamic and kinetic model of insulin folding. The highest lifetime, lowest free-energy ensemble identified consisted of native conformations adopted by a folded insulin monomer in solution, namely, the R-, the R f -, and the T-states of insulin. The lowest free-energy structure had a root mean square deviation of only 0.15 nm from native x-ray structure. The second longest-lived metastable state was an unfolded, compact monomer with little similarity to the native structure. We have identified three additional long-lived, metastable states from the bin-based model. We then carried out an exhaustive structural characterization of metastable states on the basis of tertiary contact maps and per-residue accessible surface areas. We have also determined the lowest free-energy path between two longest-lived metastable states and confirm earlier findings of non-two-state folding for insulin through a folding intermediate. The ensemble containing the monomeric intermediate retained 58% of native hydrophobic contacts, however, accompanied by a complete loss of native secondary structure. We have discussed the relative importance of nativelike versus nonnative tertiary contacts for the folding transition. We also provide a simple measure to determine the importance of an individual residue for folding transition. Finally, we have compared and contrasted this intermediate with experimental data obtained in spectroscopic, crystallographic, and calorimetric measurements during early stages of insulin aggregation. We have also determined stability of monomeric insulin by incubation at a very low concentration to isolate protein-protein interaction effects. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mode 1 stress intensity factors for round compact specimens

NASA Technical Reports Server (NTRS)

Gross, B.

1976-01-01

The mode 1 stress intensity factors were computed for round compact specimens by the boundary collocation method. Results are presented for ratios A sub T/R sub 0 in the range 0.3 to 0.8, where A sub t is the distance from the specimen center to the crack tip for a specimen of diameter 2R sub 0.

Radiotherapy using a laser proton accelerator

NASA Astrophysics Data System (ADS)

Murakami, Masao; Hishikawa, Yoshio; Miyajima, Satoshi; Okazaki, Yoshiko; Sutherland, Kenneth L.; Abe, Mitsuyuki; Bulanov, Sergei V.; Daido, Hiroyuki; Esirkepov, Timur Zh.; Koga, James; Yamagiwa, Mitsuru; Tajima, Toshiki

2008-06-01

Laser acceleration promises innovation in particle beam therapy of cancer where an ultra-compact accelerator system for cancer beam therapy can become affordable to a broad range of patients. This is not feasible without the introduction of a technology that is radically different from the conventional accelerator-based approach. Because of its compactness and other novel characteristics, the laser acceleration method provides many enhanced capabilities

Water-level altitudes 2013 and water-level changes in the Chicot, Evangeline, and Jasper aquifers and compaction 1973--2012 in the Chicot and Evangeline aquifers, Houston-Galveston region, Texas

USGS Publications Warehouse

Kasmarek, Mark C.; Johnson, Michaela R.; Ramage, Jason K.

2013-01-01

Compaction of subsurface sediments (mostly in the clay and silt layers) of the Chicot and Evangeline aquifers was recorded continuously by 13 borehole extensometers at 11 sites that were either activated or installed between 1973 and 1980. For the period of record beginning in 1973 (or later depending on activation or installation date) and ending in December 2012, cumulative measured compaction by 12 of the 13 extensometers ranged from 0.100 ft at the Texas City-Moses Lake extensometer to 3.632 ft at the Addicks extensometer (data were used from only one of two extensometers at one site). The rate of compaction varies from site to site because of differences in groundwater withdrawals near each site and differences among sites in the clay-to-sand ratio in the subsurface sediments. Therefore, it is not possible to extrapolate or infer a rate of compaction for adjacent areas based on the rate of compaction measured at a nearby extensometer.

Water-level altitudes 2014 and water-level changes in the Chicot, Evangeline, and Jasper aquifers and compaction 1973-2013 in the Chicot and Evangeline aquifers, Houston-Galveston region, Texas

USGS Publications Warehouse

Kasmarek, Mark C.; Johnson, Michaela R.; Ramage, Jason K.

2014-01-01

Compaction of subsurface sediments (mostly in the fine-grained clay and silt layers) composing the Chicot and Evangeline aquifers was recorded continuously by using analog technology at the 13 borehole extensometers at 11 sites that were either activated or installed between 1973 and 1980. For the period of record beginning in 1973 (or later depending on activation or installation date) and ending in December 2013, measured cumulative compaction at the 13 extensometers ranged from 0.100 ft at the Texas City-Moses Lake extensometer to 3.654 ft at the Addicks extensometer. The rate of compaction varies from site to site because of differences in rates of groundwater withdrawal in the areas adjacent to each extensometer site and differences among sites in the ratios of clay, silt, and sand and compressibility of the subsurface sediments. Therefore, it is not appropriate to extrapolate or infer a rate of compaction for an adjacent area on the basis of the rate of compaction measured at nearby extensometers.

The Milky Way Project: What are Yellowballs?

NASA Astrophysics Data System (ADS)

Kerton, C. R.; Wolf-Chase, G.; Arvidsson, K.; Lintott, C. J.; Simpson, R. J.

2015-02-01

Yellowballs are a collection of approximately 900 compact, infrared sources identified and named by volunteers participating in the Milky Way Project (MWP), a citizen science project that uses GLIMPSE/MIPSGAL images from Spitzer to explore topics related to Galactic star formation. In this paper, through a combination of catalog cross-matching and infrared color analysis, we show that yellowballs are a mix of compact star-forming regions, including ultra-compact and compact H II regions, as well as analogous regions for less massive B-type stars. The resulting MWP yellowball catalog provides a useful complement to the Red MSX Source survey. It similarly highlights regions of massive star formation, but the selection of objects purely on the basis of their infrared morphology and color in Spitzer images identifies a signature of compact star-forming regions shared across a broad range of luminosities and, by inference, masses. We discuss the origin of their striking mid-infrared appearance and suggest that future studies of the yellowball sample will improve our understanding of how massive and intermediate-mass star-forming regions transition from compact to more extended bubble-like structures.

Water-level altitudes 2016 and water-level changes in the Chicot, Evangeline, and Jasper aquifers and compaction 1973–2015 in the Chicot and Evangeline aquifers, Houston-Galveston region, Texas

USGS Publications Warehouse

Kasmarek, Mark C.; Ramage, Jason K.; Johnson, Michaela R.

2016-10-07

Most of the land-surface subsidence in the Houston-Galveston region, Texas, has occurred as a direct result of groundwater withdrawals for municipal supply, commercial and industrial use, and irrigation that depressured and dewatered the Chicot and Evangeline aquifers, thereby causing compaction of the aquifer sediments, mostly in the fine-grained silt and clay layers. This report, prepared by the U.S. Geological Survey in cooperation with the Harris-Galveston Subsidence District, City of Houston, Fort Bend Subsidence District, Lone Star Groundwater Conservation District, and Brazoria County Groundwater Conservation District, is one in an annual series of reports depicting water-level altitudes and water-level changes in the Chicot, Evangeline, and Jasper aquifers and measured cumulative compaction of subsurface sediments in the Chicot and Evangeline aquifers in the Houston-Galveston region. The report contains regional-scale maps depicting approximate 2016 water-level altitudes (represented by measurements made during December 2015–March 2016) for the Chicot, Evangeline, and Jasper aquifers; maps depicting 1-year (2015–16) water-level changes for each aquifer; maps depicting approximate contoured 5-year (2011–16) water-level changes for each aquifer; maps depicting approximate contoured long-term (1990–2016 and 1977–2016) water-level changes for the Chicot and Evangeline aquifers; a map depicting approximate contoured long-term (2000–16) water-level changes for the Jasper aquifer; a map depicting locations of borehole-extensometer sites; and graphs depicting measured long-term cumulative compaction of subsurface sediments at the extensometers during 1973–2015. Tables listing the water-level data used to construct each water-level map for each aquifer and the measured long-term cumulative compaction data for each extensometer site are included. Graphs depicting water-level measurement data also are included; these graphs can be used to approximate changes in effective stress caused by changes in groundwater withdrawal from the Chicot and Evangeline aquifers.In 2016, water-level-altitude contours for the Chicot aquifer ranged from 200 feet (ft) below the vertical datum (North American Vertical Datum of 1988; hereinafter, datum) in a localized area in northwestern Harris County to 200 ft above datum in west-central Montgomery County. Water-level changes during 2015–16 in the Chicot aquifer ranged from a 39-ft decline to a 26-ft rise. Contoured 5-year and long-term changes in water-level altitudes of the Chicot aquifer ranged from a 30-ft decline to a 20-ft rise (2011–16), from a 140-ft decline to a 160-ft rise (1990–2016), and from a 120-ft decline to a 200-ft rise (1977–2016). In 2016, water-level-altitude contours for the Evangeline aquifer ranged from 250 ft below datum in three separate areas in south-central Montgomery County and extending into north-central Harris County, in west-central Harris County, and in southwestern Harris County to 200 ft above datum in southeastern Grimes and northwestern Montgomery Counties. Water-level changes during 2015–16 in the Evangeline aquifer ranged from a 65-ft decline to a 61-ft rise. Contoured 5-year and long-term changes in water-level altitudes of the Evangeline aquifer ranged from a 60-ft decline to a 40-ft rise (2011–16), from a 160-ft decline to a 160-ft rise (1990–2016), and from a 320-ft decline to a 240-ft rise (1977–2016). In 2016, water-level-altitude contours for the Jasper aquifer ranged from 200 ft below datum in south-central Montgomery County extending into north-central Harris County to 250 ft above datum in northwestern Montgomery County and extending into eastern Grimes County and southwestern Walker County. Water-level changes during 2015–16 in the Jasper aquifer ranged from a 38-ft decline to a 51-ft rise. Contoured 5-year and long-term changes in water-level altitudes of the Jasper aquifer ranged from a 60-ft decline to a 40-ft rise (2011–16) and from a 220-ft decline to a 20-ft decline (2000–16).Compaction of subsurface sediments (mostly in the fine-grained silt and clay layers) in the Chicot and Evangeline aquifers was recorded continuously by using 13 extensometers at 11 sites that were either activated or installed between 1973 and 1980. During the period of record beginning in 1973 (or later depending on activation or installation date) and ending in December 2015, measured cumulative compaction at the 13 extensometers ranged from 0.095 ft at the Texas City-Moses Lake extensometer to 3.666 ft at the Addicks extensometer. From January through December 2015, the Northeast, Southwest, Addicks, Johnson Space Center, and Clear Lake (deep) extensometers recorded net decreases in land-surface elevation, but the Lake Houston, East End, Texas City-Moses Lake, Baytown C–1 (shallow), Baytown C–2 (deep), Seabrook, Clear Lake (shallow), and Pasadena extensometers recorded net increases in land-surface elevation. For the 11 extensometer sites during the selected years 1988, 1998, 2008, 2012, and 2015, the smallest effective stress (20.12 pounds per square inch [psi]) was estimated at the Texas City-Moses Lake extensometer site and was produced by a measured water level of 46.42 ft below land-surface datum (blsd) in January 2008. The corresponding net compaction during 2007 at this site was 0.001 ft. The largest effective stress (174.86 psi) was estimated at the Addicks extensometer site and was produced by a measured water level of 403.38 ft blsd in January 1998. The corresponding net compaction at the Addicks site was 0.067 ft in 1997.The 2011 drought caused water-level declines in the aquifers that were documented by the water-level-measurement data collected in January 2012. During the 2011 drought, the 13 extensometers recorded varying amounts of compaction that ranged from a net compaction value of 0.002 ft recorded by the Texas City-Moses Lake extensometer to a net compaction value of 0.192 ft recorded by the Pasadena extensometer. Water-level data for 1988, 1998, 2008, 2012, and 2015 and the corresponding net compaction values recorded by the extensometers for 1987, 1997, 2007, 2011, and 2014 were used to illustrate the cause and effect relations between changes in water level caused by groundwater withdrawals and resulting changes in effective stress. Changes in effective stress are related to changes in land-surface elevations caused by compaction of the fine-grained sediments composing the Chicot and Evangeline aquifers.The rate of compaction varies from site to site because of differences in rates of groundwater withdrawal in the areas adjacent to each extensometer site; differences among sites in the ratios of sand, silt, and clay and their corresponding compressibilities; and previously established preconsolidation heads. It is not appropriate, therefore, to extrapolate or infer a rate of compaction for an adjacent area on the basis of the rate of compaction recorded by proximal extensometers.

Two modes of longe-range orientation of DNA bases realized upon compaction.

PubMed Central

Yevdokimov YuM; Salyanov, V I; Berg, H

1981-01-01

Formation of compact particles from linear DNA-anthracycline complexes is accompanied by appearance of intense bands in the CD spectra in the region of absorption of DNA bases (UV-region) and in the region of absorption of anthracycline chromophores (visible region). The intense (positive or negative) bands in the region of anthracycline absorption demonstrate an ordered helical location of anthracycline molecules on the DNA template. This fact, in its turn, is related to formation of the DNA superstructure in PEG-containing water-salt solutions with a long-range orientation of nitrogen bases. Possible types of DNA superstructures and the relation between the local- and the long-range order of bases in the DNA superstructure are discussed. PMID:6938929

First report of field evolved resistance to agrochemicals in dengue mosquito, Aedes albopictus (Diptera: Culicidae), from Pakistan.

PubMed

Khan, Hafiz Azhar Ali; Akram, Waseem; Shehzad, Khurram; Shaalan, Essam A

2011-07-22

Agrochemicals have been widely used in Pakistan for several years. This exposes mosquito populations, particularly those present around agricultural settings, to an intense selection pressure for insecticide resistance. The aim of the present study was to investigate the toxicity of representative agrochemicals against various populations of Aedes albopictus (Skuse) collected from three different regions from 2008-2010. For organophosphates and pyrethroids, the resistance ratios compared with susceptible Lab-PK were in the range of 157-266 fold for chlorpyrifos, 24-52 fold for profenofos, 41-71 fold for triazofos, and 15-26 fold for cypermethrin, 15-53 fold for deltamethrin and 21-58 fold for lambdacyhalothrin. The resistance ratios for carbamates and new insecticides were in the range of 13-22 fold for methomyl, 24-30 fold for thiodicarb, and 41-101 fold for indoxacarb, 14-27 fold for emamectin benzoate and 23-50 fold for spinosad. Pair wise comparisons of the log LC50s of insecticides revealed correlation among several insecticides, suggesting a possible cross resistance mechanism. Moreover, resistance remained stable across 3 years, suggesting field selection for general fitness had also taken place for various populations of Ae. albopictus. Moderate to high level of resistance to agrochemicals in Pakistani field populations of Ae. albopictus is reported here first time. The geographic extent of resistance is unknown but, if widespread, may lead to problems in future vector control.

Designing a compact high performance brain PET scanner—simulation study

NASA Astrophysics Data System (ADS)

Gong, Kuang; Majewski, Stan; Kinahan, Paul E.; Harrison, Robert L.; Elston, Brian F.; Manjeshwar, Ravindra; Dolinsky, Sergei; Stolin, Alexander V.; Brefczynski-Lewis, Julie A.; Qi, Jinyi

2016-05-01

The desire to understand normal and disordered human brain function of upright, moving persons in natural environments motivates the development of the ambulatory micro-dose brain PET imager (AMPET). An ideal system would be light weight but with high sensitivity and spatial resolution, although these requirements are often in conflict with each other. One potential approach to meet the design goals is a compact brain-only imaging device with a head-sized aperture. However, a compact geometry increases parallax error in peripheral lines of response, which increases bias and variance in region of interest (ROI) quantification. Therefore, we performed simulation studies to search for the optimal system configuration and to evaluate the potential improvement in quantification performance over existing scanners. We used the Cramér-Rao variance bound to compare the performance for ROI quantification using different scanner geometries. The results show that while a smaller ring diameter can increase photon detection sensitivity and hence reduce the variance at the center of the field of view, it can also result in higher variance in peripheral regions when the length of detector crystal is 15 mm or more. This variance can be substantially reduced by adding depth-of-interaction (DOI) measurement capability to the detector modules. Our simulation study also shows that the relative performance depends on the size of the ROI, and a large ROI favors a compact geometry even without DOI information. Based on these results, we propose a compact ‘helmet’ design using detectors with DOI capability. Monte Carlo simulations show the helmet design can achieve four-fold higher sensitivity and resolve smaller features than existing cylindrical brain PET scanners. The simulations also suggest that improving TOF timing resolution from 400 ps to 200 ps also results in noticeable improvement in image quality, indicating better timing resolution is desirable for brain imaging.

Designing a compact high performance brain PET scanner—simulation study

PubMed Central

Gong, Kuang; Majewski, Stan; Kinahan, Paul E; Harrison, Robert L; Elston, Brian F; Manjeshwar, Ravindra; Dolinsky, Sergei; Stolin, Alexander V; Brefczynski-Lewis, Julie A; Qi, Jinyi

2016-01-01

The desire to understand normal and disordered human brain function of upright, moving persons in natural environments motivates the development of the ambulatory micro-dose brain PET imager (AMPET). An ideal system would be light weight but with high sensitivity and spatial resolution, although these requirements are often in conflict with each other. One potential approach to meet the design goals is a compact brain-only imaging device with a head-sized aperture. However, a compact geometry increases parallax error in peripheral lines of response, which increases bias and variance in region of interest (ROI) quantification. Therefore, we performed simulation studies to search for the optimal system configuration and to evaluate the potential improvement in quantification performance over existing scanners. We used the Cramér–Rao variance bound to compare the performance for ROI quantification using different scanner geometries. The results show that while a smaller ring diameter can increase photon detection sensitivity and hence reduce the variance at the center of the field of view, it can also result in higher variance in peripheral regions when the length of detector crystal is 15 mm or more. This variance can be substantially reduced by adding depth-of- interaction (DOI) measurement capability to the detector modules. Our simulation study also shows that the relative performance depends on the size of the ROI, and a large ROI favors a compact geometry even without DOI information. Based on these results, we propose a compact ‘helmet’ design using detectors with DOI capability. Monte Carlo simulations show the helmet design can achieve four-fold higher sensitivity and resolve smaller features than existing cylindrical brain PET scanners. The simulations also suggest that improving TOF timing resolution from 400 ps to 200 ps also results in noticeable improvement in image quality, indicating better timing resolution is desirable for brain imaging. PMID:27081753

The Optical Green Valley Versus Mid-infrared Canyon in Compact Groups

NASA Technical Reports Server (NTRS)

Walker, Lisa May; Butterfield, Natalie; Johnson, Kelsey; Zucker, Catherine; Gallagher, Sarah; Konstantopoulos, Iraklis; Zabludoff, Ann; Hornschemeier, Ann E.; Tzanavaris, Panayiotis; Charlton, Jane C.

2013-01-01

Compact groups of galaxies provide conditions similar to those experienced by galaxies in the earlier universe. Recent work on compact groups has led to the discovery of a dearth of mid-infrared transition galaxies (MIRTGs) in Infrared Array Camera (3.6-8.0 micrometers) color space as well as at intermediate specific star formation rates. However, we find that in compact groups these MIRTGs have already transitioned to the optical ([g-r]) red sequence. We investigate the optical color-magnitude diagram (CMD) of 99 compact groups containing 348 galaxies and compare the optical CMD with mid-infrared (mid-IR) color space for compact group galaxies. Utilizing redshifts available from Sloan Digital Sky Survey, we identified new galaxy members for four groups. By combining optical and mid-IR data, we obtain information on both the dust and the stellar populations in compact group galaxies. We also compare with more isolated galaxies and galaxies in the Coma Cluster, which reveals that, similar to clusters, compact groups are dominated by optically red galaxies. While we find that compact group transition galaxies lie on the optical red sequence, LVL (Local Volume Legacy) + (plus) SINGS (Spitzer Infrared Nearby Galaxies Survey) mid-IR (infrared) transition galaxies span the range of optical colors. The dearth of mid-IR transition galaxies in compact groups may be due to a lack of moderately star-forming low mass galaxies; the relative lack of these galaxies could be due to their relatively small gravitational potential wells. This makes them more susceptible to this dynamic environment, thus causing them to more easily lose gas or be accreted by larger members.

Role of Hydrophobic Clusters and Long-Range Contact Networks in the Folding of (α/β)8 Barrel Proteins

PubMed Central

Selvaraj, S.; Gromiha, M. Michael

2003-01-01

Analysis on the three dimensional structures of (α/β)8 barrel proteins provides ample light to understand the factors that are responsible for directing and maintaining their common fold. In this work, the hydrophobically enriched clusters are identified in 92% of the considered (α/β)8 barrel proteins. The residue segments with hydrophobic clusters have high thermal stability. Further, these clusters are formed and stabilized through long-range interactions. Specifically, a network of long-range contacts connects adjacent β-strands of the (α/β)8 barrel domain and the hydrophobic clusters. The implications of hydrophobic clusters and long-range networks in providing a feasible common mechanism for the folding of (α/β)8 barrel proteins are proposed. PMID:12609894

Compression and compaction properties of plasticised high molecular weight hydroxypropylmethylcellulose (HPMC) as a hydrophilic matrix carrier.

PubMed

Hardy, I J; Cook, W G; Melia, C D

2006-03-27

The compression and compaction properties of plasticised high molecular weight USP2208 HPMC were investigated with the aim of improving tablet formation in HPMC matrices. Experiments were conducted on binary polymer-plasticiser mixtures containing 17 wt.% plasticiser, and on a model hydrophilic matrix formulation. A selection of common plasticisers, propylene glycol (PG) glycerol (GLY), dibutyl sebacate (DBS) and triacetin (TRI), were chosen to provide a range of plasticisation efficiencies. T(g) values of binary mixtures determined by Dynamic Mechanical Thermal Analysis (DMTA) were in rank order PG>GLY>DBS>TRI>unplasticised HPMC. Mean yield pressure, strain rate sensitivity (SRS) and plastic compaction energy were measured during the compression process, and matrix properties were monitored by tensile strength and axial expansion post-compression. Compression of HPMC:PG binary mixtures resulted in a marked reduction in mean yield pressure and a significant increase in SRS, suggesting a classical plasticisation of HPMC analogous to that produced by water. The effect of PG was also reflected in matrix properties. At compression pressures below 70 MPa, compacts had greater tensile strength than those from native polymer, and over the range 35 and 70 MPa, lower plastic compaction values showed that less energy was required to produce the compacts. Axial expansion was also reduced. Above 70 MPa tensile strength was limited to 3 MPa. These results suggest a useful improvement of HPMC compaction and matrix properties by PG plasticisation, with lowering of T(g) resulting in improved deformation and internal bonding. These effects were also detectable in the model formulation containing a minimal polymer content for an HPMC matrix. Other plasticisers were largely ineffective, matrix strength was poor and axial expansion high. The hydrophobic plasticisers (DBS, TRI) reduced yield pressure substantially, but were poor plasticisers and showed compaction mechanisms that could be attributed to phase separation. The effect of different plasticisers suggests that the deformation characteristics of this HPMC in the solid state is dominated by hydroxyl mediated bonding, rather than by hydrophobic interactions between methoxyl-rich regions.

Explosive Compations of Intermetallic-Forming Powder Mixtures for Fabricating Structural Energetic Materials

NASA Astrophysics Data System (ADS)

Du, S. W.; Aydelotte, B.; Fondse, D.; Wei, C.-T.; Jiang, F.; Herbold, E.; Vecchio, K.; Meyers, M. A.; Thadhani, N. N.

2009-12-01

A double-tube implosion geometry is used to explosively shock consolidate intermetallic-forming Ni-Al, Ta-Al, Nb-Al, Mo-Al and W-Al powder mixtures for fabricating bulk structural energetic materials, with mechanical strength and ability to undergo impact-initiated exothermic reactions. The compacts are characterized based on uniformity of micro structure and degree of densification. Mechanical properties of the compacts are characterized over the strain-rate range of 10-3 to 104 s-1. The impact reactivity is determined using rod-on-anvil experiments, in which disk-shaped compacts mounted on a copper projectile, are impacted against a steel anvil in using a 7.62 mm gas gun. The impact reactivity of the various explosively-consolidated reactive powder mixture compacts is correlated with overall kinetic energy and impact stress to determine their influence on threshold for reaction initiation. The characteristics of the various compacts, their mechanical properties and impact-initiated chemical reactivity will be described in this paper.

Quasiperiodic Oscillations in X-ray Binaries

NASA Astrophysics Data System (ADS)

van der Klis, M.; Murdin, P.

2000-11-01

The term quasiperiodic oscillation (QPO) is used in high-energy astrophysics for any type of non-periodic variability that is constrained to a relatively narrow range of variability frequencies. X-RAY BINARIES are systems in which a `compact object', either a BLACK HOLE or a NEUTRON STAR, orbits a normal star and captures matter from it. The matter spirals down to the compact object and heats up ...

Compact and low cross-talk silicon-on-insulator crossing using a periodic dielectric waveguide.

PubMed

Feng, Junbo; Li, Qunqing; Fan, Shoushan

2010-12-01

We propose and experimentally demonstrate a compact, highly efficient, and negligible cross-talk silicon-on-insulator crossing using a periodic dielectric waveguide. The crossing occupies a footprint of less than 4 μm × 4 μm. Around 0.7 dB insertion loss and lower than -40 dB, cross talk was achieved experimentally over a broad wavelength range.

The shear modulus of the human vocal fold, preliminary results from 20 larynxes.

PubMed

Goodyer, Eric; Hemmerich, Sandra; Müller, Frank; Kobler, James B; Hess, Markus

2007-01-01

Quantification of the elastic properties of the human vocal fold provides invaluable data for researchers deriving mathematical models of phonation, developing tissue engineering therapies, and as normative data for comparison between healthy and scarred tissue. This study measured the shear modulus of excised cadaver vocal folds from 20 subjects. Twenty freshly excised human larynxes were evaluated less than four days post-mortem. They were split along the saggital plane and mounted without tension. Shear modulus was obtained by two different methods. For method 1 cyclical shear stress was applied transversely to the mid-membranous portion of the vocal fold, and shear modulus derived by applying a simple shear model. For method 2 the apparatus was configured as an indentometer, and shear modulus obtained from the stress/strain data by applying an established analytical technique. Method 1 shear model for male larynxes yielded a range from 246 to 3,356 Pa, with a mean value of 1,008 and SD of 380. The range for female larynxes was 286-3,332 Pa, with a mean value of 1,237 and SD of 768. Method 2 indentometer model for male larynxes yielded a range from 552 to 2,741 Pa, with a mean value of 1,000 and SD of 460. The range for female larynxes was 509-1,989 Pa, with a mean value of 1,332 and SD of 428. We have successfully demonstrated two methodologies that are capable of directly measuring the shear modulus of the human vocal fold, without dissecting out the vocal fold cover tissue. The sample size of nine female and 11 male larynxes is too small to validate a general conclusion. The high degree of variability in this small cohort of subjects indicates that factors such as age, health status, and post-mortem delay may be significant; and that there is range of 'normality' for vocal fold tissue.

Abnormally high formation pressures, Potwar Plateau, Pakistan

USGS Publications Warehouse

Law, B.E.; Shah, S.H.A.; Malik, M.A.

1998-01-01

Abnormally high formation pressures in the Potwar Plateau of north-central Pakistan are major obstacles to oil and gas exploration. Severe drilling problems associated with high pressures have, in some cases, prevented adequate evaluation of reservoirs and significantly increased drilling costs. Previous investigations of abnormal pressure in the Potwar Plateau have only identified abnormal pressures in Neogene rocks. We have identified two distinct pressure regimes in this Himalayan foreland fold and thrust belt basin: one in Neogene rocks and another in pre-Neogene rocks. Pore pressures in Neogene rocks are as high as lithostatic and are interpreted to be due to tectonic compression and compaction disequilibrium associated with high rates of sedimentation. Pore pressure gradients in pre-Neogene rocks are generally less than those in Neogene rocks, commonly ranging from 0.5 to 0.7 psi/ft (11.3 to 15.8 kPa/m) and are most likely due to a combination of tectonic compression and hydrocarbon generation. The top of abnormally high pressure is highly variable and doesn't appear to be related to any specific lithologic seal. Consequently, attempts to predict the depth to the top of overpressure prior to drilling are precluded.

(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.

