Molecular phylogenetic diversity of the emerging mucoralean fungus Apophysomyces: proposal of three new species.

PubMed

Alvarez, Eduardo; Stchigel, Alberto M; Cano, Josep; Sutton, Deanna A; Fothergill, Annette W; Chander, Jagdish; Salas, Valentina; Rinaldi, Michael G; Guarro, Josep

2010-06-30

Apophysomyces is a monotypic genus belonging to the order Mucorales. The species Apophysomyces elegans has been reported to cause severe infections in immunocompromised and immunocompetent people. In a previous study of Alvarez et al.(3) [J Clin Microbiol 2009;47:1650-6], we demonstrated a high variability among the 5.8S rRNA gene sequences of clinical strains of A. elegans. We performed a polyphasic study based on the analysis of the sequences of the histone 3 gene, the internal transcribed spacer region of the rDNA gene, and domains D1 and D2 of the 28S rRNA gene, as well as by evaluation of some relevant morphological and physiological characteristics of a set of clinical and environmental strains of A. elegans. We have demonstrated that A. elegans is a complex of species. We propose as new species Apophysomyces ossiformis, characterised by bone-shaped sporangiospores, Apophysomyces trapeziformis, with trapezoid-shaped sporangiospores, and Apophysomyces variabilis, with variable-shaped sporangiospores. These species failed to assimilate esculin, whereas A. elegans was able to assimilate that glycoside. Amphotericin B and posaconazole are the most active in vitro drugs against Apophysomyces. Copyright 2009 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Rotor-stator molecular crystals of fullerenes with cubane.

PubMed

Pekker, Sándor; Kováts, Eva; Oszlányi, Gábor; Bényei, Gyula; Klupp, Gyöngyi; Bortel, Gábor; Jalsovszky, István; Jakab, Emma; Borondics, Ferenc; Kamarás, Katalin; Bokor, Mónika; Kriza, György; Tompa, Kálmán; Faigel, Gyula

2005-10-01

Cubane (C8H8) and fullerene (C60) are famous cage molecules with shapes of platonic or archimedean solids. Their remarkable chemical and solid-state properties have induced great scientific interest. Both materials form polymorphic crystals of molecules with variable orientational ordering. The idea of intercalating fullerene with cubane was raised several years ago but no attempts at preparation have been reported. Here we show that C60 and similarly C70 form high-symmetry molecular crystals with cubane owing to topological molecular recognition between the convex surface of fullerenes and the concave cubane. Static cubane occupies the octahedral voids of the face-centred-cubic structures and acts as a bearing between the rotating fullerene molecules. The smooth contact of the rotor and stator molecules decreases significantly the temperature of orientational ordering. These materials have great topochemical importance: at elevated temperatures they transform to high-stability covalent derivatives although preserving their crystalline appearance. The size-dependent molecular recognition promises selective formation of related structures with higher fullerenes and/or substituted cubanes.

Investigation of Sclerotinia sclerotiorum strains variability in Brazil.

PubMed

Abreu, M J; Souza, E A

2015-06-18

White mold is a common bean disease caused by the fungus Sclerotinia sclerotiorum, resulting in economic losses in Brazil and worldwide. Lack of knowledge about the population structure of the pathogen makes it difficult to control the disease. The aim of this study was to characterize strains of S. sclerotiorum obtained from ex-perimental and commercial common bean fields in Brazil. We analyzed 50 strains of S. sclerotiorum collected at several locations in the state of Minas Gerais. The strains were characterized according to their ability and time for developing apothecia. Morphological and physiological analyses such as the mycelial growth index, colony color, the time re-quired to form the first sclerotia on media, the number of sclerotia per plate, average sclerotium size, and sclerotium shape were performed. We determined the mycelial compatibility, conducted molecular analy-sis of microsatellites, and evaluated the aggressiveness of 28 strains. Most strains had the ability to form apothecia. A small group of strains showed mycelial compatibility, and the strains showed different aggres-siveness levels. Overall, the population studied here demonstrated wide variability based on the morphological, physiological, and molecular traits analyzed. The average size and shape of sclerotia presented a cor-relation of 0.617, whereas the times required to form sclerotia and the number of sclerotia per plate showed a correlation of -0.455. The char-acterization of the pathogen population described herein will provide an important tool for promoting the development of bean cultivars re-sistant to white mold.

The effect of molecular shape on oligomerization of hydrophobic drugs: Molecular simulations of ciprofloxacin and nutlin

NASA Astrophysics Data System (ADS)

Li, Jianguo; Beuerman, Roger; Verma, Chandra

2018-03-01

Molecular aggregation plays a significant role in modulating the solubility, permeability, and bioactivity of drugs. The propensity to aggregate depends on hydrophobicity and on molecular shape. Molecular dynamics simulations coupled with enhanced sampling methods are used to explore the early stages of oligomerization of two drug molecules which have a strong aggregation propensity, but with contrasting molecule shapes: the antibiotic ciprofloxacin and the anticancer drug Nutlin-3A. The planar shape of ciprofloxacin induces the formation of stable oligomers at all cluster sizes. The aggregation of ciprofloxacin is driven by two-body interactions, and transferring one ciprofloxacin molecule to an existing cluster involves the desolvation of two faces and the concomitant hydrophobic interactions between the two faces; thus, the corresponding free energy of oligomerization weakly depends on the oligomer size. By contrast, Nutlin-3A has a star-shape and hence can only form stable oligomers when the cluster size is greater than 8. Free energy simulations further confirmed that the free energy of oligomer formation for Nutlin-3A becomes more favorable as the oligomer becomes larger. The aggregation of star-shaped Nutlin-3A results from many-body interactions and hence the free energy of cluster formation is strongly dependent on the size. The findings of this study provide atomistic insights into how molecular shape modulates the aggregation behavior of molecules and may be factored into the design of drugs or nano-particles.

The conformation of the monomethyl ethers of methyl beta-lactoside in D2O and Me2SO-d6 solutions.

PubMed

Fernández, P; Jiménez-Barbero, J

1993-10-04

The solution conformations of all the possible monomethyl ethers of methyl beta-lactoside have been analysed using molecular mechanics and dynamics calculations and nuclear magnetic resonance data (variable temperature and NOE experiments). The overall shape of all the compounds studied is fairly similar and may be described by conformers included in a low-energy region with phi = -100 +/- 40 degrees and psi = -135 +/- 35 degrees, which is ca. 5% of the total potential energy surface for the glycosidic linkages of the disaccharides.

Molecular moment similarity between several nucleoside analogs of thymidine and thymidine. sil@watson.ibm.com.

PubMed

Silverman, B D; Pitman, M C; Platt, D E

1999-06-01

Molecular moment descriptors of the shape and charge distributions of twenty five nucleoside structures have been examined. The structures include thymidine as well as the difluorotoluene nucleoside analog which has been found to pair efficiently with adenine by polymerase catalysis. The remaining twenty three structures have been chosen to be as structurally similar to thymidine and to the difluorotoluene nucleoside analog as possible. The moment descriptors which include a description of the relationship of molecular charge to shape show the difluorotoluene nucleoside to be one of the most proximate molecules to thymidine in the space of the molecular moments. The calculations, therefore, suggest that polymerase specificity might be not only a consequence of molecular steric features alone but also of the molecular electrostatic environment and its registration with molecular shape.

Noonan syndrome.

PubMed

Turner, Anne M

2014-10-01

Noonan syndrome is a common autosomal dominant condition, readily recognisable in childhood. It is characterised by a pattern of typical facial dysmorphism and malformations including congenital cardiac defects, short stature, abnormal chest shape, broad or webbed neck, and a variable learning disability. Mildly affected adults may not be diagnosed until the birth of a more obviously affected child. The phenotype is highly variable. Important progress in understanding the molecular basis of this and other related conditions was made in 2001 when germline mutations in the PTPN11 gene were found to account for ∼50% of cases. Since then, mutations in additional genes in the rat sarcoma (RAS) pathway have been identified in a proportion of the remainder. Molecular confirmation of diagnosis is now possible for many families and has become increasingly important in guiding management. Increased awareness by paediatricians will lead to earlier diagnosis, and provide patients and their families with accurate genetic counselling, including options when planning pregnancy. © 2011 The Author. Journal of Paediatrics and Child Health © 2011 Paediatrics and Child Health Division (Royal Australasian College of Physicians).

Improving of Mechanical and Shape-Memory Properties in Hyperbranched Epoxy Shape-Memory Polymers

NASA Astrophysics Data System (ADS)

Santiago, David; Fabregat-Sanjuan, Albert; Ferrando, Francesc; De la Flor, Silvia

2016-09-01

A series of shape-memory epoxy polymers were synthesized using an aliphatic amine and two different commercial hyperbranched poly(ethyleneimine)s with different molecular weights as crosslinking agents. Thermal, mechanical, and shape-memory properties in materials modified with different hyperbranched polymers were analyzed and compared in order to establish the effect of the structure and the molecular weight of the hyperbranched polymers used. The presence of hyperbranched polymers led to more heterogeneous networks, and the crosslinking densities of which increase as the hyperbranched polymer content increases. The transition temperatures can be tailored from 56 to 117 °C depending on the molecular weight and content of the hyperbranched polymer. The mechanical properties showed excellent values in all formulations at room temperature and, specially, at T_{{g}}^{{E^' with stress at break as high as 15 MPa and strain at break as high as 60 %. The shape-memory performances revealed recovery ratios around 95 %, fixity ratios around 97 %, and shape-recovery velocities as high as 22 %/min. The results obtained in this study reveal that hyperbranched polymers with different molecular weights can be used to enhance the thermal and mechanical properties of epoxy-based SMPs while keeping excellent shape-memory properties.

Unique pattern of dietary adaptation in the dentition of Carnivora: its advantage and developmental origin

PubMed Central

Saito, Kazuyuki; Kishida, Takushi; Takahashi, Katsu; Bessho, Kazuhisa

2016-01-01

Carnivora is a successful taxon in terms of dietary diversity. We investigated the dietary adaptations of carnivoran dentition and the developmental background of their dental diversity, which may have contributed to the success of the lineage. A developmental model was tested and extended to explain the unique variability and exceptional phenotypes observed in carnivoran dentition. Carnivorous mammalian orders exhibited two distinct patterns of dietary adaptation in molars and only Carnivora evolved novel variability, exhibiting a high correlation between relative molar size and the shape of the first molar. Studies of Bmp7-hetero-deficient mice, which may exhibit lower Bmp7 expression, suggested that Bmp7 has pleiotropic effects on these two dental traits. Its effects are consistent with the pattern of dietary adaptation observed in Carnivora, but not that observed in other carnivorous mammals. A molecular evolutionary analysis revealed that Bmp7 sequence evolved by natural selection during ursid evolution, suggesting that it plays an evolutionary role in the variation of carnivoran dentition. Using mouse experiments and a molecular evolutionary analysis, we extrapolated the causal mechanism of the hitherto enigmatic ursid dentition (larger M2 than M1 and M3). Our results demonstrate how carnivorans acquired novel dental variability that benefits their dietary divergence.

Selection of molecular descriptors with artificial intelligence for the understanding of HIV-1 protease peptidomimetic inhibitors-activity.

PubMed

Sirois, S; Tsoukas, C M; Chou, Kuo-Chen; Wei, Dongqing; Boucher, C; Hatzakis, G E

2005-03-01

Quantitative Structure Activity Relationship (QSAR) techniques are used routinely by computational chemists in drug discovery and development to analyze datasets of compounds. Quantitative numerical methods like Partial Least Squares (PLS) and Artificial Neural Networks (ANN) have been used on QSAR to establish correlations between molecular properties and bioactivity. However, ANN may be advantageous over PLS because it considers the interrelations of the modeled variables. This study focused on the HIV-1 Protease (HIV-1 Pr) inhibitors belonging to the peptidomimetic class of compounds. The main objective was to select molecular descriptors with the best predictive value for antiviral potency (Ki). PLS and ANN were used to predict Ki activity of HIV-1 Pr inhibitors and the results were compared. To address the issue of dimensionality reduction, Genetic Algorithms (GA) were used for variable selection and their performance was compared against that of ANN. Finally, the structure of the optimum ANN achieving the highest Pearson's-R coefficient was determined. On the basis of Pearson's-R, PLS and ANN were compared to determine which exhibits maximum performance. Training and validation of models was performed on 15 random split sets of the master dataset consisted of 231 compounds. For each compound 192 molecular descriptors were considered. The molecular structure and constant of inhibition (Ki) were selected from the NIAID database. Study findings suggested that non-covalent interactions such as hydrophobicity, shape and hydrogen bonding describe well the antiviral activity of the HIV-1 Pr compounds. The significance of lipophilicity and relationship to HIV-1 associated hyperlipidemia and lipodystrophy syndrome warrant further investigation.

Study of Molecular-Shape Selectivity of Zeolites by Gas Chromatography

ERIC Educational Resources Information Center

Chao, Pei-Yu; Chuang, Yao-Yuan; Ho, Grace Hsiuying; Chuang, Shiow-Huey; Tsai, Tseng-Chang; Lee, Chi-Young; Tsai, Shang-Tien; Huang, Jun-Fu

2008-01-01

A sorption experiment using a gas chromatograph is described that can help students understand the "molecular-shape selectivity" behavior of zeolites in the subnano regime. Hexane isomers are used as probe molecules to demonstrate the sorption phenomena. In the experiment, a zeolite adsorbs certain hexane isomers with molecular sizes smaller than…

From Molecular Docking to 3D-Quantitative Structure-Activity Relationships (3D-QSAR): Insights into the Binding Mode of 5-Lipoxygenase Inhibitors.

PubMed

Eren, Gokcen; Macchiarulo, Antonio; Banoglu, Erden

2012-02-01

Pharmacological intervention with 5-Lipoxygenase (5-LO) is a promising strategy for treatment of inflammatory and allergic ailments, including asthma. With the aim of developing predictive models of 5-LO affinity and gaining insights into the molecular basis of ligand-target interaction, we herein describe QSAR studies of 59 diverse nonredox-competitive 5-LO inhibitors based on the use of molecular shape descriptors and docking experiments. These studies have successfully yielded a predictive model able to explain much of the variance in the activity of the training set compounds while predicting satisfactorily the 5-LO inhibitory activity of an external test set of compounds. The inspection of the selected variables in the QSAR equation unveils the importance of specific interactions which are observed from docking experiments. Collectively, these results may be used to design novel potent and selective nonredox 5-LO inhibitors. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gender differences in foot shape: a study of Chinese young adults.

PubMed

Hong, Youlian; Wang, Lin; Xu, Dong Qing; Li, Jing Xian

2011-06-01

One important extrinsic factor that causes foot deformity and pain in women is footwear. Women's sports shoes are designed as smaller versions of men's shoes. Based on this, the current study aims to identify foot shape in 1,236 Chinese young adult men and 1,085 Chinese young adult women. Three-dimensional foot shape data were collected through video filming. Nineteen foot shape variables were measured, including girth (4 variables), length (4 variables), width (3 variables), height (7 variables), and angle (1 variable). A comparison of foot measures within the range of the common foot length (FL) categories indicates that women showed significantly smaller values of foot measures in width, height, and girth than men. Three foot types were classified, and distributions of different foot shapes within the same FL were found between women and men. Foot width, medial ball length, ball angle, and instep height showed significant differences among foot types in the same FL for both genders. There were differences in the foot shape between Chinese young women and men, which should be considered in the design of Chinese young adults' sports shoes.

SHAPEMOL: the companion to SHAPE in the molecular era of ALMA and HERSCHEL

NASA Astrophysics Data System (ADS)

Santander-García, M.; Bujarrabal, V.; Alcolea, J.

2013-05-01

Modern instrumentation in radioastronomy constitutes a valuable tool for studying the Universe: ALMA will reach unprecedented sensitivities and spatial resolution, while Herschel/HIFI has opened a new window (most of the sub-mm and far infrared ranges are only accessible from space) for probing molecular warm gas (˜50-1000 K), complementing ground-based telescopes, which are better suited to study molecular molecular gas with temperatures under ˜100 K. On the other hand, the SHAPE software has emerged in the last few years as the standard tool for determinging the morphology and velocity field of different kinds of gaseous nebulae (mainly planetary nebulae, protoplanetary nebulae and nebulae around massive stars, although it can also be applied to H II regions and molecular clouds) via spatio-kinematical modelling. Standard SHAPE implements radiative transfer solving, but it is only available for atomic species and not for molecules. Being aware of the growing importance of the development of tools for easying the analyses of molecular data from new era observatories, we introduce the computer code shapemol, a plug-in for SHAPE with which we intend to fill the so far empty molecular niche. shapemol enables spatio-kinematic modeling with accurate non-LTE calculations of line excitation and radiative transfer in molecular species. This code has been succesfully tested in the study of the excitation conditions of the molecular envelope of the planetary nebula NGC 7027 using data from Herschel/HIFI and IRAM 30m. Currently, it allows radiative transfer solving in the ^{12}CO and ^{13}CO J=1-0 to J=17-16 lines. shapemol, used along SHAPE, allows to easily generate synthetic maps to test against interferometric observations, as well as synthetic line profiles to match single-dish observations.

SABRE: ligand/structure-based virtual screening approach using consensus molecular-shape pattern recognition.

PubMed

Wei, Ning-Ning; Hamza, Adel

2014-01-27

We present an efficient and rational ligand/structure shape-based virtual screening approach combining our previous ligand shape-based similarity SABRE (shape-approach-based routines enhanced) and the 3D shape of the receptor binding site. Our approach exploits the pharmacological preferences of a number of known active ligands to take advantage of the structural diversities and chemical similarities, using a linear combination of weighted molecular shape density. Furthermore, the algorithm generates a consensus molecular-shape pattern recognition that is used to filter and place the candidate structure into the binding pocket. The descriptor pool used to construct the consensus molecular-shape pattern consists of four dimensional (4D) fingerprints generated from the distribution of conformer states available to a molecule and the 3D shapes of a set of active ligands computed using SABRE software. The virtual screening efficiency of SABRE was validated using the Database of Useful Decoys (DUD) and the filtered version (WOMBAT) of 10 DUD targets. The ligand/structure shape-based similarity SABRE algorithm outperforms several other widely used virtual screening methods which uses the data fusion of multiscreening tools (2D and 3D fingerprints) and demonstrates a superior early retrieval rate of active compounds (EF(0.1%) = 69.0% and EF(1%) = 98.7%) from a large size of ligand database (∼95,000 structures). Therefore, our developed similarity approach can be of particular use for identifying active compounds that are similar to reference molecules and predicting activity against other targets (chemogenomics). An academic license of the SABRE program is available on request.

Crystallization of micrometer-sized particles with molecular contours.

PubMed

Song, Pengcheng; Olmsted, Brian K; Chaikin, Paul; Ward, Michael D

2013-11-12

The crystallization of micrometer-sized particles with shapes mimicking those of tetrabenzoheptacene (TBH) and 1,2:5,6-dibenzanthracene (DBT), both flat polyacenes, in an electric field results in the formation of ordered 2D packings that mimic the plane group symmetries in their respective molecular crystal equivalents. Whereas the particles packed in low-density disordered arrangements under a gravitational gradient, dielectrophoresis (under an ac electric field) produced ordered high-density packings with readily identifiable plane group symmetry. The ordered colloidal assemblies were stable for hours, with the packing density decreasing slowly but with recognizable symmetry for up to 12 h for the TBH-shaped particles and up to 4 h for the DBT-shaped particles. This unexpected stability is attributed to jamming behavior associated with interlocking of the dogbone-shaped (TBH) and Z-block (DBT) particles, contrasting with the more rapid reduction of packing density and loss of hexagonal symmetry for disk-shaped particles upon removal of the electric field. The TBH-shaped and DBT-shaped particles assemble into the p2 plane group, which corresponds to the densest particle packing among the possible close-packed plane groups for these particle symmetries. The p2 symmetry observed for the TBH-shaped and DBT-shaped colloid crystal emulates the p2 symmetry of the (010) layers in their respective molecular crystals, which crystallize in monoclinic lattices. Notably, DBT-shaped particles also form ordered domains with pgg symmetry, replicating the plane group symmetry of the (100) layer in the orthorhombic polymorph of DBT. These observations illustrate that the 2D ordering of colloid particles can mimic the packing of molecules with similar shapes, demonstrating that packing can transcend length scales from the molecular to the colloidal.

Stock discrimination of spottedtail goby ( Synechogobius ommaturus) in the Yellow Sea by analysis of otolith shape

NASA Astrophysics Data System (ADS)

Wang, Yingjun; Ye, Zhenjiang; Liu, Qun; Cao, Liang

2011-01-01

Otolith shape is species specific and is an ideal marker of fish population affiliation. In this study, otolith shape of spottedtail goby Synechogobius ommaturus is used to identify stocks in different spawning locations in the Yellow Sea. The main objectives of this study are to explore the potential existence of local stocks of spottedtail goby in the Yellow Sea by analysis of otolith shape, and to investigate ambient impacts on otolith shape. Spottedtail goby was sampled in five locations in the Yellow Sea in 2007 and 2008. Otoliths are described using variables correlated to size (otolith area, perimeter, length, width, and weight) and shape (rectangularity, circularity, and 20 Fourier harmonics). Only standardized otolith variables are used so that the effect of otolith size on the shape variables could be eliminated. There is no significant difference among variables of sex, year, and side (left and right). However, the otolith shapes of the spring stocks and the autumn stocks differ significantly. Otolith shape differences are greater among locations than between years. Correct classification rate of spottedtail goby with the otolith shape at different sampling locations range from 29.7%-77.4%.

Dielectric properties of crystalline organic molecular films in the limit of zero overlap

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

D’Avino, Gabriele, E-mail: gabriele.davino@gmail.com; Vanzo, Davide; Soos, Zoltán G., E-mail: soos@princeton.edu

2016-01-21

We present the calculation of the static dielectric susceptibility tensor and dipole field sums in thin molecular films in the well-defined limit of zero intermolecular overlap. Microelectrostatic and charge redistribution approaches are applied to study the evolution of dielectric properties from one to a few molecular layers in films of different conjugated molecules with organic electronics applications. Because of the conditional convergence of dipolar interactions, dipole fields depend on the shape of the sample and different values are found in the middle layer of a thick film and in the bulk. The shape dependence is eliminated when depolarization is takenmore » into account, and the dielectric tensor of molecular films converges to the bulk limit within a few molecular layers. We quantify the magnitude of surface effects and interpret general trends among different systems in terms of molecular properties, such as shape, polarizability anisotropy, and supramolecular organization. A connection between atomistic models for molecular dielectrics and simpler theories for polarizable atomic lattices is also provided.« less

Visual variability affects early verb learning.

PubMed

Twomey, Katherine E; Lush, Lauren; Pearce, Ruth; Horst, Jessica S

2014-09-01

Research demonstrates that within-category visual variability facilitates noun learning; however, the effect of visual variability on verb learning is unknown. We habituated 24-month-old children to a novel verb paired with an animated star-shaped actor. Across multiple trials, children saw either a single action from an action category (identical actions condition, for example, travelling while repeatedly changing into a circle shape) or multiple actions from that action category (variable actions condition, for example, travelling while changing into a circle shape, then a square shape, then a triangle shape). Four test trials followed habituation. One paired the habituated verb with a new action from the habituated category (e.g., 'dacking' + pentagon shape) and one with a completely novel action (e.g., 'dacking' + leg movement). The others paired a new verb with a new same-category action (e.g., 'keefing' + pentagon shape), or a completely novel category action (e.g., 'keefing' + leg movement). Although all children discriminated novel verb/action pairs, children in the identical actions condition discriminated trials that included the completely novel verb, while children in the variable actions condition discriminated the out-of-category action. These data suggest that - as in noun learning - visual variability affects verb learning and children's ability to form action categories. © 2014 The British Psychological Society.

Prediction of quantum interference in molecular junctions using a parabolic diagram: Understanding the origin of Fano and anti- resonances

NASA Astrophysics Data System (ADS)

Nozaki, Daijiro; Avdoshenko, Stanislav M.; Sevinçli, Hâldun; Gutierrez, Rafael; Cuniberti, Gianaurelio

2013-03-01

Recently the interest in quantum interference (QI) phenomena in molecular devices (molecular junctions) has been growing due to the unique features observed in the transmission spectra. In order to design single molecular devices exploiting QI effects as desired, it is necessary to provide simple rules for predicting the appearance of QI effects such as anti-resonances or Fano line shapes and for controlling them. In this study, we derive a transmission function of a generic molecular junction with a side group (T-shaped molecular junction) using a minimal toy model. We developed a simple method to predict the appearance of quantum interference, Fano resonances or anti- resonances, and its position in the conductance spectrum by introducing a simple graphical representation (parabolic model). Using it we can easily visualize the relation between the key electronic parameters and the positions of normal resonant peaks and anti-resonant peaks induced by quantum interference in the conductance spectrum. We also demonstrate Fano and anti-resonance in T-shaped molecular junctions using a simple tight-binding model. This parabolic model enables one to infer on-site energies of T-shaped molecules and the coupling between side group and main conduction channel from transmission spectra.

Some Causes of the Variable Shape of Flocks of Birds

PubMed Central

Hemelrijk, Charlotte K.; Hildenbrandt, Hanno

2011-01-01

Flocks of birds are highly variable in shape in all contexts (while travelling, avoiding predation, wheeling above the roost). Particularly amazing in this respect are the aerial displays of huge flocks of starlings (Sturnus vulgaris) above the sleeping site at dawn. The causes of this variability are hardly known, however. Here we hypothesise that variability of shape increases when there are larger local differences in movement behaviour in the flock. We investigate this hypothesis with the help of a model of the self-organisation of travelling groups, called StarDisplay, since such a model has also increased our understanding of what causes the oblong shape of schools of fish. The flocking patterns in the model prove to resemble those of real birds, in particular of starlings and rock doves. As to shape, we measure the relative proportions of the flock in several ways, which either depend on the direction of movement or do not. We confirm that flock shape is usually more variable when local differences in movement in the flock are larger. This happens when a) flock size is larger, b) interacting partners are fewer, c) the flock turnings are stronger, and d) individuals roll into the turn. In contrast to our expectations, when variability of speed in the flock is higher, flock shape and the positions of members in the flock are more static. We explain this and indicate the adaptive value of low variability of speed and spatial restriction of interaction and develop testable hypotheses. PMID:21829627

First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs.

PubMed

Clissmann, Fionn; Fiore-Donno, Anna Maria; Hoppe, Björn; Krüger, Dirk; Kahl, Tiemo; Unterseher, Martin; Schnittler, Martin

2015-06-01

Decaying wood hosts a large diversity of seldom investigated protists. Environmental sequencing offers novel insights into communities, but has rarely been applied to saproxylic protists. We investigated the diversity of bright-spored wood-inhabiting Myxomycetes by environmental sequencing. Myxomycetes have a complex life cycle culminating in the formation of mainly macroscopic fruiting bodies, highly variable in shape and colour that are often found on decaying logs. Our hypothesis was that diversity of bright-spored Myxomycetes would increase with decay. DNA was extracted from wood chips collected from 17 beech logs of varying decay stages from the Hainich-Dün region in Central Germany. We obtained 260 partial small subunit ribosomal RNA gene sequences of bright-spored Myxomycetes that were assembled into 29 OTUs, of which 65% were less than 98% similar to those in the existing database. The OTU richness revealed by molecular analysis surpassed that of a parallel inventory of fruiting bodies. We tested several environmental variables and identified pH, rather than decay stage, as the main structuring factor of myxomycete distribution. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Study of silicon crystal surface formation based on molecular dynamics simulation results

NASA Astrophysics Data System (ADS)

Barinovs, G.; Sabanskis, A.; Muiznieks, A.

2014-04-01

The equilibrium shape of <110>-oriented single crystal silicon nanowire, 8 nm in cross-section, was found from molecular dynamics simulations using LAMMPS molecular dynamics package. The calculated shape agrees well to the shape predicted from experimental observations of nanocavities in silicon crystals. By parametrization of the shape and scaling to a known value of {111} surface energy, Wulff form for solid-vapor interface was obtained. The Wulff form for solid-liquid interface was constructed using the same model of the shape as for the solid-vapor interface. The parameters describing solid-liquid interface shape were found using values of surface energies in low-index directions known from published molecular dynamics simulations. Using an experimental value of the liquid-vapor interface energy for silicon and graphical solution of Herring's equation, we constructed angular diagram showing relative equilibrium orientation of solid-liquid, liquid-vapor and solid-vapor interfaces at the triple phase line. The diagram gives quantitative predictions about growth angles for different growth directions and formation of facets on the solid-liquid and solid-vapor interfaces. The diagram can be used to describe growth ridges appearing on the crystal surface grown from a melt. Qualitative comparison to the ridges of a Float zone silicon crystal cone is given.

SHAPEMOL: Modelling molecular line emission in protoplanetary and planetary nebulae with SHAPE

NASA Astrophysics Data System (ADS)

Santander-García, M.; Bujarrabal, V.; Steffen, W.; Koning, N.

2014-04-01

Modern instrumentation in radioastronomy constitutes a valuable tool for studying the Universe: ALMA will reach unprecedented sensitivities and spatial resolution, while Herschel/HIFI has opened a new window for probing molecular warm gas (˜50-1000 K). On the other hand, the SHAPE software has emerged in the last few years as the standard tool for determining the morphology and velocity field of different kinds of gaseous emission nebulae via spatio-kinematical modelling. Standard SHAPE implements radiative transfer solving, but it is only available for atomic species and not for molecules. Being aware of the growing importance of the development of tools for easying the analyses of molecular data from new era observatories, we introduce the computer code shapemol, a plug-in for SHAPE v5.0 with which we intend to fill the so far empty molecular niche. Shapemol enables spatio-kinematic modeling with accurate non-LTE calculations of line excitation and radiative transfer in molecular species. This code has been succesfully tested in the study of the excitation conditions of the molecular envelope of the young planetary nebula NGC 7027 using data from Herschel/HIFI and IRAM 30m. Currently, it allows radiative transfer solving in the 12CO and 13CO J=1-0 to J=17-16 lines. Shapemol, used along SHAPE, allows to easily generate synthetic maps to test against interferometric observations, as well as synthetic line profiles to match single-dish observations.

InN island shape and its dependence on growth condition of molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Cao, Y. G.; Xie, M. H.; Liu, Y.; Ng, Y. F.; Wu, H. S.; Tong, S. Y.

2003-12-01

During molecular-beam epitaxy of InN films on GaN(0001) surface, three-dimensional (3D) islands are observed following an initial wetting layer formation. Depending on deposition condition, the 3D islands take different shapes. Pyramidal islands form when excess nitrogen fluxes are used, whereas pillar-shaped islands are obtained when excess indium fluxes are employed. The pillar-shaped islands are identified to represent the equilibrium shape, whereas the pyramidal ones are limited by kinetics. As the size of islands increases, their aspect ratio shows a decreasing trend, which is attributed to a gradual relaxation of strain in the layer by defects.

Manipulation of Molecular Weight Distribution Shape as a New Strategy to Control Processing Parameters.

PubMed

Nadgorny, Milena; Gentekos, Dillon T; Xiao, Zeyun; Singleton, S Parker; Fors, Brett P; Connal, Luke A

2017-10-01

Molecular weight and dispersity (Ð) influence physical and rheological properties of polymers, which are of significant importance in polymer processing technologies. However, these parameters provide only partial information about the precise composition of polymers, which is reflected by the shape and symmetry of molecular weight distribution (MWD). In this work, the effect of MWD symmetry on thermal and rheological properties of polymers with identical molecular weights and Ð is demonstrated. Remarkably, when the MWD is skewed to higher molecular weight, a higher glass transition temperature (T g ), increased stiffness, increased thermal stability, and higher apparent viscosities are observed. These observed differences are attributed to the chain length composition of the polymers, easily controlled by the synthetic strategy. This work demonstrates a versatile approach to engineer the properties of polymers using controlled synthesis to skew the shape of MWD. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SIMPLE METHOD FOR THE REPRESENTATION, QUANTIFICATION, AND COMPARISON OF THE VOLUMES AND SHAPES OF CHEMICAL COMPOUNDS

EPA Science Inventory

A conceptually and computationally simple method for the definition, display, quantification, and comparison of the shapes of three-dimensional mathematical molecular models is presented. Molecular or solvent-accessible volume and surface area can also be calculated. Algorithms, ...

A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes.

PubMed

Xu, Rosalind J; Blasiak, Bartosz; Cho, Minhaeng; Layfield, Joshua P; Londergan, Casey H

2018-05-17

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.

Structure of a monolayer of molecular rotors on aqueous subphase from grazing-incidence X-ray diffraction.

PubMed

Kaleta, Jiří; Wen, Jin; Magnera, Thomas F; Dron, Paul I; Zhu, Chenhui; Michl, Josef

2018-03-23

In situ grazing-incidence X-ray scattering shows that a monolayer of artificial rod-shaped dipolar molecular rotors produced on the surface of an aqueous subphase in a Langmuir trough has a structure conducive to a 2D ferroelectric phase. The axes of the rotors stand an average of 0.83 nm apart in a triangular grid, perpendicular to the surface within experimental error. They carry 2,3-dichlorophenylene rotators near rod centers, between two decks of interlocked triptycenes installed axially on the rotor axle. The analysis is based first on simultaneous fitting of observed Bragg rods and second on fitting the reflectivity curve with only three adjustable parameters and the calculated rotor electron density, which also revealed the presence of about seven molecules of water near each rotator. Dependent on preparation conditions, a minor and variable amount of a different crystal phase may also be present in the monolayer.

Solvent-coordinate free-energy landscape view of water-mediated ion-pair dissociation

NASA Astrophysics Data System (ADS)

Yonetani, Yoshiteru

2017-12-01

Water-mediated ion-pair dissociation is studied by molecular dynamics simulations of NaCl in water. Multidimensional free-energy analysis clarifies the relation between two essential solvent coordinates: the water coordination number and water-bridge formation. These two are related in a complex way. Both are necessary to describe ion-pair dissociation. The mechanism constructed with both solvent variables clearly shows the individual roles. The water coordination number is critical for starting ion-pair dissociation. Water-bridge formation is also important because it increases the likelihood of ion-pair dissociation by reducing the dissociation free-energy barrier. Additional Ca-Cl and NH4-Cl calculations show that these conclusions are unaffected by changes in the ion charge and shape. The present results will contribute to future explorations of many other molecular events such as surface water exchange and protein-ligand dissociation because the same mechanism is involved in such events.

Epithelial Folding Driven by Apical or Basal-Lateral Modulation: Geometric Features, Mechanical Inference, and Boundary Effects.

PubMed

Wen, Fu-Lai; Wang, Yu-Chiun; Shibata, Tatsuo

2017-06-20

During embryonic development, epithelial sheets fold into complex structures required for tissue and organ functions. Although substantial efforts have been devoted to identifying molecular mechanisms underlying epithelial folding, far less is understood about how forces deform individual cells to sculpt the overall sheet morphology. Here we describe a simple and general theoretical model for the autonomous folding of monolayered epithelial sheets. We show that active modulation of intracellular mechanics along the basal-lateral as well as the apical surfaces is capable of inducing fold formation in the absence of buckling instability. Apical modulation sculpts epithelia into shallow and V-shaped folds, whereas basal-lateral modulation generates deep and U-shaped folds. These characteristic tissue shapes remain unchanged when subject to mechanical perturbations from the surroundings, illustrating that the autonomous folding is robust against environmental variabilities. At the cellular scale, how cells change shape depends on their initial aspect ratios and the modulation mechanisms. Such cell deformation characteristics are verified via experimental measurements for a canonical folding process driven by apical modulation, indicating that our theory could be used to infer the underlying folding mechanisms based on experimental data. The mechanical principles revealed in our model could potentially guide future studies on epithelial folding in diverse systems. Copyright © 2017. Published by Elsevier Inc.

Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments.

PubMed

Karaboga, Arnaud S; Petronin, Florent; Marchetti, Gino; Souchet, Michel; Maigret, Bernard

2013-04-01

Since 3D molecular shape is an important determinant of biological activity, designing accurate 3D molecular representations is still of high interest. Several chemoinformatic approaches have been developed to try to describe accurate molecular shapes. Here, we present a novel 3D molecular description, namely harmonic pharma chemistry coefficient (HPCC), combining a ligand-centric pharmacophoric description projected onto a spherical harmonic based shape of a ligand. The performance of HPCC was evaluated by comparison to the standard ROCS software in a ligand-based virtual screening (VS) approach using the publicly available directory of useful decoys (DUD) data set comprising over 100,000 compounds distributed across 40 protein targets. Our results were analyzed using commonly reported statistics such as the area under the curve (AUC) and normalized sum of logarithms of ranks (NSLR) metrics. Overall, our HPCC 3D method is globally as efficient as the state-of-the-art ROCS software in terms of enrichment and slightly better for more than half of the DUD targets. Since it is largely admitted that VS results depend strongly on the nature of the protein families, we believe that the present HPCC solution is of interest over the current ligand-based VS methods. Copyright © 2013 Elsevier Inc. All rights reserved.

Polymeric amphiphile branching leads to rare nanodisc shaped planar self-assemblies.

PubMed

Qu, Xiaozhong; Omar, Leila; Le, Thi Bich Hang; Tetley, Laurence; Bolton, Katherine; Chooi, Kar Wai; Wang, Wei; Uchegbu, Ijeoma F

2008-09-16

Self-assembly is fundamental to the biological function of cells and the fabrication of nanomaterials. However, the origin of the shape of various self-assemblies, such as the shape of cells, is not altogether clear. Polymeric, oligomeric, or low molecular weight amphiphiles are a rich source of nanomaterials, and controlling their self-assembly is the route to tailored nanosystems with specific functionalities. Here, we provide direct evidence that a particular molecular architecture, polymeric branching, leads to a rare form of self-assembly, the planar nanodisc. Cholesterol containing self-assemblies formed from amphiphilic linear or branched cetyl poly(ethylenimine) (Mn approximately 1000 Da) or amphiphilic cetyl poly(propylenimine) dendrimer derivatives (Mn approximately 2000 Da) show that branching, by reducing the hydrophilic headgroup area, alters the shape of the self-assemblies transforming closed 60 nm spherical bilayer vesicles to rare 50 nm x 10 nm planar bilayer discs. Increasing the hydrophilic headgroup area, by the inclusion of methoxy poly(ethylene glycol) moieties into the amphiphilic headgroup, transforms the planar discs to 100 nm spherical bilayer vesicles. This study provides insight into the key role played by molecular shape on molecular self-organization into rare nanodiscs.

Mapping and genomic targeting of the major leaf shape gene (L) in Upland cotton (Gossypium hirsutum L.).

PubMed

Andres, Ryan J; Bowman, Daryl T; Kaur, Baljinder; Kuraparthy, Vasu

2014-01-01

A major leaf shape locus (L) was mapped with molecular markers and genomically targeted to a small region in the D-genome of cotton. By using expression analysis and candidate gene mapping, two LMI1 -like genes are identified as possible candidates for leaf shape trait in cotton. Leaf shape in cotton is an important trait that influences yield, flowering rates, disease resistance, lint trash, and the efficacy of foliar chemical application. The leaves of okra leaf cotton display a significantly enhanced lobing pattern, as well as ectopic outgrowths along the lobe margins when compared with normal leaf cotton. These phenotypes are the hallmark characteristics of mutations in various known modifiers of leaf shape that culminate in the mis/over-expression of Class I KNOX genes. To better understand the molecular and genetic processes underlying leaf shape in cotton, a normal leaf accession (PI607650) was crossed to an okra leaf breeding line (NC05AZ21). An F2 population of 236 individuals confirmed the incompletely dominant single gene nature of the okra leaf shape trait in Gossypium hirsutum L. Molecular mapping with simple sequence repeat markers localized the leaf shape gene to 5.4 cM interval in the distal region of the short arm of chromosome 15. Orthologous mapping of the closely linked markers with the sequenced diploid D-genome (Gossypium raimondii) tentatively resolved the leaf shape locus to a small genomic region. RT-PCR-based expression analysis and candidate gene mapping indicated that the okra leaf shape gene (L (o) ) in cotton might be an upstream regulator of Class I KNOX genes. The linked molecular markers and delineated genomic region in the sequenced diploid D-genome will assist in the future high-resolution mapping and map-based cloning of the leaf shape gene in cotton.

Membrane re-modelling by BAR domain superfamily proteins via molecular and non-molecular factors.

PubMed

Nishimura, Tamako; Morone, Nobuhiro; Suetsugu, Shiro

2018-04-17

Lipid membranes are structural components of cell surfaces and intracellular organelles. Alterations in lipid membrane shape are accompanied by numerous cellular functions, including endocytosis, intracellular transport, and cell migration. Proteins containing Bin-Amphiphysin-Rvs (BAR) domains (BAR proteins) are unique, because their structures correspond to the membrane curvature, that is, the shape of the lipid membrane. BAR proteins present at high concentration determine the shape of the membrane, because BAR domain oligomers function as scaffolds that mould the membrane. BAR proteins co-operate with various molecular and non-molecular factors. The molecular factors include cytoskeletal proteins such as the regulators of actin filaments and the membrane scission protein dynamin. Lipid composition, including saturated or unsaturated fatty acid tails of phospholipids, also affects the ability of BAR proteins to mould the membrane. Non-molecular factors include the external physical forces applied to the membrane, such as tension and friction. In this mini-review, we will discuss how the BAR proteins orchestrate membrane dynamics together with various molecular and non-molecular factors. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Influence of Molecular Shape on Molecular Orientation and Stability of Vapor-Deposited Organic Semiconductors

NASA Astrophysics Data System (ADS)

Walters, Diane M.; Johnson, Noah D.; Ediger, M. D.

Physical vapor deposition is commonly used to prepare active layers in organic electronics. Recently, it has been shown that molecular orientation and packing can be tuned by changing the substrate temperature during deposition, while still producing macroscopically homogeneous films. These amorphous materials can be highly anisotropic when prepared with low substrate temperatures, and they can exhibit exceptional kinetic stability; films retain their favorable packing when heated to high temperatures. Here, we study the influence of molecular shape on molecular orientation and stability. We investigate disc-shaped molecules, such as TCTA and m-MTDATA, nearly spherical molecules, such as Alq3, and linear molecules covering a broad range of aspect ratios, such as p-TTP and BSB-Cz. Disc-shaped molecules have preferential horizontal orientation when deposited at low substrate temperatures, and their orientation can be tuned by changing the substrate temperature. Alq3 forms stable, amorphous films that are optically isotropic when vapor deposited over a broad range of substrate temperatures. This work may guide the choice of material and deposition conditions for vapor-deposited films used in organic electronics and allow for more efficient devices to be fabricated.

QSAR analyses of 3-(4-benzylpiperidin-1-yl)-N-phenylpropylamine derivatives as potent CCR5 antagonists.

PubMed

Roy, Kunal; Leonard, J Thomas

2005-01-01

CCR5 receptor binding affinity of a series of 3-(4-benzylpiperidin-1-yl)propylamine congeners was subjected to QSAR study using the linear free energy related (LFER) model of Hansch. Appropriate indicator variables encoding different group contributions and different physicochemical variables such as hydrophobicity (pi), electronic (Hammett sigma), and steric (molar refractivity, STERIMOL values) parameters of phenyl ring substituents of the compounds were used as predictor variables. The Hansch analysis explores the importance of the lipophilicity and electron-donating substituents for the binding affinity. However, this method could not give more insight into the structure-activity relationships because of the diverse molecular features in the data set. 3D-QSAR analyses of the same data set using Molecular Shape Analysis (MSA), Receptor Surface Analysis (RSA), and Molecular Field Analysis (MFA) techniques were also performed. The best model with acceptable statistical quality was derived from the MSA, which showed the importance of the relative negative charge (RNCG): substituents with a high RNCG value have more binding affinity than the unsubstituted piperidine and phenyl (R1 position) congeners. The relative negative charge surface area (RNCS) is detrimental (e.g. R2 = 3,4-Cl2) for the activity. An increase in the length of the molecule in the Z dimension (Lz) is conducive (e.g. R3 = sulfonylmorpholino), while an increase in the area of the molecular shadow in the XZ plane (Sxz) is detrimental (e.g. R1 = N-c-hexylmethyl-5-oxopyrrolidin-3-yl) for the binding affinity. The presence of a chiral center makes the molecule less active (e.g. R1 = N-methyl-5-oxopyrrolidin-3-yl). An increase in the van der Waals area, the molecular volume, and the difference between the volume of the individual molecule and the shape reference compound are conducive (e.g. R3 = (CH3)2NSO2-) for the binding affinity. Substituents with higher JursFPSA_2 values (fractional charged partial surface area) like the N-methylsulfonylpiperidin-4-yl (R1 position) group have better binding affinity than the substituents such as 4-chlorophenylamino (R1 position). Unsubstituted piperidines (R1 position) with less JursFNSA_1 values have lower binding affinity than the 4-chlorophenyl substituted compounds. The MFA derived equation shows interaction energies at different grid points, while the RSA model shows the importance of hydrophobicity and charge at different regions of the molecules. The models were validated through the leave-one-out, leave-15%-out, and leave-25%-out cross-validation techniques. The developed models were also subjected to a randomization test (99% confidence level). Although the MSA derived models had excellent statistical qualities both for the training as well as test sets, RSA and MFA results for the test sets are not comparable statistically with the MSA derived models.

Effect of molecular weight of polystyrensulfonic acid sodium salt polymers on the precipitation kinetics of sodium bicarbonate

NASA Astrophysics Data System (ADS)

Martínez-Cruz, Nancy; Carrillo-Romo, Felipe; Jaramillo-Vigueras, David

2004-10-01

This paper analyzes the effect of polystyrensulfonic acid sodium salt (NaPSS), obtained by kinetic precipitation from solutions of polymers of molecular weight 245 000 and 38 000 g mol-1 in sodium bicarbonate (NaHCO3) itself precipitated from synthetic brine. Crystal size, shape and the additive adsorbed are reported. X shaped and hexagonal prisms crystals with different aspect ratios were obtained. The results show that with increasing polymer concentration the crystal size decreases, from 0.27 to 0.48 mm. Additionally, the higher molecular weight polymer shows both higher adsorption capacity and higher crystal habit modification. Crystal shape patterns were similar for both polymers; however, the higher molecular weight material induced changes at lower concentration. It was observed that the precipitation rate reached a minimum with increasing additive concentration.

Representation and visualization of variability in a 3D anatomical atlas using the kidney as an example

NASA Astrophysics Data System (ADS)

Hacker, Silke; Handels, Heinz

2006-03-01

Computer-based 3D atlases allow an interactive exploration of the human body. However, in most cases such 3D atlases are derived from one single individual, and therefore do not regard the variability of anatomical structures concerning their shape and size. Since the geometric variability across humans plays an important role in many medical applications, our goal is to develop a framework of an anatomical atlas for representation and visualization of the variability of selected anatomical structures. The basis of the project presented is the VOXEL-MAN atlas of inner organs that was created from the Visible Human data set. For modeling anatomical shapes and their variability we utilize "m-reps" which allow a compact representation of anatomical objects on the basis of their skeletons. As an example we used a statistical model of the kidney that is based on 48 different variants. With the integration of a shape description into the VOXEL-MAN atlas it is now possible to query and visualize different shape variations of an organ, e.g. by specifying a person's age or gender. In addition to the representation of individual shape variants, the average shape of a population can be displayed. Besides a surface representation, a volume-based representation of the kidney's shape variants is also possible. It results from the deformation of the reference kidney of the volume-based model using the m-rep shape description. In this way a realistic visualization of the shape variants becomes possible, as well as the visualization of the organ's internal structures.

Sensitivity analysis for axis rotation diagrid structural systems according to brace angle changes

NASA Astrophysics Data System (ADS)

Yang, Jae-Kwang; Li, Long-Yang; Park, Sung-Soo

2017-10-01

General regular shaped diagrid structures can express diverse shapes because braces are installed along the exterior faces of the structures and the structures have no columns. However, since irregular shaped structures have diverse variables, studies to assess behaviors resulting from various variables are continuously required to supplement the imperfections related to such variables. In the present study, materials elastic modulus and yield strength were selected as variables for strength that would be applied to diagrid structural systems in the form of Twisters among the irregular shaped buildings classified by Vollers and that affect the structural design of these structural systems. The purpose of this study is to conduct sensitivity analysis for axial rotation diagrid structural systems according to changes in brace angles in order to identify the design variables that have relatively larger effects and the tendencies of the sensitivity of the structures according to changes in brace angles and axial rotation angles.

Molecular Modeling of Lipid Membrane Curvature Induction by a Peptide: More than Simply Shape

PubMed Central

Sodt, Alexander J.; Pastor, Richard W.

2014-01-01

Molecular dynamics simulations of an amphipathic helix embedded in a lipid bilayer indicate that it will induce substantial positive curvature (e.g., a tube of diameter 20 nm at 16% surface coverage). The induction is twice that of a continuum model prediction that only considers the shape of the inclusion. The discrepancy is explained in terms of the additional presence of specific interactions described only by the molecular model. The conclusion that molecular shape alone is insufficient to quantitatively model curvature is supported by contrasting molecular and continuum models of lipids with large and small headgroups (choline and ethanolamine, respectively), and of the removal of a lipid tail (modeling a lyso-lipid). For the molecular model, curvature propensity is analyzed by computing the derivative of the free energy with respect to bending. The continuum model predicts that the inclusion will soften the bilayer near the headgroup region, an effect that may weaken curvature induction. The all-atom predictions are consistent with experimental observations of the degree of tubulation by amphipathic helices and variation of the free energy of binding to liposomes. PMID:24806928

Visualization of the variability of 3D statistical shape models by animation.

PubMed

Lamecker, Hans; Seebass, Martin; Lange, Thomas; Hege, Hans-Christian; Deuflhard, Peter

2004-01-01

Models of the 3D shape of anatomical objects and the knowledge about their statistical variability are of great benefit in many computer assisted medical applications like images analysis, therapy or surgery planning. Statistical model of shapes have successfully been applied to automate the task of image segmentation. The generation of 3D statistical shape models requires the identification of corresponding points on two shapes. This remains a difficult problem, especially for shapes of complicated topology. In order to interpret and validate variations encoded in a statistical shape model, visual inspection is of great importance. This work describes the generation and interpretation of statistical shape models of the liver and the pelvic bone.

General shape optimization capability

NASA Technical Reports Server (NTRS)

Chargin, Mladen K.; Raasch, Ingo; Bruns, Rudolf; Deuermeyer, Dawson

1991-01-01

A method is described for calculating shape sensitivities, within MSC/NASTRAN, in a simple manner without resort to external programs. The method uses natural design variables to define the shape changes in a given structure. Once the shape sensitivities are obtained, the shape optimization process is carried out in a manner similar to property optimization processes. The capability of this method is illustrated by two examples: the shape optimization of a cantilever beam with holes, loaded by a point load at the free end (with the shape of the holes and the thickness of the beam selected as the design variables), and the shape optimization of a connecting rod subjected to several different loading and boundary conditions.

Environmental effects on the shape variation of male ultraviolet patterns in the Brimstone butterfly ( Gonepteryx rhamni, Pieridae, Lepidoptera)

NASA Astrophysics Data System (ADS)

Pecháček, Pavel; Stella, David; Keil, Petr; Kleisner, Karel

2014-12-01

The males of the Brimstone butterfly ( Gonepteryx rhamni) have ultraviolet pattern on the dorsal surfaces of their wings. Using geometric morphometrics, we have analysed correlations between environmental variables (climate, productivity) and shape variability of the ultraviolet pattern and the forewing in 110 male specimens of G. rhamni collected in the Palaearctic zone. To start with, we subjected the environmental variables to principal component analysis (PCA). The first PCA axis (precipitation, temperature, latitude) significantly correlated with shape variation of the ultraviolet patterns across the Palaearctic. Additionally, we have performed two-block partial least squares (PLS) analysis to assess co-variation between intraspecific shape variation and the variation of 11 environmental variables. The first PLS axis explained 93 % of variability and represented the effect of precipitation, temperature and latitude. Along this axis, we observed a systematic increase in the relative area of ultraviolet colouration with increasing temperature and precipitation and decreasing latitude. We conclude that the shape variation of ultraviolet patterns on the forewings of male Brimstones is correlated with large-scale environmental factors.

Control of nitromethane photoionization efficiency with shaped femtosecond pulses.

PubMed

Roslund, Jonathan; Shir, Ofer M; Dogariu, Arthur; Miles, Richard; Rabitz, Herschel

2011-04-21

The applicability of adaptive femtosecond pulse shaping is studied for achieving selectivity in the photoionization of low-density polyatomic targets. In particular, optimal dynamic discrimination (ODD) techniques exploit intermediate molecular electronic resonances that allow a significant increase in the photoionization efficiency of nitromethane with shaped near-infrared femtosecond pulses. The intensity bias typical of high-photon number, nonresonant ionization is accounted for by reference to a strictly intensity-dependent process. Closed-loop adaptive learning is then able to discover a pulse form that increases the ionization efficiency of nitromethane by ∼150%. The optimally induced molecular dynamics result from entry into a region of parameter space inaccessible with intensity-only control. Finally, the discovered pulse shape is demonstrated to interact with the molecular system in a coherent fashion as assessed from the asymmetry between the response to the optimal field and its time-reversed counterpart.

Effect of molecular shape on rotation under severe confinement

DOE PAGES

Dhiman, Indu; Bhowmik, Debsindhu; Shrestha, Utsab R.; ...

2018-01-31

Orientational structure and dynamics of molecules is known to be affected by confinement in space comparable in size to the molecule itself. ZSM-5 with porous channels of ≈0.55 nm is such a porous medium, which offers a strict spatial confinement on low molecular weight hydrocarbons. An important factor that determines these properties is the shape of the confined molecules. In this work, we employed molecular dynamics simulation to study the orientational structure and dynamics of four molecules that differ in shape but have similar kinetic diameters and moments of inertia, confined in ZSM-5. The effect of molecular shape on themore » orientational structure and dynamics of propane, acetonitrile, acetaldehyde and acetone in ZSM-5 is studied by means of probing the differences in the orientational distribution of molecules in the ZSM-5 channels, and extracting time scales of the decay of correlation functions related to rotational motion. Orientational correlation functions of all the four molecules exhibit two regimes of rotational motion. While the short time regime represents free rotation of the molecules before they collide with the pore walls, the long time orientational jumps driven by inter-channel migrations give rise to a very slow varying second regime. Of the molecules studied, orientational structure and dynamics of propane is found to be least affected by confinement under ZSM-5, whereas charge and shape asymmetry of other molecules makes their interchannel migration-driven rotation slow. The time scales involved in the rotational motion for the molecules studied are compared with similar studies reported in literature. Lastly, this study reveals the important role that molecular shape plays in the behavior of confined molecules.« less

Effect of molecular shape on rotation under severe confinement

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

Dhiman, Indu; Bhowmik, Debsindhu; Shrestha, Utsab R.

Orientational structure and dynamics of molecules is known to be affected by confinement in space comparable in size to the molecule itself. ZSM-5 with porous channels of ≈0.55 nm is such a porous medium, which offers a strict spatial confinement on low molecular weight hydrocarbons. An important factor that determines these properties is the shape of the confined molecules. In this work, we employed molecular dynamics simulation to study the orientational structure and dynamics of four molecules that differ in shape but have similar kinetic diameters and moments of inertia, confined in ZSM-5. The effect of molecular shape on themore » orientational structure and dynamics of propane, acetonitrile, acetaldehyde and acetone in ZSM-5 is studied by means of probing the differences in the orientational distribution of molecules in the ZSM-5 channels, and extracting time scales of the decay of correlation functions related to rotational motion. Orientational correlation functions of all the four molecules exhibit two regimes of rotational motion. While the short time regime represents free rotation of the molecules before they collide with the pore walls, the long time orientational jumps driven by inter-channel migrations give rise to a very slow varying second regime. Of the molecules studied, orientational structure and dynamics of propane is found to be least affected by confinement under ZSM-5, whereas charge and shape asymmetry of other molecules makes their interchannel migration-driven rotation slow. The time scales involved in the rotational motion for the molecules studied are compared with similar studies reported in literature. Lastly, this study reveals the important role that molecular shape plays in the behavior of confined molecules.« less

Variable area nozzle for gas turbine engines driven by shape memory alloy actuators

NASA Technical Reports Server (NTRS)

Rey, Nancy M. (Inventor); Miller, Robin M. (Inventor); Tillman, Thomas G. (Inventor); Rukus, Robert M. (Inventor); Kettle, John L. (Inventor); Dunphy, James R. (Inventor); Chaudhry, Zaffir A. (Inventor); Pearson, David D. (Inventor); Dreitlein, Kenneth C. (Inventor); Loffredo, Constantino V. (Inventor)

2001-01-01

A gas turbine engine includes a variable area nozzle having a plurality of flaps. The flaps are actuated by a plurality of actuating mechanisms driven by shape memory alloy (SMA) actuators to vary fan exist nozzle area. The SMA actuator has a deformed shape in its martensitic state and a parent shape in its austenitic state. The SMA actuator is heated to transform from martensitic state to austenitic state generating a force output to actuate the flaps. The variable area nozzle also includes a plurality of return mechanisms deforming the SMA actuator when the SMA actuator is in its martensitic state.

The FPase properties and morphology changes of a cellulolytic bacterium, Sporocytophaga sp. JL-01, on decomposing filter paper cellulose.

PubMed

Wang, Xiuran; Peng, Zhongqi; Sun, Xiaoling; Liu, Dongbo; Chen, Shan; Li, Fan; Xia, Hongmei; Lu, Tiancheng

2012-01-01

Sporocytophaga sp. JL-01 is a sliding cellulose degrading bacterium that can decompose filter paper (FP), carboxymethyl cellulose (CMC) and cellulose CF11. In this paper, the morphological characteristics of S. sp. JL-01 growing in FP liquid medium was studied by Scanning Electron Microscope (SEM), and one of the FPase components of this bacterium was analyzed. The results showed that the cell shapes were variable during the process of filter paper cellulose decomposition and the rod shape might be connected with filter paper decomposing. After incubating for 120 h, the filter paper was decomposed significantly, and it was degraded absolutely within 144 h. An FPase1 was purified from the supernatant and its characteristics were analyzed. The molecular weight of the FPase1 was 55 kDa. The optimum pH was pH 7.2 and optimum temperature was 50°C under experiment conditions. Zn(2+) and Co(2+) enhanced the enzyme activity, but Fe(3+) inhibited it.

Evidence from mixed hydrate nucleation for a funnel model of crystallization.

PubMed

Hall, Kyle Wm; Carpendale, Sheelagh; Kusalik, Peter G

2016-10-25

The molecular-level details of crystallization remain unclear for many systems. Previous work has speculated on the phenomenological similarities between molecular crystallization and protein folding. Here we demonstrate that molecular crystallization can involve funnel-shaped potential energy landscapes through a detailed analysis of mixed gas hydrate nucleation, a prototypical multicomponent crystallization process. Through this, we contribute both: (i) a powerful conceptual framework for exploring and rationalizing molecular crystallization, and (ii) an explanation of phenomenological similarities between protein folding and crystallization. Such funnel-shaped potential energy landscapes may be typical of broad classes of molecular ordering processes, and can provide a new perspective for both studying and understanding these processes.

Evidence from mixed hydrate nucleation for a funnel model of crystallization

PubMed Central

Hall, Kyle Wm.; Carpendale, Sheelagh; Kusalik, Peter G.

2016-01-01

The molecular-level details of crystallization remain unclear for many systems. Previous work has speculated on the phenomenological similarities between molecular crystallization and protein folding. Here we demonstrate that molecular crystallization can involve funnel-shaped potential energy landscapes through a detailed analysis of mixed gas hydrate nucleation, a prototypical multicomponent crystallization process. Through this, we contribute both: (i) a powerful conceptual framework for exploring and rationalizing molecular crystallization, and (ii) an explanation of phenomenological similarities between protein folding and crystallization. Such funnel-shaped potential energy landscapes may be typical of broad classes of molecular ordering processes, and can provide a new perspective for both studying and understanding these processes. PMID:27790987

International Journal of Quantum Chemistry, Quantum Biology Symposium No. 24. Proceedings of the International Symposium on the Application of Fundamental Theory to Problems of Biology and Pharmacology, Held at Ponce de Leon Resort, St. Augustine, Florida on March 1-7, 1997. Volume 65, No. 6, 1997.

DTIC Science & Technology

1997-03-01

characteristic musk odor [7]. Molecular shape is important in circular dichroism and chirality. Enantiomers, if viewed in isolation, have identical all...simply a function of the length of the elon - gated structure). We can introduce V/S as an index of molecular shape by using computed molecular

Influence of temperature on the rhombic shape of paracetamol molecular crystals

NASA Astrophysics Data System (ADS)

Belyaev, A. P.; Rubets, V. P.; Antipov, V. V.

2017-04-01

The method of differential scanning ellipsometry has been used to study the influence of heating on the rhombic shape of paracetamol molecular crystals. Rhombic molecular paracetamol crystals have been synthesized in vacuum from the vapor phase of paracetamol as a result of complex transformation, which includes a second-order transition that gives rise to a pretransition phase. It has been found that these crystals contain monoclinic nuclei, which favor the form I-to-form II polymorphic transformation during heating.

Environmental and biological characteristics of Atlantic bluefin tuna and albacore spawning habitats based on their egg distributions

NASA Astrophysics Data System (ADS)

Reglero, Patricia; Santos, Maria; Balbín, Rosa; Laíz-Carrión, Raul; Alvarez-Berastegui, Diego; Ciannelli, Lorenzo; Jiménez, Elisa; Alemany, Francisco

2017-06-01

Tuna spawning habitats are traditionally characterized using data sets of larvae or gonads from mature adults and concurrent environmental variables. Data on egg distributions have never previously been used since molecular analyses are mandatory to identify tuna eggs to species level. However, in this study we use molecularly derived egg distribution data, in addition to larval data, to characterize hydrographic and biological drivers of the spatial distribution of eggs and larvae of bluefin Thunnus thynnus and albacore tuna Thunnus alalunga in the Balearic Sea, a main spawning area of these species in the Mediterranean. The effects of the hydrography, characterized by salinity, temperature and geostrophic velocity, on the spatial distributions of the eggs and larvae are investigated. Three biological variables are used to describe the productivity in the area: chlorophyll a in the mixed layer, chlorophyll a in the deep chlorophyll maximum and mesozooplankton biomass in the mixed layer. Our results point to the importance of salinity fronts and temperatures above a minimum threshold in shaping the egg and larval distribution of both species. The spatial distribution of the biotic variables was very scattered, and they did not emerge as significant variables in the presence-absence models. However, they became significant when modeling egg and larval abundances. The lack of correlation between the three biotic variables challenges the use of chlorophyll a to describe trophic scenarios for the larvae and suggests that the spatial distribution of resources is not persistent in time. The different patterns in relation to biotic variables across species and stages found in this and other studies indicate a still elusive understanding of the link between trophic levels involving tuna early larval stages. Our ability to improve short-term forecasting and long-term predictions of climate effects on the egg and larval distributions is discussed based on the consistency of the environmentally driven spatial patterns for the two species.

CO{sub 2} isolated line shapes by classical molecular dynamics simulations: Influence of the intermolecular potential and comparison with new measurements

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

Larcher, G.; Tran, H., E-mail: ha.tran@lisa.u-pec.fr; Schwell, M.

2014-02-28

Room temperature absorption spectra of various transitions of pure CO{sub 2} have been measured in a broad pressure range using a tunable diode-laser and a cavity ring-down spectrometer, respectively, in the 1.6 μm and 0.8 μm regions. Their spectral shapes have been calculated by requantized classical molecular dynamics simulations. From the time-dependent auto-correlation function of the molecular dipole, including Doppler and collisional effects, spectral shapes are directly computed without the use of any adjusted parameter. Analysis of the spectra calculated using three different anisotropic intermolecular potentials shows that the shapes of pure CO{sub 2} lines, in terms of both themore » Lorentz widths and non-Voigt effects, slightly depend on the used potential. Comparisons between these ab initio calculations and the measured spectra show satisfactory agreement for all considered transitions (from J = 6 to J = 46). They also show that non-Voigt effects on the shape of CO{sub 2} transitions are almost independent of the rotational quantum number of the considered lines.« less

Monitor Variability of Millimeter Lines in IRC+10216

NASA Astrophysics Data System (ADS)

He, J. H.; Dinh-V-Trung; Hasegawa, T. I.

2017-08-01

A single dish monitoring of millimeter maser lines SiS J = 14-13 and HCN {ν }2={1}f J = 3-2 and several other rotational lines is reported for the archetypal carbon star IRC+10216. Relative line strength variations of 5% ∼ 30% are found for eight molecular line features with respect to selected reference lines. Definite line-shape variations are found in limited velocity intervals of the SiS and HCN line profiles. The asymmetrical line profiles of the two lines are mainly due to the varying components. The dominant varying components of the line profiles have similar periods and phases to the IR light variation, though both quantities show some degree of velocity dependence; there is also variability asymmetry between the blue and red line wings of both lines. Combining the velocities and amplitudes with a wind velocity model, we suggest that the line profile variations are due to SiS and HCN masing lines emanating from the wind acceleration zone. The possible link of the variabilities to thermal, dynamical, and/or chemical processes within or under this region is also discussed.