PubMed

Shaw, Neil; Cheng, Chongyun; Tempel, Wolfram; Chang, Jessie; Ng, Joseph; Wang, Xin-Yu; Perrett, Sarah; Rose, John; Rao, Zihe; Wang, Bi-Cheng; Liu, Zhi-Jie

2007-07-07

The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallization Here, we report the successful crystallization of a nuclease employing a reductive methylation protocol. The key to crystallization was the successful introduction of 44 new cohesive (NZ) CH...O contacts (3.2-3.7 A) by the addition of 2 methyl groups to the side chain amine nitrogen (NZ) of 9 lysine residues of the nuclease. The new contacts dramatically altered the crystallization properties of the protein, resulting in crystals that diffracted to 1.2 A resolution. Analytical ultracentrifugation analysis and thermodynamics results revealed a more compact protein structure with better solvent exclusion of buried Trp residues in the folded state of the methylated protein, assisting crystallization. In this study, introduction of novel cohesive (NZ)CH...O contacts by reductive methylation resulted in the crystallization of a protein that had previously resisted crystallization in spite of extensive purification and crystallization space screening. Introduction of (NZ)CH...O contacts could provide a solution to crystallization problems for a broad range of protein targets.

Design and characterizations of two novel cellulases through single-gene shuffling of Cel12A (EG3) gene from Trichoderma reseei.

PubMed

Yenenler, Asli; Sezerman, Osman Ugur

2016-06-01

Cellulases have great potential to be widely used for industrial applications. In general, naturally occurring cellulases are not optimized and limited to meet the industrial needs. These limitations lead to demand for novel cellulases with enhanced enzymatic properties. Here, we describe the enzymatic and structural properties of two novel enzymes, EG3_S1 and EG3_S2, obtained through the single-gene shuffling approach of Cel12A(EG3) gene from Trichoderma reseei EG3_S1 and EG3_S2 shuffled enzymes display 59 and 75% identity in protein sequence with respect to native, respectively. Toward 4-MUC, the minimum activity of EG3_S1 was reported as 5.9-fold decrease in native at 35°C, whereas the maximum activity of EG3_S2 was reported as 15.4-fold increase in native activity at 40°C. Also, the diminished enzyme activity of EG3_S1 was reported within range of 0.6- to 0.8-fold of native and within range of 0.5- to 0.7-fold of native toward CMC and Na-CMC, respectively. For EG3_S2 enzyme, the improved enzymatic activities within range of 1.1- to 1.4-fold of native and within range of 1.1- to 1.6-fold of native were reported toward CMC and Na-CMC, respectively. Moreover, we have reported 6.5-fold increase in the kcat/Km ratio of EG3_S2 with respect to native and suggested EG3_S2 enzyme as more efficient catalysis for hydrolysis reactions than its native counterpart. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Ultraefficient Cap-Exchange Protocol To Compact Biofunctional Quantum Dots for Sensitive Ratiometric Biosensing and Cell Imaging

PubMed Central

2017-01-01

An ultraefficient cap-exchange protocol (UCEP) that can convert hydrophobic quantum dots (QDs) into stable, biocompatible, and aggregation-free water-dispersed ones at a ligand:QD molar ratio (LQMR) as low as 500, some 20–200-fold less than most literature methods, has been developed. The UCEP works conveniently with air-stable lipoic acid (LA)-based ligands by exploiting tris(2-carboxylethyl phosphine)-based rapid in situ reduction. The resulting QDs are compact (hydrodynamic radius, Rh, < 4.5 nm) and bright (retaining > 90% of original fluorescence), resist nonspecific adsorption of proteins, and display good stability in biological buffers even with high salt content (e.g., 2 M NaCl). These advantageous properties make them well suited for cellular imaging and ratiometric biosensing applications. The QDs prepared by UCEP using dihydrolipoic acid (DHLA)-zwitterion ligand can be readily conjugated with octa-histidine (His8)-tagged antibody mimetic proteins (known as Affimers). These QDs allow rapid, ratiometric detection of the Affimer target protein down to 10 pM via a QD-sensitized Förster resonance energy transfer (FRET) readout signal. Moreover, compact biotinylated QDs can be readily prepared by UCEP in a facile, one-step process. The resulting QDs have been further employed for ratiometric detection of protein, exemplified by neutravidin, down to 5 pM, as well as for fluorescence imaging of target cancer cells. PMID:28421739

Extreme Folding

NASA Astrophysics Data System (ADS)

Demaine, Erik

2012-02-01

Our understanding of the mathematics and algorithms behind paper folding, and geometric folding in general, has increased dramatically over the past several years. These developments have found a surprisingly broad range of applications. In the art of origami, it has helped spur the technical origami revolution. In engineering and science, it has helped solve problems in areas such as manufacturing, robotics, graphics, and protein folding. On the recreational side, it has led to new kinds of folding puzzles and magic. I will give an overview of the mathematics and algorithms of folding, with a focus on new mathematics and sculpture.

Structure of the virulence-associated protein VapD from the intracellular pathogen Rhodococcus equi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whittingham, Jean L.; Blagova, Elena V.; Finn, Ciaran E.

2014-08-01

VapD is one of a set of highly homologous virulence-associated proteins from the multi-host pathogen Rhodococcus equi. The crystal structure reveals an eight-stranded β-barrel with a novel fold and a glycine rich ‘bald’ surface. Rhodococcus equi is a multi-host pathogen that infects a range of animals as well as immune-compromised humans. Equine and porcine isolates harbour a virulence plasmid encoding a homologous family of virulence-associated proteins associated with the capacity of R. equi to divert the normal processes of endosomal maturation, enabling bacterial survival and proliferation in alveolar macrophages. To provide a basis for probing the function of the Vapmore » proteins in virulence, the crystal structure of VapD was determined. VapD is a monomer as determined by multi-angle laser light scattering. The structure reveals an elliptical, compact eight-stranded β-barrel with a novel strand topology and pseudo-twofold symmetry, suggesting evolution from an ancestral dimer. Surface-associated octyl-β-d-glucoside molecules may provide clues to function. Circular-dichroism spectroscopic analysis suggests that the β-barrel structure is preceded by a natively disordered region at the N-terminus. Sequence comparisons indicate that the core folds of the other plasmid-encoded virulence-associated proteins from R. equi strains are similar to that of VapD. It is further shown that sequences encoding putative R. equi Vap-like proteins occur in diverse bacterial species. Finally, the functional implications of the structure are discussed in the light of the unique structural features of VapD and its partial structural similarity to other β-barrel proteins.« less

Remagne California margin

USGS Publications Warehouse

Hagstrum, J.T.; Sedlock, R.L.

1998-01-01

Paleomagnetic data for two sections of Cretaceous forearc strata with different structural attitudes on Santa Margarita and Magdalena Islands in Baja California Sur, Mexico, indicate that these rocks have been remagnetized, probably during the late Cenozoic. The in situ paleomagnetic directions, however, are similar to data from other Cretaceous rocks on peninsular California with unexpectedly shallow inclinations and easterly declinations. These data have been interpreted as indicating either northward tectonic transport (10??15?? of latitude) and clockwise rotation (>20??) or compaction shallowing of magnetic inclinations in sedimentary rocks combined with southwestward tilting of plutonic rocks. The available paleomagnetic data for Cretaceous forearc strata in southern and Baja California can be divided into three groups: (1) sections with normal-polarity magnetizations that fail fold tests and are remagnetized, (2) sections with normal-polarity magnetizations with no or inconclusive fold tests that may or may not be remagnetized, and (3) sections with both normaland reversed-polarity intervals where pervasive remagnetization has not occurred. Other rocks of the Mesozoic Great Valley Group, Coast Range ophiolite, and Franciscan Complex in California also have secondary magnetizations with directions similar to younger geomagnetic field directions. Although these widespread remagnetizations could have variable local causes, we propose regional burial and uplift, related to changes in subduction parameters, as a possible explanation. Two episodes of remagnetization are apparent: one in the Late Cretaceous and a second in the late Cenozoic. On the other hand, the unremagnetized and apparently reliable data from sedimentary and plutonic rocks on the Baja Peninsula consistently indicate northward translation (14???? 3??) and clockwise rotation (29???? 8??) with respect to North America since the Late Cretaceous. Copyright 1998 by the American Geophysical Union.

Molecular Architecture of the Cleavage-Dependent Mannose Patch on a Soluble HIV-1 Envelope Glycoprotein Trimer

PubMed Central

Behrens, Anna-Janina; Harvey, David J.; Milne, Emilia; Cupo, Albert; Kumar, Abhinav; Zitzmann, Nicole; Struwe, Weston B.; Moore, John P.

2016-01-01

ABSTRACT The formation of a correctly folded and natively glycosylated HIV-1 viral spike is dependent on protease cleavage of the gp160 precursor protein in the Golgi apparatus. Cleavage induces a compact structure which not only renders the spike capable of fusion but also limits further maturation of its extensive glycosylation. The redirection of the glycosylation pathway to preserve underprocessed oligomannose-type glycans is an important feature in immunogen design, as glycans contribute to or influence the epitopes of numerous broadly neutralizing antibodies. Here we present a quantitative site-specific analysis of a recombinant, trimeric mimic of the native HIV-1 viral spike (BG505 SOSIP.664) compared to the corresponding uncleaved pseudotrimer and the matched gp120 monomer. We present a detailed molecular map of a trimer-associated glycan remodeling that forms a localized subdomain of the native mannose patch. The formation of native trimers is a critical design feature in shaping the glycan epitopes presented on recombinant vaccine candidates. IMPORTANCE The envelope spike of human immunodeficiency virus type 1 (HIV-1) is a target for antibody-based neutralization. For some patients infected with HIV-1, highly potent antibodies have been isolated that can neutralize a wide range of circulating viruses. It is a goal of HIV-1 vaccine research to elicit these antibodies by immunization with recombinant mimics of the viral spike. These antibodies have evolved to recognize the dense array of glycans that coat the surface of the viral molecule. We show how the structure of these glycans is shaped by steric constraints imposed upon them by the native folding of the viral spike. This information is important in guiding the development of vaccine candidates. PMID:27807235

Ultrafast Hydration Dynamics and Coupled Water-Protein Fluctuations in Apomyoglobin

NASA Astrophysics Data System (ADS)

Yang, Yi; Zhang, Luyuan; Wang, Lijuan; Zhong, Dongping

2009-06-01

Protein hydration dynamics are of fundamental importance to its structure and function. Here, we characterize the global solvation dynamics and anisotropy dynamics around the apomyoglobin surface in different conformational states (native and molten globule) by measuring the Stokes shift and anisotropy decay of tryptophan with femtosecond-resolved fluorescence upconversion. With site-directed mutagenesis, we designed sixteen mutants with one tryptophan in each, and placed the probe at a desirable position ranging from buried in the protein core to fully solvent-exposed on the protein surface. In all protein sites studied, two distinct solvation relaxations (1-8 ps and 20-200 ps) were observed, reflecting the initial collective water relaxation and subsequent hydrogen-bond network restructuring, respectively, and both are strongly correlated with protein's local structures and chemical properties. The hydration dynamics of the mutants in molten globule state are faster than those observed in native state, indicating that the protein becomes more flexible and less structured when its conformation is converted from fully-folded native state to partially-folded molten globule state. Complementary, fluorescence anisotropy dynamics of all mutants in native state show an increasing trend of wobbling times (40-260 ps) when the location of the probe is changed from a loop, to a lateral helix, and then, to the compact protein core. Such an increase in wobbling times is related to the local protein structural rigidity, which relates the interaction of water with side chains. The ultrafast hydration dynamics and related side-chain motion around the protein surface unravel the coupled water-protein fluctuations on the picosecond time scales and indicate that the local protein motions are slaved by hydrating water fluctuations.

Wavefront-sensor-based electron density measurements for laser-plasma accelerators.

PubMed

Plateau, G R; Matlis, N H; Geddes, C G R; Gonsalves, A J; Shiraishi, S; Lin, C; van Mourik, R A; Leemans, W P

2010-03-01

Characterization of the electron density in laser produced plasmas is presented using direct wavefront analysis of a probe laser beam. The performance of a laser-driven plasma-wakefield accelerator depends on the plasma wavelength and hence on the electron density. Density measurements using a conventional folded-wave interferometer and using a commercial wavefront sensor are compared for different regimes of the laser-plasma accelerator. It is shown that direct wavefront measurements agree with interferometric measurements and, because of the robustness of the compact commercial device, offer greater phase sensitivity and straightforward analysis, improving shot-to-shot plasma density diagnostics.

The Steerable Microcatheter: A New Device for Selective Catheterisation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soyama, Takeshi; Yoshida, Daisuke; Sakuhara, Yusuke, E-mail: yusaku@med.hokudai.ac.jp

The steerable microcatheter (SwiftNINJA, Sumitomo Bakelite, Tokyo, Japan), which has a remote-controlled flexible tip manipulated using a dial in the handgrip, was recently developed and delivered to the market. This device enables the user to change the angle of the microcatheter tip manually, and potentially makes selective catheterisation easier. We evaluated its unique characteristics and utility in selective catheterisation and coil embolization. This article describes: (1) the advantages of this device in catheterisations involving acute angle branches, and (2) a new technique of compact coil packing with the use of intentional folding by the bendable tip of the catheter.

Wavefront-sensor-based electron density measurements for laser-plasma accelerators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plateau, Guillaume; Matlis, Nicholas; Geddes, Cameron

2010-02-20

Characterization of the electron density in laser produced plasmas is presented using direct wavefront analysis of a probe laser beam. The performance of a laser-driven plasma-wakefield accelerator depends on the plasma wavelength, hence on the electron density. Density measurements using a conventional folded-wave interferometer and using a commercial wavefront sensor are compared for different regimes of the laser-plasma accelerator. It is shown that direct wavefront measurements agree with interferometric measurements and, because of the robustness of the compact commercial device, have greater phase sensitivity, straightforward analysis, improving shot-to-shot plasma-density diagnostics.

Paleomagnetic and structural evidence for oblique slip in a fault-related fold, Grayback monocline, Colorado

USGS Publications Warehouse

Tetreault, J.; Jones, C.H.; Erslev, E.; Larson, S.; Hudson, M.; Holdaway, S.

2008-01-01

Significant fold-axis-parallel slip is accommodated in the folded strata of the Grayback monocline, northeastern Front Range, Colorado, without visible large strike-slip displacement on the fold surface. In many cases, oblique-slip deformation is partitioned; fold-axis-normal slip is accommodated within folds, and fold-axis-parallel slip is resolved onto adjacent strike-slip faults. Unlike partitioning strike-parallel slip onto adjacent strike-slip faults, fold-axis-parallel slip has deformed the forelimb of the Grayback monocline. Mean compressive paleostress orientations in the forelimb are deflected 15??-37?? clockwise from the regional paleostress orientation of the northeastern Front Range. Paleomagnetic directions from the Permian Ingleside Formation in the forelimb are rotated 16??-42?? clockwise about a bedding-normal axis relative to the North American Permian reference direction. The paleostress and paleomagnetic rotations increase with the bedding dip angle and decrease along strike toward the fold tip. These measurements allow for 50-120 m of fold-axis-parallel slip within the forelimb, depending on the kinematics of strike-slip shear. This resolved horizontal slip is nearly equal in magnitude to the ???180 m vertical throw across the fold. For 200 m of oblique-slip displacement (120 m of strike slip and 180 m of reverse slip), the true shortening direction across the fold is N90??E, indistinguishable from the regionally inferred direction of N90??E and quite different from the S53??E fold-normal direction. Recognition of this deformational style means that significant amounts of strike slip can be accommodated within folds without axis-parallel surficial faulting. ?? 2008 Geological Society of America.

Diffusion of cesium and iodine in compressed IG-110 graphite compacts

NASA Astrophysics Data System (ADS)

Carter, L. M.; Brockman, J. D.; Robertson, J. D.; Loyalka, S. K.

2016-08-01

Nuclear graphite grade IG-110 is currently used in the High Temperature Engineering Test Reactor (HTTR) in Japan for certain permanent and replaceable core components, and is a material of interest in general. Therefore, transport parameters for fission products in this material are needed. Measurement of diffusion through pressed compacts of IG-110 graphite is experimentally attractive because they are easy to prepare with homogeneous distributions of fission product surrogates. In this work, we measured diffusion coefficients for Cs and I in pressed compacts made from IG-110 powder in the 1079-1290 K temperature range, and compared them to those obtained in as-received IG-110.

Compact scanning transmission x-ray microscope at the photon factory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Takeichi, Yasuo, E-mail: yasuo.takeichi@kek.jp; Inami, Nobuhito; Ono, Kanta

We report the design and performance of a compact scanning transmission X-ray microscope developed at the Photon Factory. Piezo-driven linear stages are used as coarse stages of the microscope to realize excellent compactness, mobility, and vibrational and thermal stability. An X-ray beam with an intensity of ∼10{sup 7} photons/s was focused to a diameter of ∼40 nm at the sample. At the soft X-ray undulator beamline used with the microscope, a wide range of photon energies (250–1600 eV) is available. The microscope has been used to research energy materials and in environmental sciences.

A method to design blended rolled edges for compact range reflectors

NASA Technical Reports Server (NTRS)

Gupta, Inder J.; Burnside, Walter D.

1989-01-01

A method to design blended rolled edges for arbitrary rim shape compact range reflectors is presented. The reflectors may be center-fed or offset-fed. The method leads to rolled edges with minimal surface discontinuities. It is shown that the reflectors designed using the prescribed method can be defined analytically using simple expressions. A procedure to obtain optimum rolled edges parameter is also presented. The procedure leads to blended rolled edges that minimize the diffracted fields emanating from the junction between the paraboloid and the rolled edge surface while satisfying certain constraints regarding the reflector size and the minimum operating frequency of the system.

A compact, large-range interferometer for precision measurement and inertial sensing

NASA Astrophysics Data System (ADS)

Cooper, S. J.; Collins, C. J.; Green, A. C.; Hoyland, D.; Speake, C. C.; Freise, A.; Mow-Lowry, C. M.

2018-05-01

We present a compact, fibre-coupled interferometer with high sensitivity and a large working range. We propose to use this interferometer as a readout mechanism for future inertial sensors, removing a major limiting noise source, and in precision positioning systems. The interferometer’s peak sensitivity is 2 × 10-{14} m \\sqrt{Hz-1} at 70 Hz and 7 × 10-{11} m \\sqrt{Hz-1} at 10 mHz. If deployed on a GS-13 geophone, the resulting inertial sensing output will be limited by the suspension thermal noise of the reference mass from 10 mHz to 2 Hz.

Ground-states for the liquid drop and TFDW models with long-range attraction

NASA Astrophysics Data System (ADS)

Alama, Stan; Bronsard, Lia; Choksi, Rustum; Topaloglu, Ihsan

2017-10-01

We prove that both the liquid drop model in R 3 with an attractive background nucleus and the Thomas-Fermi-Dirac-von Weizsäcker (TFDW) model attain their ground-states for all masses as long as the external potential V(x) in these models is of long range, that is, it decays slower than Newtonian (e.g., V ( x ) ≫ | x | - 1 for large |x|.) For the TFDW model, we adapt classical concentration-compactness arguments by Lions, whereas for the liquid drop model with background attraction, we utilize a recent compactness result for sets of finite perimeter by Frank and Lieb.

A method to design blended rolled edges for compact range reflectors

NASA Technical Reports Server (NTRS)

Gupta, Inder J.; Ericksen, Kurt P.; Burnside, Walter D.

1990-01-01

A method to design blended rolled edges for arbitrary rim shape compact range reflectors is presented. The reflectors may be center-fed or offset-fed. The method leads to rolled edges with minimal surface discontinuities. It is shown that the reflectors designed using the prescribed method can be defined analytically using simple expressions. A procedure to obtain optimum rolled edges parameters is also presented. The procedure leads to blended rolled edges that minimize the diffracted fields emanating from the junction between the paraboloid and the rolled edge surface while satisfying certain constraints regarding the reflector size and the minimum operating frequency of the system.

First report of field evolved resistance to agrochemicals in dengue mosquito, Aedes albopictus (Diptera: Culicidae), from Pakistan

PubMed Central

2011-01-01

Background Agrochemicals have been widely used in Pakistan for several years. This exposes mosquito populations, particularly those present around agricultural settings, to an intense selection pressure for insecticide resistance. The aim of the present study was to investigate the toxicity of representative agrochemicals against various populations of Aedes albopictus (Skuse) collected from three different regions from 2008-2010. Results For organophosphates and pyrethroids, the resistance ratios compared with susceptible Lab-PK were in the range of 157-266 fold for chlorpyrifos, 24-52 fold for profenofos, 41-71 fold for triazofos, and 15-26 fold for cypermethrin, 15-53 fold for deltamethrin and 21-58 fold for lambdacyhalothrin. The resistance ratios for carbamates and new insecticides were in the range of 13-22 fold for methomyl, 24-30 fold for thiodicarb, and 41-101 fold for indoxacarb, 14-27 fold for emamectin benzoate and 23-50 fold for spinosad. Pair wise comparisons of the log LC50s of insecticides revealed correlation among several insecticides, suggesting a possible cross resistance mechanism. Moreover, resistance remained stable across 3 years, suggesting field selection for general fitness had also taken place for various populations of Ae. albopictus. Conclusion Moderate to high level of resistance to agrochemicals in Pakistani field populations of Ae. albopictus is reported here first time. The geographic extent of resistance is unknown but, if widespread, may lead to problems in future vector control. PMID:21781290

Note: Compact and light displacement sensor for a precision measurement system in large motion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Sang Heon, E-mail: shlee@andong.ac.kr

We developed a compact and light displacement sensor applicable to systems that require wide range motions of its sensing device. The proposed sensor utilized the optical pickup unit of the optical disk drive, which has been used applied to atomic force microscopy (AFM) because of its compactness and lightness as well as its high performance. We modified the structure of optical pickup unit and made the compact sensor driver attachable to a probe head of AFM to make large rotation. The feasibilities of the developed sensor for a general probe-moving measurement device and for probe-rotating AFM were verified. Moreover, amore » simple and precise measurement of alignment between centers of rotator and probe tip in probe-rotation AFM was experimentally demonstrated using the developed sensor.« less

Structural geology of western part of Lemhi Range, east-central Idaho

USGS Publications Warehouse

Tysdal, Russell G.

2002-01-01

The Poison Creek Anticline is a major fold that occupies a large part of the western part of the Lemhi Range. The fold is now broken by normal faults, but removal of displacement on the normal faults permitted reconstruction of the anticline. The fold formed during late Mesozoic compressional deformation in the hinterland of the Cordilleran thrust belt. It is in the hanging wall of the Poison Creek thrust fault, a major fault in east-central Idaho, that displaced Proterozoic strata over lower Paleozoic rocks.

Overlooked Short Toxin-Like Proteins: A Shortcut to Drug Design

PubMed Central

Linial, Michal

2017-01-01

Short stable peptides have huge potential for novel therapies and biosimilars. Cysteine-rich short proteins are characterized by multiple disulfide bridges in a compact structure. Many of these metazoan proteins are processed, folded, and secreted as soluble stable folds. These properties are shared by both marine and terrestrial animal toxins. These stable short proteins are promising sources for new drug development. We developed ClanTox (classifier of animal toxins) to identify toxin-like proteins (TOLIPs) using machine learning models trained on a large-scale proteomic database. Insects proteomes provide a rich source for protein innovations. Therefore, we seek overlooked toxin-like proteins from insects (coined iTOLIPs). Out of 4180 short (<75 amino acids) secreted proteins, 379 were predicted as iTOLIPs with high confidence, with as many as 30% of the genes marked as uncharacterized. Based on bioinformatics, structure modeling, and data-mining methods, we found that the most significant group of predicted iTOLIPs carry antimicrobial activity. Among the top predicted sequences were 120 termicin genes from termites with antifungal properties. Structural variations of insect antimicrobial peptides illustrate the similarity to a short version of the defensin fold with antifungal specificity. We also identified 9 proteins that strongly resemble ion channel inhibitors from scorpion and conus toxins. Furthermore, we assigned functional fold to numerous uncharacterized iTOLIPs. We conclude that a systematic approach for finding iTOLIPs provides a rich source of peptides for drug design and innovative therapeutic discoveries. PMID:29109389

Active mode locking of quantum cascade lasers in an external ring cavity.

PubMed

Revin, D G; Hemingway, M; Wang, Y; Cockburn, J W; Belyanin, A

2016-05-05

Stable ultrashort light pulses and frequency combs generated by mode-locked lasers have many important applications including high-resolution spectroscopy, fast chemical detection and identification, studies of ultrafast processes, and laser metrology. While compact mode-locked lasers emitting in the visible and near infrared range have revolutionized photonic technologies, the systems operating in the mid-infrared range where most gases have their strong absorption lines, are bulky and expensive and rely on nonlinear frequency down-conversion. Quantum cascade lasers are the most powerful and versatile compact light sources in the mid-infrared range, yet achieving their mode-locked operation remains a challenge, despite dedicated effort. Here we report the demonstration of active mode locking of an external-cavity quantum cascade laser. The laser operates in the mode-locked regime at room temperature and over the full dynamic range of injection currents.

Active mode locking of quantum cascade lasers in an external ring cavity

PubMed Central

Revin, D. G.; Hemingway, M.; Wang, Y.; Cockburn, J. W.; Belyanin, A.

2016-01-01

Stable ultrashort light pulses and frequency combs generated by mode-locked lasers have many important applications including high-resolution spectroscopy, fast chemical detection and identification, studies of ultrafast processes, and laser metrology. While compact mode-locked lasers emitting in the visible and near infrared range have revolutionized photonic technologies, the systems operating in the mid-infrared range where most gases have their strong absorption lines, are bulky and expensive and rely on nonlinear frequency down-conversion. Quantum cascade lasers are the most powerful and versatile compact light sources in the mid-infrared range, yet achieving their mode-locked operation remains a challenge, despite dedicated effort. Here we report the demonstration of active mode locking of an external-cavity quantum cascade laser. The laser operates in the mode-locked regime at room temperature and over the full dynamic range of injection currents. PMID:27147409

A Compact Immunoassay Platform Based on a Multicapillary Glass Plate

PubMed Central

Xue, Shuhua; Zeng, Hulie; Yang, Jianmin; Nakajima, Hizuru; Uchiyama, Katsumi

2014-01-01

A highly sensitive, rapid immunoassay performed in the multi-channels of a micro-well array consisting of a multicapillary glass plate (MCP) and a polydimethylsiloxane (PDMS) slide is described. The micro-dimensions and large surface area of the MCP permitted the diffusion distance to be decreased and the reaction efficiency to be increased. To confirm the concept of the method, human immunoglobulin A (h-IgA) was measured using both the proposed immunoassay system and the traditional 96-well plate method. The proposed method resulted in a 1/5-fold decrease of immunoassay time, and a 1/56-fold cut in reagent consumption with a 0.05 ng/mL of limit of detection (LOD) for IgA. The method was also applied to saliva samples obtained from healthy volunteers. The results correlated well to those obtained by the 96-well plate method. The method has the potential for use in disease diagnostic or on-site immunoassays. PMID:24859022

Proton acceleration: new developments for focusing and energy selection, and applications in plasma physics

NASA Astrophysics Data System (ADS)

Audebert, P.

2007-11-01

In the last few years, intense research has been conducted on laser-accelerated ion sources and their applications. These sources have exceptional properties, i.e. high brightness and high spectral cut-off, high directionality and laminarity, short burst duration. We have shown that for proton energies >10 MeV, the transverse and longitudinal emittance are respectively <0.004 mm-mrad and <10-4 eV-s, i.e. at least 100-fold and may be as much as 10^4-fold better than conventional accelerators beams. Thanks to these properties, these sources allow for example point-projection radiography with unprecedented resolution. We will show example of such time and space-resolved radiography of fast evolving fields, either of associated with the expansion of a plasma in vacuum [*] or with the propagation of a ICF-relevant laser beam in an underdense plasma. These proton sources also open new opportunities for ion beam generation and control, and could stimulate development of compact ion accelerators for many applications.

Bright and compact macromolecular probes for bioimaging applications

NASA Astrophysics Data System (ADS)

Thapaliya, Ek Raj; Zhang, Yang; Dhakal, Pravat; Brown, Adrienne S.; Wilson, James N.; Collins, Kevin M.; Raymo, Françisco M.

2018-02-01

Amphiphilic macromolecules with multiple borondipyrromethene (BODIPY) chromophores appended to a common poly(methacrylate) backbone were synthesized by the random co-polymerization of appropriate methacrylate monomers. The resulting polymers incorporate also hydrophilic oligo(ethylene glycol) and hydrophobic decyl side chains designed to impose aqueous solubility and insulate the chromophoric components from each other respectively. The presence of multiple chromophores translates into a significant enhancement in molar absorption coefficient, relative to a model BODIPY monomer. The effective insulation of the fluorophores minimizes interchromophoric interactions and mitigates depressive effects on the fluorescence quantum yield. The overall result is a 6-fold enhancement in brightness, relative to the model monomer. These macromolecular probes can be injected into live Caenorhabditis elegans to allow their visualization with a 4-fold increase in signal intensity, relative to the model system. Furthermore, they can be conjugated to secondary antibodies, under standard amide-coupling conditions, with negligible influence on the binding affinity of the biomoleucles to allow the implementation of immunolabeling protocols.