Structure-function covariation with nonfeeding ecological variables influences evolution of feeding specialization in Carnivora

PubMed Central

Tseng, Z. Jack; Flynn, John J.

2018-01-01

Skull shape convergence is pervasive among vertebrates. Although this is frequently inferred to indicate similar functional underpinnings, neither the specific structure-function linkages nor the selective environments in which the supposed functional adaptations arose are commonly identified and tested. We demonstrate that nonfeeding factors relating to sexual maturity and precipitation-related arboreality also can generate structure-function relationships in the skulls of carnivorans (dogs, cats, seals, and relatives) through covariation with masticatory performance. We estimated measures of masticatory performance related to ecological variables that covary with cranial shape in the mammalian order Carnivora, integrating geometric morphometrics and finite element analyses. Even after accounting for phylogenetic autocorrelation, cranial shapes are significantly correlated to both feeding and nonfeeding ecological variables, and covariation with both variable types generated significant masticatory performance gradients. This suggests that mechanisms of obligate shape covariation with nonfeeding variables can produce performance changes resembling those arising from feeding adaptations in Carnivora. PMID:29441363

The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland.

PubMed

Magalhaes, Isabel S; D'Agostino, Daniele; Hohenlohe, Paul A; MacColl, Andrew D C

2016-09-01

There has been a large focus on the genetics of traits involved in adaptation, but knowledge of the environmental variables leading to adaptive changes is surprisingly poor. Combined use of environmental data with morphological and genomic data should allow us to understand the extent to which patterns of phenotypic and genetic diversity within a species can be explained by the structure of the environment. Here, we analyse the variation of populations of three-spined stickleback from 27 freshwater lakes on North Uist, Scotland, that vary greatly in their environment, to understand how environmental and genetic constraints contribute to phenotypic divergence. We collected 35 individuals per population and 30 abiotic and biotic environmental parameters to characterize variation across lakes and analyse phenotype-environment associations. Additionally, we used RAD sequencing to estimate the genetic relationships among a subset of these populations. We found a large amount of phenotypic variation among populations, most prominently in armour and spine traits. Despite large variation in the abiotic environment, namely in ion composition, depth and dissolved organic Carbon, more phenotypic variation was explained by the biotic variables (presence of predators and density of predator and competitors), than by associated abiotic variables. Genetic structure among populations was partly geographic, with closer populations being more similar. Altogether, our results suggest that differences in body shape among stickleback populations are the result of both canalized genetic and plastic responses to environmental factors, which shape fish morphology in a predictable direction regardless of their genetic starting point. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Revisiting shape selectivity in liquid chromatography for polycyclic aromatic hydrocarbons (PAHs) - six-ring and seven-ring Cata-condensed PAH isomers of molecular mass 328 Da and 378 Da.

PubMed

Oña-Ruales, Jorge O; Sander, Lane C; Wilson, Walter B; Wise, Stephen A

2018-01-01

The relationship of reversed-phase liquid chromatography (RPLC) retention on a polymeric C 18 stationary phase and the shape of polycyclic aromatic hydrocarbons (PAHs) was investigated for three-ring to seven-ring cata-condensed isomers. We report the first RPLC separation for six-ring and seven-ring cata-condensed PAH isomers. Correlations of LC retention and shape parameters (length-to-breath ratio, L/B and thickness, T) were investigated for 2 three-ring isomers (molecular mass 178 Da), 5 four-ring isomers (molecular mass 228 Da), 11 five-ring isomers (molecular mass 278 Da), 17 six-ring isomers (molecular mass 328 Da), and 20 seven-ring isomers (molecular mass 378 Da). Significant linear correlations were found for all isomer groups (r = 0.71 to 0.94). Nonplanarity of the PAH isomers was found to influence retention (i.e., nonplanar isomers eluting earlier than expected based on L/B) and linear correlations of retention vs. T for isomer groups containing nonplanar isomers were significant (r = 0.71 to 0.86). Graphical abstract.

Microbial oceanography: paradigms, processes and promise.

PubMed

Karl, David M

2007-10-01

Life on Earth most likely originated as microorganisms in the sea. Over the past approximately 3.5 billion years, microorganisms have shaped and defined Earth's biosphere and have created conditions that have allowed the evolution of macroorganisms and complex biological communities, including human societies. Recent advances in technology have highlighted the vast and previously unknown genetic information that is contained in extant marine microorganisms, from new protein families to novel metabolic processes. Now there is a unique opportunity, using recent advances in molecular ecology, metagenomics, remote sensing of microorganisms and ecological modelling, to achieve a comprehensive understanding of marine microorganisms and their susceptibility to environmental variability and climate change. Contemporary microbial oceanography is truly a sea of opportunity and excitement.

Molecular chirality and domain shapes in lipid monolayers on aqueous surfaces

NASA Astrophysics Data System (ADS)

Krüger, Peter; Lösche, Mathias

2000-11-01

The shapes of domain boundaries in the mesoscopic phase separation of phospholipids in aqueous surface monolayers are analyzed with particular attention to the influence of molecular chirality. We have calculated equilibrium shapes of such boundaries, and show that the concept of spontaneous curvature-derived from an effective pair potential between the chiral molecules-yields an adequate description of the contribution of chirality to the total energy of the system. For enantiomeric dipalmitoylphosphatidylcholine in pure monolayers, and in mixtures with impurities that adsorb preferentially at the (one-dimensional) boundary line between the isotropic and anisotropic fluid phases, such as cyanobiphenyl (5CB), a total energy term that includes line tension, electrostatic dipole-dipole interaction, and spontaneous curvature is sufficient to describe the shapes of well-separated domain boundaries in full detail. As soon as interdomain distances fall below the domain sizes upon compression of a monolayer, fluctuations take over in determining its detailed structural morphology. Using Minkowski measures for the well-studied dimyristoyl phosphatidic acid (DMPA)/cholesterol system, we show that calculations accounting for line tension, electrostatic repulsion, and molecular chirality yield boundary shapes that are of the same topology as the experimentally observed structures. At a fixed molecular area in the phase coexistence region, the DMPA/cholesterol system undergoes an exponential decay of the line tension λ with decreasing subphase temperature T.

On the Symmetry of Molecular Flows Through the Pipe of an Arbitrary Shape (I) Diffusive Reflection

NASA Astrophysics Data System (ADS)

Kusumoto, Yoshiro

Molecular gas flows through the pipe of an arbitrary shape is mathematically considered based on a diffusive reflection model. To avoid a perpetual motion, the magnitude of the molecular flow rate must remain invariant under the exchange of inlet and outlet pressures. For this flow symmetry, the cosine law reflection at the pipe wall was found to be sufficient and necessary, on the assumption that the molecular flux is conserved in a collision with the wall. It was also shown that a spontaneous flow occurs in a hemispherical apparatus, if the reflection obeys the n-th power of cosine law with n other than unity. This apparatus could work as a molecular pump with no moving parts.

Convergence and Divergence in the Evolution of Cat Skulls: Temporal and Spatial Patterns of Morphological Diversity

PubMed Central

Sakamoto, Manabu; Ruta, Marcello

2012-01-01

Background Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats. Methodology/Principal Findings A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various saber-toothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats. Conclusions/Significance Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional diversity studies, and may reveal novel patterns of morphospace occupation. PMID:22792186

Effects of Shapes of Solute Molecules on Diffusion: A Study of Dependences on Solute Size, Solvent, and Temperature.

PubMed

Chan, T C; Li, H T; Li, K Y

2015-12-24

Diffusivities of basically linear, planar, and spherical solutes at infinite dilution in various solvents are studied to unravel the effects of solute shapes on diffusion. On the basis of the relationship between the reciprocal of diffusivity and the molecular volume of solute molecules with similar shape in a given solvent at constant temperature, the diffusivities of solutes of equal molecular volume but different shapes are evaluated and the effects due to different shapes of two equal-sized solute molecules on diffusion are determined. It is found that the effects are dependent on the size of the solute pairs studied. Evidence of the dependence of the solute-shape effects on solvent properties is also demonstrated and discussed. Here, some new diffusion data of aromatic compounds in methanol at different temperatures are reported. The result for methanol in this study indicates that the effects of solute shape on diffusivity are only weakly dependent on temperature.

Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations.

PubMed

Ollila, O H Samuli; Heikkinen, Harri A; Iwaï, Hideo

2018-06-14

Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.

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

Asahina, Yuta; Kawashima, Tomohisa; Furukawa, Naoko

The formation mechanism of CO clouds observed with the NANTEN2 and Mopra telescopes toward the stellar cluster Westerlund 2 is studied by 3D magnetohydrodynamic simulations, taking into account the interstellar cooling. These molecular clouds show a peculiar shape composed of an arc-shaped cloud on one side of the TeV γ -ray source HESS J1023-575 and a linear distribution of clouds (jet clouds) on the other side. We propose that these clouds are formed by the interaction of a jet with clumps of interstellar neutral hydrogen (H i). By studying the dependence of the shape of dense cold clouds formed bymore » shock compression and cooling on the filling factor of H i clumps, we found that the density distribution of H i clumps determines the shape of molecular clouds formed by the jet–cloud interaction: arc clouds are formed when the filling factor is large. On the other hand, when the filling factor is small, molecular clouds align with the jet. The jet propagates faster in models with small filling factors.« less

A Marked Poisson Process Driven Latent Shape Model for 3D Segmentation of Reflectance Confocal Microscopy Image Stacks of Human Skin.

PubMed

Ghanta, Sindhu; Jordan, Michael I; Kose, Kivanc; Brooks, Dana H; Rajadhyaksha, Milind; Dy, Jennifer G

2017-01-01

Segmenting objects of interest from 3D data sets is a common problem encountered in biological data. Small field of view and intrinsic biological variability combined with optically subtle changes of intensity, resolution, and low contrast in images make the task of segmentation difficult, especially for microscopy of unstained living or freshly excised thick tissues. Incorporating shape information in addition to the appearance of the object of interest can often help improve segmentation performance. However, the shapes of objects in tissue can be highly variable and design of a flexible shape model that encompasses these variations is challenging. To address such complex segmentation problems, we propose a unified probabilistic framework that can incorporate the uncertainty associated with complex shapes, variable appearance, and unknown locations. The driving application that inspired the development of this framework is a biologically important segmentation problem: the task of automatically detecting and segmenting the dermal-epidermal junction (DEJ) in 3D reflectance confocal microscopy (RCM) images of human skin. RCM imaging allows noninvasive observation of cellular, nuclear, and morphological detail. The DEJ is an important morphological feature as it is where disorder, disease, and cancer usually start. Detecting the DEJ is challenging, because it is a 2D surface in a 3D volume which has strong but highly variable number of irregularly spaced and variably shaped "peaks and valleys." In addition, RCM imaging resolution, contrast, and intensity vary with depth. Thus, a prior model needs to incorporate the intrinsic structure while allowing variability in essentially all its parameters. We propose a model which can incorporate objects of interest with complex shapes and variable appearance in an unsupervised setting by utilizing domain knowledge to build appropriate priors of the model. Our novel strategy to model this structure combines a spatial Poisson process with shape priors and performs inference using Gibbs sampling. Experimental results show that the proposed unsupervised model is able to automatically detect the DEJ with physiologically relevant accuracy in the range 10- 20 μm .

A Marked Poisson Process Driven Latent Shape Model for 3D Segmentation of Reflectance Confocal Microscopy Image Stacks of Human Skin

PubMed Central

Ghanta, Sindhu; Jordan, Michael I.; Kose, Kivanc; Brooks, Dana H.; Rajadhyaksha, Milind; Dy, Jennifer G.

2016-01-01

Segmenting objects of interest from 3D datasets is a common problem encountered in biological data. Small field of view and intrinsic biological variability combined with optically subtle changes of intensity, resolution and low contrast in images make the task of segmentation difficult, especially for microscopy of unstained living or freshly excised thick tissues. Incorporating shape information in addition to the appearance of the object of interest can often help improve segmentation performance. However, shapes of objects in tissue can be highly variable and design of a flexible shape model that encompasses these variations is challenging. To address such complex segmentation problems, we propose a unified probabilistic framework that can incorporate the uncertainty associated with complex shapes, variable appearance and unknown locations. The driving application which inspired the development of this framework is a biologically important segmentation problem: the task of automatically detecting and segmenting the dermal-epidermal junction (DEJ) in 3D reflectance confocal microscopy (RCM) images of human skin. RCM imaging allows noninvasive observation of cellular, nuclear and morphological detail. The DEJ is an important morphological feature as it is where disorder, disease and cancer usually start. Detecting the DEJ is challenging because it is a 2D surface in a 3D volume which has strong but highly variable number of irregularly spaced and variably shaped “peaks and valleys”. In addition, RCM imaging resolution, contrast and intensity vary with depth. Thus a prior model needs to incorporate the intrinsic structure while allowing variability in essentially all its parameters. We propose a model which can incorporate objects of interest with complex shapes and variable appearance in an unsupervised setting by utilizing domain knowledge to build appropriate priors of the model. Our novel strategy to model this structure combines a spatial Poisson process with shape priors and performs inference using Gibbs sampling. Experimental results show that the proposed unsupervised model is able to automatically detect the DEJ with physiologically relevant accuracy in the range 10 – 20µm. PMID:27723590

A new lizard species of the Phymaturus patagonicus group (Squamata: Liolaemini) from northern Patagonia, Neuquén, Argentina.

PubMed

Marín, Andrea González; Pérez, Cristian Hernán Fulvio; Minoli, Ignacio; Morando, Mariana; Avila, Luciano Javier

2016-06-10

The integrative taxonomy framework allows developing robust hypotheses of species limits based on the integration of results from different data sets and analytical methods. In this work, we test a candidate species hypothesis previously suggested based on molecular data, with geometric and traditional morphometrics analyses (multivariate and univariate). This new lizard species is part of the Phymaturus patagonicus group (payuniae clade) that is distributed in Neuquén and Mendoza provinces (Argentina). Our results showed that Phymaturus rahuensis sp. nov. differs from the other species of the payuniae clade by a higher number of midbody scales, and fewer supralabials scales, finger lamellae and toe lamellae. Also, its multidimensional spaces, both based on continuous lineal variables and geometric morphometrics (shape) characters, do not overlap with those of the other species in this clade. The results of the morphometric and geometric morphometric analyses presented here, coupled with previously published molecular data, represent three independent lines of evidence that support the diagnosis of this new taxon.

An issue encountered in solving problems in electricity and magnetism: curvilinear coordinates

NASA Astrophysics Data System (ADS)

Gülçiçek, Çağlar; Damlı, Volkan

2016-11-01

In physics lectures on electromagnetic theory and mathematical methods, physics teacher candidates have some difficulties with curvilinear coordinate systems. According to our experience, based on both in-class interactions and teacher candidates’ answers in test papers, they do not seem to have understood the variables in curvilinear coordinate systems very well. For this reason, the problems that physics teacher candidates have with variables in curvilinear coordinate systems have been selected as a study subject. The aim of this study is to find the physics teacher candidates’ problems with determining the variables of drawn shapes, and problems with drawing shapes based on given variables in curvilinear coordinate systems. Two different assessment tests were used in the study to achieve this aim. The curvilinear coordinates drawing test (CCDrT) was used to discover their problems related to drawing shapes, and the curvilinear coordinates detection test (CCDeT) was used to find out about problems related to determining variables. According to the findings obtained from both tests, most physics teacher candidates have problems with the ϕ variable, while they have limited problems with the r variable. Questions that are mostly answered wrongly have some common properties, such as value. According to inferential statistics, there is no significant difference between the means of the CCDeT and CCDrT scores. The mean of the CCDeT scores is only 4.63 and the mean of the CCDrT is only 4.66. Briefly, we can say that most physics teacher candidates have problems with drawing a shape using the variables of curvilinear coordinate systems or in determining the variables of drawn shapes. Part of this study was presented at the XI. National Science and Mathematics Education Congress (UFBMEK) in 2014.

Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility.

PubMed

Mlýnský, Vojtěch; Bussi, Giovanni

2018-01-18

The function of RNA molecules usually depends on their overall fold and on the presence of specific structural motifs. Chemical probing methods are routinely used in combination with nearest-neighbor models to determine RNA secondary structure. Among the available methods, SHAPE is relevant due to its capability to probe all RNA nucleotides and the possibility to be used in vivo. However, the structural determinants for SHAPE reactivity and its mechanism of reaction are still unclear. Here molecular dynamics simulations and enhanced sampling techniques are used to predict the accessibility of nucleotide analogs and larger RNA structural motifs to SHAPE reagents. We show that local RNA reconformations are crucial in allowing reagents to reach the 2'-OH group of a particular nucleotide and that sugar pucker is a major structural factor influencing SHAPE reactivity.

Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain.

PubMed

Selwa, Edithe; Huynh, Tru; Ciccotti, Giovanni; Maragliano, Luca; Malliavin, Thérèse E

2014-10-01

The catalytic domain of the adenyl cyclase (AC) toxin from Bordetella pertussis is activated by interaction with calmodulin (CaM), resulting in cAMP overproduction in the infected cell. In the X-ray crystallographic structure of the complex between AC and the C terminal lobe of CaM, the toxin displays a markedly elongated shape. As for the structure of the isolated protein, experimental results support the hypothesis that more globular conformations are sampled, but information at atomic resolution is still lacking. Here, we use temperature-accelerated molecular dynamics (TAMD) simulations to generate putative all-atom models of globular conformations sampled by CaM-free AC. As collective variables, we use centers of mass coordinates of groups of residues selected from the analysis of standard molecular dynamics (MD) simulations. Results show that TAMD allows extended conformational sampling and generates AC conformations that are more globular than in the complexed state. These structures are then refined via energy minimization and further unrestrained MD simulations to optimize inter-domain packing interactions, thus resulting in the identification of a set of hydrogen bonds present in the globular conformations. © 2014 Wiley Periodicals, Inc.

Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies

NASA Astrophysics Data System (ADS)

Xiao, Xueliang; Hu, Jinlian

2016-05-01

Animal hairs consisting of α-keratin biopolymers existing broadly in nature may be responsive to water for recovery to the innate shape from their fixed deformation, thus possess smart behavior, namely shape memory effect (SME). In this article, three typical animal hair fibers were first time investigated for their water-stimulated SME, and therefrom to identify the corresponding net-points and switches in their molecular and morphological structures. Experimentally, the SME manifested a good stability of high shape fixation ratio and reasonable recovery rate after many cycles of deformation programming under water stimulation. The effects of hydration on hair lateral size, recovery kinetics, dynamic mechanical behaviors and structural components (crystal, disulfide and hydrogen bonds) were then systematically studied. SME mechanisms were explored based on the variations of structural components in molecular assemblies of such smart fibers. A hybrid structural network model with single-switch and twin-net-points was thereafter proposed to interpret the water-stimulated shape memory mechanism of animal hairs. This original work is expected to provide inspiration for exploring other natural materials to reveal their smart functions and natural laws in animals including human as well as making more remarkable synthetic smart materials.

Performances and working mechanism of a novel polycarboxylate superplasticizer synthesized through changing molecular topological structure.

PubMed

Liu, Xiao; Guan, Jianan; Lai, Guanghong; Wang, Ziming; Zhu, Jie; Cui, Suping; Lan, Mingzhang; Li, Huiqun

2017-10-15

A novel star-shaped polycarboxylate superplasticizer (SPCE) was synthesized through a simple two-step method. 1 H Nuclear Magnetic Resonance ( 1 H NMR) and Infrared Spectroscopy (IR) measurements were used for structural characterization. SPCE and comb-shaped polycarboxylate superplasticizer (CPCE) with same molecular weights were designed and synthesized. The cement paste containing SPCE exhibited better fluidity, fluidity retention, water reduction, 25% lower saturated dosage of PCE, 10% longer setting time, lower hydration heat, more delayed hydration heat evolution and lower amount of hydration products at early ages. Furthermore, the adsorption behavior of SPCE and CPCE in cement pastes and the zeta potential were investigated, and then the working mechanism of SPCE was theoretically explained. It is interesting that changing topological structure from comb-shape to star-shape can achieve the optimization of dispersion effect, and further improve the working effectiveness. The aims of this study are to provide a new avenue to synthesize superplasticizer with novel structure achieving the chemical diversity of superplasticizer structure, and to verify the contribution of optimizing molecular shape. This new type of superplasticizer can be used as a rheology modifying agent in fresh cement-based materials. Copyright © 2017 Elsevier Inc. All rights reserved.

Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies

PubMed Central

Xiao, Xueliang; Hu, Jinlian

2016-01-01

Animal hairs consisting of α-keratin biopolymers existing broadly in nature may be responsive to water for recovery to the innate shape from their fixed deformation, thus possess smart behavior, namely shape memory effect (SME). In this article, three typical animal hair fibers were first time investigated for their water-stimulated SME, and therefrom to identify the corresponding net-points and switches in their molecular and morphological structures. Experimentally, the SME manifested a good stability of high shape fixation ratio and reasonable recovery rate after many cycles of deformation programming under water stimulation. The effects of hydration on hair lateral size, recovery kinetics, dynamic mechanical behaviors and structural components (crystal, disulfide and hydrogen bonds) were then systematically studied. SME mechanisms were explored based on the variations of structural components in molecular assemblies of such smart fibers. A hybrid structural network model with single-switch and twin-net-points was thereafter proposed to interpret the water-stimulated shape memory mechanism of animal hairs. This original work is expected to provide inspiration for exploring other natural materials to reveal their smart functions and natural laws in animals including human as well as making more remarkable synthetic smart materials. PMID:27230823

Landmark-free statistical analysis of the shape of plant leaves.

PubMed

Laga, Hamid; Kurtek, Sebastian; Srivastava, Anuj; Miklavcic, Stanley J

2014-12-21

The shapes of plant leaves are important features to biologists, as they can help in distinguishing plant species, measuring their health, analyzing their growth patterns, and understanding relations between various species. Most of the methods that have been developed in the past focus on comparing the shape of individual leaves using either descriptors or finite sets of landmarks. However, descriptor-based representations are not invertible and thus it is often hard to map descriptor variability into shape variability. On the other hand, landmark-based techniques require automatic detection and registration of the landmarks, which is very challenging in the case of plant leaves that exhibit high variability within and across species. In this paper, we propose a statistical model based on the Squared Root Velocity Function (SRVF) representation and the Riemannian elastic metric of Srivastava et al. (2011) to model the observed continuous variability in the shape of plant leaves. We treat plant species as random variables on a non-linear shape manifold and thus statistical summaries, such as means and covariances, can be computed. One can then study the principal modes of variations and characterize the observed shapes using probability density models, such as Gaussians or Mixture of Gaussians. We demonstrate the usage of such statistical model for (1) efficient classification of individual leaves, (2) the exploration of the space of plant leaf shapes, which is important in the study of population-specific variations, and (3) comparing entire plant species, which is fundamental to the study of evolutionary relationships in plants. Our approach does not require descriptors or landmarks but automatically solves for the optimal registration that aligns a pair of shapes. We evaluate the performance of the proposed framework on publicly available benchmarks such as the Flavia, the Swedish, and the ImageCLEF2011 plant leaf datasets. Copyright © 2014 Elsevier Ltd. All rights reserved.

Shape-Memory Hydrogels: Evolution of Structural Principles To Enable Shape Switching of Hydrophilic Polymer Networks.

PubMed

Löwenberg, Candy; Balk, Maria; Wischke, Christian; Behl, Marc; Lendlein, Andreas

2017-04-18

The ability of hydrophilic chain segments in polymer networks to strongly interact with water allows the volumetric expansion of the material and formation of a hydrogel. When polymer chain segments undergo reversible hydration depending on environmental conditions, smart hydrogels can be realized, which are able to shrink/swell and thus alter their volume on demand. In contrast, implementing the capacity of hydrogels to switch their shape rather than volume demands more sophisticated chemical approaches and structural concepts. In this Account, the principles of hydrogel network design, incorporation of molecular switches, and hydrogel microstructures are summarized that enable a spatially directed actuation of hydrogels by a shape-memory effect (SME) without major volume alteration. The SME involves an elastic deformation (programming) of samples, which are temporarily fixed by reversible covalent or physical cross-links resulting in a temporary shape. The material can reverse to the original shape when these molecular switches are affected by application of a suitable stimulus. Hydrophobic shape-memory polymers (SMPs), which are established with complex functions including multiple or reversible shape-switching, may provide inspiration for the molecular architecture of shape-memory hydrogels (SMHs), but cannot be identically copied in the world of hydrophilic soft materials. For instance, fixation of the temporary shape requires cross-links to be formed also in an aqueous environment, which may not be realized, for example, by crystalline domains from the hydrophilic main chains as these may dissolve in presence of water. Accordingly, dual-shape hydrogels have evolved, where, for example, hydrophobic crystallizable side chains have been linked into hydrophilic polymer networks to act as temperature-sensitive temporary cross-links. By incorporating a second type of such side chains, triple-shape hydrogels can be realized. Considering the typically given light permeability of hydrogels and the fully hydrated state with easy permeation by small molecules, other types of stimuli like light, pH, or ions can be employed that may not be easily used in hydrophobic SMPs. In some cases, those molecular switches can respond to more than one stimulus, thus increasing the number of opportunities to induce actuation of these synthetic hydrogels. Beyond this, biopolymer-based hydrogels can be equipped with a shape switching function when facilitating, for example, triple helix formation in proteins or ionic interactions in polysaccharides. Eventually, microstructured SMHs such as hybrid or porous structures can combine the shape-switching function with an improved performance by helping to overcome frequent shortcomings of hydrogels such as low mechanical strength or volume change upon temporary cross-link cleavage. Specifically, shape switching without major volume alteration is possible in porous SMHs by decoupling small volume changes of pore walls on the microscale and the macroscopic sample size. Furthermore, oligomeric rather than short aliphatic side chains as molecular switches allow stabilization of the sample volumes. Based on those structural principles and switching functionalities, SMHs have already entered into applications as soft actuators and are considered, for example, for cell manipulation in biomedicine. In the context of those applications, switching kinetics, switching forces, and reversibility of switching are aspects to be further explored.

From the molecular structure to spectroscopic and material properties: computational investigation of a bent-core nematic liquid crystal.

PubMed

Greco, Cristina; Marini, Alberto; Frezza, Elisa; Ferrarini, Alberta

2014-05-19

We present a computational investigation of the nematic phase of the bent-core liquid crystal A131. We use an integrated approach that bridges density functional theory calculations of molecular geometry and torsional potentials to elastic properties through the molecular conformational and orientational distribution function. This unique capability to simultaneously access different length scales enables us to consistently describe molecular and material properties. We can reassign (13)C NMR chemical shifts and analyze the dependence of phase properties on molecular shape. Focusing on the elastic constants we can draw some general conclusions on the unconventional behavior of bent-core nematics and highlight the crucial role of a properly-bent shape. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An Observation of Diamond-Shaped Particle Structure in a Soya Phosphatidylcohline and Bacteriorhodopsin Composite Langmuir Blodgett Film Fabricated by Multilayer Molecular Thin Film Method

NASA Astrophysics Data System (ADS)

Tsujiuchi, Y.; Makino, Y.

A composite film of soya phosphatidylcohline (soya PC) and bacteriorhodopsin (BR) was fabricated by the multilayer molecular thin film method using fatty acid and lipid on a quartz substrate. Direct Force Microscopy (DFM), UV absorption spectra and IR absorption spectra of the film were characterized on the detail of surface structure of the film. The DFM data revealed that many rhombus (diamond-shaped) particles were observed in the film. The spectroscopic data exhibited the yield of M-intermediate of BR in the film. On our modelling of molecular configuration indicate that the coexistence of the strong inter-molecular interaction and the strong inter-molecular interaction between BR trimmers attributed to form the particles.

Molecular mimicry between protein and tRNA.

PubMed

Nakamura, Y

2001-01-01

Mimicry is a sophisticated development in animals, fish, and plants that allows them to fool others by imitating a shape or color for diverse purposes, such as to prey, evade, lure, pollinate, or threaten. This is not restricted to the macro-world, but extends to the micro-world as molecular mimicry. Recent advances in structural and molecular biology uncovered a set of translation factors that resembles a tRNA shape and, in one case, even mimics a tRNA function for deciphering the genetic code. Nature must have evolved this art of molecular mimicry between protein and ribonucleic acid by using different protein structures until the translation factors sat in the cockpit of a ribosome machine, on behalf of tRNA, and achieved diverse actions. Structural, functional, and evolutionary aspects of molecular mimicry will be discussed.

Variable-Domain Displacement Transfer Functions for Converting Surface Strains into Deflections for Structural Deformed Shape Predictions

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2015-01-01

Variable-Domain Displacement Transfer Functions were formulated for shape predictions of complex wing structures, for which surface strain-sensing stations must be properly distributed to avoid jointed junctures, and must be increased in the high strain gradient region. Each embedded beam (depth-wise cross section of structure along a surface strain-sensing line) was discretized into small variable domains. Thus, the surface strain distribution can be described with a piecewise linear or a piecewise nonlinear function. Through discretization, the embedded beam curvature equation can be piece-wisely integrated to obtain the Variable-Domain Displacement Transfer Functions (for each embedded beam), which are expressed in terms of geometrical parameters of the embedded beam and the surface strains along the strain-sensing line. By inputting the surface strain data into the Displacement Transfer Functions, slopes and deflections along each embedded beam can be calculated for mapping out overall structural deformed shapes. A long tapered cantilever tubular beam was chosen for shape prediction analysis. The input surface strains were analytically generated from finite-element analysis. The shape prediction accuracies of the Variable- Domain Displacement Transfer Functions were then determined in light of the finite-element generated slopes and deflections, and were fofound to be comparable to the accuracies of the constant-domain Displacement Transfer Functions

Molecular structural property and potential energy dependence on nonequilibrium-thermodynamic state point of liquid n-hexadecane under shear.

PubMed

Tseng, Huan-Chang; Chang, Rong-Yeu; Wu, Jiann-Shing

2011-01-28

Extensive computer experiments have been conducted in order to shed light on the macroscopic shear flow behavior of liquid n-hexadecane fluid under isobaric-isothermal conditions through the nonequilibrium molecular dynamic methodology. With respect to shear rates, the accompanying variations in structural properties of the fluid span the microscopic range of understanding from the intrinsic to extrinsic characteristics. As drawn from the average value of bond length and bond angle, the distribution of dihedral angle, and the radius distribution function of intramolecular and intermolecular van der Waals distances, these intrinsic structures change with hardness, except in the situation of extreme shear rates. The shear-induced variation of thermodynamic state curve along with the shear rate studied is shown to consist of both the quasiequilibrium state plateau and the nonequilibrium-thermodynamic state slope. Significantly, the occurrence of nonequilibrium-thermodynamic state behavior is attributed to variations in molecular potential energies, which include bond stretching, bond bending, bond torsion, and intra- and intermolecular van der Waals interactions. To unfold the physical representation of extrinsic structural deformation, under the aggressive influence of a shear flow field, the molecular dimension and appearance can be directly described via the squared radius of gyration and the sphericity angle, R(g)(2) and ϕ, respectively. In addition, a specific orientational order S(x) defines the alignment of the molecules with the flow direction of the x-axis. As a result, at low shear rates, the overall molecules are slightly stretched and shaped in a manner that is increasingly ellipsoidal. Simultaneously, there is an obvious enhancement in the order. In contrast to high shear rates, the molecules spontaneously shrink themselves with a decreased value of R(g)(2), while their shape and order barely vary with an infinite value of ϕ and S(x). It is important to note that under different temperatures and pressures, these three parameters are integrated within a molecular description in response to thermodynamic state variable of density and rheological material function of shear viscosity.

The Geometric Phase of Stock Trading.

PubMed

Altafini, Claudio

2016-01-01

Geometric phases describe how in a continuous-time dynamical system the displacement of a variable (called phase variable) can be related to other variables (shape variables) undergoing a cyclic motion, according to an area rule. The aim of this paper is to show that geometric phases can exist also for discrete-time systems, and even when the cycles in shape space have zero area. A context in which this principle can be applied is stock trading. A zero-area cycle in shape space represents the type of trading operations normally carried out by high-frequency traders (entering and exiting a position on a fast time-scale), while the phase variable represents the cash balance of a trader. Under the assumption that trading impacts stock prices, even zero-area cyclic trading operations can induce geometric phases, i.e., profits or losses, without affecting the stock quote.

Fluid models and simulations of biological cell phenomena

NASA Technical Reports Server (NTRS)

Greenspan, H. P.

1982-01-01

The dynamics of coated droplets are examined within the context of biofluids. Of specific interest is the manner in which the shape of a droplet, the motion within it as well as that of aggregates of droplets can be controlled by the modulation of surface properties and the extent to which such fluid phenomena are an intrinsic part of cellular processes. From the standpoint of biology, an objective is to elucidate some of the general dynamical features that affect the disposition of an entire cell, cell colonies and tissues. Conventionally averaged field variables of continuum mechanics are used to describe the overall global effects which result from the myriad of small scale molecular interactions. An attempt is made to establish cause and effect relationships from correct dynamical laws of motion rather than by what may have been unnecessary invocation of metabolic or life processes. Several topics are discussed where there are strong analogies droplets and cells including: encapsulated droplets/cell membranes; droplet shape/cell shape; adhesion and spread of a droplet/cell motility and adhesion; and oams and multiphase flows/cell aggregates and tissues. Evidence is presented to show that certain concepts of continuum theory such as suface tension, surface free energy, contact angle, bending moments, etc. are relevant and applicable to the study of cell biology.

Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

PubMed Central

2011-01-01

Background Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies. Results The mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci. Conclusion The occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for resolving phylogenetic issues concerning copepods. The variable site maps of C. sinicus mitogenomes provide a solid foundation for population genetic studies. PMID:21269523

Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors.

PubMed

Venkatraman, Vishwesh; Sael, Lee; Kihara, Daisuke

2009-01-01

With structure databases expanding at a rapid rate, the task at hand is to provide reliable clues to their molecular function and to be able to do so on a large scale. This, however, requires suitable encodings of the molecular structure which are amenable to fast screening. To this end, moment-based representations provide a compact and nonredundant description of molecular shape and other associated properties. In this article, we present an overview of some commonly used representations with specific focus on two schemes namely spherical harmonics and their extension, the 3D Zernike descriptors. Key features and differences of the two are reviewed and selected applications are highlighted. We further discuss recent advances covering aspects of shape and property-based comparison at both global and local levels and demonstrate their applicability through some of our studies.

Coarse-grained simulation of molecular mechanisms of recovery in thermally activated shape-memory polymers

NASA Astrophysics Data System (ADS)

Abberton, Brendan C.; Liu, Wing Kam; Keten, Sinan

2013-12-01

Thermally actuated shape-memory polymers (SMPs) are capable of being programmed into a temporary shape and then recovering their permanent reference shape upon exposure to heat, which facilitates a phase transition that allows dramatic increase in molecular mobility. Experimental, analytical, and computational studies have established empirical relations of the thermomechanical behavior of SMPs that have been instrumental in device design. However, the underlying mechanisms of the recovery behavior and dependence on polymer microstructure remain to be fully understood for copolymer systems. This presents an opportunity for bottom-up studies through molecular modeling; however, the limited time-scales of atomistic simulations prohibit the study of key performance metrics pertaining to recovery. In order to elucidate the effects of phase fraction, recovery temperature, and deformation temperature on shape recovery, here we investigate the shape-memory behavior in a copolymer model with coarse-grained potentials using a two-phase molecular model that reproduces physical crosslinking. Our simulation protocol allows observation of upwards of 90% strain recovery in some cases, at time-scales that are on the order of the timescale of the relevant relaxation mechanism (stress relaxation in the unentangled soft-phase). Partial disintegration of the glassy phase during mechanical deformation is found to contribute to irrecoverable strain. Temperature dependence of the recovery indicates nearly full elastic recovery above the trigger temperature, which is near the glass-transition temperature of the rubbery switching matrix. We find that the trigger temperature is also directly correlated with the deformation temperature, indicating that deformation temperature influences the recovery temperatures required to obtain a given amount of shape recovery, until the plateau regions overlap above the transition region. Increasing the fraction of glassy phase results in higher strain recovery at low to intermediate temperatures, a widening of the transition region, and an eventual crossover at high temperatures. Our results corroborate experimental findings on shape-memory behavior and provide new insight into factors governing deformation recovery that can be leveraged in biomaterials design. The established computational methodology can be extended in straightforward ways to investigate the effects of monomer chemistry, low-molecular-weight solvents, physical and chemical crosslinking, different phase-separation morphologies, and more complicated mechanical deformation toward predictive modeling capabilities for stimuli-responsive polymers.

European early modern humans and the fate of the Neandertals

PubMed Central

Trinkaus, Erik

2007-01-01

A consideration of the morphological aspects of the earliest modern humans in Europe (more than ≈33,000 B.P.) and the subsequent Gravettian human remains indicates that they possess an anatomical pattern congruent with the autapomorphic (derived) morphology of the earliest (Middle Paleolithic) African modern humans. However, they exhibit a variable suite of features that are either distinctive Neandertal traits and/or plesiomorphic (ancestral) aspects that had been lost among the African Middle Paleolithic modern humans. These features include aspects of neurocranial shape, basicranial external morphology, mandibular ramal and symphyseal form, dental morphology and size, and anteroposterior dental proportions, as well as aspects of the clavicles, scapulae, metacarpals, and appendicular proportions. The ubiquitous and variable presence of these morphological features in the European earlier modern human samples can only be parsimoniously explained as a product of modest levels of assimilation of Neandertals into early modern human populations as the latter dispersed across Europe. This interpretation is in agreement with current analyses of recent and past human molecular data. PMID:17452632

Distribution and predictors of wing shape and size variability in three sister species of solitary bees

PubMed Central

Prunier, Jérôme G.; Dewulf, Alexandre; Kuhlmann, Michael; Michez, Denis

2017-01-01

Morphological traits can be highly variable over time in a particular geographical area. Different selective pressures shape those traits, which is crucial in evolutionary biology. Among these traits, insect wing morphometry has already been widely used to describe phenotypic variability at the inter-specific level. On the contrary, fewer studies have focused on intra-specific wing morphometric variability. Yet, such investigations are relevant to study potential convergences of variation that could highlight micro-evolutionary processes. The recent sampling and sequencing of three solitary bees of the genus Melitta across their entire species range provides an excellent opportunity to jointly analyse genetic and morphometric variability. In the present study, we first aim to analyse the spatial distribution of the wing shape and centroid size (used as a proxy for body size) variability. Secondly, we aim to test different potential predictors of this variability at both the intra- and inter-population levels, which includes genetic variability, but also geographic locations and distances, elevation, annual mean temperature and precipitation. The comparison of spatial distribution of intra-population morphometric diversity does not reveal any convergent pattern between species, thus undermining the assumption of a potential local and selective adaptation at the population level. Regarding intra-specific wing shape differentiation, our results reveal that some tested predictors, such as geographic and genetic distances, are associated with a significant correlation for some species. However, none of these predictors are systematically identified for the three species as an important factor that could explain the intra-specific morphometric variability. As a conclusion, for the three solitary bee species and at the scale of this study, our results clearly tend to discard the assumption of the existence of a common pattern of intra-specific signal/structure within the intra-specific wing shape and body size variability. PMID:28273178

Assembling oppositely charged lock and key responsive colloids: A mesoscale analog of adaptive chemistry

PubMed Central

Mihut, Adriana M.; Stenqvist, Björn; Lund, Mikael; Schurtenberger, Peter; Crassous, Jérôme J.

2017-01-01

We have seen a considerable effort in colloid sciences to copy Nature’s successful strategies to fabricate complex functional structures through self-assembly. This includes attempts to design colloidal building blocks and their intermolecular interactions, such as creating the colloidal analogs of directional molecular interactions, molecular recognition, host-guest systems, and specific binding. We show that we can use oppositely charged thermoresponsive particles with complementary shapes, such as spherical and bowl-shaped particles, to implement an externally controllable lock-and-key self-assembly mechanism. The use of tunable electrostatic interactions combined with the temperature-dependent size and shape and van der Waals interactions of these building blocks provides an exquisite control over the selectivity and specificity of the interactions and self-assembly process. The dynamic nature of the mechanism allows for reversibly cycling through various structures that range from weakly structured dense liquids to well-defined molecule-shaped clusters with different configurations through variations in temperature and ionic strength. We link this complex and dynamic self-assembly behavior to the relevant molecular interactions, such as screened Coulomb and van der Waals forces and the geometrical complementarity of the two building blocks, and discuss our findings in the context of the concepts of adaptive chemistry recently introduced to molecular systems. PMID:28929133

A consistent methodology for optimal shape design of graphene sheets to maximize their fundamental frequencies considering topological defects

NASA Astrophysics Data System (ADS)

Shi, Jin-Xing; Ohmura, Keiichiro; Shimoda, Masatoshi; Lei, Xiao-Wen

2018-07-01

In recent years, shape design of graphene sheets (GSs) by introducing topological defects for enhancing their mechanical behaviors has attracted the attention of scholars. In the present work, we propose a consistent methodology for optimal shape design of GSs using a combination of the molecular mechanics (MM) method, the non-parametric shape optimization method, the phase field crystal (PFC) method, Voronoi tessellation, and molecular dynamics (MD) simulation to maximize their fundamental frequencies. At first, we model GSs as continuum frame models using a link between the MM method and continuum mechanics. Then, we carry out optimal shape design of GSs in fundamental frequency maximization problem based on a developed shape optimization method for frames. However, the obtained optimal shapes of GSs only consisting of hexagonal carbon rings are unstable that do not satisfy the principle of least action, so we relocate carbon atoms on the optimal shapes by introducing topological defects using the PFC method and Voronoi tessellation. At last, we perform the structural relaxation through MD simulation to determine the final optimal shapes of GSs. We design two examples of GSs and the optimal results show that the fundamental frequencies of GSs can be significantly enhanced according to the optimal shape design methodology.

The use of generalised additive models (GAM) in dentistry.

PubMed

Helfenstein, U; Steiner, M; Menghini, G

1997-12-01

Ordinary multiple regression and logistic multiple regression are widely applied statistical methods which allow a researcher to 'explain' or 'predict' a response variable from a set of explanatory variables or predictors. In these models it is usually assumed that quantitative predictors such as age enter linearly into the model. During recent years these methods have been further developed to allow more flexibility in the way explanatory variables 'act' on a response variable. The methods are called 'generalised additive models' (GAM). The rigid linear terms characterising the association between response and predictors are replaced in an optimal way by flexible curved functions of the predictors (the 'profiles'). Plotting the 'profiles' allows the researcher to visualise easily the shape by which predictors 'act' over the whole range of values. The method facilitates detection of particular shapes such as 'bumps', 'U-shapes', 'J-shapes, 'threshold values' etc. Information about the shape of the association is not revealed by traditional methods. The shapes of the profiles may be checked by performing a Monte Carlo simulation ('bootstrapping'). After the presentation of the GAM a relevant case study is presented in order to demonstrate application and use of the method. The dependence of caries in primary teeth on a set of explanatory variables is investigated. Since GAMs may not be easily accessible to dentists, this article presents them in an introductory condensed form. It was thought that a nonmathematical summary and a worked example might encourage readers to consider the methods described. GAMs may be of great value to dentists in allowing visualisation of the shape by which predictors 'act' and obtaining a better understanding of the complex relationships between predictors and response.

Simulation of size-exclusion chromatography distribution coefficients of comb-shaped molecules in spherical pores comparison of simulation and experiment.

PubMed

Radke, Wolfgang

2004-03-05

Simulations of the distribution coefficients of linear polymers and regular combs with various spacings between the arms have been performed. The distribution coefficients were plotted as a function of the number of segments in order to compare the size exclusion chromatography (SEC)-elution behavior of combs relative to linear molecules. By comparing the simulated SEC-calibration curves it is possible to predict the elution behavior of comb-shaped polymers relative to linear ones. In order to compare the results obtained by computer simulations with experimental data, a variety of comb-shaped polymers varying in side chain length, spacing between the side chains and molecular weights of the backbone were analyzed by SEC with light-scattering detection. It was found that the computer simulations could predict the molecular weights of linear molecules having the same retention volume with an accuracy of about 10%, i.e. the error in the molecular weight obtained by calculating the molecular weight of the comb-polymer based on a calibration curve constructed using linear standards and the results of the computer simulations are of the same magnitude as the experimental error of absolute molecular weight determination.

Sex-related shape dimorphism in the human radiocarpal and midcarpal joints.

PubMed

Kivell, Tracy L; Guimont, Isabelle; Wall, Christine E

2013-01-01

Previous research has revealed significant size differences between human male and female carpal bones but it is unknown if there are significant shape differences as well. This study investigated sex-related shape variation and allometric patterns in five carpal bones that make up the radiocarpal and midcarpal joints in modern humans. We found that many aspects of carpal shape (76% of all variables quantified) were similar between males and females, despite variation in size. However, 10 of the shape ratios were significantly different between males and females, with at least one significant shape difference observed in each carpal bone. Within-sex standard major axis regressions (SMA) of the numerator (i.e., the linear variables) on the denominator (i.e., the geometric mean) for each significantly different shape ratio indicated that most linear variables scaled with positive allometry in both males and females, and that for eight of the shape ratios, sex-related shape variation is associated with statistically similar sex-specific scaling relationships. Only the length of the scaphoid body and the height of the lunate triquetrum facet showed a significantly higher SMA slope in females compared with males. These findings indicate that the significant differences in the majority of the shape ratios are a function of subtle (i.e., not statistically significant) scaling differences between males and females. There are a number of potential developmental, functional, and evolutionary factors that may cause sex-related shape differences in the human carpus. The results highlight the potential for subtle differences in scaling to result in functionally significant differences in shape. Copyright © 2012 Wiley Periodicals, Inc.

CIDR

Science.gov Websites

Diagnostic Laboratory and the Molecular Pathology Laboratory. Johns Hopkins Genomics is staffed with clinical molecular geneticists, bioinformaticists, statistical geneticists, clinical geneticists and molecular shape Claes, Peter et al, Nature Genetics, 2018 February GAME-ON & OncoArray: An International

Origin and Consequences of the Relationship between Protein Mean and Variance

PubMed Central

Vallania, Francesco Luigi Massimo; Sherman, Marc; Goodwin, Zane; Mogno, Ilaria; Cohen, Barak Alon; Mitra, Robi David

2014-01-01

Cell-to-cell variance in protein levels (noise) is a ubiquitous phenomenon that can increase fitness by generating phenotypic differences within clonal populations of cells. An important challenge is to identify the specific molecular events that control noise. This task is complicated by the strong dependence of a protein's cell-to-cell variance on its mean expression level through a power-law like relationship (σ2∝μ1.69). Here, we dissect the nature of this relationship using a stochastic model parameterized with experimentally measured values. This framework naturally recapitulates the power-law like relationship (σ2∝μ1.6) and accurately predicts protein variance across the yeast proteome (r2 = 0.935). Using this model we identified two distinct mechanisms by which protein variance can be increased. Variables that affect promoter activation, such as nucleosome positioning, increase protein variance by changing the exponent of the power-law relationship. In contrast, variables that affect processes downstream of promoter activation, such as mRNA and protein synthesis, increase protein variance in a mean-dependent manner following the power-law. We verified our findings experimentally using an inducible gene expression system in yeast. We conclude that the power-law-like relationship between noise and protein mean is due to the kinetics of promoter activation. Our results provide a framework for understanding how molecular processes shape stochastic variation across the genome. PMID:25062021

Sexual Dimorphism and Allometric Effects Associated With the Wing Shape of Seven Moth Species of Sphingidae (Lepidoptera: Bombycoidea)

PubMed Central

de Camargo, Nícholas Ferreira; Corrêa, Danilo do Carmo Vieira; de Camargo, Amabílio J. Aires; Diniz, Ivone Rezende

2015-01-01

Sexual dimorphism is a pronounced pattern of intraspecific variation in Lepidoptera. However, moths of the family Sphingidae (Lepidoptera: Bombycoidea) are considered exceptions to this rule. We used geometric morphometric techniques to detect shape and size sexual dimorphism in the fore and hindwings of seven hawkmoth species. The shape variables produced were then subjected to a discriminant analysis. The allometric effects were measured with a simple regression between the canonical variables and the centroid size. We also used the normalized residuals to assess the nonallometric component of shape variation with a t-test. The deformations in wing shape between sexes per species were assessed with a regression between the nonreduced shape variables and the residuals. We found sexual dimorphism in both wings in all analyzed species, and that the allometric effects were responsible for much of the wing shape variation between the sexes. However, when we removed the size effects, we observed shape sexual dimorphism. It is very common for females to be larger than males in Lepidoptera, so it is expected that the shape of structures such as wings suffers deformations in order to preserve their function. However, sources of variation other than allometry could be a reflection of different reproductive flight behavior (long flights in search for sexual mates in males, and flight in search for host plants in females). PMID:26206895

Direct Prediction of EPR Spectra from Lipid Bilayers: Understanding Structure and Dynamics in Biological Membranes.

PubMed

Catte, Andrea; White, Gaye F; Wilson, Mark R; Oganesyan, Vasily S

2018-06-02

Of the many biophysical techniques now being brought to bear on studies of membranes, electron paramagnetic resonance (EPR) of nitroxide spin probes was the first to provide information about both mobility and ordering in lipid membranes. Here, we report the first prediction of variable temperature EPR spectra of model lipid bilayers in the presence and absence of cholesterol from the results of large scale fully atomistic molecular dynamics (MD) simulations. Three types of structurally different spin probes were employed in order to study different parts of the bilayer. Our results demonstrate very good agreement with experiment and thus confirm the accuracy of the latest lipid force fields. The atomic resolution of the simulations allows the interpretation of the molecular motions and interactions in terms of their impact on the sensitive EPR line shapes. Direct versus indirect effects of cholesterol on the dynamics of spin probes are analysed. Given the complexity of structural organisation in lipid bilayers, the advantage of using a combined MD-EPR simulation approach is two-fold. Firstly, prediction of EPR line shapes directly from MD trajectories of actual phospholipid structures allows unambiguous interpretation of EPR spectra of biological membranes in terms of complex motions. Secondly, such an approach provides an ultimate test bed for the up-to-date MD simulation models employed in the studies of biological membranes, an area that currently attracts great attention. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Geometric Phase of Stock Trading

PubMed Central

2016-01-01

Geometric phases describe how in a continuous-time dynamical system the displacement of a variable (called phase variable) can be related to other variables (shape variables) undergoing a cyclic motion, according to an area rule. The aim of this paper is to show that geometric phases can exist also for discrete-time systems, and even when the cycles in shape space have zero area. A context in which this principle can be applied is stock trading. A zero-area cycle in shape space represents the type of trading operations normally carried out by high-frequency traders (entering and exiting a position on a fast time-scale), while the phase variable represents the cash balance of a trader. Under the assumption that trading impacts stock prices, even zero-area cyclic trading operations can induce geometric phases, i.e., profits or losses, without affecting the stock quote. PMID:27556642

{bold {ital Ab initio}} studies of the structural and electronic properties of solid cubane

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

Richardson, S.L.; Martins, J.L.

1998-12-01

In this paper, we report {ital ab initio} calculation of the structural and electronic properties of solid cubane (s-C{sub 8}H{sub 8}) in the local-density approximation. By using an {ital ab initio} constant pressure extended molecular dynamics method with variable cell shape proposed by Wentzcovitch, Martins, and Price, we compute a lattice parameter {ital a} and a bond angle {alpha} for the rhombohedral Bravais lattice and compare it with experimental x-ray data. We obtain bond lengths for the mononuclear C{sub 8}H{sub 8} unit of basis atoms, as well as a density of states and heat of formation. {copyright} {ital 1998} {italmore » The American Physical Society}« less

Entropic effects, shape, and size of mixed micelles formed by copolymers with complex architectures

NASA Astrophysics Data System (ADS)

Kalogirou, Andreas; Gergidis, Leonidas N.; Moultos, Othonas; Vlahos, Costas

2015-11-01

The entropic effects in the comicellization behavior of amphiphilic A B copolymers differing in the chain size of solvophilic A parts were studied by means of molecular dynamics simulations. In particular, mixtures of miktoarm star copolymers differing in the molecular weight of solvophilic arms were investigated. We found that the critical micelle concentration values show a positive deviation from the analytical predictions of the molecular theory of comicellization for chemically identical copolymers. This can be attributed to the effective interactions between copolymers originated from the arm size asymmetry. The effective interactions induce a very small decrease in the aggregation number of preferential micelles triggering the nonrandom mixing between the solvophilic moieties in the corona. Additionally, in order to specify how the chain architecture affects the size distribution and the shape of mixed micelles we studied star-shaped, H-shaped, and homo-linked-rings-linear mixtures. In the first case the individual constituents form micelles with preferential and wide aggregation numbers and in the latter case the individual constituents form wormlike and spherical micelles.

Entropic effects, shape, and size of mixed micelles formed by copolymers with complex architectures.

PubMed

Kalogirou, Andreas; Gergidis, Leonidas N; Moultos, Othonas; Vlahos, Costas

2015-11-01

The entropic effects in the comicellization behavior of amphiphilic AB copolymers differing in the chain size of solvophilic A parts were studied by means of molecular dynamics simulations. In particular, mixtures of miktoarm star copolymers differing in the molecular weight of solvophilic arms were investigated. We found that the critical micelle concentration values show a positive deviation from the analytical predictions of the molecular theory of comicellization for chemically identical copolymers. This can be attributed to the effective interactions between copolymers originated from the arm size asymmetry. The effective interactions induce a very small decrease in the aggregation number of preferential micelles triggering the nonrandom mixing between the solvophilic moieties in the corona. Additionally, in order to specify how the chain architecture affects the size distribution and the shape of mixed micelles we studied star-shaped, H-shaped, and homo-linked-rings-linear mixtures. In the first case the individual constituents form micelles with preferential and wide aggregation numbers and in the latter case the individual constituents form wormlike and spherical micelles.

Computing Shapes Of Cascade Diffuser Blades

NASA Technical Reports Server (NTRS)

Tran, Ken; Prueger, George H.

1993-01-01

Computer program generates sizes and shapes of cascade-type blades for use in axial or radial turbomachine diffusers. Generates shapes of blades rapidly, incorporating extensive cascade data to determine optimum incidence and deviation angle for blade design based on 65-series data base of National Advisory Commission for Aeronautics and Astronautics (NACA). Allows great variability in blade profile through input variables. Also provides for design of three-dimensional blades by allowing variable blade stacking. Enables designer to obtain computed blade-geometry data in various forms: as input for blade-loading analysis; as input for quasi-three-dimensional analysis of flow; or as points for transfer to computer-aided design.

Study of hadronic event-shape variables in multijet final states in pp collisions at √s = 7 TeV

DOE PAGES

Khachatryan, V.

2014-10-14

Event-shape variables, which are sensitive to perturbative and nonperturbative aspects of quantum chromodynamic (QCD) interactions, are studied in multijet events recorded in proton-proton collisions at √s = 7 TeV. Events are selected with at least one jet with transverse momentum p T > 110 GeV and pseudorapidity |η| < 2.4, in a data sample corresponding to integrated luminosities of up to 5 fb –1. As a result, the distributions of five event-shape variables in various leading jet p T ranges are compared to predictions from different QCD Monte Carlo event generators.

Structural Characterization of Vapor-deposited Organic Glasses

NASA Astrophysics Data System (ADS)

Gujral, Ankit

Physical vapor deposition, a common route of thin film fabrication for organic electronic devices, has recently been shown to produce organic glassy films with enhanced kinetic stability and anisotropic structure. Anisotropic structures are of interest in the organic electronics community as it has been shown that certain structures lead to enhanced device performance, such as higher carrier mobility and better light outcoupling. A mechanism proposed to explain the origin of the stability and anisotropy of vapor-deposited glasses relies on two parameters: 1) enhanced molecular mobility at the free surface (vacuum interface) of a glass, and 2) anisotropic molecular packing at the free surface of the supercooled liquid of the glass-forming system. By vapor-depositing onto a substrate maintained at Tsubstrate < Tg (where Tg is the glass transition temperature), the enhanced molecular mobility at the free surface allows every molecule that lands on the surface to at least partially equilibrate to the preferred anisotropic molecular packing motifs before being buried by further deposition. The extent of equilibration depends on the mobility at the surface, controlled by Tsubstrate, and the residence time on the free surface, controlled by the rate of deposition. This body of work deals with the optimization of deposition conditions and system chemistry to prepare and characterize films with functional anisotropic structures. Here, we show that structural anisotropy can be attained for a variety of molecular systems including a rod-shaped non-mesogen, TPD, a rod-shaped smectic mesogen, itraconazole, two discotic mesogens, phenanthroperylene-ester and triphenylene-ester, and a disc-shaped non-mesogen, m-MTDATA. Experimental evidence is also provided of the anisotropic molecular packing at the free surface (vacuum interface) for the disc-shaped systems that are consistent with the expectations of the proposed mechanism and the final bulk state of the vapor-deposited glasses.

Exploring Conceptual Frameworks of Models of Atomic Structures and Periodic Variations, Chemical Bonding, and Molecular Shape and Polarity: A Comparison of Undergraduate General Chemistry Students with High and Low Levels of Content Knowledge

ERIC Educational Resources Information Center

Wang, Chia-Yu; Barrow, Lloyd H.

2013-01-01

The purpose of the study was to explore students' conceptual frameworks of models of atomic structure and periodic variations, chemical bonding, and molecular shape and polarity, and how these conceptual frameworks influence their quality of explanations and ability to shift among chemical representations. This study employed a purposeful sampling…

Soft particles at a fluid interface

NASA Astrophysics Data System (ADS)

Mehrabian, Hadi; Harting, Jens; Snoeijer, Jacco H.

2015-11-01

Particles added to a fluid interface can be used as a surface stabilizer in the food, oil and cosmetic industries. As an alternative to rigid particles, it is promising to consider highly deformable particles that can adapt their conformation at the interface. In this study, we compute the shapes of soft elastic particles using molecular dynamics simulations of a cross-linked polymer gel, complemented by continuum calculations based on the linear elasticity. It is shown that the particle shape is not only affected by the Young's modulus of the particle, but also strongly depends on whether the gel is partially or completely wetting the fluid interface. We find that the molecular simulations for the partially wetting case are very accurately described by the continuum theory. By contrast, when the gel is completely wetting the fluid interface the linear theory breaks down and we reveal that molecular details have a strong influence on the equilibrium shape.

Measurement of event shape variables in deep inelastic e p scattering

NASA Astrophysics Data System (ADS)

Adloff, C.; Aid, S.; Anderson, M.; Andreev, V.; Andrieu, B.; Arkadov, V.; Arndt, C.; Ayyaz, I.; Babaev, A.; Bähr, J.; Bán, J.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Bassler, U.; Beck, H. P.; Beck, M.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bertrand-Coremans, G.; Beyer, R.; Biddulph, P.; Bizot, J. C.; Borras, K.; Botterweck, F.; Boudry, V.; Bourov, S.; Braemer, A.; Braunschweig, W.; Brisson, V.; Brown, D. P.; Brückner, W.; Bruel, P.; Bruncko, D.; Brune, C.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Buschhorn, G.; Calvet, D.; Campbell, A. J.; Carli, T.; Charlet, M.; Clarke, D.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Cousinou, M.-C.; Cox, B. E.; Cozzika, G.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; de Roeck, A.; de Wolf, E. A.; Delcourt, B.; Dirkmann, M.; Dixon, P.; Dlugosz, W.; Dollfus, C.; Donovan, K. T.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Elsen, E.; Erdmann, M.; Fahr, A. B.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Formánek, J.; Foster, J. M.; Franke, G.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gebauer, M.; Gerhards, R.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Gonzalez-Pineiro, B.; Gorelov, I.; Grab, C.; Grässler, H.; Greenshaw, T.; Griffiths, R. K.; Grindhammer, G.; Gruber, A.; Gruber, C.; Hadig, T.; Haidt, D.; Hajduk, L.; Haller, T.; Hampel, M.; Haynes, W. J.; Heinemann, B.; Heinzelmann, G.; Henderson, R. C. W.; Hengstmann, S.; Henschel, H.; Herynek, I.; Hess, M. F.; Hewitt, K.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Höppner, M.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hütte, M.; Ibbotson, M.; İşsever, Ç.; Itterbeck, H.; Jacquet, M.; Jaffre, M.; Janoth, J.; Jansen, D. M.; Jönsson, L.; Johnson, D. P.; Jung, H.; Kalmus, P. I. P.; Kander, M.; Kant, D.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kaufmann, O.; Kausch, M.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kolya, S. D.; Korbel, V.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Küpper, A.; Küster, H.; Kuhlen, M.; Kurča, T.; Laforge, B.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Lebedev, A.; Lehner, F.; Lemaitre, V.; Levonian, S.; Lindstroem, M.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Lytkin, L.; Magnussen, N.; Mahlke-Krüger, H.; Malinovski, E.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, G.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Merkel, P.; Metlica, F.; Meyer, A.; Meyer, A.; Meyer, H.; Meyer, J.; Meyer, P.-O.; Migliori, A.; Mikocki, S.; Milstead, D.; Moeck, J.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, D.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Négri, I.; Newman, P. R.; Newton, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nowak, G.; Nunnemann, T.; Oberlack, H.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panaro, E.; Panitch, A.; Pascaud, C.; Passaggio, S.; Patel, G. D.; Pawletta, H.; Peppel, E.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pöschl, R.; Pope, G.; Povh, B.; Rabbertz, K.; Reimer, P.; Rick, H.; Reiss, S.; Rizvi, E.; Robmann, P.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleif, S.; Schleper, P.; von Schlippe, W.; Schmidt, D.; Schmidt, G.; Schoeffel, L.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Sefkow, F.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Sloan, T.; Smirnov, P.; Smith, M.; Solochenko, V.; Soloviev, Y.; Specka, A.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Squinabol, F.; Steffen, P.; Steinberg, R.; Steinhart, J.; Stella, B.; Stellberger, A.; Stiewe, J.; Stößlein, U.; Stolze, K.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thompson, G.; Thompson, P. D.; Tobien, N.; Todenhagen, R.; Truöl, P.; Tsipolitis, G.; Turnau, J.; Tzamariudaki, E.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; van Esch, P.; van Mechelen, P.; Vandenplas, D.; Vazdik, Y.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Wallny, R.; Walter, T.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wiesand, S.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wobisch, M.; Wollatz, H.; Wünsch, E.; ŽáČek, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zini, P.; Zomer, F.; Zsembery, J.; Zurnedden, M.

1997-02-01

Deep inelastic e p scattering data, taken with the H1 detector at HERA, are used to study the event shape variables thrust, jet broadening and jet mass in the current hemisphere of the Breit frame over a large range of momentum transfers Q between 7 GeV and 100 GeV. The data are compared with results from e+e- experiments. Using second order QCD calculations and an approach to relate hadronisation effects to power corrections an analysis of the Q dependences of the means of the event shape parameters is presented, from which both the power corrections and the strong coupling constant are determined without any assumption on fragmentation models. The power corrections of all event shape variables investigated follow a 1/Q behaviour and can be described by a common parameter α0.

Molecular quantum control landscapes in von Neumann time-frequency phase space

NASA Astrophysics Data System (ADS)

Ruetzel, Stefan; Stolzenberger, Christoph; Fechner, Susanne; Dimler, Frank; Brixner, Tobias; Tannor, David J.

2010-10-01

Recently we introduced the von Neumann representation as a joint time-frequency description for femtosecond laser pulses and suggested its use as a basis for pulse shaping experiments. Here we use the von Neumann basis to represent multidimensional molecular control landscapes, providing insight into the molecular dynamics. We present three kinds of time-frequency phase space scanning procedures based on the von Neumann formalism: variation of intensity, time-frequency phase space position, and/or the relative phase of single subpulses. The shaped pulses produced are characterized via Fourier-transform spectral interferometry. Quantum control is demonstrated on the laser dye IR140 elucidating a time-frequency pump-dump mechanism.

Molecular quantum control landscapes in von Neumann time-frequency phase space.

PubMed

Ruetzel, Stefan; Stolzenberger, Christoph; Fechner, Susanne; Dimler, Frank; Brixner, Tobias; Tannor, David J

2010-10-28

Recently we introduced the von Neumann representation as a joint time-frequency description for femtosecond laser pulses and suggested its use as a basis for pulse shaping experiments. Here we use the von Neumann basis to represent multidimensional molecular control landscapes, providing insight into the molecular dynamics. We present three kinds of time-frequency phase space scanning procedures based on the von Neumann formalism: variation of intensity, time-frequency phase space position, and/or the relative phase of single subpulses. The shaped pulses produced are characterized via Fourier-transform spectral interferometry. Quantum control is demonstrated on the laser dye IR140 elucidating a time-frequency pump-dump mechanism.

Mono- and multilayers of molecular spoked carbazole wheels on graphite

PubMed Central

Aggarwal, A Vikas; Kalle, Daniel; Höger, Sigurd

2014-01-01

Summary Self-assembled monolayers of a molecular spoked wheel (a shape-persistent macrocycle with an intraannular spoke/hub system) and its synthetic precursor are investigated by scanning tunneling microscopy (STM) at the liquid/solid interface of 1-octanoic acid and highly oriented pyrolytic graphite. The submolecularly resolved STM images reveal that the molecules indeed behave as more or less rigid objects of certain sizes and shapes – depending on their chemical structures. In addition, the images provide insight into the multilayer growth of the molecular spoked wheels (MSWs), where the first adlayer acts as a template for the commensurate adsorption of molecules in the second layer. PMID:25550744

Mono- and multilayers of molecular spoked carbazole wheels on graphite.

PubMed

Jester, Stefan-S; Aggarwal, A Vikas; Kalle, Daniel; Höger, Sigurd

2014-01-01

Self-assembled monolayers of a molecular spoked wheel (a shape-persistent macrocycle with an intraannular spoke/hub system) and its synthetic precursor are investigated by scanning tunneling microscopy (STM) at the liquid/solid interface of 1-octanoic acid and highly oriented pyrolytic graphite. The submolecularly resolved STM images reveal that the molecules indeed behave as more or less rigid objects of certain sizes and shapes - depending on their chemical structures. In addition, the images provide insight into the multilayer growth of the molecular spoked wheels (MSWs), where the first adlayer acts as a template for the commensurate adsorption of molecules in the second layer.

Redescription of two species of Thaparocleidus (Monogenea: Dactylogyridae), with the description of T. armillatus sp. n. from Wallago attu and a phylogenetic analysis based on 18S rDNA sequences.

PubMed

Verma, Chandni; Chaudhary, Anshu; Shanker Singh, Hridaya

2017-09-26

The phylogenetic studies on monogeneans of the genus Thaparocleidus parasitizing W. attu in India was inferred from 18S rDNA gene data. Out of species of Thaparocleidus, one new, T. armillatus sp. n., is described herein which distinguished from its congener species in the shapes and sizes of sclerotized structures and rest of the two species, T. indicus and T. wallagonius are redescribed morphologically as well as validated and confirmed by molecular means also. Besides the above, T. gangus was also included in the molecular analysis as it is recently described on the basis of morphology only. The phylogenetic tree was also reconstructed in order to elucidate the taxonomic status of Thaparocleidus armillatus sp. n., T. indicus, T. wallagonius and T. gangus. This research reports for the first time, the molecular phylogenetic analysis of 18S rDNA gene for four species belonging to the genus Thaparocleidus from W. attu collected off the River Ganga in India. In phylogram, all four species of Thapaocleidus come in a single clade that confirmed their monophyletic status. A very low interspecific variability was observed in T. armillatus sp. n. and T. wallagonius suggesting that these species are highly similar in morphology. Correspondingly, T. indicus and T. gangus also showed low interspecific variability which too signifies their morphological similarities in their sclerotized structures. Our result suggested that all four species taken in the present investigation from India are monophyletic and it is also observed that morphological similarities in the sclerotized structures are well correlated with phylogeny.

Formation mechanism and mechanics of dip-pen nanolithography using molecular dynamics.

PubMed

Wu, Cheng-Da; Fang, Te-Hua; Lin, Jen-Fin

2010-03-02

Molecular dynamics simulations are used to investigate the mechanisms of molecular transference, pattern formation, and mechanical behavior in the dip-pen nanolithography (DPN) process. The effects of deposition temperature were studied using molecular trajectories, the meniscus characteristic, surface absorbed energy, and pattern formation analysis. At the first transferred stage (at the initial indentation depth), the conformation of SAM molecules lies almost on the substrate surface. The molecules start to stand on the substrate due to the pull and drag forces at the second transferred stage (after the tip is pulled up). According to the absorbed energy behavior, the second transferred stage has larger transferred amounts and the transfer rate is strongly related to temperature. When molecules were deposited at low temperature (e.g., room temperature), the pattern shape was more highly concentrated. The pattern shape at high temperatures expanded and the area increased because of good molecular diffusion.

Controlled Folding, Motional, and Constitutional Dynamic Processes of Polyheterocyclic Molecular Strands.

PubMed

Barboiu, Mihail; Stadler, Adrian-Mihail; Lehn, Jean-Marie

2016-03-18

General design principles have been developed for the control of the structural features of polyheterocyclic strands and their effector-modulated shape changes. Induced defined molecular motions permit designed enforcement of helical as well as linear molecular shapes. The ability of such molecular strands to bind metal cations allows the generation of coiling/uncoiling processes between helically folded and extended linear states. Large molecular motions are produced on coordination of metal ions, which may be made reversible by competition with an ancillary complexing agent and fueled by sequential acid/base neutralization energy. The introduction of hydrazone units into the strands confers upon them constitutional dynamics, whereby interconversion between different strand compositions is achieved through component exchange. These features have relevance for nanomechanical devices. We present a morphological and functional analysis of such systems developed in our laboratories. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Configuration control on the shape memory stiffness of molecularly imprinted polymer for specific uptake of creatinine

NASA Astrophysics Data System (ADS)

Ang, Qian Yee; Zolkeflay, Muhammad Helmi; Low, Siew Chun

2016-04-01

In this study, sol-gel processing was proposed to prepare a creatinine (Cre)-imprinted molecularly imprinted polymer (MIP). The intermolecular interaction constituted by the cross-linkers, i.e., 2-acrylamido-2-methylpropane-sulfonic acid (AMPS) and aluminium ion (Al3+), was studied and compared in order to form a confined matrix that promises the effectiveness of molecular imprinting. In view of the shape recognition, the hydrogen bonded Cre-AMPS did not demonstrate good recognition of Cre, with Cre binding found only at 5.70 ± 0.15 mg g-1 of MIP. Whilst, MIP cross-linked using Al3+ was able to attain an excellent Cre adsorption capacity of 19.48 ± 0.64 mg g-1 of MIP via the stronger ionic interaction of Cre-Al3+. Based on the Scatchard analysis, a higher Cre concentration in testing solution required greater driving force to resolve the binding resistance of Cre molecules, so as to have a precise Cre binding with shape factor. The molecular recognition ability of Cre-MIP in present work was shape-specific for Cre as compared to its structural analogue, 2-pyrrolidinone (2-pyr), by an ideal selectivity coefficient of 6.57 ± 0.10. In overall, this study has come up with a practical approach on the preparation of MIP for the detection of renal dysfunction by point-of-care Cre testing.

Sexual Dimorphism and Allometric Effects Associated With the Wing Shape of Seven Moth Species of Sphingidae (Lepidoptera: Bombycoidea).

PubMed

de Camargo, Willian Rogers Ferreira; de Camargo, Nícholas Ferreira; Corrêa, Danilo do Carmo Vieira; de Camargo, Amabílio J Aires; Diniz, Ivone Rezende

2015-01-01

Sexual dimorphism is a pronounced pattern of intraspecific variation in Lepidoptera. However, moths of the family Sphingidae (Lepidoptera: Bombycoidea) are considered exceptions to this rule. We used geometric morphometric techniques to detect shape and size sexual dimorphism in the fore and hindwings of seven hawkmoth species. The shape variables produced were then subjected to a discriminant analysis. The allometric effects were measured with a simple regression between the canonical variables and the centroid size. We also used the normalized residuals to assess the nonallometric component of shape variation with a t-test. The deformations in wing shape between sexes per species were assessed with a regression between the nonreduced shape variables and the residuals. We found sexual dimorphism in both wings in all analyzed species, and that the allometric effects were responsible for much of the wing shape variation between the sexes. However, when we removed the size effects, we observed shape sexual dimorphism. It is very common for females to be larger than males in Lepidoptera, so it is expected that the shape of structures such as wings suffers deformations in order to preserve their function. However, sources of variation other than allometry could be a reflection of different reproductive flight behavior (long flights in search for sexual mates in males, and flight in search for host plants in females). © The Author 2015. Published by Oxford University Press on behalf of the Entomological Society of America.

Body shape by 3-D photonic scanning in Thai and UK adults: comparison of national sizing surveys.

PubMed

Wells, J C K; Treleaven, P; Charoensiriwath, S

2012-01-01

Body mass index (BMI) cut-offs associated with increased risk of diabetes and cardiovascular disease differ between European and Asian populations, and among Asian populations. Within-population and ethnic variability in body shape has likewise been linked with variability in cardiovascular risk in western settings. To explore differences between Thai and White UK adults in body shape and its associations with height, age and BMI. Data on weight and body shape by 3-D photonic scanning from National Sizing Surveys of UK (3542 men, 4130 women) and Thai (5889 men, 6499 women) adults aged 16-90 years, using a common protocol and methodology, were analysed. Thai adults in both sexes had significantly smaller body girths than UK adults after adjusting for age and height. Matching for BMI, and adjusting for height and age, Thais in both sexes tended to have similar or greater limb girths, but significantly smaller torso girths (especially waist and hip) than UK individuals. These results were replicated within narrow BMI bands at ∼20 and ∼25 kg m(-2). Shape-age associations also differed between the populations. Young Thai adults have a significantly slighter physique than White UK adults, with a less central distribution of body weight. However these differences reduce with age, especially in males. The 3-D photonic scanning provides detailed digital anthropometric data capable of monitoring between- and within-individual shape variability. The technology merits further application to investigate whether variability in body shape is more sensitive to metabolic risk than BMI within and between-populations.

Evaluation of a laser scanning sensor on detection of complex shaped targets for variable-rate sprayer development

USDA-ARS?s Scientific Manuscript database

Sensors that can accurately measure canopy structures are prerequisites for development of advanced variable-rate sprayers. A 270° radial range laser sensor was evaluated for its accuracy to measure dimensions of target surfaces with complex shapes and sizes. An algorithm for data acquisition and 3-...

Modeling of DNA-Mediated Self-Assembly from Anisotropic Nanoparticles: A Molecular Dynamics Study

NASA Astrophysics Data System (ADS)

Millan, Jaime; Girard, Martin; Brodin, Jeffrey; O'Brien, Matt; Mirkin, Chad; Olvera de La Cruz, Monica

The programmable selectivity of DNA recognition constitutes an elegant scheme to self-assemble a rich variety of superlattices from versatile nanoscale building blocks, where the natural interactions between building blocks are traded by complementary DNA hybridization interactions. Recently, we introduced and validated a scale-accurate coarse-grained model for a molecular dynamics approach that captures the dynamic nature of DNA hybridization events and reproduces the experimentally-observed crystallization behavior of various mixtures of spherical DNA-modified nanoparticles. Here, we have extended this model to robustly reproduce the assembly of nanoparticles with the anisotropic shapes observed experimentally. In particular, we are interested in two different particle types: (i) regular shapes, namely the cubic and octahedral polyhedra shapes commonly observed in gold nanoparticles, and (ii) irregular shapes akin to those exhibited by enzymes. Anisotropy in shape can provide an analog to the atomic orbitals exhibited by conventional atomic crystals. We present results for the assembly of enzymes or anisotropic nanoparticles and the co-assembly of enzymes and nanoparticles.

Toward a four-toothed molecular bevel gear with C2-symmetrical rotors.

PubMed

Kao, Chen-Yi; Hsu, Ya-Ting; Lu, Hsiu-Feng; Chao, Ito; Huang, Shou-Ling; Lin, Ying-Chih; Sun, Wei-Ting; Yang, Jye-Shane

2011-07-15

The design, synthesis, conformational analysis, and variable-temperature NMR studies of pentiptycene-based molecular gears Pp(2)X, where Pp is the unlabeled (in 1H) or methoxy groups-labeled (in 1OM) pentiptycene rotor and X is the phenylene stator containing ortho-bridged ethynylene axles, are reported. The approach of using shape-persistent rotors of four teeth but C(2) symmetry for constructing four-toothed molecular gears is unprecedented. In addition, the first example of enantioresolution of chiral pentiptycene scaffolds is demonstrated. Density functional theory (DFT) and AM1 calculations on these Pp(2)X systems suggest two possible correlated torsional motions, geared rocking and four-toothed geared rotations, which compete with the uncorrelated gear slippage. The DFT-derived torsional barriers in 1H for rocking, four-toothed rotation, and gear slippage are approximately 2.9, 5.5, and 4.7 kcal mol(-1), respectively. The low energy barriers for these torsional motions result from the low energy cost of bending the ethynylene axles. Comparison of the NMR spectra of 1OM in a mixture of stereoisomers (1OM-mix) and in an enantiopure form (1OM-op) confirms a fast gear slippage in these Pp(2)X systems. The effect of the methoxy labels on rotational potential energy surface and inter-rotor dynamics is also discussed.

Reconstruction of fluorescence molecular tomography with a cosinoidal level set method.

PubMed

Zhang, Xuanxuan; Cao, Xu; Zhu, Shouping

2017-06-27

Implicit shape-based reconstruction method in fluorescence molecular tomography (FMT) is capable of achieving higher image clarity than image-based reconstruction method. However, the implicit shape method suffers from a low convergence speed and performs unstably due to the utilization of gradient-based optimization methods. Moreover, the implicit shape method requires priori information about the number of targets. A shape-based reconstruction scheme of FMT with a cosinoidal level set method is proposed in this paper. The Heaviside function in the classical implicit shape method is replaced with a cosine function, and then the reconstruction can be accomplished with the Levenberg-Marquardt method rather than gradient-based methods. As a result, the priori information about the number of targets is not required anymore and the choice of step length is avoided. Numerical simulations and phantom experiments were carried out to validate the proposed method. Results of the proposed method show higher contrast to noise ratios and Pearson correlations than the implicit shape method and image-based reconstruction method. Moreover, the number of iterations required in the proposed method is much less than the implicit shape method. The proposed method performs more stably, provides a faster convergence speed than the implicit shape method, and achieves higher image clarity than the image-based reconstruction method.

Surface facial modelling and allometry in relation to sexual dimorphism.

PubMed

Velemínská, J; Bigoni, L; Krajíček, V; Borský, J; Šmahelová, D; Cagáňová, V; Peterka, M

2012-04-01

Sexual dimorphism is responsible for a substantial part of human facial variability, the study of which is essential for many scientific fields ranging from evolution to special biomedical topics. Our aim was to analyse the relationship between size variability and shape facial variability of sexual traits in the young adult Central European population and to construct average surface models of adult males and females. The method of geometric morphometrics allowed not only the identification of dimorphic traits, but also the evaluation of static allometry and the visualisation of sexual facial differences. Facial variability in the studied sample was characterised by a strong relationship between facial size and shape of sexual dimorphic traits. Large size of face was associated with facial elongation and vice versa. Regarding shape sexual dimorphic traits, a wide, vaulted and high forehead in combination with a narrow and gracile lower face were typical for females. Variability in shape dimorphic traits was smaller in females compared to males. For female classification, shape sexual dimorphic traits are more important, while for males the stronger association is with face size. Males generally had a closer inter-orbital distance and a deeper position of the eyes in relation to the facial plane, a larger and wider straight nose and nostrils, and more massive lower face. Using pseudo-colour maps to provide a detailed schematic representation of the geometrical differences between the sexes, we attempted to clarify the reasons underlying the development of such differences. Copyright © 2012 Elsevier GmbH. All rights reserved.

Investigation of the spatially isotropic component of the laterally averaged molecular hydrogen/Ag(111) physisorption potential

NASA Astrophysics Data System (ADS)

Yu, Chien-fan; Whaley, K. Birgitta; Hogg, C. S.; Sibener, S. J.

1985-10-01

A comprehensive study of the spatially isotropic component of the laterally averaged molecular hydrogen/Ag(111) physisorption potential is presented. Diffractive selective adsorption scattering resonances for rotationally state-selected H2 and D2 on Ag(111) have been mapped out as a function of incident polar angle for several crystal azimuths and beam energies. These resonances have been used to determine the bound eigenvalues, and subsequently the shape, of the potential well. Best fit Lennard-Jones, Morse, variable exponent, and exponential-3 potentials having well depths of ˜32 meV are derived from the data. These measurements are supported by rotationally inelastic scattering measurements for HD and exact close-coupled quantum scattering calculations. Debye-Waller attenuation measurements are also presented for H2, D2, and HD. The ability to detect these diffractively coupled resonances on a closest-packed metallic surface, i.e., a surface of extremely low corrugation, suggests that such measurements can be carried out on a much wider class of surfaces than previously envisioned.

Investigation of the spatially isotropic component of the laterally averaged molecular hydrogen/Ag(3) physisorption potential

NASA Astrophysics Data System (ADS)

Yu, C. F.; Whaley, K. B.; Hogg, C. S.; Sibener, S. J.

1985-08-01

A comprehensive study of the spatially isotropic component of the laterally averaged molecular hydrogen/Ag(111) physisorption potential is presented. Diffractive selective adsorption scattering resonances for rotationally state-selected H2 and D2 on Ag(111) have been mapped out as a function of incident polar angle for several crystal azimuths and beam energies. These resonances have been used to determine the bound eigenvalues, and subsequently the shape, of the potential well. Best fit Lennard-Jones, Morse, variable exponent, and exponential-3 potentials having well depths of approximately 32 MeV are derived from the data. These measurements are supported by rotationally inelastic scattering measurements for HD and exact close-coupled quantum scattering calculations. Debye-Waller attenuation measurements are also presented for H2, D2, and HD. The ability to detect these diffractively coupled resonances on a closest-packed metallic surface, i.e., a surface of extremely low corrugation, suggests that such measurements can be carried out on a much wider class of surfaces than previously envisioned.

Molecular Orientation in Two Component Vapor-Deposited Glasses: Effect of Substrate Temperature and Molecular Shape

NASA Astrophysics Data System (ADS)

Powell, Charles; Jiang, Jing; Walters, Diane; Ediger, Mark

Vapor-deposited glasses are widely investigated for use in organic electronics including the emitting layers of OLED devices. These materials, while macroscopically homogenous, have anisotropic packing and molecular orientation. By controlling this orientation, outcoupling efficiency can be increased by aligning the transition dipole moment of the light-emitting molecules parallel to the substrate. Light-emitting molecules are typically dispersed in a host matrix, as such, it is imperative to understand molecular orientation in two-component systems. In this study we examine two-component vapor-deposited films and the orientations of the constituent molecules using spectroscopic ellipsometry, UV-vis and IR spectroscopy. The role of temperature, composition and molecular shape as it effects molecular orientation is examined for mixtures of DSA-Ph in Alq3 and in TPD. Deposition temperature relative to the glass transition temperature of the two-component mixture is the primary controlling factor for molecular orientation. In mixtures of DSA-Ph in Alq3, the linear DSA-Ph has a horizontal orientation at low temperatures and slight vertical orientation maximized at 0.96Tg,mixture, analogous to one-component films.

Effects of rotation and tidal distortions on the shapes of radial velocity curves of polytropic models of pulsating variable stars

NASA Astrophysics Data System (ADS)

Kumar, Tarun; Lal, Arvind Kumar; Pathania, Ankush

2018-06-01

Anharmonic oscillations of rotating stars have been studied by various authors in literature to explain the observed features of certain variable stars. However, there is no study available in literature that has discussed the combined effect of rotation and tidal distortions on the anharmonic oscillations of stars. In this paper, we have created a model to determine the effect of rotation and tidal distortions on the anharmonic radial oscillations associated with various polytropic models of pulsating variable stars. For this study we have used the theory of Rosseland to obtain the anharmonic pulsation equation for rotationally and tidally distorted polytropicmodels of pulsating variable stars. The main objective of this study is to investigate the effect of rotation and tidal distortions on the shapes of the radial velocity curves for rotationally and tidally distorted polytropic models of pulsating variable stars. The results of the present study show that the rotational effects cause more deviations in the shapes of radial velocity curves of pulsating variable stars as compared to tidal effects.

Cytoskeletal Reorganization Drives Mesenchymal Condensation and Regulates Downstream Molecular Signaling.

PubMed

Ray, Poulomi; Chapman, Susan C

2015-01-01

Skeletal condensation occurs when specified mesenchyme cells self-organize over several days to form a distinctive cartilage template. Here, we determine how and when specified mesenchyme cells integrate mechanical and molecular information from their environment, forming cartilage condensations in the pharyngeal arches of chick embryos. By disrupting cytoskeletal reorganization, we demonstrate that dynamic cell shape changes drive condensation and modulate the response of the condensing cells to Fibroblast Growth Factor (FGF), Bone Morphogenetic Protein (BMP) and Transforming Growth Factor beta (TGF-β) signaling pathways. Rho Kinase (ROCK)-driven actomyosin contractions and Myosin II-generated differential cell cortex tension regulate these cell shape changes. Disruption of the condensation process inhibits the differentiation of the mesenchyme cells into chondrocytes, demonstrating that condensation regulates the fate of the mesenchyme cells. We also find that dorsal and ventral condensations undergo distinct cell shape changes. BMP signaling is instructive for dorsal condensation-specific cell shape changes. Moreover, condensations exhibit ventral characteristics in the absence of BMP signaling, suggesting that in the pharyngeal arches ventral morphology is the ground pattern. Overall, this study characterizes the interplay between cytoskeletal dynamics and molecular signaling in a self-organizing system during tissue morphogenesis.

Cytoskeletal Reorganization Drives Mesenchymal Condensation and Regulates Downstream Molecular Signaling

PubMed Central

Ray, Poulomi; Chapman, Susan C.

2015-01-01

Skeletal condensation occurs when specified mesenchyme cells self-organize over several days to form a distinctive cartilage template. Here, we determine how and when specified mesenchyme cells integrate mechanical and molecular information from their environment, forming cartilage condensations in the pharyngeal arches of chick embryos. By disrupting cytoskeletal reorganization, we demonstrate that dynamic cell shape changes drive condensation and modulate the response of the condensing cells to Fibroblast Growth Factor (FGF), Bone Morphogenetic Protein (BMP) and Transforming Growth Factor beta (TGF-β) signaling pathways. Rho Kinase (ROCK)-driven actomyosin contractions and Myosin II-generated differential cell cortex tension regulate these cell shape changes. Disruption of the condensation process inhibits the differentiation of the mesenchyme cells into chondrocytes, demonstrating that condensation regulates the fate of the mesenchyme cells. We also find that dorsal and ventral condensations undergo distinct cell shape changes. BMP signaling is instructive for dorsal condensation-specific cell shape changes. Moreover, condensations exhibit ventral characteristics in the absence of BMP signaling, suggesting that in the pharyngeal arches ventral morphology is the ground pattern. Overall, this study characterizes the interplay between cytoskeletal dynamics and molecular signaling in a self-organizing system during tissue morphogenesis. PMID:26237312

Morphological and molecular characterization of Sarcocystis taeniata and Sarcocystis pilosa n. sp. from the sika deer (Cervus nippon) in Lithuania.

PubMed

Prakas, Petras; Butkauskas, Dalius; Rudaitytė, Eglė; Kutkienė, Liuda; Sruoga, Aniolas; Pūraitė, Irma

2016-08-01

The diaphragm muscles of eight sika deer (Cervus nippon) bred in Lithuania were examined for Sarcocystis cysts. Two Sarcocystis species, Sarcocystis taeniata, which were previously reported in Canadian moose (Alces alces) and Argentinean red deer (Cervus elaphus), and Sarcocystis pilosa n. sp. were described using light microscopy (LM), transmission electron microscopy (TEM), 18S ribosomal DNA (rDNA), and subunit I of cytochrome c oxidase (cox1) sequences analysis. By LM, cysts of S. taeniata were 424.8 × 57.9 (200-837 × 30-100) μm in size and had a thin (up to 1 μm) and smooth cyst wall, while short ribbon-like protrusions arising from broadened cone-shaped bases were seen under TEM. Cysts of S. pilosa (by LM) were ribbon-shaped, measured 848.5 × 63.8 (350-1700 × 30-125) μm and had thin 7-8-μm long hair-like protrusions. By TEM, cyst wall was type 7a-like; protrusions arose from 0.3 μm wide dome-shaped base with minute indentations of the parasitophorous vacuolar membrane near it, the surface of protrusions seemed to be smooth, and the ground substance layer was thin (0.18-0.22 μm). The 18S rDNA, in contrast to the cox1, lacked variability to discriminate S. pilosa from closely related Sarcocystis hjorti from the red deer and moose. S. taeniata, but not S. pilosa, showed a considerable intraspecific variation in both genes analyzed. The phylogenetic analyses based on 18S rDNA and cox1 sequences suggest that canids are definitive hosts of both S. taeniata and S. pilosa. This paper represents the first identification of Sarcocystis species in the sika deer by morphological and molecular methods.

Effects of interstellar dust scattering on the X-ray eclipses of the LMXB AX J1745.6-2901 in the Galactic Centre

NASA Astrophysics Data System (ADS)

Jin, Chichuan; Ponti, Gabriele; Haberl, Frank; Smith, Randall; Valencic, Lynne

2018-07-01

AX J1745.6-2901 is an eclipsing low-mass X-ray binary in the Galactic Centre (GC). It shows significant X-ray excess emission during the eclipse phase, and its eclipse light curve shows an asymmetric shape. We use archival XMM-Newton and Chandra observations to study the origin of these peculiar X-ray eclipsing phenomena. We find that the shape of the observed X-ray eclipse light curves depends on both photon energy and the shape of the source extraction region, and also shows differences between the two instruments. By performing detailed simulations for the time-dependent X-ray dust-scattering halo, as well as directly modelling the observed eclipse and non-eclipse halo profiles of AX J1745.6-2901, we obtained solid evidence that its peculiar eclipse phenomena are indeed caused by the X-ray dust scattering in multiple foreground dust layers along the line of sight (LOS). The apparent dependence on the instruments is caused by different instrumental point spread functions. Our results can be used to assess the influence of dust-scattering in other eclipsing X-ray sources, and raise the importance of considering the timing effects of dust-scattering halo when studying the variability of other X-ray sources in the GC, such as Sgr A⋆. Moreover, our study of halo eclipse reinforces the existence of a dust layer local to AX J1745.6-2901 as reported by Jin et al. (2017), as well as identifying another dust layer within a few hundred parsecs to the Earth, containing up to several tens of percent LOS dust, which is likely to be associated with the molecular clouds in the Solar neighbourhood. The remaining LOS dust is likely to be associated with the molecular clouds located in the Galactic disc in-between.

Geographic in wing morphology relate to colonization history in New World but not Old World populations of yellow dung flies.

PubMed

Schäfer, Martin A; Berger, David; Rohner, Patrick T; Kjaersgaard, Anders; Bauerfeind, Stephanie S; Guillaume, Frédéric; Fox, Charles W; Blanckenhorn, Wolf U

2018-06-17

Geographic clines offer insights about putative targets and agents of natural selection as well as tempo and mode of adaptation. However, demographic processes can lead to clines that are indistinguishable from adaptive divergence. Using the widespread yellow dung fly Scathophaga stercoraria (Diptera: Scathophagidae), we examine quantitative genetic differentiation (Q ST ) of wing shape across North America, Europe and Japan, and compare this differentiation with that of ten microsatellites (F ST ). Morphometric analyses of 28 populations reared at three temperatures revealed significant thermal plasticity, sexual dimorphism and geographic differentiation in wing shape. In North America morphological differentiation followed the decline in microsatellite variability along the presumed route of recent colonization from the southeast to the northwest. Across Europe, where S. stercoraria presumably existed for much longer time and where no molecular pattern of isolation by distance was evident, clinal variation was less pronounced despite significant morphological differentiation (Q ST >F ST ). Shape vector comparisons further indicate that thermal plasticity (hot-to-cold) does not mirror patterns of latitudinal divergence (south-to-north), as might have been expected under a scenario with temperature as the major agent of selection. Our findings illustrate the importance of detailed phylogeographic information when interpreting geographic clines of dispersal traits in an adaptive evolutionary framework. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Differing Roles of Functional Movement Variability as Experience Increases in Gymnastics

PubMed Central

Busquets, Albert; Marina, Michel; Davids, Keith; Angulo-Barroso, Rosa

2016-01-01

Current theories, like Ecological Dynamics, propose that inter-trial movement variability is functional when acquiring or refining movement coordination. Here, we examined how age-based experience levels of gymnasts constrained differences in emergent movement pattern variability during task performance. Specifically, we investigated different roles of movement pattern variability when gymnasts in different age groups performed longswings on a high bar, capturing the range of experience from beginner to advanced status. We also investigated the functionality of the relationships between levels of inter-trial variability and longswing amplitude during performance. One-hundred and thirteen male gymnasts in five age groups were observed performing longswings (with three different experience levels: beginners, intermediates and advanced performers). Performance was evaluated by analysis of key events in coordination of longswing focused on the arm-trunk and trunk-thigh segmental relations. Results revealed that 10 of 18 inter-trial variability measures changed significantly as a function of increasing task experience. Four of ten variability measures conformed to a U-shaped function with age implying exploratory strategies amongst beginners and functional adaptive variability amongst advanced performers. Inter-trial variability of arm-trunk coordination variables (6 of 10) conformed to a \\-shaped curve, as values were reduced to complete the longswings. Changes in coordination variability from beginner to intermediate status were largely restrictive, with only one variability measure related to exploration. Data revealed how inter-trial movement variability in gymnastics, relative to performance outcomes, needs careful interpretation, implying different roles as task experience changes. Key points Inter-trial variability while performing longswings on a high bar was assessed in a large sample (113 participants) divided into five age groups (form beginners to advanced gymnasts). Longswing assessment allowed us to evaluate inter-trial variability in representative performance context. Coordination variability presented two different configurations across experience levels depending on the variable of interest: either a U-shaped or a L- or \\-shaped graph. Increased inter-trial variability of the functional phase events offered flexibility to adapt the longswing performance in the advanced gymnasts, while decreasing variability in arm-trunk coordination modes was critical to improve longswing and to achieve the most advanced level. In addition, the relationship between variability measures and the global performance outcome (i.e. the swing amplitude) revealed different functional roles of movement variability (exploratory or restrictive) as a function of changes in experience levels. PMID:27274664

The implementation of non-Voigt line profiles in the HITRAN database: H2 case study

NASA Astrophysics Data System (ADS)

Wcisło, P.; Gordon, I. E.; Tran, H.; Tan, Y.; Hu, S.-M.; Campargue, A.; Kassi, S.; Romanini, D.; Hill, C.; Kochanov, R. V.; Rothman, L. S.

2016-07-01

Experimental capabilities of molecular spectroscopy and its applications nowadays require a sub-percent or even sub-per mille accuracy of the representation of the shapes of molecular transitions. This implies the necessity of using more advanced line-shape models which are characterized by many more parameters than a simple Voigt profile. It is a great challenge for modern molecular spectral databases to store and maintain the extended set of line-shape parameters as well as their temperature dependences. It is even more challenging to reliably retrieve these parameters from experimental spectra over a large range of pressures and temperatures. In this paper we address this problem starting from the case of the H2 molecule for which the non-Voigt line-shape effects are exceptionally pronounced. For this purpose we reanalyzed the experimental data reported in the literature. In particular, we performed detailed line-shape analysis of high-quality spectra obtained with cavity-enhanced techniques. We also report the first high-quality cavity-enhanced measurement of the H2 fundamental vibrational mode. We develop a correction to the Hartmann-Tran profile (HTP) which adjusts the HTP to the particular model of the velocity-changing collisions. This allows the measured spectra to be better represented over a wide range of pressures. The problem of storing the HTP parameters in the HITRAN database together with their temperature dependences is also discussed.

VizieR Online Data Catalog: uvby photometry of 4 CP stars (Adelman, 1997)

NASA Astrophysics Data System (ADS)

Adelman, S. J.

1996-07-01

Differential Stroemgren uvby photometric observations from the Four College Automated Photoelectric Telescope refine the rotational periods and define the shapes of the light curves of four magnetic Chemically Peculiar stars. HD 32633 (P=6.43000d) exhibits an in-phase variability with asymmetrically shaped light curves. 25 Sex (P=4.37900d) has a complex variability with the v, b, and y light variability crudely in phase, but quite different from that of u. HR 7224 (P=1.123095d) shows in-phase variability with two nearly equal secondary minima. HD 200311 (P=26.0042d), which was previous thought to be a long period variable, is found to be a modest photometric variable. (5 data files).

Molecular Innovation in Ciliates with Complex Genome Rearrangements

NASA Astrophysics Data System (ADS)

Neme, R.; Landweber, L. F.

2017-07-01

We study molecular innovation in several ciliate species with unique massive genome rearrangements to understand how a radically distinct genome architecture can shape the process of acquiring new functions, genes and structures.

Core-level spectra and molecular deformation in adsorption: V-shaped pentacene on Al(001)

PubMed Central

Lin, He; Brivio, Gian Paolo; Floreano, Luca; Fratesi, Guido

2015-01-01

Summary By first-principle simulations we study the effects of molecular deformation on the electronic and spectroscopic properties as it occurs for pentacene adsorbed on the most stable site of Al(001). The rationale for the particular V-shaped deformed structure is discussed and understood. The molecule–surface bond is made evident by mapping the charge redistribution. Upon X-ray photoelectron spectroscopy (XPS) from the molecule, the bond with the surface is destabilized by the electron density rearrangement to screen the core hole. This destabilization depends on the ionized carbon atom, inducing a narrowing of the XPS spectrum with respect to the molecules adsorbed hypothetically undistorted, in full agreement to experiments. When looking instead at the near-edge X-ray absorption fine structure (NEXAFS) spectra, individual contributions from the non-equivalent C atoms provide evidence of the molecular orbital filling, hybridization, and interchange induced by distortion. The alteration of the C–C bond lengths due to the V-shaped bending decreases by a factor of two the azimuthal dichroism of NEXAFS spectra, i.e., the energy splitting of the sigma resonances measured along the two in-plane molecular axes. PMID:26734516

Free Surface Relaxations of Star-Shaped Polymer Films

DOE PAGES

Glynos, Emmanouil; Johnson, Kyle J.; Frieberg, Bradley; ...

2017-11-28

Here, the surface relaxation dynamics of supported star-shaped polymer thin films are shown to be slower than the bulk, persisting up to temperatures at least 50 degrees above the bulk glass transition temperature Tmore » $$bulk\\atop{g}$$. This behavior, exhibited by star-shaped polystyrenes (SPSs) with functionality f = 8 arms and molecular weights per arm M arm < M e (M e is the entanglement molecular weight), is shown by molecular dynamics simulations to be associated with a preferential localization of these macromolecules at the free surface. This new phenomenon is in notable contrast to that of linear chain polymer thin film systems where the surface relaxations are enhanced in relation to the bulk; this enhancement persists only for a limited temperature range above the bulk T$$bulk\\atop{g}$$. Finally, evidence of the slow surface dynamics, compared to the bulk, for temperatures well above T g and at length and time scales not associated with the glass transition has not previously been reported for polymers.« less

Mesoscale Graphene-like Honeycomb Mono- and Multilayers Constructed via Self-Assembly of Coclusters.

PubMed

Hou, Xue-Sen; Zhu, Guo-Long; Ren, Li-Jun; Huang, Zi-Han; Zhang, Rui-Bin; Ungar, Goran; Yan, Li-Tang; Wang, Wei

2018-02-07

Honeycomb structure endows graphene with extraordinary properties. But could a honeycomb monolayer superlattice also be generated via self-assembly of colloids or nanoparticles? Here we report the construction of mono- and multilayer molecular films with honeycomb structure that can be regarded as self-assembled artificial graphene (SAAG). We construct fan-shaped molecular building blocks by covalently connecting two kinds of clusters, one polyoxometalate and four polyhedral oligomeric silsesquioxanes. The precise shape control enables these complex molecules to self-assemble into a monolayer 2D honeycomb superlattice that mirrors that of graphene but on the mesoscale. The self-assembly of the SAAG was also reproduced via coarse-grained molecular simulations of a fan-shaped building block. It revealed a hierarchical process and the key role of intermediate states in determining the honeycomb structure. Experimental images also show a diversity of bi- and trilayer stacking modes. The successful creation of SAAG and its stacks opens up prospects for the preparation of novel self-assembled nanomaterials with unique properties.

Sombrero-shaped plasmonic nanoparticles with molecular-level sensitivity and multifunctionality.

PubMed

Wi, Jung-Sub; Barnard, Edward S; Wilson, Robert J; Zhang, Mingliang; Tang, Mary; Brongersma, Mark L; Wang, Shan X

2011-08-23

We demonstrate top-down synthesis of monodisperse plasmonic nanoparticles designed to contain internal Raman hot spots. Our Raman-active nanoparticles are fabricated using nanoimprint lithography and thin-film deposition and are composed of novel internal structures with sublithographic dimensions: a disk-shaped Ag core, a Petri-dish-shaped SiO(2) base whose inner surface is coated with Ag film, and a sub-10 nm scale circular gap between the core and the base. Confocal Raman measurements and electromagnetic simulations show that Raman hot spots appear at the inside perimeter of individual nanoparticles and serve as the source of a 1000-fold improvement of minimum molecular detection level that enables detection of signals from a few molecules near hot spots. A multimodality version of these nanoparticles, which includes the functionality offered by magnetic multilayers, is also demonstrated. These results illustrate the potential of direct fabrication for creating exotic monodisperse nanoparticles, which combine engineered internal nanostructures and multilayer composite materials, for use in nanoparticle-based molecular imaging and detection. © 2011 American Chemical Society

Conformations of low-molecular-weight lignin polymers in water

DOE PAGES

Petridis, Loukas; Smith, Jeremy C.

2016-01-13

Low-molecular-weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a criticalmore » degree of polymerization, N c=15, the polymer adopts less spherical conformations than above N c. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. As a result, an implication relevant to cellulosic biofuel production is that lignin will self-aggregate even at high pretreatment temperatures.« less

Conformations of Low-Molecular-Weight Lignin Polymers in Water.

PubMed

Petridis, Loukas; Smith, Jeremy C

2016-02-08

Low-molecular-weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a critical degree of polymerization, Nc =15, the polymer adopts less spherical conformations than above Nc. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. An implication relevant to cellulosic biofuel production is that lignin will self-aggregate even at high pretreatment temperatures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Shape variation in the human pelvis and limb skeleton: Implications for obstetric adaptation.

PubMed

Kurki, Helen K; Decrausaz, Sarah-Louise

2016-04-01

Under the obstetrical dilemma (OD) hypothesis, selection acts on the human female pelvis to ensure a sufficiently sized obstetric canal for birthing a large-brained, broad shouldered neonate, while bipedal locomotion selects for a narrower and smaller pelvis. Despite this female-specific stabilizing selection, variability of linear dimensions of the pelvic canal and overall size are not reduced in females, suggesting shape may instead be variable among females of a population. Female canal shape has been shown to vary among populations, while male canal shape does not. Within this context, we examine within-population canal shape variation in comparison with that of noncanal aspects of the pelvis and the limbs. Nine skeletal samples (total female n = 101, male n = 117) representing diverse body sizes and shapes were included. Principal components analysis was applied to size-adjusted variables of each skeletal region. A multivariate variance was calculated using the weighted PC scores for all components in each model and F-ratios used to assess differences in within-population variances between sexes and skeletal regions. Within both sexes, multivariate canal shape variance is significantly greater than noncanal pelvis and limb variances, while limb variance is greater than noncanal pelvis variance in some populations. Multivariate shape variation is not consistently different between the sexes in any of the skeletal regions. Diverse selective pressures, including obstetrics, locomotion, load carrying, and others may act on canal shape, as well as genetic drift and plasticity, thus increasing variation in morphospace while protecting obstetric sufficiency. © 2015 Wiley Periodicals, Inc.

Shape optimization using a NURBS-based interface-enriched generalized FEM

DOE PAGES

Najafi, Ahmad R.; Safdari, Masoud; Tortorelli, Daniel A.; ...

2016-11-26

This study presents a gradient-based shape optimization over a fixed mesh using a non-uniform rational B-splines-based interface-enriched generalized finite element method, applicable to multi-material structures. In the proposed method, non-uniform rational B-splines are used to parameterize the design geometry precisely and compactly by a small number of design variables. An analytical shape sensitivity analysis is developed to compute derivatives of the objective and constraint functions with respect to the design variables. Subtle but important new terms involve the sensitivity of shape functions and their spatial derivatives. As a result, verification and illustrative problems are solved to demonstrate the precision andmore » capability of the method.« less

Structural Conversion of Aβ17–42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways

PubMed Central

Cheon, Mookyung; Hall, Carol K.; Chang, Iksoo

2015-01-01

Discovering the mechanisms by which proteins aggregate into fibrils is an essential first step in understanding the molecular level processes underlying neurodegenerative diseases such as Alzheimer’s and Parkinson's. The goal of this work is to provide insights into the structural changes that characterize the kinetic pathways by which amyloid-β peptides convert from monomers to oligomers to fibrils. By applying discontinuous molecular dynamics simulations to PRIME20, a force field designed to capture the chemical and physical aspects of protein aggregation, we have been able to trace out the entire aggregation process for a system containing 8 Aβ17–42 peptides. We uncovered two fibrillization mechanisms that govern the structural conversion of Aβ17–42 peptides from disordered oligomers into protofilaments. The first mechanism is monomeric conversion templated by a U-shape oligomeric nucleus into U-shape protofilament. The second mechanism involves a long-lived and on-pathway metastable oligomer with S-shape chains, having a C-terminal turn, en route to the final U-shape protofilament. Oligomers with this C-terminal turn have been regarded in recent experiments as a major contributing element to cell toxicity in Alzheimer’s disease. The internal structures of the U-shape protofilaments from our PRIME20/DMD simulation agree well with those from solid state NMR experiments. The approach presented here offers a simple molecular-level framework to describe protein aggregation in general and to visualize the kinetic evolution of a putative toxic element in Alzheimer’s disease in particular. PMID:25955249

The Case for the L-Shaped Classroom.

ERIC Educational Resources Information Center

Dyck, James A.

1994-01-01

Classroom shape is an important variable in educational quality. The traditional squat rectangle may be counterproductive to the learning process. The fat L-shaped classroom, compared to H, X, and T shapes, offers good separation, is more compact, and provides good visibility and ease of movement for the teacher. It has excellent nesting…

Instrumental Variable Analysis with a Nonlinear Exposure–Outcome Relationship

PubMed Central

Davies, Neil M.; Thompson, Simon G.

2014-01-01

Background: Instrumental variable methods can estimate the causal effect of an exposure on an outcome using observational data. Many instrumental variable methods assume that the exposure–outcome relation is linear, but in practice this assumption is often in doubt, or perhaps the shape of the relation is a target for investigation. We investigate this issue in the context of Mendelian randomization, the use of genetic variants as instrumental variables. Methods: Using simulations, we demonstrate the performance of a simple linear instrumental variable method when the true shape of the exposure–outcome relation is not linear. We also present a novel method for estimating the effect of the exposure on the outcome within strata of the exposure distribution. This enables the estimation of localized average causal effects within quantile groups of the exposure or as a continuous function of the exposure using a sliding window approach. Results: Our simulations suggest that linear instrumental variable estimates approximate a population-averaged causal effect. This is the average difference in the outcome if the exposure for every individual in the population is increased by a fixed amount. Estimates of localized average causal effects reveal the shape of the exposure–outcome relation for a variety of models. These methods are used to investigate the relations between body mass index and a range of cardiovascular risk factors. Conclusions: Nonlinear exposure–outcome relations should not be a barrier to instrumental variable analyses. When the exposure–outcome relation is not linear, either a population-averaged causal effect or the shape of the exposure–outcome relation can be estimated. PMID:25166881

Raining on black holes and massive galaxies: the top-down multiphase condensation model

NASA Astrophysics Data System (ADS)

Gaspari, M.; Temi, P.; Brighenti, F.

2017-04-01

The plasma haloes filling massive galaxies, groups and clusters are shaped by active galactic nucleus (AGN) heating and subsonic turbulence (σv ˜ 150 km s-1), as probed by Hitomi. Novel 3D high-resolution simulations show the soft X-ray, keV hot plasma cools rapidly via radiative emission at the high-density interface of the turbulent eddies, stimulating a top-down condensation cascade of warm 104 K filaments. The kpc-scale ionized (optical/ultraviolet) filaments form a skin enveloping the neutral filaments (optical/infrared/21 cm). The peaks of the warm filaments further condense into cold molecular clouds (<50 K; radio) with total mass of several 107 M⊙ and inheriting the turbulent kinematics. In the core, the clouds collide inelastically, mixing angular momentum and leading to Chaotic Cold Accretion (CCA). The black hole accretion rate (BHAR) can be modelled via quasi-spherical viscous accretion, dot{M}_bullet ∝ ν _c, with clump collisional viscosity νc ≡ λc σv and λc ˜ 100 pc. Beyond the core, pressure torques shape the angular momentum transport. In CCA, the BHAR is recurrently boosted up to 2 dex compared with the disc evolution, which arises as turbulence becomes subdominant. With negligible rotation too, compressional heating inhibits the molecular phase. The CCA BHAR distribution is lognormal with pink noise, f-1 power spectrum characteristic of fractal phenomena. Such chaotic fluctuations can explain the rapid luminosity variability of AGN and high-mass X-ray binaries. An improved criterium to trace non-linear condensation is proposed: σv/vcool ≲ 1. The three-phase CCA reproduces key observations of cospatial multiphase gas in massive galaxies, including Chandra X-ray images, SOAR Hα filaments and kinematics, Herschel [C+] emission and ALMA molecular associations. CCA plays important role in AGN feedback and unification, the evolution of BHs, galaxies and clusters.

Negative differential resistance by molecular resonant tunneling between neutral tribenzosubporphine anchored to a Au(111) surface and tribenzosubporphine cation adsorbed on to a tungsten tip.

PubMed

Majima, Yutaka; Ogawa, Daisuke; Iwamoto, Masachika; Azuma, Yasuo; Tsurumaki, Eiji; Osuka, Atsuhiro

2013-09-25

Tribenzosubporphyrins are boron(III)-chelated triangular bowl-shaped ring-contracted porphyrins that possess a 14π-aromatic circuit. Their flat molecular shapes and discrete molecular orbital diagrams make them ideal for observation by scanning tunneling microscopy (STM). Expanding their applications toward single molecule-based devices requires a fundamental knowledge of single molecular conductance between tribenzosubporphines and the STM metal tip. We utilized a tungsten (W) STM tip to investigate the electronic properties of B-(5-mercaptopentoxy)tribenzosubporphine 1 at the single molecular level. B-(5-mercaptopentoxy)-tribenzosubporphine 1 was anchored to the Au(111) surface via reaction with 1-heptanethiol linkers that were preorganized as a self-assembled monolayer (C7S SAM) on the Au(111) substrate. This arrangement ensured that 1 was electronically decoupled from the metal surface. Differential conductance (dI/dV - V) measurements with the bare W tip exhibited a broad gap region of low conductance and three distinct responses at 2.4,-1.3, and -2.1 V. Bias-voltage-dependent STM imaging of 1 at 65 K displayed a triangle shape at -2.1 < V < -1.3 V and a circle shape at V < -2.1 V, reflecting its HOMO and HOMO-1, respectively. In addition, different conductance behaviors were reproducibly observed, which has been ascribed to the adsorption of a tribenzosubporphine-cation on the W tip. When using a W tip doped with preadsorbed tribenzosubporphine-cation, negative differential resistance (NDR) phenomena were clearly observed in a reproducible manner with a peak-to-valley ratio of 2.6, a value confirmed by spatial mapping conductance measurements. Collectively, the observed NDR phenomena have been attributed to effective molecular resonant tunneling between a neutral tribenzosubporphine anchored to the metal surface and a tribenzosubporphine cation adsorbed on a W tip.

Shape memory polymer network with thermally distinct elasticity and plasticity.

PubMed

Zhao, Qian; Zou, Weike; Luo, Yingwu; Xie, Tao

2016-01-01

Stimuli-responsive materials with sophisticated yet controllable shape-changing behaviors are highly desirable for real-world device applications. Among various shape-changing materials, the elastic nature of shape memory polymers allows fixation of temporary shapes that can recover on demand, whereas polymers with exchangeable bonds can undergo permanent shape change via plasticity. We integrate the elasticity and plasticity into a single polymer network. Rational molecular design allows these two opposite behaviors to be realized at different temperature ranges without any overlap. By exploring the cumulative nature of the plasticity, we demonstrate easy manipulation of highly complex shapes that is otherwise extremely challenging. The dynamic shape-changing behavior paves a new way for fabricating geometrically complex multifunctional devices.

Gender differences in adult foot shape: implications for shoe design.

PubMed

Wunderlich, R E; Cavanagh, P R

2001-04-01

To analyze gender differences in foot shape in a large sample of young individuals. Univariate t-tests and multivariate discriminant analyses were used to assess 1) significant differences between men and women for each foot and leg dimension, standardized to foot length, 2) the reliability of classification into gender classes using the absolute and standardized variable sets, and 3) the relative importance of each variable to the discrimination between men and women. Men have longer and broader feet than women for a given stature. After normalization of the measurements by foot length, men and women were found to differ significantly in two calf, five ankle, and four foot shape variables. Classification by gender using absolute values was correct at least 93% of the time. Using the variables standardized to foot length, gender was correctly classified 85% of the time. This study demonstrates that female feet and legs are not simply scaled-down versions of male feet but rather differ in a number of shape characteristics, particularly at the arch, the lateral side of the foot, the first toe, and the ball of the foot. These differences should be taken into account in the design and manufacture of women's sport shoes.

A serine protease homologue Bombyx mori scarface induces a short and fat body shape in silkworm.

PubMed

Wang, R-X; Tong, X-L; Gai, T-T; Li, C-L; Qiao, L; Hu, H; Han, M-J; Xiang, Z-H; Lu, C; Dai, F-Y

2018-06-01

Body shape is one of the most prominent and basic characteristics of any organism. In insects, abundant variations in body shape can be observed both within and amongst species. However, the molecular mechanism underlying body shape fine-tuning is very complex and has been largely unknown until now. In the silkworm Bombyx mori, the tubby (tub) mutant has an abnormal short fat body shape and the abdomen of tub larvae expands to form a fusiform body shape. Morphological investigation revealed that the body length was shorter and the body width was wider than that of the Dazao strain. Thus, this mutant is a good model for studying the molecular mechanisms of body shape fine-tuning. Using positional cloning, we identified a gene encoding the serine protease homologue, B. mori scarface (Bmscarface), which is associated with the tub phenotype. Sequence analysis revealed a specific 312-bp deletion from an exon of Bmscarface in the tub strain. In addition, recombination was not observed between the tub and Bmscarface loci. Moreover, RNA interference of Bmscarface resulted in the tub-like phenotype. These results indicate that Bmscarface is responsible for the tub mutant phenotype. This is the first study to report that mutation of a serine protease homologue can induce an abnormal body shape in insects. © 2018 The Royal Entomological Society.

A Simple Demonstration of Atomic and Molecular Orbitals Using Circular Magnets

ERIC Educational Resources Information Center

Chakraborty, Maharudra; Mukhopadhyay, Subrata; Das, Ranendu Sekhar

2014-01-01

A quite simple and inexpensive technique is described here to represent the approximate shapes of atomic orbitals and the molecular orbitals formed by them following the principles of the linear combination of atomic orbitals (LCAO) method. Molecular orbitals of a few simple molecules can also be pictorially represented. Instructors can employ the…

Stabilizing detached Bridgman melt crystal growth: Proportional-integral feedback control

NASA Astrophysics Data System (ADS)

Yeckel, Andrew; Daoutidis, Prodromos; Derby, Jeffrey J.

2012-10-01

The dynamics, operability limits, and tuning of a proportional-integral feedback controller to stabilize detached vertical Bridgman crystal growth are analyzed using a capillary model of shape stability. The manipulated variable is the pressure difference between upper and lower vapor spaces, and the controlled variable is the gap width at the triple-phase line. Open and closed loop dynamics of step changes in these state variables are analyzed under both shape stable and shape unstable growth conditions. Effects of step changes in static contact angle and growth angle are also studied. Proportional and proportional-integral control can stabilize unstable growth, but only within tight operability limits imposed by the narrow range of allowed meniscus shapes. These limits are used to establish safe operating ranges of controller gain. Strong nonlinearity of the capillary model restricts the range of perturbations that can be stabilized, and under some circumstances, stabilizes a spurious operating state far from the set point. Stabilizing detachment at low growth angle proves difficult and becomes impossible at zero growth angle.

Use of inter-simple sequence repeats and amplified fragment length polymorphisms to analyze genetic relationships among small grain-infecting species of ustilago.

PubMed

Menzies, J G; Bakkeren, G; Matheson, F; Procunier, J D; Woods, S

2003-02-01

ABSTRACT In the smut fungi, few features are available for use as taxonomic criteria (spore size, shape, morphology, germination type, and host range). DNA-based molecular techniques are useful in expanding the traits considered in determining relationships among these fungi. We examined the phylogenetic relationships among seven species of Ustilago (U. avenae, U. bullata, U. hordei, U. kolleri, U. nigra, U. nuda, and U. tritici) using inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs) to compare their DNA profiles. Fifty-four isolates of different Ustilago spp. were analyzed using ISSR primers, and 16 isolates of Ustilago were studied using AFLP primers. The variability among isolates within species was low for all species except U. bullata. The isolates of U. bullata, U. nuda, and U. tritici were well separated and our data supports their speciation. U. avenae and U. kolleri isolates did not separate from each other and there was little variability between these species. U. hordei and U. nigra isolates also showed little variability between species, but the isolates from each species grouped together. Our data suggest that U. avenae and U. kolleri are monophyletic and should be considered one species, as should U. hordei and U. nigra.

Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere

PubMed Central

Peredo, Elena L.; Simmons, Sheri L.

2018-01-01

Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents. PMID:29375531

Dropping the Other U: An Alternative Approach to U-Shaped Developmental Functions

ERIC Educational Resources Information Center

Brainerd, C. J.

2004-01-01

The aim of this article is to introduce readers to an alternative way of applying U-shaped functions to understand development, especially cognitive development. In classical developmental applications, age is the abscissa; that is, in the fundamental equation B = f(A), some behavioral variable (B) plots as a U-shaped or inverted U-shaped function…

Development for 2D pattern quantification method on mask and wafer

NASA Astrophysics Data System (ADS)

Matsuoka, Ryoichi; Mito, Hiroaki; Toyoda, Yasutaka; Wang, Zhigang

2010-03-01

We have developed the effective method of mask and silicon 2-dimensional metrology. The aim of this method is evaluating the performance of the silicon corresponding to Hotspot on a mask. The method adopts a metrology management system based on DBM (Design Based Metrology). This is the high accurate contouring created by an edge detection algorithm used in mask CD-SEM and silicon CD-SEM. Currently, as semiconductor manufacture moves towards even smaller feature size, this necessitates more aggressive optical proximity correction (OPC) to drive the super-resolution technology (RET). In other words, there is a trade-off between highly precise RET and mask manufacture, and this has a big impact on the semiconductor market that centers on the mask business. 2-dimensional Shape quantification is important as optimal solution over these problems. Although 1-dimensional shape measurement has been performed by the conventional technique, 2-dimensional shape management is needed in the mass production line under the influence of RET. We developed the technique of analyzing distribution of shape edge performance as the shape management technique. On the other hand, there is roughness in the silicon shape made from a mass-production line. Moreover, there is variation in the silicon shape. For this reason, quantification of silicon shape is important, in order to estimate the performance of a pattern. In order to quantify, the same shape is equalized in two dimensions. And the method of evaluating based on the shape is popular. In this study, we conducted experiments for averaging method of the pattern (Measurement Based Contouring) as two-dimensional mask and silicon evaluation technique. That is, observation of the identical position of a mask and a silicon was considered. It is possible to analyze variability of the edge of the same position with high precision. The result proved its detection accuracy and reliability of variability on two-dimensional pattern (mask and silicon) and is adaptable to following fields of mask quality management. - Estimate of the correlativity of shape variability and a process margin. - Determination of two-dimensional variability of pattern. - Verification of the performance of the pattern of various kinds of Hotspots. In this report, we introduce the experimental results and the application. We expect that the mask measurement and the shape control on mask production will make a huge contribution to mask yield-enhancement and that the DFM solution for mask quality control process will become much more important technology than ever. It is very important to observe the shape of the same location of Design, Mask, and Silicon in such a viewpoint.

Can BI-RADS features on mammography be used as a surrogate for expensive genomic testing in breast cancer patients?

NASA Astrophysics Data System (ADS)

Harowicz, Michael R.; Marks, Jeffrey R.; Marcom, P. Kelly; Mazurowski, Maciej A.

2017-03-01

Medical oncologists increasingly rely on expensive genomic analysis to stratify patients for different treatment. The genomic markers are able to divide patients into groups that behave differently in terms of tumor presentation, likelihood of metastatic spread, and response to chemotherapy and radiation therapy. In recent years there has been a rapid increase in the number of genomic tests available, like the Oncotype DX test, which provides the risk of cancer recurrence for a subset of patients. Radiogenomics, a new field that investigates the relationship between imaging phenotypes and genomic characteristics, may offer a less expensive and less invasive imaging surrogate for molecular subtype and Oncotype DX recurrence score (ODRS). This retrospective study analyzes the relationship between Breast Imaging-Reporting and Data System (BI-RADS) features as assessed by radiologists on mammograms with molecular subtype and ODRS. We used data from patients with BI-RADS features (shape or margin) and a genomic feature (subtype or ODRS) for the following cohort: shape vs. subtype (n=69), margin vs. subtype (n=78), shape vs. ODRS (n=20), and margin vs. ODRS (n=18). The association between features was assessed using a Fisher's exact test. Our results show that shape assessed by radiologists according to the BI-RADS lexicon is associated with molecular subtype (p=0.0171), while BI-RADS features of shape and margin were not significantly associated with ODRS (p=0.7839, p=0.6047 respectively).

Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors.

PubMed

Hu, Ben; Kuang, Zheng-Kun; Feng, Shi-Yu; Wang, Dong; He, Song-Bing; Kong, De-Xin

2016-11-17

The crystallized ligands in the Protein Data Bank (PDB) can be treated as the inverse shapes of the active sites of corresponding proteins. Therefore, the shape similarity between a molecule and PDB ligands indicated the possibility of the molecule to bind with the targets. In this paper, we proposed a shape similarity profile that can be used as a molecular descriptor for ligand-based virtual screening. First, through three-dimensional (3D) structural clustering, 300 diverse ligands were extracted from the druggable protein-ligand database, sc-PDB. Then, each of the molecules under scrutiny was flexibly superimposed onto the 300 ligands. Superimpositions were scored by shape overlap and property similarity, producing a 300 dimensional similarity array termed the "Three-Dimensional Biologically Relevant Spectrum (BRS-3D)". Finally, quantitative or discriminant models were developed with the 300 dimensional descriptor using machine learning methods (support vector machine). The effectiveness of this approach was evaluated using 42 benchmark data sets from the G protein-coupled receptor (GPCR) ligand library and the GPCR decoy database (GLL/GDD). We compared the performance of BRS-3D with other 2D and 3D state-of-the-art molecular descriptors. The results showed that models built with BRS-3D performed best for most GLL/GDD data sets. We also applied BRS-3D in histone deacetylase 1 inhibitors screening and GPCR subtype selectivity prediction. The advantages and disadvantages of this approach are discussed.

Shape of the orbital opening: individual characterization and analysis of variability in modern humans, Gorilla gorilla, and Pan troglodytes.

PubMed

Schmittbuhl, M; Le Minor, J M; Allenbach, B; Schaaf, A

1999-05-01

The description of the human orbital shape is principally qualitative in the classical literature, and characterised by adjectives such as circular, rectangular or quadrangular. In order to provide a precise quantification and interpretation of this shape, a study based on automatic image analysis and Fourier analysis was carried out on 45 human skulls (30 males, 15 females), and for comparison on 61 skulls of Gorilla gorilla (40 males, 21 females), and 34 skulls of Pan troglodytes (20 males, 14 females). Sexual dimorphism in the shape of the orbital opening was not demonstrated. Its dominant morphological features could be characterized by Fourier analysis; elliptical elongation and quadrangularity were dominant morphological features of the shape of the orbital opening in the three species. Elliptical elongation was more marked in humans and Pan, whereas quadrangularity was particularly emphasized in Gorilla. An intraspecific variability of the shape of the orbital opening existed in humans, Gorilla and Pan, and seemed close in the three species. Interspecific partition between humans, Gorilla and Pan was demonstrated despite the variability observed in the three species studied. Interspecific differences between Gorilla and the Pan-humans group were principally explained by the differences in quadrangularity, and by differences in orientation of triangularity and pentagonality. Differences in the shape of the orbital opening between humans and Pan were principally explained by differences in hexagonality, and by differences in orientation of quadrangularity. A closeness of shape between some humans and some individuals in Pan and, to a lesser degree, with some individuals in Gorilla was observed, demonstrating the existence of a morphological continuum of the shape of the orbital opening in hominoids.

The inter-rater reliability of estimating the size of burns from various burn area chart drawings.

PubMed

Wachtel, T L; Berry, C C; Wachtel, E E; Frank, H A

2000-03-01

The accuracy and variability of burn size calculations using four Lund and Browder charts currently in clinical use and two Rule of Nine's diagrams were evaluated. The study showed that variability in estimation increased with burn size initially, plateaued in large burns and then decreased slightly in extensive burns. The Rule of Nine's technique often overestimates the burn size and is more variable, but can be performed somewhat faster than the Lund and Browder method. More burn experience leads to less variability in burn area chart drawing estimates. Irregularly shaped burns and burns on the trunk and thighs had greater variability than less irregularly shaped burns or burns on more defined anatomical parts of the body.

Shape memory polymer network with thermally distinct elasticity and plasticity

PubMed Central

Zhao, Qian; Zou, Weike; Luo, Yingwu; Xie, Tao

2016-01-01

Stimuli-responsive materials with sophisticated yet controllable shape-changing behaviors are highly desirable for real-world device applications. Among various shape-changing materials, the elastic nature of shape memory polymers allows fixation of temporary shapes that can recover on demand, whereas polymers with exchangeable bonds can undergo permanent shape change via plasticity. We integrate the elasticity and plasticity into a single polymer network. Rational molecular design allows these two opposite behaviors to be realized at different temperature ranges without any overlap. By exploring the cumulative nature of the plasticity, we demonstrate easy manipulation of highly complex shapes that is otherwise extremely challenging. The dynamic shape-changing behavior paves a new way for fabricating geometrically complex multifunctional devices. PMID:26824077

Demonstration of the Principles of Restriction Endonuclease Cleavage Reactions Using Thermostable Bfl I from "Anoxybacillus Flavithermus"

ERIC Educational Resources Information Center

Sharma, Prince; D'Souza, David R.; Bhandari, Deepali; Parashar, Vijay; Capalash, Neena

2003-01-01

Restriction enzymes are basic tools in recombinant DNA technology. To shape the molecular biology experiments, the students must know how to work with these molecular scissors. Here, we describe an integrated set of experiments, introduced in the "Advances in Molecular Biology and Biotechnology" postgraduate course, which covers the important…

Synchrotron X-ray scattering characterization of the molecular structures of star polystyrenes with varying numbers of arms.

PubMed

Jin, Sangwoo; Higashihara, Tomoya; Jin, Kyeong Sik; Yoon, Jinhwan; Rho, Yecheol; Ahn, Byungcheol; Kim, Jehan; Hirao, Akira; Ree, Moonhor

2010-05-20

We have synthesized well-defined multiarmed star polystyrenes, with 6, 9, 17, 33, and 57 arms, and studied their molecular shapes and structural characteristics in a good solvent (tetrahydrofuran at 25 degrees C) and in a theta (Theta) solvent (cyclohexane at 35 degrees C) by small-angle X-ray scattering (SAXS) using a synchrotron radiation source. Analysis of the SAXS data provided a detailed characterization of the molecular shapes, including the contributions of the blob morphology of the arms, the radius of gyration, the paired distance distribution, the radial electron density distribution, and the Zimm-Stockmayer and Roovers g-factor, for the multiarmed star polystyrenes. In particular, the molecular shapes of the star polystyrenes were found to change from a fuzzy ellipsoid, for the 6-armed polystyrene, to a fuzzy sphere, for the 57-armed polystyrene, with an increasing number of arms. The ellipsoidal character of the star polystyrenes with fewer arms may originate from the extended anisotropically branched architecture at the center of the molecule. The arms of the star polystyrenes were found to be more extended than those of the linear polystyrenes. Furthermore, the degree of chain extension in the arms increased with the number of arms.