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation.

PubMed

Umbarger, Mark A; Toro, Esteban; Wright, Matthew A; Porreca, Gregory J; Baù, Davide; Hong, Sun-Hae; Fero, Michael J; Zhu, Lihua J; Marti-Renom, Marc A; McAdams, Harley H; Shapiro, Lucy; Dekker, Job; Church, George M

2011-10-21

We have determined the three-dimensional (3D) architecture of the Caulobacter crescentus genome by combining genome-wide chromatin interaction detection, live-cell imaging, and computational modeling. Using chromosome conformation capture carbon copy (5C), we derive ~13 kb resolution 3D models of the Caulobacter genome. The resulting models illustrate that the genome is ellipsoidal with periodically arranged arms. The parS sites, a pair of short contiguous sequence elements known to be involved in chromosome segregation, are positioned at one pole, where they anchor the chromosome to the cell and contribute to the formation of a compact chromatin conformation. Repositioning these elements resulted in rotations of the chromosome that changed the subcellular positions of most genes. Such rotations did not lead to large-scale changes in gene expression, indicating that genome folding does not strongly affect gene regulation. Collectively, our data suggest that genome folding is globally dictated by the parS sites and chromosome segregation. Copyright © 2011 Elsevier Inc. All rights reserved.

Phase distribution and microstructural changes of self-compacting cement paste at elevated temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye, G.; Liu, X.; De Schutter, G.

2007-06-15

Self-compacting concrete, as a new smart building material with various advanced properties, has been used for a wide range of structures and infrastructures. However little investigation have been reported on the properties of Self-compacting when it is exposed to elevated temperatures. Previous experiments on fire test have shown the differences between high performance concrete and traditional concrete at elevated temperature. This difference is largely depending on the microstructural properties of concrete matrix, i.e. the cement paste, especially on the porosity, pore size distribution and the connectivity of pores in cement pastes. In this contribution, the investigations are focused on themore » cement paste. The phase distribution and microstructural changes of self-compacting cement paste at elevated temperatures are examined by mercury intrusion porosimetry and scanning electron microscopy. The chemical decomposition of self-compacting cement paste at different temperatures is determined by thermogravimetric analysis. The experimental results of self-compacting cement paste are compared with those of high performance cement paste and traditional cement paste. It was found that self-compacting cement paste shows a higher change of the total porosity in comparison with high performance cement paste. When the temperature is higher than 700 deg. C, a dramatic loss of mass was observed in the self-compacting cement paste samples with addition of limestone filler. This implies that the SCC made by this type of self-compacting cement paste will probably show larger damage once exposed to fire. Investigation has shown that 0.5 kg/m{sup 3} of Polypropylene fibers in the self-compacting cement paste can avoid the damage efficiently.« less

Structural elucidation of the interaction between neurodegenerative disease-related tau protein with model lipid membranes

NASA Astrophysics Data System (ADS)

Jones, Emmalee M.

A protein's sequence of amino acids determines how it folds. That folded structure is linked to protein function, and misfolding to dysfunction. Protein misfolding and aggregation into beta-sheet rich fibrillar aggregates is connected with over 20 neurodegenerative diseases, including Alzheimer's disease (AD). AD is characterized in part by misfolding, aggregation and deposition of the microtubule associated tau protein into neurofibrillary tangles (NFTs). However, two questions remain: What is tau's fibrillization mechanism, and what is tau's cytotoxicity mechanism? Tau is prone to heterogeneous interactions, including with lipid membranes. Lipids have been found in NFTs, anionic lipid vesicles induced aggregation of the microtubule binding domain of tau, and other protein aggregates induced ion permeability in cells. This evidence prompted our investigation of tau's interaction with model lipid membranes to elucidate the structural perturbations those interactions induced in tau protein and in the membrane. We show that although tau is highly charged and soluble, it is highly surface active and preferentially interacts with anionic membranes. To resolve molecular-scale structural details of tau and model membranes, we utilized X-ray and neutron scattering techniques. X-ray reflectivity indicated tau aggregated at air/water and anionic lipid membrane interfaces and penetrated into membranes. More significantly, membrane interfaces induced tau protein to partially adopt a more compact conformation with density similar to folded protein and ordered structure characteristic of beta-sheet formation. This suggests possible membrane-based mechanisms of tau aggregation. Membrane morphological changes were seen using fluorescence microscopy, and X-ray scattering techniques showed tau completely disrupts anionic membranes, suggesting an aggregate-based cytotoxicity mechanism. Further investigation of protein constructs and a "hyperphosphorylation" disease mimic helped clarify the role of the microtubule binding domain in anionic lipid affinity and demonstrated even "hyperphosphorylation" did not prevent interaction with anionic membranes. Additional studies investigated more complex membrane models to increase physiological relevance. These insights revealed structural changes in tau protein and lipid membranes after interaction. We observed tau's affinity for interfaces, and aggregation and compaction once tau partitions to interfaces. We observed the beginnings of beta-sheet formation in tau at anionic lipid membranes. We also examined disruption to the membrane on a molecular scale.

Optical properties of ultrarough silver films on silicon

NASA Astrophysics Data System (ADS)

Neff, H.; Henkel, S.; Sass, J. K.; Steinbeiss, E.; Ratz, P.; Müller, J.; Michalke, W.

1996-07-01

The optical properties of inhomogeneously grown rough silver films have been analyzed on the basis of reflectance measurements. Data have been recorded within the wave number range 50 cm-1<λ-1<50 000 cm-1. The results are compared with compact and fairly smooth films, made from the same metal. Rough films reveal very low reflectance and high absorptivity values of nearly 1, at wave numbers ≳200 cm-1. The reflectance of these films is peaking at the bulk plasma resonance hvp of silver at 3.87 eV. Smooth compact films, in contrast, show a pronounced minimum at the same energy. Based on an effective medium approach and available literature data, the dielectric function (DF) and absorption coefficient have been calculated. For rough films, the real part of the DF remains positive within the whole spectral range, but is negative for compact films below hvp, in agreement with published data. The calculated DF of the inhomogeneously grown films fully resembles the experimental observations.

A compact model and direct parameters extraction techniques For amorphous gallium-indium-zinc-oxide thin film transistors

NASA Astrophysics Data System (ADS)

Moldovan, Oana; Castro-Carranza, Alejandra; Cerdeira, Antonio; Estrada, Magali; Barquinha, Pedro; Martins, Rodrigo; Fortunato, Elvira; Miljakovic, Slobodan; Iñiguez, Benjamin

2016-12-01

An advanced compact and analytical drain current model for the amorphous gallium indium zinc oxide (GIZO) thin film transistors (TFTs) is proposed. Its output saturation behavior is improved by introducing a new asymptotic function. All model parameters were extracted using an adapted version of the Universal Method and Extraction Procedure (UMEM) applied for the first time for GIZO devices in a simple and direct form. We demonstrate the correct behavior of the model for negative VDS, a necessity for a complete compact model. In this way we prove the symmetry of source and drain electrodes and extend the range of applications to both signs of VDS. The model, in Verilog-A code, is implemented in Electronic Design Automation (EDA) tools, such as Smart Spice, and compared with measurements of TFTs. It describes accurately the experimental characteristics in the whole range of GIZO TFTs operation, making the model suitable for the design of circuits using these types of devices.

A compact holographic optical tweezers instrument

NASA Astrophysics Data System (ADS)

Gibson, G. M.; Bowman, R. W.; Linnenberger, A.; Dienerowitz, M.; Phillips, D. B.; Carberry, D. M.; Miles, M. J.; Padgett, M. J.

2012-11-01

Holographic optical tweezers have found many applications including the construction of complex micron-scale 3D structures and the control of tools and probes for position, force, and viscosity measurement. We have developed a compact, stable, holographic optical tweezers instrument which can be easily transported and is compatible with a wide range of microscopy techniques, making it a valuable tool for collaborative research. The instrument measures approximately 30×30×35 cm and is designed around a custom inverted microscope, incorporating a fibre laser operating at 1070 nm. We designed the control software to be easily accessible for the non-specialist, and have further improved its ease of use with a multi-touch iPad interface. A high-speed camera allows multiple trapped objects to be tracked simultaneously. We demonstrate that the compact instrument is stable to 0.5 nm for a 10 s measurement time by plotting the Allan variance of the measured position of a trapped 2 μm silica bead. We also present a range of objects that have been successfully manipulated.

Proline 54 trans-cis isomerization is responsible for the kinetic partitioning at the last-step photocycle of photoactive yellow protein

PubMed Central

Lee, Byoung-Chul; Hoff, Wouter D.

2008-01-01

Photoactive yellow protein (PYP), a blue-light photoreceptor for Ectothiorhodospira halophila, has provided a unique system for studying protein folding that is coupled with a photocycle. Upon receptor activation by blue light, PYP proceeds through a photocycle that includes a partially folded signaling state. The last-step photocycle is a thermal recovery reaction from the signaling state to the native state. Bi-exponential kinetics had been observed for the last-step photocycle; however, the slow phase of the bi-exponential kinetics has not been extensively studied. Here we analyzed both fast and slow phases of the last-step photocycle in PYP. From the analysis of the denaturant dependence of the fast and slow phases, we found that the last-step photocycle proceeds through parallel channels of the folding pathway. The burial of the solvent-accessible area was responsible for the transition state of the fast phase, while structural rearrangement from the compact state to the native state was responsible for the transition state of the slow phase. The photocycle of PYP was linked to the thermodynamic cycle that includes both unfolding and refolding of the fast- and slow-phase intermediates. In order to test the hypothesis of proline-limited folding for the slow phase, we constructed two proline mutants: P54A and P68A. We found that only a single phase of the last-step photocycle was observed in P54A. This suggests that there is a low energy barrier between trans to cis conformation in P54 in the light-induced state of PYP, and the resulting cis conformation of P54 generates a slow-phase kinetic trap during the photocycle-coupled folding pathway of PYP. PMID:18794212

On the die compaction of powders used in pharmaceutics.

PubMed

Aryanpour, Gholamreza; Farzaneh, Masoud

2018-07-01

Die compaction is widely used in the compaction of pharmaceutical powders (tableting). It is well known that the powder densification is a result of particle rearrangement and particle deformation. The former is considered to be the governing mechanism of densification in an initial stage of compaction and the latter is regarded as the governing mechanism in the compaction at the higher pressure range. As a more realistic assumption, one can consider that a simultaneous performance of both the rearrangement and deformation mechanisms takes place from the beginning of compaction. To mathematically formulate this assumption, a piston equation is presented where the material relative density is given as a function of the applied pressure on the powder. From the equation, it is possible to obtain the contribution of each mechanism to the material densification at each value of the applied pressure. In the continuation, the piston equation is applied to the tabletting of some pharmaceutical powders. These are the powders of Ascorbic Acid, Avicel ® PH 101, Avicel ® PH 301, Emcompress ® , Sodium Chloride, and Tablettose ® whose tableting results have been previously published in the literature. The results show the piston equation as a suitable approach to describe the tabletting of pharmaceutical powders.

Compaction behaviour and mechanical strength of lactose-sodium starch glycolate and lactose-croscarmellose sodium binary tablets

NASA Astrophysics Data System (ADS)

Ashikin Yaakub, Nur; Shamsul Anuar, Mohd; Tahir, Suraya Mohd

2018-04-01

The focus of this study is to elucidate the effects of adding super disintegrants (SSG and Acdisol) to a filler (lactose) in terms of the compaction behaviour and mechanical strength of the formed binary tablets. The tablets were formed in a uniaxial die compaction process with compaction pressures ranging from 37.7MPa to 150.7 MPa. Consequently, the findings indicated that the increasing of the compaction pressure and the percentage mass composition of the super disintegrants would led to the increased in the strength of the tablets as well as their plastic energies, where this was more apparent for the case of the binary lactose/Acdisol tablets. In addition, as the compaction pressure increased, the maximum ejection pressure required to eject the tablet from the die cavity also increased. In contrast, a decreased in the maximum ejection pressure was observed as the composition of both super disintegrants increased in the lactose-super disintegrant binary tablets. In conclusion, the addition of super disintegrant; SSG with lactose and Acdisol with lactose; would enhanced the mechanical strength of lactose based tablets especially for the case of acdisol-lactose binary tablets in the experimental conditions adopted in this current work.

The effect of processing on the mechanical properties of self-reinforced composites

NASA Astrophysics Data System (ADS)

Hassani, Farzaneh; Martin, Peter J.; Falzon, Brian G.

2018-05-01

Hot-compaction is one of the most common manufacturing methods for creating recyclable all thermoplastic composites. The current work investigates the compaction of highly oriented self-reinforced fabrics with three processing methods to study the effect of pressure and temperature in the tensile mechanical properties of the consolidated laminates. Hot-press, calender roller and vacuum bag technique were adopted to consolidate bi-component polypropylene woven fabrics in a range of pressures and compaction temperatures. Hot-pressed samples exhibited the highest quality of compaction. The modulus of the hot-pressed samples increased with compaction temperature initially due to the improved interlayer bonding and decreased after a maximum at 150°C because of partial melting of the reinforcement phase. The calender roller technique exhibited to have smaller processing temperature window as the pressure is only applied for a short time and the fabrics start to shrink with increasing the processing temperature. The need for constraining the fabrics through the process is therefore found to be paramount. The Vacuum bag results showed this technique to be the least efficient method because of the low compaction pressure. Microscopic images and void content measurement of the consolidated samples further validate the results from tensile testing.

Soil compaction effects of forwarding and its relationship with 6- and 8-wheel drive machines

Treesearch

Fernando Seixas; Tim McDonald

1997-01-01

A study was done to determine the impact, if any, of a range of drive train options on the soil compaction effects of forwarders. The purpose of the study was to evaluate the cost of optional forwarder equipment versus its ability to reduce detrimental soil physical property changes. Tests were done on forwarders equipped with wide and narrow tires, rear steel tracks,...

Compact power reactor

DOEpatents

Wetch, Joseph R.; Dieckamp, Herman M.; Wilson, Lewis A.

1978-01-01

There is disclosed a small compact nuclear reactor operating in the epithermal neutron energy range for supplying power at remote locations, as for a satellite. The core contains fuel moderator elements of Zr hydride with 7 w/o of 93% enriched uranium alloy. The core has a radial beryllium reflector and is cooled by liquid metal coolant such as NaK. The reactor is controlled and shut down by moving portions of the reflector.

Changes in soil physical and chemical properties following organic matter removal and compaction: 20-year response of the aspen Lake-States Long Term Soil Productivity installations

Treesearch

Robert A. Slesak; Brian J. Palik; Anthony W. D' Amato; Valerie J. Kurth

2017-01-01

Soil functions that control plant resource availability can be altered by management activities such as increased organic matter (OM) removal and soil compaction during forest harvesting. The Long Term Soil Productivity study was established to evaluate how these practices influence soil and site productivity using experimental treatments that span a range of forest...

Compressibility of binary powder formulations: investigation and evaluation with compaction equations.

PubMed

Gentis, Nicolaos D; Betz, Gabriele

2012-02-01

The purpose of this work was to investigate and evaluate the powder compressibility of binary mixtures containing a well-compressible compound (microcrystalline cellulose) and a brittle active drug (paracetamol and mefenamic acid) and its progression after a drug load increase. Drug concentration range was 0%-100% (m/m) with 10% intervals. The powder formulations were compacted to several relative densities with the Zwick material tester. The compaction force and tensile strength were fitted to several mathematical models that give representative factors for the powder compressibility. The factors k and C (Heckel and modified Heckel equation) showed mostly a nonlinear correlation with increasing drug load. The biggest drop in both factors occurred at far regions and drug load ranges. This outcome is crucial because in binary mixtures the drug load regions with higher changeover of plotted factors could be a hint for an existing percolation threshold. The susceptibility value (Leuenberger equation) showed varying values for each formulation without the expected trend of decrease for higher drug loads. The outcomes of this study showed the main challenges for good formulation design. Thus, we conclude that such mathematical plots are mandatory for a scientific evaluation and prediction of the powder compaction process. Copyright © 2011 Wiley Periodicals, Inc.

Modeling of Firn Compaction for Estimating Ice-Sheet Mass Change from Observed Ice-Sheet Elevation Change

NASA Technical Reports Server (NTRS)

Li, Jun; Zwally, H. Jay

2011-01-01

Changes in ice-sheet surface elevation are caused by a combination of ice-dynamic imbalance, ablation, temporal variations in accumulation rate, firn compaction and underlying bedrock motion. Thus, deriving the rate of ice-sheet mass change from measured surface elevation change requires information on the rate of firn compaction and bedrock motion, which do not involve changes in mass, and requires an appropriate firn density to associate with elevation changes induced by recent accumulation rate variability. We use a 25 year record of surface temperature and a parameterization for accumulation change as a function of temperature to drive a firn compaction model. We apply this formulation to ICESat measurements of surface elevation change at three locations on the Greenland ice sheet in order to separate the accumulation-driven changes from the ice-dynamic/ablation-driven changes, and thus to derive the corresponding mass change. Our calculated densities for the accumulation-driven changes range from 410 to 610 kg/cu m, which along with 900 kg/cu m for the dynamic/ablation-driven changes gives average densities ranging from 680 to 790 kg/cu m. We show that using an average (or "effective") density to convert elevation change to mass change is not valid where the accumulation and the dynamic elevation changes are of opposite sign.

Frequency and amplitude modulation of ultra-compact terahertz quantum cascade lasers using an integrated avalanche diode oscillator.

PubMed

Castellano, Fabrizio; Li, Lianhe; Linfield, Edmund H; Davies, A Giles; Vitiello, Miriam S

2016-03-15

Mode-locked comb sources operating at optical frequencies underpin applications ranging from spectroscopy and ultrafast physics, through to absolute frequency measurements and atomic clocks. Extending their operation into the terahertz frequency range would greatly benefit from the availability of compact semiconductor-based sources. However, the development of any compact mode-locked THz laser, which itself is inherently a frequency comb, has yet to be achieved without the use of an external stimulus. High-power, electrically pumped quantum cascade lasers (QCLs) have recently emerged as a promising solution, owing to their octave spanning bandwidths, the ability to achieve group-velocity dispersion compensation and the possibility of obtaining active mode-locking. Here, we propose an unprecedented compact architecture to induce both frequency and amplitude self-modulation in a THz QCL. By engineering a microwave avalanche oscillator into the laser cavity, which provides a 10 GHz self-modulation of the bias current and output power, we demonstrate multimode laser emission centered around 3 THz, with distinct multiple sidebands. The resulting microwave amplitude and frequency self-modulation of THz QCLs opens up intriguing perspectives, for engineering integrated self-mode-locked THz lasers, with impact in fields such as nano- and ultrafast photonics and optical metrology.

Frequency and amplitude modulation of ultra-compact terahertz quantum cascade lasers using an integrated avalanche diode oscillator

PubMed Central

Castellano, Fabrizio; Li, Lianhe; Linfield, Edmund H.; Davies, A. Giles; Vitiello, Miriam S.

2016-01-01

Mode-locked comb sources operating at optical frequencies underpin applications ranging from spectroscopy and ultrafast physics, through to absolute frequency measurements and atomic clocks. Extending their operation into the terahertz frequency range would greatly benefit from the availability of compact semiconductor-based sources. However, the development of any compact mode-locked THz laser, which itself is inherently a frequency comb, has yet to be achieved without the use of an external stimulus. High-power, electrically pumped quantum cascade lasers (QCLs) have recently emerged as a promising solution, owing to their octave spanning bandwidths, the ability to achieve group-velocity dispersion compensation and the possibility of obtaining active mode-locking. Here, we propose an unprecedented compact architecture to induce both frequency and amplitude self-modulation in a THz QCL. By engineering a microwave avalanche oscillator into the laser cavity, which provides a 10 GHz self-modulation of the bias current and output power, we demonstrate multimode laser emission centered around 3 THz, with distinct multiple sidebands. The resulting microwave amplitude and frequency self-modulation of THz QCLs opens up intriguing perspectives, for engineering integrated self-mode-locked THz lasers, with impact in fields such as nano- and ultrafast photonics and optical metrology. PMID:26976199

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

PubMed

Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

2015-10-26

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

Web servlet-assisted, dial-in flow cytometry data analysis.

PubMed

Battye, F

2001-02-01

The obvious benefits of centralized data storage notwithstanding, the size of modern flow cytometry data files discourages their transmission over commonly used telephone modem connections. The proposed solution is to install at the central location a web servlet that can extract compact data arrays, of a form dependent on the requested display type, from the stored files and transmit them to a remote client computer program for display. A client program and a web servlet, both written in the Java programming language, were designed to communicate over standard network connections. The client program creates familiar numerical and graphical display types and allows the creation of gates from combinations of user-defined regions. Data compression techniques further reduce transmission times for data arrays that are already much smaller than the data file itself. For typical data files, network transmission times were reduced more than 700-fold for extraction of one-dimensional (1-D) histograms, between 18 and 120-fold for 2-D histograms, and 6-fold for color-coded dot plots. Numerous display formats are possible without further access to the data file. This scheme enables telephone modem access to centrally stored data without restricting flexibility of display format or preventing comparisons with locally stored files. Copyright 2001 Wiley-Liss, Inc.

A folding-dependent mechanism of antimicrobial peptide resistance to degradation unveiled by solution structure of distinctin

PubMed Central

Raimondo, Domenico; Andreotti, Giuseppina; Saint, Nathalie; Amodeo, Pietro; Renzone, Giovanni; Sanseverino, Marina; Zocchi, Ivana; Molle, Gerard; Motta, Andrea; Scaloni, Andrea

2005-01-01

Many bioactive peptides, presenting an unstructured conformation in aqueous solution, are made resistant to degradation by posttranslational modifications. Here, we describe how molecular oligomerization in aqueous solution can generate a still unknown transport form for amphipathic peptides, which is more compact and resistant to proteases than forms related to any possible monomer. This phenomenon emerged from 3D structure, function, and degradation properties of distinctin, a heterodimeric antimicrobial compound consisting of two peptide chains linked by a disulfide bond. After homodimerization in water, this peptide exhibited a fold consisting of a symmetrical full-parallel four-helix bundle, with a well secluded hydrophobic core and exposed basic residues. This fold significantly stabilizes distinctin against proteases compared with other linear amphipathic peptides, without affecting its antimicrobial, hemolytic, and ion-channel formation properties after membrane interaction. This full-parallel helical orientation represents a perfect compromise between formation of a stable structure in water and requirement of a drastic structural rearrangement in membranes to elicit antimicrobial potential. Thus, distinctin can be claimed as a prototype of a previously unrecognized class of antimicrobial derivatives. These results suggest a critical revision of the role of peptide oligomerization whenever solubility or resistance to proteases is known to affect biological properties. PMID:15840728

DOE Office of Scientific and Technical Information (OSTI.GOV)

Helander, Sara; Montecchio, Meri; Lemak, Alexander

Highlights: • We describe the structure of a novel fold in FKBP25 and HectD. • The new fold is named the Basic Tilted Helix Bundle (BTHB) domain. • A conserved basic surface patch is presented, suggesting a functional role. - Abstract: In this paper, we describe the structure of a N-terminal domain motif in nuclear-localized FKBP25{sub 1–73}, a member of the FKBP family, together with the structure of a sequence-related subdomain of the E3 ubiquitin ligase HectD1 that we show belongs to the same fold. This motif adopts a compact 5-helix bundle which we name the Basic Tilted Helix Bundlemore » (BTHB) domain. A positively charged surface patch, structurally centered around the tilted helix H4, is present in both FKBP25 and HectD1 and is conserved in both proteins, suggesting a conserved functional role. We provide detailed comparative analysis of the structures of the two proteins and their sequence similarities, and analysis of the interaction of the proposed FKBP25 binding protein YY1. We suggest that the basic motif in BTHB is involved in the observed DNA binding of FKBP25, and that the function of this domain can be affected by regulatory YY1 binding and/or interactions with adjacent domains.« less

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

PubMed Central

Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

2015-01-01

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer’s disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements. PMID:26498066

The unique N-terminal zinc finger of synaptotagmin-like protein 4 reveals FYVE structure.

PubMed

Miyamoto, Kazuhide; Nakatani, Arisa; Saito, Kazuki

2017-12-01

Synaptotagmin-like protein 4 (Slp4), expressed in human platelets, is associated with dense granule release. Slp4 is comprised of the N-terminal zinc finger, Slp homology domain, and C2 domains. We synthesized a compact construct (the Slp4N peptide) corresponding to the Slp4 N-terminal zinc finger. Herein, we have determined the solution structure of the Slp4N peptide by nuclear magnetic resonance (NMR). Furthermore, experimental, chemical modification of Cys residues revealed that the Slp4N peptide binds two zinc atoms to mediate proper folding. NMR data showed that eight Cys residues coordinate zinc atoms in a cross-brace fashion. The Simple Modular Architecture Research Tool database predicted the structure of Slp4N as a RING finger. However, the actual structure of the Slp4N peptide adopts a unique C 4 C 4 -type FYVE fold and is distinct from a RING fold. To create an artificial RING finger (ARF) with specific ubiquitin-conjugating enzyme (E2)-binding capability, cross-brace structures with eight zinc-ligating residues are needed as the scaffold. The cross-brace structure of the Slp4N peptide could be utilized as the scaffold for the design of ARFs. © 2017 The Protein Society.

950 keV X-Band Linac For Material Recognition Using Two-Fold Scintillator Detector As A Concept Of Dual-Energy X-Ray System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Kiwoo; Natsui, Takuya; Hirai, Shunsuke

2011-06-01

One of the advantages of applying X-band linear accelerator (Linac) is the compact size of the whole system. That shows us the possibility of on-site system such as the custom inspection system in an airport. As X-ray source, we have developed X-band Linac and achieved maximum X-ray energy 950 keV using the low power magnetron (250 kW) in 2 {mu}s pulse length. The whole size of the Linac system is 1x1x1 m{sup 3}. That is realized by introducing X-band system. In addition, we have designed two-fold scintillator detector in dual energy X-ray concept. Monte carlo N-particle transport (MCNP) code wasmore » used to make up sensor part of the design with two scintillators, CsI and CdWO4. The custom inspection system is composed of two equipments: 950 keV X-band Linac and two-fold scintillator and they are operated simulating real situation such as baggage check in an airport. We will show you the results of experiment which was performed with metal samples: iron and lead as targets in several conditions.« less

New Structural Interpretation of the Central Confusion Range, Western Utah, Based On Balanced Cross Sections

NASA Astrophysics Data System (ADS)

Yezerski, D.; Greene, D. C.

2009-12-01

The Confusion Range is a topographically low mountain range in the Basin and Range of west-central Utah, located east of and in the hanging wall of the Snake Range core complex. Previous workers have used a gravity sliding model to interpret the Confusion Range as a large structural trough or synclinorium (e.g. Hose, 1977). Based on existing mapping (Hose, 1965; Hintze, 1974) and new field data, we use balanced and restored cross sections to reinterpret the structure of the Confusion Range as an east-vergent fold-and-thrust belt formed during the Sevier Orogeny. The Confusion Range consists of Cambro-Ordovician through Triassic strata, with predominantly thick-bedded, competent carbonate rocks in the lower Paleozoic (lPz) section and incompetent shales and thin-bedded carbonates in the upper Paleozoic (uPz) section. The contrasting mechanical behavior of these stratigraphic sections results in faulted folds within uPz carbonates above detachments in shale-rich units, deforming in response to ramp-flat thrust faulting of the underlying lPz units. East of the axis of the Conger Mountain (Mtn) syncline, we attribute the increase in structural elevation of lPz rocks to a subsurface thrust sheet consisting of lPz strata that advanced eastward via a high-angle ramp from a lower detachment in the Kanosh Shale to an upper detachment in the Pilot Shale. The doubling of lPz strata that resulted continues through the eastern Confusion Range where a series of small-displacement thrust faults comprising the Kings Canyon thrust system gently tilt strata to the west. In the Conger Range, west of the Conger Mtn syncline, our analysis focuses on reinterpreting the geometrically unlikely folding depicted in previous cross sections as more admissible, fault-cored, asymmetric, detached folding. In our interpretation, resistance created by a steeply-dipping thrust ramp in the lPz section west of Conger Mtn resulted in folding of uPz strata into an east-vergent anticline. Continued east-vergent contraction against the ramp resulted in the west-dipping limb of the anticline, consisting of Ely Limestone, developing into an overturned, west-vergent, synclinal backfold detached in the Chainman Shale. Further contraction exceeded the fold capacity of the detachment fold and resulted in the formation of the Browns Wash fault as an east-vergent thrust fault. The Browns Wash fault is a key component in the development of the present structural geometry, emplacing a west-vergent overturned syncline (detachment fold) in the hanging wall against an east-vergent overturned syncline (footwall syncline) in the footwall. Further west, underlying the western Conger Range and Buckskin Hills, lPz strata are exposed in what we interpret to be a ramp anticline overlying a subsurface thrust ramp. This interpretation implies a lateral ramp separating lPz rocks in the Buckskin Hills from uPz rocks exposed in the Knoll Hill anticline to the north. UPz and Mesozoic strata exposed to the west on the edge of Snake Valley were emplaced by a Tertiary west-dipping normal fault that truncated the west limb of the ramp anticline.

Paleomagnetic, structural, and seismological evidence for oblique-slip deformation in fault-related folds in the Rocky Mountain Foreland, Colorado Plateau, and central Coast Ranges

NASA Astrophysics Data System (ADS)

Tetreault, Joya Liana

The two geologic questions I address in this research are: do fault-related folds accommodate oblique-slip shortening, and how is oblique-slip deformation absorbed within the folded strata? If the strata is deforming as a strike-slip shear zone, then we should be able to observe material rotations produced by strike-slip shear by measuring paleomagnetic vertical-axis rotations. I have approached these problems by applying paleomagnetic vertical-axis rotations, minor fault analyses, and focal mechanism strain inversions to identify evidence of strike-slip shear and to quantify oblique-slip deformation within fault-related folds in the Rocky Mountain Foreland, Colorado Plateau, and the central Coast Ranges. Clockwise paleomagnetic vertical-axis rotations and compressive paleostress rotations of 15-40º in the forelimb of the Grayback Monocline, northeastern Front Range Colorado, indicate that this Laramide fold is absorbing right-lateral shear from a N90E regional shortening direction. This work shows that paleomagnetic vertical-axis rotations in folded strata can be used to identify strike-slip motion on an underlying fault, and that oblique-slip deformation is localized in the forelimb of the fold. I applied the same paleomagnetic methods to identify oblique-slip on the underlying faults of the Nacimiento, East Kaibab, San Rafael, and Grand Hogback monoclines of the Colorado Plateau. The absence of paleomagnetic rotations and structural evidence for small displacements at the Nacimiento and East Kaibab monoclines indicate minor (<1km) right-lateral slip is being accommodated in these folds. Paleomagnetic vertical-axis rotations are found in the forelimbs of the San Rafael and Grand Hogback monoclines, yielding strike-slip displacements of ˜5km within these two folds. These results are consistent with a northeast Laramide compressive stress direction. In the Coalinga anticline, central Coast Ranges, California, clockwise paleomagnetic rotations and an 8º counterclockwise deflection of the maximum shortening direction (derived from focal mechanisms strain inversions of the upper 7km) are compatible with right-lateral shear. The maximum shortening direction in the area of the mainshock rupture is fold-normal, indicating that strike-slip displacement is confined to the main fault plane and not distributed to the hanging wall. The San Andreas Fault is therefore partitioning a small amount of strike-slip to the Coalinga anticline.

Paleomagnetic and Seismologic Evidence for Oblique-Slip Partitioning to the Coalinga Anticline From the San Andreas Fault

NASA Astrophysics Data System (ADS)

Tetreault, J. L.; Jones, C. H.

2007-12-01

The Coalinga Anticline is a one of a series of fault-related folds in the central Coast Ranges, California, oriented subparallel to the San Andreas Fault (SAF). The development of the Central Coast Range anticlines can be related to the relative strength of the SAF. If positing a weak SAF, fault-normal slip is partitioned to these subparallel compressional folds. If the SAF is strong, these folds rotated to their current orientation during wrenching. Another possibility is that the Coast Range anticlines are accommodating oblique-slip partitioned from the SAF. The 1983 Coalinga earthquake does not have a purely thrusting focal mechanism (rake =100°), reflecting the likelihood that oblique slip is being partitioned to this anticline, even though surface expression of fold-axis-parallel slip has not been identified. Paleomagnetic vertical-axis rotations and focal mechanism strain inversions were used to quantify oblique-slip deformation within the Coalinga Anticline. Clockwise rotations of 10° to 16° are inferred from paleomagnetic sites located in late Miocene to Pliocene beds on the steeply dipping forelimb and backlimb of the fold. Significant vertical-axis rotations are not identified in the paleomagnetic sites within the nose of the anticline. The varying vertical axis rotations conflict with wrench tectonics (strong SAF) as the mechanism of fold development. We use focal mechanisms inversions of earthquakes that occurred between 1983 to 2006 to constrain the seismogenic strain within the fold that presumably help to build it over time. In the upper 7 km, the principal shortening axis is oriented N37E to N40E, statistically indistinguishable from normal to the fold (N45E). The right-lateral shear in the folded strata above the fault tip, evident from the paleomagnetically determined clockwise vertical-axis rotations, is being accommodated aseismically or interseismically. In the region between 7 and 11 km, where the mainshock occurred, the shortening direction ranges from oblique to normal to the fold trend. Our results show that right-lateral slip is resolved along the main fault plane and not distributed to the smaller aftershocks at depths of 7-11 km. The principal strain axes and clockwise paleomagnetic rotations indicate that the Coalinga Anticline is accommodating minor right-lateral shearing and thus shares some of the strike-slip motion of the San Andreas system.

Vocal fold paralysis secondary to phonotrauma.

PubMed

Klein, Travis A L; Gaziano, Joy E; Ridley, Marion B

2014-01-01

A unique case of acute onset vocal fold paralysis secondary to phonotrauma is presented. The cause was forceful vocalization by a drill instructor on a firearm range. Imaging studies revealed extensive intralaryngeal and retropharyngeal hemorrhage. Laryngoscopy showed a complete left vocal fold paralysis. Relative voice rest was recommended, and the patient regained normal vocal fold mobility and function after approximately 12 weeks. Copyright © 2014 The Voice Foundation. All rights reserved.

Variable food absorption by Antarctic krill: Relationships between diet, egestion rate and the composition and sinking rates of their fecal pellets

NASA Astrophysics Data System (ADS)

Atkinson, A.; Schmidt, K.; Fielding, S.; Kawaguchi, S.; Geissler, P. A.

2012-01-01

The kinetics of food processing by zooplankton affects both their energy budgets and the biogeochemical fate of their fecal pellets. We sampled 40 schools of krill across the Scotia Sea during spring, summer and autumn and found that in all 3 seasons, every aspect of their absorption and defecation varied greatly. The C content of fecal pellets varied from 0.85% to 29% of their dry mass (median 9.8%) and C egestion rates varied 75-fold. C:N mass ratios of pellets ranged from 4.9 to 13.2 (median 7.8), higher than values of 3.9 in the krill and 5.4 in their food, pointing to enhanced uptake of N. Pellet sinking rates equated to 27-1218 m d -1 (median 304 m d -1), being governed mainly by pellet diameter (80-600 μm, mean 183 μm) and density (1.038-1.391 g cm -3, mean 1.121 g cm -3). Pellets showed little loss of C or N in filtered seawater over the first 2 days and were physically robust. When feeding rates were low, slow gut passage time and high absorption efficiency resulted in low egestion rates of pellets that were low in C and N content. These pellets were compact, dense and fast-sinking. Conversely, in good feeding conditions much food tended to pass quickly through the gut and was not efficiently absorbed, producing C and N-rich, slow-sinking pellets. Such "superfluous feeding" probably maximises the absolute rates of nutrient absorption. Food composition was also important: diatom-rich diets depressed the C content of the pellets but increased their sinking rates, likely due to silica ballasting. So depending on how krill process food, their pellets could represent both vehicles for rapid export and slow sinking, C and N-rich food sources for pelagic scavengers. C egestion rates by krill averaged 3.4% of summer primary production (and ingestion rates would be 2-10-fold higher than this) so whatever the fate of the pellets, krill are an important re-packager within the food web. While salp pellets tend to sink faster than those of krill, it is the latter that tend to prevail in sediment traps. We suggest that this is because krill schools are more compact, producing "rain showers" of pellets that exceed the capacity of pelagic scavengers to reprocess them.

Biogeochemical Processes That Produce Dissolved Organic Matter From Wheat Straw

USGS Publications Warehouse

Wershaw, Robert L.; Rutherford, David W.; Leenheer, Jerry A.; Kennedy, Kay R.; Cox, Larry G.; Koci, Donald R.

2003-01-01

The chemical reactions that lead to the formation of dissolved organic matter (DOM) in natural waters are poorly understood. Studies on the formation of DOM generally are complicated because almost all DOM isolates have been derived from mixtures of plant species composed of a wide variety of different types of precursor compounds for DOM formation. This report describes a study of DOM derived mainly from bales of wheat straw that had been left in a field for several years. During this period of time, black water from the decomposing wheat straw accumulated in pools in the field. The nuclear magnetic resonance and infrared spectra of the black water DOM indicate that it is composed almost entirely of lignin and carbohydrate polymeric units. Analysis by high-performance size-exclusion chromatography with multi-angle laser-light scattering detection indicates that the number average molecular weight of the DOM is 124,000 daltons. The results presented in this report indicate that the black water DOM is composed of hemicellulose chains cross-linked to lignin oligomers. These types of structures have been shown to exist in the hemicellulose matrix of plant cell walls. The cross-linked lignin-hemicellulose complexes apparently were released from partially degraded wheat-straw cell walls with little alteration. In solution in the black water, these lignin-hemicellulose polymers fold into compact globular particles in which the nonpolar parts of the polymer form the interiors of the particles and the polar groups are on the exterior surfaces of the particles. The tightly folded, compact conformation of these particles probably renders them relatively resistant to microbial degradation. This should be especially the case for the aromatic lignin structures that will be buried in the interiors of the particles.

Occurrence and morphology of carbonate concretions in the Beulah-Zap coal bed, Williston basin, North Dakota

USGS Publications Warehouse

Keighin, C.W.M.; Flores, R.M.; Rowland, T.

1996-01-01

Carbonate concretionary bodies were encountered during mining of the Beulah-Zap lignite seam in the Coteau Properties' Freedom mine, Mercer County, North Dakota. Preliminary studies show that areal and vertical distribution of the concretions are variable. All concretions examined are composed almost entirely of calcite. They occur as thin tabular bodies, as more or less elliptical forms, or as tear shaped bodies, and may occur individually or as clusters of buff-colored, poorly consolidated to solidly crystalline material. The carbonate masses vary in size from a few millimeters to tens of centimeters. Bedding in the lignite may display some compactional folding over dense spheroidal to elliptical concretions, indicating formation of the concretions prior to compaction. Internal morphology of the concretions is complex, and includes cone-in-cone structure, cross-cutting calcite veinlets, and multiple generations of calcite. Carbon isotope values suggest the concretions are composed of biogenic carbonate, probably related to early diagenesis and decomposition of organic matter (peat); oxygen isotope values are light, and consistent with a freshwater origin.

Influence of chain topology on polymer crystallization: poly(ethylene oxide) (PEO) rings vs. linear chains.

PubMed

Zardalidis, George; Mars, Julian; Allgaier, Jürgen; Mezger, Markus; Richter, Dieter; Floudas, George

2016-10-04

The absence of entanglements, the more compact structure and the faster diffusion in melts of cyclic poly(ethylene oxide) (PEO) chains have consequences on their crystallization behavior at the lamellar and spherulitic length scales. Rings with molecular weight below the entanglement molecular weight (M < M e ), attain the equilibrium configuration composed from twice-folded chains with a lamellar periodicity that is half of the corresponding linear chains. Rings with M > M e undergo distinct step-like conformational changes to a crystalline lamellar with the equilibrium configuration. Rings melt from this configuration in the absence of crystal thickening in sharp contrast to linear chains. In general, rings more easily attain their extended equilibrium configuration due to strained segments and the absence of entanglements. In addition, rings have a higher equilibrium melting temperature. At the level of the spherulitic superstructure, growth rates are much faster for rings reflecting the faster diffusion and more compact structure. With respect to the segmental dynamics in their semi-crystalline state, ring PEOs with a steepness index of ∼34 form some of the "strongest" glasses.

Light funneling from a photonic crystal laser cavity to a nano-antenna: overcoming the diffraction limit in optical energy transfer down to the nanoscale.

PubMed

Mivelle, Mathieu; Viktorovitch, Pierre; Baida, Fadi I; El Eter, Ali; Xie, Zhihua; Vo, Than-Phong; Atie, Elie; Burr, Geoffrey W; Nedeljkovic, Dusan; Rauch, Jean-Yves; Callard, Ségolène; Grosjean, Thierry

2014-06-16

We show that the near-field coupling between a photonic crystal microlaser and a nano-antenna can enable hybrid photonic systems that are both physically compact (free from bulky optics) and efficient at transferring optical energy into the nano-antenna. Up to 19% of the laser power from a micron-scale photonic crystal laser cavity is experimentally transferred to a bowtie aperture nano-antenna (BNA) whose area is 400-fold smaller than the overall emission area of the microlaser. Instead of a direct deposition of the nano-antenna onto the photonic crystal, it is fabricated at the apex of a fiber tip to be accurately placed in the microlaser near-field. Such light funneling within a hybrid structure provides a path for overcoming the diffraction limit in optical energy transfer to the nanoscale and should thus open promising avenues in the nanoscale enhancement and confinement of light in compact architectures, impacting applications such as biosensing, optical trapping, local heating, spectroscopy, and nanoimaging.

DNAPL distribution in the source zone: Effect of soil structure and uncertainty reduction with increased sampling density

NASA Astrophysics Data System (ADS)

Pantazidou, Marina; Liu, Ke

2008-02-01

This paper focuses on parameters describing the distribution of dense nonaqueous phase liquid (DNAPL) contaminants and investigates the variability of these parameters that results from soil heterogeneity. In addition, it quantifies the uncertainty reduction that can be achieved with increased density of soil sampling. Numerical simulations of DNAPL releases were performed using stochastic realizations of hydraulic conductivity fields generated with the same geostatistical parameters and conditioning data at two sampling densities, thus generating two simulation ensembles of low and high density (three-fold increase) of soil sampling. The results showed that DNAPL plumes in aquifers identical in a statistical sense exhibit qualitatively different patterns, ranging from compact to finger-like. The corresponding quantitative differences were expressed by defining several alternative measures that describe the DNAPL plume and computing these measures for each simulation of the two ensembles. The uncertainty in the plume features under study was affected to different degrees by the variability of the soil, with coefficients of variation ranging from about 20% to 90%, for the low-density sampling. Meanwhile, the increased soil sampling frequency resulted in reductions of uncertainty varying from 7% to 69%, for low- and high-uncertainty variables, respectively. In view of the varying uncertainty in the characteristics of a DNAPL plume, remedial designs that require estimates of the less uncertain features of the plume may be preferred over others that need a more detailed characterization of the source zone architecture.

Shape Memory Alloy-Based Soft Gripper with Variable Stiffness for Compliant and Effective Grasping.

PubMed

Wang, Wei; Ahn, Sung-Hoon

2017-12-01

Soft pneumatic actuators and motor-based mechanisms being concomitant with the cumbersome appendages have many challenges to making the independent robotic system with compact and lightweight configuration. Meanwhile, shape memory actuators have shown a promising alternative solution in many engineering applications ranging from artificial muscle to aerospace industry. However, one of the main limitations of such systems is their inherent softness resulting in a small actuation force, which prevents them from more effective applications. This issue can be solved by combining shape memory actuators and the mechanism of stiffness modulation. As a first, this study describes a shape memory alloy-based soft gripper composed of three identical fingers with variable stiffness for adaptive grasping in low stiffness state and effective holding in high stiffness state. Each finger with two hinges is fabricated through integrating soft composite actuator with stiffness changeable material where each hinge can approximately achieve a 55-fold changeable stiffness independently. Besides, each finger with two hinges can actively achieve multiple postures by both selectively changing the stiffness of hinges and actuating the relevant SMA wire. Based on these principles, the gripper is applicable for grasping objects with deformable shapes and varying shapes with a large range of weight where its maximum grasping force is increased to ∼10 times through integrating with the stiffness changeable mechanism. The final demonstration shows that the finger with desired shape-retained configurations enables the gripper to successfully pick up a frustum-shaped object.

Experimental investigation of protein folding and misfolding.

PubMed

Dobson, Christopher M

2004-09-01

Newly synthesised proteins need to fold, often to intricate and close-packed structures, in order to function. The underlying mechanism by which this complex process takes place both in vitro and in vivo is now becoming understood, at least in general terms, as a result of the application of a wide range of biophysical and computational methods used in combination with the techniques of biochemistry and protein engineering. It is increasingly apparent, however, that folding is not only crucial for generating biological activity, but that it is also coupled to a wide range of processes within the cell, ranging from the trafficking of proteins to specific organelles to the regulation of cell growth and differentiation. Not surprisingly, therefore, the failure of proteins to fold appropriately, or to remain correctly folded, is associated with a large number of cellular malfunctions that give rise to disease. Misfolding, and its consequences such as aggregation, can be investigated by extending the types of techniques used to study the normal folding process. Application of these techniques is enabling the development of a unified description of the interconversion and regulation of the different conformational states available to proteins in living systems. Such a description proves a generic basis for understanding the fundamental links between protein misfolding and its associated clinical disorders, such as Alzheimer's disease and Type II diabetes, and for exploring novel therapeutic strategies directed at their prevention and treatment on a rational basis.

Permeability During Magma Expansion and Compaction

NASA Astrophysics Data System (ADS)

Gonnermann, Helge. M.; Giachetti, Thomas; Fliedner, Céline; Nguyen, Chinh T.; Houghton, Bruce F.; Crozier, Joshua A.; Carey, Rebecca J.

2017-12-01

Plinian lapilli from the 1060 Common Era Glass Mountain rhyolitic eruption of Medicine Lake Volcano, California, were collected and analyzed for vesicularity and permeability. A subset of the samples were deformed at a temperature of 975°, under shear and normal stress, and postdeformation porosities and permeabilities were measured. Almost all undeformed samples fall within a narrow range of vesicularity (0.7-0.9), encompassing permeabilities between approximately 10-15 m2 and 10-10 m2. A percolation threshold of approximately 0.7 is required to fit the data by a power law, whereas a percolation threshold of approximately 0.5 is estimated by fitting connected and total vesicularity using percolation modeling. The Glass Mountain samples completely overlap with a range of explosively erupted silicic samples, and it remains unclear whether the erupting magmas became permeable at porosities of approximately 0.7 or at lower values. Sample deformation resulted in compaction and vesicle connectivity either increased or decreased. At small strains permeability of some samples increased, but at higher strains permeability decreased. Samples remain permeable down to vesicularities of less than 0.2, consistent with a potential hysteresis in permeability-porosity between expansion (vesiculation) and compaction (outgassing). We attribute this to retention of vesicle interconnectivity, albeit at reduced vesicle size, as well as bubble coalescence during shear deformation. We provide an equation that approximates the change in permeability during compaction. Based on a comparison with data from effusively erupted silicic samples, we propose that this equation can be used to model the change in permeability during compaction of effusively erupting magmas.

Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection.

PubMed

Zopf, Agnes; Raim, Roman; Danzer, Martin; Niklas, Norbert; Spilka, Rita; Pröll, Johannes; Gabriel, Christian; Nechansky, Andreas; Roucka, Markus

2015-03-01

The detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performance of compact sequencing using the novel hybcell technology with 454 next-generation sequencing (454-NGS), Sanger sequencing, and pyrosequencing, using an evaluation panel of 35 specimens. A total of 32 mutations and 10 wild-type cases were reported using 454-NGS as the reference method. Specificity ranged from 100% for Sanger sequencing to 80% for pyrosequencing. Sanger sequencing and hybcell-based compact sequencing achieved a sensitivity of 96%, whereas pyrosequencing had a sensitivity of 88%. Accuracy was 97% for Sanger sequencing, 85% for pyrosequencing, and 94% for hybcell-based compact sequencing. Quantitative results were obtained for 454-NGS and hybcell-based compact sequencing data, resulting in a significant correlation (r = 0.914). Whereas pyrosequencing and Sanger sequencing were not able to detect multiple mutated cell clones within one tumor specimen, 454-NGS and the hybcell-based compact sequencing detected multiple mutations in two specimens. Our comparison shows that the hybcell-based compact sequencing is a valuable alternative to state-of-the-art methodologies used for detection of clinically relevant point mutations.

Single Folding Optical Potential for Elastic Scattering of Protons from 14N and 16O in a Wide Range of Energies

NASA Astrophysics Data System (ADS)

Hamada, Sh.

2018-03-01

Available experimental data for protons elastically scattered from 14N and 16O target nuclei are reanalyzed within the framework of single folding optical potential (SFOP) model. In this model, the real part of the potential is derived on the basis of single folding potential. The renormalization factor N r is extracted for the two aforementioned nuclear systems. Theoretical calculations fairly reproduce the experimental data in the whole angular range. Energy dependence of real and imaginary volume integrals as well as reaction cross sections are discussed.

On the Influence of Material Parameters in a Complex Material Model for Powder Compaction

NASA Astrophysics Data System (ADS)

Staf, Hjalmar; Lindskog, Per; Andersson, Daniel C.; Larsson, Per-Lennart

2016-10-01

Parameters in a complex material model for powder compaction, based on a continuum mechanics approach, are evaluated using real insert geometries. The parameter sensitivity with respect to density and stress after compaction, pertinent to a wide range of geometries, is studied in order to investigate completeness and limitations of the material model. Finite element simulations with varied material parameters are used to build surrogate models for the sensitivity study. The conclusion from this analysis is that a simplification of the material model is relevant, especially for simple insert geometries. Parameters linked to anisotropy and the plastic strain evolution angle have a small impact on the final result.

Modeling coupled aerodynamics and vocal fold dynamics using immersed boundary methods.

PubMed

Duncan, Comer; Zhai, Guangnian; Scherer, Ronald

2006-11-01

The penalty immersed boundary (PIB) method, originally introduced by Peskin (1972) to model the function of the mammalian heart, is tested as a fluid-structure interaction model of the closely coupled dynamics of the vocal folds and aerodynamics in phonation. Two-dimensional vocal folds are simulated with material properties chosen to result in self-oscillation and volume flows in physiological frequency ranges. Properties of the glottal flow field, including vorticity, are studied in conjunction with the dynamic vocal fold motion. The results of using the PIB method to model self-oscillating vocal folds for the case of 8 cm H20 as the transglottal pressure gradient are described. The volume flow at 8 cm H20, the transglottal pressure, and vortex dynamics associated with the self-oscillating model are shown. Volume flow is also given for 2, 4, and 12 cm H2O, illustrating the robustness of the model to a range of transglottal pressures. The results indicate that the PIB method applied to modeling phonation has good potential for the study of the interdependence of aerodynamics and vocal fold motion.

High-frequency electric field measurement using a toroidal antenna

DOEpatents

Lee, Ki Ha

2002-01-01

A simple and compact method and apparatus for detecting high frequency electric fields, particularly in the frequency range of 1 MHz to 100 MHz, uses a compact toroidal antenna. For typical geophysical applications the sensor will be used to detect electric fields for a wide range of spectrum starting from about 1 MHz, in particular in the frequency range between 1 to 100 MHz, to detect small objects in the upper few meters of the ground. Time-varying magnetic fields associated with time-varying electric fields induce an emf (voltage) in a toroidal coil. The electric field at the center of (and perpendicular to the plane of) the toroid is shown to be linearly related to this induced voltage. By measuring the voltage across a toroidal coil one can easily and accurately determine the electric field.

Small image laser range finder for planetary rover

NASA Technical Reports Server (NTRS)

Wakabayashi, Yasufumi; Honda, Masahisa; Adachi, Tadashi; Iijima, Takahiko

1994-01-01

A variety of technical subjects need to be solved before planetary rover navigation could be a part of future missions. The sensors which will perceive terrain environment around the rover will require critical development efforts. The image laser range finder (ILRF) discussed here is one of the candidate sensors because of its advantage in providing range data required for its navigation. The authors developed a new compact-sized ILRF which is a quarter of the size of conventional ones. Instead of the current two directional scanning system which is comprised of nodding and polygon mirrors, the new ILRF is equipped with the new concept of a direct polygon mirror driving system, which successfully made its size compact to accommodate the design requirements. The paper reports on the design concept and preliminary technical specifications established in the current development phase.

On-chip photonic particle sensor

NASA Astrophysics Data System (ADS)

Singh, Robin; Ma, Danhao; Agarwal, Anu; Anthony, Brian

2018-02-01

We propose an on-chip photonic particle sensor design that can perform particle sizing and counting for various environmental applications. The sensor is based on micro photonic ring resonators that are able to detect the presence of the free space particles through the interaction with their evanescent electric field tail. The sensor can characterize a wide range of the particle size ranging from a few nano meters to micron ( 1 micron). The photonic platform offers high sensitivity, compactness, fast response of the device. Further, FDTD simulations are performed to analyze different particle-light interactions. Such a compact and portable platform, packaged with integrated photonic circuit provides a useful sensing modality in space shuttle and environmental applications.

pH-dependent structures and properties of casein micelles.

PubMed

Liu, Yan; Guo, Rong

2008-08-01

The association behavior of casein over a broad pH range has first been investigated by fluorescent technique together with DLS and turbidity measurements. Casein molecules can self-assemble into casein micelles in the pH ranges 2.0 to 3.0, and 5.5 to 12.0. The hydrophobic interaction, hydrogen bond and electrostatic action are the main interactions in the formation of casein micelles. The results show that the structure of casein micelles is more compact at low pH and looser at high pH. The casein micelle has the most compact structure at pH 5.5, when it has almost no electrostatic repulsion between casein molecules.

High temperature structural insulating material

DOEpatents

Chen, Wayne Y.

1987-01-06

A high temperature structural insulating material useful as a liner for cylinders of high temperature engines through the favorable combination of high service temperature (above about 800.degree. C.), low thermal conductivity (below about 0.2 W/m.degree. C.), and high compressive strength (above about 250 psi). The insulating material is produced by selecting hollow ceramic beads with a softening temperature above about 800.degree. C., a diameter within the range of 20-200 .mu.m, and a wall thickness in the range of about 2-4 .mu.m; compacting the beads and a compatible silicate binder composition under pressure and sintering conditions to provide the desired structural form with the structure having a closed-cell, compact array of bonded beads.

High temperature structural insulating material

DOEpatents

Chen, Wayne Y.

1987-01-01

A high temperature structural insulating material useful as a liner for cylinders of high temperature engines through the favorable combination of high service temperature (above about 800.degree. C.), low thermal conductivity (below about 0.2 W/m.degree. C.), and high compressive strength (above about 250 psi). The insulating material is produced by selecting hollow ceramic beads with a softening temperature above about 800.degree. C., a diameter within the range of 20-200 .mu.m, and a wall thickness in the range of about 2-4 .mu.m; compacting the beads and a compatible silicate binder composition under pressure and sintering conditions to provide the desired structural form with the structure having a closed-cell, compact array of bonded beads.

Soybean nodulation and symbiotic nitrogen fixation in response to soil compaction and mulching

NASA Astrophysics Data System (ADS)

Siczek, A.; Lipiec, J.

2009-04-01

Symbiotic nitrogen fixation by legume crops such as soybean plays a key role in supplying nitrogen for agricultural systems. In symbiotic associations with Bradyrhizobium japonicum soybean can fix up to 200 kg N ha-1 yr-1. This reduces the need for expensive and often environmentally harmful because of leaching nitrogen fertilization. However both soybean nodulation and nitrogen fixation are sensitive to soil conditions. One of the critical soil constraints is soil compaction. Increasing use of heavy equipment and intensive cropping in modern agriculture leads to excessive soil compaction. Compaction often is found as a result of field operations that have to be performed in a very short period of time and when soils are wet and more susceptible to compaction. This results in unfavourable water content, temperature, aeration, pore size distribution, strength for plant growth and microbial activity. The surface mulching can alleviate the adverse effect of the environmental factors on soil by decreasing fluctuation of soil temperature, increasing moisture by controlling evaporation from the soil surface, decreasing bulk density, preventing soil crusting. The effect of mulch on soil conditions largely depends on soil compaction and weather conditions during growing season. The positive effect of the straw mulch on soil moisture has been seen under seasons with insufficient rainfalls. However thicker layers of mulch can act as diffusion barrier, especially when the mulch is wet. Additionally, low soil temperature prevalent during early spring under mulch can impede development of nodule, nodule size and delay onset of nodulation. The aim of this study was to determine the effect of the straw mulch on nodulation and nitrogen fixation of soybean in variously compacted soil. The experimental field was 192 m2and was divided into three parts composed of 6 micro-plots with area 7 m2. Three degrees of soil compaction obtained in each field part through tractor passes were compared: low, medium and heavy (0, 3 or 5 passes, respectively). This resulted in a wide range of soil bulk density (1.2 to 1.65 Mg m-3) that can occur in the arable fields. To obtain uniform conditions for seed germination and initial seedling growth the entire plot area was tilled with a cultivator-harrow to a depth of 5 cm after soil compaction. Soybean "Aldana" seeds inoculated with B. japonicum were sown in rows with spacing of 0.3 m. After sowing half of each micro-plot was mulched with wheat straw (0.5 kg m-2) and another one - not. Nodulation was evaluated by using the parameters of nodule number and nodule weight and acetylene reduction assay was used for the measurement of nitrogenase activity. Number of nodules on root system under mulched and not mulched soil was the highest in not compacted and medium compacted soil, respectively and the lowest - in most compacted soil with mulch. Nitrogenase activity ( mol C2H4 h-1 plant-1) decreased as soil compaction increased but the more pronounced tendency and higher values were obtained in mulched plots. The results indicate that mulching in some range of soil compaction can improve soybean nodulation and nitrogen fixation. This work was funded in part by the Polish Ministry of Science and Higher Education (Grant No N N310 149635).