Optical frequency comb Fourier transform spectroscopy with sub-nominal resolution and precision beyond the Voigt profile

NASA Astrophysics Data System (ADS)

Rutkowski, Lucile; Masłowski, Piotr; Johansson, Alexandra C.; Khodabakhsh, Amir; Foltynowicz, Aleksandra

2018-01-01

Broadband precision spectroscopy is indispensable for providing high fidelity molecular parameters for spectroscopic databases. We have recently shown that mechanical Fourier transform spectrometers based on optical frequency combs can measure broadband high-resolution molecular spectra undistorted by the instrumental line shape (ILS) and with a highly precise frequency scale provided by the comb. The accurate measurement of the power of the comb modes interacting with the molecular sample was achieved by acquiring single-burst interferograms with nominal resolution matched to the comb mode spacing. Here we describe in detail the experimental and numerical steps needed to achieve sub-nominal resolution and retrieve ILS-free molecular spectra, i.e. with ILS-induced distortion below the noise level. We investigate the accuracy of the transition line centers retrieved by fitting to the absorption lines measured using this method. We verify the performance by measuring an ILS-free cavity-enhanced low-pressure spectrum of the 3ν1 + ν3 band of CO2 around 1575 nm with line widths narrower than the nominal resolution. We observe and quantify collisional narrowing of absorption line shape, for the first time with a comb-based spectroscopic technique. Thus retrieval of line shape parameters with accuracy not limited by the Voigt profile is now possible for entire absorption bands acquired simultaneously.

PubChem3D: Shape compatibility filtering using molecular shape quadrupoles

PubMed Central

2011-01-01

Background PubChem provides a 3-D neighboring relationship, which involves finding the maximal shape overlap between two static compound 3-D conformations, a computationally intensive step. It is highly desirable to avoid this overlap computation, especially if it can be determined with certainty that a conformer pair cannot meet the criteria to be a 3-D neighbor. As such, PubChem employs a series of pre-filters, based on the concept of volume, to remove approximately 65% of all conformer neighbor pairs prior to shape overlap optimization. Given that molecular volume, a somewhat vague concept, is rather effective, it leads one to wonder: can the existing PubChem 3-D neighboring relationship, which consists of billions of shape similar conformer pairs from tens of millions of unique small molecules, be used to identify additional shape descriptor relationships? Or, put more specifically, can one place an upper bound on shape similarity using other "fuzzy" shape-like concepts like length, width, and height? Results Using a basis set of 4.18 billion 3-D neighbor pairs identified from single conformer per compound neighboring of 17.1 million molecules, shape descriptors were computed for all conformers. These steric shape descriptors included several forms of molecular volume and shape quadrupoles, which essentially embody the length, width, and height of a conformer. For a given 3-D neighbor conformer pair, the volume and each quadrupole component (Qx, Qy, and Qz) were binned and their frequency of occurrence was examined. Per molecular volume type, this effectively produced three different maps, one per quadrupole component (Qx, Qy, and Qz), of allowed values for the similarity metric, shape Tanimoto (ST) ≥ 0.8. The efficiency of these relationships (in terms of true positive, true negative, false positive and false negative) as a function of ST threshold was determined in a test run of 13.2 billion conformer pairs not previously considered by the 3-D neighbor set. At an ST ≥ 0.8, a filtering efficiency of 40.4% of true negatives was achieved with only 32 false negatives out of 24 million true positives, when applying the separate Qx, Qy, and Qz maps in a series (Qxyz). This efficiency increased linearly as a function of ST threshold in the range 0.8-0.99. The Qx filter was consistently the most efficient followed by Qy and then by Qz. Use of a monopole volume showed the best overall performance, followed by the self-overlap volume and then by the analytic volume. Application of the monopole-based Qxyz filter in a "real world" test of 3-D neighboring of 4,218 chemicals of biomedical interest against 26.1 million molecules in PubChem reduced the total CPU cost of neighboring by between 24-38% and, if used as the initial filter, removed from consideration 48.3% of all conformer pairs at almost negligible computational overhead. Conclusion Basic shape descriptors, such as those embodied by size, length, width, and height, can be highly effective in identifying shape incompatible compound conformer pairs. When performing a 3-D search using a shape similarity cut-off, computation can be avoided by identifying conformer pairs that cannot meet the result criteria. Applying this methodology as a filter for PubChem 3-D neighboring computation, an improvement of 31% was realized, increasing the average conformer pair throughput from 154,000 to 202,000 per second per CPU core. PMID:21774809

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

Glynos, Emmanouil; Johnson, Kyle J.; Frieberg, Bradley

The surface relaxation dynamics of supported star-shaped polymer thin films are shown to be slower than the bulk, persisting up to temperatures at least 50 K above the bulk glass transition temperature Tgbulk. This behavior, exhibited by star-shaped polystyrenes with functionality f=8 arms and molecular weights per arm Marm

Basic mechanisms of MCD in animal models.

PubMed

Battaglia, Giorgio; Becker, Albert J; LoTurco, Joseph; Represa, Alfonso; Baraban, Scott C; Roper, Steven N; Vezzani, Annamaria

2009-09-01

Epilepsy-associated glioneuronal malformations (malformations of cortical development [MCD]) include focal cortical dysplasias (FCD) and highly differentiated glioneuronal tumors, most frequently gangliogliomas. The neuropathological findings are variable but suggest aberrant proliferation, migration, and differentiation of neural precursor cells as essential pathogenetic elements. Recent advances in animal models for MCDs allow new insights in the molecular pathogenesis of these epilepsy-associated lesions. Novel approaches, presented here, comprise RNA interference strategies to generate and study experimental models of subcortical band heterotopia and study functional aspects of aberrantly shaped and positioned neurons. Exciting analyses address impaired NMDA receptor expression in FCD animal models compared to human FCDs and excitatory imbalances in MCD animal models such as lissencephaly gene ablated mice as well as in utero irradiated rats. An improved understanding of relevant pathomechanisms will advance the development of targeted treatment strategies for epilepsy-associated malformations.

Profiling charge complementarity and selectivity for binding at the protein surface.

PubMed

Sulea, Traian; Purisima, Enrico O

2003-05-01

A novel analysis and representation of the protein surface in terms of electrostatic binding complementarity and selectivity is presented. The charge optimization methodology is applied in a probe-based approach that simulates the binding process to the target protein. The molecular surface is color coded according to calculated optimal charge or according to charge selectivity, i.e., the binding cost of deviating from the optimal charge. The optimal charge profile depends on both the protein shape and charge distribution whereas the charge selectivity profile depends only on protein shape. High selectivity is concentrated in well-shaped concave pockets, whereas solvent-exposed convex regions are not charge selective. This suggests the synergy of charge and shape selectivity hot spots toward molecular selection and recognition, as well as the asymmetry of charge selectivity at the binding interface of biomolecular systems. The charge complementarity and selectivity profiles map relevant electrostatic properties in a readily interpretable way and encode information that is quite different from that visualized in the standard electrostatic potential map of unbound proteins.

Mechanism study of biopolymer hair as a coupled thermo-water responsive smart material

NASA Astrophysics Data System (ADS)

Xiao, Xueliang; Zhou, Hongtao; Qian, Kun

2017-03-01

Animal hairs existing broadly in nature are found to be effectively responsive to stimuli of heat and water in sequence for shape deformation and recovery, namely, coupled shape memory function (CSMF). In the paper, the ability of thermo-water sensitive CSMF was first time investigated for animal hairs, the structural and molecular networks for net-points and switches were therefrom identified. Experimentally, animal hair manifested a high ability of shape fixation in thermal processing and good shape recovery by water stimulus. Characterizations of two stimuli (heating and hydration) were performed systematically on hair’s deformation, recovery, viscoelasticity and chemical components (crystalline phase, key bonds inamorphous area). The variations of related chemical components in molecular networks were also explored. A hybrid structural network model was thereafter proposed to interpret the thermo-water sensitive CSMF of hair. This study of two-sequential-stimuli CSMF is original and inspired to explore more complex functions of other smart natural materials and expected to make much smarter synthetic polymers.

Variable stiffness corrugated composite structure with shape memory polymer for morphing skin applications

NASA Astrophysics Data System (ADS)

Gong, Xiaobo; Liu, Liwu; Scarpa, Fabrizio; Leng, Jinsong; Liu, Yanju

2017-03-01

This work presents a variable stiffness corrugated structure based on a shape memory polymer (SMP) composite with corrugated laminates as reinforcement that shows smooth aerodynamic surface, extreme mechanical anisotropy and variable stiffness for potential morphing skin applications. The smart composite corrugated structure shows a low in-plane stiffness to minimize the actuation energy, but also possess high out-of-plane stiffness to transfer the aerodynamic pressure load. The skin provides an external smooth aerodynamic surface because of the one-sided filling with the SMP. Due to variable stiffness of the shape memory polymer the morphing skin exhibits a variable stiffness with a change of temperature, which can help the skin adjust its stiffness according different service environments and also lock the temporary shape without external force. Analytical models related to the transverse and bending stiffness are derived and validated using finite element techniques. The stiffness of the morphing skin is further investigated by performing a parametric analysis against the geometry of the corrugation and various sets of SMP fillers. The theoretical and numerical models show a good agreement and demonstrate the potential of this morphing skin concept for morphing aircraft applications. We also perform a feasibility study of the use of this morphing skin in a variable camber morphing wing baseline. The results show that the morphing skin concept exhibits sufficient bending stiffness to withstand the aerodynamic load at low speed (less than 0.3 Ma), while demonstrating a large transverse stiffness variation (up to 191 times) that helps to create a maximum mechanical efficiency of the structure under varying external conditions.

Pupil shape in the animal kingdom: from the pseudopupil to the vertical pupil.

PubMed

González-Martín-Moro, J; Gómez-Sanz, F; Sales-Sanz, A; Huguet-Baudin, E; Murube-del-Castillo, J

2014-12-01

To study the different pupil shapes adopted by the different animal species. Review of the related literature, using PubMed database. The initial search strategy was pupil shape (limited to animals). The first volume of System of Ophthalmology (Duke-Elder) and Evolution's witness (I. Schwab) were also reviewed. An optic illusion called pseudopupil is usually observed in the compound eyes of insects. The pupil is circular in most vertebrates, however slit vertical pupils are present in cats and in some snake species. Vertical pupils could have a photoprotective function, as it makes a more complete closure possible in photopic conditions, and helps to camouflage the predator. It has also been hypothesized that it could help to correct chromatic aberration. Ruminants are usually endowed with horizontal pupils. This shape could improve the capacity of the eye to detect vertical silhouettes. Some marine animals have crescent-shaped pupils. In these animals, a superior operculum helps to protect the inferior retina from the great amount of light coming from above. There is a surprising variability in pupil shape. Through this variability, nature has fitted the eye to different circumstances. The theories proposed to explain this high variability are discussed in detail in the article. Copyright © 2012 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.

Aggregation work at polydisperse micellization: ideal solution and "dressed micelle" models comparing to molecular dynamics simulations.

PubMed

Burov, S V; Shchekin, A K

2010-12-28

General thermodynamic relations for the work of polydisperse micelle formation in the model of ideal solution of molecular aggregates in nonionic surfactant solution and the model of "dressed micelles" in ionic solution have been considered. In particular, the dependence of the aggregation work on the total concentration of nonionic surfactant has been analyzed. The analogous dependence for the work of formation of ionic aggregates has been examined with regard to existence of two variables of a state of an ionic aggregate, the aggregation numbers of surface active ions and counterions. To verify the thermodynamic models, the molecular dynamics simulations of micellization in nonionic and ionic surfactant solutions at two total surfactant concentrations have been performed. It was shown that for nonionic surfactants, even at relatively high total surfactant concentrations, the shape and behavior of the work of polydisperse micelle formation found within the model of the ideal solution at different total surfactant concentrations agrees fairly well with the numerical experiment. For ionic surfactant solutions, the numerical results indicate a strong screening of ionic aggregates by the bound counterions. This fact as well as independence of the coefficient in the law of mass action for ionic aggregates on total surfactant concentration and predictable behavior of the "waterfall" lines of surfaces of the aggregation work upholds the model of "dressed" ionic aggregates.

Quantifying Three-Dimensional Morphology and RNA from Individual Embryos

PubMed Central

Green, Rebecca M.; Leach, Courtney L.; Hoehn, Natasha; Marcucio, Ralph S.; Hallgrímsson, Benedikt

2017-01-01

Quantitative analysis of morphogenesis aids our understanding of developmental processes by providing a method to link changes in shape with cellular and molecular processes. Over the last decade many methods have been developed for 3D imaging of embryos using microCT scanning to quantify the shape of embryos during development. These methods generally involve a powerful, cross-linking fixative such as paraformaldehyde to limit shrinkage during the CT scan. However, the extended time frames that these embryos are incubated in such fixatives prevent use of the tissues for molecular analysis after microCT scanning. This is a significant problem because it limits the ability to correlate variation in molecular data with morphology at the level of individual embryos. Here, we outline a novel method that allows RNA, DNA or protein isolation following CT scan while also allowing imaging of different tissue layers within the developing embryo. We show shape differences early in craniofacial development (E11.5) between common mouse genetic backgrounds, and demonstrate that we are able to generate RNA from these embryos after CT scanning that is suitable for downstream RT-PCR and RNAseq analyses. PMID:28152580

High hydrostatic pressure specifically affects molecular dynamics and shape of low-density lipoprotein particles

PubMed Central

Golub, M.; Lehofer, B.; Martinez, N.; Ollivier, J.; Kohlbrecher, J.; Prassl, R.; Peters, J.

2017-01-01

Lipid composition of human low-density lipoprotein (LDL) and its physicochemical characteristics are relevant for proper functioning of lipid transport in the blood circulation. To explore dynamical and structural features of LDL particles with either a normal or a triglyceride-rich lipid composition we combined coherent and incoherent neutron scattering methods. The investigations were carried out under high hydrostatic pressure (HHP), which is a versatile tool to study the physicochemical behavior of biomolecules in solution at a molecular level. Within both neutron techniques we applied HHP to probe the shape and degree of freedom of the possible motions (within the time windows of 15 and 100 ps) and consequently the flexibility of LDL particles. We found that HHP does not change the types of motion in LDL, but influences the portion of motions participating. Contrary to our assumption that lipoprotein particles, like membranes, are highly sensitive to pressure we determined that LDL copes surprisingly well with high pressure conditions, although the lipid composition, particularly the triglyceride content of the particles, impacts the molecular dynamics and shape arrangement of LDL under pressure. PMID:28382948

High hydrostatic pressure specifically affects molecular dynamics and shape of low-density lipoprotein particles

NASA Astrophysics Data System (ADS)

Golub, M.; Lehofer, B.; Martinez, N.; Ollivier, J.; Kohlbrecher, J.; Prassl, R.; Peters, J.

2017-04-01

Lipid composition of human low-density lipoprotein (LDL) and its physicochemical characteristics are relevant for proper functioning of lipid transport in the blood circulation. To explore dynamical and structural features of LDL particles with either a normal or a triglyceride-rich lipid composition we combined coherent and incoherent neutron scattering methods. The investigations were carried out under high hydrostatic pressure (HHP), which is a versatile tool to study the physicochemical behavior of biomolecules in solution at a molecular level. Within both neutron techniques we applied HHP to probe the shape and degree of freedom of the possible motions (within the time windows of 15 and 100 ps) and consequently the flexibility of LDL particles. We found that HHP does not change the types of motion in LDL, but influences the portion of motions participating. Contrary to our assumption that lipoprotein particles, like membranes, are highly sensitive to pressure we determined that LDL copes surprisingly well with high pressure conditions, although the lipid composition, particularly the triglyceride content of the particles, impacts the molecular dynamics and shape arrangement of LDL under pressure.

Yield impact for wafer shape misregistration-based binning for overlay APC diagnostic enhancement

NASA Astrophysics Data System (ADS)

Jayez, David; Jock, Kevin; Zhou, Yue; Govindarajulu, Venugopal; Zhang, Zhen; Anis, Fatima; Tijiwa-Birk, Felipe; Agarwal, Shivam

2018-03-01

The importance of traditionally acceptable sources of variation has started to become more critical as semiconductor technologies continue to push into smaller technology nodes. New metrology techniques are needed to pursue the process uniformity requirements needed for controllable lithography. Process control for lithography has the advantage of being able to adjust for cross-wafer variability, but this requires that all processes are close in matching between process tools/chambers for each process. When this is not the case, the cumulative line variability creates identifiable groups of wafers1 . This cumulative shape based effect is described as impacting overlay measurements and alignment by creating misregistration of the overlay marks. It is necessary to understand what requirements might go into developing a high volume manufacturing approach which leverages this grouping methodology, the key inputs and outputs, and what can be extracted from such an approach. It will be shown that this line variability can be quantified into a loss of electrical yield primarily at the edge of the wafer and proposes a methodology for root cause identification and improvement. This paper will cover the concept of wafer shape based grouping as a diagnostic tool for overlay control and containment, the challenges in implementing this in a manufacturing setting, and the limitations of this approach. This will be accomplished by showing that there are identifiable wafer shape based signatures. These shape based wafer signatures will be shown to be correlated to overlay misregistration, primarily at the edge. It will also be shown that by adjusting for this wafer shape signal, improvements can be made to both overlay as well as electrical yield. These improvements show an increase in edge yield, and a reduction in yield variability.

Grid sensitivity capability for large scale structures

NASA Technical Reports Server (NTRS)

Nagendra, Gopal K.; Wallerstein, David V.

1989-01-01

The considerations and the resultant approach used to implement design sensitivity capability for grids into a large scale, general purpose finite element system (MSC/NASTRAN) are presented. The design variables are grid perturbations with a rather general linking capability. Moreover, shape and sizing variables may be linked together. The design is general enough to facilitate geometric modeling techniques for generating design variable linking schemes in an easy and straightforward manner. Test cases have been run and validated by comparison with the overall finite difference method. The linking of a design sensitivity capability for shape variables in MSC/NASTRAN with an optimizer would give designers a powerful, automated tool to carry out practical optimization design of real life, complicated structures.

TRIANGLE-SHAPED DC CORONA DISCHARGE DEVICE FOR MOLECULAR DECOMPOSITION

EPA Science Inventory

The paper discusses the evaluation of electrostatic DC corona discharge devices for the application of molecular decomposition. A point-to-plane geometry corona device with a rectangular cross section demonstrated low decomposition efficiencies in earlier experimental work. The n...

Molecular Phylogenies Support Homoplasy of Multiple Morphological Characters Used in the Taxonomy of Heteroscleromorpha (Porifera: Demospongiae)

PubMed Central

Morrow, Christine C.; Redmond, Niamh E.; Picton, Bernard E.; Thacker, Robert W.; Collins, Allen G.; Maggs, Christine A.; Sigwart, Julia D.; Allcock, A. Louise

2013-01-01

Sponge classification has long been based mainly on morphocladistic analyses but is now being greatly challenged by more than 12 years of accumulated analyses of molecular data analyses. The current study used phylogenetic hypotheses based on sequence data from 18S rRNA, 28S rRNA, and the CO1 barcoding fragment, combined with morphology to justify the resurrection of the order Axinellida Lévi, 1953. Axinellida occupies a key position in different morphologically derived topologies. The abandonment of Axinellida and the establishment of Halichondrida Vosmaer, 1887 sensu lato to contain Halichondriidae Gray, 1867, Axinellidae Carter, 1875, Bubaridae Topsent, 1894, Heteroxyidae Dendy, 1905, and a new family Dictyonellidae van Soest et al., 1990 was based on the conclusion that an axially condensed skeleton evolved independently in separate lineages in preference to the less parsimonious assumption that asters (star-shaped spicules), acanthostyles (club-shaped spicules with spines), and sigmata (C-shaped spicules) each evolved more than once. Our new molecular trees are congruent and contrast with the earlier, morphologically based, trees. The results show that axially condensed skeletons, asters, acanthostyles, and sigmata are all homoplasious characters. The unrecognized homoplasious nature of these characters explains much of the incongruence between molecular-based and morphology-based phylogenies. We use the molecular trees presented here as a basis for re-interpreting the morphological characters within Heteroscleromorpha. The implications for the classification of Heteroscleromorpha are discussed and a new order Biemnida ord. nov. is erected. PMID:23753661

The influence of polymer architecture on the assembly of poly(ethylene oxide) grafted C60 fullerene clusters in aqueous solution: a molecular dynamics simulation study.

PubMed

Hooper, Justin B; Bedrov, Dmitry; Smith, Grant D

2009-03-28

The effect of polymer architecture on the aggregation behavior of C60 fullerenes tethered with a single chain of poly(ethylene oxide) (PEO) in aqueous solution has been investigated using coarse-grained, implicit solvent molecular dynamics simulations. The PEO-grafted fullerenes were comprised of a single tether of 60 repeat units represented as a linear polymer, a three-arm star (20 repeat units/arm) or a six-arm star (10 repeat units/arm). Additionally, the influence of arm length on self-assembly of the PEO-fullerene conjugates was investigated for the three-arm stars. Self-assembly is driven by favorable fullerene-fullerene and fullerene-PEO interactions. Our simulations reveal that it should be possible to control the size and geometry of the self-assembled fullerene aggregates in water through variation of PEO architecture and PEO molecular weight. We found that aggregate size and shape could be understood qualitatively in terms of the packing parameter concept that has been employed for diblock polymer and surfactant self-assembly. Higher molecular weight PEO (longer arms) and more compact PEO (more arms for the same molecular weight) resulted in greater steric repulsion between fullerenes, engendering greater aggregate surface curvature and hence the formation of smaller, more spherically shaped aggregates. Finally, weak attractive interactions between PEO and the fullerenes were found to play an important role in determining aggregate shape, size and the dynamics of self-assembly.

Variability of O3 and NO2 profile shapes during DISCOVER-AQ: Implications for satellite observations and comparisons to model-simulated profiles

NASA Astrophysics Data System (ADS)

Flynn, Clare Marie; Pickering, Kenneth E.; Crawford, James H.; Weinheimer, Andrew J.; Diskin, Glenn; Thornhill, K. Lee; Loughner, Christopher; Lee, Pius; Strode, Sarah A.

2016-12-01

To investigate the variability of in situ profile shapes under a variety of meteorological and pollution conditions, results are presented of an agglomerative hierarchical cluster analysis of the in situ O3 and NO2 profiles for each of the four campaigns of the NASA DISCOVER-AQ mission. Understanding the observed profile variability for these trace gases is useful for understanding the accuracy of the assumed profile shapes used in satellite retrieval algorithms as well as for understanding the correlation between satellite column observations and surface concentrations. The four campaigns of the DISCOVER-AQ mission took place in Maryland during July 2011, the San Joaquin Valley of California during January-February 2013, the Houston, Texas, metropolitan region during September 2013, and the Denver-Front Range region of Colorado during July-August 2014. Several distinct profile clusters emerged for the California, Texas, and Colorado campaigns for O3, indicating significant variability of O3 profile shapes, while the Maryland campaign presented only one distinct O3 cluster. In contrast, very few distinct profile clusters emerged for NO2 during any campaign for this particular clustering technique, indicating the NO2 profile behavior was relatively uniform throughout each campaign. However, changes in NO2 profile shape were evident as the boundary layer evolved through the day, but they were apparently not significant enough to yield more clusters. The degree of vertical mixing (as indicated by temperature lapse rate) associated with each cluster exerted an important influence on the shapes of the median cluster profiles for O3, as well as impacted the correlations between the associated column and surface data for each cluster for O3. The correlation analyses suggest satellites may have the best chance to relate to surface O3 under the conditions encountered during the Maryland campaign Clusters 1 and 2, which include deep, convective boundary layers and few interruptions to this connection from complex meteorology, chemical environments, or orography. The regional CMAQ model captured the shape factors for O3, and moderately well captured the NO2 shape factors, for the conditions associated with the Maryland campaign, suggesting that a regional air quality model may adequately specify a priori profile shapes for remote sensing retrievals. CMAQ shape factor profiles were not as well represented for the other regions.

Accurate deuterium spectroscopy for fundamental studies

NASA Astrophysics Data System (ADS)

Wcisło, P.; Thibault, F.; Zaborowski, M.; Wójtewicz, S.; Cygan, A.; Kowzan, G.; Masłowski, P.; Komasa, J.; Puchalski, M.; Pachucki, K.; Ciuryło, R.; Lisak, D.

2018-07-01

We present an accurate measurement of the weak quadrupole S(2) 2-0 line in self-perturbed D2 and theoretical ab initio calculations of both collisional line-shape effects and energy of this rovibrational transition. The spectra were collected at the 247-984 Torr pressure range with a frequency-stabilized cavity ring-down spectrometer linked to an optical frequency comb (OFC) referenced to a primary time standard. Our line-shape modeling employed quantum calculations of molecular scattering (the pressure broadening and shift and their speed dependencies were calculated, while the complex frequency of optical velocity-changing collisions was fitted to experimental spectra). The velocity-changing collisions are handled with the hard-sphere collisional kernel. The experimental and theoretical pressure broadening and shift are consistent within 5% and 27%, respectively (the discrepancy for shift is 8% when referred not to the speed averaged value, which is close to zero, but to the range of variability of the speed-dependent shift). We use our high pressure measurement to determine the energy, ν0, of the S(2) 2-0 transition. The ab initio line-shape calculations allowed us to mitigate the expected collisional systematics reaching the 410 kHz accuracy of ν0. We report theoretical determination of ν0 taking into account relativistic and QED corrections up to α5. Our estimation of the accuracy of the theoretical ν0 is 1.3 MHz. We observe 3.4σ discrepancy between experimental and theoretical ν0.

Rotator side chains trigger cooperative transition for shape and function memory effect in organic semiconductors.

PubMed

Chung, Hyunjoong; Dudenko, Dmytro; Zhang, Fengjiao; D'Avino, Gabriele; Ruzié, Christian; Richard, Audrey; Schweicher, Guillaume; Cornil, Jérôme; Beljonne, David; Geerts, Yves; Diao, Ying

2018-01-18

Martensitic transition is a solid-state phase transition involving cooperative movement of atoms, mostly studied in metallurgy. The main characteristics are low transition barrier, ultrafast kinetics, and structural reversibility. They are rarely observed in molecular crystals, and hence the origin and mechanism are largely unexplored. Here we report the discovery of martensitic transition in single crystals of two different organic semiconductors. In situ microscopy, single-crystal X-ray diffraction, Raman and nuclear magnetic resonance spectroscopy, and molecular simulations combined indicate that the rotating bulky side chains trigger cooperative transition. Cooperativity enables shape memory effect in single crystals and function memory effect in thin film transistors. We establish a molecular design rule to trigger martensitic transition in organic semiconductors, showing promise for designing next-generation smart multifunctional materials.

Variable expression of molecular markers in juvenile nasopharyngeal angiofibroma.

PubMed

Mishra, A; Pandey, A; Mishra, S C

2017-09-01

Molecular categorisation may explain the wide variation in the clinical characteristics of juvenile nasopharyngeal angiofibroma. Variations in molecular markers in juvenile nasopharyngeal angiofibroma in an Indian population were investigated and compared with global reports. Variable molecular marker expression was demonstrated at the regional and global levels. A wide variation in molecular characteristics is evident. Molecular data have been reported for only 11 countries, indicating a clear geographical bias. Only 58 markers have been studied, and most are yet to be validated. Research into the molecular epidemiology of juvenile nasopharyngeal angiofibroma is still in its infancy. Although the molecular variation is not well understood, data obtained so far have prompted important research questions. Hence, multicentre collaborative molecular studies are needed to establish the aetiopathogenesis and establish molecular surrogates for clinical characteristics.

Determination of the topological shape of integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria in the detergent solution by small-angle X-ray scattering.

PubMed

Hong, Xinguo; Weng, Yu-Xiang; Li, Ming

2004-02-01

The topological shape of the integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria Rhodobacter spheroides 2.4.1 in detergent solution has been determined from synchrotron small-angle X-ray scattering data using direct curve-fitting by the ellipsoid, ab initio shape determination methods of simulated annealing algorithm and multipole expansion, respectively. The results indicate that the LH2 protein in aqueous solution is encapsulated by a monolayered detergent shell. The detergent-stabilized structure has the shape of an oblate plate, with a thickness of 40 A, a long axis of 110 A, and a short axis of 85 A. After correction for the detergent shell, the shape of the LH2 core is also an oblate plate with a height of 40 A, a long axis of 80 A, and a short axis of 55 A. In contrast to the cylindrical crystal structure with a height of 40 A and a diameter of 68 A, the molecular shape of the LH2 complex in detergent solution clearly deviates from the ringlike crystal structure, with an eccentricity found to be 0.59-consistent with the result of single molecular spectroscopy study of the isolated single LH2 molecules.

Determination of the Topological Shape of Integral Membrane Protein Light-Harvesting Complex LH2 from Photosynthetic Bacteria in the Detergent Solution by Small-Angle X-Ray Scattering

PubMed Central

Hong, Xinguo; Weng, Yu-Xiang; Li, Ming

2004-01-01

The topological shape of the integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria Rhodobacter spheroides 2.4.1 in detergent solution has been determined from synchrotron small-angle X-ray scattering data using direct curve-fitting by the ellipsoid, ab initio shape determination methods of simulated annealing algorithm and multipole expansion, respectively. The results indicate that the LH2 protein in aqueous solution is encapsulated by a monolayered detergent shell. The detergent-stabilized structure has the shape of an oblate plate, with a thickness of 40 Å, a long axis of 110 Å, and a short axis of 85 Å . After correction for the detergent shell, the shape of the LH2 core is also an oblate plate with a height of 40 Å, a long axis of 80 Å, and a short axis of 55 Å. In contrast to the cylindrical crystal structure with a height of 40 Å and a diameter of 68 Å, the molecular shape of the LH2 complex in detergent solution clearly deviates from the ringlike crystal structure, with an eccentricity found to be 0.59—consistent with the result of single molecular spectroscopy study of the isolated single LH2 molecules. PMID:14747343

Rational Design and Synthesis of Carboxylate Gemini Surfactants with an Excellent Aggregate Behavior for Nano-La2O3 Morphology-Controllable Preparation.

PubMed

Liao, Xueming; Gao, Zhinong; Xia, Yan; Niu, Fei; Zhai, Wenzhong

2017-04-04

A series of carboxylate gemini surfactants (CGS, C n -Φ-C n , n = 12, 14, 16, 18) with diphenyl ketone as a spacer group were prepared using a simple and feasible synthetic method. These CGS exhibited an excellent surface activity with extremely low critical micelle concentration (CMC) value (approximately 10 -5 mol/L), good performance in reducing surface tension (nearly 30 mN/m), and the ability of molecular self-assembly into different aggregate morphologies via adjusting the concentrations, which is attributed to the introduction of diphenyl ketone and carboxylic acid ammonium salt in the molecular structure. Moreover, the surface activity and self-assembly ability of CGS were further optimized by tuning the length of the tail chain. These excellent properties imply that CGS can be a soft template to prepare nanomaterials, especially in morphology-controllable synthesis. By adjusting the concentration of one of CGS (C 12 -Φ-C 12 ), nano-La 2 O 3 particles with diverse morphologies were obtained, including spherical shape, bead-chain shape, rod shape, velvet-antler shape, cedar shape, and bowknot shape. This work offers a vital insight into the rational design of template agents for the development of morphology-controllable nanomaterials.

Shape Morphing Adaptive Radiator Technology (SMART) for Variable Heat Rejection

NASA Technical Reports Server (NTRS)

Erickson, Lisa

2016-01-01

The proposed technology leverages the temperature dependent phase change of shape memory alloys (SMAs) to drive the shape of a flexible radiator panel. The opening/closing of the radiator panel, as a function of temperature, passively adapts the radiator's rate of heat rejection in response to a vehicle's needs.

Intra-individual metameric variation expressed at the enamel-dentine junction of lower post-canine dentition of South African fossil hominins and modern humans.

PubMed

Pan, Lei; Thackeray, John Francis; Dumoncel, Jean; Zanolli, Clément; Oettlé, Anna; de Beer, Frikkie; Hoffman, Jakobus; Duployer, Benjamin; Tenailleau, Christophe; Braga, José

2017-08-01

The aim of this study is to compare the degree and patterning of inter- and intra-individual metameric variation in South African australopiths, early Homo and modern humans. Metameric variation likely reflects developmental and taxonomical issues, and could also be used to infer ecological and functional adaptations. However, its patterning along the early hominin postcanine dentition, particularly among South African fossil hominins, remains unexplored. Using microfocus X-ray computed tomography (µXCT) and geometric morphometric tools, we studied the enamel-dentine junction (EDJ) morphology and we investigated the intra- and inter-individual EDJ metameric variation among eight australopiths and two early Homo specimens from South Africa, as well as 32 modern humans. Along post-canine dentition, shape changes between metameres represented by relative positions and height of dentine horns, outlines of the EDJ occlusal table are reported in modern and fossil taxa. Comparisons of EDJ mean shapes and multivariate analyses reveal substantial variation in the direction and magnitude of metameric shape changes among taxa, but some common trends can be found. In modern humans, both the direction and magnitude of metameric shape change show increased variability in M 2 -M 3 compared to M 1 -M 2 . Fossil specimens are clustered together showing similar magnitudes of shape change. Along M 2 -M 3 , the lengths of their metameric vectors are not as variable as those of modern humans, but they display considerable variability in the direction of shape change. The distalward increase of metameric variation along the modern human molar row is consistent with the odontogenetic models of molar row structure (inhibitory cascade model). Though much remains to be tested, the variable trends and magnitudes in metamerism in fossil hominins reported here, together with differences in the scale of shape change between modern humans and fossil hominins may provide valuable information regarding functional morphology and developmental processes in fossil species. © 2017 Wiley Periodicals, Inc.

Framework for shape analysis of white matter fiber bundles.

PubMed

Glozman, Tanya; Bruckert, Lisa; Pestilli, Franco; Yecies, Derek W; Guibas, Leonidas J; Yeom, Kristen W

2018-02-15

Diffusion imaging coupled with tractography algorithms allows researchers to image human white matter fiber bundles in-vivo. These bundles are three-dimensional structures with shapes that change over time during the course of development as well as in pathologic states. While most studies on white matter variability focus on analysis of tissue properties estimated from the diffusion data, e.g. fractional anisotropy, the shape variability of white matter fiber bundle is much less explored. In this paper, we present a set of tools for shape analysis of white matter fiber bundles, namely: (1) a concise geometric model of bundle shapes; (2) a method for bundle registration between subjects; (3) a method for deformation estimation. Our framework is useful for analysis of shape variability in white matter fiber bundles. We demonstrate our framework by applying our methods on two datasets: one consisting of data for 6 normal adults and another consisting of data for 38 normal children of age 11 days to 8.5 years. We suggest a robust and reproducible method to measure changes in the shape of white matter fiber bundles. We demonstrate how this method can be used to create a model to assess age-dependent changes in the shape of specific fiber bundles. We derive such models for an ensemble of white matter fiber bundles on our pediatric dataset and show that our results agree with normative human head and brain growth data. Creating these models for a large pediatric longitudinal dataset may improve understanding of both normal development and pathologic states and propose novel parameters for the examination of the pediatric brain. Copyright © 2017 Elsevier Inc. All rights reserved.

An improved quasistatic line-shape theory: The effects of molecular motion on the line wings

NASA Technical Reports Server (NTRS)

Ma, Q.; Tipping, Richard H.

1994-01-01

A theory is presented for the modification of the line-shape functions and absorption coefficient due to the breakdown of the quasistatic approximation. This breakdown arises from the effects of molecular motion and increases the absorption in the near wings. Numerical calculations for the high-frequency wing of the nu(sub 3) band of CO2 broadened by Ar are reported and it is shown that these effects are significant near the bandhead. The importance of such corrections in other spectral regions and for other systems is discussed briefly.

Constructing Molecular Models with Low-Cost Toy Beads

ERIC Educational Resources Information Center

Ng, Pun-hon; Wong, Siu-ling; Mak, Se-yuen

2012-01-01

In teaching the science of the nano world, ball-and-stick molecular models are frequently used as 3D representations of molecules. Unlike a chemical formula, a molecular model allows us to visualise the 3D shape of the molecule and the relative positions of its atoms, the bonds between atoms and why a pair of mirror isomers with the same atoms,…

Phylogenetic, ecological, and allometric correlates of cranial shape in Malagasy lemuriforms.

PubMed

Baab, Karen L; Perry, Jonathan M G; Rohlf, F James; Jungers, William L

2014-05-01

Adaptive radiations provide important insights into many aspects of evolution, including the relationship between ecology and morphological diversification as well as between ecology and speciation. Many such radiations include divergence along a dietary axis, although other ecological variables may also drive diversification, including differences in diel activity patterns. This study examines the role of two key ecological variables, diet and activity patterns, in shaping the radiation of a diverse clade of primates, the Malagasy lemurs. When phylogeny was ignored, activity pattern and several dietary variables predicted a significant proportion of cranial shape variation. However, when phylogeny was taken into account, only typical diet accounted for a significant proportion of shape variation. One possible explanation for this discrepancy is that this radiation was characterized by a relatively small number of dietary shifts (and possibly changes in body size) that occurred in conjunction with the divergence of major clades. This pattern may be difficult to detect with the phylogenetic comparative methods used here, but may characterize not just lemurs but other mammals. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

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

Krasheninnikov, S. I.

The equations of motion of a dust grain with non-spherical shape in plasma are generalized by incorporating the effects associated with propeller-like features of the grain's shape. For the grain shape close to rotationally symmetric, the stability of “stationary” (in terms of variables used in the grain dynamic equations) solutions are considered. It is found that propeller-like features of the grain's shape can crucially alter stability of such “stationary” states.

A molecular dynamics study of ambient and high pressure phases of silica: structure and enthalpy variation with molar volume.

PubMed

Rajappa, Chitra; Sringeri, S Bhuvaneshwari; Subramanian, Yashonath; Gopalakrishnan, J

2014-06-28

Extensive molecular dynamics studies of 13 different silica polymorphs are reported in the isothermal-isobaric ensemble with the Parrinello-Rahman variable shape simulation cell. The van Beest-Kramer-van Santen (BKS) potential is shown to predict lattice parameters for most phases within 2%-3% accuracy, as well as the relative stabilities of different polymorphs in agreement with experiment. Enthalpies of high-density polymorphs - CaCl2-type, α-PbO2-type, and pyrite-type - for which no experimental data are available as yet, are predicted here. Further, the calculated enthalpies exhibit two distinct regimes as a function of molar volume-for low and medium-density polymorphs, it is almost independent of volume, while for high-pressure phases a steep dependence is seen. A detailed analysis indicates that the increased short-range contributions to enthalpy in the high-density phases arise not only from an increased coordination number of silicon but also shorter Si-O bond lengths. Our results indicate that amorphous phases of silica exhibit better optimization of short-range interactions than crystalline phases at the same density while the magnitude of Coulombic contributions is lower in the amorphous phase.

Oligometastatic prostate cancer: shaping the definition with molecular imaging and an improved understanding of tumor biology.

PubMed

Joice, Gregory A; Rowe, Steven P; Pienta, Kenneth J; Gorin, Michael A

2017-11-01

The aim of this review is to discuss how novel imaging modalities and molecular markers are shaping the definition of oligometastatic prostate cancer. To effectively classify a patient as having oligometastatic prostate cancer, diagnostic tests must be sensitive enough to detect subtle sites of metastatic disease. Conventional imaging modalities can readily detect widespread polymetastatic disease but do not have the sensitivity necessary to reliably classify patients as oligometastatic. Molecular imaging using both metabolic- and molecularly-targeted radiotracers has demonstrated great promise in aiding in our ability to define the oligometastatic state. Perhaps the most promising data to date have been generated with radiotracers targeting prostate-specific membrane antigen. In addition, early studies are beginning to define biologic markers in the oligometastatic state that may be indicative of disease with minimal metastatic potential. Recent developments in molecular imaging have allowed for improved detection of metastatic prostate cancer allowing for more accurate staging of patients with oligometastatic disease. Future development of biologic markers may assist in defining the oligometastatic state and determining prognosis.

Bond-valence methods for pKa prediction. II. Bond-valence, electrostatic, molecular geometry, and solvation effects

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

Bickmore, Barry R.; Rosso, Kevin M.; Tadanier, Christopher J.

2006-08-15

In a previous contribution, we outlined a method for predicting (hydr)oxy-acid and oxide surface acidity constants based on three main factors: bond valence, Me?O bond ionicity, and molecular shape. Here electrostatics calculations and ab initio molecular dynamics simulations are used to qualitatively show that Me?O bond ionicity controls the extent to which the electrostatic work of proton removal departs from ideality, bond valence controls the extent of solvation of individual functional groups, and bond valence and molecular shape controls local dielectric response. These results are consistent with our model of acidity, but completely at odds with other methods of predictingmore » acidity constants for use in multisite complexation models. In particular, our ab initio molecular dynamics simulations of solvated monomers clearly indicate that hydrogen bonding between (hydr)oxo-groups and water molecules adjusts to obey the valence sum rule, rather than maintaining a fixed valence based on the coordination of the oxygen atom as predicted by the standard MUSIC model.« less

Reviews: The Molecular Animator.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1987

1987-01-01

Provided is a review of a chemical software package. The package makes possible an instructional technique that is not effective by any other means, namely the ability to view molecular shapes in three dimensions. The program can be used with either IBM or Apple hardware. (RH)

DNA Shape Dominates Sequence Affinity in Nucleosome Formation

NASA Astrophysics Data System (ADS)

Freeman, Gordon S.; Lequieu, Joshua P.; Hinckley, Daniel M.; Whitmer, Jonathan K.; de Pablo, Juan J.

2014-10-01

Nucleosomes provide the basic unit of compaction in eukaryotic genomes, and the mechanisms that dictate their position at specific locations along a DNA sequence are of central importance to genetics. In this Letter, we employ molecular models of DNA and proteins to elucidate various aspects of nucleosome positioning. In particular, we show how DNA's histone affinity is encoded in its sequence-dependent shape, including subtle deviations from the ideal straight B-DNA form and local variations of minor groove width. By relying on high-precision simulations of the free energy of nucleosome complexes, we also demonstrate that, depending on DNA's intrinsic curvature, histone binding can be dominated by bending interactions or electrostatic interactions. More generally, the results presented here explain how sequence, manifested as the shape of the DNA molecule, dominates molecular recognition in the problem of nucleosome positioning.

Isosteric And Non-Isosteric Base Pairs In RNA Motifs: Molecular Dynamics And Bioinformatics Study Of The Sarcin-Ricin Internal Loop

PubMed Central

Havrila, Marek; Réblová, Kamila; Zirbel, Craig L.; Leontis, Neocles B.; Šponer, Jiří

2013-01-01

The Sarcin-Ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, i.e., in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of SR motif. SHAPE probing experiment was also performed to confirm fidelity of MD simulations. We identified 57 instances of the SR motif in a non-redundant subset of the RNA X-ray structure database and analyzed their basepairing, base-phosphate, and backbone-backbone interactions. We extracted sequences aligned to these instances from large ribosomal RNA alignments to determine frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. Non isosteric base substitutions led to unstable structures, but so did isosteric substitutions which were unable to make key base-phosphate interactions. MD technique explains why some potentially isosteric SR motifs are not realized during evolution. We also found that inability to form stable cWW geometry is an important factor in case of the first base pair of the flexible region of the SR motif. Comparison of structural, bioinformatics, SHAPE probing and MD simulation data reveals that explicit solvent MD simulations neatly reflect viability of different sequence variants of the SR motif. Thus, MD simulations can efficiently complement bioinformatics tools in studies of conservation patterns of RNA motifs and provide atomistic insight into the role of their different signature interactions. PMID:24144333

Multi-region statistical shape model for cochlear implantation

NASA Astrophysics Data System (ADS)

Romera, Jordi; Kjer, H. Martin; Piella, Gemma; Ceresa, Mario; González Ballester, Miguel A.

2016-03-01

Statistical shape models are commonly used to analyze the variability between similar anatomical structures and their use is established as a tool for analysis and segmentation of medical images. However, using a global model to capture the variability of complex structures is not enough to achieve the best results. The complexity of a proper global model increases even more when the amount of data available is limited to a small number of datasets. Typically, the anatomical variability between structures is associated to the variability of their physiological regions. In this paper, a complete pipeline is proposed for building a multi-region statistical shape model to study the entire variability from locally identified physiological regions of the inner ear. The proposed model, which is based on an extension of the Point Distribution Model (PDM), is built for a training set of 17 high-resolution images (24.5 μm voxels) of the inner ear. The model is evaluated according to its generalization ability and specificity. The results are compared with the ones of a global model built directly using the standard PDM approach. The evaluation results suggest that better accuracy can be achieved using a regional modeling of the inner ear.

Entropy analysis of frequency and shape change in horseshoe bat biosonar

NASA Astrophysics Data System (ADS)

Gupta, Anupam K.; Webster, Dane; Müller, Rolf

2018-06-01

Echolocating bats use ultrasonic pulses to collect information about their environments. Some of this information is encoded at the baffle structures—noseleaves (emission) and pinnae (reception)—that act as interfaces between the bats' biosonar systems and the external world. The baffle beam patterns encode the direction-dependent sensory information as a function of frequency and hence represent a view of the environment. To generate diverse views of the environment, the bats can vary beam patterns by changes to (1) the wavelengths of the pulses or (2) the baffle geometries. Here we compare the variability in sensory information encoded by just the use of frequency or baffle shape dynamics in horseshoe bats. For this, we use digital and physical prototypes of both noseleaf and pinnae. The beam patterns for all prototypes were either measured or numerically predicted. Entropy was used as a measure to compare variability as a measure of sensory information encoding capacity. It was found that new information was acquired as a result of shape dynamics. Furthermore, the overall variability available for information encoding was similar in the case of frequency or shape dynamics. Thus, shape dynamics allows the horseshoe bats to generate diverse views of the environment in the absence of broadband biosonar signals.

A method to calculate fission-fragment yields Y(Z,N) versus proton and neutron number in the Brownian shape-motion model

DOE PAGES

Moller, Peter; Ichikawa, Takatoshi

2015-12-23

In this study, we propose a method to calculate the two-dimensional (2D) fission-fragment yield Y(Z,N) versus both proton and neutron number, with inclusion of odd-even staggering effects in both variables. The approach is to use the Brownian shape-motion on a macroscopic-microscopic potential-energy surface which, for a particular compound system is calculated versus four shape variables: elongation (quadrupole moment Q 2), neck d, left nascent fragment spheroidal deformation ϵ f1, right nascent fragment deformation ϵ f2 and two asymmetry variables, namely proton and neutron numbers in each of the two fragments. The extension of previous models 1) introduces a method tomore » calculate this generalized potential-energy function and 2) allows the correlated transfer of nucleon pairs in one step, in addition to sequential transfer. In the previous version the potential energy was calculated as a function of Z and N of the compound system and its shape, including the asymmetry of the shape. We outline here how to generalize the model from the “compound-system” model to a model where the emerging fragment proton and neutron numbers also enter, over and above the compound system composition.« less

Self-assembly programming of DNA polyominoes.

PubMed

Ong, Hui San; Syafiq-Rahim, Mohd; Kasim, Noor Hayaty Abu; Firdaus-Raih, Mohd; Ramlan, Effirul Ikhwan

2016-10-20

Fabrication of functional DNA nanostructures operating at a cellular level has been accomplished through molecular programming techniques such as DNA origami and single-stranded tiles (SST). During implementation, restrictive and constraint dependent designs are enforced to ensure conformity is attainable. We propose a concept of DNA polyominoes that promotes flexibility in molecular programming. The fabrication of complex structures is achieved through self-assembly of distinct heterogeneous shapes (i.e., self-organised optimisation among competing DNA basic shapes) with total flexibility during the design and assembly phases. In this study, the plausibility of the approach is validated using the formation of multiple 3×4 DNA network fabricated from five basic DNA shapes with distinct configurations (monomino, tromino and tetrominoes). Computational tools to aid the design of compatible DNA shapes and the structure assembly assessment are presented. The formations of the desired structures were validated using Atomic Force Microscopy (AFM) imagery. Five 3×4 DNA networks were successfully constructed using combinatorics of these five distinct DNA heterogeneous shapes. Our findings revealed that the construction of DNA supra-structures could be achieved using a more natural-like orchestration as compared to the rigid and restrictive conventional approaches adopted previously. Copyright © 2016 Elsevier B.V. All rights reserved.

Building better water models using the shape of the charge distribution of a water molecule

NASA Astrophysics Data System (ADS)

Dharmawardhana, Chamila Chathuranga; Ichiye, Toshiko

2017-11-01

The unique properties of liquid water apparently arise from more than just the tetrahedral bond angle between the nuclei of a water molecule since simple three-site models of water are poor at mimicking these properties in computer simulations. Four- and five-site models add partial charges on dummy sites and are better at modeling these properties, which suggests that the shape of charge distribution is important. Since a multipole expansion of the electrostatic potential describes a charge distribution in an orthogonal basis set that is exact in the limit of infinite order, multipoles may be an even better way to model the charge distribution. In particular, molecular multipoles up to the octupole centered on the oxygen appear to describe the electrostatic potential from electronic structure calculations better than four- and five-site models, and molecular multipole models give better agreement with the temperature and pressure dependence of many liquid state properties of water while retaining the computational efficiency of three-site models. Here, the influence of the shape of the molecular charge distribution on liquid state properties is examined by correlating multipoles of non-polarizable water models with their liquid state properties in computer simulations. This will aid in the development of accurate water models for classical simulations as well as in determining the accuracy needed in quantum mechanical/molecular mechanical studies and ab initio molecular dynamics simulations of water. More fundamentally, this will lead to a greater understanding of how the charge distribution of a water molecule leads to the unique properties of liquid water. In particular, these studies indicate that p-orbital charge out of the molecular plane is important.

Applications of SHAPES screening in drug discovery.

PubMed

Lepre, Christopher A; Peng, Jeffrey; Fejzo, Jasna; Abdul-Manan, Norzehan; Pocas, Jennifer; Jacobs, Marc; Xie, Xiaoling; Moore, Jonathan M

2002-12-01

The SHAPES strategy combines nuclear magnetic resonance (NMR) screening of a library of small drug-like molecules with a variety of complementary methods, such as virtual screening, high throughput enzymatic assays, combinatorial chemistry, X-ray crystallography, and molecular modeling, in a directed search for new medicinal chemistry leads. In the past few years, the SHAPES strategy has found widespread utility in pharmaceutical research. To illustrate a variety of different implementations of the method, we will focus in this review on recent applications of the SHAPES strategy in several drug discovery programs at Vertex Pharmaceuticals.

Place, Poverty, and Algebra: A Statewide Comparative Spatial Analysis of Variable Relationships

ERIC Educational Resources Information Center

Hogrebe, Mark C.; Tate, William F.

2012-01-01

Place matters in moderating variable relationships between algebra performance and educational variables because there are differences on the socioeconomic (SES) poverty-affluence continuum that shape local contexts. This article examines relationships between variables for school district demographic composition, teaching and financial contexts,…

Spatial structure of morphological and neutral genetic variation in Brook Trout

USGS Publications Warehouse

Kazyak, David C.; Hilderbrand, Robert H.; Keller, Stephen R.; Colaw, Mark C.; Holloway, Amanda E.; Morgan, Raymond P.; King, Timothy L.

2015-01-01

Brook Trout Salvelinus fontinalis exhibit exceptional levels of life history variation, remarkable genetic variability, and fine-scale population structure. In many cases, neighboring populations may be highly differentiated from one another to an extent that is comparable with species-level distinctions in other taxa. Although genetic samples have been collected from hundreds of populations and tens of thousands of individuals, little is known about whether differentiation at neutral markers reflects phenotypic differences among Brook Trout populations. We compared differentiation in morphology and neutral molecular markers among populations from four geographically proximate locations (all within 24 km) to examine how genetic diversity covaries with morphology. We found significant differences among and/or within streams for all three morphological axes examined and identified the source stream of many individuals based on morphology (52.3% classification efficiency). Although molecular and morphological differentiation among streams ranged considerably (mean pairwise FST: 0.023–0.264; pairwise PST: 0.000–0.339), the two measures were not significantly correlated. While in some cases morphological characters appear to have diverged to a greater extent than expected by neutral genetic drift, many traits were conserved to a greater extent than were neutral genetic markers. Thus, while Brook Trout exhibit fine-scale spatial patterns in both morphology and neutral genetic diversity, these types of biological variabilities are being structured by different ecological and evolutionary processes. The relative influences of genetic drift versus selection and phenotypic plasticity in shaping morphology appear to vary among populations occupying nearby streams.

Alike but different: the evolution of the Tubifex tubifex species complex (Annelida, Clitellata) through polyploidization.

PubMed

Marotta, Roberto; Crottini, Angelica; Raimondi, Elena; Fondello, Cristina; Ferraguti, Marco

2014-04-02

Tubifex tubifex is a widespread annelid characterized by considerable variability in its taxonomic characteristics and by a mixed reproductive strategy, with both parthenogenesis and biparental reproduction. In a molecular phylogenetic analysis, we detected substantial genetic variability among sympatric Tubifex spp. from the Lambro River (Milano, Italy), which we suggested comprise several cryptic species. To gain insights into the evolutionary events that generated this differentiation, we performed a cytogenetic analysis in parallel with a molecular assay. Approximately 80 cocoons of T. tubifex and T. blanchardi were collected and dissected. For each cocoon, we sequenced a fragment of the 16S rRNA from half of the sibling embryos and karyotyped the other half. To generate a robust phylogeny enabling the reconstruction of the evolutionary processes shaping the diversity of these sympatric lineages, we complemented our original 16S rRNA gene sequences with additional COI sequences. The chromosome number distribution was consistent with the presence of at least six sympatric euploid chromosome complements (one diploid, one triploid, three tetraploids and one hexaploid), as confirmed by a FISH assay performed with an homologous 18S rDNA probe. All the worms with 2n = 50 chromosomes belonged to an already identified sibling species of T. tubifex, T. blanchardi. The six euploid sets were coherently arranged in the phylogeny, with each lineage grouping specimens with the same chromosome complement. These results are compatible with the hypothesis that multiple polyploidization events, possibly enhanced by parthenogenesis, may have driven the evolution of the T. tubifex species complex.

Interaction between a pulsating jet and a surrounding disk wind. A hydrodynamical perspective

NASA Astrophysics Data System (ADS)

Tabone, B.; Raga, A.; Cabrit, S.; Pineau des Forêts, G.

2018-06-01

Context. The molecular richness of fast protostellar jets within 20-100 au of their source, despite strong ultraviolet irradiation, remains a challenge for the models investigated so far. Aim.We aim to investigate the effect of interaction between a time-variable jet and a surrounding steady disk wind, to assess the possibility of jet chemical enrichement by the wind, and the characteristic signatures of such a configuration. Methods: We have constructed an analytic model of a jet bow shock driven into a surrounding slower disk wind in the thin shell approximation. The refilling of the post bow shock cavity from below by the disk wind is also studied. An extension of the model to the case of two or more successive internal working surfaces (IWS) is made. We then compared this analytic model with numerical simulations with and without a surrounding disk wind. Results: We find that at early times (of order the variability period), jet bow shocks travel in refilled pristine disk wind material, before interacting with the cocoon of older bow shocks. This opens the possibility of bow shock chemical enrichment (if the disk wind is molecular and dusty) and of probing the unperturbed disk wind structure near the jet base. Several distinctive signatures of the presence of a surrounding disk wind are identified, in the bow shock morphology and kinematics. Numerical simulations validate our analytical approach and further show that at large scale, the passage of many jet IWS inside a disk wind produces a stationary V-shaped cavity, closing down onto the axis at a finite distance from the source.

Genetic divergence among accessions of melon from traditional agriculture of the Brazilian Northeast.

PubMed

Aragão, F A S; Torres Filho, J; Nunes, G H S; Queiróz, M A; Bordallo, P N; Buso, G S C; Ferreira, M A; Costa, Z P; Bezerra Neto, F

2013-12-06

The genetic divergence of 38 melon accessions from traditional agriculture of the Brazilian Northeast and three commercial hybrids were evaluated using fruit descriptors and microsatellite markers. The melon germplasm belongs to the botanic varieties cantalupensis (19), momordica (7), conomon (4), and inodorus (3), and to eight genotypes that were identified only at the species level. The fruit descriptors evaluated were: number of fruits per plant (NPF), fruit mass (FM; kg), fruit longitudinal diameter (LD; cm), fruit transversal diameter (TD; cm), shape index based on the LD/TD ratio, flesh pulp thickness, cavity thickness (CT; cm), firmness fruit pulp (N), and soluble solids (SS; °Brix). The results showed high variability for all descriptors, especially for NPF, LD, and FM. The grouping analysis based on fruit descriptors produced eight groups without taxonomic criteria. The LD (22.52%), NPF (19.70%), CT (16.13%), and SS (9.57%) characteristics were the descriptors that contributed the most to genotype dissimilarity. The 17 simple sequence repeat polymorphic markers amplified 41 alleles with an average of 2.41 alleles and three genotypes per locus. Some markers presented a high frequency for the main allele. The genetic diversity ranged from 0.07 to 0.60, the observed heterozygosity had very low values, and the mean polymorphism information content was 0.32. Molecular genetic similarity analyses clustered the accessions in 13 groups, also not following taxonomic ranks. There was no association between morphoagronomic and molecular groupings. In conclusion, there was great variability among the accessions and among and within botanic groups.

Programmable thermal emissivity structures based on bioinspired self-shape materials

NASA Astrophysics Data System (ADS)

Athanasopoulos, N.; Siakavellas, N. J.

2015-12-01

Programmable thermal emissivity structures based on the bioinspired self-shape anisotropic materials were developed at macro-scale, and further studied theoretically at smaller scale. We study a novel concept, incorporating materials that are capable of transforming their shape via microstructural rearrangements under temperature stimuli, while avoiding the use of exotic shape memory materials or complex micro-mechanisms. Thus, programmed thermal emissivity behaviour of a surface is achievable. The self-shape structure reacts according to the temperature of the surrounding environment or the radiative heat flux. A surface which incorporates self-shape structures can be designed to quickly absorb radiative heat energy at low temperature levels, but is simultaneously capable of passively controlling its maximum temperature in order to prevent overheating. It resembles a “game” of colours, where two or more materials coexist with different values of thermal emissivity/ absorptivity/ reflectivity. The transformation of the structure conceals or reveals one of the materials, creating a surface with programmable - and therefore, variable- effective thermal emissivity. Variable thermal emissivity surfaces may be developed with a total hemispherical emissivity ratio (ɛEff_H/ɛEff_L) equal to 28.

Insights into Inverse Materials Design from Phase Transitions in Shape Space

NASA Astrophysics Data System (ADS)

Cersonsky, Rose; van Anders, Greg; Dodd, Paul M.; Glotzer, Sharon C.

In designing new materials for synthesis, the inverse materials design approach posits that, given a structure, we can predict a building block optimized for self- assembly. How does that building block change as pressure is varied to maintain the same crystal structure? We address this question for entropically stabilized colloidal crystals by working in a generalized statistical thermodynamic ensemble where an alchemical potential variable is fixed and its conjugate variable, particle shape, is allowed to fluctuate. We show that there are multiple regions of shape behavior and phase transitions in shape space between these regions. Furthermore, while past literature has looked towards packing arguments for proposing shape-filling candidate building blocks for structure formation, we show that even at very high pressures, a structure will attain lowest free energy by modifying these space-filling shapes. U.S. Army Research Office under Grant Award No. W911NF-10-1-0518, Emerging Frontiers in Research and Innovation Award EFRI-1240264, National Science Foundation Grant Number ACI- 1053575, XSEDE award DMR 140129, Rackham Merit Fellowship Program.

Programmable thermal emissivity structures based on bioinspired self-shape materials

PubMed Central

Athanasopoulos, N.; Siakavellas, N. J.

2015-01-01

Programmable thermal emissivity structures based on the bioinspired self-shape anisotropic materials were developed at macro-scale, and further studied theoretically at smaller scale. We study a novel concept, incorporating materials that are capable of transforming their shape via microstructural rearrangements under temperature stimuli, while avoiding the use of exotic shape memory materials or complex micro-mechanisms. Thus, programmed thermal emissivity behaviour of a surface is achievable. The self-shape structure reacts according to the temperature of the surrounding environment or the radiative heat flux. A surface which incorporates self-shape structures can be designed to quickly absorb radiative heat energy at low temperature levels, but is simultaneously capable of passively controlling its maximum temperature in order to prevent overheating. It resembles a “game” of colours, where two or more materials coexist with different values of thermal emissivity/ absorptivity/ reflectivity. The transformation of the structure conceals or reveals one of the materials, creating a surface with programmable – and therefore, variable- effective thermal emissivity. Variable thermal emissivity surfaces may be developed with a total hemispherical emissivity ratio (εEff_H/εEff_L) equal to 28. PMID:26635316

Chiral symmetry breaking by spatial confinement in tactoidal droplets of lyotropic chromonic liquid crystals

PubMed Central

Tortora, Luana; Lavrentovich, Oleg D.

2011-01-01

In many colloidal systems, an orientationally ordered nematic (N) phase emerges from the isotropic (I) melt in the form of spindle-like birefringent tactoids. In cases studied so far, the tactoids always reveal a mirror-symmetric nonchiral structure, sometimes even when the building units are chiral. We report on chiral symmetry breaking in the nematic tactoids formed in molecularly nonchiral polymer-crowded aqueous solutions of low-molecular weight disodium cromoglycate. The parity is broken by twisted packing of self-assembled molecular aggregates within the tactoids as manifested by the observed optical activity. Fluorescent confocal microscopy reveals that the chiral N tactoids are located at the boundaries of cells. We explain the chirality induction as a replacement of energetically costly splay packing of the aggregates within the curved bipolar tactoidal shape with twisted packing. The effect represents a simple pathway of macroscopic chirality induction in an organic system with no molecular chirality, as the only requirements are orientational order and curved shape of confinement. PMID:21402929

Champagne flutes and brandy snifters: modelling protostellar outflow-cloud chemical interfaces

NASA Astrophysics Data System (ADS)

Rollins, R. P.; Rawlings, J. M. C.; Williams, D. A.; Redman, M. P.

2014-10-01

A rich variety of molecular species has now been observed towards hot cores in star-forming regions and in the interstellar medium. An increasing body of evidence from millimetre interferometers suggests that many of these form at the interfaces between protostellar outflows and their natal molecular clouds. However, current models have remained unable to explain the origin of the observational bias towards wide-angled `brandy snifter' shaped outflows over narrower `champagne flute' shapes in carbon monoxide imaging. Furthermore, these wide-angled systems exhibit unusually high abundances of the molecular ion HCO+. We present results from a chemodynamic model of such regions where a rich chemistry arises naturally as a result of turbulent mixing between cold, dense molecular gas and the hot, ionized outflow material. The injecta drives a rich and rapid ion-neutral chemistry in qualitative and quantitative agreement with the observations. The observational bias towards wide-angled outflows is explained naturally by the geometry-dependent ion injection rate causing rapid dissociation of CO in the younger systems.

A Structural Approach to Establishing a Platform Chemistry for the Tunable, Bulk Electron Beam Cross-Linking of Shape Memory Polymer Systems

PubMed Central

Hearon, Keith; Besset, Celine J.; Lonnecker, Alexander T.; Ware, Taylor; Voit, Walter E.; Wilson, Thomas S.; Wooley, Karen L.; Maitland, Duncan J.

2014-01-01

The synthetic design and thermomechanical characterization of shape memory polymers (SMPs) built from a new polyurethane chemistry that enables facile, bulk and tunable cross-linking of low-molecular weight thermoplastics by electron beam irradiation is reported in this study. SMPs exhibit stimuli-induced geometry changes and are being proposed for applications in numerous fields. We have previously reported a polyurethane SMP system that exhibits the complex processing capabilities of thermoplastic polymers and the mechanical robustness and tunability of thermomechanical properties that are often characteristic of thermoset materials. These previously reported polyurethanes suffer practically because the thermoplastic molecular weights needed to achieve target cross-link densities severely limit high-throughput thermoplastic processing and because thermally unstable radiation-sensitizing additives must be used to achieve high enough cross-link densities to enable desired tunable shape memory behavior. In this study, we demonstrate the ability to manipulate cross-link density in low-molecular weight aliphatic thermoplastic polyurethane SMPs (Mw as low as ~1.5 kDa) without radiation-sensitizing additives by incorporating specific structural motifs into the thermoplastic polymer side chains that we hypothesized would significantly enhance susceptibility to e-beam cross-linking. A custom diol monomer was first synthesized and then implemented in the synthesis of neat thermoplastic polyurethane SMPs that were irradiated at doses ranging from 1 to 500 kGy. Dynamic mechanical analysis (DMA) demonstrated rubbery moduli to be tailorable between 0.1 and 55 MPa, and both DMA and sol/gel analysis results provided fundamental insight into our hypothesized mechanism of electron beam cross-linking, which enables controllable bulk cross-linking to be achieved in highly processable, low-molecular weight thermoplastic shape memory polymers without sensitizing additives. PMID:25411511

Matrix superpotentials

NASA Astrophysics Data System (ADS)

Nikitin, Anatoly G.; Karadzhov, Yuri

2011-07-01

We present a collection of matrix-valued shape invariant potentials which give rise to new exactly solvable problems of SUSY quantum mechanics. It includes all irreducible matrix superpotentials of the generic form W=kQ+\\frac{1}{k} R+P, where k is a variable parameter, Q is the unit matrix multiplied by a real-valued function of independent variable x, and P and R are the Hermitian matrices depending on x. In particular, we recover the Pron'ko-Stroganov 'matrix Coulomb potential' and all known scalar shape invariant potentials of SUSY quantum mechanics. In addition, five new shape invariant potentials are presented. Three of them admit a dual shape invariance, i.e. the related Hamiltonians can be factorized using two non-equivalent superpotentials. We find discrete spectrum and eigenvectors for the corresponding Schrödinger equations and prove that these eigenvectors are normalizable.

A statistical shape model of the human second cervical vertebra.

PubMed

Clogenson, Marine; Duff, John M; Luethi, Marcel; Levivier, Marc; Meuli, Reto; Baur, Charles; Henein, Simon

2015-07-01

Statistical shape and appearance models play an important role in reducing the segmentation processing time of a vertebra and in improving results for 3D model development. Here, we describe the different steps in generating a statistical shape model (SSM) of the second cervical vertebra (C2) and provide the shape model for general use by the scientific community. The main difficulties in its construction are the morphological complexity of the C2 and its variability in the population. The input dataset is composed of manually segmented anonymized patient computerized tomography (CT) scans. The alignment of the different datasets is done with the procrustes alignment on surface models, and then, the registration is cast as a model-fitting problem using a Gaussian process. A principal component analysis (PCA)-based model is generated which includes the variability of the C2. The SSM was generated using 92 CT scans. The resulting SSM was evaluated for specificity, compactness and generalization ability. The SSM of the C2 is freely available to the scientific community in Slicer (an open source software for image analysis and scientific visualization) with a module created to visualize the SSM using Statismo, a framework for statistical shape modeling. The SSM of the vertebra allows the shape variability of the C2 to be represented. Moreover, the SSM will enable semi-automatic segmentation and 3D model generation of the vertebra, which would greatly benefit surgery planning.

Comment on "The shape and composition of interstellar silicate grains"

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

Bradley, J P; Ishii, H

2007-09-27

In the paper entitled 'The shape and composition of interstellar silicate grains' (A & A, 462, 667-676 (2007)), Min et al. explore non-spherical grain shape and composition in modeling the interstellar 10 and 20 {micro}m extinction features. This progression towards more realistic models is vitally important to enabling valid comparisons between dust observations and laboratory measurements. Min et al. proceed to compare their model results with GEMS (glass with embedded metals and sulfides) from IDPs (interplanetary dust particles) and to discuss the nature and origin of GEMS. Specifically, they evaluate the hypothesis of Bradley (1994) that GEMS are interstellar (IS)more » amorphous silicates. From a comparison of the mineralogy, chemical compositions, and infrared (IR) spectral properties of GEMS with their modeling results, Min et al. conclude: 'GEMS are, in general, not unprocessed leftovers from the diffuse ISM'. This conclusion is based, however, on erroneous and incomplete GEMS data. It is important to clarify first that Bradley (1994) never proposed that GEMS are unprocessed leftovers from the diffuse ISM, nor did he suggest that individual subnanogram mass GEMS are a representative sampling of the enormous mass of silicates in the diffuse ISM. Bradley (1994) simply showed that GEMS properties are consistent with those of IS amorphous silicates. It is widely accepted that circumstellar outflows are important sources of IS silicates, and whether GEMS are processed or not, the circumstellar heritage of some has been rigorously confirmed through measurements of non-solar oxygen (O) isotope abundances (Messenger et al., 2003; Floss et al., 2006). Keller et al. (2000) assert that even GEMS without detectable O isotope anomalies are probably also extrasolar IS silicates because they are embedded in carbonaceous material with non-solar D/H isotopic composition. (Much of the silicate dust in the ISM may be isotopically homogenized (Zhukovska et al., 2007)). Recent measurements show that the elemental compositions of GEMS with non-solar isotopic compositions are 'remarkably similar' to those with solar isotopic compositions (Keller & Messenger, 2007). About 80% of all isotopically anomalous IS silicates identified to date are GEMS with detectable and variable O isotopic memories of a circumstellar ancestry (Messenger, 2007). Bradley (1999) proposed that GEMS are IS silicates from 'a presolar interstellar molecular cloud, presumably the local molecular cloud from which the solar system formed'. Although based on incorrect data (detailed below), Min et al. propose that most GEMS actually formed in the presolar molecular cloud, and they further propose that none of them are IS silicates. IS silicate sources include molecular clouds, circumstellar outflows, supernovae, and even recently discovered black hole winds (Molster & Waters; 2003; Jones, 2005; Zhukovska et al. 2007; Markwick-Kemper et al. 2007). The average IS 10 {micro}m extinction feature observed along lines of sight towards the galactic center (modeled by Min et al.) presumably provides a good average for IS silicates, but it cannot distinguish amorphous silicates originating in the presolar molecular cloud from amorphous silicates originating in other interstellar molecular clouds or indeed other sources of amorphous IS silicates. Even if most GEMS accreted in the presolar molecular cloud, then they must also be representatives of some portion of the IS amorphous silicate population. Laboratory heating experiments indicate it is highly unlikely that GEMS were modified in a protoplanetary accretion disk environment (Brownlee et al. 2005). In summary, Min et al. conclude from their modeling of the shape and composition of IS silicates that the properties of GEMS are generally inconsistent with those of IS silicates. First, it has been rigorously confirmed via ion microprobe measurements that some GEMS are indeed presolar IS silicates. Second, regardless of whether GEMS, or components of GEMS, originated in presolar circumstellar outflows or a presolar molecular cloud they are all IS silicates. Third, key GEMS data reported in Min et al. are inaccurate. Had complete isotopic, chemical, mineralogical and infrared (IR) spectral properties of GEMS been considered, Min et al. may have concluded that the properties of GEMS, although not an exact match, are generally consistent with those of amorphous silicates in the ISM.« less

Novel Breast Cancer Therapeutics Based on Bacterial Cupredoxin

DTIC Science & Technology

2008-09-01

M. and Lim, C. (1999) Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the...crowding has structural effects on the folded ensemble of polypeptides. energy landscape theory excluded volume effect molecular simulations protein... molecular simulations (51). Thermo- dynamic properties such as the radius of gyration (Rg), shape parameters ( and S) (11), and the fraction of native

Hiding in the swamp: new capillariid nematode parasitizing New Zealand brown mudfish.

PubMed

Jorge, F; White, R S A; Paterson, R A

2018-05-01

The extent of New Zealand's freshwater fish-parasite diversity has yet to be fully revealed, with host-parasite relationships still to be described from nearly half the known fish community. While advances in the number of fish species examined and parasite taxa described are being made, some parasite groups, such as nematodes, remain poorly understood. In the present study we combined morphological and molecular analyses to characterize a capillariid nematode found infecting the swim bladder of the brown mudfish Neochanna apoda, an endemic New Zealand fish from peat-swamp-forests. Morphologically, the studied nematodes are distinct from other Capillariinae taxa by the features of the male posterior end, namely the shape of the bursa lobes, and shape of spicule distal end. Male specimens were classified into three different types according to differences in the shape of the bursa lobes at the posterior end, but only one was successfully characterized molecularly. Molecular analysis indicated that the studied capillariid is distinct from other genera. However, inferences about the phylogenetic position of the capillariid reported here will remain uncertain, due to the limited number of Capillariinae taxa characterized molecularly. The discovery of this new capillariid, which atypically infects the swim bladder of its host, which itself inhabits a very unique ecosystem, underlines the very interesting evolutionary history of this parasite, which for now will remain unresolved.

Measurement of Size-dependent Dynamic Shape Factors of Quartz Particles in Two Flow Regimes

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

Alexander, Jennifer M.; Bell, David M.; Imre, D.

2016-08-02

Understanding and modeling the behavior of quartz dust particles, commonly found in the atmosphere, requires knowledge of many relevant particles properties, including particle shape. This study uses a single particle mass spectrometer, a differential mobility analyzer, and an aerosol particle mass analyzer to measure quartz aerosol particles mobility, aerodynamic, and volume equivalent diameters, mass, composition, effective density, and dynamic shape factor as a function of particle size, in both the free molecular and transition flow regimes. The results clearly demonstrate that dynamic shape factors can vary significantly as a function of particle size. For the quartz samples studied here, themore » dynamic shape factors increase with size, indicating that larger particles are significantly more aspherical than smaller particles. In addition, dynamic shape factors measured in the free-molecular (χv) and transition (χt) flow regimes can be significantly different, and these differences vary with the size of the quartz particles. For quartz, χv of small (d < 200 nm) particles is 1.25, while χv of larger particles (d ~ 440 nm) is 1.6, with a continuously increasing trend with particle size. In contrast χt, of small particles starts at 1.1 increasing slowly to 1.34 for 550 nm diameter particles. The multidimensional particle characterization approach used here goes beyond determination of average properties for each size, to provide additional information about how the particle dynamic shape factor may vary even for particles with the same mass and volume equivalent diameter.« less

Shape-shifting corals: Molecular markers show morphology is evolutionarily plastic in Porites

PubMed Central

Forsman, Zac H; Barshis, Daniel J; Hunter, Cynthia L; Toonen, Robert J

2009-01-01

Background Corals are notoriously difficult to identify at the species-level due to few diagnostic characters and variable skeletal morphology. This 'coral species problem' is an impediment to understanding the evolution and biodiversity of this important and threatened group of organisms. We examined the evolution of the nuclear ribosomal internal transcribed spacer (ITS) and mitochondrial markers (COI, putative control region) in Porites, one of the most taxonomically challenging and ecologically important genera of reef-building corals. Results Nuclear and mitochondrial markers were congruent, clearly resolving many traditionally recognized species; however, branching and mounding varieties were genetically indistinguishable within at least two clades, and specimens matching the description of 'Porites lutea' sorted into three genetically divergent groups. Corallite-level features were generally concordant with genetic groups, although hyper-variability in one group (Clade I) overlapped and obscured several others, and Synarea (previously thought to be a separate subgenus) was closely related to congeners despite its unique morphology. Scanning electron microscopy revealed subtle differences between genetic groups that may have been overlooked previously as taxonomic characters. Conclusion This study demonstrates that the coral skeleton can be remarkably evolutionarily plastic, which may explain some taxonomic difficulties, and obscure underlying patterns of endemism and diversity. PMID:19239678

Identification and detection of simple 3D objects with severely blurred vision.

PubMed

Kallie, Christopher S; Legge, Gordon E; Yu, Deyue

2012-12-05

Detecting and recognizing three-dimensional (3D) objects is an important component of the visual accessibility of public spaces for people with impaired vision. The present study investigated the impact of environmental factors and object properties on the recognition of objects by subjects who viewed physical objects with severely reduced acuity. The experiment was conducted in an indoor testing space. We examined detection and identification of simple convex objects by normally sighted subjects wearing diffusing goggles that reduced effective acuity to 20/900. We used psychophysical methods to examine the effect on performance of important environmental variables: viewing distance (from 10-24 feet, or 3.05-7.32 m) and illumination (overhead fluorescent and artificial window), and object variables: shape (boxes and cylinders), size (heights from 2-6 feet, or 0.61-1.83 m), and color (gray and white). Object identification was significantly affected by distance, color, height, and shape, as well as interactions between illumination, color, and shape. A stepwise regression analysis showed that 64% of the variability in identification could be explained by object contrast values (58%) and object visual angle (6%). When acuity is severely limited, illumination, distance, color, height, and shape influence the identification and detection of simple 3D objects. These effects can be explained in large part by the impact of these variables on object contrast and visual angle. Basic design principles for improving object visibility are discussed.

Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank

PubMed Central

Alves, Alexandre Alonso; Bhering, Leonardo Lopes; Rosado, Tatiana Barbosa; Laviola, Bruno Galvêas; Formighieri, Eduardo Fernandes; Cruz, Cosme Damião

2013-01-01

The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought. PMID:24130445

Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank.

PubMed

Alves, Alexandre Alonso; Bhering, Leonardo Lopes; Rosado, Tatiana Barbosa; Laviola, Bruno Galvêas; Formighieri, Eduardo Fernandes; Cruz, Cosme Damião

2013-09-01

The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought.

Symptoms Moderating the Association Between Recent Suicide Attempts and Trauma Levels: Fan-Shaped Effects.

PubMed

Afzali, Mohammad H; Birmes, Philippe; Vautier, Stéphane

2015-01-01

The present study focuses on variables moderating the incidence of recent suicide attempt in a large community sample (n = 39,617) of French citizens with various levels of trauma. Five trauma levels were established based on posttraumatic stress disorder items of the Mini International Neuropsychiatric Interview. Twenty-three symptoms were examined as potential moderating variables with a fan-shaped pattern. Seven symptoms regarding desire for death, self-harm intention, suicidal ideation, lifetime suicide attempt, depressed mood, loss of interest, and panic attack exhibited the fan-shaped pattern. The absence of these moderating symptoms decreases the incidence of suicide attempt and their presence leads to a gradual increase.

Variable Number Of Tandem Repeats (VNTR) and its application in bacterial epidemiology.

PubMed

Ramazanzadeh, Rashid; McNerney, Ruth

2007-08-15

Molecular epidemiology is the using of molecular techniques to study bacterial distribution in human populations. Recently molecular epidemiologist benefit from several techniques such as Variable Number Tandem Repeat (VNTR) typing method to typing bacterial strains. Variable Number Tandem Repeat (VNTR) typing is a tool for genotyping and provides data in a simple and numeric format based on the number of repetitive sequences. VNTR for first time identified in M. tuberculosis as Mycobacterial Interspersed Repeat Units (MIRUs). General terms of VNTR have now been reported in Bacillus anthracis, Legionella pneumophila, Pseudomonas aeruginosa, Salmonella enterica and Escherichia coli O157.

Hairpin-shaped tetranuclear palladium(II) complex: synthesis, crystal structure, DNA binding and cytotoxicity activity studies.

PubMed

Gao, En-Jun; Wang, Ke-Hua; Zhu, Ming-Chang; Liu, Lei

2010-07-01

A novel tetranuclear palladium(II) complex [Pd(4)(phen)(4) (micro-pydc)(4)].10H(2)O (phen = 1,10-phenanthroline, pydc = pyridine-3,4-dicarboxylate) has been synthesized and characterized. In the tetranuclear complex, two pairs of dipalladated [Pd(phen)] moieties are bridged together by four pydc, presenting a hairpin molecular shape. The binding of the title complex with fish sperm DNA (FS-DNA) has been investigated by UV spectrum and fluorescence spectrum. All the results indicate that the complex bind to DNA in an intercalative mode and considerating the molecular shape and size, the dipalladated phenanthroline moieties bisintercalate to the base pairs of DNA. Agarose gel electrophoresis assay demonstrates the ability of the complex to cleave the pBR322 plasmid DNA. Cytotoxic activity studies show the complex exhibited good cytotoxic activity against four different cancer cell lines. Crown Copyright (c) 2010. Published by Elsevier Masson SAS. All rights reserved.

Reagent-Free Programming of Shape-Memory Behavior in Gelatin by Electron Beams: Experiments and Modeling

NASA Astrophysics Data System (ADS)

Riedel, Stefanie; Mayr, Stefan G.

2018-02-01

Recent years have seen a paradigm shift in biomaterials toward stimuli-responsive switchable systems that actively interact with their environment. This work demonstrates how to turn the ubiquitous off-the-shelf material gelatin into such a smart biomaterial. This is achieved by realizing the shape-memory effect, viz., a temperature-induced transition from a secondary into a primary shape that has been programmed in the first place merely by exposure to energetic electrons without addition of potentially hazardous cross-linkers. While this scenario is experimentally quantified for exemplary actuators, a theoretical framework capable of unraveling the molecular foundations and predicting experiments is also presented. It particularly employs molecular dynamics modeling based on force fields that are also derived within this work. Implementing this functionality into a highly accepted material, these findings open an avenue for large-scale application in a broad range of areas.

A Multidimensional Diversity‐Oriented Synthesis Strategy for Structurally Diverse and Complex Macrocycles

PubMed Central

Nie, Feilin; Kunciw, Dominique L.; Wilcke, David; Stokes, Jamie E.; Galloway, Warren R. J. D.; Bartlett, Sean; Sore, Hannah F.

2016-01-01

Abstract Synthetic macrocycles are an attractive area in drug discovery. However, their use has been hindered by a lack of versatile platforms for the generation of structurally (and thus shape) diverse macrocycle libraries. Herein, we describe a new concept in library synthesis, termed multidimensional diversity‐oriented synthesis, and its application towards macrocycles. This enabled the step‐efficient generation of a library of 45 novel, structurally diverse, and highly‐functionalized macrocycles based around a broad range of scaffolds and incorporating a wide variety of biologically relevant structural motifs. The synthesis strategy exploited the diverse reactivity of aza‐ylides and imines, and featured eight different macrocyclization methods, two of which were novel. Computational analyses reveal a broad coverage of molecular shape space by the library and provides insight into how the various diversity‐generating steps of the synthesis strategy impact on molecular shape. PMID:27484830

Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

NASA Astrophysics Data System (ADS)

Awasthi, Shalini; Nair, Nisanth N.

2017-03-01

Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective variables, which severely limits the predictive power of the enhanced sampling approaches. Here we propose a method called Temperature Accelerated Sliced Sampling (TASS) that combines temperature accelerated molecular dynamics with umbrella sampling and metadynamics to sample the collective variable space in an efficient manner. The presented method can sample a large number of collective variables and is advantageous for controlled exploration of broad and unbound free energy basins. TASS is also shown to achieve quick free energy convergence and is practically usable with ab initio molecular dynamics techniques.

Four-dimensional Printing of Liquid Crystal Elastomers.

PubMed

Ambulo, Cedric P; Burroughs, Julia J; Boothby, Jennifer M; Kim, Hyun; Shankar, M Ravi; Ware, Taylor H

2017-10-25

Three-dimensional structures capable of reversible changes in shape, i.e., four-dimensional-printed structures, may enable new generations of soft robotics, implantable medical devices, and consumer products. Here, thermally responsive liquid crystal elastomers (LCEs) are direct-write printed into 3D structures with a controlled molecular order. Molecular order is locally programmed by controlling the print path used to build the 3D object, and this order controls the stimulus response. Each aligned LCE filament undergoes 40% reversible contraction along the print direction on heating. By printing objects with controlled geometry and stimulus response, magnified shape transformations, for example, volumetric contractions or rapid, repetitive snap-through transitions, are realized.

Application of 3D Zernike descriptors to shape-based ligand similarity searching.

PubMed

Venkatraman, Vishwesh; Chakravarthy, Padmasini Ramji; Kihara, Daisuke

2009-12-17

The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed. In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, a graph matching algorithm that compares atom environments. Three benchmark datasets are used to thoroughly test the methods in terms of their ability for molecular classification, retrieval rate, and performance under the situation that simulates actual virtual screening tasks over a large pharmaceutical database. The 3DZD performed better than or comparable to the other methods examined, depending on the datasets and evaluation metrics used. Reasons for the success and the failure of the shape based methods for specific cases are investigated. Based on the results for the three datasets, general conclusions are drawn with regard to their efficiency and applicability. The 3DZD has unique ability for fast comparison of three-dimensional shape of compounds. Examples analyzed illustrate the advantages and the room for improvements for the 3DZD.

Application of 3D Zernike descriptors to shape-based ligand similarity searching

PubMed Central

2009-01-01

Background The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed. Results In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, a graph matching algorithm that compares atom environments. Three benchmark datasets are used to thoroughly test the methods in terms of their ability for molecular classification, retrieval rate, and performance under the situation that simulates actual virtual screening tasks over a large pharmaceutical database. The 3DZD performed better than or comparable to the other methods examined, depending on the datasets and evaluation metrics used. Reasons for the success and the failure of the shape based methods for specific cases are investigated. Based on the results for the three datasets, general conclusions are drawn with regard to their efficiency and applicability. Conclusion The 3DZD has unique ability for fast comparison of three-dimensional shape of compounds. Examples analyzed illustrate the advantages and the room for improvements for the 3DZD. PMID:20150998

Fast surface-based travel depth estimation algorithm for macromolecule surface shape description.

PubMed

Giard, Joachim; Alface, Patrice Rondao; Gala, Jean-Luc; Macq, Benoît

2011-01-01

Travel Depth, introduced by Coleman and Sharp in 2006, is a physical interpretation of molecular depth, a term frequently used to describe the shape of a molecular active site or binding site. Travel Depth can be seen as the physical distance a solvent molecule would have to travel from a point of the surface, i.e., the Solvent-Excluded Surface (SES), to its convex hull. Existing algorithms providing an estimation of the Travel Depth are based on a regular sampling of the molecule volume and the use of the Dijkstra's shortest path algorithm. Since Travel Depth is only defined on the molecular surface, this volume-based approach is characterized by a large computational complexity due to the processing of unnecessary samples lying inside or outside the molecule. In this paper, we propose a surface-based approach that restricts the processing to data defined on the SES. This algorithm significantly reduces the complexity of Travel Depth estimation and makes possible the analysis of large macromolecule surface shape description with high resolution. Experimental results show that compared to existing methods, the proposed algorithm achieves accurate estimations with considerably reduced processing times.

Dipole saturated absorption modeling in gas phase: Dealing with a Gaussian beam

NASA Astrophysics Data System (ADS)

Dupré, Patrick

2018-01-01

With the advent of new accurate and sensitive spectrometers, cf. combining optical cavities (for absorption enhancement), the requirement for reliable molecular transition modeling is becoming more pressing. Unfortunately, there is no trivial approach which can provide a definitive formalism allowing us to solve the coupled systems of equations associated with nonlinear absorption. Here, we propose a general approach to deal with any spectral shape of the electromagnetic field interacting with a molecular species under saturation conditions. The development is specifically applied to Gaussian-shaped beams. To make the analytical expressions tractable, approximations are proposed. Finally, two or three numerical integrations are required for describing the Lamb-dip profile. The implemented model allows us to describe the saturated absorption under low pressure conditions where the broadening by the transit-time may dominate the collision rates. The model is applied to two specific overtone transitions of the molecular acetylene. The simulated line shapes are discussed versus the collision and the transit-time rates. The specific collisional and collision-free regimes are illustrated, while the Rabi frequency controls the intermediate regime. We illustrate how to recover the input parameters by fitting the simulated profiles.

NMR and molecular dynamics study of the size, shape, and composition of reverse micelles in a cetyltrimethylammonium bromide (CTAB)/n-hexane/pentanol/water microemulsion.

PubMed

Mills, Amanda J; Wilkie, John; Britton, Melanie M

2014-09-11

The size, shape, and composition of reverse micelles (RMs) in a cetyltrimethylammonium bromide (CTAB)/pentanol/n-hexane/water microemulsion were investigated using pulsed gradient stimulated echo (PGSTE) nuclear magnetic resonance (NMR) measurements and molecular modeling. PGSTE data were collected at observation times (Δ) of 10, 40, and 450 ms. At long observation times, CTAB and pentanol exhibited single diffusion coefficients. However, at short (Δ ≤ 40 ms) observation times both CTAB and pentanol exhibited slow and fast diffusion coefficients. These NMR data indicate that both CTAB and pentanol molecules reside in different environments within the microemulsion and that there is exchange between regions on the millisecond time scale. Molecular dynamic simulations of the CTAB RM, in a solvent box containing n-hexane and pentanol, produced an ellipsoid shaped RM. Using structural parameters from these simulations and the Stokes-Einstein relation, the structure factor and dimensions of the reverse micelle were determined. Analysis of the composition of the interphase also showed that there was a variation in the ratio of surfactant to cosurfactant molecules depending on the curvature of the interphase.

Electronic structure of the benzene dimer cation

NASA Astrophysics Data System (ADS)

Pieniazek, Piotr A.; Krylov, Anna I.; Bradforth, Stephen E.

2007-07-01

The benzene and benzene dimer cations are studied using the equation-of-motion coupled-cluster model with single and double substitutions for ionized systems. The ten lowest electronic states of the dimer at t-shaped, sandwich, and displaced sandwich configurations are described and cataloged based on the character of the constituent fragment molecular orbitals. The character of the states, bonding patterns, and important features of the electronic spectrum are explained using qualitative dimer molecular orbital linear combination of fragment molecular orbital framework. Relaxed ground state geometries are obtained for all isomers. Calculations reveal that the lowest energy structure of the cation has a displaced sandwich structure and a binding energy of 20kcal/mol, while the t-shaped isomer is 6kcal/mol higher. The calculated electronic spectra agree well with experimental gas phase action spectra and femtosecond transient absorption in liquid benzene. Both sandwich and t-shaped structures feature intense charge resonance bands, whose location is very sensitive to the interfragment distance. Change in the electronic state ordering was observed between σ and πu states, which correlate to the B˜ and C˜ bands of the monomer, suggesting a reassignment of the local excitation peaks in the gas phase experimental spectrum.

Profiling Charge Complementarity and Selectivity for Binding at the Protein Surface

PubMed Central

Sulea, Traian; Purisima, Enrico O.

2003-01-01

A novel analysis and representation of the protein surface in terms of electrostatic binding complementarity and selectivity is presented. The charge optimization methodology is applied in a probe-based approach that simulates the binding process to the target protein. The molecular surface is color coded according to calculated optimal charge or according to charge selectivity, i.e., the binding cost of deviating from the optimal charge. The optimal charge profile depends on both the protein shape and charge distribution whereas the charge selectivity profile depends only on protein shape. High selectivity is concentrated in well-shaped concave pockets, whereas solvent-exposed convex regions are not charge selective. This suggests the synergy of charge and shape selectivity hot spots toward molecular selection and recognition, as well as the asymmetry of charge selectivity at the binding interface of biomolecular systems. The charge complementarity and selectivity profiles map relevant electrostatic properties in a readily interpretable way and encode information that is quite different from that visualized in the standard electrostatic potential map of unbound proteins. PMID:12719221

Barbell-shaped stir bar sorptive extraction using dummy template molecularly imprinted polymer coatings for analysis of bisphenol A in water.

PubMed

Liu, Ruimei; Feng, Feng; Chen, Guolin; Liu, Zhimin; Xu, Zhigang

2016-07-01

This study reports the development of a novel dummy template molecularly imprinted polymer (MIP)-coated barbell-shaped stir bar. The MIP stir bar coatings were prepared by using 2,2-bis(4-hydroxyphenyl)butane (BPB), 4,4'-dihydroxydiphenylmethane (BPF), 4-tert-butylphenol (PTBP), and tetrabromobisphenol A (TBBA) as dummy templates using a capillary in situ polymerization method. Uniform coatings can be prepared controllably. The method is simple, easy, and reproducible. The barbell-shaped stir bar was developed by using medical silicone tubes as wheels. The wheels could be removed and reinstalled when necessary; therefore, the barbell-shaped stir bar was easy to disassemble and reassemble. The novel MIP-coated stir bar showed good selectivity for the target analyte, bisphenol A (BPA). The established method is selective and sensitive with a lower detection limit for BPA of 0.003 μg/L. The dummy template MIP-coated stir bar is suitable for trace BPA analysis in real environmental water samples without template leakage. The novel stir bar can be used at least 100 times.

The role of nicotinic receptors in shaping and functioning of the glutamatergic system: a window into cognitive pathology.

PubMed

Molas, Susanna; Dierssen, Mara

2014-10-01

The involvement of the cholinergic system in learning, memory and attention has long been recognized, although its neurobiological mechanisms are not fully understood. Recent evidence identifies the endogenous cholinergic signaling via nicotinic acetylcholine receptors (nAChRs) as key players in determining the morphological and functional maturation of the glutamatergic system. Here, we review the available experimental and clinical evidence of nAChRs contribution to the establishment of the glutamatergic system, and therefore to cognitive function. We provide some clues of the putative underlying molecular mechanisms and discuss recent human studies that associate genetic variability of the genes encoding nAChR subunits with cognitive disorders. Finally, we discuss the new avenues to therapeutically targeting nAChRs in persons with cognitive dysfunction for which the α7-nAChR subunit is an important etiological mechanism. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mass analysis of neutral particles and ions released during electrical breakdowns on spacecraft surfaces

NASA Technical Reports Server (NTRS)

Kendall, B. R. F.

1983-01-01

A specialized spectrometer was designed and developed to measure the mass and velocity distributions of neutral particles (molecules and molecular clusters) released from metal-backed Teflon and Kapton films. Promising results were obtained with an insulation breakdown initiation system based on a moveable contact touching the insulated surfaces. A variable energy, high voltage pulse is applied to the contact. The resulting surface damage sites can be made similar in size and shape to those produced by a high voltage electron beam system operating at similar discharge energies. The point discharge apparatus was used for final development of several high speed recording systems and for measurements of the composition of the materials given off by the discharge. Results with this apparatus show evolution of large amounts of fluorocarbon fragments from discharge through Teflon FEP, while discharges through Kapton produce mainly very light hydrocarbon fragments at masses below about 80 a.m.u.

Plant xylem hydraulics: What we understand, current research, and future challenges.

PubMed

Venturas, Martin D; Sperry, John S; Hacke, Uwe G

2017-06-01

Herein we review the current state-of-the-art of plant hydraulics in the context of plant physiology, ecology, and evolution, focusing on current and future research opportunities. We explain the physics of water transport in plants and the limits of this transport system, highlighting the relationships between xylem structure and function. We describe the great variety of techniques existing for evaluating xylem resistance to cavitation. We address several methodological issues and their connection with current debates on conduit refilling and exponentially shaped vulnerability curves. We analyze the trade-offs existing between water transport safety and efficiency. We also stress how little information is available on molecular biology of cavitation and the potential role of aquaporins in conduit refilling. Finally, we draw attention to how plant hydraulic traits can be used for modeling stomatal responses to environmental variables and climate change, including drought mortality. © 2017 Institute of Botany, Chinese Academy of Sciences.

A linear-encoding model explains the variability of the target morphology in regeneration

PubMed Central

Lobo, Daniel; Solano, Mauricio; Bubenik, George A.; Levin, Michael

2014-01-01

A fundamental assumption of today's molecular genetics paradigm is that complex morphology emerges from the combined activity of low-level processes involving proteins and nucleic acids. An inherent characteristic of such nonlinear encodings is the difficulty of creating the genetic and epigenetic information that will produce a given self-assembling complex morphology. This ‘inverse problem’ is vital not only for understanding the evolution, development and regeneration of bodyplans, but also for synthetic biology efforts that seek to engineer biological shapes. Importantly, the regenerative mechanisms in deer antlers, planarian worms and fiddler crabs can solve an inverse problem: their target morphology can be altered specifically and stably by injuries in particular locations. Here, we discuss the class of models that use pre-specified morphological goal states and propose the existence of a linear encoding of the target morphology, making the inverse problem easy for these organisms to solve. Indeed, many model organisms such as Drosophila, hydra and Xenopus also develop according to nonlinear encodings producing linear encodings of their final morphologies. We propose the development of testable models of regeneration regulation that combine emergence with a top-down specification of shape by linear encodings of target morphology, driving transformative applications in biomedicine and synthetic bioengineering. PMID:24402915

Evolutionary mechanisms shaping the genetic population structure of coastal fish: insight from populations of Coilia nasus in Northwestern Pacific.

PubMed

Gao, Tianxiang; Wan, Zhenzhen; Song, Na; Zhang, Xiumei; Han, Zhiqiang

2014-12-01

A number of evolutionary mechanisms have been suggested for generating significant genetic structuring among marine fish populations in Northwestern Pacific. We used mtDNA control region to assess the factors in shaping the genetic structure of Japanese grenadier anchovy, Coilia nasus, an anadromous and estuarine coastal species, in Northwestern Pacific. Sixty seven individuals from four locations in Northwestern Pacific were sequenced for mitochondrial control region, detecting 61 haplotypes. The length of amplified control region varied from 677 to 754 bp. This length variability was due to the presence of varying numbers of a 38-bp tandemly repeated sequence. Two distinct lineages were detected, which might have diverged during Pleistocene low sea levels. There were strong differences in the geographical distribution of the two lineages. Analyses of molecular variance and the population statistic ΦST revealed significant genetic structure between China and Ariake Bay populations. Based on the frequency distribution of tandem repeat units, significant genetic differentiation was also detected between China and Ariake Bay populations. Isolation by distance seems to be the main factor driving present genetic structuring of C. nasus populations, indicating coastal dispersal pattern in this coastal species. Such an evolutionary process agrees well with some of the biological features characterizing this species.

Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology.

PubMed

Ruths, Troy; Nakhleh, Luay

2013-05-07

Cis-regulatory networks (CRNs) play a central role in cellular decision making. Like every other biological system, CRNs undergo evolution, which shapes their properties by a combination of adaptive and nonadaptive evolutionary forces. Teasing apart these forces is an important step toward functional analyses of the different components of CRNs, designing regulatory perturbation experiments, and constructing synthetic networks. Although tests of neutrality and selection based on molecular sequence data exist, no such tests are currently available based on CRNs. In this work, we present a unique genotype model of CRNs that is grounded in a genomic context and demonstrate its use in identifying portions of the CRN with properties explainable by neutral evolutionary forces at the system, subsystem, and operon levels. We leverage our model against experimentally derived data from Escherichia coli. The results of this analysis show statistically significant and substantial neutral trends in properties previously identified as adaptive in origin--degree distribution, clustering coefficient, and motifs--within the E. coli CRN. Our model captures the tightly coupled genome-interactome of an organism and enables analyses of how evolutionary events acting at the genome level, such as mutation, and at the population level, such as genetic drift, give rise to neutral patterns that we can quantify in CRNs.

Molecular relaxation behavior and isothermal crystallization above glass transition temperature of amorphous hesperetin.

PubMed

Shete, Ganesh; Khomane, Kailas S; Bansal, Arvind Kumar

2014-01-01

The purpose of this paper was to investigate the relaxation behavior of amorphous hesperetin (HRN), using dielectric spectroscopy, and assessment of its crystallization kinetics above glass transition temperature (Tg ). Amorphous HRN exhibited both local (β-) and global (α-) relaxations. β-Relaxation was observed below Tg , whereas α-relaxation prominently emerged above Tg . β-Relaxation was found to be of Johari-Goldstein type and was correlated with α-process by coupling model. Secondly, isothermal crystallization experiments were performed at 363 K (Tg + 16.5 K), 373 K (Tg + 26.5 K), and 383 K (Tg + 36.5 K). The kinetics of crystallization, obtained from the normalized dielectric strength, was modeled using the Avrami model. Havriliak-Negami (HN) shape parameters, αHN and αHN .βHN , were analyzed during the course of crystallization to understand the dynamics of amorphous phase during the emergence of crystallites. HN shape parameters indicated that long range (α-like) were motions affected to a greater extent than short range (β-like) motions during isothermal crystallization studies at all temperature conditions. The variable behavior of α-like motions at different isothermal crystallization temperatures was attributed to evolving crystallites with time and increase in electrical conductivity with temperature. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.

Effect of polyvinylpyrrolidone on mesoporous silica morphology and esterification of lauric acid with 1-butanol catalyzed by immobilized enzyme

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

Zhang, Jinyu; Zhou, Guowei, E-mail: guoweizhou@hotmail.com; Jiang, Bin

2014-05-01

Mesoporous silica materials with a range of morphology evolution, i.e., from curved rod-shaped mesoporous silica to straight rod-shaped mesoporous silica, were successfully prepared using polyvinylpyrrolidone (PVP) and triblock copolymer as dual template. The effects of PVP molecular weight and concentration on mesoporous silica structure parameters were studied. Results showed that surface area and pore volume continuously decreased with increased PVP molecular weight. Mesoporous silica prepared with PVP K30 also possessed larger pore diameter, interplanar spacing (d{sub 100}), and cell parameter (a{sub 0}) than that prepared with PVP K15 and PVP K90. In addition, with increased PVP concentration, d{sub 100} andmore » a{sub 0} continuously decreased. The mechanism of morphology evolution caused by the change in PVP concentration was investigated. The conversion rate of lauric acid with 1-butanol catalyzed by immobilized Porcine pancreatic lipase (PPL) was also evaluated. Results showed that PPL immobilized on amino-functionalized straight rod-shaped mesoporous silica maintained 50% of its esterification conversion rate even after five cycles of use with a maximum conversion rate was about 90.15%. - Graphical abstract: Curved rod-shaped mesoporous silica can be obtained at low and the highest PVP concentration, while straight rod-shaped mesoporous silica can be obtained at higher PVP concentration. - Highlights: • Mesoporous silica with morphology evolution from CRMS to SRMS were prepared. • Effects of PVP molecular weight and concentration on silica morphology were studied. • A possible mechanism for the formation of morphology evolution SiO{sub 2} was proposed. • Esterification of lauric acid with 1-butanol catalyzed by immobilized PPL.« less

Ultrahigh-resolution spectroscopy with atomic or molecular dark resonances: Exact steady-state line shapes and asymptotic profiles in the adiabatic pulsed regime

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

Zanon-Willette, Thomas; Clercq, Emeric de; Arimondo, Ennio

2011-12-15

Exact and asymptotic line shape expressions are derived from the semiclassical density matrix representation describing a set of closed three-level {Lambda} atomic or molecular states including decoherences, relaxation rates, and light shifts. An accurate analysis of the exact steady-state dark-resonance profile describing the Autler-Townes doublet, the electromagnetically induced transparency or coherent population trapping resonance, and the Fano-Feshbach line shape leads to the linewidth expression of the two-photon Raman transition and frequency shifts associated to the clock transition. From an adiabatic analysis of the dynamical optical Bloch equations in the weak field limit, a pumping time required to efficiently trap amore » large number of atoms into a coherent superposition of long-lived states is established. For a highly asymmetrical configuration with different decay channels, a strong two-photon resonance based on a lower states population inversion is established when the driving continuous-wave laser fields are greatly unbalanced. When time separated resonant two-photon pulses are applied in the adiabatic pulsed regime for atomic or molecular clock engineering, where the first pulse is long enough to reach a coherent steady-state preparation and the second pulse is very short to avoid repumping into a new dark state, dark-resonance fringes mixing continuous-wave line shape properties and coherent Ramsey oscillations are created. Those fringes allow interrogation schemes bypassing the power broadening effect. Frequency shifts affecting the central clock fringe computed from asymptotic profiles and related to the Raman decoherence process exhibit nonlinear shapes with the three-level observable used for quantum measurement. We point out that different observables experience different shifts on the lower-state clock transition.« less

Editorial: The Advent of a Molecular Genetics of General Intelligence.

ERIC Educational Resources Information Center

Weiss, Volkmar

1995-01-01

Raw IQ scores do not demonstrate the bell curve created by normalized scores, even the bell-shaped distribution does not require large numbers of underlying genes. Family data support a major gene locus of IQ. The correlation between glutathione peroxidase and IQ should be investigated through molecular genetics. (SLD)

Beyond [lambda][subscript max] Part 2: Predicting Molecular Color

ERIC Educational Resources Information Center

Williams, Darren L.; Flaherty, Thomas J.; Alnasleh, Bassam K.

2009-01-01

A concise roadmap for using computational chemistry programs (i.e., Gaussian 03W) to predict the color of a molecular species is presented. A color-predicting spreadsheet is available with the online material that uses transition wavelengths and peak-shape parameters to predict the visible absorbance spectrum, transmittance spectrum, chromaticity…

The Case for "Story-Driven" Biology Education

ERIC Educational Resources Information Center

Schattner, Peter

2015-01-01

Can learning molecular biology and genetics be enjoyable? Of course it can. Biologists know their field is exciting and fascinating and that learning how cells and molecules shape the living world is extraordinarily interesting. But can students who are not already inclined towards science also be convinced that learning molecular biology is…

Geomorphic effectiveness of a long profile shape and the role of inherent geological controls in the Himalayan hinterland area of the Ganga River basin, India

NASA Astrophysics Data System (ADS)

Sonam; Jain, Vikrant

2018-03-01

Long profiles of rivers provide a platform to analyse interaction between geological and geomorphic processes operating at different time scales. Identification of an appropriate model for river long profile becomes important in order to establish a quantitative relationship between the profile shape, its geomorphic effectiveness, and inherent geological characteristics. This work highlights the variability in the long profile shape of the Ganga River and its major tributaries, its impact on stream power distribution pattern, and role of the geological controls on it. Long profile shapes are represented by the sum of two exponential functions through the curve fitting method. We have shown that coefficients of river long profile equations are governed by the geological characteristics of subbasins. These equations further define the spatial distribution pattern of stream power and help to understand stream power variability in different geological terrains. Spatial distribution of stream power in different geological terrains successfully explains spatial variability in geomorphic processes within the Himalayan hinterland area. In general, the stream power peaks of larger rivers lie in the Higher Himalaya, and rivers in the eastern hinterland area are characterised by the highest magnitude of stream power.

Excess electron is trapped in a large single molecular cage C60F60.

PubMed

Wang, Yin-Feng; Li, Zhi-Ru; Wu, Di; Sun, Chia-Chung; Gu, Feng-Long

2010-01-15

A new kind of solvated electron systems, sphere-shaped e(-)@C60F60 (I(h)) and capsule-shaped e(-)@C60F60 (D6h), in contrast to the endohedral complex M@C60, is represented at the B3LYP/6-31G(d) + dBF (diffusive basis functions) density functional theory. It is proven, by examining the singly occupied molecular orbital (SOMO) and the spin density map of e(-)@C60F60, that the excess electron is indeed encapsulated inside the C60F60 cage. The shape of the electron cloud in SOMO matches with the shape of C60F60 cage. These cage-like single molecular solvated electrons have considerably large vertical electron detachment energies VDE of 4.95 (I(h)) and 4.67 eV (D6h) at B3LYP/6-31+G(3df) + dBF level compared to the VDE of 3.2 eV for an electron in bulk water (Coe et al., Int Rev Phys Chem 2001, 20, 33) and that of 3.66 eV for e(-)@C20F20 (Irikura, J Phys Chem A 2008, 112, 983), which shows their higher stability. The VDE of the sphere-shaped e(-)@C60F60 (I(h)) is greater than that of the capsule-shaped e(-)@C60F60 (D6h), indicating that the excess electron prefers to reside in the cage with the higher symmetry to form the more stable solvated electron. It is also noticed that the cage size [7.994 (I(h)), 5.714 and 9.978 A (D6h) in diameter] is much larger than that (2.826 A) of (H2O)20- dodecahedral cluster (Khan, Chem Phys Lett 2005, 401, 85). Copyright 2009 Wiley Periodicals, Inc.

Tuning the Direction of Intramolecular Charge Transfer and the Nature of the Fluorescent State in a T-Shaped Molecular Dyad.

PubMed

Felouat, Abdellah; D'Aléo, Anthony; Charaf-Eddin, Azzam; Jacquemin, Denis; Le Guennic, Boris; Kim, Eunsun; Lee, Kwang Jin; Woo, Jae Heun; Ribierre, Jean-Charles; Wu, Jeong Weon; Fages, Frédéric

2015-06-18

Controlling photoinduced intramolecular charge transfer at the molecular scale is key to the development of molecular devices for nanooptoelectronics. Here, we describe the design, synthesis, electronic characterization, and photophysical properties of two electron donor-acceptor molecular systems that consist of tolane and BF2-containing curcuminoid chromophoric subunits connected in a T-shaped arrangement. The two π-conjugated segments intersect at the electron acceptor dioxaborine core. From steady-state electronic absorption and fluorescence emission, we find that the photophysics of the dialkylamino-substituted analogue is governed by the occurrence of two closely lying excited states. From DFT calculations, we show that excitation in either of these two states results in a distinct shift of the electron density, whether it occurs along the curcuminoid or tolane moiety. Femtosecond transient absorption spectroscopy confirmed these findings. As a consequence, the nature of the emitting state and the photophysical properties are strongly dependent on solvent polarity. Moreover, these characteristics can also be switched by protonation or complexation at the nitrogen atom of the amino group. These features set new approaches toward the construction of a three-terminal molecular system in which the lateral branch would transduce a change of electronic state and ultimately control charge transport in a molecular-scale device.

Pursuit of STEM: Factors shaping degree completion for African American females in STEM

NASA Astrophysics Data System (ADS)

Wilkins, Ashlee N.

The primary purpose of the study was to examine secondary data from the Cooperative Institutional Research Program (CIRP) Freshman and College Senior Surveys to investigate factors shaping degree aspirations for African American female undergraduates partaking in science, technology, engineering, and mathematics (STEM) majors. Hierarchical multiple regression was used to analyze the data and identify relationships between independent variables in relation to the dependent variable. The findings of the study reveal four key variables that were predictive of degree completion for African American females in STEM. Father's education, SAT composite, highest degree planned, and self-perception were positive predictors for females; while independent variable overall sense of community among students remained a negative predictor. Lastly implications for education and recommendations for future research were discussed.

Shuttlecock-Shaped Molecular Rectifier: Asymmetric Electron Transport Coupled with Controlled Molecular Motion.

PubMed

Ryu, Taekhee; Lansac, Yves; Jang, Yun Hee

2017-07-12

A fullerene derivative with five hydroxyphenyl groups attached around a pentagon, (4-HOC 6 H 4 ) 5 HC 60 (1), has shown an asymmetric current-voltage (I-V) curve in a conducting atomic force microscopy experiment on gold. Such molecular rectification has been ascribed to the asymmetric distribution of frontier molecular orbitals over its shuttlecock-shaped structure. Our nonequilibrium Green's function (NEGF) calculations based on density functional theory (DFT) indeed exhibit an asymmetric I-V curve for 1 standing up between two Au(111) electrodes, but the resulting rectification ratio (RR ∼ 3) is insufficient to explain the wide range of RR observed in experiments performed under a high bias voltage. Therefore, we formulate a hypothesis that high RR (>10) may come from molecular orientation switching induced by a strong electric field applied between two electrodes. Indeed, molecular dynamics simulations of a self-assembled monolayer of 1 on Au(111) show that the orientation of 1 can be switched between standing-up and lying-on-the-side configurations in a manner to align its molecular dipole moment with the direction of the applied electric field. The DFT-NEGF calculations taking into account such field-induced reorientation between up and side configurations indeed yield RR of ∼13, which agrees well with the experimental value obtained under a high bias voltage.

Systematic study of aggregation structure and thermal behavior of a series of unique H-shape alkane molecules.

PubMed

Yamamoto, Hiroko; Tashiro, Kohji; Nemoto, Norio; Motoyama, Yukihiro; Takahashi, Yoshiaki

2011-08-11

The H-shape alkanes of various arm lengths have been synthesized successfully through the Grignard reaction. The detailed investigation of these novel compounds may allow us to widen the topological chemistry field furthermore. The molecular form and molecular packing structure in the crystal lattice have been revealed successfully on the basis of X-ray structure analysis as well as the analysis of Raman longitudinal acoustic modes (LAM) sensitive to the alkyl zigzag chain segments. The molecular conformation in the crystal lattice is deformed markedly from the originally imagined H-shape. In the cases of C3HOH to C6HOH, for example, the molecules are packed in a complicated manner and the OH···O hydrogen bonds govern the whole intermolecular interactions mainly. Since the alkyl segmental length is not very long, the conformational change is not very drastic, i.e., the small configurational entropy. Synergic effect of the hydrogen bonds and the small configurational entropy gives the higher melting point as known from the thermal data. On the other hand, in the cases of C10HOH and C12HOH, one of the long alkyl chain arms is found to be bent by 90° so that all of the alky chain segments of planar-zigzag conformation can be packed as closely as possible, and the intermolecular OH···O hydrogen bonds are also formed effectively without any mistake. As a result, the contribution of nonbonded intra- and intermolecular van der Waals interactions between the trans-zigzag alkyl chain segments become major, and the coupling of this enthalpy effect with the larger configurational entropy effect of the molecular shape results in the decrement of the melting point which approaches gradually that of longer n-alkane compound. In this way a sensitive balance between the nonbonded van der Waals interactions, the OH···O hydrogen bonds, as well as the configurational entropy effect gives the characteristic thermal behavior of the H-shape compounds. The thus-newly synthesized H-shape alkane compounds should give us new insight into the packing topology of complicated molecules, leading to the development of new functionality unexpected for normal linear alkane compounds. © 2011 American Chemical Society

Mechanical stress and network structure drive protein dynamics during cytokinesis.

PubMed

Srivastava, Vasudha; Robinson, Douglas N

2015-03-02

Cell-shape changes associated with processes like cytokinesis and motility proceed on several-second timescales but are derived from molecular events, including protein-protein interactions, filament assembly, and force generation by molecular motors, all of which occur much faster [1-4]. Therefore, defining the dynamics of such molecular machinery is critical for understanding cell-shape regulation. In addition to signaling pathways, mechanical stresses also direct cytoskeletal protein accumulation [5-7]. A myosin-II-based mechanosensory system controls cellular contractility and shape during cytokinesis and under applied stress [6, 8]. In Dictyostelium, this system tunes myosin II accumulation by feedback through the actin network, particularly through the crosslinker cortexillin I. Cortexillin-binding IQGAPs are major regulators of this system. Here, we defined the short timescale dynamics of key cytoskeletal proteins during cytokinesis and under mechanical stress, using fluorescence recovery after photobleaching and fluorescence correlation spectroscopy, to examine the dynamic interplay between these proteins. Equatorially enriched proteins including cortexillin I, IQGAP2, and myosin II recovered much more slowly than actin and polar crosslinkers. The mobility of equatorial proteins was greatly reduced at the furrow compared to the interphase cortex, suggesting their stabilization during cytokinesis. This mobility shift did not arise from a single biochemical event, but rather from a global inhibition of protein dynamics by mechanical-stress-associated changes in the cytoskeletal structure. Mechanical tuning of contractile protein dynamics provides robustness to the cytoskeletal framework responsible for regulating cell shape and contributes to cytokinesis fidelity. Copyright © 2015 Elsevier Ltd. All rights reserved.

Morphometric study of phylogenetic and ecologic signals in procyonid (mammalia: carnivora) endocasts.

PubMed

Ahrens, Heather E

2014-12-01

Endocasts provide a proxy for brain morphology but are rarely incorporated in phylogenetic analyses despite the potential for new suites of characters. The phylogeny of Procyonidae, a carnivoran family with relatively limited taxonomic diversity, is not well resolved because morphological and molecular data yield conflicting topologies. The presence of phylogenetic and ecologic signals in the endocasts of procyonids will be determined using three-dimensional geometric morphometrics. Endocasts of seven ingroup species and four outgroup species were digitally rendered and 21 landmarks were collected from the endocast surface. Two phylogenetic hypotheses of Procyonidae will be examined using methods testing for phylogenetic signal in morphometric data. In analyses of all taxa, there is significant phylogenetic signal in brain shape for both the morphological and molecular topologies. However, the analyses of ingroup taxa recover a significant phylogenetic signal for the morphological topology only. These results indicate support for the molecular outgroup topology, but not the ingroup topology given the brain shape data. Further examination of brain shape using principal components analysis and wireframe comparisons suggests procyonids possess more developed areas of the brain associated with motor control, spatial perception, and balance relative to the basal musteloid condition. Within Procyonidae, similar patterns of variation are present, and may be associated with increased arboreality in certain taxa. Thus, brain shape derived from endocasts may be used to test for phylogenetic signal and preliminary analyses suggest an association with behavior and ecology. © 2014 Wiley Periodicals, Inc.

The Shape of Protein Crowders is a Major Determinant of Protein Diffusion

PubMed Central

Balbo, Jessica; Mereghetti, Paolo; Herten, Dirk-Peter; Wade, Rebecca C.

2013-01-01

As a model for understanding how molecular crowding influences diffusion and transport of proteins in cellular environments, we combined experimental and theoretical approaches to study the diffusion of proteins in highly concentrated protein solutions. Bovine serum albumin and γ-Globulin were chosen as molecular crowders and as tracers. These two proteins are representatives of the main types of plasma protein and have different shapes and sizes. Solutions consisting of one or both proteins were studied. The self-diffusion coefficients of the fluorescently labeled tracer proteins were measured by means of fluorescence correlation spectroscopy at a total protein concentration of up to 400 g/L. γ-Globulin is found to have a stronger influence as a crowder on the tracer self-diffusion coefficient than Bovine serum albumin. Brownian dynamics simulations show that the excluded volume and the shape of the crowding protein have a significantly stronger influence on translational and rotational diffusion coefficients, as well as transient oligomerization, than hydrodynamic or direct interactions. Anomalous subdiffusion, which is not observed at the experimental fluorescence correlation spectroscopy timescales (>100 μs), appears only at very short timescales (<1 μs) in the simulations due to steric effects of the proteins. We envision that the combined experimental and computational approach employed here can be developed to unravel the different biophysical contributions to protein motion and interaction in cellular environments by systematically varying protein properties such as molecular weight, size, shape, and electrostatic interactions. PMID:23561534

Computer-aided design of customized foot orthoses: reproducibility and effect of method used to obtain foot shape.

PubMed

Telfer, Scott; Gibson, Kellie S; Hennessy, Kym; Steultjens, Martijn P; Woodburn, Jim

2012-05-01

To determine, for a number of techniques used to obtain foot shape based around plaster casting, foam box impressions, and 3-dimensional scanning, (1) the effect the technique has on the overall reproducibility of custom foot orthoses (FOs) in terms of inter- and intracaster reliability and (2) the reproducibility of FO design by using computer-aided design (CAD) software in terms of inter- and intra-CAD operator reliability for all these techniques. Cross-sectional study. University laboratory. Convenience sample of individuals (N=22) with noncavus foot types. Not applicable. Parameters of the FO design (length, width at forefoot, width at rearfoot, and peak medial arch height), the forefoot to rearfoot angle of the foot shape, and overall volume match between device designs. For intra- and intercaster reliability of the different methods of obtaining the foot shape, all methods fell below the reproducibility quality threshold for the medial arch height of the device, and volume matching was <80% for all methods. The more experienced CAD operator was able to achieve excellent reliability (intraclass correlation coefficients >0.75) for all variables with the exception of forefoot to rearfoot angle, with overall volume matches of >87% of the devices. None of the techniques for obtaining foot shape met all the criteria for excellent reproducibility, with the peak arch height being particularly variable. Additional variability is added at the CAD stage of the FO design process, although with adequate operator experience good to excellent reproducibility may be achieved at this stage. Taking only basic linear or angular measurement parameters from the device may fail to fully capture the variability in FO design. Copyright © 2012 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Molecular Evolution of the Neural Crest Regulatory Network in Ray-Finned Fish

PubMed Central

Kratochwil, Claudius F.; Geissler, Laura; Irisarri, Iker; Meyer, Axel

2015-01-01

Abstract Gene regulatory networks (GRN) are central to developmental processes. They are composed of transcription factors and signaling molecules orchestrating gene expression modules that tightly regulate the development of organisms. The neural crest (NC) is a multipotent cell population that is considered a key innovation of vertebrates. Its derivatives contribute to shaping the astounding morphological diversity of jaws, teeth, head skeleton, or pigmentation. Here, we study the molecular evolution of the NC GRN by analyzing patterns of molecular divergence for a total of 36 genes in 16 species of bony fishes. Analyses of nonsynonymous to synonymous substitution rate ratios (dN/dS) support patterns of variable selective pressures among genes deployed at different stages of NC development, consistent with the developmental hourglass model. Model-based clustering techniques of sequence features support the notion of extreme conservation of NC-genes across the entire network. Our data show that most genes are under strong purifying selection that is maintained throughout ray-finned fish evolution. Late NC development genes reveal a pattern of increased constraints in more recent lineages. Additionally, seven of the NC-genes showed signs of relaxation of purifying selection in the famously species-rich lineage of cichlid fishes. This suggests that NC genes might have played a role in the adaptive radiation of cichlids by granting flexibility in the development of NC-derived traits—suggesting an important role for NC network architecture during the diversification in vertebrates. PMID:26475317

Amino Acid Properties Conserved in Molecular Evolution

PubMed Central

Rudnicki, Witold R.; Mroczek, Teresa; Cudek, Paweł

2014-01-01

That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts – one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications. PMID:24967708

The kinematics of the molecular gas in Centaurus A

NASA Technical Reports Server (NTRS)

Quillen, A. C.; De Zeeuw, P. T.; Phinney, E. S.; Phillips, T. G.

1992-01-01

The CO (2-1) emission along the inner dust lane of Centaurus A, observed with the Caltech Submillimeter Observatory on Mauna Kea, shows the molecular gas to be in a thin disk, with a velocity dispersion of only about 10 km/s. The observed line profiles are broadened considerably due to beam smearing of the gas velocity field. The profile shapes are inconsistent with planar circular and noncircular motion. However, a warped disk in a prolate potential provides a good fit to the profile shapes. The morphology and kinematics of the molecular gas is similar to that of the ionized material, seen in H-alpha. The best-fitting warped disk model not only matches the optical appearance of the dust lane but also agrees with the large-scale map of the CO emission and is consistent with H I measurements at larger radii.

Free-standing supramolecular hydrogel objects by reaction-diffusion

PubMed Central

Lovrak, Matija; Hendriksen, Wouter E. J.; Maity, Chandan; Mytnyk, Serhii; van Steijn, Volkert; Eelkema, Rienk; van Esch, Jan H.

2017-01-01

Self-assembly provides access to a variety of molecular materials, yet spatial control over structure formation remains difficult to achieve. Here we show how reaction–diffusion (RD) can be coupled to a molecular self-assembly process to generate macroscopic free-standing objects with control over shape, size, and functionality. In RD, two or more reactants diffuse from different positions to give rise to spatially defined structures on reaction. We demonstrate that RD can be used to locally control formation and self-assembly of hydrazone molecular gelators from their non-assembling precursors, leading to soft, free-standing hydrogel objects with sizes ranging from several hundred micrometres up to centimeters. Different chemical functionalities and gradients can easily be integrated in the hydrogel objects by using different reactants. Our methodology, together with the vast range of organic reactions and self-assembling building blocks, provides a general approach towards the programmed fabrication of soft microscale objects with controlled functionality and shape. PMID:28580948

Self-Healing Composite of Thermoset Polymer and Programmed Super Contraction Fibers

NASA Technical Reports Server (NTRS)

Li, Guoqiang (Inventor); Meng, Harper (Inventor)

2016-01-01

A composition comprising thermoset polymer, shape memory polymer to facilitate macro scale damage closure, and a thermoplastic polymer for molecular scale healing is disclosed; the composition has the ability to resolve structural defects by a bio-mimetic close-then heal process. In use, the shape memory polymer serves to bring surfaces of a structural defect into approximation, whereafter use of the thermoplastic polymer for molecular scale healing allowed for movement of the thermoplastic polymer into the defect and thus obtain molecular scale healing. The thermoplastic can be fibers, particles or spheres which are used by heating to a level at or above the thermoplastic's melting point, then cooling of the composition below the melting temperature of the thermoplastic. Compositions of the invention have the ability to not only close macroscopic defects, but also to do so repeatedly even if another wound/damage occurs in a previously healed/repaired area.

Vibrational Detection of Odorant Functional Groups by Drosophila melanogaster

PubMed Central

Maniati, Klio; Haralambous, Katherine-Joanne

2017-01-01

Abstract A remarkable feature of olfaction, and perhaps the hardest one to explain by shape-based molecular recognition, is the ability to detect the presence of functional groups in odorants, irrespective of molecular context. We previously showed that Drosophila trained to avoid deuterated odorants could respond to a molecule bearing a nitrile group, which shares the vibrational stretch frequency with the CD bond. Here, we reproduce and extend this finding by showing analogous olfactory responses of Drosophila to the chemically vastly different functional groups, thiols and boranes, that nevertheless possess a common vibration at 2600 cm−1. Furthermore, we show that Drosophila do not respond to a cyanohydrin structure that renders nitrile groups invisible to IR spectroscopy. We argue that the response of Drosophila to these odorants which parallels their perception in humans, supports the hypothesis that odor character is encoded in odorant molecular vibrations, not in the specific shape-based activation pattern of receptors. PMID:29094064

Spatial variability of organic matter molecular composition and elemental geochemistry in surface sediments of a small boreal Swedish lake

NASA Astrophysics Data System (ADS)

Tolu, Julie; Rydberg, Johan; Meyer-Jacob, Carsten; Gerber, Lorenz; Bindler, Richard

2017-04-01

The composition of sediment organic matter (OM) exerts a strong control on biogeochemical processes in lakes, such as those involved in the fate of carbon, nutrients and trace metals. While between-lake spatial variability of OM quality is increasingly investigated, we explored in this study how the molecular composition of sediment OM varies spatially within a single lake and related this variability to physical parameters and elemental geochemistry. Surface sediment samples (0-10 cm) from 42 locations in Härsvatten - a small boreal forest lake with a complex basin morphometry - were analyzed for OM molecular composition using pyrolysis gas chromatography mass spectrometry for the contents of 23 major and trace elements and biogenic silica. We identified 162 organic compounds belonging to different biochemical classes of OM (e.g., carbohydrates, lignin and lipids). Close relationships were found between the spatial patterns of sediment OM molecular composition and elemental geochemistry. Differences in the source types of OM (i.e., terrestrial, aquatic plant and algal) were linked to the individual basin morphometries and chemical status of the lake. The variability in OM molecular composition was further driven by the degradation status of these different source pools, which appeared to be related to sedimentary physicochemical parameters (e.g., redox conditions) and to the molecular structure of the organic compounds. Given the high spatial variation in OM molecular composition within Härsvatten and its close relationship with elemental geochemistry, the potential for large spatial variability across lakes should be considered when studying biogeochemical processes involved in the cycling of carbon, nutrients and trace elements or when assessing lake budgets.

Jig-Shape Optimization of a Low-Boom Supersonic Aircraft

NASA Technical Reports Server (NTRS)

Pak, Chan-gi

2018-01-01

A simple approach for optimizing the jig-shape is proposed in this study. This simple approach is based on an unconstrained optimization problem and applied to a low-boom supersonic aircraft. In this study, the jig-shape optimization is performed using the two-step approach. First, starting design variables are computed using the least squares surface fitting technique. Next, the jig-shape is further tuned using a numerical optimization procedure based on in-house object-oriented optimization tool.

Analysis of the semi-permanent house in Merauke city in terms of aesthetic value in architecture

NASA Astrophysics Data System (ADS)

Topan, Anton; Octavia, Sari; Soleman, Henry

2018-05-01

Semi permanent houses are also used called “Rumah Kancingan” is the houses that generally exist in the Merauke city. Called semi permanent because the main structure use is woods even if the walls uses bricks. This research tries to analyze more about Semi permanent house in terms of aesthethics value. This research is a qualitative research with data collection techniques using questionnaire method and direct observation field and study of literature. The result of questionnaire data collection then processed using SPSS to get the influence of independent variable against the dependent variable and found that color, ornament, shape of the door-window and shape of roof (independent) gives 97,1% influence to the aesthetics of the Semi permanent house and based on the output coefficient SPSS obtained that the dependent variable has p-value < 0.05 which means independent variables have an effect on significant to aesthetic variable. For variables of semi permanent and wooden structure gives an effect of 98,6% to aesthetics and based on the result of SPSS coefficient it is found that free variable has p-value < 0.05 which means independent variables have an effect on significant to aesthetic variable.

Variable-pulse-shape pulsed-power accelerator

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

Stoltzfus, Brian S.; Austin, Kevin; Hutsel, Brian Thomas

A variable-pulse-shape pulsed-power accelerator is driven by a large number of independent LC drive circuits. Each LC circuit drives one or more coaxial transmission lines that deliver the circuit's output power to several water-insulated radial transmission lines that are connected in parallel at small radius by a water-insulated post-hole convolute. The accelerator can be impedance matched throughout. The coaxial transmission lines are sufficiently long to transit-time isolate the LC drive circuits from the water-insulated transmission lines, which allows each LC drive circuit to be operated without being affected by the other circuits. This enables the creation of any power pulsemore » that can be mathematically described as a time-shifted linear combination of the pulses of the individual LC drive circuits. Therefore, the output power of the convolute can provide a variable pulse shape to a load that can be used for magnetically driven, quasi-isentropic compression experiments and other applications.« less

An analysis of autism as a contingency-shaped disorder of verbal behavior

PubMed Central

Drash, Philip W.; Tudor, Roger M.