Physiologically Based Pharmacokinetic (PBPK) Modeling of ...

EPA Pesticide Factsheets

Background: Quantitative estimation of toxicokinetic variability in the human population is a persistent challenge in risk assessment of environmental chemicals. Traditionally, inter-individual differences in the population are accounted for by default assumptions or, in rare cases, are based on human toxicokinetic data.Objectives: To evaluate the utility of genetically diverse mouse strains for estimating toxicokinetic population variability for risk assessment, using trichloroethylene (TCE) metabolism as a case study. Methods: We used data on oxidative and glutathione conjugation metabolism of TCE in 16 inbred and one hybrid mouse strains to calibrate and extend existing physiologically-based pharmacokinetic (PBPK) models. We added one-compartment models for glutathione metabolites and a two-compartment model for dichloroacetic acid (DCA). A Bayesian population analysis of inter-strain variability was used to quantify variability in TCE metabolism. Results: Concentration-time profiles for TCE metabolism to oxidative and glutathione conjugation metabolites varied across strains. Median predictions for the metabolic flux through oxidation was less variable (5-fold range) than that through glutathione conjugation (10-fold range). For oxidative metabolites, median predictions of trichloroacetic acid production was less variable (2-fold range) than DCA production (5-fold range), although uncertainty bounds for DCA exceeded the predicted variability. Conclusions:

Roller compaction: Effect of relative humidity of lactose powder.

PubMed

Omar, Chalak S; Dhenge, Ranjit M; Palzer, Stefan; Hounslow, Michael J; Salman, Agba D

2016-09-01

The effect of storage at different relative humidity conditions, for various types of lactose, on roller compaction behaviour was investigated. Three types of lactose were used in this study: anhydrous lactose (SuperTab21AN), spray dried lactose (SuperTab11SD) and α-lactose monohydrate 200M. These powders differ in their amorphous contents, due to different manufacturing processes. The powders were stored in a climatic chamber at different relative humidity values ranging from 10% to 80% RH. It was found that the roller compaction behaviour and ribbon properties were different for powders conditioned to different relative humidities. The amount of fines produced, which is undesirable in roller compaction, was found to be different at different relative humidity. The minimum amount of fines produced was found to be for powders conditioned at 20-40% RH. The maximum amount of fines was produced for powders conditioned at 80% RH. This was attributed to the decrease in powder flowability, as indicated by the flow function coefficient ffc and the angle of repose. Particle Image Velocimetry (PIV) was also applied to determine the velocity of primary particles during ribbon production, and it was found that the velocity of the powder during the roller compaction decreased with powders stored at high RH. This resulted in less powder being present in the compaction zone at the edges of the rollers, which resulted in ribbons with a smaller overall width. The relative humidity for the storage of powders has shown to have minimal effect on the ribbon tensile strength at low RH conditions (10-20%). The lowest tensile strength of ribbons produced from lactose 200M and SD was for powders conditioned at 80% RH, whereas, ribbons produced from lactose 21AN at the same condition of 80% RH showed the highest tensile strength. The storage RH range 20-40% was found to be an optimum condition for roll compacting three lactose powders, as it resulted in a minimum amount of fines in the product. Copyright © 2016 Elsevier B.V. All rights reserved.

Compact characterization of liquid absorption and emission spectra using linear variable filters integrated with a CMOS imaging camera.

PubMed

Wan, Yuhang; Carlson, John A; Kesler, Benjamin A; Peng, Wang; Su, Patrick; Al-Mulla, Saoud A; Lim, Sung Jun; Smith, Andrew M; Dallesasse, John M; Cunningham, Brian T

2016-07-08

A compact analysis platform for detecting liquid absorption and emission spectra using a set of optical linear variable filters atop a CMOS image sensor is presented. The working spectral range of the analysis platform can be extended without a reduction in spectral resolution by utilizing multiple linear variable filters with different wavelength ranges on the same CMOS sensor. With optical setup reconfiguration, its capability to measure both absorption and fluorescence emission is demonstrated. Quantitative detection of fluorescence emission down to 0.28 nM for quantum dot dispersions and 32 ng/mL for near-infrared dyes has been demonstrated on a single platform over a wide spectral range, as well as an absorption-based water quality test, showing the versatility of the system across liquid solutions for different emission and absorption bands. Comparison with a commercially available portable spectrometer and an optical spectrum analyzer shows our system has an improved signal-to-noise ratio and acceptable spectral resolution for discrimination of emission spectra, and characterization of colored liquid's absorption characteristics generated by common biomolecular assays. This simple, compact, and versatile analysis platform demonstrates a path towards an integrated optical device that can be utilized for a wide variety of applications in point-of-use testing and point-of-care diagnostics.

A long-term soil structure observatory for post-compaction soil structure evolution: design and initial soil structure recovery observations

NASA Astrophysics Data System (ADS)

Keller, Thomas; Colombi, Tino; Ruiz, Siul; Grahm, Lina; Reiser, René; Rek, Jan; Oberholzer, Hans-Rudolf; Schymanski, Stanislaus; Walter, Achim; Or, Dani

2016-04-01

Soil compaction due to agricultural vehicular traffic alters the geometrical arrangement of soil constituents, thereby modifying mechanical properties and pore spaces that affect a range of soil hydro-ecological functions. The ecological and economic costs of soil compaction are dependent on the immediate impact on soil functions during the compaction event, and a function of the recovery time. In contrast to a wealth of soil compaction information, mechanisms and rates of soil structure recovery remain largely unknown. A long-term (>10-yr) soil structure observatory (SSO) was established in 2014 on a loamy soil in Zurich, Switzerland, to quantify rates and mechanisms of structure recovery of compacted arable soil under different post-compaction management treatments. We implemented three initial compaction treatments (using a two-axle agricultural vehicle with 8 Mg wheel load): compaction of the entire plot area (i.e. track-by-track), compaction in wheel tracks, and no compaction. After compaction, we implemented four post-compaction soil management systems: bare soil (BS), permanent grass (PG), crop rotation without mechanical loosening (NT), and crop rotation under conventional tillage (CT). BS and PG provide insights into uninterrupted natural processes of soil structure regeneration under reduced (BS) and normal biological activity (PG). The two cropping systems (NT and CT) enable insights into soil structure recovery under common agricultural practices with minimal (NT) and conventional mechanical soil disturbance (CT). Observations include periodic sampling and measurements of soil physical properties, earthworm abundance, crop measures, electrical resistivity and ground penetrating radar imaging, and continuous monitoring of state variables - soil moisture, temperature, CO2 and O2 concentrations, redox potential and oxygen diffusion rates - for which a network of sensors was installed at various depths (0-1 m). Initial compaction increased soil bulk density to about half a metre, decreased gas and water transport functions (air permeability, gas diffusivity, saturated hydraulic conductivity), and increased mechanical impedance. Water infiltration at the soil surface was initially reduced by three orders of magnitude, but significantly recovered within a year. However, within the soil profile, recovery of transport properties is much smaller. Air permeability tended to recover more than gas diffusivity, suggesting that initial post-compaction recovery is initiated by new macropores (e.g. biopores). Tillage recovered topsoil bulk density but not topsoil transport functions. Compaction changed grass species composition in PG, and significantly reduced grass biomass in PG and crop yields in NT and CT.

Shear-enhanced compaction bands formed at shallow burial conditions; implications for fluid flow (Provence, France)

NASA Astrophysics Data System (ADS)

Ballas, Gregory; Soliva, Roger; Sizun, Jean-Pierre; Fossen, Haakon; Benedicto, Antonio; Skurtveit, Elin

2013-02-01

Field observations of highly porous and permeable sandstone in the Orange area (S-E Basin, France) show that networks of shear-enhanced compaction bands can form in a contractional regime at burial depths of about 400 m ± 100 m. These bands show equal compaction and shear displacements, are organized in conjugate and densely distributed networks, and are restricted to the coarse-grained (mean grain diameter of 0.6 ± 0.1 mm) and less porous (porosity of 26 ± 2%) sand layers. The bands are crush microbreccia with limited grain comminution and high grain microfracture density. They show reductions of permeability (mD) ranging from 0 to little more than 1 order of magnitude. They show no control on the alteration products related to meteoric water flow, which suggests that these shear-enhanced compaction bands have no or only negligible influence on subsurface fluid flow. Their selective occurrence and small (20%) reduction in transmissibility in densely populated layers prevented them from compartmentalizing the sandstone reservoirs. A comparison with compaction-band populations in the Navajo and Aztec sandtsones (western U.S.) emphasizes the role of burial depth and the presence of chemical compaction processes for the sealing potential of deformation bands.

Study of the suitability of a commercial hydroxyapatite powder to obtain sintered compacts for medical applications

NASA Astrophysics Data System (ADS)

Palacio, C.; Jaramillo, D.; Correa, S.; Arroyave, M.

2017-06-01

Hydroxyapatite (HA) is a material widely used by the medical community due to its Ca/P ratio is comparable to the Ca/P ratio of bones and teeth, which promotes osteoinduction and osteoconduction processes when in contact with bone tissue, either as volume piece or coating. This work focuses on studying the quality of the commercial HA powder MKnano-#MKN-HXAP-S12 µm, after processing, to obtain sintered compact discs with suitable physical and chemical characteristics for implants applications. The HA powder was processed through calcination, grinding, pressing and sintering to evaluate the effect of such as procedures in the compacts dics quality. The raw powder was characterized by laser diffraction, SEM, XRF, XRD, TGA and DSC while the characteristics of the obtained compact discs were determined by dilatometry and XRD to identify the sintering temperature range, constituent phases, the amorphous content and the crystallinity degree, parameters that allow determining their suitability for implants applications. Although, it was not possible to obtain sintered compacts with the suitable chemical composition and without fractures, this work allowed to identify the parameters that determine the suitability of a HA powder to obtain sintered compacts for medical applications, as well as the characterization protocol that allows the evaluation of such parameters.

Hurricane Katrina sediment slowed elevation loss in subsiding brackish marshes of the Mississippi River delta

USGS Publications Warehouse

McKee, K.L.; Cherry, J.A.

2009-01-01

Although hurricanes can damage or destroy coastal wetlands, they may play a beneficial role in reinvigorating marshes by delivering sediments that raise soil elevations and stimulate organic matter production. Hurricane Katrina altered elevation dynamics of two subsiding brackish marshes in the Mississippi River deltaic plain by adding 3 to 8 cm of sediment to the soil surface in August 2005. Soil elevations at both sites subsequently declined due to continued subsidence, but net elevation gain was still positive at both Pearl River (+1.7 cm) and Big Branch (+0.7 cm) marshes two years after the hurricane. At Big Branch where storm sediments had higher organic matter and water contents, post-storm elevation loss was more rapid due to initial compaction of the storm layer in combination with root-zone collapse. In contrast, elevation loss was slower at Pearl River where the storm deposit (high sand content) did not compact and the root zone did not collapse. Vegetation at both sites fully recovered within one year, and accumulation of root matter at Big Branch increased 10-fold from 2005 to 2006, suggesting that the hurricane stimulated belowground productivity. Results of this study imply that hurricane sediment may benefit subsiding marshes by slowing elevation loss. However, long-term effects of hurricane sediment on elevation dynamics will depend not only on the amount of sediment deposited, but on sediment texture and resistance to compaction as well as on changes in organic matter accumulation in the years following the hurricane.

Feasibility study of a cyclotron complex for hadron therapy

NASA Astrophysics Data System (ADS)

Smirnov, V.; Vorozhtsov, S.

2018-04-01

An accelerator complex for hadron therapy based on a chain of cyclotrons is under development at JINR (Dubna, Russia), and the corresponding conceptual design is under preparation. The complex mainly consists of two superconducting cyclotrons. The first accelerator is a compact cyclotron used as an injector to the main accelerator, which is a six-fold separated sector machine. The facility is intended for generation of protons and carbon beams. The H2+ and 12C6+ ions from the corresponding ECR ion sources are accelerated in the injector-cyclotron up to the output energy of 70 MeV/u. Then, the H2+ ions are extracted from the injector by a stripping foil, and the resulting proton beam with the energy of 70 MeV is used for medical purposes. After acceleration in the main cyclotron, the carbon beam can be either used directly for therapy or introduced to the main cyclotron for obtaining the final energy of 400 MeV/u. The basic requirements to the project are the following: compliance to medical requirements, compact size, feasible design, and high reliability of all systems of the complex. The advantages of the dual cyclotron design can help reaching these goals. The initial calculations show that this design is technically feasible with acceptable beam dynamics. The accelerator complex with a relatively compact size can be a good solution for medical applications. The basic parameters of the facility and detailed investigation of the magnetic system and beam dynamics are described.

Fabry-Perot confocal resonator optical associative memory

NASA Astrophysics Data System (ADS)

Burns, Thomas J.; Rogers, Steven K.; Vogel, George A.

1993-03-01

A unique optical associative memory architecture is presented that combines the optical processing environment of a Fabry-Perot confocal resonator with the dynamic storage and recall properties of volume holograms. The confocal resonator reduces the size and complexity of previous associative memory architectures by folding a large number of discrete optical components into an integrated, compact optical processing environment. Experimental results demonstrate the system is capable of recalling a complete object from memory when presented with partial information about the object. A Fourier optics model of the system's operation shows it implements a spatially continuous version of a discrete, binary Hopfield neural network associative memory.

Geometrical optics design of a compact range Gregorian subreflector system by the principle of the central ray

NASA Technical Reports Server (NTRS)

Clerici, Giancarlo; Burnside, Walter D.

1989-01-01

In recent years, the compact range has become very popular for measuring Radar Cross Section (RCS) and antenna patterns. The compact range, in fact, offers several advantages due to reduced size, a controlled environment, and privacy. On the other hand, it has some problems of its own, which must be solved properly in order to achieve high quality measurement results. For example, diffraction from the edges of the main reflector corrupts the plane wave in the target zone and creates spurious scattering centers in RCS measurements. While diffraction can be minimized by using rolled edges, the field of an offset single reflector compact range is corrupted by three other errors: the taper of the reflected field, the cross polarization introduced by the tilt of the feed and the aperture blockage introduced by the feed itself. These three errors can be eliminated by the use of a subreflector system. A properly designed subreflector system offers very little aperture blockage, no cross-polarization introduced and a minimization of the taper of the reflected field. A Gregorian configuration has been adopted in order to enclose the feed and the ellipsoidal subreflector in a lower chamber, which is isolated by absorbers from the upper chamber, where the main parabolic reflector and the target zone are enclosed. The coupling between the two rooms is performed through a coupling aperture. The first cut design for such a subreflector system is performed through Geometrical Optics ray tracing techniques (GO), and is greatly simplified by the use of the concept of the central ray introduced by Dragone. The purpose of the GO design is to establish the basic dimensions of the main reflector and subreflector, the size of the primary and secondary illuminating surfaces, the tilt angles of the subreflector and feed, and estimate the feed beamwidth. At the same time, the shape of the coupling aperture is initially determined.

Studies of compact objects with Einstein - Review and prospects

NASA Technical Reports Server (NTRS)

Grindlay, Jonathan E.

1990-01-01

X-ray images and spectra of a wide range of systems containing compact objects were obtained with the Einstein X-ray Observatory. Accreting white dwarfs, neutron stars and black holes were observed in binary systems in the Galaxy, and new constraints were derived for their formation, nature and evolution. Massive black holes were studied in active galactic nuclei, and X-ray spectra (and evolution) of AGN have led to a new model for the diffuse X-ray background.

Long Range Materials Research

DTIC Science & Technology

1976-01-01

the "weight In water -weight In air" method. The compact Is first weighed dry and then weighed while Immersed completely In water . The density was...calculated from the following: (Wdry) ^ compact W. - W dry wet (1) where P^-o ^8 ’^ density of water corrected for temperature. The weight wet...PPh9) ’"NXV 2 (4) ’ X CH20TS + EtO e These bonds are easily cleaved by water and alcohols . Thererore, it should be possible to

Compaction Control of Earth-Rock Mixtures

DTIC Science & Technology

1991-08-01

specifications have avoided dealing with the full-scale materials. For example, the specified range for water contenz and the value of minimum de - sired percent...Record Samples taken from that embankment or concerning the satisfactory result sof tets perfornt d on t lous. s c p s relative to de ~sgn r, q:.irements...precision of the compaction test provided that the lines of optimums of the families of curves are neatly de - fined. That is to say that the

Compact near-IR and mid-IR cavity ring down spectroscopy device

NASA Technical Reports Server (NTRS)

Miller, J. Houston (Inventor)

2011-01-01

This invention relates to a compact cavity ring down spectrometer for detection and measurement of trace species in a sample gas using a tunable solid-state continuous-wave mid-infrared PPLN OPO laser or a tunable low-power solid-state continuous wave near-infrared diode laser with an algorithm for reducing the periodic noise in the voltage decay signal which subjects the data to cluster analysis or by averaging of the interquartile range of the data.

``Sequence space soup'' of proteins and copolymers

NASA Astrophysics Data System (ADS)

Chan, Hue Sun; Dill, Ken A.

1991-09-01

To study the protein folding problem, we use exhaustive computer enumeration to explore ``sequence space soup,'' an imaginary solution containing the ``native'' conformations (i.e., of lowest free energy) under folding conditions, of every possible copolymer sequence. The model is of short self-avoiding chains of hydrophobic (H) and polar (P) monomers configured on the two-dimensional square lattice. By exhaustive enumeration, we identify all native structures for every possible sequence. We find that random sequences of H/P copolymers will bear striking resemblance to known proteins: Most sequences under folding conditions will be approximately as compact as known proteins, will have considerable amounts of secondary structure, and it is most probable that an arbitrary sequence will fold to a number of lowest free energy conformations that is of order one. In these respects, this simple model shows that proteinlike behavior should arise simply in copolymers in which one monomer type is highly solvent averse. It suggests that the structures and uniquenesses of native proteins are not consequences of having 20 different monomer types, or of unique properties of amino acid monomers with regard to special packing or interactions, and thus that simple copolymers might be designable to collapse to proteinlike structures and properties. A good strategy for designing a sequence to have a minimum possible number of native states is to strategically insert many P monomers. Thus known proteins may be marginally stable due to a balance: More H residues stabilize the desired native state, but more P residues prevent simultaneous stabilization of undesired native states.

Hexafluoroisopropanol-induced helix-sheet transition of stem bromelain: correlation to function.

PubMed

Dave, Sandeep; Dkhar, H Kitdorlang; Singh, Manvendra Pratap; Gupta, Garima; Chandra, Vemika; Mahajan, Sahil; Gupta, Pawan

2010-06-01

Stem bromelain is a proteolytic phytoprotein with a variety of therapeutic effects. Understanding its structural properties could provide insight into the mechanisms underlying its clinical utility. Stem bromelain was evaluated for its conformational and folding properties at the pH conditions it encounters when administered orally. It exists as a partially folded intermediate at pH 2.0. The conformational changes to this intermediate state were evaluated using fluorinated alcohols known to induce changes similar to those seen in vivo. Studies using circular dichroism, fluorescence emission spectroscopy, binding of the hydrophobic dye 1-anilino-8-naphthalene sulfonic acid and mass spectrometry indicate that treatment with 10-30% hexafluoroisopropanol induces the partially folded intermediate to adopt much of the native protein's secondary structure, but only a rudimentary tertiary structure, characteristic of the molten globule state. Addition of slightly higher concentrations of hexafluoroisopropanol caused transformation from an alpha-helix to a beta-sheet and induced formation of a compact nonnative structure. This nonnative form was more inhibitory of cell survival than either the native or the partially folded intermediate forms, as measured by enhanced suppression of proliferative cues (e.g., extracellular-signal-regulated kinase) and initiation of apoptotic events. The nonnative form also showed better antitumorigenic properties, as evaluated using an induced two-stage mouse skin papilloma model. In contrast, the nonnative state showed only a fraction of the proteolytic activity of the native form. This study demonstrates that hexafluoroisopropanol can induce a conformational change in stem bromelain to a form with potentially useful therapeutic properties different from those of the native protein. Copyright 2010 Elsevier Ltd. All rights reserved.

Powder metallurgy technology of NiTi shape memory alloy

NASA Astrophysics Data System (ADS)

Dutkiewicz, J. M.; Maziarz, W.; Czeppe, T.; Lityńska, L.; Nowacki, W. K.; Gadaj, S. P.; Luckner, J.; Pieczyska, E. A.

2008-05-01

Powder metallurgy technology was elaborated for consolidation of shape memory NiTi powders. The shape memory alloy was compacted from the prealloyed powder delivered by Memry SA. The powder shows Ms = 10°C and As = -34°C as results from DSC measurements. The samples were hot pressed in the as delivered spherical particle's state. The hot compaction was performed in a specially constructed vacuum press, at temperature of 680°C and pressure of 400 MPa. The alloy powder was encapsulated in copper capsules prior to hot pressing to avoid oxidation or carbides formation. The alloy after hot vacuum compaction at 680°C (i.e. within the B2 NiTi stability range) has shown similar transformation range as the powder. The porosity of samples compacted in the as delivered state was only 1%. The samples tested in compression up to ɛ = 0.06 have shown partial superelastic effect due to martensitic reversible transform- ation which started at the stress above 300 MPa and returned back to ɛ = 0.015 after unloading. They have shown also a high ultimate compression strength of 1600 MPa. Measurements of the samples temperature changes during the process allowed to detect the temperature increase above 12°C for the strain rate 10-2 s-1 accompanied the exothermic martensite transformation during loading and the temperature decrease related to the reverse endothermic transformation during unloading.

Compact hydrogen production systems for solid polymer fuel cells

NASA Astrophysics Data System (ADS)

Ledjeff-Hey, K.; Formanski, V.; Kalk, Th.; Roes, J.

Generally there are several ways to produce hydrogen gas from carbonaceous fuels like natural gas, oil or alcohols. Most of these processes are designed for large-scale industrial production and are not suitable for a compact hydrogen production system (CHYPS) in the power range of 1 kW. In order to supply solid polymer fuel cells (SPFC) with hydrogen, a compact fuel processor is required for mobile applications. The produced hydrogen-rich gas has to have a low level of harmful impurities; in particular the carbon monoxide content has to be lower than 20 ppmv. Integrating the reaction step, the gas purification and the heat supply leads to small-scale hydrogen production systems. The steam reforming of methanol is feasible at copper catalysts in a low temperature range of 200-350°C. The combination of a small-scale methanol reformer and a metal membrane as purification step forms a compact system producing high-purity hydrogen. The generation of a SPFC hydrogen fuel gas can also be performed by thermal or catalytic cracking of liquid hydrocarbons such as propane. At a temperature of 900°C the decomposition of propane into carbon and hydrogen takes place. A fuel processor based on this simple concept produces a gas stream with a hydrogen content of more than 90 vol.% and without CO and CO2.

Atomic-level description of ubiquitin folding

PubMed Central

Piana, Stefano; Lindorff-Larsen, Kresten; Shaw, David E.

2013-01-01

Equilibrium molecular dynamics simulations, in which proteins spontaneously and repeatedly fold and unfold, have recently been used to help elucidate the mechanistic principles that underlie the folding of fast-folding proteins. The extent to which the conclusions drawn from the analysis of such proteins, which fold on the microsecond timescale, apply to the millisecond or slower folding of naturally occurring proteins is, however, unclear. As a first attempt to address this outstanding issue, we examine here the folding of ubiquitin, a 76-residue-long protein found in all eukaryotes that is known experimentally to fold on a millisecond timescale. Ubiquitin folding has been the subject of many experimental studies, but its slow folding rate has made it difficult to observe and characterize the folding process through all-atom molecular dynamics simulations. Here we determine the mechanism, thermodynamics, and kinetics of ubiquitin folding through equilibrium atomistic simulations. The picture emerging from the simulations is in agreement with a view of ubiquitin folding suggested from previous experiments. Our findings related to the folding of ubiquitin are also consistent, for the most part, with the folding principles derived from the simulation of fast-folding proteins, suggesting that these principles may be applicable to a wider range of proteins. PMID:23503848

Nuclear Power in Space.

ERIC Educational Resources Information Center

Department of Energy, Washington, DC. Nuclear Energy Office.

Research has shown that nuclear radioisotope power generators can supply compact, reliable, and efficient sources of energy for a broad range of space missions. These missions range from televising views of planetary surfaces to communicating scientific data to Earth. This publication presents many applications of the advancing technology and…

Novel, ultra-compact, high-performance, eye-safe laser rangefinder for demanding applications

NASA Astrophysics Data System (ADS)

Silver, M.; Lee, S. T.; Borthwick, A.; Morton, G.; McNeill, C.; McSporran, D.; McRae, I.; McKinlay, G.; Jackson, D.; Alexander, W.

2016-05-01

Compact eye-safe laser rangefinders (LRFs) are a key technology for future sensors. In addition to reduced size, weight and power (SWaP), compact LRFs are increasingly being required to deliver a higher repetition rate, burst mode capability. Burst mode allows acquisition of telemetry data from fast moving targets or while sensing-on-the-move. We will describe a new, ultra-compact, long-range, eye-safe laser rangefinder that incorporates a novel transmitter that can deliver a burst capability. The transmitter is a diode-pumped, erbium:glass, passively Q-switched, solid-state laser which uses design and packaging techniques adopted from the telecom components sector. The key advantage of this approach is that the transmitter can be engineered to match the physical dimensions of the active laser components and the submillimetre sized laser spot. This makes the transmitter significantly smaller than existing designs, leading to big improvements in thermal management, and allowing higher repetition rates. In addition, the design approach leads to devices that have higher reliability, lower cost, and smaller form-factor, than previously possible. We present results from the laser rangefinder that incorporates the new transmitter. The LRF has dimensions (L x W x H) of 100 x 55 x 34 mm and achieves ranges of up to 15km from a single shot, and over a temperature range of -32°C to +60°C. Due to the transmitter's superior thermal performance, the unit is capable of repetition rates of 1Hz continuous operation and short bursts of up to 4Hz. Short bursts of 10Hz have also been demonstrated from the transmitter in the laboratory.

A study of radar cross section measurement techniques

NASA Technical Reports Server (NTRS)

Mcdonald, Malcolm W.

1986-01-01

Past, present, and proposed future technologies for the measurement of radar cross section were studied. The purpose was to determine which method(s) could most advantageously be implemented in the large microwave anechoic chamber facility which is operated at the antenna test range site. The progression toward performing radar cross section measurements of space vehicles with which the Orbital Maneuvering Vehicle will be called upon to rendezvous and dock is a natural outgrowth of previous work conducted in recent years of developing a high accuracy range and velocity sensing radar system. The radar system was designed to support the rendezvous and docking of the Orbital Maneuvering Vehicle with various other space vehicles. The measurement of radar cross sections of space vehicles will be necessary in order to plan properly for Orbital Maneuvering Vehicle rendezvous and docking assignments. The methods which were studied include: standard far-field measurements; reflector-type compact range measurements; lens-type compact range measurement; near field/far field transformations; and computer predictive modeling. The feasibility of each approach is examined.

Compact FPGA-based beamformer using oversampled 1-bit A/D converters.