2004-01-01

This paper analyzes autism as a contingency-shaped disorder of verbal behavior. Contingencies of reinforcement in effect during the first to third year of a child's life may operate to establish and maintain those behaviors that later result in a diagnosis of autism. While neurobiological variables may, in some cases, predispose some children to be more or less responsive to environmental variables than others, our analysis suggests that reliance on neurobiological variables as causal factors in autism is unnecessary. We present six paradigms that may play critical etiologic roles in the development of behaviors labeled as autistic. Recognizing these contingencies and their resulting behaviors during the first two years of a child's life may contribute substantially to earlier identification, more effective treatment and, quite possibly, to the development of Applied Behavior Analysis programs for the prevention of autism that could be implemented immediately. Conceptualizing autism as a contingency-shaped disorder of verbal behavior may provide a new and potentially more effective paradigm for behavioral research and treatment in autism. PMID:22477283

The analysis of morphometric data on rocky mountain wolves and artic wolves using statistical method

NASA Astrophysics Data System (ADS)

Ammar Shafi, Muhammad; Saifullah Rusiman, Mohd; Hamzah, Nor Shamsidah Amir; Nor, Maria Elena; Ahmad, Noor’ani; Azia Hazida Mohamad Azmi, Nur; Latip, Muhammad Faez Ab; Hilmi Azman, Ahmad

2018-04-01

Morphometrics is a quantitative analysis depending on the shape and size of several specimens. Morphometric quantitative analyses are commonly used to analyse fossil record, shape and size of specimens and others. The aim of the study is to find the differences between rocky mountain wolves and arctic wolves based on gender. The sample utilised secondary data which included seven variables as independent variables and two dependent variables. Statistical modelling was used in the analysis such was the analysis of variance (ANOVA) and multivariate analysis of variance (MANOVA). The results showed there exist differentiating results between arctic wolves and rocky mountain wolves based on independent factors and gender.

Lipids, curvature, and nano-medicine*

PubMed Central

Mouritsen, Ole G

2011-01-01

The physical properties of the lamellar lipid-bilayer component of biological membranes are controlled by a host of thermodynamic forces leading to overall tensionless bilayers with a conspicuous lateral pressure profile and build-in curvature-stress instabilities that may be released locally or globally in terms of morphological changes. In particular, the average molecular shape and the propensity of the different lipid and protein species for forming non-lamellar and curved structures are a source of structural transitions and control of biological function. The effects of different lipids, sterols, and proteins on membrane structure are discussed and it is shown how one can take advantage of the curvature-stress modulations brought about by specific molecular agents, such as fatty acids, lysolipids, and other amphiphilic solutes, to construct intelligent drug-delivery systems that function by enzymatic triggering via curvature. Practical applications: The simple concept of lipid molecular shape and how it impacts on the structure of lipid aggregates, in particular the curvature and curvature stress in lipid bilayers and liposomes, can be exploited to construct liposome-based drug-delivery systems, e.g., for use as nano-medicine in cancer therapy. Non-lamellar-forming lysolipids and fatty acids, some of which may be designed to be prodrugs, can be created by phospholipase action in diseased tissues thereby providing for targeted drug release and proliferation of molecular entities with conical shape that break down the permeability barrier of the target cells and may hence enhance efficacy. PMID:22164124

A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds.

PubMed

Isidro-Llobet, Albert; Hadje Georgiou, Kathy; Galloway, Warren R J D; Giacomini, Elisa; Hansen, Mette R; Méndez-Abt, Gabriela; Tan, Yaw Sing; Carro, Laura; Sore, Hannah F; Spring, David R

2015-04-21

Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity.

Observation of the de Vries behavior in SmA* phase of a liquid crystal using polarised Raman scattering and infrared spectroscopy

NASA Astrophysics Data System (ADS)

Kocot, A.; Vij, J. K.; Perova, T. S.; Merkel, K.; Swaminathan, V.; Sreenilayam, S. P.; Yadav, N.; Panov, V. P.; Stevenson, P. J.; Panov, A.; Rodriguez-Lojo, D.

2017-09-01

Two approaches exist in the literature for describing the orientational distribution function (ODF) of the molecular directors in SmA* phase of liquid crystals, though several models are recently proposed in the literature for explaining the de Vries behaviour. These ODFs correspond to either the conventional unimodal arrangements of molecular directors arising from the mean field theory that leads to the broad or sugar-loaf like distribution or to the "diffuse-cone-shaped" type distribution proposed by de Vries. The hypothesis by de Vries provides for a realistic explanation as to how at a molecular level, a first-order SmA* to SmC* transition can occur where the uniform molecular director azimuthal distributions condense to values lying within a narrow range of angles; finally these condense to a single value while at the same time ensuring a little or no concomitant shrinkage in the layer spacing. The azimuthal distribution of the in-layer directors is probed using IR and polarized Raman spectroscopic techniques. The latter allows us to obtain the ODF and the various order parameters for the uniaxial and the biaxial phases. Based on the results of these measurements, we conclude that the "cone-shaped" (or volcano-shaped) de Vries type of distribution can most preferably describe SmA* where "a first-order phase transition from SmA* to SmC*" and a low layer shrinkage can both be easily explained.

An analysis of the kinetics of molecular response during the first trimester of treatment with nilotinib in newly diagnosed chronic myeloid leukemia patients in chronic phase.

PubMed

Steegmann, Juan Luis; Colomer, Dolors; Gómez-Casares, Maria-Teresa; García-Gutiérrez, Valentín; Ortí, Guillermo; Ramírez-Payer, Angel; Olavarria, Eduardo; Vall-Llovera, Ferrán; Giraldo, Pilar; Conde, Eulogio; Vallansot, Rolando; López-Lorenzo, Jose Luis; Palomera, Luis; Álvarez-Larrán, Alberto; Conesa, Venancio; Bautista, Guiomar; Casas, Laura; Giles, Frank; Hochhaus, Andreas; Casado-Montero, Luis Felipe

2017-10-01

This study was aimed to analyze the association of very early molecular response to nilotinib with the achievement of deep molecular response (MR4) at 18 months. We hypothesized that the BCR-ABL1 levels during the first 3 months of therapy, and the kinetics of their descent in this period, could be predictive of deep molecular response thereafter. This substudy of the ENEST1st trial included 60 patients with chronic myeloid leukemia in chronic phase treated with front-line nilotinib, and BCR-ABL1IS levels were measured using GUS as the control gene. The analysis included seven time points during the first trimester of treatment (baseline and fortnightly thereafter). The rates of MMR at 12 months, and of MR4 at 18 months (primary variable of the study), were 70 and 41%, respectively, similar to those obtained in the core study. BCR-ABL1IS ≤10% was achieved at 1, 1.5, 2 and 3 months in 50, 70, 83 and 93% of the patients, respectively. The observed shape of the BCR-ABL1IS descent was biphasic, with a faster slope during the first trimester and a median halving time (HT) of 11 days, the shortest reported in the literature. An HT ≤13 days was predictive of MMR at 12 months and MR4 at 18 months. The association of a shorter HT with response provides a rationale for exploring very early kinetics patterns in all patients treated with potent TKIs such as nilotinib.

Predictors of Dropout by Female Obese Patients Treated with a Group Cognitive Behavioral Therapy to Promote Weight Loss.

PubMed

Sawamoto, Ryoko; Nozaki, Takehiro; Furukawa, Tomokazu; Tanahashi, Tokusei; Morita, Chihiro; Hata, Tomokazu; Komaki, Gen; Sudo, Nobuyuki

2016-01-01

To investigate predictors of dropout from a group cognitive behavioral therapy (CBT) intervention for overweight or obese women. 119 overweight and obese Japanese women aged 25-65 years who attended an outpatient weight loss intervention were followed throughout the 7-month weight loss phase. Somatic characteristics, socioeconomic status, obesity-related diseases, diet and exercise habits, and psychological variables (depression, anxiety, self-esteem, alexithymia, parenting style, perfectionism, and eating attitude) were assessed at baseline. Significant variables, extracted by univariate statistical analysis, were then used as independent variables in a stepwise multiple logistic regression analysis with dropout as the dependent variable. 90 participants completed the weight loss phase, giving a dropout rate of 24.4%. The multiple logistic regression analysis demonstrated that compared to completers the dropouts had significantly stronger body shape concern, tended to not have jobs, perceived their mothers to be less caring, and were more disorganized in temperament. Of all these factors, the best predictor of dropout was shape concern. Shape concern, job condition, parenting care, and organization predicted dropout from the group CBT weight loss intervention for overweight or obese Japanese women. © 2016 S. Karger GmbH, Freiburg.

Predictors of Dropout by Female Obese Patients Treated with a Group Cognitive Behavioral Therapy to Promote Weight Loss

PubMed Central

Sawamoto, Ryoko; Nozaki, Takehiro; Furukawa, Tomokazu; Tanahashi, Tokusei; Morita, Chihiro; Hata, Tomokazu; Komaki, Gen; Sudo, Nobuyuki

2016-01-01

Objective To investigate predictors of dropout from a group cognitive behavioral therapy (CBT) intervention for overweight or obese women. Methods 119 overweight and obese Japanese women aged 25-65 years who attended an outpatient weight loss intervention were followed throughout the 7-month weight loss phase. Somatic characteristics, socioeconomic status, obesity-related diseases, diet and exercise habits, and psychological variables (depression, anxiety, self-esteem, alexithymia, parenting style, perfectionism, and eating attitude) were assessed at baseline. Significant variables, extracted by univariate statistical analysis, were then used as independent variables in a stepwise multiple logistic regression analysis with dropout as the dependent variable. Results 90 participants completed the weight loss phase, giving a dropout rate of 24.4%. The multiple logistic regression analysis demonstrated that compared to completers the dropouts had significantly stronger body shape concern, tended to not have jobs, perceived their mothers to be less caring, and were more disorganized in temperament. Of all these factors, the best predictor of dropout was shape concern. Conclusion Shape concern, job condition, parenting care, and organization predicted dropout from the group CBT weight loss intervention for overweight or obese Japanese women. PMID:26745715

Indian Craniometric Variability and Affinities

PubMed Central

Raghavan, Pathmanathan; Bulbeck, David; Pathmanathan, Gayathiri; Rathee, Suresh Kanta

2013-01-01

Recently published craniometric and genetic studies indicate a predominantly indigenous ancestry of Indian populations. We address this issue with a fuller coverage of Indian craniometrics than any done before. We analyse metrical variability within Indian series, Indians' sexual dimorphism, differences between northern and southern Indians, index-based differences of Indian males from other series, and Indians' multivariate affinities. The relationship between a variable's magnitude and its variability is log-linear. This relationship is strengthened by excluding cranial fractions and series with a sample size less than 30. Male crania are typically larger than female crania, but there are also shape differences. Northern Indians differ from southern Indians in various features including narrower orbits and less pronounced medial protrusion of the orbits. Indians resemble Veddas in having small crania and similar cranial shape. Indians' wider geographic affinities lie with “Caucasoid” populations to the northwest, particularly affecting northern Indians. The latter finding is confirmed from shape-based Mahalanobis-D distances calculated for the best sampled male and female series. Demonstration of a distinctive South Asian craniometric profile and the intermediate status of northern Indians between southern Indians and populations northwest of India confirm the predominantly indigenous ancestry of northern and especially southern Indians. PMID:24455409

Nottingham Prognostic Index Plus (NPI+): a modern clinical decision making tool in breast cancer.

PubMed

Rakha, E A; Soria, D; Green, A R; Lemetre, C; Powe, D G; Nolan, C C; Garibaldi, J M; Ball, G; Ellis, I O

2014-04-02

Current management of breast cancer (BC) relies on risk stratification based on well-defined clinicopathologic factors. Global gene expression profiling studies have demonstrated that BC comprises distinct molecular classes with clinical relevance. In this study, we hypothesised that molecular features of BC are a key driver of tumour behaviour and when coupled with a novel and bespoke application of established clinicopathologic prognostic variables can predict both clinical outcome and relevant therapeutic options more accurately than existing methods. In the current study, a comprehensive panel of biomarkers with relevance to BC was applied to a large and well-characterised series of BC, using immunohistochemistry and different multivariate clustering techniques, to identify the key molecular classes. Subsequently, each class was further stratified using a set of well-defined prognostic clinicopathologic variables. These variables were combined in formulae to prognostically stratify different molecular classes, collectively known as the Nottingham Prognostic Index Plus (NPI+). The NPI+ was then used to predict outcome in the different molecular classes. Seven core molecular classes were identified using a selective panel of 10 biomarkers. Incorporation of clinicopathologic variables in a second-stage analysis resulted in identification of distinct prognostic groups within each molecular class (NPI+). Outcome analysis showed that using the bespoke NPI formulae for each biological BC class provides improved patient outcome stratification superior to the traditional NPI. This study provides proof-of-principle evidence for the use of NPI+ in supporting improved individualised clinical decision making.

Combining computational chemistry and crystallography for a better understanding of the structure of cellulose

USDA-ARS?s Scientific Manuscript database

The approaches in this article seek to enhance understanding of cellulose at the molecular level, independent of the source and the particular crystalline form of cellulose. Four main areas of structure research are reviewed. Initially the molecular shape is inferred from the crystal structures of m...

Correlates across the Structural, Functional, and Molecular Phenotypes of Fragile X Syndrome

ERIC Educational Resources Information Center

Beckel-Mitchener, Andrea; Greenough, William T.

2004-01-01

Fragile X syndrome (FXS) is characterized by a pattern of morphological, functional, and molecular characteristics with, in at least some cases, apparent relationships among phenotypic features at different levels. Gross morphology differences in the sizes of some human brain regions are accompanied by fine structural alterations in the shapes and…

Fabrication of sophisticated two-dimensional organic nanoarchitectures thought hydrogen bond mediated molecular self assembly

NASA Astrophysics Data System (ADS)

Silly, Fabien

2012-02-01

Complex supramolecular two-dimensional (2D) networks are attracting considerable interest as highly ordered functional materials for applications in nanotechnology. The challenge consists in tailoring the ordering of one or more molecular species into specific architectures over an extended length scale with molecular precision. Highly organized supramolecular arrays can be obtained through self-assembly of complementary molecules which can interlock via intermolecular interactions. Molecules forming hydrogen bonds (H-bonds) are especially interesting building blocks for creating sophisticated organic architectures due to high selectivity and directionality of these bindings. We used scanning tunnelling microscopy to investigate at the atomic scale the formation of H-bonded 2D organic nanoarchitectures on surfaces. We mixed perylene derivatives having rectangular shape with melamine and DNA base having triangular and non symmetric shape respectively. We observe that molecule substituents play a key role in formation of the multicomponent H-bonded architectures. We show that the 2D self-assembly of these molecules can be tailored by adjusting the temperature and molecular ratio. We used these stimuli to successfully create numerous close-packed and porous 2D multicomponent structures.

Exploring the Molecular Growth of Two Gigantic Half‐Closed Polyoxometalate Clusters {Mo180} and {Mo130Ce6}

PubMed Central

Xuan, Weimin; Pow, Robert; Long, De‐Liang

2017-01-01

Abstract Understanding the process of the self‐assembly of gigantic polyoxometalates and their subsequent molecular growth, by the addition of capping moieties onto the oxo‐frameworks, is critical for the development of the designed assembly of complex high‐nuclearity cluster species, yet such processes remain far from being understood. Herein we describe the molecular growth from {Mo150} and {Mo120Ce6} to afford two half‐closed gigantic molybdenum blue clusters {Mo180} (1) and {Mo130Ce6} (2), respectively. Compound 1 features a hat‐shaped structure with the parent wheel‐shaped {Mo150} being capped by a {Mo30} unit on one side. Similarly, 2 exhibits an elliptical lanthanide‐doped wheel {Mo120Ce6} that is sealed by a {Mo10} unit on one side. Moreover, the observation of the parent uncapped {Mo150} and {Mo120Ce6} clusters as minor products during the synthesis of 1 and 2 strongly suggests that the molecular growth process can be initialized from {Mo150} and {Mo120Ce6} in solution, respectively. PMID:28508585

Effects of aging on the relationship between cognitive demand and step variability during dual-task walking.

PubMed

Decker, Leslie M; Cignetti, Fabien; Hunt, Nathaniel; Potter, Jane F; Stergiou, Nicholas; Studenski, Stephanie A

2016-08-01

A U-shaped relationship between cognitive demand and gait control may exist in dual-task situations, reflecting opposing effects of external focus of attention and attentional resource competition. The purpose of the study was twofold: to examine whether gait control, as evaluated from step-to-step variability, is related to cognitive task difficulty in a U-shaped manner and to determine whether age modifies this relationship. Young and older adults walked on a treadmill without attentional requirement and while performing a dichotic listening task under three attention conditions: non-forced (NF), forced-right (FR), and forced-left (FL). The conditions increased in their attentional demand and requirement for inhibitory control. Gait control was evaluated by the variability of step parameters related to balance control (step width) and rhythmic stepping pattern (step length and step time). A U-shaped relationship was found for step width variability in both young and older adults and for step time variability in older adults only. Cognitive performance during dual tasking was maintained in both young and older adults. The U-shaped relationship, which presumably results from a trade-off between an external focus of attention and competition for attentional resources, implies that higher-level cognitive processes are involved in walking in young and older adults. Specifically, while these processes are initially involved only in the control of (lateral) balance during gait, they become necessary for the control of (fore-aft) rhythmic stepping pattern in older adults, suggesting that attentional resources turn out to be needed in all facets of walking with aging. Finally, despite the cognitive resources required by walking, both young and older adults spontaneously adopted a "posture second" strategy, prioritizing the cognitive task over the gait task.

Emission control of InGaN nanocolumns grown by molecular-beam epitaxy on Si(111) substrates

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

Albert, S.; Bengoechea-Encabo, A.; Sanchez-Garcia, M. A.

This work studies the effect of the growth temperature on the morphology and emission characteristics of self-assembled InGaN nanocolumns grown by plasma assisted molecular beam epitaxy. Morphology changes are assessed by scanning electron microscopy, while emission is measured by photoluminescence. Within the growth temperature range of 750 to 650 deg. C, an increase in In incorporation for decreasing temperature is observed. This effect allows tailoring the InGaN nanocolumns emission line shape by using temperature gradients during growth. Depending on the gradient rate, span, and sign, broad emission line shapes are obtained, covering the yellow to green range, even yielding whitemore » emission.« less

Towards the identification of the loci of adaptive evolution

PubMed Central

Pardo-Diaz, Carolina; Salazar, Camilo; Jiggins, Chris D

2015-01-01

1. Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. 2. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability. In most cases, a combination of DNA, RNA and functional methodologies with field experiments will be needed to uncover the genes and mechanisms shaping adaptation in nature. PMID:25937885

Spin filter and molecular switch based on bowtie-shaped graphene nanoflake

NASA Astrophysics Data System (ADS)

Kang, Jun; Wu, Fengmin; Li, Jingbo

2012-11-01

The magnetic and transport properties of bowtie-shaped graphene nanoflake (BGNF) are investigated from first principles calculations. The eigen states of ferromagnetic (FM) BGNF near Fermi level are found to be delocalized over the whole flake, whereas those of antiferromagnetic (AFM) BGNF are localized in one side. The different characters result in different transport properties for FM and AFM BGNFs. FM BGNF exhibits perfect spin filtering effect and can serve as a spin filter. Moreover, the conductance of BGNF is much larger in FM state than in AFM state, thus BGNF can serve as a molecular switch. These results suggest that BGNF is a good candidate for future nanoelectronics.

A molecular heterojunction of zinc phthalocyanine and peanut-shaped fullerene polymer: A density functional study

NASA Astrophysics Data System (ADS)

Tanikawa, Kousei; Ohno, Kaoru; Noda, Yusuke; Ono, Shota; Kuwahara, Riichi; Takashima, Akito; Nakaya, Masato; Onoe, Jun

2017-10-01

We have performed first-principles density functional calculations of a molecular heterojunction of a zinc phthalocyanine (ZnPc) molecule and a peanut-shaped fullerene polymer (PSFP) made from several coalesced cross-linked C60 molecules. The PSFP has many isomers and all have both spatially localized (near ZnPc) and metallic conducting levels. Here we consider four typical isomers. From the resulting electronic structure, we discuss the applicability of these isomers to organic photovoltaics (OPV), electrodes, and light harvesting materials. If one of the isomers called T3, which has the largest energy gap, is used together with ZnPc for OPV, this system shows more than 20% energy conversion efficiency.

Highly Resolved Studies of Vacuum Ultraviolet Photoionization Dynamics

NASA Astrophysics Data System (ADS)

Kakar, Sandeep

We use measurements of dispersed fluorescence from electronically excited photoions to study fundamental aspects of intramolecular dynamics. Our experimental innovations make it possible to obtain highly resolved photoionization data that offer qualitative insights into molecular scattering. In particular, we obtain vibrationally resolved data to probe coupling between the electronic and nuclear degrees of freedom by studying the distribution of vibrational energy among photoions. Vibrationally resolved branching ratios are measured over a broad spectral range of excitation energy and their non-Franck-Condon behavior is used as a tool to investigate two diverse aspects of shape resonant photoionization. First, vibrational branching ratios are obtained for the SiF_4 5a _1^{-1} and CS_2 5sigma_{rm u} ^{-1} photoionization channels to help elucidate the microscopic aspects of shape resonant wavefunction for polyatomic molecules. It is shown that in such molecules the shape resonant wavefunction is not necessarily attributable to a specific bond in the molecule. Second, the multichannel aspect of shape resonant photoionization dynamics, reflected in continuum channel coupling, is investigated by obtaining vibrational branching ratios for the 2 sigma_{rm u}^{ -1} and 4sigma^{ -1} photoionization of the isoelectronic molecules N_2 and CO, respectively. These data indicate that effects of continuum coupling may be widespread. We also present the first set of rotationally resolved data over a wide energy range for the 2 sigma_{rm u}^{ -1} photoionization of N_2. These data probe the partitioning of the angular momentum between the photoelectron and photoion, and highlight the multicenter nature of the molecular potential. These case studies illustrate the utility of dispersed fluorescence measurements as a complement to photoelectron spectroscopy for obtaining highly resolved data for molecular photoionization. These measurements makes it possible to probe intrinsically molecular aspects, such as the vibration and rotation, of photoionization dynamics over an extended spectral range when used in conjunction with synchrotron radiation as the exciting source. Furthermore, the high resolution made possible by this technique provides high selectivity for accessing weaker ionization channels which are the ones strongly affected by resonant activity, and the present study repeatedly stresses the importance of this capability in discovering and deciphering new trends in resonant molecular ionization dynamics.

SHAPEMOL: a 3D code for calculating CO line emission in planetary and protoplanetary nebulae. Detailed model-fitting of the complex nebula NGC 6302

NASA Astrophysics Data System (ADS)

Santander-García, M.; Bujarrabal, V.; Koning, N.; Steffen, W.

2015-01-01

Context. Modern instrumentation in radioastronomy constitutes a valuable tool for studying the Universe: ALMA has reached unprecedented sensitivities and spatial resolution, while Herschel/HIFI has opened a new window (most of the sub-mm and far-infrared ranges are only accessible from space) for probing molecular warm gas (~50-1000 K). On the other hand, the software SHAPE has emerged in the past few years as a standard tool for determining the morphology and velocity field of different kinds of gaseous emission nebulae via spatio-kinematical modelling. Standard SHAPE implements radiative transfer solving, but it is only available for atomic species and not for molecules. Aims: Being aware of the growing importance of the development of tools for simplifying the analyses of molecular data from new-era observatories, we introduce the computer code shapemol, a complement to SHAPE, with which we intend to fill the so-far under-developed molecular niche. Methods: shapemol enables user-friendly, spatio-kinematic modelling with accurate non-LTE calculations of excitation and radiative transfer in CO lines. Currently, it allows radiative transfer solving in the 12CO and 13CO J = 1-0 to J = 17-16 lines, but its implementation permits easily extending the code to different transitions and other molecular species, either by the code developers or by the user. Used along SHAPE, shapemol allows easily generating synthetic maps to test against interferometric observations, as well as synthetic line profiles to match single-dish observations. Results: We give a full description of how shapemol works, and we discuss its limitations and the sources of uncertainty to be expected in the final synthetic profiles or maps. As an example of the power and versatility of shapemol, we build a model of the molecular envelope of the planetary nebula NGC 6302 and compare it with 12CO and 13CO J = 2-1 interferometric maps from SMA and high-J transitions from Herschel/HIFI. We find the molecular envelope to have a complex, broken ring-like structure with an inner, hotter region and several "fingers" and high-velocity blobs, emerging outwards from the plane of the ring. We derive a mass of 0.11 M⊙ for the molecular envelope. A copy of the code is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/573/A56

Beyond the bump-hunt: A game plan for discovering dynamical dark matter at the LHC

NASA Astrophysics Data System (ADS)

Dienes, Keith R.; Su, Shufang; Thomas, Brooks

2016-06-01

Dynamical Dark Matter (DDM) is an alternative framework for dark-matter physics in which an ensemble of individual constituent fields with a spectrum of masses, lifetimes, and cosmological abundances collectively constitute the dark-matter candidate, and in which the traditional notion of dark-matter stability is replaced by a balancing between lifetimes and abundances across the ensemble. In this talk, we discuss the prospects for distinguishing between DDM ensembles and traditional dark-matter candidates at hadron colliders - and in particular, at the upgraded LHC - via the analysis of event-shape distributions of kine-matic variables. We also examine the correlations between these kinematic variables and other relevant collider variables in order to assess how imposing cuts on these additional variables may distort - for better or worse - their event-shape distributions.

Design and analysis of variable-twist tiltrotor blades using shape memory alloy hybrid composites

NASA Astrophysics Data System (ADS)

Park, Jae-Sang; Kim, Seong-Hwan; Jung, Sung Nam; Lee, Myeong-Kyu

2011-01-01

The tiltrotor blade, or proprotor, acts as a rotor in the helicopter mode and as a propeller in the airplane mode. For a better performance, the proprotor should have different built-in twist distributions along the blade span, suitable for each operational mode. This paper proposes a new variable-twist proprotor concept that can adjust the built-in twist distribution for given flight modes. For a variable-twist control, the present proprotor adopts shape memory alloy hybrid composites (SMAHC) containing shape memory alloy (SMA) wires embedded in the composite matrix. The proprotor of the Korea Aerospace Research Institute (KARI) Smart Unmanned Aerial Vehicle (SUAV), which is based on the tiltrotor concept, is used as a baseline proprotor model. The cross-sectional properties of the variable-twist proprotor are designed to maintain the cross-sectional properties of the original proprotor as closely as possible. However, the torsion stiffness is significantly reduced to accommodate the variable-twist control. A nonlinear flexible multibody dynamic analysis is employed to investigate the dynamic characteristics of the proprotor such as natural frequency and damping in the whirl flutter mode, the blade structural loads in a transition flight and the rotor performance in hover. The numerical results show that the present proprotor is designed to have a strong similarity to the baseline proprotor in dynamic and load characteristics. It is demonstrated that the present proprotor concept could be used to improve the hover performance adaptively when the variable-twist control using the SMAHC is applied appropriately.

Hazard evaluation of ten organophosphorous insecticides against the midge, Chironomus riparius via QSAR

USGS Publications Warehouse

Landrum, Peter F.; Fisher, Susan W.; Hwang, Haejo; Hickey, James P.

1999-01-01

Toxicities of ten organophosphorus (OP) insecticides were measured against midge larvae (Chironomus riparius) under varying temperature (11, 18, and 25°C) and pH (6, 7, and 8) conditions and with and without sediment. Toxicity usually increased with increasing temperature and was greater in the absence of sediment. No trend was found with varying pH. A series of unidimensional parameters and multidimensional models were used to describe the changes in toxicity. Log Kow was able to explain about 40–60% of the variability in response data for aqueous exposures while molecular volume and aqueous solubility were less predictive. Likewise, the linear solvation energy relationship (LSER) model only explained 40–70% of the response variability, suggesting that factors other than solubility were most important for producing the observed response. Molecular connectivity was the most useful for describing the variability in the response. In the absence of sediment, 1χv and 3κ were best able to describe the variation in response among all compounds at each pH (70–90%). In the presence of sediment, even molecular connectivity could not describe the variability until the partitioning potential to sediment was accounted for by assuming equilibrium partitioning. After correcting for partitioning, the same molecular connectivity terms as in the aqueous exposures described most of the variability, 61–87%, except for the 11°C data where correlations were not significant. Molecular connectivity was a better tool than LSER or the unidimensional variables to explain the steric fitness of OP insecticides which was crucial to the toxicity.

Corallite wall and septal microstructure in scleractinian reef corals: comparison of molecular clades within the family Faviidae.

PubMed

Budd, Ann F; Stolarski, Jarosław

2011-01-01

Recent molecular phylogenies conflict with traditional scleractinian classification at ranks ranging from suborder to genus, challenging morphologists to discover new characters that better agree with molecular data. Such characters are essential for including fossils in analyses and tracing evolutionary patterns through geologic time. We examine the skeletal morphology of 36 species belonging to the traditional families Faviidae, Merulinidae, Pectiniidae, and Trachyphylliidae (3 Atlantic, 14 Indo-Pacific, 2 cosmopolitan genera) at the macromorphological, micromorphological, and microstructural levels. Molecular analyses indicate that the families are not monophyletic groups, but consist of six family-level clades, four of which are examined [clade XV = Diploastrea heliopora; clade XVI = Montastraea cavernosa; clade XVII ("Pacific faviids") = Pacific faviids (part) + merulinids (part) + pectiniids (part) + M. annularis complex; clade XXI ("Atlantic faviids") = Atlantic faviids (part) + Atlantic mussids]. Comparisons among molecular clades indicate that micromorphological and microstructural characters (singly and in combination) are clade diagnostic, but with two exceptions, macromorphologic characters are not. The septal teeth of "Atlantic faviids" are paddle-shaped (strong secondary calcification axes) or blocky, whereas the septal teeth of "Pacific faviids" are spine-shaped or multidirectional. Corallite walls in "Atlantic faviids" are usually septothecal, with occasional trabeculothecal elements; whereas corallite walls in "Pacific faviids" are usually trabeculothecal or parathecal or they contain abortive septa. Exceptions include subclades of "Pacific faviids" consisting of a) Caulastraea and Oulophyllia (strong secondary axes) and b) Cyphastrea (septothecal walls). Diploastrea has a diagnostic synapticulothecal wall and thick triangular teeth; Montastraea cavernosa is also distinct, possessing both "Pacific faviid" (abortive septa) and "Atlantic faviid" (paddle-shaped teeth) attributes. The development of secondary axes is similar in traditional Atlantic faviids and mussids, supporting molecular results placing them in the same clade. Subclades of "Pacific faviids" reveal differences in wall structure and the arrangement and distinctiveness of centers of rapid accretion. Copyright © 2010 Wiley-Liss, Inc.

Continuum Theory of Retroviral Capsids

NASA Astrophysics Data System (ADS)

Nguyen, T. T.; Bruinsma, R. F.; Gelbart, W. M.

2006-02-01

We present a self-assembly phase diagram for the shape of retroviral capsids, based on continuum elasticity theory. The spontaneous curvature of the capsid proteins drives a weakly first-order transition from spherical to spherocylindrical shapes. The conical capsid shape which characterizes the HIV-1 retrovirus is never stable under unconstrained energy minimization. Only under conditions of fixed volume and/or fixed spanning length can the conical shape be a minimum energy structure. Our results indicate that, unlike the capsids of small viruses, retrovirus capsids are not uniquely determined by the molecular structure of the constituent proteins but depend in an essential way on physical constraints present during assembly.

Evaluation of the correctness of the feed selection based on the analysis of chip's shape

NASA Astrophysics Data System (ADS)

Chodor, Jaroslaw; Kukielka, Leon; Kaldunski, Pawel; Bohdal, Lukasz; Patyk, Radoslaw; Kulakowska, Agnieszka

2018-05-01

For the experiment needs, the own experiment plan was developed. The researches were carried out to determine the effect of variable, small feed on the chip's shape. To provide orthogonal free cutting special specimens were prepared. Obtained chips were divided according to shapes and also scanned using a scanning electron microscope (SEM). Conclusions from the experiments were given.

Improving the accuracy of ultrafast ligand-based screening: incorporating lipophilicity into ElectroShape as an extra dimension.

PubMed

Armstrong, M Stuart; Finn, Paul W; Morris, Garrett M; Richards, W Graham

2011-08-01

In a previous paper, we presented the ElectroShape method, which we used to achieve successful ligand-based virtual screening. It extended classical shape-based methods by applying them to the four-dimensional shape of the molecule where partial charge was used as the fourth dimension to capture electrostatic information. This paper extends the approach by using atomic lipophilicity (alogP) as an additional molecular property and validates it using the improved release 2 of the Directory of Useful Decoys (DUD). When alogP replaced partial charge, the enrichment results were slightly below those of ElectroShape, though still far better than purely shape-based methods. However, when alogP was added as a complement to partial charge, the resulting five-dimensional enrichments shows a clear improvement in performance. This demonstrates the utility of extending the ElectroShape virtual screening method by adding other atom-based descriptors.

Highly conserved Z and molecularly diverged W chromosomes in the fish genus Triportheus (Characiformes, Triportheidae).

PubMed

Yano, C F; Bertollo, L A C; Ezaz, T; Trifonov, V; Sember, A; Liehr, T; Cioffi, M B

2017-03-01

The main objectives of this study were to test: (1) whether the W-chromosome differentiation matches to species' evolutionary divergence (phylogenetic concordance) and (2) whether sex chromosomes share a common ancestor within a congeneric group. The monophyletic genus Triportheus (Characiformes, Triportheidae) was the model group for this study. All species in this genus so far analyzed have ZW sex chromosome system, where the Z is always the largest chromosome of the karyotype, whereas the W chromosome is highly variable ranging from almost homomorphic to highly heteromorphic. We applied conventional and molecular cytogenetic approaches including C-banding, ribosomal DNA mapping, comparative genomic hybridization (CGH) and cross-species whole chromosome painting (WCP) to test our questions. We developed Z- and W-chromosome paints from T. auritus for cross-species WCP and performed CGH in a representative species (T. signatus) to decipher level of homologies and rates of differentiation of W chromosomes. Our study revealed that the ZW sex chromosome system had a common origin, showing highly conserved Z chromosomes and remarkably divergent W chromosomes. Notably, the W chromosomes have evolved to different shapes and sequence contents within ~15-25 Myr of divergence time. Such differentiation highlights a dynamic process of W-chromosome evolution within congeneric species of Triportheus.

Genome-wide evolutionary dynamics of influenza B viruses on a global scale

PubMed Central

Langat, Pinky; Bowden, Thomas A.; Edwards, Stephanie; Gall, Astrid; Rambaut, Andrew; Daniels, Rodney S.; Russell, Colin A.; Pybus, Oliver G.; McCauley, John

2017-01-01

The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally. PMID:29284042

Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates.

PubMed

Edelson, Benjamin S; Best, Timothy P; Olenyuk, Bogdan; Nickols, Nicholas G; Doss, Raymond M; Foister, Shane; Heckel, Alexander; Dervan, Peter B

2004-01-01

A pivotal step forward in chemical approaches to controlling gene expression is the development of sequence-specific DNA-binding molecules that can enter live cells and traffic to nuclei unaided. DNA-binding polyamides are a class of programmable, sequence-specific small molecules that have been shown to influence a wide variety of protein-DNA interactions. We have synthesized over 100 polyamide-fluorophore conjugates and assayed their nuclear uptake profiles in 13 mammalian cell lines. The compiled dataset, comprising 1300 entries, establishes a benchmark for the nuclear localization of polyamide-dye conjugates. Compounds in this series were chosen to provide systematic variation in several structural variables, including dye composition and placement, molecular weight, charge, ordering of the aromatic and aliphatic amino-acid building blocks and overall shape. Nuclear uptake does not appear to be correlated with polyamide molecular weight or with the number of imidazole residues, although the positions of imidazole residues affect nuclear access properties significantly. Generally negative determinants for nuclear access include the presence of a beta-Ala-tail residue and the lack of a cationic alkyl amine moiety, whereas the presence of an acetylated 2,4-diaminobutyric acid-turn is a positive factor for nuclear localization. We discuss implications of these data on the design of polyamide-dye conjugates for use in biological systems.

Molecular characterization and chromosomal distribution of Galileo, Kepler and Newton, three foldback transposable elements of the Drosophila buzzatii species complex.

PubMed

Casals, Ferran; Cáceres, Mario; Manfrin, Maura Helena; González, Josefa; Ruiz, Alfredo

2005-04-01

Galileo is a foldback transposable element that has been implicated in the generation of two polymorphic chromosomal inversions in Drosophila buzzatii. Analysis of the inversion breakpoints led to the discovery of two additional elements, called Kepler and Newton, sharing sequence and structural similarities with Galileo. Here, we describe in detail the molecular structure of these three elements, on the basis of the 13 copies found at the inversion breakpoints plus 10 additional copies isolated during this work. Similarly to the foldback elements described in other organisms, these elements have long inverted terminal repeats, which in the case of Galileo possess a complex structure and display a high degree of internal variability between copies. A phylogenetic tree built with their shared sequences shows that the three elements are closely related and diverged approximately 10 million years ago. We have also analyzed the abundance and chromosomal distribution of these elements in D. buzzatii and other species of the repleta group by Southern analysis and in situ hybridization. Overall, the results suggest that these foldback elements are present in all the buzzatti complex species and may have played an important role in shaping their genomes. In addition, we show that recombination rate is the main factor determining the chromosomal distribution of these elements.

Labeling and analysis of chicken taste buds using molecular markers in oral epithelial sheets

PubMed Central

Rajapaksha, Prasangi; Wang, Zhonghou; Venkatesan, Nandakumar; Tehrani, Kayvan F.; Payne, Jason; Swetenburg, Raymond L.; Kawabata, Fuminori; Tabata, Shoji; Mortensen, Luke J.; Stice, Steven L.; Beckstead, Robert; Liu, Hong-Xiang

2016-01-01

In chickens, the sensory organs for taste are the taste buds in the oral cavity, of which there are ~240–360 in total number as estimated by scanning electron microscopy (SEM). There is not an easy way to visualize all taste buds in chickens. Here, we report a highly efficient method for labeling chicken taste buds in oral epithelial sheets using the molecular markers Vimentin and α-Gustducin. Immediate tissue fixation following incubation with sub-epithelially injected proteases enabled us to peel off whole epithelial sheets, leaving the shape and integrity of the tissue intact. In the peeled epithelial sheets, taste buds labeled with antibodies against Vimentin and α-Gustducin were easily identified and counted under a light microscope and many more taste buds, patterned in rosette-like clusters, were found than previously reported with SEM. Broiler-type, female-line males have more taste buds than other groups and continue to increase the number of taste buds over stages after hatch. In addition to ovoid-shaped taste buds, big tube-shaped taste buds were observed in the chicken using 2-photon microscopy. Our protocol for labeling taste buds with molecular markers will factilitate future mechanistic studies on the development of chicken taste buds in association with their feeding behaviors. PMID:27853250

SHOCKED AND SCORCHED: THE TAIL OF A TADPOLE IN AN INTERSTELLAR POND

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

Sahai, R.; Morris, M. R.; Claussen, M. J., E-mail: raghvendra.sahai@jpl.nasa.gov

2012-05-20

We report multi-wavelength observations of the far-infrared source IRAS 20324+4057, including high-resolution optical imaging with the Hubble Space Telescope, and ground-based near-infrared, millimeter-wave and radio observations. These data show an extended, limb-brightened, tadpole-shaped nebula with a bright, compact, cometary nebula located inside the tadpole head. Our molecular line observations indicate that the Tadpole is predominantly molecular with a total gas mass exceeding 3.7 M{sub Sun }. Our radio continuum imaging and archival Spitzer IRAC images show the presence of additional tadpole-shaped objects in the vicinity of IRAS 20324+4057 that share a common east-west head-tail orientation: we propose that these structuresmore » are small, dense molecular cores that originated in the Cygnus cloud and are now being (1) photoevaporated by the ultraviolet radiation field of the Cyg OB2 No. 8 cluster located to the northwest; and (2) shaped by ram pressure of a distant wind source or sources located to the west, blowing ablated and photoevaporated material from their heads eastward. The ripples in the tail of the Tadpole are interpreted in terms of instabilities at the interface between the ambient wind and the dense medium of the former.« less

Labeling and analysis of chicken taste buds using molecular markers in oral epithelial sheets.

PubMed

Rajapaksha, Prasangi; Wang, Zhonghou; Venkatesan, Nandakumar; Tehrani, Kayvan F; Payne, Jason; Swetenburg, Raymond L; Kawabata, Fuminori; Tabata, Shoji; Mortensen, Luke J; Stice, Steven L; Beckstead, Robert; Liu, Hong-Xiang

2016-11-17

In chickens, the sensory organs for taste are the taste buds in the oral cavity, of which there are ~240-360 in total number as estimated by scanning electron microscopy (SEM). There is not an easy way to visualize all taste buds in chickens. Here, we report a highly efficient method for labeling chicken taste buds in oral epithelial sheets using the molecular markers Vimentin and α-Gustducin. Immediate tissue fixation following incubation with sub-epithelially injected proteases enabled us to peel off whole epithelial sheets, leaving the shape and integrity of the tissue intact. In the peeled epithelial sheets, taste buds labeled with antibodies against Vimentin and α-Gustducin were easily identified and counted under a light microscope and many more taste buds, patterned in rosette-like clusters, were found than previously reported with SEM. Broiler-type, female-line males have more taste buds than other groups and continue to increase the number of taste buds over stages after hatch. In addition to ovoid-shaped taste buds, big tube-shaped taste buds were observed in the chicken using 2-photon microscopy. Our protocol for labeling taste buds with molecular markers will factilitate future mechanistic studies on the development of chicken taste buds in association with their feeding behaviors.

Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning

PubMed Central

Mets, David G; Brainard, Michael S

2018-01-01

Abstract Background Vocal learning in songbirds has emerged as a powerful model for sensorimotor learning. Neurobehavioral studies of Bengalese finch (Lonchura striata domestica) song, naturally more variable and plastic than songs of other finch species, have demonstrated the importance of behavioral variability for initial learning, maintenance, and plasticity of vocalizations. However, the molecular and genetic underpinnings of this variability and the learning it supports are poorly understood. Findings To establish a platform for the molecular analysis of behavioral variability and plasticity, we generated an initial draft assembly of the Bengalese finch genome from a single male animal to 151× coverage and an N50 of 3.0 MB. Furthermore, we developed an initial set of gene models using RNA-seq data from 8 samples that comprise liver, muscle, cerebellum, brainstem/midbrain, and forebrain tissue from juvenile and adult Bengalese finches of both sexes. Conclusions We provide a draft Bengalese finch genome and gene annotation to facilitate the study of the molecular-genetic influences on behavioral variability and the process of vocal learning. These data will directly support many avenues for the identification of genes involved in learning, including differential expression analysis, comparative genomic analysis (through comparison to existing avian genome assemblies), and derivation of genetic maps for linkage analysis. Bengalese finch gene models and sequences will be essential for subsequent manipulation (molecular or genetic) of genes and gene products, enabling novel mechanistic investigations into the role of variability in learned behavior. PMID:29618046

Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning.

PubMed

Colquitt, Bradley M; Mets, David G; Brainard, Michael S

2018-03-01

Vocal learning in songbirds has emerged as a powerful model for sensorimotor learning. Neurobehavioral studies of Bengalese finch (Lonchura striata domestica) song, naturally more variable and plastic than songs of other finch species, have demonstrated the importance of behavioral variability for initial learning, maintenance, and plasticity of vocalizations. However, the molecular and genetic underpinnings of this variability and the learning it supports are poorly understood. To establish a platform for the molecular analysis of behavioral variability and plasticity, we generated an initial draft assembly of the Bengalese finch genome from a single male animal to 151× coverage and an N50 of 3.0 MB. Furthermore, we developed an initial set of gene models using RNA-seq data from 8 samples that comprise liver, muscle, cerebellum, brainstem/midbrain, and forebrain tissue from juvenile and adult Bengalese finches of both sexes. We provide a draft Bengalese finch genome and gene annotation to facilitate the study of the molecular-genetic influences on behavioral variability and the process of vocal learning. These data will directly support many avenues for the identification of genes involved in learning, including differential expression analysis, comparative genomic analysis (through comparison to existing avian genome assemblies), and derivation of genetic maps for linkage analysis. Bengalese finch gene models and sequences will be essential for subsequent manipulation (molecular or genetic) of genes and gene products, enabling novel mechanistic investigations into the role of variability in learned behavior.

Secondary School Students' Attitudes to Nanotechnology: What Are the Implications for Science Curriculum Development?

ERIC Educational Resources Information Center

Murcia, Karen

2013-01-01

Nanotechnology is guided by the assumption that with the ability to shape or re-shape at the molecular level, we could manipulate the physical world. Some speculate that this ability will be the beginning of the next technological revolution. Hence, an aim of secondary science education should be the development of scientifically literate citizens…

Modeling the preferred shapes of polyamine transporter ligands and dihydromotuporamine-C mimics: shovel versus hoe.

PubMed

Breitbeil, Fred; Kaur, Navneet; Delcros, Jean-Guy; Martin, Bénédicte; Abboud, Khalil A; Phanstiel, Otto

2006-04-20

Preferred conformers generated from motuporamine and anthracene-polyamine derivatives provided insight into the shapes associated with polyamine transporter (PAT) recognition and potentially dihydromotuporamine C (4a) bioactivity. Molecular modeling revealed that N(1)-(anthracen-9-ylmethyl)-3,3-triamine (6a), N(1)-(anthracen-9-ylmethyl)-4,4-triamine (6b), N(1)-(anthracen-9-ylmethyl)-N(1)-ethyl-3,3-triamine (7a), N(1)-(anthracen-9-ylmethyl)-N(1)-ethyl-4,4-triamine (7b), and 4a all preferred a hoe motif. This hoe shape was defined by the all-anti polyamine shaft extending above the relatively flat, appended ring system. The hoe geometry was also inferred by the (1)H NMR spectrum of the free amine of 7a (CDCl(3)), which showed a strong shielding effect of the anthracene ring on the chemical shifts associated with the appended polyamine chain. This shielding effect was found to be independent over a broad concentration range of 7a, which also supported an intramolecular phenomenon. The degree of substitution at the N(1)-position seems to be an important determinant of both the molecular shape preferences and biological activity of anthracenylmethyl-polyamine conjugates.

The Influence of Anion Shape on the Electrical Double Layer Microstructure and Capacitance of Ionic Liquids-Based Supercapacitors by Molecular Simulations.

PubMed

Chen, Ming; Li, Song; Feng, Guang

2017-02-16

Room-temperature ionic liquids (RTILs) are an emerging class of electrolytes for supercapacitors. In this work, we investigate the effects of different supercapacitor models and anion shape on the electrical double layers (EDLs) of two different RTILs: 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([Emim][Tf₂N]) and 1-ethyl-3-methylimidazolium 2-(cyano)pyrrolide ([Emim][CNPyr]) by molecular dynamics (MD) simulation. The EDL microstructure is represented by number densities of cations and anions, and the potential drop near neutral and charged electrodes reveal that the supercapacitor model with a single electrode has the same EDL structure as the model with two opposite electrodes. Nevertheless, the employment of the one-electrode model without tuning the bulk density of RTILs is more time-saving in contrast to the two-electrode one. With the one-electrode model, our simulation demonstrated that the shapes of anions significantly imposed effects on the microstructure of EDLs. The EDL differential capacitance vs. potential (C-V) curves of [Emim][CNPyr] electrolyte exhibit higher differential capacitance at positive potentials. The modeling study provides microscopic insight into the EDLs structure of RTILs with different anion shapes.

Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy

PubMed Central

2009-01-01

An important part of characterizing any protein molecule is to determine its size and shape. Sedimentation and gel filtration are hydrodynamic techniques that can be used for this medium resolution structural analysis. This review collects a number of simple calculations that are useful for thinking about protein structure at the nanometer level. Readers are reminded that the Perrin equation is generally not a valid approach to determine the shape of proteins. Instead, a simple guideline is presented, based on the measured sedimentation coefficient and a calculated maximum S, to estimate if a protein is globular or elongated. It is recalled that a gel filtration column fractionates proteins on the basis of their Stokes radius, not molecular weight. The molecular weight can be determined by combining gradient sedimentation and gel filtration, techniques available in most biochemistry laboratories, as originally proposed by Siegel and Monte. Finally, rotary shadowing and negative stain electron microscopy are powerful techniques for resolving the size and shape of single protein molecules and complexes at the nanometer level. A combination of hydrodynamics and electron microscopy is especially powerful. PMID:19495910

Multiblock thermoplastic polyurethanes for biomedical and shape memory applications

NASA Astrophysics Data System (ADS)

Gu, Xinzhu

Polyurethanes are a class of polymers that are capable of tailoring the overall polymer structure and thus final properties by many factors. The great potential in tailoring polymer structures imparts PUs unique mechanical properties and good cytocompatibility, which make them good candidates for many biomedical devices. In this dissertation, three families of multiblock thermoplastic polyurethanes are synthesized and characterized for biomedical and shape memory applications. In the first case described in Chapters 2, 3 and 4, a novel family of multiblock thermoplastic polyurethanes consisting of poly(ɛ-caprolactone) (PCL) and poly(ethylene glycol) (PEG) are presented. These materials were discovered to be very durable, with strain-to-break higher than 1200%. Heat-triggered reversible plasticity shape memory (RPSM) was observed, where the highly deformed samples completely recovered their as-cast shape within one minute when heating above the transition temperature. Instead of conventional "hard" blocks, entanglements, which result from high molecular weight, served as the physical crosslinks in this system, engendering shape recovery and preventing flow. Moreover, water-triggered shape memory effect of PCL-PEG TPUs is explored, wherein water permeated into the initially oriented PEG domains, causing rapid shape recovery toward the equilibrium shape upon contact with liquid water. The recovery behavior is found to be dependent on PEG weight percentage in the copolymers. By changing the material from bulk film to electrospun fibrous mat, recovery speed was greatly accelerated. The rate of water recovery was manipulated through structural variables, including thickness of bulk film and diameter of e-spun webs. A new, yet simple shape memory cycle, "wet-fixing" is also reported, where both the fixing and recovery ratios can be greatly improved. A detailed microstructural study on one particular composition is presented, revealing the evolution of microphase morphology during the shape memory cycle. Then, in Chapter 5, the role of Polyhedral oligosilsesquioxane (POSS) in suppressing enzymatic degradation of PCL-PEG TPUs is investigated. In vitro enzymatic hydrolytic biodegradation revealed that POSS incorporation significantly suppressed degradation of PCL-PEG TPUs. All TPUs were surface-eroded by enzymatic attack in which the chemical composition and the bulk mechanical properties exhibited little changes. A surface passivation mechanism is proposed to explain the protection of POSS-containing TPUs from enzymatic degradation. Finally, Chapter 6 presents another POSS-based TPUs system with PLA-based polyol as the glassy soft block. Manipulation of the final thermal and mechanical properties is discussed in terms of different polyols and POSS used. The free recovery and the constrained recovery responses of the polymer films were demonstrated as a function of the prior "fixing" deformation temperature. In addition, this family of materials was capable of memorizing their T g., where optimal recovery breadth and recovery stress were achieved when pre-deformation occurred right at Tg.

Body shape indices are predictors for estimating fat-free mass in male athletes

PubMed Central

Aoki, Toru; Komori, Daisuke; Oyamada, Kazuyuki; Murata, Kensuke; Fujita, Eiji; Akamine, Takuya; Urita, Yoshihisa; Yamamoto, Masayoshi

2018-01-01

It is unknown whether body size and body shape parameters can be predictors for estimating whole body fat-free mass (FFM) in male athletes. This study aimed to investigate whether body size and shape variables can be predictors for FFM in male athletes. Using a whole-body dual-energy X-ray absorptiometry scanner, whole body fat mass (FM) and FFM were determined in 132 male athletes and 14 sedentary males. The sample was divided into two groups: validation (N = 98) and cross-validation (N = 48) groups. Body height (BH), body mass (BM), and waist circumference at immediately above the iliac crest (W) were measured. BM-to-W and W-to-BH ratios were calculated as indices of body shapes. Stepwise multiple regression analysis revealed that BM/W and W/BH were selected as explainable variables for predicting FFM. The equation developed in the validation group was FFM (kg) = 0.883 × BM/W (kg/m) + 43.674 × W/BH (cm/cm)– 41.480 [R2 = 0.900, SEE (%SEE) = 2.3 kg (3.8%)], which was validated in the cross-validation group. Thus, the current results demonstrate that an equation using BM/W and W/BH as independent variables is applicable for predicting FFM in male athletes. PMID:29346452

A Simulation Study of Categorizing Continuous Exposure Variables Measured with Error in Autism Research: Small Changes with Large Effects.

PubMed

Heavner, Karyn; Burstyn, Igor

2015-08-24

Variation in the odds ratio (OR) resulting from selection of cutoffs for categorizing continuous variables is rarely discussed. We present results for the effect of varying cutoffs used to categorize a mismeasured exposure in a simulated population in the context of autism spectrum disorders research. Simulated cohorts were created with three distinct exposure-outcome curves and three measurement error variances for the exposure. ORs were calculated using logistic regression for 61 cutoffs (mean ± 3 standard deviations) used to dichotomize the observed exposure. ORs were calculated for five categories with a wide range for the cutoffs. For each scenario and cutoff, the OR, sensitivity, and specificity were calculated. The three exposure-outcome relationships had distinctly shaped OR (versus cutoff) curves, but increasing measurement error obscured the shape. At extreme cutoffs, there was non-monotonic oscillation in the ORs that cannot be attributed to "small numbers." Exposure misclassification following categorization of the mismeasured exposure was differential, as predicted by theory. Sensitivity was higher among cases and specificity among controls. Cutoffs chosen for categorizing continuous variables can have profound effects on study results. When measurement error is not too great, the shape of the OR curve may provide insight into the true shape of the exposure-disease relationship.

Graph Theoretical Representation of Atomic Asymmetry and Molecular Chirality of Benzenoids in Two-Dimensional Space

PubMed Central

Zhao, Tanfeng; Zhang, Qingyou; Long, Hailin; Xu, Lu

2014-01-01

In order to explore atomic asymmetry and molecular chirality in 2D space, benzenoids composed of 3 to 11 hexagons in 2D space were enumerated in our laboratory. These benzenoids are regarded as planar connected polyhexes and have no internal holes; that is, their internal regions are filled with hexagons. The produced dataset was composed of 357,968 benzenoids, including more than 14 million atoms. Rather than simply labeling the huge number of atoms as being either symmetric or asymmetric, this investigation aims at exploring a quantitative graph theoretical descriptor of atomic asymmetry. Based on the particular characteristics in the 2D plane, we suggested the weighted atomic sum as the descriptor of atomic asymmetry. This descriptor is measured by circulating around the molecule going in opposite directions. The investigation demonstrates that the weighted atomic sums are superior to the previously reported quantitative descriptor, atomic sums. The investigation of quantitative descriptors also reveals that the most asymmetric atom is in a structure with a spiral ring with the convex shape going in clockwise direction and concave shape going in anticlockwise direction from the atom. Based on weighted atomic sums, a weighted F index is introduced to quantitatively represent molecular chirality in the plane, rather than merely regarding benzenoids as being either chiral or achiral. By validating with enumerated benzenoids, the results indicate that the weighted F indexes were in accordance with their chiral classification (achiral or chiral) over the whole benzenoids dataset. Furthermore, weighted F indexes were superior to previously available descriptors. Benzenoids possess a variety of shapes and can be extended to practically represent any shape in 2D space—our proposed descriptor has thus the potential to be a general method to represent 2D molecular chirality based on the difference between clockwise and anticlockwise sums around a molecule. PMID:25032832

Blue Light-excited Light-Oxygen-Voltage-sensing Domain 2 (LOV2) Triggers a Rearrangement of the Kinase Domain to Induce Phosphorylation Activity in Arabidopsis Phototropin1.

PubMed

Oide, Mao; Okajima, Koji; Kashojiya, Sachiko; Takayama, Yuki; Oroguchi, Tomotaka; Hikima, Takaaki; Yamamoto, Masaki; Nakasako, Masayoshi

2016-09-16

Phototropin1 is a blue light (BL) receptor in plants and shows BL-dependent kinase activation. The BL-excited light-oxygen-voltage-sensing domain 2 (LOV2) is primarily responsible for the activation of the kinase domain; however, the molecular mechanism by which conformational changes in LOV2 are transmitted to the kinase domain remains unclear. Here, we investigated BL-induced structural changes of a minimum functional fragment of Arabidopsis phototropin1 composed of LOV2, the kinase domain, and a linker connecting the two domains using small-angle x-ray scattering (SAXS). The fragment existed as a dimer and displayed photoreversible SAXS changes reflected in the radii of gyration of 42.9 Å in the dark and 48.8 Å under BL irradiation. In the dark, the molecular shape reconstructed from the SAXS profiles appeared as two bean-shaped lobes in a twisted arrangement that was 170 Å long, 80 Å wide, and 50 Å thick. The molecular shape under BL became slightly elongated from that in the dark. By fitting the crystal structure of the LOV2 dimer and a homology model of the kinase domain to their inferred shapes, the BL-dependent change could be interpreted as the positional shift in the kinase domain relative to that of the LOV2 dimer. In addition, we found that lysine 475, a functionally important residue, in the N-terminal region of LOV2 plays a critical role in transmitting the structural changes in LOV2 to the kinase domain. The interface between the domains is critical for signaling, suitably changing the structure to activate the kinase in response to conformational changes in the adjoining LOV2. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Shape-dependent electronic properties of blue phosphorene nano-flakes

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

Bhatia, Pradeep; Swaroop, Ram; Kumar, Ashok, E-mail: ashok@cup.ac.in

In recent year’s considerable attention has been given to the first principles method for modifying and controlling electronic properties of nano-materials. We performed DFT-based calculations on the electronic properties of zigzag-edged nano-flakes of blue phosphorene with three possible shapes namely rectangular, triangular and hexagonal. We observed that HOMO-LUMO gap of zigzag phosphorene nano-flakes with different shapes is ∼2.9 eV with H-passivations and ∼0.7 – 1.2 eV in pristine cases. Electronic properties of blue phosphorene nano-flakes show the strong dependence on their shape. We observed that distributions of molecular orbitals were strongly affected by the different shapes. Zigzag edged considered nanostructuresmore » are non-magnetic and semiconducting in nature. The shape dependent electronic properties may find applications in tunable nano-electronics.« less

Early sound symbolism for vowel sounds.

PubMed

Spector, Ferrinne; Maurer, Daphne

2013-01-01

Children and adults consistently match some words (e.g., kiki) to jagged shapes and other words (e.g., bouba) to rounded shapes, providing evidence for non-arbitrary sound-shape mapping. In this study, we investigated the influence of vowels on sound-shape matching in toddlers, using four contrasting pairs of nonsense words differing in vowel sound (/i/ as in feet vs. /o/ as in boat) and four rounded-jagged shape pairs. Crucially, we used reduplicated syllables (e.g., kiki vs. koko) rather than confounding vowel sound with consonant context and syllable variability (e.g., kiki vs. bouba). Toddlers consistently matched words with /o/ to rounded shapes and words with /i/ to jagged shapes (p < 0.01). The results suggest that there may be naturally biased correspondences between vowel sound and shape.

Early sound symbolism for vowel sounds

PubMed Central

Spector, Ferrinne; Maurer, Daphne

2013-01-01

Children and adults consistently match some words (e.g., kiki) to jagged shapes and other words (e.g., bouba) to rounded shapes, providing evidence for non-arbitrary sound–shape mapping. In this study, we investigated the influence of vowels on sound–shape matching in toddlers, using four contrasting pairs of nonsense words differing in vowel sound (/i/ as in feet vs. /o/ as in boat) and four rounded–jagged shape pairs. Crucially, we used reduplicated syllables (e.g., kiki vs. koko) rather than confounding vowel sound with consonant context and syllable variability (e.g., kiki vs. bouba). Toddlers consistently matched words with /o/ to rounded shapes and words with /i/ to jagged shapes (p < 0.01). The results suggest that there may be naturally biased correspondences between vowel sound and shape. PMID:24349684

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.

Using tobacco mosaic virus to probe enhanced surface diffusion of molecular glasses.

PubMed

Zhang, Yue; Potter, Richard; Zhang, William; Fakhraai, Zahra

2016-11-09

Recent studies have shown that diffusion on the surface of organic glasses can be many orders of magnitude faster than bulk diffusion. Developing new probes that can readily measure surface diffusion can help study the effect of parameters such as chemical structure, intermolecular interaction, molecules' shape and size on the enhanced surface diffusion. In this study, we develop a novel probe that significantly simplifies these types of studies. Tobacco mosaic virus (TMV) is used as probe particle to measure surface diffusion coefficient of molecular glass N,N'-bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD). The evolution of the meniscus formed around TMV is probed as a function of time at various temperatures. TMV has a well-defined, mono-dispersed, cylindrical shape, with a large aspect-ratio (average diameter of 16.6 nm, length of 300 nm). As such, the shape of the meniscus around the center of TMV is semi-two dimensional, which compared to using a nanosphere as probe, increases the driving force for meniscus formation and simplifies the analysis of surface diffusion. We show that under these conditions, after a short transient time the shape of the meniscus is self-similar, allowing accurate determination of the surface diffusion coefficient. Measurements at various temperatures are then performed to investigate the temperature dependence of the surface diffusion coefficient. It is found that surface diffusion is greatly enhanced in TPD and has a lower activation barrier compared to the bulk counterpart. These observations are consistent with previous studies of surface diffusion on molecular glasses, demonstrating the accuracy of this method.

GaN nanowires with pentagon shape cross-section by ammonia-source molecular beam epitaxy

DOE PAGES

Lin, Yong; Leung, Benjamin; Li, Qiming; ...

2015-07-14

In this study, ammonia-based molecular beam epitaxy (NH 3-MBE) was used to grow catalyst-assisted GaN nanowires on (11¯02) r-plane sapphire substrates. Dislocation free [112¯0] oriented nanowires are formed with pentagon shape cross-section, instead of the usual triangular shape facet configuration. Specifically, the cross-section is the result of the additional two nonpolar {101¯0} side facets, which appear due to a decrease in relative growth rate of the {101¯0} facets to the {101¯1} and {101¯1} facets under the growth regime in NH 3-MBE. Compared to GaN nanowires grown by Ni-catalyzed metal–organic chemical vapor deposition, the NH 3-MBE grown GaN nanowires show moremore » than an order of magnitude increase in band-edge to yellow luminescence intensity ratio, as measured by cathodoluminescence, indicating improved microstructural and optical properties.« less

Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes

PubMed Central

Brangwynne, Clifford P.; Mitchison, Timothy J.; Hyman, Anthony A.

2011-01-01

For most intracellular structures with larger than molecular dimensions, little is known about the connection between underlying molecular activities and higher order organization such as size and shape. Here, we show that both the size and shape of the amphibian oocyte nucleolus ultimately arise because nucleoli behave as liquid-like droplets of RNA and protein, exhibiting characteristic viscous fluid dynamics even on timescales of < 1 min. We use these dynamics to determine an apparent nucleolar viscosity, and we show that this viscosity is ATP-dependent, suggesting a role for active processes in fluidizing internal contents. Nucleolar surface tension and fluidity cause their restructuring into spherical droplets upon imposed mechanical deformations. Nucleoli exhibit a broad distribution of sizes with a characteristic power law, which we show is a consequence of spontaneous coalescence events. These results have implications for the function of nucleoli in ribosome subunit processing and provide a physical link between activity within a macromolecular assembly and its physical properties on larger length scales. PMID:21368180

Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes.

PubMed

Brangwynne, Clifford P; Mitchison, Timothy J; Hyman, Anthony A

2011-03-15

For most intracellular structures with larger than molecular dimensions, little is known about the connection between underlying molecular activities and higher order organization such as size and shape. Here, we show that both the size and shape of the amphibian oocyte nucleolus ultimately arise because nucleoli behave as liquid-like droplets of RNA and protein, exhibiting characteristic viscous fluid dynamics even on timescales of < 1 min. We use these dynamics to determine an apparent nucleolar viscosity, and we show that this viscosity is ATP-dependent, suggesting a role for active processes in fluidizing internal contents. Nucleolar surface tension and fluidity cause their restructuring into spherical droplets upon imposed mechanical deformations. Nucleoli exhibit a broad distribution of sizes with a characteristic power law, which we show is a consequence of spontaneous coalescence events. These results have implications for the function of nucleoli in ribosome subunit processing and provide a physical link between activity within a macromolecular assembly and its physical properties on larger length scales.

Testing spatial uniformity of the CR spectrum in the local ISM with γ-ray observations

NASA Astrophysics Data System (ADS)

Prokhorov, D. A.; Colafrancesco, S.

2018-05-01

Gamma-ray observations of nearby radio-line-emitting gas structures in the interstellar medium allow us to probe the spectrum of cosmic rays (CRs). In this paper, we analysed Fermi Large Area Telescope (LAT) γ-ray observations of three such structures located near each other to check if their CR spectra are compatible with that of the CR background or might provide evidence for a population of "fresh" CRs. We found that the shape of the γ-ray spectrum in the Aquarius HI shell is consistent with the previously published stacked γ-ray spectrum of the Gould Belt molecular clouds. We also found that assumptions on the diffuse Galactic γ-ray background affect the spectral shapes of CRs derived in the R Coronae Australis and ρ Ophiuchi molecular clouds in which spectral deviations had previously been suggested. These two facts provide evidence to support the hypothesis of uniformity of the shapes of cosmic ray spectra in the local Galaxy environment.