PubMed

Tomov, Borislav Gueorguiev; Jensen, Jørgen Arendt

2005-05-01

A compact medical ultrasound beamformer architecture that uses oversampled 1-bit analog-to-digital (A/D) converters is presented. Sparse sample processing is used, as the echo signal for the image lines is reconstructed in 512 equidistant focal points along the line through its in-phase and quadrature components. That information is sufficient for presenting a B-mode image and creating a color flow map. The high sampling rate provides the necessary delay resolution for the focusing. The low channel data width (1-bit) makes it possible to construct a compact beamformer logic. The signal reconstruction is done using finite impulse reponse (FIR) filters, applied on selected bit sequences of the delta-sigma modulator output stream. The approach allows for a multichannel beamformer to fit in a single field programmable gate array (FPGA) device. A 32-channel beamformer is estimated to occupy 50% of the available logic resources in a commercially available mid-range FPGA, and to be able to operate at 129 MHz. Simulation of the architecture at 140 MHz provides images with a dynamic range approaching 60 dB for an excitation frequency of 3 MHz.

Evaluation of expansion algorithm of measurement range suited for 3D shape measurement using two pitches of projected grating with light source-stepping method

NASA Astrophysics Data System (ADS)

Sakaguchi, Toshimasa; Fujigaki, Motoharu; Murata, Yorinobu

2015-03-01

Accurate and wide-range shape measurement method is required in industrial field. The same technique is possible to be used for a shape measurement of a human body for the garment industry. Compact 3D shape measurement equipment is also required for embedding in the inspection system. A shape measurement by a phase shifting method can measure the shape with high spatial resolution because the coordinates can be obtained pixel by pixel. A key-device to develop compact equipment is a grating projector. Authors developed a linear LED projector and proposed a light source stepping method (LSSM) using the linear LED projector. The shape measurement euipment can be produced with low-cost and compact without any phase-shifting mechanical systems by using this method. Also it enables us to measure 3D shape in very short time by switching the light sources quickly. A phase unwrapping method is necessary to widen the measurement range with constant accuracy for phase shifting method. A general phase unwrapping method with difference grating pitches is often used. It is one of a simple phase unwrapping method. It is, however, difficult to apply the conventional phase unwrapping algorithm to the LSSM. Authors, therefore, developed an expansion unwrapping algorithm for the LSSM. In this paper, an expansion algorithm of measurement range suited for 3D shape measurement using two pitches of projected grating with the LSSM was evaluated.

Self-folding origami at any energy scale

NASA Astrophysics Data System (ADS)

Pinson, Matthew B.; Stern, Menachem; Carruthers Ferrero, Alexandra; Witten, Thomas A.; Chen, Elizabeth; Murugan, Arvind

2017-05-01

Programmable stiff sheets with a single low-energy folding motion have been sought in fields ranging from the ancient art of origami to modern meta-materials research. Despite such attention, only two extreme classes of crease patterns are usually studied; special Miura-Ori-based zero-energy patterns, in which crease folding requires no sheet bending, and random patterns with high-energy folding, in which the sheet bends as much as creases fold. We present a physical approach that allows systematic exploration of the entire space of crease patterns as a function of the folding energy. Consequently, we uncover statistical results in origami, finding the entropy of crease patterns of given folding energy. Notably, we identify three classes of Mountain-Valley choices that have widely varying `typical' folding energies. Our work opens up a wealth of experimentally relevant self-folding origami designs not reliant on Miura-Ori, the Kawasaki condition or any special symmetry in space.

Beam-based measurements of long-range transverse wakefields in the Compact Linear Collider main-linac accelerating structure

DOE PAGES

Zha, Hao; Latina, Andrea; Grudiev, Alexej; ...

2016-01-20

The baseline design of CLIC (Compact Linear Collider) uses X-band accelerating structures for its main linacs. In order to maintain beam stability in multibunch operation, long-range transverse wakefields must be suppressed by 2 orders of magnitude between successive bunches, which are separated in time by 0.5 ns. Such strong wakefield suppression is achieved by equipping every accelerating structure cell with four damping waveguides terminated with individual rf loads. A beam-based experiment to directly measure the effectiveness of this long-range transverse wakefield and benchmark simulations was made in the FACET test facility at SLAC using a prototype CLIC accelerating structure. Furthermore,more » the experiment showed good agreement with the simulations and a strong suppression of the wakefields with an unprecedented minimum resolution of 0.1 V/(pC mm m).« less

High-harmonic generation in amorphous solids

DOE Office of Scientific and Technical Information (OSTI.GOV)

You, Yong Sing; Yin, Yanchun; Wu, Yi

High-harmonic generation in isolated atoms and molecules has been widely utilized in extreme ultraviolet photonics and attosecond pulse metrology. Recently, high-harmonic generation has been observed in solids, which could lead to important applications such as all-optical methods to image valance charge density and reconstruct electronic band structures, as well as compact extreme ultraviolet light sources. So far these studies are confined to crystalline solids; therefore, decoupling the respective roles of long-range periodicity and high density has been challenging. Here we report the observation of high-harmonic generation from amorphous fused silica. We also decouple the role of long-range periodicity by comparingmore » harmonics generated from fused silica and crystalline quartz, which contain the same atomic constituents but differ in long-range periodicity. These results advance current understanding of the strong-field processes leading to high-harmonic generation in solids with implications for the development of robust and compact extreme ultraviolet light sources.« less

High-harmonic generation in amorphous solids

DOE PAGES

You, Yong Sing; Yin, Yanchun; Wu, Yi; ...

2017-09-28

High-harmonic generation in isolated atoms and molecules has been widely utilized in extreme ultraviolet photonics and attosecond pulse metrology. Recently, high-harmonic generation has been observed in solids, which could lead to important applications such as all-optical methods to image valance charge density and reconstruct electronic band structures, as well as compact extreme ultraviolet light sources. So far these studies are confined to crystalline solids; therefore, decoupling the respective roles of long-range periodicity and high density has been challenging. Here we report the observation of high-harmonic generation from amorphous fused silica. We also decouple the role of long-range periodicity by comparingmore » harmonics generated from fused silica and crystalline quartz, which contain the same atomic constituents but differ in long-range periodicity. These results advance current understanding of the strong-field processes leading to high-harmonic generation in solids with implications for the development of robust and compact extreme ultraviolet light sources.« less

Optimized scalable network switch

DOEpatents

Blumrich, Matthias A [Ridgefield, CT; Chen, Dong [Croton On Hudson, NY; Coteus, Paul W [Yorktown Heights, NY; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Steinmacher-Burow, Burkhard D [Mount Kisco, NY; Takken, Todd E [Mount Kisco, NY; Vranas, Pavlos M [Bedford Hills, NY

2007-12-04

In a massively parallel computing system having a plurality of nodes configured in m multi-dimensions, each node including a computing device, a method for routing packets towards their destination nodes is provided which includes generating at least one of a 2m plurality of compact bit vectors containing information derived from downstream nodes. A multilevel arbitration process in which downstream information stored in the compact vectors, such as link status information and fullness of downstream buffers, is used to determine a preferred direction and virtual channel for packet transmission. Preferred direction ranges are encoded and virtual channels are selected by examining the plurality of compact bit vectors. This dynamic routing method eliminates the necessity of routing tables, thus enhancing scalability of the switch.

Optimized scalable network switch

DOEpatents

Blumrich, Matthias A.; Chen, Dong; Coteus, Paul W.

2010-02-23

In a massively parallel computing system having a plurality of nodes configured in m multi-dimensions, each node including a computing device, a method for routing packets towards their destination nodes is provided which includes generating at least one of a 2m plurality of compact bit vectors containing information derived from downstream nodes. A multilevel arbitration process in which downstream information stored in the compact vectors, such as link status information and fullness of downstream buffers, is used to determine a preferred direction and virtual channel for packet transmission. Preferred direction ranges are encoded and virtual channels are selected by examining the plurality of compact bit vectors. This dynamic routing method eliminates the necessity of routing tables, thus enhancing scalability of the switch.

Silica-based, compact and variable-optical-attenuator integrated coherent receiver with stable optoelectronic coupling system.

PubMed

Tsunashima, Satoshi; Nakajima, Fumito; Nasu, Yusuke; Kasahara, Ryoichi; Nakanishi, Yasuhiko; Saida, Takashi; Yamada, Takashi; Sano, Kimikazu; Hashimoto, Toshikazu; Fukuyama, Hiroyuki; Nosaka, Hideaki; Murata, Koichi

2012-11-19

We demonstrate a compact and variable-optical-attenuator (VOA) integrated coherent receiver with a silica-based planar lightwave circuit (PLC). To realize the compact receiver, we integrate a VOA in a single PLC chip with polarization beam splitters and optical 90-degree hybrids, and employ a stable optoelectronic coupling system consisting of micro lens arrays and photodiode (PD) subcarriers with high-speed right-angled signal lines. We integrate a VOA and a coherent receiver in a 27x40x6 mm package, and successfully demodulate a 128-Gbit/s polarization division multiplexed (PDM) quadrature phase shift keying (QPSK) signal with a VOA-assisted wide dynamic range of more than 30 dB.

Rapid variability, dying pulse trains and black holes

NASA Technical Reports Server (NTRS)

Stoeger, W. R.

1980-01-01

After reviewing the general model and arguments by which rapid temporal variability and quasi-periodicities are considered indicative of a compact source's possible black hole character, the paper presents a scenario for 'dying pulse trains'. These originate inside the inner edge of accretion disks encircling black holes from accreting flares or other self-luminous entities executing their final few revolutions before reaching the event horizon. Confirmed detection of such phenomena with time scales in the range 0.01 (M/solar mass) to 0.5 (M/solar mass)ms, where M is the mass of the compact source, would provide much better support for its black hole candidacy. Variability on time-scales larger than this by itself places few constraints on the nature of the compact object.

A new surface-potential-based compact model for the MoS2 field effect transistors in active matrix display applications

NASA Astrophysics Data System (ADS)

Cao, Jingchen; Peng, Songang; Liu, Wei; Wu, Quantan; Li, Ling; Geng, Di; Yang, Guanhua; Ji, Zhouyu; Lu, Nianduan; Liu, Ming

2018-02-01

We present a continuous surface-potential-based compact model for molybdenum disulfide (MoS2) field effect transistors based on the multiple trapping release theory and the variable-range hopping theory. We also built contact resistance and velocity saturation models based on the analytical surface potential. This model is verified with experimental data and is able to accurately predict the temperature dependent behavior of the MoS2 field effect transistor. Our compact model is coded in Verilog-A, which can be implemented in a computer-aided design environment. Finally, we carried out an active matrix display simulation, which suggested that the proposed model can be successfully applied to circuit design.

Symmetric waterbomb origami.

PubMed

Chen, Yan; Feng, Huijuan; Ma, Jiayao; Peng, Rui; You, Zhong

2016-06-01

The traditional waterbomb origami, produced from a pattern consisting of a series of vertices where six creases meet, is one of the most widely used origami patterns. From a rigid origami viewpoint, it generally has multiple degrees of freedom, but when the pattern is folded symmetrically, the mobility reduces to one. This paper presents a thorough kinematic investigation on symmetric folding of the waterbomb pattern. It has been found that the pattern can have two folding paths under certain circumstance. Moreover, the pattern can be used to fold thick panels. Not only do the additional constraints imposed to fold the thick panels lead to single degree of freedom folding, but the folding process is also kinematically equivalent to the origami of zero-thickness sheets. The findings pave the way for the pattern being readily used to fold deployable structures ranging from flat roofs to large solar panels.

Periodic folding of viscous sheets

NASA Astrophysics Data System (ADS)

Ribe, Neil M.

2003-09-01

The periodic folding of a sheet of viscous fluid falling upon a rigid surface is a common fluid mechanical instability that occurs in contexts ranging from food processing to geophysics. Asymptotic thin-layer equations for the combined stretching-bending deformation of a two-dimensional sheet are solved numerically to determine the folding frequency as a function of the sheet’s initial thickness, the pouring speed, the height of fall, and the fluid properties. As the buoyancy increases, the system bifurcates from “forced” folding driven kinematically by fluid extrusion to “free” folding in which viscous resistance to bending is balanced by buoyancy. The systematics of the numerically predicted folding frequency are in good agreement with laboratory experiments.

Dustiness behaviour of loose and compacted Bentonite and organoclay powders: What is the difference in exposure risk?

NASA Astrophysics Data System (ADS)

Jensen, Keld Alstrup; Koponen, Ismo Kalevi; Clausen, Per Axel; Schneider, Thomas

2009-01-01

Single-drop and rotating drum dustiness testing was used to investigate the dustiness of loose and compacted montmorillonite (Bentonite) and an organoclay (Nanofil®5), which had been modified from montmorillonite-rich Bentonite. The dustiness was analysed based on filter measurements as well as particle size distributions, the particle generation rate, and the total number of generated particles. Particle monitoring was completed using a TSI Fast Mobility Particle Sizer (FMPS) and a TSI Aerosol Particle Sizer (APS) at 1 s resolution. Low-pressure uniaxial powder compaction of the starting materials showed a logarithmic compaction curve and samples subjected to 3.5 kg/cm2 were used for dustiness testing to evaluate the role of powder compaction, which could occur in powders from large shipments or high-volume storage facilities. The dustiness tests showed intermediate dustiness indices (1,077-2,077 mg/kg powder) in tests of Nanofil®5, Bentonite, and compacted Bentonite, while a high-level dustiness index was found for compacted Nanofil®5 (3,487 mg/kg powder). All powders produced multimodal particle size-distributions in the dust cloud with one mode around 300 nm (Bentonite) or 400 nm (Nanofil®5) as well as one (Nanofil®5) or two modes (Bentonite) with peaks between 1 and 2.5 μm. The dust release was found to occur either as a burst (loose Bentonite and Nanofil®5), constant rate (compacted Nanofil®5), or slowly increasing rate (compacted Bentonite). In rotating drum experiments, the number of particles generated in the FMPS and APS size-ranges were in general agreement with the mass-based dustiness index, but the same order was not observed in the single-drop tests. Compaction of Bentonite reduced the number of generated particles with app. 70 and 40% during single-drop and rotating drum dustiness tests, respectively. Compaction of Nanofil®5 reduced the dustiness in the single-drop test, but it was more than doubled in the rotating drum test. Physically relevant low-pressure compaction may reduce the risk of particle exposure if powders are handled in operations with few agitations such as pouring or tapping. Repeated agitation, e.g., mixing, of these compacted powders, would result in reduced (app. 20% for Bentonite) or highly increased (app. 225% for Nanofil®5) dustiness and thereby alter the exposure risk significantly.

Tunable continuous-wave terahertz generation/detection with compact 1.55 μm detuned dual-mode laser diode and InGaAs based photomixer.

PubMed

Kim, Namje; Han, Sang-Pil; Ko, Hyunsung; Leem, Young Ahn; Ryu, Han-Cheol; Lee, Chul Wook; Lee, Donghun; Jeon, Min Yong; Noh, Sam Kyu; Park, Kyung Hyun

2011-08-01

We demonstrate a tunable continuous-wave (CW) terahertz (THz) homodyne system with a novel detuned dual-mode laser diode (DML) and low-temperature-grown (LTG) InGaAs photomixers. The optical beat source with the detuned DML showed a beat frequency tuning range of 0.26 to over 1.07 THz. Log-spiral antenna integrated LTG InGaAs photomixers are used as THz wave generators and detectors. The CW THz radiation frequency was continuously tuned to over 1 THz. Our results clearly show the feasibility of a compact and fast scanning CW THz spectrometer consisting of a fiber-coupled detuned DML and photomixers operating in the 1.55-μm range.

Properties of soil in the San Fernando hydraulic fill dams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, K.L.

1975-08-01

Results are presented of extensive field and laboratory tests on soils from two old hydraulic fill dams that were damaged during the Feb. 9, 1971, San Fernando earthquake. The data include standard penetration, absolute and relative compaction, relative density, static strength, and cyclic triaxial test results for both the hydraulic fill silty sand and the natural silty and gravelly sand alluvium. The relative densities of the hydraulic fills ranged from about 51 to 58 percent and the relative compaction ranged from about 85 to 92 percent of Modified AASHO maximum density. The relative density of the alluvium was about 65more » to 70 percent. Other properties were consistent with previously published data from other similar soils at similar densities.« less

Low cost and compact quantum key distribution

NASA Astrophysics Data System (ADS)

Duligall, J. L.; Godfrey, M. S.; Harrison, K. A.; Munro, W. J.; Rarity, J. G.

2006-10-01

We present the design of a novel free-space quantum cryptography system, complete with purpose-built software, that can operate in daylight conditions. The transmitter and receiver modules are built using inexpensive off-the-shelf components. Both modules are compact allowing the generation of renewed shared secrets on demand over a short range of a few metres. An analysis of the software is shown as well as results of error rates and therefore shared secret yields at varying background light levels. As the system is designed to eventually work in short-range consumer applications, we also present a use scenario where the consumer can regularly 'top up' a store of secrets for use in a variety of one-time-pad (OTP) and authentication protocols.

High temperature structural insulating material

DOEpatents

Chen, W.Y.

1984-07-27

A high temperature structural insulating material useful as a liner for cylinders of high temperature engines through the favorable combination of high service temperature (above about 800/sup 0/C), low thermal conductivity (below about 0.2 W/m/sup 0/C), and high compressive strength (above about 250 psi). The insulating material is produced by selecting hollow ceramic beads with a softening temperature above about 800/sup 0/C, a diameter within the range of 20-200 ..mu..m, and a wall thickness in the range of about 2 to 4 ..mu..m; compacting the beads and a compatible silicate binder composition under pressure and sintering conditions to provide the desired structural form with the structure having a closed-cell, compact array of bonded beads.

Assessment of the Polycyclic Aromatic Hydrocarbon-Diffuse Interstellar Band Proposal

NASA Technical Reports Server (NTRS)

Salama, Farid; Bakes, F.; Allamandola, L.; Tielens, A. G. G. M.; Witteborn, Fred C. (Technical Monitor)

1995-01-01

The potential link between neutral and/or ionized polycyclic aromatic hydrocarbons (PAHs) and the diffuse interstellar band (DIB) carriers is examined. Based on the study of the general physical and chemical properties of PAHs, an assessment is made of their possible contribution to the DIB carriers. It is found that, under the conditions reigning in the diffuse interstellar medium, PAHs can be present in the form of neutral molecules as well as positive and/or negative ions. The charge distribution of small PAHs is dominated, however, by two charge states at one time with compact PAHs present only in the neutral and cationic forms. Each PAH has a distinct spectral signature depending on its charge state. Moreover, the spectra of ionized PAHs are always clearly dominated by a single band in the DIB spectral range. In the case of compact PAH ions, the strongest absorption band is of type A (i.e., the band is broad, falls in the high energy range of the spectrum, and possess a large oscillator strength), and seems to correlate with strong and broad DIBs. In the case of non-compact PAH ions, the strongest absorption band is of type I (i.e., the band is narrow, falls in the low energy range of the spectrum, and possess a small oscillator strength), and seems to correlate with weak and narrow DIBs. Potential molecular size and structure constraints for interstellar PAHs are derived by comparing known DIB characteristics to the spectroscopic properties of PAHs. It is found that: (i) Only neutral PAHs larger than about 30 carbon atoms could, if present, contribute to the DIBs. (ii) For compact PAHs, only ions with less than about 250 carbon atoms could, if present, contribute to the DIBs. (iii) The observed distribution of the DIBs between strong/moderate and broad bands on the one hand and weak and narrow bands on the other hand can easily be interpreted in the context of the PAH proposal by a distribution between compact and non-compact PAH ions, respectively. A plausible correlation between PAH charge states and DIB "families" is thus provided by the PAH-DIB proposal. Following this proposal, DIB families would provide tracers of conditions within a cloud which globally determine the relative importance of cations, anions, and neutral species, rather than tracers of a specific species. Observational predictions are given to establish the viability of the PAH hypothesis. It is concluded that small PAH ions are very promising candidates as DIB carriers provided their population is dominated by a finite number (100-200) of species. A key test for the PAH proposal, consisting of laboratory and astronomical investigations of the ultraviolet range, is called for.

Moho topography, ranges and folds of Tibet by analysis of global gravity models and GOCE data

PubMed Central

Shin, Young Hong; Shum, C.K.; Braitenberg, Carla; Lee, Sang Mook; Na, Sung -Ho; Choi, Kwang Sun; Hsu, Houtse; Park, Young-Sue; Lim, Mutaek

2015-01-01

The determination of the crustal structure is essential in geophysics, as it gives insight into the geohistory, tectonic environment, geohazard mitigation, etc. Here we present the latest advance on three-dimensional modeling representing the Tibetan Mohorovičić discontinuity (topography and ranges) and its deformation (fold), revealed by analyzing gravity data from GOCE mission. Our study shows noticeable advances in estimated Tibetan Moho model which is superior to the results using the earlier gravity models prior to GOCE. The higher quality gravity field of GOCE is reflected in the Moho solution: we find that the Moho is deeper than 65 km, which is twice the normal continental crust beneath most of the Qinghai-Tibetan plateau, while the deepest Moho, up to 82 km, is located in western Tibet. The amplitude of the Moho fold is estimated to be ranging from −9 km to 9 km with a standard deviation of ~2 km. The improved GOCE gravity derived Moho signals reveal a clear directionality of the Moho ranges and Moho fold structure, orthogonal to deformation rates observed by GPS. This geophysical feature, clearly more evident than the ones estimated using earlier gravity models, reveals that it is the result of the large compressional tectonic process. PMID:26114224

Distribution of breakage events in random packings of rodlike particles.

PubMed

Grof, Zdeněk; Štěpánek, František

2013-07-01

Uniaxial compaction and breakage of rodlike particle packing has been studied using a discrete element method simulation. A scaling relationship between the applied stress, the number of breakage events, and the number-mean particle length has been derived and compared with computational experiments. Based on results for a wide range of intrinsic particle strengths and initial particle lengths, it seems that a single universal relation can be used to describe the incidence of breakage events during compaction of rodlike particle layers.

Kinematic Dynamo In Turbulent Circumstellar Disks

NASA Technical Reports Server (NTRS)

Stepinski, T.

1993-01-01

Many circumstellar disks associated with objects ranging from protoplanetary nebulae, to accretion disks around compact stars allow for the generation of magnetic fields by an (alpha)omega dynamo. We have applied kinematic dynamo formalism to geometrically thin accretion disks. We calculate, in the framework of an adiabatic approximation, the normal mode solutions for dynamos operating in disks around compact stars. We then describe the criteria for a viable dynamo in protoplanetary nebulae, and discuss the particular features that make accretion disk dynamos different from planetary, stellar, and galactic dynamos.

Self-folding with shape memory composites at the millimeter scale

NASA Astrophysics Data System (ADS)

Felton, S. M.; Becker, K. P.; Aukes, D. M.; Wood, R. J.

2015-08-01

Self-folding is an effective method for creating 3D shapes from flat sheets. In particular, shape memory composites—laminates containing shape memory polymers—have been used to self-fold complex structures and machines. To date, however, these composites have been limited to feature sizes larger than one centimeter. We present a new shape memory composite capable of folding millimeter-scale features. This technique can be activated by a global heat source for simultaneous folding, or by resistive heaters for sequential folding. It is capable of feature sizes ranging from 0.5 to 40 mm, and is compatible with multiple laminate compositions. We demonstrate the ability to produce complex structures and mechanisms by building two self-folding pieces: a model ship and a model bumblebee.

Photonic integrated circuit implementation of a sub-GHz-selectivity frequency comb filter for optical clock multiplication.

PubMed

Geng, Zihan; Xie, Yiwei; Zhuang, Leimeng; Burla, Maurizio; Hoekman, Marcel; Roeloffzen, Chris G H; Lowery, Arthur J

2017-10-30

We report a photonic integrated circuit implementation of an optical clock multiplier, or equivalently an optical frequency comb filter. The circuit comprises a novel topology of a ring-resonator-assisted asymmetrical Mach-Zehnder interferometer in a Sagnac loop, providing a reconfigurable comb filter with sub-GHz selectivity and low complexity. A proof-of-concept device is fabricated in a high-index-contrast stoichiometric silicon nitride (Si 3 N 4 /SiO 2 ) waveguide, featuring low loss, small size, and large bandwidth. In the experiment, we show a very narrow passband for filters of this kind, i.e. a -3-dB bandwidth of 0.6 GHz and a -20-dB passband of 1.2 GHz at a frequency interval of 12.5 GHz. As an application example, this particular filter shape enables successful demonstrations of five-fold repetition rate multiplication of optical clock signals, i.e. from 2.5 Gpulses/s to 12.5 Gpulses/s and from 10 Gpulses/s to 50 Gpulses/s. This work addresses comb spectrum processing on an integrated platform, pointing towards a device-compact solution for optical clock multipliers (frequency comb filters) which have diverse applications ranging from photonic-based RF spectrum scanners and photonic radars to GHz-granularity WDM switches and LIDARs.

Magnetic field detector consisting of magnetic and semiconducting nanoparticles co-assembled in a liquid crystalline matrix

NASA Astrophysics Data System (ADS)

Amaral, Jose; Rodarte, Andrea; Wan, Jacky; Ferri, Christopher; Quint, Makiko; Pandolfi, Ron; Scheibner, Michael; Hirst, Linda; Ghosh, Sayantani

2015-03-01

An exciting area of research is using nano-constituents to create artificial materials that are multifunctional and allow for modification post-fabrication and in situ. We are investigating the ensemble behavior of iron-oxide magnetic nanoparticles (MNPs) and CdSe/ZnS quantum dots (QDs) when dispersed in an electro-optically active liquid crystalline (LC) matrix. The directed assembly of NPs in the matrix is driven by the temperature-induced transition of the LC from the isotropic to the nematic phase as the NPs are mostly expelled into the isotropic regions, finally ending up clustered around LC defect points when the transition is complete. Our results show a two-fold intensity increase of QD photoluminescence intensity with low magnetic fields (less than 100 mT). We speculate this increase is due to MNP rearrangement which produces a compaction of the clusters, resulting in the detection of increased QD emission. The individual components work together to act as a magnetic field detector and since they are direct assembled in a LC medium, they could potentially be used in a wide range of fluid-based applications. This work was funded by NSF grants DMR-1056860 and ECC-1227034. This work was funded by NSF Grants DMR-1056860 and ECC-1227034.

A Planar Microfluidic Mixer Based on Logarithmic Spirals

PubMed Central

Scherr, Thomas; Quitadamo, Christian; Tesvich, Preston; Park, Daniel Sang-Won; Tiersch, Terrence; Hayes, Daniel; Choi, Jin-Woo; Nandakumar, Krishnaswamy

2013-01-01

A passive, planar micromixer design based on logarithmic spirals is presented. The device was fabricated using polydimethylsiloxane soft photolithography techniques, and mixing performance was characterized via numerical simulation and fluorescent microscopy. Mixing efficiency initially declined as Reynolds number increased, and this trend continued until a Reynolds number of 15 where a minimum was reached at 53%. Mixing efficiency then began to increase reaching a maximum mixing efficiency of 86% at Re = 67. Three-dimensional simulations of fluid mixing in this design were compared to other planar geometries such as the Archimedes spiral and Meandering-S mixers. The implementation of logarithmic curvature offers several unique advantages that enhance mixing, namely a variable cross-sectional area and a logarithmically varying radius of curvature that creates 3-D Dean vortices. These flow phenomena were observed in simulations with multilayered fluid folding and validated with confocal microscopy. This design provides improved mixing performance over a broader range of Reynolds numbers than other reported planar mixers, all while avoiding external force fields, more complicated fabrication processes, and the introduction of flow obstructions or cavities that may unintentionally affect sensitive or particulate-containing samples. Due to the planar design requiring only single-step lithographic features, this compact geometry could be easily implemented into existing micro-total analysis systems requiring effective rapid mixing. PMID:23956497

A planar microfluidic mixer based on logarithmic spirals

NASA Astrophysics Data System (ADS)

Scherr, Thomas; Quitadamo, Christian; Tesvich, Preston; Sang-Won Park, Daniel; Tiersch, Terrence; Hayes, Daniel; Choi, Jin-Woo; Nandakumar, Krishnaswamy; Monroe, W. Todd

2012-05-01

A passive, planar micromixer design based on logarithmic spirals is presented. The device was fabricated using polydimethylsiloxane soft photolithography techniques, and mixing performance was characterized via numerical simulation and fluorescent microscopy. Mixing efficiency initially declined as the Reynolds number increased, and this trend continued until a Reynolds number of 15 where a minimum was reached at 53%. Mixing efficiency then began to increase reaching a maximum mixing efficiency of 86% at Re = 67. Three-dimensional (3D) simulations of fluid mixing in this design were compared to other planar geometries such as the Archimedes spiral and Meandering-S mixers. The implementation of logarithmic curvature offers several unique advantages that enhance mixing, namely a variable cross-sectional area and a logarithmically varying radius of curvature that creates 3D Dean vortices. These flow phenomena were observed in simulations with multilayered fluid folding and validated with confocal microscopy. This design provides improved mixing performance over a broader range of Reynolds numbers than other reported planar mixers, all while avoiding external force fields, more complicated fabrication processes and the introduction of flow obstructions or cavities that may unintentionally affect sensitive or particulate-containing samples. Due to the planar design requiring only single-step lithographic features, this compact geometry could be easily implemented into existing micro-total analysis systems requiring effective rapid mixing.