Dynamic, mechanical integration between nucleus and cell- where physics meets biology.

PubMed

Dickinson, Richard B; Neelam, Srujana; Lele, Tanmay P

2015-01-01

Nuclear motions like rotation, translation and deformation suggest that the nucleus is acted upon by mechanical forces. Molecular linkages with the cytoskeleton are thought to transfer forces to the nuclear surface. We developed an approach to apply reproducible, known mechanical forces to the nucleus in spread adherent cells and quantified the elastic response of the mechanically integrated nucleus-cell. The method is sensitive to molecular perturbations and revealed new insight into the function of the LINC complex. While these experiments revealed elastic behaviors, turnover of the cytoskeleton by assembly/disassembly and binding/unbinding of linkages are expected to dissipate any stored mechanical energy in the nucleus or the cytoskeleton. Experiments investigating nuclear forces over longer time scales demonstrated the mechanical principle that expansive/compressive stresses on the nuclear surface arise from the movement of the cell boundaries to shape and position the nucleus. Such forces can shape the nucleus to conform to cell shapes during cell movements with or without myosin activity.

Dynamic, mechanical integration between nucleus and cell- where physics meets biology

PubMed Central

Dickinson, Richard B; Neelam, Srujana; Lele, Tanmay P

2015-01-01

Nuclear motions like rotation, translation and deformation suggest that the nucleus is acted upon by mechanical forces. Molecular linkages with the cytoskeleton are thought to transfer forces to the nuclear surface. We developed an approach to apply reproducible, known mechanical forces to the nucleus in spread adherent cells and quantified the elastic response of the mechanically integrated nucleus-cell. The method is sensitive to molecular perturbations and revealed new insight into the function of the LINC complex. While these experiments revealed elastic behaviors, turnover of the cytoskeleton by assembly/disassembly and binding/unbinding of linkages are expected to dissipate any stored mechanical energy in the nucleus or the cytoskeleton. Experiments investigating nuclear forces over longer time scales demonstrated the mechanical principle that expansive/compressive stresses on the nuclear surface arise from the movement of the cell boundaries to shape and position the nucleus. Such forces can shape the nucleus to conform to cell shapes during cell movements with or without myosin activity. PMID:26338356

Stabilizing detached Bridgman melt crystal growth: Model-based nonlinear feedback control

NASA Astrophysics Data System (ADS)

Yeckel, Andrew; Daoutidis, Prodromos; Derby, Jeffrey J.

2012-12-01

The dynamics and operability limits of a nonlinear-proportional-integral controller designed to stabilize detached vertical Bridgman crystal growth are studied. The manipulated variable is the pressure difference between upper and lower vapor spaces, and the controlled variable is the gap width at the triple-phase line. The controller consists of a model-based nonlinear component coupled with a standard proportional-integral controller. The nonlinear component is based on a capillary model of shape stability. Perturbations to gap width, pressure difference, wetting angle, and growth angle are studied under both shape stable and shape unstable conditions. The nonlinear-PI controller allows a wider operating range of gain than a standard PI controller used alone, is easier to tune, and eliminates solution multiplicity from closed-loop operation.

Comparative Molecular and Morphological Variation Analysis of Siderastrea (Anthozoa, Scleractinia) Reveals the Presence of Siderastrea stellata in the Gulf of Mexico.

PubMed

García, Norberto A Colín; Campos, Jorge E; Musi, José L Tello; Forsman, Zac H; Muñoz, Jorge L Montero; Reyes, Alejandro Monsalvo; González, Jesús E Arias

2017-02-01

The genus Siderastrea exhibits high levels of morphological variability. Some of its species share similar morphological characteristics with congeners, making their identification difficult. Siderastrea stellata has been reported as an intermediary of S. siderea and S. radians in the Brazilian reef ecosystem. In an earlier study conducted in Mexico, we detected Siderastrea colonies with morphological features that were not consistent with some siderastreid species previously reported in the Gulf of Mexico. Thus, we performed a combined morphological and molecular analysis to identify Siderastrea species boundaries from the Gulf of Mexico. Some colonies presented high morphologic variability, with characteristics that corresponded to Siderastrea stellata. Molecular analysis, using the nuclear ITS and ITS2 region, corroborated the morphological results, revealing low genetic variability between S. radians and S. stellata. Since the ITS sequences did not distinguish between Siderastrea species, we used the ITS2 region to differentiate S. stellata from S. radians. This is the first report of Siderastrea stellata and its variability in the Gulf of Mexico that is supported by morphological and molecular analyses.

Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms

PubMed Central

Emmons-Bell, Maya; Durant, Fallon; Hammelman, Jennifer; Bessonov, Nicholas; Volpert, Vitaly; Morokuma, Junji; Pinet, Kaylinnette; Adams, Dany S.; Pietak, Alexis; Lobo, Daniel; Levin, Michael

2015-01-01

The shape of an animal body plan is constructed from protein components encoded by the genome. However, bioelectric networks composed of many cell types have their own intrinsic dynamics, and can drive distinct morphological outcomes during embryogenesis and regeneration. Planarian flatworms are a popular system for exploring body plan patterning due to their regenerative capacity, but despite considerable molecular information regarding stem cell differentiation and basic axial patterning, very little is known about how distinct head shapes are produced. Here, we show that after decapitation in G. dorotocephala, a transient perturbation of physiological connectivity among cells (using the gap junction blocker octanol) can result in regenerated heads with quite different shapes, stochastically matching other known species of planaria (S. mediterranea, D. japonica, and P. felina). We use morphometric analysis to quantify the ability of physiological network perturbations to induce different species-specific head shapes from the same genome. Moreover, we present a computational agent-based model of cell and physical dynamics during regeneration that quantitatively reproduces the observed shape changes. Morphological alterations induced in a genomically wild-type G. dorotocephala during regeneration include not only the shape of the head but also the morphology of the brain, the characteristic distribution of adult stem cells (neoblasts), and the bioelectric gradients of resting potential within the anterior tissues. Interestingly, the shape change is not permanent; after regeneration is complete, intact animals remodel back to G. dorotocephala-appropriate head shape within several weeks in a secondary phase of remodeling following initial complete regeneration. We present a conceptual model to guide future work to delineate the molecular mechanisms by which bioelectric networks stochastically select among a small set of discrete head morphologies. Taken together, these data and analyses shed light on important physiological modifiers of morphological information in dictating species-specific shape, and reveal them to be a novel instructive input into head patterning in regenerating planaria. PMID:26610482

Variability of Grip Kinetics during Adult Signature Writing

PubMed Central

Ghali, Bassma; Thalanki Anantha, Nayanashri; Chan, Jennifer; Chau, Tom

2013-01-01

Grip kinetics and their variation are emerging as important considerations in the clinical assessment of handwriting pathologies, fine motor rehabilitation, biometrics, forensics and ergonomic pen design. This study evaluated the intra- and inter-participant variability of grip shape kinetics in adults during signature writing. Twenty (20) adult participants wrote on a digitizing tablet using an instrumented pen that measured the forces exerted on its barrel. Signature samples were collected over 10 days, 3 times a day, to capture temporal variations in grip shape kinetics. A kinetic topography (i.e., grip shape image) was derived per signature by time-averaging the measured force at each of 32 locations around the pen barrel. The normalized cross correlations (NCC) of grip shape images were calculated within- and between-participants. Several classification algorithms were implemented to gauge the error rate of participant discrimination based on grip shape kinetics. Four different grip shapes emerged and several participants made grip adjustments (change in grip shape or grip height) or rotated the pen during writing. Nonetheless, intra-participant variation in grip kinetics was generally much smaller than inter-participant force variations. Using the entire grip shape images as a 32-dimensional input feature vector, a K-nearest neighbor classifier achieved an error rate of % in discriminating among participants. These results indicate that writers had unique grip shape kinetics that were repeatable over time but distinct from those of other participants. The topographic analysis of grip kinetics may inform the development of personalized interventions or customizable grips in clinical and industrial applications, respectively. PMID:23658812

Variability of grip kinetics during adult signature writing.

PubMed

Ghali, Bassma; Thalanki Anantha, Nayanashri; Chan, Jennifer; Chau, Tom

2013-01-01

Grip kinetics and their variation are emerging as important considerations in the clinical assessment of handwriting pathologies, fine motor rehabilitation, biometrics, forensics and ergonomic pen design. This study evaluated the intra- and inter-participant variability of grip shape kinetics in adults during signature writing. Twenty (20) adult participants wrote on a digitizing tablet using an instrumented pen that measured the forces exerted on its barrel. Signature samples were collected over 10 days, 3 times a day, to capture temporal variations in grip shape kinetics. A kinetic topography (i.e., grip shape image) was derived per signature by time-averaging the measured force at each of 32 locations around the pen barrel. The normalized cross correlations (NCC) of grip shape images were calculated within- and between-participants. Several classification algorithms were implemented to gauge the error rate of participant discrimination based on grip shape kinetics. Four different grip shapes emerged and several participants made grip adjustments (change in grip shape or grip height) or rotated the pen during writing. Nonetheless, intra-participant variation in grip kinetics was generally much smaller than inter-participant force variations. Using the entire grip shape images as a 32-dimensional input feature vector, a K-nearest neighbor classifier achieved an error rate of 1.2±0.4% in discriminating among participants. These results indicate that writers had unique grip shape kinetics that were repeatable over time but distinct from those of other participants. The topographic analysis of grip kinetics may inform the development of personalized interventions or customizable grips in clinical and industrial applications, respectively.

Cullin 5: A Destabilizing Force for Some Oncogenes | Center for Cancer Research

Cancer.gov

Cancer can result when cellular processes such as proliferation and cell death go haywire. Among the many mechanisms in place to regulate these critical processes are molecular chaperones, which help proteins attain their proper functional shape and also regulate protein degradation through the cell’s recycling program, called the ubiquitin/proteasome system. One molecular

Origami: A Versatile Modeling System for Visualising Chemical Structure and Exploring Molecular Function

ERIC Educational Resources Information Center

Davis, James; Leslie, Ray; Billington, Susan; Slater, Peter R.

2010-01-01

The use of "Origami" is presented as an accessible and transferable modeling system through which to convey the intricacies of molecular shape and highlight structure-function relationships. The implementation of origami has been found to be a versatile alternative to conventional ball-and-stick models, possessing the key advantages of being both…

The Genetics of Canine Skull Shape Variation

PubMed Central

Schoenebeck, Jeffrey J.; Ostrander, Elaine A.

2013-01-01

A dog’s craniofacial diversity is the result of continual human intervention in natural selection, a process that began tens of thousands of years ago. To date, we know little of the genetic underpinnings and developmental mechanisms that make dog skulls so morphologically plastic. In this Perspectives, we discuss the origins of dog skull shapes in terms of history and biology and highlight recent advances in understanding the genetics of canine skull shapes. Of particular interest are those molecular genetic changes that are associated with the development of distinct breeds. PMID:23396475

Exploring possible relations between optical variability time scales and broad emission line shapes in AGN

NASA Astrophysics Data System (ADS)

Bon, Edi; Jovanović, Predrag; Marziani, Paola; Bon, Nataša; Otašević, Aleksandar

2018-06-01

Here we investigate the connection of broad emission line shapes and continuum light curve variability time scales of type-1 Active Galactic Nuclei (AGN). We developed a new model to describe optical broad emission lines as an accretion disk model of a line profile with additional ring emission. We connect ring radii with orbital time scales derived from optical light curves, and using Kepler's third law, we calculate mass of central supermassive black hole (SMBH). The obtained results for central black hole masses are in a good agreement with other methods. This indicates that the variability time scales of AGN may not be stochastic, but rather connected to the orbital time scales which depend on the central SMBH mass.

Effect analysis of design variables on the disc in a double-eccentric butterfly valve.

PubMed

Kang, Sangmo; Kim, Da-Eun; Kim, Kuk-Kyeom; Kim, Jun-Oh

2014-01-01

We have performed a shape optimization of the disc in an industrial double-eccentric butterfly valve using the effect analysis of design variables to enhance the valve performance. For the optimization, we select three performance quantities such as pressure drop, maximum stress, and mass (weight) as the responses and three dimensions regarding the disc shape as the design variables. Subsequently, we compose a layout of orthogonal array (L16) by performing numerical simulations on the flow and structure using a commercial package, ANSYS v13.0, and then make an effect analysis of the design variables on the responses using the design of experiments. Finally, we formulate a multiobjective function consisting of the three responses and then propose an optimal combination of the design variables to maximize the valve performance. Simulation results show that the disc thickness makes the most significant effect on the performance and the optimal design provides better performance than the initial design.

The Gavialis-Tomistoma debate: the contribution of skull ontogenetic allometry and growth trajectories to the study of crocodylian relationships.

PubMed

Piras, Paolo; Colangelo, Paolo; Adams, Dean C; Buscalioni, Angela; Cubo, Jorge; Kotsakis, Tassos; Meloro, Carlo; Raia, Pasquale

2010-01-01

The phylogenetic placement of Tomistoma and Gavialis crocodiles depends largely upon whether molecular or morphological data are utilized. Molecular analyses consider them as sister taxa, whereas morphological/paleontological analyses set Gavialis apart from Tomistoma and other crocodylian species. Here skull allometric trajectories of Tomistoma and Gavialis were contrasted with those of two longirostral crocodylian taxa, Crocodylus acutus and Mecistops cataphractus, to examine similarities in growth trajectories in light of this phylogenetic controversy. Entire skull shape and its two main modules, rostrum and postrostrum, were analyzed separately. We tested differences for both multivariate angles between trajectories and for shape differences at early and late stages of development. Based on a multivariate regression of shape data and size, Tomistoma seems to possess a peculiar rate of growth in comparison to the remaining taxa. However, its morphology at both juvenile and adult sizes is always closer to those of Brevirostres crocodylians, for the entire head shape, as well as the shape of the postrostrum and rostrum. By contrast, the allometric trajectory of Gavialis always begins and ends in a unique region of the multidimensional morphospace. These findings concur with a morphological hypothesis that places Gavialis separate from Brevirostres, and Tomistoma closer to other crocodylids, and provides an additional, and independent, data set to inform on this ongoing phylogenetic discussion. © 2010 Wiley Periodicals, Inc.

Identifying individuality and variability in team tactics by means of statistical shape analysis and multilayer perceptrons.

PubMed

Jäger, Jörg M; Schöllhorn, Wolfgang I

2012-04-01

Offensive and defensive systems of play represent important aspects of team sports. They include the players' positions at certain situations during a match, i.e., when players have to be on specific positions on the court. Patterns of play emerge based on the formations of the players on the court. Recognition of these patterns is important to react adequately and to adjust own strategies to the opponent. Furthermore, the ability to apply variable patterns of play seems to be promising since they make it harder for the opponent to adjust. The purpose of this study is to identify different team tactical patterns in volleyball and to analyze differences in variability. Overall 120 standard situations of six national teams in women's volleyball are analyzed during a world championship tournament. Twenty situations from each national team are chosen, including the base defence position (start configuration) and the two players block with middle back deep (end configuration). The shapes of the defence formations at the start and end configurations during the defence of each national team as well as the variability of these defence formations are statistically analyzed. Furthermore these shapes data are used to train multilayer perceptrons in order to test whether artificial neural networks can recognize the teams by their tactical patterns. Results show significant differences between the national teams in both the base defence position at the start and the two players block with middle back deep at the end of the standard defence situation. Furthermore, the national teams show significant differences in variability of the defence systems and start-positions are more variable than the end-positions. Multilayer perceptrons are able to recognize the teams at an average of 98.5%. It is concluded that defence systems in team sports are highly individual at a competitive level and variable even in standard situations. Artificial neural networks can be used to recognize teams by the shapes of the players' configurations. These findings support the concept that tactics and strategy have to be adapted for the team and need to be flexible in order to be successful. Copyright © 2010 Elsevier B.V. All rights reserved.

Formation of Ordered Arrays of Proteins on Surfaces

NASA Technical Reports Server (NTRS)

Lenhoff, A. M.

1996-01-01

Van der Waals (dispersion) forces contribute to interactions of proteins with other molecules or with surfaces, but because of the structural complexity of protein molecules, the magnitude of these effects is usually estimated based on idealized models of the molecular geometry, e.g., spheres or spheroids. The calculations reported here seek to account for both the geometric irregularity of protein molecules and the material properties of the interacting media. While the latter are found to fall in the generally accepted range, the molecular shape is shown to cause the magnitudes of the interactions to differ significantly from those calculated using idealized models, with important consequences. First, the roughness of the molecular surface leads to much lower average interaction energies for both protein-protein and protein-surface cases relative to calculations in which the protein molecule is approximated as a sphere. These results indicate that a form of steric stabilization may be an important effect in protein solutions. Underlying this behavior is appreciable orientational dependence, one reflection of which is that molecules of complementary shape are found to exhibit very strong attractive dispersion interactions. Although this has been widely discussed previously in the context of molecular recognition processes, the broader implications of these phenomena may also be important at larger molecular separations, e.g., in the dynamics of aggregation, precipitation and crystal growth.

Van der Waals Interactions Involving Proteins

NASA Technical Reports Server (NTRS)

Roth, Charles M.; Neal, Brian L.; Lenhoff, Abraham M.

1996-01-01

Van der Waals (dispersion) forces contribute to interactions of proteins with other molecules or with surfaces, but because of the structural complexity of protein molecules, the magnitude of these effects is usually estimated based on idealized models of the molecular geometry, e.g., spheres or spheroids. The calculations reported here seek to account for both the geometric irregularity of protein molecules and the material properties of the interacting media. Whereas the latter are found to fall in the generally accepted range, the molecular shape is shown to cause the magnitudes of the interactions to differ significantly from those calculated using idealized models. with important consequences. First, the roughness of the molecular surface leads to much lower average interaction energies for both protein-protein and protein-surface cases relative to calculations in which the protein molecule is approximated as a sphere. These results indicate that a form of steric stabilization may be an important effect in protein solutions. Underlying this behavior is appreciable orientational dependence, one reflection of which is that molecules of complementary shape are found to exhibit very strong attractive dispersion interactions. Although this has been widely discussed previously in the context of molecular recognition processes, the broader implications of these phenomena may also be important at larger molecular separations, e.g., in the dynamics of aggregation, precipitation, and crystal growth.

Axially adjustable magnetic properties in arrays of multilayered Ni/Cu nanowires with variable segment sizes

NASA Astrophysics Data System (ADS)

Shirazi Tehrani, A.; Almasi Kashi, M.; Ramazani, A.; Montazer, A. H.

2016-07-01

Arrays of multilayered Ni/Cu nanowires (NWs) with variable segment sizes were fabricated into anodic aluminum oxide templates using a pulsed electrodeposition method in a single bath for designated potential pulse times. Increasing the pulse time between 0.125 and 2 s in the electrodeposition of Ni enabled the formation of segments with thicknesses ranging from 25 to 280 nm and 10-110 nm in 42 and 65 nm diameter NWs, respectively, leading to disk-shaped, rod-shaped and/or near wire-shaped geometries. Using hysteresis loop measurements at room temperature, the axial and perpendicular magnetic properties were investigated. Regardless of the segment geometry, the axial coercivity and squareness significantly increased with increasing Ni segment thickness, in agreement with a decrease in calculated demagnetizing factors along the NW length. On the contrary, the perpendicular magnetic properties were found to be independent of the pulse times, indicating a competition between the intrawire interactions and the shape demagnetizing field.

Moderators of the Association Between Exercise Identity and Obligatory Exercise Among Participants of an Athletic Event

PubMed Central

Karr, Trisha M.; Zunker, Christie; Thompson, Ron A.; Sherman, Roberta; Erickson, Ann; Cao, Li; Crosby, Ross D.; Mitchell, James E.

2012-01-01

Previous research has connected exercise identity with obligatory exercise, yet to date no empirical studies have identified moderator variables of this association. The current study included participants of an athletic event (full marathon, n = 582; half marathon, n = 1,106; shorter distance, n = 733) who completed questionnaires about exercise behaviors, obligatory exercise, and internalization of both the thin-ideal and athletic-ideal body shapes. General linear model analyses were conducted to examine the exercise identity-obligatory exercise relationship; moderator variables included gender, internalization of the thin-ideal body shape, and internalization of the athletic-ideal body shape. After controlling for the effects of body mass index, age, and distance group, the three-way interaction of exercise identity, gender, and internalization of the athletic-ideal body shape predicted obligatory exercise. Findings suggest that women who report high identification with exercise and high value on having an athletic physique may be vulnerable to obligatory exercise. PMID:23092850

Using collective variables to drive molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme

2013-12-01

A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.

How to Build a Bacterial Cell: MreB as the Foreman of E. coli Construction.

PubMed

Shi, Handuo; Bratton, Benjamin P; Gitai, Zemer; Huang, Kerwyn Casey

2018-03-08

Cell shape matters across the kingdoms of life, and cells have the remarkable capacity to define and maintain specific shapes and sizes. But how are the shapes of micron-sized cells determined from the coordinated activities of nanometer-sized proteins? Here, we review general principles that have surfaced through the study of rod-shaped bacterial growth. Imaging approaches have revealed that polymers of the actin homolog MreB play a central role. MreB both senses and changes cell shape, thereby generating a self-organizing feedback system for shape maintenance. At the molecular level, structural and computational studies indicate that MreB filaments exhibit tunable mechanical properties that explain their preference for certain geometries and orientations along the cylindrical cell body. We illustrate the regulatory landscape of rod-shape formation and the connectivity between cell shape, cell growth, and other aspects of cell physiology. These discoveries provide a framework for future investigations into the architecture and construction of microbes. Copyright © 2018 Elsevier Inc. All rights reserved.

Association of incident symptomatic hip osteoarthritis with differences in hip shape by active shape modeling: the Johnston County Osteoarthritis Project.

PubMed

Nelson, Amanda E; Liu, Felix; Lynch, John A; Renner, Jordan B; Schwartz, Todd A; Lane, Nancy E; Jordan, Joanne M

2014-01-01

To investigate hip shape by active shape modeling (ASM) as a potential predictor of incident radiographic hip osteoarthritis (RHOA) and symptomatic hip osteoarthritis (SRHOA). All hips developing RHOA from baseline (Kellgren/Lawrence [K/L] grade 0/1) to mean 6-year followup (K/L grade ≥2, 190 hips) and 1:1 control hips (K/L grade 0/1 at both times, 192 hips) were included. Proximal femur shape was defined on baseline anteroposterior pelvis radiographs and submitted to ASM, producing a mean shape and continuous variables representing independent modes of shape variation. Mode scores (n = 14, explaining 95% of shape variance) were simultaneously included in logistic regression models with incident RHOA and SRHOA as dependent variables, adjusted for intraperson correlations, sex, race, body mass index (BMI), baseline K/L grade, and/or symptoms. We evaluated 382 hips from 342 individuals: 61% women and 83% white, with mean age 62 years and mean BMI 29 kg/m(2) . Several modes differed by sex and race, but no modes were associated with incident RHOA overall. Among men only, modes 1 and 2 were significantly associated (for a 1-SD decrease in mode 1 score: odds ratio [OR] 1.7 [95% confidence interval (95% CI) 1.1-2.5] and for a 1-SD increase in mode 2 score: OR 1.5 [95% CI 1.0-2.2]) with incident RHOA. A 1-SD decrease in mode 2 or 3 score increased the odds of SRHOA by 50%. This study confirms other reports that variations in proximal femur shape have a modest association with incident hip OA. The observation of proximal femur shape associations with hip symptoms requires further investigation. Copyright © 2014 by the American College of Rheumatology.

Body shape analyses of large persons in South Korea.

PubMed

Park, Woojin; Park, Sungjoon

2013-01-01

Despite the prevalence of obesity and overweight, anthropometric characteristics of large individuals have not been extensively studied. This study investigated body shapes of large persons (Broca index ≥ 20, BMI ≥ 25 or WHR>1.0) using stature-normalised body dimensions data from the latest South Korean anthropometric survey. For each sex, a factor analysis was performed on the anthropometric data set to identify the key factors that explain the shape variability; and then, a cluster analysis was conducted on the factor scores data to determine a set of representative body types. The body types were labelled in terms of their distinct shape characteristics and their relative frequencies were computed for each of the four age groups considered: the 10s, 20s-30s, 40s-50s and 60s. The study findings may facilitate creating artefacts that anthropometrically accommodate large individuals, developing digital human models of large persons and designing future ergonomics studies on largeness. This study investigated body shapes of large persons using anthropometric data from South Korea. For each sex, multivariate statistical analyses were conducted to identify the key factors of the body shape variability and determine the representative body types. The study findings may facilitate designing artefacts that anthropometrically accommodate large persons.

Drugs meeting the molecular basis of diabetic kidney disease: bridging from molecular mechanism to personalized medicine.

PubMed

Lambers Heerspink, Hiddo J; Oberbauer, Rainer; Perco, Paul; Heinzel, Andreas; Heinze, Georg; Mayer, Gert; Mayer, Bernd

2015-08-01

Diabetic kidney disease (DKD) is a complex, multifactorial disease and is associated with a high risk of renal and cardiovascular morbidity and mortality. Clinical practice guidelines for diabetes recommend essentially identical treatments for all patients without taking into account how the individual responds to the instituted therapy. Yet, individuals vary widely in how they respond to medications and therefore optimal therapy differs between individuals. Understanding the underlying molecular mechanisms of variability in drug response will help tailor optimal therapy. Polymorphisms in genes related to drug pharmacokinetics have been used to explore mechanisms of response variability in DKD, but with limited success. The complex interaction between genetic make-up and environmental factors on the abundance of proteins and metabolites renders pharmacogenomics alone insufficient to fully capture response variability. A complementary approach is to attribute drug response variability to individual variability in underlying molecular mechanisms involved in the progression of disease. The interplay of different processes (e.g. inflammation, fibrosis, angiogenesis, oxidative stress) appears to drive disease progression, but the individual contribution of each process varies. Drugs at the other hand address specific targets and thereby interfere in certain disease-associated processes. At this level, biomarkers may help to gain insight into which specific pathophysiological processes are involved in an individual followed by a rational assessment whether a specific drug's mode of action indeed targets the relevant process at hand. This article describes the conceptual background and data-driven workflow developed by the SysKid consortium aimed at improving characterization of the molecular mechanisms underlying DKD at the interference of the molecular impact of individual drugs in order to tailor optimal therapy to individual patients. © The Author 2015. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

Effects of Unpredictable Variable Prenatal Stress (UVPS) on Bdnf DNA Methylation and Telomere Length in the Adult Rat Brain

NASA Technical Reports Server (NTRS)

Blaze, Jennifer; Asok, A.; Moyer, E. L.; Roth, T. L.; Ronca, A. E.

2015-01-01

In utero exposure to stress can shape neurobiological and behavioral outcomes in offspring, producing vulnerability to psychopathology later in life. Animal models of prenatal stress likewise have demonstrated long-­-term alterations in brain function and behavioral deficits in offspring. For example, using a rodent model of unpredictable variable prenatal stress (UVPS), in which dams are exposed to unpredictable, variable stress across pregnancy, we have found increased body weight and anxiety-­-like behavior in adult male, but not female, offspring. DNA methylation (addition of methyl groups to cytosines which normally represses gene transcription) and changes in telomere length (TTAGGG repeats on the ends of chromosomes) are two molecular modifications that result from stress and could be responsible for the long-­-term effects of UVPS. Here, we measured methylation of brain-­-derived neurotrophic factor (bdnf), a gene important in development and plasticity, and telomere length in the brains of adult offspring from the UVPS model. Results indicate that prenatally stressed adult males have greater methylation in the medial prefrontal cortex (mPFC) compared to non-­-stressed controls, while females have greater methylation in the ventral hippocampus compared to controls. Further, prenatally stressed males had shorter telomeres than controls in the mPFC. These findings demonstrate the ability of UVPS to produce epigenetic alterations and changes in telomere length across behaviorally-­-relevant brain regions, which may have linkages to the phenotypic outcomes.

Color visualization for fluid flow prediction

NASA Technical Reports Server (NTRS)

Smith, R. E.; Speray, D. E.

1982-01-01

High-resolution raster scan color graphics allow variables to be presented as a continuum, in a color-coded picture that is referenced to a geometry such as a flow field grid or a boundary surface. Software is used to map a scalar variable such as pressure or temperature, defined on a two-dimensional slice of a flow field. The geometric shape is preserved in the resulting picture, and the relative magnitude of the variable is color-coded onto the geometric shape. The primary numerical process for color coding is an efficient search along a raster scan line to locate the quadrilteral block in the grid that bounds each pixel on the line. Tension spline interpolation is performed relative to the grid for specific values of the scalar variable, which is then color coded. When all pixels for the field of view are color-defined, a picture is played back from a memory device onto a television screen.

Predictive variables for the biological behaviour of basal cell carcinoma of the face: relevance of morphometry of the nuclei.

PubMed

Appel, T; Bierhoff, E; Appel, K; von Lindern, J-J; Bergé, S; Niederhagen, B

2003-06-01

We did a morphometric analysis of 130 histological sections of basal cell carcinoma (BCC) of the face to find out whether morphometric variables in the structure of the nuclei of BCC cells could serve as predictors of the biological behaviour. We considered the following variables: maximum and minimum diameters, perimeter, nuclear area and five form factors that characterise and quantify the shape of a structure (axis ratio, shape factor, nuclear contour index, nuclear roundness and circumference ratio). We did a statistical analysis of primary and recurring tumours and four histology-based groups (multifocal superficial BCCs, nodular BCCs, sclerosing BCCs and miscellaneous forms) using a two-sided t test for independent samples. Multifocal superficial BCCs showed significantly smaller values for the directly measured variables (maximum and minimum diameters, perimeter and nuclear area). Morphometry could not distinguish between primary and recurring tumours.

Research on damping properties optimization of variable-stiffness plate

NASA Astrophysics Data System (ADS)

Wen-kai, QI; Xian-tao, YIN; Cheng, SHEN

2016-09-01

This paper investigates damping optimization design of variable-stiffness composite laminated plate, which means fibre paths can be continuously curved and fibre angles are distinct for different regions. First, damping prediction model is developed based on modal dissipative energy principle and verified by comparing with modal testing results. Then, instead of fibre angles, the element stiffness and damping matrixes are translated to be design variables on the basis of novel Discrete Material Optimization (DMO) formulation, thus reducing the computation time greatly. Finally, the modal damping capacity of arbitrary order is optimized using MMA (Method of Moving Asymptotes) method. Meanwhile, mode tracking technique is employed to investigate the variation of modal shape. The convergent performance of interpolation function, first order specific damping capacity (SDC) optimization results and variation of modal shape in different penalty factor are discussed. The results show that the damping properties of the variable-stiffness plate can be increased by 50%-70% after optimization.

Common developmental pathways link tooth shape to regeneration

PubMed Central

Fraser, Gareth J.; Bloomquist, Ryan F.; Streelman, J. Todd

2013-01-01

In many non-mammalian vertebrates, adult dentitions result from cyclical rounds of tooth regeneration wherein simple unicuspid teeth are replaced by more complex forms. Therefore and by contrast to mammalian models, the numerical majority of vertebrate teeth develop shape during the process of replacement. Here, we exploit the dental diversity of Lake Malawi cichlid fishes to ask how vertebrates generally replace their dentition and in turn how this process acts to influence resulting tooth morphologies. First, we used immunohistochemistry to chart organogenesis of continually replacing cichlid teeth and discovered an epithelial down-growth that initiates the replacement cycle via a labial proliferation bias. Next, we identified sets of co-expressed genes from common pathways active during de novo, lifelong tooth replacement and tooth morphogenesis. Of note, we found two distinct epithelial cell populations, expressing markers of dental competence and cell potency, which may be responsible for tooth regeneration. Related gene sets were simultaneously active in putative signaling centers associated with the differentiation of replacement teeth with complex shapes. Finally, we manipulated targeted pathways (BMP, FGF, Hh, Notch, Wnt/β-catenin) in vivo with small molecules and demonstrated dose-dependent effects on both tooth replacement and tooth shape. Our data suggest that the processes of tooth regeneration and tooth shape morphogenesis are integrated via a common set of molecular signals. This linkage has subsequently been lost or decoupled in mammalian dentitions where complex tooth shapes develop in first generation dentitions that lack the capacity for lifelong replacement. Our dissection of the molecular mechanics of vertebrate tooth replacement coupled to complex shape pinpoints aspects of odontogenesis that might be re-evolved in the lab to solve problems in regenerative dentistry. PMID:23422830

Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables

NASA Astrophysics Data System (ADS)

Hashemian, Behrooz; Millán, Daniel; Arroyo, Marino

2013-12-01

Collective variables (CVs) are low-dimensional representations of the state of a complex system, which help us rationalize molecular conformations and sample free energy landscapes with molecular dynamics simulations. Given their importance, there is need for systematic methods that effectively identify CVs for complex systems. In recent years, nonlinear manifold learning has shown its ability to automatically characterize molecular collective behavior. Unfortunately, these methods fail to provide a differentiable function mapping high-dimensional configurations to their low-dimensional representation, as required in enhanced sampling methods. We introduce a methodology that, starting from an ensemble representative of molecular flexibility, builds smooth and nonlinear data-driven collective variables (SandCV) from the output of nonlinear manifold learning algorithms. We demonstrate the method with a standard benchmark molecule, alanine dipeptide, and show how it can be non-intrusively combined with off-the-shelf enhanced sampling methods, here the adaptive biasing force method. We illustrate how enhanced sampling simulations with SandCV can explore regions that were poorly sampled in the original molecular ensemble. We further explore the transferability of SandCV from a simpler system, alanine dipeptide in vacuum, to a more complex system, alanine dipeptide in explicit water.

Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables.

PubMed

Hashemian, Behrooz; Millán, Daniel; Arroyo, Marino

2013-12-07

Collective variables (CVs) are low-dimensional representations of the state of a complex system, which help us rationalize molecular conformations and sample free energy landscapes with molecular dynamics simulations. Given their importance, there is need for systematic methods that effectively identify CVs for complex systems. In recent years, nonlinear manifold learning has shown its ability to automatically characterize molecular collective behavior. Unfortunately, these methods fail to provide a differentiable function mapping high-dimensional configurations to their low-dimensional representation, as required in enhanced sampling methods. We introduce a methodology that, starting from an ensemble representative of molecular flexibility, builds smooth and nonlinear data-driven collective variables (SandCV) from the output of nonlinear manifold learning algorithms. We demonstrate the method with a standard benchmark molecule, alanine dipeptide, and show how it can be non-intrusively combined with off-the-shelf enhanced sampling methods, here the adaptive biasing force method. We illustrate how enhanced sampling simulations with SandCV can explore regions that were poorly sampled in the original molecular ensemble. We further explore the transferability of SandCV from a simpler system, alanine dipeptide in vacuum, to a more complex system, alanine dipeptide in explicit water.

Jig-Shape Optimization of a Low-Boom Supersonic Aircraft

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi

2018-01-01

A simple approach for optimizing the jig-shape is proposed in this study. This simple approach is based on an unconstrained optimization problem and applied to a low-boom supersonic aircraft. In this study, the jig-shape optimization is performed using the two-step approach. First, starting design variables are computed using the least-squares surface fitting technique. Next, the jig-shape is further tuned using a numerical optimization procedure based on an in-house object-oriented optimization tool. During the numerical optimization procedure, a design jig-shape is determined by the baseline jig-shape and basis functions. A total of 12 symmetric mode shapes of the cruise-weight configuration, rigid pitch shape, rigid left and right stabilator rotation shapes, and a residual shape are selected as sixteen basis functions. After three optimization runs, the trim shape error distribution is improved, and the maximum trim shape error of 0.9844 inches of the starting configuration becomes 0.00367 inch by the end of the third optimization run.

Quantitative scanning thermal microscopy of ErAs/GaAs superlattice structures grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Park, K. W.; Nair, H. P.; Crook, A. M.; Bank, S. R.; Yu, E. T.

2013-02-01

A proximal probe-based quantitative measurement of thermal conductivity with ˜100-150 nm lateral and vertical spatial resolution has been implemented. Measurements on an ErAs/GaAs superlattice structure grown by molecular beam epitaxy with 3% volumetric ErAs content yielded thermal conductivity at room temperature of 9 ± 2 W/m K, approximately five times lower than that for GaAs. Numerical modeling of phonon scattering by ErAs nanoparticles yielded thermal conductivities in reasonable agreement with those measured experimentally and provides insight into the potential influence of nanoparticle shape on phonon scattering. Measurements of wedge-shaped samples created by focused ion beam milling provide direct confirmation of depth resolution achieved.

Dielectric Boundary Force in Molecular Solvation with the Poisson–Boltzmann Free Energy: A Shape Derivative Approach

PubMed Central

Li, Bo; Cheng, Xiaoliang; Zhang, Zhengfang

2013-01-01

In an implicit-solvent description of molecular solvation, the electrostatic free energy is given through the electrostatic potential. This potential solves a boundary-value problem of the Poisson–Boltzmann equation in which the dielectric coefficient changes across the solute-solvent interface—the dielectric boundary. The dielectric boundary force acting on such a boundary is the negative first variation of the electrostatic free energy with respect to the location change of the boundary. In this work, the concept of shape derivative is used to define such variations and formulas of the dielectric boundary force are derived. It is shown that such a force is always in the direction toward the charged solute molecules. PMID:24058212

Size and habit evolution of PETN crystals - a lattice Monte Carlo study

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

Zepeda-Ruiz, L A; Maiti, A; Gee, R

2006-02-28

Starting from an accurate inter-atomic potential we develop a simple scheme of generating an ''on-lattice'' molecular potential of short range, which is then incorporated into a lattice Monte Carlo code for simulating size and shape evolution of nanocrystallites. As a specific example, we test such a procedure on the morphological evolution of a molecular crystal of interest to us, e.g., Pentaerythritol Tetranitrate, or PETN, and obtain realistic facetted structures in excellent agreement with experimental morphologies. We investigate several interesting effects including, the evolution of the initial shape of a ''seed'' to an equilibrium configuration, and the variation of growth morphologymore » as a function of the rate of particle addition relative to diffusion.« less

An Easily Constructed and Versatile Molecular Model

NASA Astrophysics Data System (ADS)

Hernandez, Sandra A.; Rodriguez, Nora M.; Quinzani, Oscar

1996-08-01

Three-dimensional molecular models are powerful tools used in basic courses of general and organic chemistry when the students must visualize the spatial distributions of atoms in molecules and relate them to the physical and chemical properties of such molecules. This article discusses inexpensive, easily carried, and semipermanent molecular models that the students may build by themselves. These models are based upon two different types of arrays of thin flexible wires, like telephone hook-up wires, which may be bent easily but keep their shapes.

Exploring Biomolecular Recognition by Modeling and Simulation

NASA Astrophysics Data System (ADS)

Wade, Rebecca

2007-12-01

Biomolecular recognition is complex. The balance between the different molecular properties that contribute to molecular recognition, such as shape, electrostatics, dynamics and entropy, varies from case to case. This, along with the extent of experimental characterization, influences the choice of appropriate computational approaches to study biomolecular interactions. I will present computational studies in which we aim to make concerted use of bioinformatics, biochemical network modeling and molecular simulation techniques to study protein-protein and protein-small molecule interactions and to facilitate computer-aided drug design.

Experimental and Numerical Analysis of Narrowband Coherent Rayleigh-Brillouin Scattering in Atomic and Molecular Species (Pre Print)

DTIC Science & Technology

2012-02-01

use of polar gas species. While current simplified models have adequately predicted CRS and CRBS line shapes for a wide variety of cases, multiple ...published simplified models are presented for argon, molecular nitrogen, and methane at 300 & 500 K and 1 atm. The simplified models require uncertain gas... models are presented for argon, molecular nitrogen, and methane at 300 & 500 K and 1 atm. The simplified models require uncertain gas properties

Molecular subgroups of medulloblastoma

PubMed Central

Northcott, Paul A; Dubuc, Adrian M; Pfister, Stefan; Taylor, Michael D

2014-01-01

Recent efforts at stratifying medulloblastomas based on their molecular features have revolutionized our understanding of this morbidity. Collective efforts by multiple independent groups have subdivided medulloblastoma from a single disease into four distinct molecular subgroups characterized by disparate transcriptional signatures, mutational spectra, copy number profiles and, most importantly, clinical features. We present a summary of recent studies that have contributed to our understanding of the core medulloblastoma subgroups, focusing largely on clinically relevant discoveries that have already, and will continue to, shape research. PMID:22853794

Molecular Imprinting Techniques Used for the Preparation of Biosensors

PubMed Central

Ertürk, Gizem; Mattiasson, Bo

2017-01-01

Molecular imprinting is the technology of creating artificial recognition sites in polymeric matrices which are complementary to the template in their size, shape and spatial arrangement of the functional groups. Molecularly imprinted polymers (MIPs) and their incorporation with various transducer platforms are among the most promising approaches for detection of several analytes. There are a variety of molecular imprinting techniques used for the preparation of biomimetic sensors including bulk imprinting, surface imprinting (soft lithography, template immobilization, grafting, emulsion polymerization) and epitope imprinting. This chapter presents an overview of all of these techniques with examples from particular publications. PMID:28165419

New 'Molecular Movie' Reveals Ultrafast Chemistry in Motion

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

Minitti, Michael

2015-06-22

Scientists for the first time tracked ultrafast structural changes, captured in quadrillionths-of-a-second steps, as ring-shaped gas molecules burst open and unraveled. Ring-shaped molecules are abundant in biochemistry and also form the basis for many drug compounds. The study points the way to a wide range of real-time X-ray studies of gas-based chemical reactions that are vital to biological processes.

New 'Molecular Movie' Reveals Ultrafast Chemistry in Motion

ScienceCinema

Minitti, Michael

2018-02-14

Scientists for the first time tracked ultrafast structural changes, captured in quadrillionths-of-a-second steps, as ring-shaped gas molecules burst open and unraveled. Ring-shaped molecules are abundant in biochemistry and also form the basis for many drug compounds. The study points the way to a wide range of real-time X-ray studies of gas-based chemical reactions that are vital to biological processes.

Packing of flexible 2D materials in vesicles

NASA Astrophysics Data System (ADS)

Zou, Guijin; Yi, Xin; Zhu, Wenpeng; Gao, Huajian

2018-06-01

To understand the mechanics of cellular packing of two-dimensional (2D) materials, we perform systematic molecular dynamics simulations and theoretical analysis to investigate the packing of a flexible circular sheet in a spherical vesicle and the 2D packing problem of a strip in a cylindrical vesicle. Depending on the system dimensions and the bending rigidity ratio between the confined sheet and the vesicle membrane, a variety of packing morphologies are observed, including a conical shape, a shape of three-fold symmetry, a cylindrically curved shape, an axisymmetrically buckled shape, as well as the initial circular shape. A set of buckling analyses lead to phase diagrams of the packing morphologies of the encapsulated sheets. These results may have important implications on the mechanism of intracellular packing and toxicity of 2D materials.

Genetical genomics of Populus leaf shape variation

DOE PAGES

Drost, Derek R.; Puranik, Swati; Novaes, Evandro; ...

2015-06-30

Leaf morphology varies extensively among plant species and is under strong genetic control. Mutagenic screens in model systems have identified genes and established molecular mechanisms regulating leaf initiation, development, and shape. However, it is not known whether this diversity across plant species is related to naturally occurring variation at these genes. Quantitative trait locus (QTL) analysis has revealed a polygenic control for leaf shape variation in different species suggesting that loci discovered by mutagenesis may only explain part of the naturally occurring variation in leaf shape. Here we undertook a genetical genomics study in a poplar intersectional pseudo-backcross pedigree tomore » identify genetic factors controlling leaf shape. Here, the approach combined QTL discovery in a genetic linkage map anchored to the Populus trichocarpa reference genome sequence and transcriptome analysis.« less

DNA sequence-directed shape change of photopatterned hydrogels via high-degree swelling

NASA Astrophysics Data System (ADS)

Cangialosi, Angelo; Yoon, ChangKyu; Liu, Jiayu; Huang, Qi; Guo, Jingkai; Nguyen, Thao D.; Gracias, David H.; Schulman, Rebecca

2017-09-01

Shape-changing hydrogels that can bend, twist, or actuate in response to external stimuli are critical to soft robots, programmable matter, and smart medicine. Shape change in hydrogels has been induced by global cues, including temperature, light, or pH. Here we demonstrate that specific DNA molecules can induce 100-fold volumetric hydrogel expansion by successive extension of cross-links. We photopattern up to centimeter-sized gels containing multiple domains that undergo different shape changes in response to different DNA sequences. Experiments and simulations suggest a simple design rule for controlled shape change. Because DNA molecules can be coupled to molecular sensors, amplifiers, and logic circuits, this strategy introduces the possibility of building soft devices that respond to diverse biochemical inputs and autonomously implement chemical control programs.

Prostatic cancers: understanding their molecular pathology and the 2016 WHO classification

PubMed Central

Inamura, Kentaro

2018-01-01

Accumulating evidence suggests that prostatic cancers represent a group of histologically and molecularly heterogeneous diseases with variable clinical courses. In accordance with the increased knowledge of their clinicopathologies and genetics, the World Health Organization (WHO) classification of prostatic cancers has been revised. Additionally, recent data on their comprehensive molecular characterization have increased our understanding of the genomic basis of prostatic cancers and enabled us to classify them into subtypes with distinct molecular pathologies and clinical features. Our increased understanding of the molecular pathologies of prostatic cancers has permitted their evolution from a poorly understood, heterogeneous group of diseases with variable clinical courses to characteristic molecular subtypes that allow the implementation of personalized therapies and better patient management. This review provides perspectives on the new 2016 WHO classification of prostatic cancers as well as recent knowledge of their molecular pathologies. The WHO classification of prostatic cancers will require additional revisions to allow for reliable and clinically meaningful cancer diagnoses as a better understanding of their molecular characteristics is obtained. PMID:29581876

Comparative Analysis of Four Buckwheat Species Based on Morphology and Complete Chloroplast Genome Sequences.

PubMed

Wang, Cheng-Long; Ding, Meng-Qi; Zou, Chen-Yan; Zhu, Xue-Mei; Tang, Yu; Zhou, Mei-Liang; Shao, Ji-Rong

2017-07-26

Buckwheat is a nutritional and economically crop belonging to Polygonaceae, Fagopyrum. To better understand the mutation patterns and evolution trend in the chloroplast (cp) genome of buckwheat, and found sufficient number of variable regions to explore the phylogenetic relationships of this genus, two complete cp genomes of buckwheat including Fagopyrum dibotrys (F. dibotrys) and Fagopyrum luojishanense (F. luojishanense) were sequenced, and other two Fagopyrum cp genomes were used for comparative analysis. After morphological analysis, the main difference among these buckwheat were height, leaf shape, seeds and flower type. F. luojishanense was distinguishable from the cultivated species easily. Although the F. dibotrys and two cultivated species has some similarity, they different in habit and component contents. The cp genome of F. dibotrys was 159,320 bp while the F. luojishanense was 159,265 bp. 48 and 61 SSRs were found in F. dibotrys and F. luojishanense respectively. Meanwhile, 10 highly variable regions among these buckwheat species were located precisely. The phylogenetic relationships among four Fagopyrum species based on complete cp genomes was showed. The results suggested that F. dibotrys is more closely related to Fagopyrum tataricum. These data provided valuable genetic information for Fagopyrum species identification, taxonomy, phylogenetic study and molecular breeding.

Selecting Species Traits for Biomonitoring Applications in light of Phylogenetic Relationships among Lotic Insects

NASA Astrophysics Data System (ADS)

Poff, N.; Vieira, N. K.; Simmons, M. P.; Olden, J. D.; Kondratieff, B. C.; Finn, D. S.

2005-05-01

The use of species traits as indicators of environmental disturbance is being considered for biomonitoring programs globally. As such, methods to select relevant and informative traits for inclusion in biometrics need to be developed. In this research, we identified 20 traits of aquatic insects within six trait groups: morphology, mobility, life-history strategy, thermal tolerance, feeding guild and ecology (e.g., habitat preference). We constructed phylogenetic trees for 1) all lotic insect species of North America and 2) all Ephemeroptera, Plecoptera and Trichoptera species based on morphology- and molecular-based analyses and classifications. We then measured variability (i.e., plasticity) of the 20 traits and six trait groups across the two phylogenetic trees. Traits with higher degrees of plasticity indicated traits that were less phylogenetically constrained, and were considered informative for biomonitoring purposes. Thermal tolerance, rheophily, body size at maturity and feeding guild showed the highest plasticity across both phylogenetic trees. Two mobility traits, occurrence in drift and adult dispersal distance, showed moderate plasticity. By contrast, adult exiting ability, degree of attachment, adult lifespan and body shape showed low variability and were thus less informative. Plastic species traits that are less phylogenetically constrained may be most useful in detecting community change along environmental gradients.

Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures.

PubMed

Raherison, Elie S M; Giguère, Isabelle; Caron, Sébastien; Lamara, Mebarek; MacKay, John J

2015-07-01

Transcript profiling has shown the molecular bases of several biological processes in plants but few studies have developed an understanding of overall transcriptome variation. We investigated transcriptome structure in white spruce (Picea glauca), aiming to delineate its modular organization and associated functional and evolutionary attributes. Microarray analyses were used to: identify and functionally characterize groups of co-expressed genes; investigate expressional and functional diversity of vascular tissue preferential genes which were conserved among Picea species, and identify expression networks underlying wood formation. We classified 22 857 genes as variable (79%; 22 coexpression groups) or invariant (21%) by profiling across several vegetative tissues. Modular organization and complex transcriptome restructuring among vascular tissue preferential genes was revealed by their assignment to coexpression groups with partially overlapping profiles and partially distinct functions. Integrated analyses of tissue-based and temporally variable profiles identified secondary xylem gene networks, showed their remodelling over a growing season and identified PgNAC-7 (no apical meristerm (NAM), Arabidopsis transcription activation factor (ATAF) and cup-shaped cotyledon (CUC) transcription factor 007 in Picea glauca) as a major hub gene specific to earlywood formation. Reference profiling identified comprehensive, statistically robust coexpressed groups, revealing that modular organization underpins the evolutionary conservation of the transcriptome structure. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Controlling the shape of membrane protein polyhedra

NASA Astrophysics Data System (ADS)

Li, Di; Kahraman, Osman; Haselwandter, Christoph A.

2017-03-01

Membrane proteins and lipids can self-assemble into membrane protein polyhedral nanoparticles (MPPNs). MPPNs have a closed spherical surface and a polyhedral protein arrangement, and may offer a new route for structure determination of membrane proteins and targeted drug delivery. We develop here a general analytic model of how MPPN self-assembly depends on bilayer-protein interactions and lipid bilayer mechanical properties. We find that the bilayer-protein hydrophobic thickness mismatch is a key molecular control parameter for MPPN shape that can be used to bias MPPN self-assembly towards highly symmetric and uniform MPPN shapes. Our results suggest strategies for optimizing MPPN shape for structural studies of membrane proteins and targeted drug delivery.

Winds from accretion disks - Ultraviolet line formation in cataclysmic variables

NASA Technical Reports Server (NTRS)

Shlosman, Isaac; Vitello, Peter

1993-01-01

Winds from accretion disks in cataclysmic variable stars are ubiquitous. Observations by IUE reveal P Cygni-shaped profiles of high-ionization lines which are attributed to these winds. We have studied the formation of UV emission lines in cataclysmic variables by constructing kinematical models of biconical rotating outflows from disks around white dwarfs. The photoionization in the wind is calculated taking into account the radiation fields of the disk, the boundary layer, and the white dwarf. The 3D radiative transfer is solved in the Sobolev approximation. Effects on the line shapes of varying basic physical parameters of the wind are shown explicitly. We identify and map the resonant scattering regions in the wind which have strongly biconical character regardless of the assumed velocity and radiation fields. Rotation at the base of the wind introduces a radial shear which decreases the line optical depth and reduces the line core intensity. We find that it is possible to reproduce the observed P Cygni line shapes and make some predictions to be verified in high-resolution observations.

Random Matrix Theory in molecular dynamics analysis.

PubMed

Palese, Luigi Leonardo

2015-01-01

It is well known that, in some situations, principal component analysis (PCA) carried out on molecular dynamics data results in the appearance of cosine-shaped low index projections. Because this is reminiscent of the results obtained by performing PCA on a multidimensional Brownian dynamics, it has been suggested that short-time protein dynamics is essentially nothing more than a noisy signal. Here we use Random Matrix Theory to analyze a series of short-time molecular dynamics experiments which are specifically designed to be simulations with high cosine content. We use as a model system the protein apoCox17, a mitochondrial copper chaperone. Spectral analysis on correlation matrices allows to easily differentiate random correlations, simply deriving from the finite length of the process, from non-random signals reflecting the intrinsic system properties. Our results clearly show that protein dynamics is not really Brownian also in presence of the cosine-shaped low index projections on principal axes. Copyright © 2014 Elsevier B.V. All rights reserved.

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

Glynos, Emmanouil; Johnson, Kyle J.; Frieberg, Bradley

Here, the surface relaxation dynamics of supported star-shaped polymer thin films are shown to be slower than the bulk, persisting up to temperatures at least 50 degrees above the bulk glass transition temperature Tmore » $$bulk\\atop{g}$$. This behavior, exhibited by star-shaped polystyrenes (SPSs) with functionality f = 8 arms and molecular weights per arm M arm < M e (M e is the entanglement molecular weight), is shown by molecular dynamics simulations to be associated with a preferential localization of these macromolecules at the free surface. This new phenomenon is in notable contrast to that of linear chain polymer thin film systems where the surface relaxations are enhanced in relation to the bulk; this enhancement persists only for a limited temperature range above the bulk T$$bulk\\atop{g}$$. Finally, evidence of the slow surface dynamics, compared to the bulk, for temperatures well above T g and at length and time scales not associated with the glass transition has not previously been reported for polymers.« less

Nanomechanical DNA origami pH sensors.

PubMed

Kuzuya, Akinori; Watanabe, Ryosuke; Yamanaka, Yusei; Tamaki, Takuya; Kaino, Masafumi; Ohya, Yuichi

2014-10-16

Single-molecule pH sensors have been developed by utilizing molecular imaging of pH-responsive shape transition of nanomechanical DNA origami devices with atomic force microscopy (AFM). Short DNA fragments that can form i-motifs were introduced to nanomechanical DNA origami devices with pliers-like shape (DNA Origami Pliers), which consist of two levers of 170-nm long and 20-nm wide connected at a Holliday-junction fulcrum. DNA Origami Pliers can be observed as in three distinct forms; cross, antiparallel and parallel forms, and cross form is the dominant species when no additional interaction is introduced to DNA Origami Pliers. Introduction of nine pairs of 12-mer sequence (5'-AACCCCAACCCC-3'), which dimerize into i-motif quadruplexes upon protonation of cytosine, drives transition of DNA Origami Pliers from open cross form into closed parallel form under acidic conditions. Such pH-dependent transition was clearly imaged on mica in molecular resolution by AFM, showing potential application of the system to single-molecular pH sensors.

Geometric Morphometrics on Gene Expression Patterns Within Phenotypes: A Case Example on Limb Development

PubMed Central

Martínez-Abadías, Neus; Mateu, Roger; Niksic, Martina; Russo, Lucia; Sharpe, James

2016-01-01

How the genotype translates into the phenotype through development is critical to fully understand the evolution of phenotypes. We propose a novel approach to directly assess how changes in gene expression patterns are associated with changes in morphology using the limb as a case example. Our method combines molecular biology techniques, such as whole-mount in situ hybridization, with image and shape analysis, extending the use of Geometric Morphometrics to the analysis of nonanatomical shapes, such as gene expression domains. Elliptical Fourier and Procrustes-based semilandmark analyses were used to analyze the variation and covariation patterns of the limb bud shape with the expression patterns of two relevant genes for limb morphogenesis, Hoxa11 and Hoxa13. We devised a multiple thresholding method to semiautomatically segment gene domains at several expression levels in large samples of limb buds from C57Bl6 mouse embryos between 10 and 12 postfertilization days. Besides providing an accurate phenotyping tool to quantify the spatiotemporal dynamics of gene expression patterns within developing structures, our morphometric analyses revealed high, non-random, and gene-specific variation undergoing canalization during limb development. Our results demonstrate that Hoxa11 and Hoxa13, despite being paralogs with analogous functions in limb patterning, show clearly distinct dynamic patterns, both in shape and size, and are associated differently with the limb bud shape. The correspondence between our results and already well-established molecular processes underlying limb development confirms that this morphometric approach is a powerful tool to extract features of development regulating morphogenesis. Such multilevel analyses are promising in systems where not so much molecular information is available and will advance our understanding of the genotype–phenotype map. In systematics, this knowledge will increase our ability to infer how evolution modified a common developmental pattern to generate a wide diversity of morphologies, as in the vertebrate limb. PMID:26377442

Reconfigurable photonic crystals enabled by pressure-responsive shape-memory polymers

PubMed Central

Fang, Yin; Ni, Yongliang; Leo, Sin-Yen; Taylor, Curtis; Basile, Vito; Jiang, Peng

2015-01-01

Smart shape-memory polymers can memorize and recover their permanent shape in response to an external stimulus (for example, heat). They have been extensively exploited for a wide spectrum of applications ranging from biomedical devices to aerospace morphing structures. However, most of the existing shape-memory polymers are thermoresponsive and their performance is hindered by heat-demanding programming and recovery steps. Although pressure is an easily adjustable process variable such as temperature, pressure-responsive shape-memory polymers are largely unexplored. Here we report a series of shape-memory polymers that enable unusual ‘cold' programming and instantaneous shape recovery triggered by applying a contact pressure at ambient conditions. Moreover, the interdisciplinary integration of scientific principles drawn from two disparate fields—the fast-growing photonic crystal and shape-memory polymer technologies—enables fabrication of reconfigurable photonic crystals and simultaneously provides a simple and sensitive optical technique for investigating the intriguing shape-memory effects at nanoscale. PMID:26074349

Viscoelastic properties of dendrimers in the melt from nonequlibrium molecular dynamics

NASA Astrophysics Data System (ADS)

Bosko, Jaroslaw T.; Todd, B. D.; Sadus, Richard J.

2004-12-01

The viscoelastic properties of dendrimers of generation 1-4 are studied using nonequilibrium molecular dynamics. Flow properties of dendrimer melts under shear are compared to systems composed of linear chain polymers of the same molecular weight, and the influence of molecular architecture is discussed. Rheological material properties, such as the shear viscosity and normal stress coefficients, are calculated and compared for both systems. We also calculate and compare the microscopic properties of both linear chain and dendrimer molecules, such as their molecular alignment, order parameters and rotational velocities. We find that the highly symmetric shape of dendrimers and their highly constrained geometry allows for substantial differences in their material properties compared to traditional linear polymers of equivalent molecular weight.

Winemaking and Bioprocesses Strongly Shaped the Genetic Diversity of the Ubiquitous Yeast Torulaspora delbrueckii

PubMed Central

Comte, Guillaume; Panfili, Aurélie; Delcamp, Adline; Salin, Franck; Marullo, Philippe; Bely, Marina

2014-01-01

The yeast Torulaspora delbrueckii is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, T. delbrueckii is frequently isolated in natural environments (plant, soil, insect). T. delbrueckii is thus a remarkable ubiquitous yeast species with both wild and anthropic habitats, and appears to be a perfect yeast model to search for evidence of human domestication. For that purpose, we developed eight microsatellite markers that were used for the genotyping of 110 strains from various substrates and geographical origins. Microsatellite analysis showed four genetic clusters: two groups contained most nature strains from Old World and Americas respectively, and two clusters were associated with winemaking and other bioprocesses. Analysis of molecular variance (AMOVA) confirmed that human activities significantly shaped the genetic variability of T. delbrueckii species. Natural isolates are differentiated on the basis of geographical localisation, as expected for wild population. The domestication of T. delbrueckii probably dates back to the Roman Empire for winemaking (∼1900 years ago), and to the Neolithic era for bioprocesses (∼4000 years ago). Microsatellite analysis also provided valuable data regarding the life-cycle of the species, suggesting a mostly diploid homothallic life. In addition to population genetics and ecological studies, the microsatellite tool will be particularly useful for further biotechnological development of T. delbrueckii strains for winemaking and other bioprocesses. PMID:24718638

YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs

PubMed Central

Shigematsu, Megumi; Honda, Shozo; Loher, Phillipe; Telonis, Aristeidis G.; Rigoutsos, Isidore

2017-01-01

Abstract Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles. To unravel the emerging complexities of tRNA biology and molecular mechanisms underlying them, an efficient tRNA sequencing method is required. However, the rigid structure of tRNA has been presenting a challenge to the development of such methods. We report the development of Y-shaped Adapter-ligated MAture TRNA sequencing (YAMAT-seq), an efficient and convenient method for high-throughput sequencing of mature tRNAs. YAMAT-seq circumvents the issue of inefficient adapter ligation, a characteristic of conventional RNA sequencing methods for mature tRNAs, by employing the efficient and specific ligation of Y-shaped adapter to mature tRNAs using T4 RNA Ligase 2. Subsequent cDNA amplification and next-generation sequencing successfully yield numerous mature tRNA sequences. YAMAT-seq has high specificity for mature tRNAs and high sensitivity to detect most isoacceptors from minute amount of total RNA. Moreover, YAMAT-seq shows quantitative capability to estimate expression levels of mature tRNAs, and has high reproducibility and broad applicability for various cell lines. YAMAT-seq thus provides high-throughput technique for identifying tRNA profiles and their regulations in various transcriptomes, which could play important regulatory roles in translation and other biological processes. PMID:28108659

Winemaking and bioprocesses strongly shaped the genetic diversity of the ubiquitous yeast Torulaspora delbrueckii.

PubMed

Albertin, Warren; Chasseriaud, Laura; Comte, Guillaume; Panfili, Aurélie; Delcamp, Adline; Salin, Franck; Marullo, Philippe; Bely, Marina

2014-01-01

The yeast Torulaspora delbrueckii is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, T. delbrueckii is frequently isolated in natural environments (plant, soil, insect). T. delbrueckii is thus a remarkable ubiquitous yeast species with both wild and anthropic habitats, and appears to be a perfect yeast model to search for evidence of human domestication. For that purpose, we developed eight microsatellite markers that were used for the genotyping of 110 strains from various substrates and geographical origins. Microsatellite analysis showed four genetic clusters: two groups contained most nature strains from Old World and Americas respectively, and two clusters were associated with winemaking and other bioprocesses. Analysis of molecular variance (AMOVA) confirmed that human activities significantly shaped the genetic variability of T. delbrueckii species. Natural isolates are differentiated on the basis of geographical localisation, as expected for wild population. The domestication of T. delbrueckii probably dates back to the Roman Empire for winemaking (∼ 1900 years ago), and to the Neolithic era for bioprocesses (∼ 4000 years ago). Microsatellite analysis also provided valuable data regarding the life-cycle of the species, suggesting a mostly diploid homothallic life. In addition to population genetics and ecological studies, the microsatellite tool will be particularly useful for further biotechnological development of T. delbrueckii strains for winemaking and other bioprocesses.

Plasticity as Phenotype: G x E Interaction in a Freshwater Snail

NASA Astrophysics Data System (ADS)

Brunkow, P. E.; Calloway, S. A.

2005-05-01

Plasticity in morphological development allows species to accommodate environmental variation experienced during growth; however, genetic variation for phenotypic plasticity per se has been relatively under-studied. We utilized the well-documented plastic response of shell development to predator cues in a freshwater snail to quantify genetic variation for plasticity in growth rate and shell shape. Field-caught pairs of snails reproduced in the laboratory to create families of full siblings, which were then divided and allowed to grow in control and predator cue treatments. Predator (crayfish) cues had significant effects on both size-corrected growth rate and shell shape; family identity also significantly affected both final shell shape and growth rate. The interaction between predator treatment and family identity significantly affected snail growth rate but not final shell shape, suggesting genetic variation in the plastic response to predator cues for a physiological variable (growth rate) but not for a variable known to mechanically reduce the risk of predation (shell shape), at least in this population of snails. The possibility that risk of multiple modes of predation (i.e., both fish and crayfish) in some populations might maintain genetic variation in morphological plasticity is discussed.

Genetic variability among elite popcorn lines based on molecular and morphoagronomic characteristics.