Purification, Characterization, and Functional Role of a Novel Extracellular Protease from Pleurotus ostreatus

PubMed Central

Palmieri, Gianna; Bianco, Carmen; Cennamo, Giovanna; Giardina, Paola; Marino, Gennaro; Monti, Maria; Sannia, Giovanni

2001-01-01

A new extracellular protease (PoSl; Pleurotus ostreatus subtilisin-like protease) from P. ostreatus culture broth has been purified and characterized. PoSl is a monomeric glycoprotein with a molecular mass of 75 kDa, a pI of 4.5, and an optimum pH in the alkaline range. The inhibitory profile indicates that PoSl is a serine protease. The N-terminal and three tryptic peptide sequences of PoSl have been determined. The homology of one internal peptide with conserved sequence around the Asp residue of the catalytic triad in the subtilase family suggests that PoSl is a subtilisin-like protease. This hypothesis is further supported by the finding that PoSl hydrolysis sites of the insulin B chain match those of subtilisin. PoSl activity is positively affected by calcium. A 10-fold decrease in the Km value in the presence of calcium ions can reflect an induced structural change in the substrate recognition site region. Furthermore, Ca2+ binding slows PoSl autolysis, triggering the protein to form a more compact structure. These effects have already been observed for subtilisin and other serine proteases. Moreover, PoSl protease seems to play a key role in the regulation of P. ostreatus laccase activity by degrading and/or activating different isoenzymes. PMID:11375191

Fold-related-fracturing at the Livingstone River anticline (AB; Canada) by coupling field surveying and numerical modelling

NASA Astrophysics Data System (ADS)

Humair, Florian; Epard, Jean-Luc; Bauville, Arthur; Jaboyedoff, Michel; Pana, Dinu; Kaus, Boris; Schmalholz, Stefan

2016-04-01

The interpretation of fold-related joints and faults is of primary importance in terms of fluids prospection (e.g. water, oil, gas, C02) since anticlines are potential structural trap while fracturing can strongly influence the storage capacity as well as the migration pathways. Located at the front of the Foothills of the Rocky Mountains in Alberta (Canada), the Livingstone Range (LRA) is analogous to hydrocarbon reservoir that occur elsewhere in the Foothills (Cooley et al., 2011). The Livingstone Range fold system is related to the development of the Livingstone thrust that cuts around 1000m up-section from a regional decollement in the Palliser Formation (Devonian) to another in the Fernie Formation (Jurassic). Our study focuses on the detailed structural investigation of the Livingstone River anticline (northern part of the LRA). It aims at characterizing the anticline geometry as well as the fracturing pattern (orientation, mode, infilling, spacing, trace length, density, and cross-cutting relationships) in order to propose a kinematic interpretation of the fold-related fracturing genesis. The study area is investigated at different scales by combining field surveys with remote sensing (HR-Digital Elevation Model, Ground-based LiDAR, Gigapixel photography) and thin-sections analyses. In a second step we performed finite difference 3D numerical simulations in order to compute the evolution of local principal stress orientation during folding. We compared the fracture (or plastic bands) distribution in the field with 1) a dynamic numerical model of detachment folding; and 2) an instantaneous numerical model based on the final fold geometry. Cooley, M.A., Price, R.A., Dixon, J.M., Kyser, T.K. 2011. Along-strike variations and internal details of chevron-style flexural slip thrust-propagation folds within the southern Livingstone Range anticlinorium, a paleo-hydrocarbon reservoir in southern Alberta Foothills, Canada. AAPG bulletin, 95 (11), 1821-1849.

Analysis of folded pulse forming line operation.

PubMed

Domonkos, M T; Watrous, J; Parker, J V; Cavazos, T; Slenes, K; Heidger, S; Brown, D; Wilson, D

2014-09-01

A compact pulse forming line (CPFL) concept based on a folded transmission line and high-breakdown strength dielectric was explored through an effort combining proof-of-principle experiments with electromagnetic modeling. A small-scale folded CPFL was fabricated using surface-mount ceramic multilayer capacitors. The line consisted of 150 capacitors close-packed in parallel and delivered a 300 ns flat-top pulse. The concept was carried to a 10 kV class device using a polymer-ceramic nanocomposite dielectric with a permittivity of 37.6. The line was designed for a 161 ns FWHM length pulse into a matched load. The line delivered a 110 ns FWHM pulse, and the pulse peak amplitude exceeded the matched load ideal. Transient electromagnetic analysis using the particle-in-cell code ICEPIC was conducted to examine the nature of the unexpected pulse shortening and distortion. Two-dimensional analysis failed to capture the anomalous behavior. Three-dimensional analysis replicated the pulse shape and revealed that the bends were largely responsible for the pulse shortening. The bends not only create the expected reflection of the incident TEM wave but also produce a non-zero component of the Poynting vector perpendicular to the propagation direction of the dominant electromagnetic wave, resulting in power flow largely external to the PFL. This analysis explains both the pulse shortening and the amplitude of the pulse.

Analysis of folded pulse forming line operation

NASA Astrophysics Data System (ADS)

Domonkos, M. T.; Watrous, J.; Parker, J. V.; Cavazos, T.; Slenes, K.; Heidger, S.; Brown, D.; Wilson, D.

2014-09-01

A compact pulse forming line (CPFL) concept based on a folded transmission line and high-breakdown strength dielectric was explored through an effort combining proof-of-principle experiments with electromagnetic modeling. A small-scale folded CPFL was fabricated using surface-mount ceramic multilayer capacitors. The line consisted of 150 capacitors close-packed in parallel and delivered a 300 ns flat-top pulse. The concept was carried to a 10 kV class device using a polymer-ceramic nanocomposite dielectric with a permittivity of 37.6. The line was designed for a 161 ns FWHM length pulse into a matched load. The line delivered a 110 ns FWHM pulse, and the pulse peak amplitude exceeded the matched load ideal. Transient electromagnetic analysis using the particle-in-cell code ICEPIC was conducted to examine the nature of the unexpected pulse shortening and distortion. Two-dimensional analysis failed to capture the anomalous behavior. Three-dimensional analysis replicated the pulse shape and revealed that the bends were largely responsible for the pulse shortening. The bends not only create the expected reflection of the incident TEM wave but also produce a non-zero component of the Poynting vector perpendicular to the propagation direction of the dominant electromagnetic wave, resulting in power flow largely external to the PFL. This analysis explains both the pulse shortening and the amplitude of the pulse.

Locking hinge

NASA Technical Reports Server (NTRS)

Wesselski, Clarence J. (Inventor)

1988-01-01

The space station configuration currently studied utilizes structures which require struts to be hinged in the middle in the stowed mode and locked into place in the deployed mode. Since there are hundreds of hinges involved, it is necessary that they have simple, positive locking features with a minimum of joint looseness or slack. This invention comprises two similar housings hinged together with a spring loaded locking member which assists in making as well as breaking the lock. This invention comprises a bracket hinge and bracket members with a spring biased and movable locking member. The locking or latch member has ear parts received in locking openings where wedging surfaces on the ear parts cooperate with complimentary surfaces on the bracket members for bringing the bracket members into a tight end-to-end alignment when the bracket members are in an extended position. When the locking member is moved to an unlocking position, pivoting of the hinge about a pivot pin automatically places the locking member to retain the locking member in an unlocked position. In pivoting the hinge from an extended position to a folded position, longitudinal spring members are placed under tension over annular rollers so that the spring tension in a folded position assists in return of the hinge from a folded to an extended position. Novelty lies in the creation of a locking hinge which allows compact storage and easy assembly of structural members having a minimal number of parts.

Inter- and Intra- Field variations in soil compaction levels and subsequent impacts on hydrological extremes

NASA Astrophysics Data System (ADS)

Pattison, Ian; Coates, Victoria

2015-04-01

The rural landscape in the UK is dominated by pastoral agriculture, with about 40% of land cover classified as either improved or semi-natural grassland according to the Land Cover Map 2007. Intensification has resulted in greater levels of compaction associated with higher stocking densities. However, there is likely to be a great amount of variability in compaction levels within and between fields due to multiple controlling factors. This research focusses in on two of these factors; firstly animal species, namely sheep, cattle and horses; and secondly field zonation e.g. feeding areas, field gates, open field. Field experiments have been conducted in multiple fields in the River Skell catchment, in Yorkshire, UK, which has an area of 140km2. The effect on physical and hydrologic soil characteristics such as bulk density and moisture contents have been quantified using a wide range of field and laboratory based experiments. Results have highlighted statistically different properties between heavily compacted areas where animals congregate and less-trampled open areas. Furthermore, soil compaction has been hypothesised to contribute to increased flood risk at larger spatial scales. Previous research (Pattison, 2011) on a ~40km2 catchment (Dacre Beck, Lake District, UK) has shown that when soil characteristics are homogeneously parameterised in a hydrological model, downstream peak discharges can be 65% higher for a heavy compacted soil than for a lightly compacted soil. Here we report results from spatially distributed hydrological modelling using soil parameters gained from the field experimentation. Results highlight the importance of both the percentage of the catchment which is heavily compacted and also the spatial distribution of these fields.

Influence of wood-derived biochar on the compactibility and strength of silt loam soil

NASA Astrophysics Data System (ADS)

Ahmed, Ahmed; Gariepy, Yvan; Raghavan, Vijaya

2017-04-01

Biochar is proven to enhance soil fertility and increase crop productivity. Given that the influence of biochar on soil compaction remains unclear, selected physico-mechanical properties of soil amended with wood-derived biochar were assessed. For unamended silt loam, the bulk density, maximum bulk density, optimum moisture content, plastic limit, liquid limit, and plasticity index were 1.05 Mg m-3, 1.69 Mg m-3, 16.55, 17.1, 29.3, and 12.2%, respectively. The penetration resistance and shear strength of the unamended silt loam compacted in the standard compaction Proctor mold and at its optimum moisture content were 1800 kPa and 850 kPa, respectively. Results from amending the silt loam with 10% particle size ranges (0.5-212 μm) led to relative decreases of 18.1, 17.75, 66.66, and 97.4% in bulk density, maximum bulk density, penetration resistance, and shear strength, respectively; a 26.8% relative increase in optimum moisture content; along with absolute increases in plastic limit, liquid limit, and plasticity index of 5.3, 13.7, and 8.4%, respectively. While the biochar-amended silt loam soil was more susceptible to compaction, however, soil mechanical impedance enhanced.

Thixoforming of Stellite Powder Compacts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hogg, S. C.; Atkinson, H. V.; Kapranos, P.

2007-04-07

Thixoforming involves processing metallic alloys in the semi-solid state. The process requires the microstructure to be spheroidal when part-solid and part-liquid i.e. to consist of solid spheroids surrounded by liquid. The aim of this work was to investigate whether powder compacts can be used as feedstock for thixoforming and whether the consolidating pressure in the thixoformer can be used to remove porosity from the compact. The powder compacts were made from stellite 6 and stellite 21 alloys, cobalt-based alloys widely used for e.g. manufacturing prostheses. Isothermal heat treatments of small samples in the consolidated state showed the optimum thixoforming temperaturemore » to be in the range 1340 deg. C-1350 deg. C for both materials. The alloys were thixoformed into graphite dies and flowed easily to fill the die. Porosity in the thixoformed components was lower than in the starting material. Hardness values at various positions along the radius of the thixoformed demonstrator component were above the specification for both alloys.« less

Compact Stars with Sequential QCD Phase Transitions.

PubMed

Alford, Mark; Sedrakian, Armen

2017-10-20

Compact stars may contain quark matter in their interiors at densities exceeding several times the nuclear saturation density. We explore models of such compact stars where there are two first-order phase transitions: the first from nuclear matter to a quark-matter phase, followed at a higher density by another first-order transition to a different quark-matter phase [e.g., from the two-flavor color-superconducting (2SC) to the color-flavor-locked (CFL) phase]. We show that this can give rise to two separate branches of hybrid stars, separated from each other and from the nuclear branch by instability regions, and, therefore, to a new family of compact stars, denser than the ordinary hybrid stars. In a range of parameters, one may obtain twin hybrid stars (hybrid stars with the same masses but different radii) and even triplets where three stars, with inner cores of nuclear matter, 2SC matter, and CFL matter, respectively, all have the same mass but different radii.

Microstructure investigation of 13Cr-2Mo ODS steel components obtained by high voltage electric discharge compaction technique

DOE PAGES

Bogachev, Igor; Yudin, Artem; Grigoryev, Evgeniy; ...

2015-11-02

Refractory oxide dispersion strengthened 13Cr-2Mo steel powder was successfully consolidated to near theoretical density using high voltage electric discharge compaction. Cylindrical samples with relative density from 90% to 97% and dimensions of 10 mm in diameter and 10–15 mm in height were obtained. Consolidation conditions such as pressure and voltage were varied in some ranges to determine the optimal compaction regime. Three different concentrations of yttria were used to identify its effect on the properties of the samples. It is shown that the utilized ultra-rapid consolidation process in combination with high transmitted energy allows obtaining high density compacts, retaining themore » initial structure with minimal grain growth. The experimental results indicate some heterogeneity of the structure which may occur in the external layers of the tested samples due to various thermal and electromagnetic in-processing effects. As a result, the choice of the optimal parameters of the consolidation enables obtaining samples of acceptable quality.« less

Phase-change memory: A continuous multilevel compact model of subthreshold conduction and threshold switching

NASA Astrophysics Data System (ADS)

Pigot, Corentin; Gilibert, Fabien; Reyboz, Marina; Bocquet, Marc; Zuliani, Paola; Portal, Jean-Michel

2018-04-01

Phase-change memory (PCM) compact modeling of the threshold switching based on a thermal runaway in Poole–Frenkel conduction is proposed. Although this approach is often used in physical models, this is the first time it is implemented in a compact model. The model accuracy is validated by a good correlation between simulations and experimental data collected on a PCM cell embedded in a 90 nm technology. A wide range of intermediate states is measured and accurately modeled with a single set of parameters, allowing multilevel programing. A good convergence is exhibited even in snapback simulation owing to this fully continuous approach. Moreover, threshold properties extraction indicates a thermally enhanced switching, which validates the basic hypothesis of the model. Finally, it is shown that this model is compliant with a new drift-resilient cell-state metric. Once enriched with a phase transition module, this compact model is ready to be implemented in circuit simulators.

Microstructure Investigation of 13Cr-2Mo ODS Steel Components Obtained by High Voltage Electric Discharge Compaction Technique.

PubMed

Bogachev, Igor; Yudin, Artem; Grigoryev, Evgeniy; Chernov, Ivan; Staltsov, Maxim; Khasanov, Oleg; Olevsky, Eugene

2015-11-02

Refractory oxide dispersion strengthened 13Cr-2Mo steel powder was successfully consolidated to near theoretical density using high voltage electric discharge compaction. Cylindrical samples with relative density from 90% to 97% and dimensions of 10 mm in diameter and 10-15 mm in height were obtained. Consolidation conditions such as pressure and voltage were varied in some ranges to determine the optimal compaction regime. Three different concentrations of yttria were used to identify its effect on the properties of the samples. It is shown that the utilized ultra-rapid consolidation process in combination with high transmitted energy allows obtaining high density compacts, retaining the initial structure with minimal grain growth. The experimental results indicate some heterogeneity of the structure which may occur in the external layers of the tested samples due to various thermal and electromagnetic in-processing effects. The choice of the optimal parameters of the consolidation enables obtaining samples of acceptable quality.

Compact piezoelectric tripod manipulator based on a reverse bridge-type amplification mechanism

NASA Astrophysics Data System (ADS)

Na, Tae-Won; Choi, Jun-Ho; Jung, Jin-Young; Kim, Hyeong-Geon; Han, Jae-Hung; Park, Kwang-Chun; Oh, Il-Kwon

2016-09-01

We report a hierarchical piezoelectric tripod manipulator based on a reverse bridge-type displacement amplifier. The reverse bridge-type amplification mechanism is pre-strained by each piezo-stack actuator up to 60 μm and is cross-stacked in a series arrangement to make a compact and high-stroke manipulator having load-bearing characteristics. The designed manipulator with three degrees of freedom is compact with a height of 56.0 mm, a diameter of 48.6 mm and total weight of 115 g. It achieves a translational stroke of up to 880 μm in heaving motion and a tilting angle of up to 2.0° in rotational motion within the operating voltage and power range of the piezoelectric stack actuator. A key feature of the present design is built-in and pre-strained displacement amplification mechanisms integrated with piezoelectric stacked actuators, resulting in a compact tripod manipulator having exceptionally high stroke and load-bearing capacity.

VLBI observations of 6 GHz OH masers in three ultra-compact H Ii regions

NASA Astrophysics Data System (ADS)

Desmurs, J. F.; Baudry, A.

1998-12-01

Following our successful analysis of VLBI observations of the (2) Pi_ {3/ 2}, J={5/ 2}, F=3-3 and F=2-2 excited OH emission at 6035 and 6031 MHz in W3(OH), we have analyzed the same transitions in three other ultra-compact HII regions, M17, ON1, and W51. The restoring beams were in the range 6 to 30 milliarc sec. The F=3-3 and 2-2 hyperfine transitions of OH were both mapped in ON1. Seven 6035 MHz LCP or RCP maser components were identified in ON1. They are distributed over a region whose diameter is similar to that of the compact HII region, namely ~ 0.4 - 0.5 arc sec. In contrast with the F=3-3 line emission, the F=2-2 transition at 6031 MHz is nearly an order of magnitude weaker than the peak 6035 MHz emission. In M17, we observed fringes only in the 6035 MHz line. The detected OH components appear to be projected on to the compact HII region. We report also on weak VLBI detection of the 6035 MHz emission from W51. This emission seems to be located between two active ultra-compact HII regions in a complex area which deserves further investigation. The 5 cm OH minimum brightness temperatures range from about 3 10(7) K in W51 to 8 10(9) K in ON1. Variability of the 6035 or 6031 MHz emission is well established and suggests that the 5 cm OH masers are not fully saturated. The high spectral and spatial resolutions achieved in this work allowed us to identify Zeeman pairs and hence to derive the magnetic field strength. In ON1 and W51 the field lies in the range 4 to 6 mG with a trend for higher field at 6031 MHz than at 6035 MHz in ON1. In M17 no Zeeman splitting was observed and the magnetic field appears to be weaker than 1 mG.

Basic Tilted Helix Bundle - a new protein fold in human FKBP25/FKBP3 and HectD1.

PubMed

Helander, Sara; Montecchio, Meri; Lemak, Alexander; Farès, Christophe; Almlöf, Jonas; Yi, Yanjun; Yee, Adelinda; Arrowsmith, Cheryl; DhePaganon, Sirano; Sunnerhagen, Maria

2014-04-25

In this paper, we describe the structure of a N-terminal domain motif in nuclear-localized FKBP251-73, a member of the FKBP family, together with the structure of a sequence-related subdomain of the E3 ubiquitin ligase HectD1 that we show belongs to the same fold. This motif adopts a compact 5-helix bundle which we name the Basic Tilted Helix Bundle (BTHB) domain. A positively charged surface patch, structurally centered around the tilted helix H4, is present in both FKBP25 and HectD1 and is conserved in both proteins, suggesting a conserved functional role. We provide detailed comparative analysis of the structures of the two proteins and their sequence similarities, and analysis of the interaction of the proposed FKBP25 binding protein YY1. We suggest that the basic motif in BTHB is involved in the observed DNA binding of FKBP25, and that the function of this domain can be affected by regulatory YY1 binding and/or interactions with adjacent domains. Copyright © 2014 Elsevier Inc. All rights reserved.

Advanced collapsible tank for liquid containment

NASA Technical Reports Server (NTRS)

Flanagan, David T.; Hopkins, Robert C.

1993-01-01

Tanks for bulk liquid containment will be required to support advanced planetary exploration programs. Potential applications include storage of potable, process, and waste water, and fuels and process chemicals. The launch mass and volume penalties inherent in rigid tanks suggest that collapsible tanks may be more efficient. Collapsible tanks are made of lightweight flexible material and can be folded compactly for storage and transport. Although collapsible tanks for terrestrial use are widely available, a new design was developed that has significantly less mass and bulk than existing models. Modelled after the shape of a sessible drop, this design features a dual membrane with a nearly uniform stress distribution and a low surface-to-volume ratio. It can be adapted to store a variety of liquids in nearly any environment with constant acceleration field. Three models of 10L, 50L, and 378L capacity have been constructed and tested. The 378L (100 gallon) model weighed less than 10 percent of a commercially available collapsible tank of equivalent capacity, and required less than 20 percent of the storage space when folded for transport.

A model for the origin of Martian polygonal terrain

NASA Technical Reports Server (NTRS)

Mcgill, G. E.

1993-01-01

Extensive areas of the Martian northern plains in Utopia and Acidalia Planitiae are characterized by 'polygonal terrain.' Polygonal terrain consists of material cut by complex troughs defining a pattern resembling mudcracks, columnar joints, or frost-wedge polygons on the Earth. However, the Martian polygons are orders of magnitude larger than these potential Earth analogs, leading to severe mechanical difficulties for genetic models based on simple analogy arguments. Stratigraphic studies show that the polygonally fractured material in Utopia Planitia was deposited on a land surface with significant topography, including scattered knobs and mesas, fragments of ancient crater rims, and fresh younger craters. Sediments or volcanics deposited over topographically irregular surfaces can experience differential compaction producing drape folds. Bending stresses due to these drape folds would be superposed on the pervasive tensile stresses due to desiccation or cooling, such that the probability of fracturing is enhanced above buried topographic highs and suppressed above buried topographic lows. Thus it was proposed that the scale of the Martian polygons is controlled by the spacing of topographic highs on the buried surface rather than by the physics of the shrinkage process.

Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme

PubMed Central

Xie, Zheng; Srividya, Narayanan; Sosnick, Tobin R.; Pan, Tao; Scherer, Norbert F.

2004-01-01

The equilibrium folding of the catalytic domain of Bacillus subtilis RNase P RNA is investigated by single-molecule fluorescence resonance energy transfer (FRET). Previous ensemble studies of this 255-nucleotide ribozyme described the equilibrium folding with two transitions, U-to-Ieq-to-N, and focused on the Ieq-to-N transition. The present study focuses on the U-to-Ieq transition. Comparative ensemble measurements of the ribozyme construct labeled with fluorescein at the 5′ end and Cy3 at the 3′ end show that modifications required for labeling do not interfere with folding and help to define the Mg2+ concentration range for the U-to-Ieq transition. Histogram analysis of the Mg2+-dependent single-molecule FRET efficiency reveals two previously undetermined folding intermediates. The single-molecule FRET trajectories exhibit non-two-state and nonergodic behaviors at intermediate Mg2+ concentrations on the time scale of seconds. The trajectories at intermediate Mg2+ concentrations are classified into five classes based on three FRET levels and their dynamics of interconversion within the measured time range. This heterogeneity, together with the observation of “nonsudden jump” FRET transitions, indicates that the early folding steps of this ribozyme involve a series of intermediates with different degrees of kinetic isolation and that folding occurs under kinetic control and involves many “local” conformational switches. A free energy contour is constructed to illustrate the complex folding surface. PMID:14704266

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes.

PubMed

Pervouchine, Dmitri D

2018-06-15

The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the “first-align-then-fold” principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite “first-fold-then-align” approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA⁻RNA interactions across the transcriptome.

UFO (UnFold Operator) computer program abstract

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kissel, L.; Biggs, F.

UFO (UnFold Operator) is an interactive user-oriented computer program designed to solve a wide range of problems commonly encountered in physical measurements. This document provides a summary of the capabilities of version 3A of UFO.

Range-Gated Metrology with Compact Optical Head

NASA Technical Reports Server (NTRS)

Dubovitsky, Serge; Shaddock, Daniel; Ware, Brent; Lay, Oliver

2008-01-01

This work represents a radical simplification in the design of the optical head needed for high-precision laser ranging applications. The optical head is now a single fiber-optic collimator with dimensions of order of 1 1 2 cm, which can be easily integrated into the system being measured with minimal footprint.

Water-level altitudes 2015 and water-level changes in the Chicot, Evangeline, and Jasper aquifers and compaction 1973-2014 in the Chicot and Evangeline aquifers, Houston-Galveston region, Texas

USGS Publications Warehouse

Kasmarek, Mark C.; Ramage, Jason K.; Houston, Natalie A.; Johnson, Michaela R.; Schmidt, Tiffany S.

2015-01-01

Compaction of subsurface sediments (mostly in the fine-grained silt and clay layers) composing the Chicot and Evangeline aquifers was recorded continuously by using analog technology at the 13 borehole extensometers at 11 sites that were either activated or installed between 1973 and 1980. For the period of record beginning in 1973 (or later depending on activation or installation date) and ending in December 2014, measured cumulative compaction at the 13 extensometers ranged from 0.101 ft at the Texas City-Moses Lake extensometer to 3.668 ft at the Addicks extensometer. During 2014, a total of 10 of the 13 extensometers recorded a slight net decrease of land-surface elevation; the extensometers at the Lake Houston and Clear Lake (shallow) sites recorded slight net increases of land-surface elevation, and the extensometer at the Texas City-Moses Lake site recorded no change in elevation. The rate of compaction varies from site to site because of differences in rates of groundwater withdrawal in the areas adjacent to each extensometer site and differences among sites in the ratios of sand, silt, and clay and compressibilities of the subsurface sediments. It is not appropriate, therefore, to extrapolate or infer a rate of compaction for an adjacent area on the basis of the rate of compaction measured at nearby extensometers.

Modelling the Deformation Front of a Fold-Thrust Belt: the Effect of an Upper Detachment Horizon

NASA Astrophysics Data System (ADS)

Burberry, C. M.; Koyi, H.; Nilfouroushan, F.; Cosgrove, J. W.

2008-12-01

Structures found at the deformation fronts of fold-thrust belts are variable in type, geometry and spatial organisation, as can be demonstrated from comparisons between structures in the Zagros Fold-Thrust Belt, Iran and the Sawtooth Range, Montana. A range of influencing factors has been suggested to account for this variation, including the mechanical properties and distribution of any detachment horizons within the cover rock succession. A series of analogue models was designed to test this hypothesis, under conditions scaled to represent the Sawtooth Range, Montana. A brittle sand pack, containing an upper ductile layer with variable geometry, was shortened above a ductile base and the evolution of the deformation front was monitored throughout the deformation using a high-accuracy laser scanner. In none of the experiments did the upper detachment horizon cover the entire model. In experiments where it pinched out perpendicular to the shortening direction, a triangle zone was formed when the deformation front reached the pinch out. This situation is analogous to the Teton Canyon region structures in the Sawtooth Range, Montana, where the Cretaceous Colorado Shale unit pinches out at the deformation front, favouring the development of a triangle zone in this region. When the pinch out was oblique to the shortening direction, a more complex series of structures was formed. However, when shortening stopped before the detachment pinch out was reached, the deformation front structures were foreland-propagating and no triangle zone was observed. This situation is analogous to foreland-propagating thrust structures developed at the deformation front in the Swift Dam region of the Sawtooth Range, Montana and to the development of fault-bend folds at the deformation front of the Zagros Fold-Thrust Belt, Iran. We suggest that the presence of a suitable intermediate detachment horizon within a sediment pile can be invoked as a valid explanation for the development of varied deformation front structures in fold-thrust belts. Specifically, the spatial extent of the upper detachment horizon with respect to the spatial extent of the deformed region is a key influence on the development of deformation front structures. However, we acknowledge that factors such as basement structure and variable sedimentation within the foreland basin may also be key influences on deformation front structures in other fold-thrust belts.

Room temperature thermal conductivity measurements of neat MOF-5 compacts with high pressure hydrogen and helium

DOE PAGES

Semelsberger, Troy Allen; Veenstra, Mike; Dixon, Craig

2016-02-09

Metal-organic frameworks (MOFs) are a highly porous crystalline material with potential in various applications including on-board vehicle hydrogen storage for fuel cell vehicles. The thermal conductivity of MOFs is an important parameter in the design and ultimate performance of an on-board hydrogen storage system. However, in-situ thermal conductivity measurements have not been previously reported. The present study reports room temperature thermal conductivity and thermal diffusivity measurements performed on neat MOF-5 cylindrical compacts (ρ = 0.4 g/mL) as a function of pressure (0.27–90 bar) and gas type (hydrogen and helium). The transient plane source technique was used to measure both themore » non-directional thermal properties (isotropic method) and the directional thermal properties (anisotropic method). High pressure measurements were made using our in-house built low-temperature, high pressure thermal conductivity sample cell. The intrinsic thermal properties of neat MOF-5 measured under vacuum were—Isotropic: k isotropic = 0.1319 W/m K, α isotropic = 0.4165 mm 2/s; Anisotropic: k axial = 0.1477 W/m K, k radial = 0.1218 W/m K, α axial = 0.5096 mm 2/s, and α radial = 0.4232 mm 2/s. The apparent thermal properties of neat MOF-5 increased with increasing hydrogen and helium pressure, with the largest increase occurring in the narrow pressure range of 0–10 bar and then monotonically asymptoting with increasing pressures up to around 90 bar. On average, a greater than two-fold enhancement in the apparent thermal properties was observed with neat MOF-5 in the presence of helium and hydrogen compared to the intrinsic values of neat MOF-5 measured under vacuum. The apparent thermal properties of neat MOF-5 measured with hydrogen were higher than those measured with helium, which were directly related to the gas-specific thermal properties of helium and hydrogen. Neat MOF-5 exhibited a small degree of anisotropy under all conditions measured with thermal conductivities and diffusivities in the axial direction being higher than those in the radial direction. As a result, the low temperature specific heat capacities of neat MOF-5 were also measured and reported for the temperature range of 93–313 K (–180–40 °C).« less

Room temperature thermal conductivity measurements of neat MOF-5 compacts with high pressure hydrogen and helium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Semelsberger, Troy Allen; Veenstra, Mike; Dixon, Craig

Metal-organic frameworks (MOFs) are a highly porous crystalline material with potential in various applications including on-board vehicle hydrogen storage for fuel cell vehicles. The thermal conductivity of MOFs is an important parameter in the design and ultimate performance of an on-board hydrogen storage system. However, in-situ thermal conductivity measurements have not been previously reported. The present study reports room temperature thermal conductivity and thermal diffusivity measurements performed on neat MOF-5 cylindrical compacts (ρ = 0.4 g/mL) as a function of pressure (0.27–90 bar) and gas type (hydrogen and helium). The transient plane source technique was used to measure both themore » non-directional thermal properties (isotropic method) and the directional thermal properties (anisotropic method). High pressure measurements were made using our in-house built low-temperature, high pressure thermal conductivity sample cell. The intrinsic thermal properties of neat MOF-5 measured under vacuum were—Isotropic: k isotropic = 0.1319 W/m K, α isotropic = 0.4165 mm 2/s; Anisotropic: k axial = 0.1477 W/m K, k radial = 0.1218 W/m K, α axial = 0.5096 mm 2/s, and α radial = 0.4232 mm 2/s. The apparent thermal properties of neat MOF-5 increased with increasing hydrogen and helium pressure, with the largest increase occurring in the narrow pressure range of 0–10 bar and then monotonically asymptoting with increasing pressures up to around 90 bar. On average, a greater than two-fold enhancement in the apparent thermal properties was observed with neat MOF-5 in the presence of helium and hydrogen compared to the intrinsic values of neat MOF-5 measured under vacuum. The apparent thermal properties of neat MOF-5 measured with hydrogen were higher than those measured with helium, which were directly related to the gas-specific thermal properties of helium and hydrogen. Neat MOF-5 exhibited a small degree of anisotropy under all conditions measured with thermal conductivities and diffusivities in the axial direction being higher than those in the radial direction. As a result, the low temperature specific heat capacities of neat MOF-5 were also measured and reported for the temperature range of 93–313 K (–180–40 °C).« less

Geologic Map of the Pahranagat Range 30' x 60' Quadrangle, Lincoln and Nye Counties, Nevada

USGS Publications Warehouse

Jayko, A.S.

2007-01-01

Introduction The Pahranagat Range 30' x 60' quadrangle lies within an arid, sparsely populated part of Lincoln and Nye Counties, southeastern Nevada. Much of the area is public land that includes the Desert National Wildlife Range, the Pahranagat National Wildlife Refuge, and the Nellis Air Force Base. The topography, typical of much of the Basin and Range Province, consists of north-south-trending ranges and intervening broad alluvial valleys. Elevations range from about 1,000 to 2,900 m. At the regional scale, the Pahranagat Range quadrangle lies within the Mesozoic and early Tertiary Sevier Fold-and-Thrust Belt and the Cenozoic Basin and Range Province. The quadrangle is underlain by a Proterozoic to Permian miogeoclinal section, a nonmarine clastic and volcanic section of middle Oligocene or older to late Miocene age, and alluvial deposits of late Cenozoic age. The structural features that are exposed reflect relatively shallow crustal deformation. Mesozoic deformation is dominated by thrust faults and asymmetric or open folds. Cenozoic deformation is dominated by faults that dip more than 45i and dominostyle tilted blocks. At least three major tectonic events have affected the area: Mesozoic (Sevier) folding and thrust faulting, pre-middle Oligocene extensional deformation, and late Cenozoic (mainly late Miocene to Holocene) extensional deformation. Continued tectonic activity is expressed in the Pahranagat Range area by seismicity and faults having scarps that cut alluvial deposits.

Compact characterization of liquid absorption and emission spectra using linear variable filters integrated with a CMOS imaging camera

PubMed Central

Wan, Yuhang; Carlson, John A.; Kesler, Benjamin A.; Peng, Wang; Su, Patrick; Al-Mulla, Saoud A.; Lim, Sung Jun; Smith, Andrew M.; Dallesasse, John M.; Cunningham, Brian T.

2016-01-01

A compact analysis platform for detecting liquid absorption and emission spectra using a set of optical linear variable filters atop a CMOS image sensor is presented. The working spectral range of the analysis platform can be extended without a reduction in spectral resolution by utilizing multiple linear variable filters with different wavelength ranges on the same CMOS sensor. With optical setup reconfiguration, its capability to measure both absorption and fluorescence emission is demonstrated. Quantitative detection of fluorescence emission down to 0.28 nM for quantum dot dispersions and 32 ng/mL for near-infrared dyes has been demonstrated on a single platform over a wide spectral range, as well as an absorption-based water quality test, showing the versatility of the system across liquid solutions for different emission and absorption bands. Comparison with a commercially available portable spectrometer and an optical spectrum analyzer shows our system has an improved signal-to-noise ratio and acceptable spectral resolution for discrimination of emission spectra, and characterization of colored liquid’s absorption characteristics generated by common biomolecular assays. This simple, compact, and versatile analysis platform demonstrates a path towards an integrated optical device that can be utilized for a wide variety of applications in point-of-use testing and point-of-care diagnostics. PMID:27389070

Compact characterization of liquid absorption and emission spectra using linear variable filters integrated with a CMOS imaging camera

NASA Astrophysics Data System (ADS)

Wan, Yuhang; Carlson, John A.; Kesler, Benjamin A.; Peng, Wang; Su, Patrick; Al-Mulla, Saoud A.; Lim, Sung Jun; Smith, Andrew M.; Dallesasse, John M.; Cunningham, Brian T.

2016-07-01

A compact analysis platform for detecting liquid absorption and emission spectra using a set of optical linear variable filters atop a CMOS image sensor is presented. The working spectral range of the analysis platform can be extended without a reduction in spectral resolution by utilizing multiple linear variable filters with different wavelength ranges on the same CMOS sensor. With optical setup reconfiguration, its capability to measure both absorption and fluorescence emission is demonstrated. Quantitative detection of fluorescence emission down to 0.28 nM for quantum dot dispersions and 32 ng/mL for near-infrared dyes has been demonstrated on a single platform over a wide spectral range, as well as an absorption-based water quality test, showing the versatility of the system across liquid solutions for different emission and absorption bands. Comparison with a commercially available portable spectrometer and an optical spectrum analyzer shows our system has an improved signal-to-noise ratio and acceptable spectral resolution for discrimination of emission spectra, and characterization of colored liquid’s absorption characteristics generated by common biomolecular assays. This simple, compact, and versatile analysis platform demonstrates a path towards an integrated optical device that can be utilized for a wide variety of applications in point-of-use testing and point-of-care diagnostics.

Limits on the Mass and Abundance of Primordial Black Holes from Quasar Gravitational Microlensing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mediavilla, E.; Jiménez-Vicente, J.; Calderón-Infante, J.

The idea that dark matter can be made of intermediate-mass primordial black holes (PBHs) in the 10 M {sub ⊙} ≲ M ≲ 200 M {sub ⊙} range has recently been reconsidered, particularly in the light of the detection of gravitational waves by the LIGO experiment. The existence of even a small fraction of dark matter in black holes should nevertheless result in noticeable quasar gravitational microlensing. Quasar microlensing is sensitive to any type of compact objects in the lens galaxy, to their abundance, and to their mass. We have analyzed optical and X-ray microlensing data from 24 gravitationally lensedmore » quasars to estimate the abundance of compact objects in a very wide range of masses. We conclude that the fraction of mass in black holes or any type of compact objects is negligible outside of the 0.05 M {sub ⊙} ≲ M ≲ 0.45 M {sub ⊙} mass range and that it amounts to 20% ± 5% of the total matter, in agreement with the expected masses and abundances of the stellar component. Consequently, the existence of a significant population of intermediate-mass PBHs appears to be inconsistent with current microlensing observations. Therefore, primordial massive black holes are a very unlikely source of the gravitational radiation detected by LIGO.« less

Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding.

PubMed

Tomić, A; Berynskyy, M; Wade, R C; Tomić, S

2015-11-01

The experimentally determined structures of human dipeptidyl peptidase III (DPP III) for the wild-type protein and for the complex of its E451A mutant with the peptide substrate, tynorphin, differ significantly in their overall shape. The two domains of the enzyme are separated by a wide cleft in the structure of the ligand-free enzyme, while in the ligand-bound mutant they are very close to each other, and the protein structure is extremely compact. Here, we applied a range of molecular dynamics simulation techniques to investigate the DPP III conformational landscape and the influence of ligand binding on the protein structure and dynamics. We used conventional, accelerated and steered methods to simulate DPP III and its complexes with tynorphin and with the preferred, synthetic, substrate Arg-Arg-2-naphthylamide. We found that DPP III can adopt a number of different forms in solution. The compact forms are more stable, but the open and partially closed states, spanning a wide range of conformations, can more effectively recognize the substrate which preferentially binds to the five-stranded β-core of the lower DPP III domain. The simulations indicated the existence of a dynamic equilibrium between open and semi-closed states and revealed two ways that the protein can close, leading to two distinct compact structures. The way in which the protein closes depends on the presence of the ligand.

Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues

NASA Astrophysics Data System (ADS)

Negi, Sunita; Rana Atilgan, Ali; Atilgan, Canan

2012-12-01

Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca+2 ion between the two lobes.

A mixed-effects model approach for the statistical analysis of vocal fold viscoelastic shear properties.

PubMed

Xu, Chet C; Chan, Roger W; Sun, Han; Zhan, Xiaowei

2017-11-01

A mixed-effects model approach was introduced in this study for the statistical analysis of rheological data of vocal fold tissues, in order to account for the data correlation caused by multiple measurements of each tissue sample across the test frequency range. Such data correlation had often been overlooked in previous studies in the past decades. The viscoelastic shear properties of the vocal fold lamina propria of two commonly used laryngeal research animal species (i.e. rabbit, porcine) were measured by a linear, controlled-strain simple-shear rheometer. Along with published canine and human rheological data, the vocal fold viscoelastic shear moduli of these animal species were compared to those of human over a frequency range of 1-250Hz using the mixed-effects models. Our results indicated that tissues of the rabbit, canine and porcine vocal fold lamina propria were significantly stiffer and more viscous than those of human. Mixed-effects models were shown to be able to more accurately analyze rheological data generated from repeated measurements. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Quaternary thrust system of the northern Alaska Range

USGS Publications Warehouse

Bemis, Sean P.; Carver, Gary A.; Koehler, Richard D.

2012-01-01

The framework of Quaternary faults in Alaska remains poorly constrained. Recent studies in the Alaska Range north of the Denali fault add significantly to the recognition of Quaternary deformation in this active orogen. Faults and folds active during the Quaternary occur over a length of ∼500 km along the northern flank of the Alaska Range, extending from Mount McKinley (Denali) eastward to the Tok River valley. These faults exist as a continuous system of active structures, but we divide the system into four regions based on east-west changes in structural style. At the western end, the Kantishna Hills have only two known faults but the highest rate of shallow crustal seismicity. The western northern foothills fold-thrust belt consists of a 50-km-wide zone of subparallel thrust and reverse faults. This broad zone of deformation narrows to the east in a transition zone where the range-bounding fault of the western northern foothills fold-thrust belt terminates and displacement occurs on thrust and/or reverse faults closer to the Denali fault. The eastern northern foothills fold-thrust belt is characterized by ∼40-km-long thrust fault segments separated across left-steps by NNE-trending left-lateral faults. Altogether, these faults accommodate much of the topographic growth of the northern flank of the Alaska Range.Recognition of this thrust fault system represents a significant concern in addition to the Denali fault for infrastructure adjacent to and transecting the Alaska Range. Although additional work is required to characterize these faults sufficiently for seismic hazard analysis, the regional extent and structural character should require the consideration of the northern Alaska Range thrust system in regional tectonic models.

A compressibility based model for predicting the tensile strength of directly compressed pharmaceutical powder mixtures.

PubMed

Reynolds, Gavin K; Campbell, Jacqueline I; Roberts, Ron J

2017-10-05

A new model to predict the compressibility and compactability of mixtures of pharmaceutical powders has been developed. The key aspect of the model is consideration of the volumetric occupancy of each powder under an applied compaction pressure and the respective contribution it then makes to the mixture properties. The compressibility and compactability of three pharmaceutical powders: microcrystalline cellulose, mannitol and anhydrous dicalcium phosphate have been characterised. Binary and ternary mixtures of these excipients have been tested and used to demonstrate the predictive capability of the model. Furthermore, the model is shown to be uniquely able to capture a broad range of mixture behaviours, including neutral, negative and positive deviations, illustrating its utility for formulation design. Copyright © 2017 Elsevier B.V. All rights reserved.

Tableting Properties and Compression Models of Labisia pumila Tablets.

PubMed

Etti, C J; Yusof, Y A; Chin, N L; Mohd Tahir, S

2017-03-04

The tableting properties of Labisia pumila herbal powder, which is well known for its therapeutic benefits was investigated. The herbal powder was compressed into tablets using a stainless steel cylindrical uniaxial die of 13-mm- diameter with compaction pressures ranging from 7 to 25 MPa. Two feed weights, 0.5 and 1.0 g were used to form tablets. Some empirical models were used to describe the compressibility behavior of Labisia pumila tablets. The strength and density of tablets increased with increase in compaction pressure and resulted in reduction in porosity of the tablets. Smaller feeds, higher forces and increase in compaction pressure, contributed to more coherent tablets. These findings can be used to enhance the approach and understanding of tableting properties of Labisia pumila herbal powder tablets.

Compact plasma Pockels cell for TIL of SGIII laser facility

NASA Astrophysics Data System (ADS)

Zhang, Xiongjun; Wu, Dengsheng; Lin, Doughui; Yu, Haiwu; Zhang, Jun

2008-01-01

Compact plasma Pockel's cells (PPC) with 70mm aperture driven by one-pulse process have been constructed for technical integration line (TIL) of SGIII laser facility. The experimental results indicate that the working range of gas pressure is wide, and the delay of gas breakdown is steady. Measurements of the optical performance show static transmittance of 93.1%, static extinction ratio of 3900, and average switching efficiency of 99.7%. Eight compact PPCs are used for the second-stage integrating experiments of TIL. By using of parallel driving technology, one driver can work for four PPCs. An analyzer of optical switch is replaced with Brewster-angle Nd-glass slabs in amplifier. Two years application results show that the PPCs can effectively minimize the growth of parasitic-oscillation, and have a high reliability.

Compact stars in the non-minimally coupled electromagnetic fields to gravity

NASA Astrophysics Data System (ADS)

Sert, Özcan

2018-03-01

We investigate the gravitational models with the non-minimal Y(R)F^2 coupled electromagnetic fields to gravity, in order to describe charged compact stars, where Y( R) denotes a function of the Ricci curvature scalar R and F^2 denotes the Maxwell invariant term. We determine two parameter family of exact spherically symmetric static solutions and the corresponding non-minimal model without assuming any relation between energy density of matter and pressure. We give the mass-radius, electric charge-radius ratios and surface gravitational redshift which are obtained by the boundary conditions. We reach a wide range of possibilities for the parameters k and α in these solutions. Lastly we show that the models can describe the compact stars even in the more simple case α =3.

Generalized slow roll in the unified effective field theory of inflation

NASA Astrophysics Data System (ADS)

Motohashi, Hayato; Hu, Wayne

2017-07-01

We provide a compact and unified treatment of power spectrum observables for the effective field theory (EFT) of inflation with the complete set of operators that lead to second-order equations of motion in metric perturbations in both space and time derivatives, including Horndeski and Gleyzes-Langlois-Piazza-Vernizzi theories. We relate the EFT operators in ADM form to the four additional free functions of time in the scalar and tensor equations. Using the generalized slow-roll formalism, we show that each power spectrum can be described by an integral over a single source that is a function of its respective sound horizon. With this correspondence, existing model independent constraints on the source function can be simply reinterpreted in the more general inflationary context. By expanding these sources around an optimized freeze-out epoch, we also provide characterizations of these spectra in terms of five slow-roll hierarchies whose leading-order forms are compact and accurate as long as EFT coefficients vary only on time scales greater than an e -fold. We also clarify the relationship between the unitary gauge observables employed in the EFT and the comoving gauge observables of the postinflationary universe.

Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake.

PubMed

Yildiz, Ozkan; Kalthoff, Christoph; Raunser, Stefan; Kühlbrandt, Werner

2007-01-24

A binary complex of the ammonia channel Amt1 from Methanococcus jannaschii and its cognate P(II) signalling protein GlnK1 has been produced and characterized. Complex formation is prevented specifically by the effector molecules Mg-ATP and 2-ketoglutarate. Single-particle electron microscopy of the complex shows that GlnK1 binds on the cytoplasmic side of Amt1. Three high-resolution X-ray structures of GlnK1 indicate that the functionally important T-loop has an extended, flexible conformation in the absence of Mg-ATP, but assumes a compact, tightly folded conformation upon Mg-ATP binding, which in turn creates a 2-ketoglutarate-binding site. We propose a regulatory mechanism by which nitrogen uptake is controlled by the binding of both effector molecules to GlnK1. At normal effector levels, a 2-ketoglutarate molecule binding at the apex of the compact T-loop would prevent complex formation, ensuring uninhibited ammonia uptake. At low levels of Mg-ATP, the extended loops would seal the ammonia channels in the complex. Binding of both effector molecules to P(II) signalling proteins may thus represent an effective feedback mechanism for regulating ammonium uptake through the membrane.

MICRO/NANO-STRUCTURAL EXAMINATION AND FISSION PRODUCT IDENTIFICATION IN NEUTRON IRRADIATED AGR-1 TRISO FUEL

DOE Office of Scientific and Technical Information (OSTI.GOV)

van Rooyen, I. J.; Lillo, T. M.; Wen, H. M.

Advanced microscopic and microanalysis techniques were developed and applied to study irradiation effects and fission product behavior in selected low-enriched uranium oxide/uranium carbide TRISO-coated particles from fuel compacts in six capsules irradiated to burnups of 11.2 to 19.6% FIMA. Although no TRISO coating failures were detected during the irradiation, the fraction of Ag-110m retained in individual particles often varied considerably within a single compact and at the capsule level. At the capsule level Ag-110m release fractions ranged from 1.2 to 38% and within a single compact, silver release from individual particles often spanned a range that extended from 100% retentionmore » to nearly 100% release. In this paper, selected irradiated particles from Baseline, Variant 1 and Variant 3 type fueled TRISO coated particles were examined using Scanning Electron Microscopy, Atom Probe Tomography; Electron Energy Loss Spectroscopy; Precession Electron Diffraction, Transmission Electron Microscopy, Scanning Transmission Electron Microscopy (STEM), High Resolution Electron Microscopy (HRTEM) examinations and Electron Probe Micro-Analyzer. Particle selection in this study allowed for comparison of the fission product distribution with Ag retention, fuel type and irradiation level. Nano sized Ag-containing features were predominantly identified in SiC grain boundaries and/or triple points in contrast with only two sitings of Ag inside a SiC grain in two different compacts (Baseline and Variant 3 fueled compacts). STEM and HRTEM analysis showed evidence of Ag and Pd co-existence in some cases and it was found that fission product precipitates can consist of multiple or single phases. STEM analysis also showed differences in precipitate compositions between Baseline and Variant 3 fuels. A higher density of fission product precipitate clusters were identified in the SiC layer in particles from the Variant 3 compact compared with the Variant 1 compact. Trend analysis shows precipitates were randomly distributed along the perimeter of the IPyC-SiC interlayer but only weakly associated with kernel protrusion and buffer fractures. There has been no evidence that the general release of silver is related to cracks or significant degradation of the microstructure. The results presented in this paper provide new insights to Ag transport mechanism(s) in intact SiC layer of TRISO coated particles.« less

Flat-top MZI filters: a novel robust design based on MMI splitters

NASA Astrophysics Data System (ADS)

Cherchi, Matteo; Harjanne, Mikko; Ylinen, Sami; Kapulainen, Markku; Vehmas, Tapani; Aalto, Timo

2016-03-01

Multimode Interferometers (MMIs) are an attractive alternative to directional couplers, ensuring more relaxed tolerances to fabrication errors and broader operation bandwidth. The drawback is that only a limited discrete set of splitting ratios is achievable with MMIs of constant cross section. This issue clearly limits their use in flat-top interferometric filters, which design requires, in general, free choice of the splitting ratios. Here we show for the first time that it is possible to design 4-stage flat-top interferometers using only standard MMIs with 50:50 and 85:15 splitting ratios. The design approach is based on the representation of the system on the Bloch sphere. Flat-top interleavers with different free spectral ranges have been designed and fabricated on the silicon photonics platform of VTT, based on 3 μm thick rib and strip waveguides. Two different layouts have been explored: one where all components are collinear and a more compact one which elements have been folded in a spiral shape. All interleavers have been designed for TE polarization, and they work in a wavelength range comparable with the 100 nm bandwidth of the MMI splitters. Even though fabrication imperfections and non-ideal behaviour of both waveguide bends and MMIs led to reduced extinction compared to simulations, most devices show in-band extinction exceeding 15 dB. The in-band losses of the most central channels did not exceed 1.5 dB compared to the reference straight waveguide. The designed interleavers can be employed in cascaded configurations to achieve broadband and fabrication tolerant flat-top wavelength (de)multiplexers.

Compacting biomass waste materials for use as fuel

NASA Astrophysics Data System (ADS)

Zhang, Ou

Every year, biomass waste materials are produced in large quantity. The combustibles in biomass waste materials make up over 70% of the total waste. How to utilize these waste materials is important to the nation and the world. The purpose of this study is to test optimum processes and conditions of compacting a number of biomass waste materials to form a densified solid fuel for use at coal-fired power plants or ordinary commercial furnaces. Successful use of such fuel as a substitute for or in cofiring with coal not only solves a solid waste disposal problem but also reduces the release of some gases from burning coal which cause health problem, acid rain and global warming. The unique punch-and-die process developed at the Capsule Pipeline Research Center, University of Missouri-Columbia was used for compacting the solid wastes, including waste paper, plastics (both film and hard products), textiles, leaves, and wood. The compaction was performed to produce strong compacts (biomass logs) under room temperature without binder and without preheating. The compaction conditions important to the commercial production of densified biomass fuel logs, including compaction pressure, pressure holding time, back pressure, moisture content, particle size, binder effects, and mold conditions were studied and optimized. The properties of the biomass logs were evaluated in terms of physical, mechanical, and combustion characteristics. It was found that the compaction pressure and the initial moisture content of the biomass material play critical roles in producing high-quality biomass logs. Under optimized compaction conditions, biomass waste materials can be compacted into high-quality logs with a density of 0.8 to 1.2 g/cm3. The logs made from the combustible wastes have a heating value in the range 6,000 to 8,000 Btu/lb which is only slightly (10 to 30%) less than that of subbituminous coal. To evaluate the feasibility of cofiring biomass logs with coal, burn tests were conducted in a stoke boiler. A separate burning test was also carried out by burning biomass logs alone in an outdoor hot-water furnace for heating a building. Based on a previous coal compaction study, the process of biomass compaction was studied numerically by use of a non-linear finite element code. A constitutive model with sufficient generality was adapted for biomass material to deal with pore contraction during compaction. A contact node algorithm was applied to implement the effect of mold wall friction into the finite element program. Numerical analyses were made to investigate the pressure distribution in a die normal to the axis of compaction, and to investigate the density distribution in a biomass log after compaction. The results of the analyses gave generally good agreement with theoretical analysis of coal log compaction, although assumptions had to be made about the variation in the elastic modulus of the material and the Poisson's ratio during the compaction cycle.

Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein.

PubMed

Lazim, Raudah; Mei, Ye; Zhang, Dawei

2012-03-01

Replica exchange molecular dynamics (REMD) simulation provides an efficient conformational sampling tool for the study of protein folding. In this study, we explore the mechanism directing the structure variation from α/4β-fold protein to 3α-fold protein after mutation by conducting REMD simulation on 42 replicas with temperatures ranging from 270 K to 710 K. The simulation began from a protein possessing the primary structure of GA88 but the tertiary structure of GB88, two G proteins with "high sequence identity." Albeit the large Cα-root mean square deviation (RMSD) of the folded protein (4.34 Å at 270 K and 4.75 Å at 304 K), a variation in tertiary structure was observed. Together with the analysis of secondary structure assignment, cluster analysis and principal component, it provides insights to the folding and unfolding pathway of 3α-fold protein and α/4β-fold protein respectively paving the way toward the understanding of the ongoings during conformational variation.

Free Energy Landscape and Multiple Folding Pathways of an H-Type RNA Pseudoknot

PubMed Central

Bian, Yunqiang; Zhang, Jian; Wang, Jun; Wang, Jihua; Wang, Wei

2015-01-01

How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias-exchange metadynamics. The folding free energy landscapes are obtained and several folding intermediates are identified. It is suggested that the folding occurs via multiple mechanisms, including a step-wise mechanism starting either from the first helix or the second, and a cooperative mechanism with both helices forming simultaneously. Despite of the multiple mechanism nature, the ensemble folding kinetics estimated from a Markov state model is single-exponential. It is also found that the correlation between folding and binding of metal ions is significant, and the bound ions mediate long-range interactions in the intermediate structures. Non-native interactions are found to be dominant in the unfolded state and also present in some intermediates, possibly hinder the folding process of the RNA. PMID:26030098

Denaturant-Dependent Conformational Changes in a [beta]-Trefoil Protein: Global and Residue-Specific Aspects of an Equilibrium Denaturation Process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Latypov, Ramil F.; Liu, Dingjiang; Jacob, Jaby

2010-01-12

Conformational properties of the folded and unfolded ensembles of human interleukin-1 receptor antagonist (IL-1ra) are strongly denaturant-dependent as evidenced by high-resolution two-dimensional nuclear magnetic resonance (NMR), limited proteolysis, and small-angle X-ray scattering (SAXS). The folded ensemble was characterized in detail in the presence of different urea concentrations by 1H-15N HSQC NMR. The {beta}-trefoil fold characteristic of native IL-1ra was preserved until the unfolding transition region beginning at 4 M urea. At the same time, a subset of native resonances disappeared gradually starting at low denaturant concentrations, indicating noncooperative changes in the folded state. Additional evidence of structural perturbations came frommore » the chemical shift analysis, nonuniform and bell-shaped peak intensity profiles, and limited proteolysis. In particular, the following nearby regions of the tertiary structure became progressively destabilized with increasing urea concentrations: the {beta}-hairpin interface of trefoils 1 and 2 and the H2a-H2 helical region. These regions underwent small-scale perturbations within the native baseline region in the absence of populated molten globule-like states. Similar regions were affected by elevated temperatures known to induce irreversible aggregation of IL-1ra. Further evidence of structural transitions invoking near-native conformations came from an optical spectroscopy analysis of its single-tryptophan variant W17A. The increase in the radius of gyration was associated with a single equilibrium unfolding transition in the case of two different denaturants, urea and guanidine hydrochloride (GuHCl). However, the compactness of urea- and GuHCl-unfolded molecules was comparable only at high denaturant concentrations and deviated under less denaturing conditions. Our results identified the role of conformational flexibility in IL-1ra aggregation and shed light on the nature of structural transitions within the folded ensembles of other {beta}-trefoil proteins, such as IL-1{beta} and hFGF-1.« less