PubMed

Dos Santos, J F; Mangolin, C A; Machado, M F P S; Scapim, C A; Giordani, W; Gonçalves, L S A

2017-06-29

Knowledge of genetic diversity among genotypes and relationships among elite lines is of great importance for the development of breeding programs. Therefore, the objective of this study was to evaluate genetic variability based on the morphoagronomic and molecular characterization of 18 elite popcorn (Zea mays var. everta) lines to be used by Universidade Estadual de Maringá breeding programs. We used 31 microsatellite primers (widely distributed in the genome), and 16 morphological descriptors (including the resistance to maize white spot, common rust, polysora rust of maize, cercospora and leaf blights). The molecular data revealed variability among the lines, which were divided into four groups that were partially concordant with unweighted pair group method with arithmetic mean (UPMGA) and Bayesian clusters. The lines G3, G4, G11, and G13 exhibited favorable morphological characters and low disease incidence rates. The four groups were confirmed using the Gower distance in the UPGMA cluster; however, there was no association with the dissimilarity patterns obtained using the molecular data. The absence of a correlation suggests that both characterizations (morphoagronomic and molecular) are important for discriminating among elite popcorn lines.

Ultra Low Density and Highly Crosslinked Biocompatible Shape Memory Polyurethane Foams

PubMed Central

Singhal, Pooja; Rodriguez, Jennifer N.; Small, Ward; Eagleston, Scott; Van de Water, Judy; Maitland, Duncan J.; Wilson, Thomas S.

2012-01-01

We report the development of highly chemically crosslinked, ultra low density (~0.015 g/cc) polyurethane shape memory foams synthesized from symmetrical, low molecular weight and branched hydroxyl monomers. Sharp single glass transitions (Tg) customizable in the functional range of 45–70 °C were achieved. Thermomechanical testing confirmed shape memory behavior with 97–98% shape recovery over repeated cycles, a glassy storage modulus of 200–300 kPa and recovery stresses of 5–15 kPa. Shape holding tests under constrained storage above the Tg showed stable shape memory. A high volume expansion of up to 70 times was seen on actuation of these foams from a fully compressed state. Low in-vitro cell activation induced by the foam compared to controls demonstrates low acute bio-reactivity. We believe these porous polymeric scaffolds constitute an important class of novel smart biomaterials with multiple potential applications. PMID:22570509

Early brain development toward shaping of human mind: an integrative psychoneurodevelopmental model in prenatal and perinatal medicine.

PubMed

Hruby, Radovan; Maas, Lili M; Fedor-Freybergh, P G

2013-01-01

The article introduces an integrative psychoneurodevelopmental model of complex human brain and mind development based on the latest findings in prenatal and perinatal medicine in terms of integrative neuroscience. The human brain development is extraordinarily complex set of events and could be influenced by a lot of factors. It is supported by new insights into the early neuro-ontogenic processes with the help of structural 3D magnetic resonance imaging or diffusion tensor imaging of fetal human brain. Various factors and targets for neural development including birth weight variability, fetal and early-life programming, fetal neurobehavioral states and fetal behavioral responses to various stimuli and others are discussed. Molecular biology reveals increasing sets of genes families as well as transcription and neurotropic factors together with critical epigenetic mechanisms to be deeply employed in the crucial neurodevelopmental events. Another field of critical importance is psychoimmuno-neuroendocrinology. Various effects of glucocorticoids as well as other hormones, prenatal stress and fetal HPA axis modulation are thought to be of special importance for brain development. The early postnatal period is characterized by the next intense shaping of complex competences, induced mainly by the very unique mother - newborn´s interactions and bonding. All these mechanisms serve to shape individual human mind with complex abilities and neurobehavioral strategies. Continuous research elucidating these special competences of human fetus and newborn/child supports integrative neuroscientific approach to involve various scientific disciplines for the next progress in human brain and mind research, and opens new scientific challenges and philosophic attitudes. New findings and approaches in this field could establish new methods in science, in primary prevention and treatment strategies, and markedly contribute to the development of modern integrative and personalized medicine.

Shape Mode Analysis Exposes Movement Patterns in Biology: Flagella and Flatworms as Case Studies

PubMed Central

Werner, Steffen; Rink, Jochen C.; Riedel-Kruse, Ingmar H.; Friedrich, Benjamin M.

2014-01-01

We illustrate shape mode analysis as a simple, yet powerful technique to concisely describe complex biological shapes and their dynamics. We characterize undulatory bending waves of beating flagella and reconstruct a limit cycle of flagellar oscillations, paying particular attention to the periodicity of angular data. As a second example, we analyze non-convex boundary outlines of gliding flatworms, which allows us to expose stereotypic body postures that can be related to two different locomotion mechanisms. Further, shape mode analysis based on principal component analysis allows to discriminate different flatworm species, despite large motion-associated shape variability. Thus, complex shape dynamics is characterized by a small number of shape scores that change in time. We present this method using descriptive examples, explaining abstract mathematics in a graphic way. PMID:25426857

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

PubMed

Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal

2016-08-23

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

CH4 dissociation on Ru(0001): A view from both sides of the barrier

NASA Astrophysics Data System (ADS)

Mortensen, H.; Diekhöner, L.; Baurichter, A.; Luntz, A. C.

2002-04-01

This paper reports measurements of both dissociative adsorption on and associative desorption from CH4 on Ru(0001). We consider the former a view of dissociation from the front side of the barrier, while the latter is considered as a view of dissociation from the back side of the barrier. A combination of both previous and new molecular beam measurements of dissociative adsorption shows that S0 depends on all experimental variables (E, Tn, Ts and isotope) in a manner similar to other close-packed transition metals. The interpretation of this behavior in terms of a theoretical description of the dissociation is discussed critically, with special emphasis on insights from new theoretical studies. The energy-resolved desorption flux Df(E,Ts) is obtained in associative desorption experiments using the technique of laser assisted associative desorption (LAAD). Measurements at several Ts allow both a direct determination of the adiabatic barrier V*(0) and considerable insight into the dynamics of dissociation. The V*(0) obtained from Df(E,Ts) is in excellent agreement with density functional theory (DFT) calculations and with the value indirectly inferred from molecular beam experiments. The chief dynamic conclusion from an analysis of Df(E,Ts) is that both bending and stretching coordinates must be produced in associative desorption, although they are not populated statistically. The absence of an isotope effect in the shape of Df(E,Ts) argues against the importance of tunneling in the desorption/adsorption. When reactive fluxes are compared via detailed balance, both the molecular beam experiment and the LAAD experiment are in good agreement.

Universal aspects of adhesion and atomic force microscopy

NASA Technical Reports Server (NTRS)

Banerjea, Amitava; Smith, John R.; Ferrante, John

1990-01-01

Adhesive energies are computed for flat and atomically sharp tips as a function of the normal distance to the substrate. The dependence of binding energies on tip shape is investigated. The magnitudes of the binding energies for the atomic force microscope are found to depend sensitively on tip material, tip shape and the sample site being probed. The form of the energy-distance curve, however, is universal and independent of these variables, including tip shape.

The A and m coefficients in the Bruun/Dean equilibrium profile equation seen from the Arctic

USGS Publications Warehouse

Are, F.; Reimnitz, E.

2008-01-01

The Bruun/Dean relation between water depth and distance from the shore with a constant profile shape factor is widely used to describe shoreface profiles in temperate environments. However, it has been shown that the sediment scale parameter (A) and the profile shape factor (m) are interrelated variables. An analysis of 63 Arctic erosional shoreface profiles shows that both coefficients are highly variable. Relative frequency of the average m value is only 16% by the class width 0.1. No other m value frequency exceeds 21%. Therefore, there is insufficient reason to use average m to characterize Arctic shoreface profile shape. The shape of each profile has a definite combination of A and m values. Coefficients A and m show a distinct inverse relationship, as in temperate climate. A dependence of m values on coastal sediment grain size is seen, and m decreases with increasing grain size. With constant m = 0.67, parameter A obtains a dimension unit m1/3. But A equals the water depth in meters 1 m from the water edge. This fact and the variability of parameter m testify that the Bruun/Dean equation is essentially an empirical formula. There is no need to give any measurement unit to parameter A. But the International System of Units (SI) has to be used in applying the Bruun/Dean equation for shoreface profiles. A comparison of the shape of Arctic shoreface profiles with those of temperate environments shows surprising similarity. Therefore, the conclusions reached in this Arctic paper seem to apply also to temperate environments.

Molecular filter-based diagnostics in high speed flows

NASA Technical Reports Server (NTRS)

Elliott, Gregory S.; Samimy, MO; Arnette, Stephen A.

1993-01-01

The use of iodine molecular filters in nonintrusive planar velocimetry methods is examined. Detailed absorption profiles are obtained to highlight the effects that determine the profile shape. It is shown that pressure broadening induced by the presence of a nonabsorbing vapor can be utilized to significantly change the slopes bounding the absorbing region while remaining in the optically-thick regime.

Applying Hand-Held 3D Printing Technology to the Teaching of VSEPR Theory

ERIC Educational Resources Information Center

Dean, Natalie L.; Ewan, Corrina; McIndoe, J. Scott

2016-01-01

The use of hand-held 3D printing technology provides a unique and engaging approach to learning VSEPR theory by enabling students to draw three-dimensional depictions of different molecular geometries, giving them an appreciation of the shapes of the building blocks of complex molecular structures. Students are provided with 3D printing pens and…

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

McLaughlin, E.; Gupta, S.

This project mainly involves a molecular dynamics and Monte Carlo study of the effect of molecular shape on thermophysical properties of bulk fluids with an emphasis on the aromatic hydrocarbon liquids. In this regard we have studied the modeling, simulation methodologies, and predictive and correlating methods for thermodynamic properties of fluids of nonspherical molecules. In connection with modeling we have studied the use of anisotropic site-site potentials, through a modification of the Gay-Berne Gaussian overlap potential, to successfully model the aromatic rings after adding the necessary electrostatic moments. We have also shown these interaction sites should be located at themore » geometric centers of the chemical groups. In connection with predictive methods, we have shown two perturbation type theories to work well for fluids modeled using one-center anisotropic potentials and the possibility exists for extending these to anisotropic site-site models. In connection with correlation methods, we have studied, through simulations, the effect of molecular shape on the attraction term in the generalized van der Waals equation of state for fluids of nonspherical molecules and proposed a possible form which is to be studied further. We have successfully studied the vector and parallel processing aspects of molecular simulations for fluids of nonspherical molecules.« less

Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution

NASA Astrophysics Data System (ADS)

Egwolf, Bernhard; Tavan, Paul

2004-01-01

We extend our continuum description of solvent dielectrics in molecular-dynamics (MD) simulations [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)], which has provided an efficient and accurate solution of the Poisson equation, to ionic solvents as described by the linearized Poisson-Boltzmann (LPB) equation. We start with the formulation of a general theory for the electrostatics of an arbitrarily shaped molecular system, which consists of partially charged atoms and is embedded in a LPB continuum. This theory represents the reaction field induced by the continuum in terms of charge and dipole densities localized within the molecular system. Because these densities cannot be calculated analytically for systems of arbitrary shape, we introduce an atom-based discretization and a set of carefully designed approximations. This allows us to represent the densities by charges and dipoles located at the atoms. Coupled systems of linear equations determine these multipoles and can be rapidly solved by iteration during a MD simulation. The multipoles yield the reaction field forces and energies. Finally, we scrutinize the quality of our approach by comparisons with an analytical solution restricted to perfectly spherical systems and with results of a finite difference method.

Geomorphic effectiveness of long profile shape and role of inherent geological controls, Ganga River Basin, India

NASA Astrophysics Data System (ADS)

Sonam, Sonam; Jain, Vikrant

2017-04-01

River long profile is one of the fundamental geomorphic parameters which provides a platform to study interaction of geological and geomorphic processes at different time scales. Long profile shape is governed by geological processes at 10 ^ 5 - 10 ^ 6 years' time scale and it controls the modern day (10 ^ 0 - 10 ^ 1 years' time scale) fluvial processes by controlling the spatial variability of channel slope. Identification of an appropriate model for river long profile may provide a tool to analyse the quantitative relationship between basin geology, profile shape and its geomorphic effectiveness. A systematic analysis of long profiles has been carried for the Himalayan tributaries of the Ganga River basin. Long profile shape and stream power distribution pattern is derived using SRTM DEM data (90 m spatial resolution). Peak discharge data from 34 stations is used for hydrological analysis. Lithological variability and major thrusts are marked along the river long profile. The best fit of long profile is analysed for power, logarithmic and exponential function. Second order exponential function provides the best representation of long profiles. The second order exponential equation is Z = K1*exp(-β1*L) + K2*exp(-β2*L), where Z is elevation of channel long profile, L is the length, K and β are coefficients of the exponential function. K1 and K2 are the proportion of elevation change of the long profile represented by β1 (fast) and β2 (slow) decay coefficients of the river long profile. Different values of coefficients express the variability in long profile shapes and is related with the litho-tectonic variability of the study area. Channel slope of long profile is estimated taking the derivative of exponential function. Stream power distribution pattern along long profile is estimated by superimposing the discharge and long profile slope. Sensitivity analysis of stream power distribution with decay coefficients of the second order exponential equation is evaluated for a range of coefficient values. Our analysis suggests that the amplitude of stream power peak value is dependent on K1, the proportion of elevation change coming under the fast decay exponent and the location of stream power peak is dependent of the long profile decay coefficient (β1). Different long profile shapes owing to litho-tectonic variability across the Himalayas are responsible for spatial variability of stream power distribution pattern. Most of the stream power peaks lie in the Higher Himalaya. In general, eastern rivers have higher stream power in hinterland area and low stream power in the alluvial plains. This is responsible for, 1) higher erosion rate and sediment supply in hinterland of eastern rivers, 2) the incised and stable nature of channels in the western alluvial plains and 3) aggrading channels with dynamic nature in the eastern alluvial plains. Our study shows that the spatial variability of litho-units defines the coefficients of long profile function which in turn controls the position and magnitude of stream power maxima and hence the geomorphic variability in a fluvial system.

Procedures for shape optimization of gas turbine disks

NASA Technical Reports Server (NTRS)

Cheu, Tsu-Chien

1989-01-01

Two procedures, the feasible direction method and sequential linear programming, for shape optimization of gas turbine disks are presented. The objective of these procedures is to obtain optimal designs of turbine disks with geometric and stress constraints. The coordinates of the selected points on the disk contours are used as the design variables. Structural weight, stress and their derivatives with respect to the design variables are calculated by an efficient finite element method for design senitivity analysis. Numerical examples of the optimal designs of a disk subjected to thermo-mechanical loadings are presented to illustrate and compare the effectiveness of these two procedures.

Shaping effective communication skills and therapeutic relationships at work: the foundation of collaboration.

PubMed

Grover, Susan M

2005-04-01

Effective communication is essential to practice and can result in improved interpersonal relationships at the workplace. Effective communication is shaped by basic techniques such as open-ended questions, listening, empathy, and assertiveness. However, the relationship between effective communication and successful interpersonal relationships is affected by intervening variables. The variables of gender, generation, context, collegiality, cooperation, self-disclosure, and reciprocity can impede or enhance the outcome of quality communication. It is essential for occupational health nurses to qualitatively assess the degree to which each of these concepts affects communication and, in turn, relationships at work.

A simple, analytical, axisymmetric microburst model for downdraft estimation

NASA Technical Reports Server (NTRS)

Vicroy, Dan D.

1991-01-01

A simple analytical microburst model was developed for use in estimating vertical winds from horizontal wind measurements. It is an axisymmetric, steady state model that uses shaping functions to satisfy the mass continuity equation and simulate boundary layer effects. The model is defined through four model variables: the radius and altitude of the maximum horizontal wind, a shaping function variable, and a scale factor. The model closely agrees with a high fidelity analytical model and measured data, particularily in the radial direction and at lower altitudes. At higher altitudes, the model tends to overestimate the wind magnitude relative to the measured data.

Interfractional variability of respiration-induced esophageal tumor motion quantified using fiducial markers and four-dimensional cone-beam computed tomography.

PubMed

Jin, Peng; Hulshof, Maarten C C M; van Wieringen, Niek; Bel, Arjan; Alderliesten, Tanja

2017-07-01

To investigate the interfractional variability of respiration-induced esophageal tumor motion using fiducial markers and four-dimensional cone-beam computed tomography (4D-CBCT) and assess if a 4D-CT is sufficient for predicting the motion during the treatment. Twenty-four patients with 63 markers visible in the retrospectively reconstructed 4D-CBCTs were included. For each marker, we calculated the amplitude and trajectory of the respiration-induced motion. Possible time trends of the amplitude over the treatment course and the interfractional variability of amplitudes and trajectory shapes were assessed. Further, the amplitudes measured in the 4D-CT were compared to those in the 4D-CBCTs. The amplitude was largest in the cranial-caudal direction of the distal esophagus (mean: 7.1mm) and proximal stomach (mean: 7.8mm). No time trend was observed in the amplitude over the treatment course. The interfractional variability of amplitudes and trajectory shapes was limited (mean: ≤1.4mm). Moreover, small and insignificant deviation was found between the amplitudes quantified in the 4D-CT and in the 4D-CBCT (mean absolute difference: ≤1.0mm). The limited interfractional variability of amplitudes and trajectory shapes and small amplitude difference between 4D-CT-based and 4D-CBCT-based measurements imply that a single 4D-CT would be sufficient for predicting the respiration-induced esophageal tumor motion during the treatment course. Copyright © 2017 Elsevier B.V. All rights reserved.

Global MHD Simulations of the Earth's Bow Shock Shape and Motion Under Variable Solar Wind Conditions

NASA Astrophysics Data System (ADS)

Mejnertsen, L.; Eastwood, J. P.; Hietala, H.; Schwartz, S. J.; Chittenden, J. P.

2018-01-01

Empirical models of the Earth's bow shock are often used to place in situ measurements in context and to understand the global behavior of the foreshock/bow shock system. They are derived statistically from spacecraft bow shock crossings and typically treat the shock surface as a conic section parameterized according to a uniform solar wind ram pressure, although more complex models exist. Here a global magnetohydrodynamic simulation is used to analyze the variability of the Earth's bow shock under real solar wind conditions. The shape and location of the bow shock is found as a function of time, and this is used to calculate the shock velocity over the shock surface. The results are compared to existing empirical models. Good agreement is found in the variability of the subsolar shock location. However, empirical models fail to reproduce the two-dimensional shape of the shock in the simulation. This is because significant solar wind variability occurs on timescales less than the transit time of a single solar wind phase front over the curved shock surface. Empirical models must therefore be used with care when interpreting spacecraft data, especially when observations are made far from the Sun-Earth line. Further analysis reveals a bias to higher shock speeds when measured by virtual spacecraft. This is attributed to the fact that the spacecraft only observes the shock when it is in motion. This must be accounted for when studying bow shock motion and variability with spacecraft data.

Molecular and supramolecular control of the work function of an inorganic electrode with self-assembled monolayer of umbrella-shaped fullerene derivatives.

PubMed

Lacher, Sebastian; Matsuo, Yutaka; Nakamura, Eiichi

2011-10-26

The surface properties of inorganic substrates can be altered by coating with organic molecules, which may result in the improvement of the properties suitable for electronic or biological applications. This article reports a systematic experimental study on the influence of the molecular and supramolecular properties of umbrella-shaped penta(organo)[60]fullerene derivatives, and on the work function and the water contact angle of indium-tin oxide (ITO) and gold surfaces. We could relate these macroscopic characteristics to single-molecular level properties, such as ionization potential and molecular dipole. The results led us to conclude that the formation of a SAM of a polar compound generates an electronic field through intermolecular interaction of the molecular charges, and this field makes the overall dipole of the SAM much smaller than the one expected from the simple sum of the dipoles of all molecules in the SAM. This effect, which was called depolarization and previously discussed theoretically, is now quantitatively probed by experiments. The important physical properties in surface science such as work function, ionization potential, and water contact angles have been mutually correlated at the level of molecular structures and molecular orientations on the substrate surface. We also found that the SAMs on ITO and gold operate under the same principle except that the "push-back" effect operates specifically for gold. The study also illustrates the ability of the photoelectron yield spectroscopy technique to rapidly measure the work function of a SAM-covered substrate and the ionization potential value of a molecule on the surface.

A log-normal distribution model for the molecular weight of aquatic fulvic acids

USGS Publications Warehouse

Cabaniss, S.E.; Zhou, Q.; Maurice, P.A.; Chin, Y.-P.; Aiken, G.R.

2000-01-01

The molecular weight of humic substances influences their proton and metal binding, organic pollutant partitioning, adsorption onto minerals and activated carbon, and behavior during water treatment. We propose a lognormal model for the molecular weight distribution in aquatic fulvic acids to provide a conceptual framework for studying these size effects. The normal curve mean and standard deviation are readily calculated from measured M(n) and M(w) and vary from 2.7 to 3 for the means and from 0.28 to 0.37 for the standard deviations for typical aquatic fulvic acids. The model is consistent with several types of molecular weight data, including the shapes of high- pressure size-exclusion chromatography (HP-SEC) peaks. Applications of the model to electrostatic interactions, pollutant solubilization, and adsorption are explored in illustrative calculations.The molecular weight of humic substances influences their proton and metal binding, organic pollutant partitioning, adsorption onto minerals and activated carbon, and behavior during water treatment. We propose a log-normal model for the molecular weight distribution in aquatic fulvic acids to provide a conceptual framework for studying these size effects. The normal curve mean and standard deviation are readily calculated from measured Mn and Mw and vary from 2.7 to 3 for the means and from 0.28 to 0.37 for the standard deviations for typical aquatic fulvic acids. The model is consistent with several type's of molecular weight data, including the shapes of high-pressure size-exclusion chromatography (HP-SEC) peaks. Applications of the model to electrostatic interactions, pollutant solubilization, and adsorption are explored in illustrative calculations.

[Application of the elliptic fourier functions to the description of avian egg shape].

PubMed

Ávila, Dennis Denis

2014-12-01

Egg shape is difficult to quantify due to the lack of an exact formula to describe its geometry. Here I described a simple algorithm to characterize and compare egg shapes using Fourier functions. These functions can delineate any closed contour and had been previously applied to describe several biological objects. I described, step by step, the process of data acquisition, processing and the use of the SHAPE software to extract function coefficients in a study case. I compared egg shapes in three birds' species representing different reproductive strategies: Cuban Parakeet (Aratinga euops), Royal Tern (Thalasseus maximus) and Cuban Blackbird (Dives atroviolaceus). Using 73 digital pictures of eggs kept in Cuban scientific collections, I calculated Fourier descriptors with 4, 6, 8, 16 and 20 harmonics. Descriptors were reduced by a Principal Component Analysis and the scores of the eigen-values that account for 90% of variance were used in a Lineal Discriminant Function to analyze the possibility to differentiate eggs according to its shapes. Using four harmonics, the first five component accounted for 97% of shape variances; more harmonics diluted the variance increasing to eight the number of components needed to explain most of the variation. Convex polygons in the discriminant space showed a clear separation between species, allowing trustful discrimination (classification errors between 7-15%). Misclassifications were related to specific egg shape variability between species. In the study case, A. euops eggs were perfectly classified, but for the other species, errors ranged from 5 to 29% of misclassifications, in relation to the numbers or harmonics and components used. The proposed algorithm, despite its apparent mathematical complexity, showed many advantages to describe eggs shape allowing a deeper understanding of factors related to this variable.

Anabolic Heterogeneity Following Resistance Training: A Role for Circadian Rhythm?

PubMed

Camera, Donny M

2018-01-01

It is now well established that resistance exercise stimulates muscle protein synthesis and promotes gains in muscle mass and strength. However, considerable variability exists following standardized resistance training programs in the magnitude of muscle cross-sectional area and strength responses from one individual to another. Several studies have recently posited that alterations in satellite cell population, myogenic gene expression and microRNAs may contribute to individual variability in anabolic adaptation. One emerging factor that may also explain the variability in responses to resistance exercise is circadian rhythms and underlying molecular clock signals. The molecular clock is found in most cells within the body, including skeletal muscle, and principally functions to optimize the timing of specific cellular events around a 24 h cycle. Accumulating evidence investigating the skeletal muscle molecular clock indicates that exercise-induced contraction and its timing may regulate gene expression and protein synthesis responses which, over time, can influence and modulate key physiological responses such as muscle hypertrophy and increased strength. Therefore, the circadian clock may play a key role in the heterogeneous anabolic responses with resistance exercise. The central aim of this Hypothesis and Theory is to discuss and propose the potential interplay between the circadian molecular clock and established molecular mechanisms mediating muscle anabolic responses with resistance training. This article begins with a current review of the mechanisms associated with the heterogeneity in muscle anabolism with resistance training before introducing the molecular pathways regulating circadian function in skeletal muscle. Recent work showing members of the core molecular clock system can regulate myogenic and translational signaling pathways is also discussed, forming the basis for a possible role of the circadian clock in the variable anabolic responses with resistance exercise.

Crystal engineering of giant molecules based on perylene diimide conjugated polyhedral oligomeric silsesquioxane nano-atom

NASA Astrophysics Data System (ADS)

Ren, He

Molecular architectures and topologies are found contributing to the formation of supramolecular structures of giant molecules. Dr. Cheng's research group developed a diverse of giant molecules via precisely controlled chemistry synthetic routes. These giant molecules can be categorized into several different families, namely giant surfactants, giant shape amphiphiles and giant polyhedron. By analyzing the hierarchical structures of these carefully designed and precisely synthesized giant molecules, the structural factors which affect, or even dominates, in some cases, the formation of supramolecular structures are revealed in these intensive researches. The results will further contribute to the understanding of dependence of supramolecular structures on molecular designs as well as molecular topology, and providing a practical solution to the scaling up of microscopic molecular functionalities to macroscopic material properties. Molecular Nano Particles (MNPs), including fullerene (C60), POSS, Polyoxometalate (POM) and proteins etc., is defined and applied as a specific type of building blocks in the design and synthesis of giant molecules. The persistence in shape and symmetry is considered as one of the major properties of MNPs. This persistence will support the construction of giant molecules for further supramolecular structures' study by introducing specific shapes, or precisely located side groups which will facilitate self-assembling behaviors with pre-programmed secondary interactions. Dictating material physical properties by its chemical composition is an attractive yet currently failed approach in the study of materials. However, the pursuit of determining material properties by microscopic molecular level properties is never seized, and found its solution when the idea of crystal engineering is raised: should each atom in the material is located exactly where it is designed to be and is properly bonded, the property of the material is hence determined. In such "bottom-up" approach, the precise fabrication of 2 nm 100 nm nanostructures, is of great research interest. In this thesis, crystal engineering of giant molecules based on PDI conjugated POSS Nano-Atom (PDI-BPOSS) nano-atoms via self-assembly is performed and studied. Herein, three different giant molecules were synthesized: shape amphiphile, m-phenyl-(PDI-BPOSS)2 (S1) and tetrahedron, R-(PDI-BPOSS)4 (S2) and S-(PDI-BPOSS)4 (S3). Single crystals were grown for S1 and S2, X-ray diffraction (XRD), Scanning Electron Microscopy (SEM) and transmission electron microscopy (TEM) were performed, and crystal structures of these samples were determined, while hexagonal superlattice without crystal order can be observed for S3 to exhibit crystal-like morphology.

Design, Synthesis, and Self-Assembly of Well-Defined Hybrid Materials Including Polymer Amphiphiles and Giant Tetrahedra Molecules Based on Poss Nanoparticles

NASA Astrophysics Data System (ADS)

Huang, Mingjun

"Bottom-up" techniques-based self-assembly are always attracting people's interests since this technology provides relatively low economic cost and fast route to construct organized structures at different scales. Considering unprecedented benefits from polymer materials, self-assemblies utilizing polymer building blocks have been extensively studied to achieve diverse hierarchical structures and various attractive properties. However, precise controls of chemical primary structures and compositions and exact constructions of hierarchal ordered structures in synthetic polymers are far from being fully appreciated. In this dissertation, a novel approach has been utilized to construct diverse well-defined nano-building blocks, giant molecules, via conjugating different, and functionalized molecular nanoparticles (MNPs) which are shape- and volume-persistent nano-objects with precise molecular structure and specific symmetry. The representative examples of the three basic categories of giant molecules, "giant polyhedra", "giant surfactants", and "giant shape amphiphiles" were discussed in details. First, a class of precisely defined, nanosized giant tetrahedra was constructed by placing different polyhedral oligomeric silsesquioxane (POSS) molecular nanoparticles at the vertices of a rigid tetrahedral framework. Designed symmetry breaking of these giant tetrahedra introduces accurate positional interactions and results in diverse selectively assembled, highly ordered supramolecular lattices including a Frank-Kasper (FK) A15 phase. The FK and quasicrystal phases are originally identified in metal alloys and only sporadically observed in soft matters. It remains unclear how to correlate their stability with the chemical composition and molecular topology in the self-assembling systems. We then for this purpose designed and studied the self-assembly phase transition sequences of four series of hybrid giant surfactants based on hydrophilic POSS cages tethered with one to four polystyrene (PS) tails. With increasing the number of tails, molecular topological variations not only affect phase boundaries in terms of the PS volume fraction, but also open a window to stabilize supramolecular FK and quasicrystal phases in the spherical phase region, demonstrating the critical role of molecular topology in dictating the formation of unconventional supramolecular lattices of "soft" spherical motifs. The FK A15 phase was even surprisingly observed in the giant shape amphiphile molecule, triphenylene-6BPOSS, which has a disk-like flat triphenylene core connected with six hydrophobic POSS cages by sides. Without conical molecular shape, triphenylene-6BPOSS self-assembled and stabilized into supramolecular sphere via pi-pi interactions through a completely different mechanism with precious two cases. These studies indicate that "bottom-up" self-assemble based on well-defined giant molecules approach can be rather powerful to fabricate usually complicated hierarchical structures and open up a wide field of supramolecular self-assembly with unexpected structure and properties.

Variability among Capsicum baccatum accessions from Goiás, Brazil, assessed by morphological traits and molecular markers.

PubMed

Martinez, A L A; Araújo, J S P; Ragassi, C F; Buso, G S C; Reifschneider, F J B

2017-07-06

Capsicum peppers are native to the Americas, with Brazil being a significant diversity center. Capsicum baccatum accessions at Instituto Federal (IF) Goiano represent a portion of the species genetic resources from central Brazil. We aimed to characterize a C. baccatum working collection comprising 27 accessions and 3 commercial cultivars using morphological traits and molecular markers to describe its genetic and morphological variability and verify the occurrence of duplicates. This set included 1 C. baccatum var. praetermissum and 29 C. baccatum var. pendulum with potential for use in breeding programs. Twenty-two morphological descriptors, 57 inter-simple sequence repeat, and 34 random amplified polymorphic DNA markers were used. Genetic distance was calculated through the Jaccard similarity index and genetic variability through cluster analysis using the unweighted pair group method with arithmetic mean, resulting in dendrograms for both morphological analysis and molecular analysis. Genetic variability was found among C. baccatum var. pendulum accessions, and the distinction between the two C. baccatum varieties was evident in both the morphological and molecular analyses. The 29 C. baccatum var. pendulum genotypes clustered in four groups according to fruit type in the morphological analysis. They formed seven groups in the molecular analysis, without a clear correspondence with morphology. No duplicates were found. The results describe the genetic and morphological variability, provide a detailed characterization of genotypes, and discard the possibility of duplicates within the IF Goiano C. baccatum L. collection. This study will foment the use of this germplasm collection in C. baccatum breeding programs.

Steady state temperature distribution in dermal regions of an irregular tapered shaped human limb with variable eccentricity.

PubMed

Agrawal, M; Pardasani, K R; Adlakha, N

2014-08-01

The investigators in the past have developed some models of temperature distribution in the human limb assuming it as a regular circular or elliptical tapered cylinder. But in reality the limb is not of regular tapered cylindrical shape. The radius and eccentricity are not same throughout the limb. In view of above a model of temperature distribution in the irregular tapered elliptical shaped human limb is proposed for a three dimensional steady state case in this paper. The limb is assumed to be composed of multiple cylindrical substructures with variable radius and eccentricity. The mathematical model incorporates the effect of blood mass flow rate, metabolic activity and thermal conductivity. The outer surface is exposed to the environment and appropriate boundary conditions have been framed. The finite element method has been employed to obtain the solution. The temperature profiles have been computed in the dermal layers of a human limb and used to study the effect of shape, microstructure and biophysical parameters on temperature distribution in human limbs. The proposed model is one of the most realistic model as compared to conventional models as this can be effectively employed to every regular and nonregular structures of the body with variable radius and eccentricity to study the thermal behaviour. Copyright © 2014 Elsevier Ltd. All rights reserved.

LIGSIFT: an open-source tool for ligand structural alignment and virtual screening.

PubMed

Roy, Ambrish; Skolnick, Jeffrey

2015-02-15

Shape-based alignment of small molecules is a widely used approach in computer-aided drug discovery. Most shape-based ligand structure alignment applications, both commercial and freely available ones, use the Tanimoto coefficient or similar functions for evaluating molecular similarity. Major drawbacks of using such functions are the size dependence of the score and the fact that the statistical significance of the molecular match using such metrics is not reported. We describe a new open-source ligand structure alignment and virtual screening (VS) algorithm, LIGSIFT, that uses Gaussian molecular shape overlay for fast small molecule alignment and a size-independent scoring function for efficient VS based on the statistical significance of the score. LIGSIFT was tested against the compounds for 40 protein targets available in the Directory of Useful Decoys and the performance was evaluated using the area under the ROC curve (AUC), the Enrichment Factor (EF) and Hit Rate (HR). LIGSIFT-based VS shows an average AUC of 0.79, average EF values of 20.8 and a HR of 59% in the top 1% of the screened library. LIGSIFT software, including the source code, is freely available to academic users at http://cssb.biology.gatech.edu/LIGSIFT. Supplementary data are available at Bioinformatics online. skolnick@gatech.edu. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Exploiting Molecular Weight Distribution Shape to Tune Domain Spacing in Block Copolymer Thin Films.

PubMed

Gentekos, Dillon T; Jia, Junteng; Tirado, Erika S; Barteau, Katherine P; Smilgies, Detlef-M; DiStasio, Robert A; Fors, Brett P

2018-04-04

We report a method for tuning the domain spacing ( D sp ) of self-assembled block copolymer thin films of poly(styrene- block-methyl methacrylate) (PS- b-PMMA) over a large range of lamellar periods. By modifying the molecular weight distribution (MWD) shape (including both the breadth and skew) of the PS block via temporal control of polymer chain initiation in anionic polymerization, we observe increases of up to 41% in D sp for polymers with the same overall molecular weight ( M n ≈ 125 kg mol -1 ) without significantly changing the overall morphology or chemical composition of the final material. In conjunction with our experimental efforts, we have utilized concepts from population statistics and least-squares analysis to develop a model for predicting D sp based on the first three moments of the MWDs. This statistical model reproduces experimental D sp values with high fidelity (with mean absolute errors of 1.2 nm or 1.8%) and provides novel physical insight into the individual and collective roles played by the MWD moments in determining this property of interest. This work demonstrates that both MWD breadth and skew have a profound influence over D sp , thereby providing an experimental and conceptual platform for exploiting MWD shape as a simple and modular handle for fine-tuning D sp in block copolymer thin films.

ARE LARGE, COMETARY-SHAPED PROPLYDS REALLY (FREE-FLOATING) EVAPORATING GAS GLOBULES?

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

Sahai, R.; Guesten, R.; Morris, M. R., E-mail: raghvendra.sahai@jpl.nasa.gov

2012-12-20

We report the detection of strong and compact molecular line emission (in the CO J = 3-2, 4-3, 6-5, 7-6, {sup 13}CO J = 3-2, HCN, and HCO{sup +} J = 4-3 transitions) from a cometary-shaped object (Carina-frEGG1) in the Carina star-forming region (SFR) previously classified as a photoevaporating protoplanetary disk (proplyd). We derive a molecular mass of 0.35 M{sub Sun} for Carina-frEGG1, which shows that it is not a proplyd, but belongs to a class of free-floating evaporating gas globules (frEGGs) recently found in the Cygnus SFR by Sahai et al. Archival adaptive optics near-IR (Ks) images show amore » central hourglass-shaped nebula. The derived source luminosity (about 8-18 L{sub Sun }), the hourglass morphology, and the presence of collimated jets seen in Hubble Space Telescope images imply the presence of a jet-driving, young, low-mass star deeply embedded in the dust inside Carina-frEGG1. Our results suggest that the true nature of many or most such cometary-shaped objects seen in massive SFRs and previously labeled as proplyds has been misunderstood, and that these are really frEGGs.« less

Disentangling the role of the Y(4260) in e+e- →D*Dbar* and Ds* Dbars* via line shape studies

NASA Astrophysics Data System (ADS)

Xue, Si-Run; Jing, Hao-Jie; Guo, Feng-Kun; Zhao, Qiang

2018-04-01

Whether the Y (4260) can couple to open charm channels has been a crucial issue for understanding its nature. The available experimental data suggest that the cross section line shapes of exclusive processes in e+e- annihilations have nontrivial structures around the mass region of the Y (4260). As part of a series of studies of the Y (4260) as mainly a D bar D1 (2420) + c . c . molecular state, we show that the partial widths of the Y (4260) to the two-body open charm channels of e+e- →D*Dbar* and Ds* D bars* are much smaller than that to D bar D* π + c . c . . The line shapes measured by the Belle Collaboration for these two channels can be well described by the vector charmonium states ψ (4040), ψ (4160) and ψ (4415) together with the Y (4260). It turns out that the interference of the Y (4260) with the other charmonia produces a dip around 4.22 GeV in the e+e- →D*Dbar* cross section line shape. The data also show an evidence for the strong coupling of the Y (4260) to the DDbar1 (2420), in line with the expectation in the hadronic molecular scenario for the Y (4260).

Impact of P/In flux ratio and epilayer thickness on faceting for nanoscale selective area growth of InP by molecular beam epitaxy.

PubMed

Fahed, M; Desplanque, L; Coinon, C; Troadec, D; Wallart, X

2015-07-24

The impact of the P/In flux ratio and the deposited thickness on the faceting of InP nanostructures selectively grown by molecular beam epitaxy (MBE) is reported. Homoepitaxial growth of InP is performed inside 200 nm wide stripe openings oriented either along a [110] or [1-10] azimuth in a 10 nm thick SiO2 film deposited on an InP(001) substrate. When varying the P/In flux ratio, no major shape differences are observed for [1-10]-oriented apertures. On the other hand, the InP nanostructure cross sections strongly evolve for [110]-oriented apertures for which (111)B facets are more prominent and (001) ones shrink for large P/In flux ratio values. These results show that the growth conditions allow tailoring the nanocrystal shape. They are discussed in the framework of the equilibrium crystal shape model using existing theoretical calculations of the surface energies of different low-index InP surfaces as a function of the phosphorus chemical potential, directly related to the P/In ratio. Experimental observations strongly suggest that the relative (111)A surface energy is probably smaller than the calculated value. We also discuss the evolution of the nanostructure shape with the InP-deposited thickness.

Universal shape characteristics for the mesoscopic star-shaped polymer via dissipative particle dynamics simulations

NASA Astrophysics Data System (ADS)

Kalyuzhnyi, O.; Ilnytskyi, J. M.; Holovatch, Yu; von Ferber, C.

2018-05-01

In this paper we study the shape characteristics of star-like polymers in various solvent quality using a mesoscopic level of modeling. The dissipative particle dynamics simulations are performed for the homogeneous and four different heterogeneous star polymers with the same molecular weight. We analyse the gyration radius and asphericity at the poor, good and θ-solvent regimes. Detailed explanation based on interplay between enthalpic and entropic contributions to the free energy and analyses on of the asphericity of individual branches are provided to explain the increase of the apsphericity in θ-solvent regime.

Host–guest complexes between cryptophane-C and chloromethanes revisited

PubMed Central

Takacs, Z; Soltesova, M; Kowalewski, J; Lang, J; Brotin, T; Dutasta, J-P

2013-01-01

Cryptophane-C is composed of two nonequivalent cyclotribenzylene caps, one of which contains methoxy group substituents on the phenyl rings. The two caps are connected by three OCH2CH2O linkers in an anti arrangement. Host–guest complexes of cryptophane-C with dichloromethane and chloroform in solution were investigated in detail by nuclear magnetic resonance techniques and density functional theory (DFT) calculations. Variable temperature proton and carbon-13 spectra show a variety of dynamic processes, such as guest exchange and host conformational transitions. The guest exchange was studied quantitatively by exchange spectroscopy measurements or by line-shape analysis. The conformational preferences of the guest-containing host were interpreted through cross-relaxation measurements, providing evidence of the gauche+2 and gauche−2 conformations of the linkers. In addition, the mobility of the chloroform guest inside the cavity was studied by carbon-13 relaxation experiments. Combining different types of evidence led to a detailed picture of molecular recognition, interpreted in terms of conformational selection. Copyright © 2012 John Wiley & Sons, Ltd. PMID:23132654

A cell-based computational model of early embryogenesis coupling mechanical behaviour and gene regulation

NASA Astrophysics Data System (ADS)

Delile, Julien; Herrmann, Matthieu; Peyriéras, Nadine; Doursat, René

2017-01-01

The study of multicellular development is grounded in two complementary domains: cell biomechanics, which examines how physical forces shape the embryo, and genetic regulation and molecular signalling, which concern how cells determine their states and behaviours. Integrating both sides into a unified framework is crucial to fully understand the self-organized dynamics of morphogenesis. Here we introduce MecaGen, an integrative modelling platform enabling the hypothesis-driven simulation of these dual processes via the coupling between mechanical and chemical variables. Our approach relies upon a minimal `cell behaviour ontology' comprising mesenchymal and epithelial cells and their associated behaviours. MecaGen enables the specification and control of complex collective movements in 3D space through a biologically relevant gene regulatory network and parameter space exploration. Three case studies investigating pattern formation, epithelial differentiation and tissue tectonics in zebrafish early embryogenesis, the latter with quantitative comparison to live imaging data, demonstrate the validity and usefulness of our framework.

Epigenomics and human adaptation to high altitude.

PubMed

Julian, Colleen G

2017-11-01

Over the past decade, major technological and analytical advancements have propelled efforts toward identifying the molecular mechanisms that govern human adaptation to high altitude. Despite remarkable progress with respect to the identification of adaptive genomic signals that are strongly associated with the "hypoxia-tolerant" physiological characteristics of high-altitude populations, many questions regarding the fundamental biological processes underlying human adaptation remain unanswered. Vital to address these enduring questions will be determining the role of epigenetic processes, or non-sequence-based features of the genome, that are not only critical for the regulation of transcriptional responses to hypoxia but heritable across generations. This review proposes that epigenomic processes are involved in shaping patterns of adaptation to high altitude by influencing adaptive potential and phenotypic variability under conditions of limited oxygen supply. Improved understanding of the interaction between genetic, epigenetic, and environmental factors holds great promise to provide deeper insight into the mechanisms underlying human adaptive potential, and clarify its implications for biomedical research. Copyright © 2017 the American Physiological Society.

Are there laws of genome evolution?

PubMed

Koonin, Eugene V

2011-08-01

Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics" in the same sense "law" is understood in modern physics.

Redox Regulation of Endothelial Cell Fate

PubMed Central

Song, Ping; Zou, Ming-Hui

2014-01-01

Endothelial cells (ECs) are present throughout blood vessels and have variable roles in both physiological and pathological settings. EC fate is altered and regulated by several key factors in physiological or pathological conditions. Reactive nitrogen species and reactive oxygen species derived from NAD(P)H oxidases, mitochondria, or nitric oxide-producing enzymes are not only cytotoxic but also compose a signaling network in the redox system. The formation, actions, key molecular interactions, and physiological and pathological relevance of redox signals in ECs remain unclear. We review the identities, sources, and biological actions of oxidants and reductants produced during EC function or dysfunction. Further, we discuss how ECs shape key redox sensors and examine the biological functions, transcriptional responses, and post-translational modifications evoked by the redox system in ECs. We summarize recent findings regarding the mechanisms by which redox signals regulate the fate of ECs and address the outcome of altered EC fate in health and disease. Future studies will examine if the redox biology of ECs can be targeted in pathophysiological conditions. PMID:24633153

Spontaneous assembly of chemically encoded two-dimensional coacervate droplet arrays by acoustic wave patterning

PubMed Central

Tian, Liangfei; Martin, Nicolas; Bassindale, Philip G.; Patil, Avinash J.; Li, Mei; Barnes, Adrian; Drinkwater, Bruce W.; Mann, Stephen

2016-01-01

The spontaneous assembly of chemically encoded, molecularly crowded, water-rich micro-droplets into periodic defect-free two-dimensional arrays is achieved in aqueous media by a combination of an acoustic standing wave pressure field and in situ complex coacervation. Acoustically mediated coalescence of primary droplets generates single-droplet per node micro-arrays that exhibit variable surface-attachment properties, spontaneously uptake dyes, enzymes and particles, and display spatial and time-dependent fluorescence outputs when exposed to a reactant diffusion gradient. In addition, coacervate droplet arrays exhibiting dynamical behaviour and exchange of matter are prepared by inhibiting coalescence to produce acoustically trapped lattices of droplet clusters that display fast and reversible changes in shape and spatial configuration in direct response to modulations in the acoustic frequencies and fields. Our results offer a novel route to the design and construction of ‘water-in-water' micro-droplet arrays with controllable spatial organization, programmable signalling pathways and higher order collective behaviour. PMID:27708286

Culture observation and molecular phylogenetic analysis on the blooming green alga Chaetomorpha valida (Cladophorales, Chlorophyta) from China

NASA Astrophysics Data System (ADS)

Deng, Yunyan; Tang, Xiaorong; Zhan, Zifeng; Teng, Linhong; Ding, Lanping; Huang, Bingxin

2013-05-01

The marine green alga Chaetomorpha valida fouls aquaculture ponds along the coastal cities of Dalian and Rongcheng, China. Unialgal cultures were observed under a microscope to determine the developmental morphological characters of C. valida. Results reveal that gametophytic filaments often produce lateral branches under laboratory culture conditions, suggesting an atypical heteromorphic life cycle of C. valida between unbranched sporophytes and branched gametophytes, which differs from typical isomorphic alternation of Chaetomorpha species. The shape of the basal attachment cell, an important taxonomic character within the genus, was found variable depending on environmental conditions. The 18S rDNA and 28S rDNA regions were used to explore the phylogenetic affinity of the taxa. Inferred trees from 18S rDNA sequences revealed a close relationship between C. valida and Chaetomorpha moniligera. These results would enrich information in general biology and morphological plasticity of C. valida and provided a basis for future identification of green tide forming algae.

Avian egg shape: Form, function, and evolution.

PubMed

Stoddard, Mary Caswell; Yong, Ee Hou; Akkaynak, Derya; Sheard, Catherine; Tobias, Joseph A; Mahadevan, L

2017-06-23

Avian egg shape is generally explained as an adaptation to life history, yet we currently lack a global synthesis of how egg-shape differences arise and evolve. Here, we apply morphometric, mechanistic, and macroevolutionary analyses to the egg shapes of 1400 bird species. We characterize egg-shape diversity in terms of two biologically relevant variables, asymmetry and ellipticity, allowing us to quantify the observed morphologies in a two-dimensional morphospace. We then propose a simple mechanical model that explains the observed egg-shape diversity based on geometric and material properties of the egg membrane. Finally, using phylogenetic models, we show that egg shape correlates with flight ability on broad taxonomic scales, suggesting that adaptations for flight may have been critical drivers of egg-shape variation in birds. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Heritability of Wing Size and Shape of the Rice and Corn Strains of Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae).

PubMed

Cañas-Hoyos, N; Márquez, E J; Saldamando-Benjumea, C I

2016-08-01

Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) represents a pest of economic importance in all Western Hemisphere. This polyphagous species has diverged into two populations that have been mainly recognized with various mitochondrial and nuclear molecular markers and named "the rice" and "the corn" strains. In Colombia, both strains have evolved prezygotic and postzygotic isolation. They differ in tolerance to Bacillus thuringiensis (Cry1Ac and Cry1Ab endotoxins) and the insecticides lambda-cyhalothrin and methomyl. In 2014, a wing morphometric analysis made in 159 individuals from a colony showed that both strains significantly differ in wing shape. The species also exhibits sexual dimorphism in the rice strain as in females wing size is larger than in males. Here, we continued this work with another wing morphometric approach in laboratory-reared strains to calculate wing size and shape heritabilities using a full-sib design and in wild populations to determine if this method distinguishes these strains. Our results show that male heritabilities of both traits were higher than female ones. Wild populations were significantly different in wing shape and size. These results suggest that wing morphometrics can be used as an alternative method to molecular markers to differentiate adults from laboratory-reared populations and wild populations of this pest, particularly in males of this species. Finally, Q ST values obtained for wing size and shape further demonstrated that both strains are genetically differentiated in nature.

Universal analytical scattering form factor for shell-, core-shell, or homogeneous particles with continuously variable density profile shape.

PubMed

Foster, Tobias

2011-09-01

A novel analytical and continuous density distribution function with a widely variable shape is reported and used to derive an analytical scattering form factor that allows us to universally describe the scattering from particles with the radial density profile of homogeneous spheres, shells, or core-shell particles. Composed by the sum of two Fermi-Dirac distribution functions, the shape of the density profile can be altered continuously from step-like via Gaussian-like or parabolic to asymptotically hyperbolic by varying a single "shape parameter", d. Using this density profile, the scattering form factor can be calculated numerically. An analytical form factor can be derived using an approximate expression for the original Fermi-Dirac distribution function. This approximation is accurate for sufficiently small rescaled shape parameters, d/R (R being the particle radius), up to values of d/R ≈ 0.1, and thus captures step-like, Gaussian-like, and parabolic as well as asymptotically hyperbolic profile shapes. It is expected that this form factor is particularly useful in a model-dependent analysis of small-angle scattering data since the applied continuous and analytical function for the particle density profile can be compared directly with the density profile extracted from the data by model-free approaches like the generalized inverse Fourier transform method. © 2011 American Chemical Society

Shapes of soot aerosol particles and implications for their effects on climate

NASA Astrophysics Data System (ADS)

Adachi, Kouji; Chung, Serena H.; Buseck, Peter R.

2010-08-01

Soot aerosol particles (also called light-absorbing, black, or elemental carbon) are major contributors to global warming through their absorption of solar radiation. When embedded in organic matter or sulfate, as is common in polluted areas such as over Mexico City (MC) and other megacities, their optical properties are affected by their shapes and positions within their host particles. However, large uncertainties remain regarding those variables and how they affect warming by soot. Using electron tomography with a transmission electron microscope, three-dimensional (3-D) images of individual soot particles embedded within host particles collected from MC and its surroundings were obtained. From those 3-D images, we calculated the optical properties using a discrete dipole approximation. Many soot particles have open, chainlike shapes even after being surrounded by organic matter and are located in off-center positions within their host materials. Such embedded soot absorbs sunlight less efficiently than if compact and located near the center of its host particle. In the case of our MC samples, their contribution to direct radiative forcing is ˜20% less than if they had a simple core-shell shape, which is the shape assumed in many climate models. This study shows that the shapes and positions of soot within its host particles have an important effect on particle optical properties and should be recognized as potentially important variables when evaluating global climate change.

Evaluation of INL Supplied MOOSE/OSPREY Model: Modeling Water Adsorption on Type 3A Molecular Sieve

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

Pompilio, L. M.; DePaoli, D. W.; Spencer, B. B.

The purpose of this study was to evaluate Idaho National Lab’s Multiphysics Object-Oriented Simulation Environment (MOOSE) software in modeling the adsorption of water onto type 3A molecular sieve (3AMS). MOOSE can be thought-of as a computing framework within which applications modeling specific coupled-phenomena can be developed and run. The application titled Off-gas SeParation and REcoverY (OSPREY) has been developed to model gas sorption in packed columns. The sorbate breakthrough curve calculated by MOOSE/OSPREY was compared to results previously obtained in the deep bed hydration tests conducted at Oak Ridge National Laboratory. The coding framework permits selection of various options, whenmore » they exist, for modeling a process. For example, the OSPREY module includes options to model the adsorption equilibrium with a Langmuir model or a generalized statistical thermodynamic adsorption (GSTA) model. The vapor solid equilibria and the operating conditions of the process (e.g., gas phase concentration) are required to calculate the concentration gradient driving the mass transfer between phases. Both the Langmuir and GSTA models were tested in this evaluation. Input variables were either known from experimental conditions, or were available (e.g., density) or were estimated (e.g., thermal conductivity of sorbent) from the literature. Variables were considered independent of time, i.e., rather than having a mass transfer coefficient that varied with time or position in the bed, the parameter was set to remain constant. The calculated results did not coincide with data from laboratory tests. The model accurately estimated the number of bed volumes processed for the given operating parameters, but breakthrough times were not accurately predicted, varying 50% or more from the data. The shape of the breakthrough curves also differed from the experimental data, indicating a much wider sorption band. Model modifications are needed to improve its utility and predictive capability. Recommended improvements include: greater flexibility for input of mass transfer parameters, time-variable gas inlet concentration, direct output of loading and temperature profiles along the bed, and capability to conduct simulations of beds in series.« less

Multiscale equation-free algorithms for molecular dynamics

NASA Astrophysics Data System (ADS)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

Promoter architecture dictates cell-to-cell variability in gene expression.

PubMed

Jones, Daniel L; Brewster, Robert C; Phillips, Rob

2014-12-19

Variability in gene expression among genetically identical cells has emerged as a central preoccupation in the study of gene regulation; however, a divide exists between the predictions of molecular models of prokaryotic transcriptional regulation and genome-wide experimental studies suggesting that this variability is indifferent to the underlying regulatory architecture. We constructed a set of promoters in Escherichia coli in which promoter strength, transcription factor binding strength, and transcription factor copy numbers are systematically varied, and used messenger RNA (mRNA) fluorescence in situ hybridization to observe how these changes affected variability in gene expression. Our parameter-free models predicted the observed variability; hence, the molecular details of transcription dictate variability in mRNA expression, and transcriptional noise is specifically tunable and thus represents an evolutionarily accessible phenotypic parameter. Copyright © 2014, American Association for the Advancement of Science.

Cartilage.

ERIC Educational Resources Information Center

Caplan, Arnold I.

1984-01-01

Cartilage is a fundamental biological material that helps to shape the body and then helps to support it. Its fundamental properties of strength and resilience are explained in terms of the tissue's molecular structure. (JN)

Monte Carlo simulation of energy deposition by low-energy electrons in molecular hydrogen

NASA Technical Reports Server (NTRS)

Heaps, M. G.; Furman, D. R.; Green, A. E. S.

1975-01-01

A set of detailed atomic cross sections has been used to obtain the spatial deposition of energy by 1-20-eV electrons in molecular hydrogen by a Monte Carlo simulation of the actual trajectories. The energy deposition curve (energy per distance traversed) is quite peaked in the forward direction about the entry point for electrons with energies above the threshold of the electronic states, but the peak decreases and broadens noticeably as the electron energy decreases below 10 eV (threshold for the lowest excitable electronic state of H2). The curve also assumes a very symmetrical shape for energies below 10 eV, indicating the increasing importance of elastic collisions in determining the shape of the curve, although not the mode of energy deposition.

One ligand in dual roles: self-assembly of a bis-rhomboidal-shaped, three-dimensional molecular wheel.

PubMed

Lu, Xiaocun; Li, Xiaopeng; Guo, Kai; Wang, Jing; Huang, Mingjun; Wang, Jin-Liang; Xie, Ting-Zheng; Moorefield, Charles N; Cheng, Stephen Z D; Wesdemiotis, Chrys; Newkome, George R

2014-10-06

A facile high yield, self-assembly process that leads to a terpyridine-based, three-dimensional, bis-rhomboidal-shaped, molecular wheel is reported. The desired coordination-driven supramolecular wheel involves eight structurally distorted tristerpyridine (tpy) ligands possessing a 60° angle between the adjacent tpy units and twelve Zn(2+) ions. The tpy ligand plays dual roles in the self-assembly process: two are staggered at 180° to create the internal hub, while six produce the external rim. The wheel can be readily generated by mixing the tpy ligand and Zn(2+) in a stoichiometric ratio of 2:3; full characterization is provided by ESI-MS, NMR spectroscopy, and TEM imaging. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Double-Staining Method for Differentiation of Morphological Changes and Membrane Integrity of Campylobacter coli Cells

PubMed Central

Alonso, Jose L.; Mascellaro, Salvatore; Moreno, Yolanda; Ferrús, María A.; Hernández, Javier

2002-01-01

We developed a double-staining procedure involving NanoOrange dye (Molecular Probes, Eugene, Oreg.) and membrane integrity stains (LIVE/DEAD BacLight kit; Molecular Probes) to show the morphological and membrane integrity changes of Campylobacter coli cells during growth. The conversion from a spiral to a coccoid morphology via intermediary forms and the membrane integrity changes of the C. coli cells can be detected with the double-staining procedure. Our data indicate that young or actively growing cells are mainly spiral shaped (green-stained cells), but older cells undergo a degenerative change to coccoid forms (red-stained cells). Club-shaped transition cell forms were observed with NanoOrange stain. Chlorinated drinking water affected the viability but not the morphology of C. coli cells. PMID:12324366

Excited state dynamics & optical control of molecular motors

NASA Astrophysics Data System (ADS)

Wiley, Ted; Sension, Roseanne

2014-03-01

Chiral overcrowded alkenes are likely candidates for light driven rotary molecular motors. At their core, these molecular motors are based on the chromophore stilbene, undergoing ultrafast cis/trans photoisomerization about their central double bond. Unlike stilbene, the photochemistry of molecular motors proceeds in one direction only. This unidirectional rotation is a result of helicity in the molecule induced by steric hindrance. However, the steric hindrance which ensures unidirectional excited state rotation, has the unfortunate consequence of producing large ground state barriers which dramatically decrease the overall rate of rotation. These molecular scale ultrafast motors have only recently been studied by ultrafast spectroscopy. Our lab has studied the photochemistry and photophysics of a ``first generation'' molecular motor with UV-visible transient absorption spectroscopy. We hope to use optical pulse shaping to enhance the efficiency and turnover rate of these molecular motors.

Shape Optimization for Navier-Stokes Equations with Algebraic Turbulence Model: Numerical Analysis and Computation

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

Haslinger, Jaroslav, E-mail: hasling@karlin.mff.cuni.cz; Stebel, Jan, E-mail: stebel@math.cas.cz

2011-04-15

We study the shape optimization problem for the paper machine headbox which distributes a mixture of water and wood fibers in the paper making process. The aim is to find a shape which a priori ensures the given velocity profile on the outlet part. The mathematical formulation leads to the optimal control problem in which the control variable is the shape of the domain representing the header, the state problem is represented by the generalized Navier-Stokes system with nontrivial boundary conditions. This paper deals with numerical aspects of the problem.

Development of non-conventional instrument transformers (NCIT) using smart materials

NASA Astrophysics Data System (ADS)

Nikolić, Bojan; Khan, Sanowar; Gabdullin, Nikita

2016-11-01

In this paper is presented a novel approach for current measurement using smart materials, magnetic shape memory (MSM) alloys. Their shape change can be controlled by the application of magnetic field or mechanical stress. This gives the possibility to measure currents by correlating the magnetic field produced by the current, shape change in an MSM- based sensor and the voltage output of a Linear Variable Differential Transducer (LVDT) actuated by this shape change. In the first part of the paper is presented a review of existing current measurement sensors by comparing their properties and highlighting their advantages and disadvantages.

Shape design sensitivity analysis using domain information

NASA Technical Reports Server (NTRS)

Seong, Hwal-Gyeong; Choi, Kyung K.

1985-01-01

A numerical method for obtaining accurate shape design sensitivity information for built-up structures is developed and demonstrated through analysis of examples. The basic character of the finite element method, which gives more accurate domain information than boundary information, is utilized for shape design sensitivity improvement. A domain approach for shape design sensitivity analysis of built-up structures is derived using the material derivative idea of structural mechanics and the adjoint variable method of design sensitivity analysis. Velocity elements and B-spline curves are introduced to alleviate difficulties in generating domain velocity fields. The regularity requirements of the design velocity field are studied.

Shape Optimization for Navier-Stokes Equations with Algebraic Turbulence Model: Existence Analysis

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

Bulicek, Miroslav; Haslinger, Jaroslav; Malek, Josef

2009-10-15

We study a shape optimization problem for the paper machine headbox which distributes a mixture of water and wood fibers in the paper making process. The aim is to find a shape which a priori ensures the given velocity profile on the outlet part. The mathematical formulation leads to an optimal control problem in which the control variable is the shape of the domain representing the header, the state problem is represented by a generalized stationary Navier-Stokes system with nontrivial mixed boundary conditions. In this paper we prove the existence of solutions both to the generalized Navier-Stokes system and tomore » the shape optimization problem.« less

Self-Latching Piezocomposite Actuator

NASA Technical Reports Server (NTRS)

Wilkie, William K. (Inventor); Lynch, Christopher S. (Inventor); Bryant, Robert G. (Inventor)

2017-01-01

A self-latching piezocomposite actuator includes a plurality of shape memory ceramic fibers. The actuator can be latched by applying an electrical field to the shape memory ceramic fibers. The actuator remains in a latched state/shape after the electrical field is no longer present. A reverse polarity electric field may be applied to reset the actuator to its unlatched state/shape. Applied electric fields may be utilized to provide a plurality of latch states between the latched and unlatched states of the actuator. The self-latching piezocomposite actuator can be used for active/adaptive airfoils having variable camber, trim tabs, active/deformable engine inlets, adaptive or adjustable vortex generators, active optical components such as mirrors that change shapes, and other morphing structures.

Extended q -Gaussian and q -exponential distributions from gamma random variables

NASA Astrophysics Data System (ADS)

Budini, Adrián A.

2015-05-01

The family of q -Gaussian and q -exponential probability densities fit the statistical behavior of diverse complex self-similar nonequilibrium systems. These distributions, independently of the underlying dynamics, can rigorously be obtained by maximizing Tsallis "nonextensive" entropy under appropriate constraints, as well as from superstatistical models. In this paper we provide an alternative and complementary scheme for deriving these objects. We show that q -Gaussian and q -exponential random variables can always be expressed as a function of two statistically independent gamma random variables with the same scale parameter. Their shape index determines the complexity q parameter. This result also allows us to define an extended family of asymmetric q -Gaussian and modified q -exponential densities, which reduce to the standard ones when the shape parameters are the same. Furthermore, we demonstrate that a simple change of variables always allows relating any of these distributions with a beta stochastic variable. The extended distributions are applied in the statistical description of different complex dynamics such as log-return signals in financial markets and motion of point defects in a fluid flow.

Application of shape memory alloy (SMA) spars for aircraft maneuver enhancement

NASA Astrophysics Data System (ADS)

Nam, Changho; Chattopadhyay, Aditi; Kim, Youdan

2002-07-01

Modern combat aircraft are required to achieve aggressive maneuverability and high agility performance, while maintaining handling qualities over a wide range of flight conditions. Recently, a new adaptive-structural concept called variable stiffness spar is proposed in order to increase the maneuverability of the flexible aircraft. The variable stiffness spar controls wing torsional stiffness to enhance roll performance in the complete flight envelope. However, variable stiffness spar requires the mechanical actuation system in order to rotate the Variable stiffness spar during flight. The mechanical actuation system to rotate variable stiffness spar may cause an additional weight increase. In this paper, we will apply Shape Memory Alloy (SMA) spars for aeroelastic performance enhancement. In order to explore the potential of SMA spar design, roll performance of the composite smart wings will be investigated using ASTROS. Parametric study will be conducted to investigate the SMA spar effects by changing the spar locations and geometry. The results show that with activation of the SMA spar, the roll effectiveness can be increased up to 61% compared with the baseline model.

Climate history shapes contemporary leaf litter decomposition

Treesearch

Michael S. Strickland; Ashley D. Keiser; Mark A. Bradford

2015-01-01

Litter decomposition is mediated by multiple variables, of which climate is expected to be a dominant factor at global scales. However, like other organisms, traits of decomposers and their communities are shaped not just by the contemporary climate but also their climate history. Whether or not this affects decomposition rates is underexplored. Here we source...

A Qualitative Examination of Mexican Immigrants' Career Development: Perceived Barriers and Motivators

ERIC Educational Resources Information Center

Shinnar, Rachel Sheli

2007-01-01

This study examines the variables shaping career development among Mexican immigrants. Based on qualitative interviews with 17 adult, Mexican immigrants, a model describing the barriers and motivators to career development for this sample is offered. Findings indicate that Mexican immigrants' careers are shaped by three sets of interrelated…

A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds† †Electronic supplementary information (ESI) available: Experimental procedures, characterization data and details of the computational analyses. See DOI: 10.1039/c5ob00371g Click here for additional data file.

PubMed Central

Isidro-Llobet, Albert; Hadje Georgiou, Kathy; Galloway, Warren R. J. D.; Giacomini, Elisa; Hansen, Mette R.; Méndez-Abt, Gabriela; Tan, Yaw Sing; Carro, Laura; Sore, Hannah F.

2015-01-01

Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity. PMID:25778821

Robust Airfoil Optimization in High Resolution Design Space

NASA Technical Reports Server (NTRS)

Li, Wu; Padula, Sharon L.

2003-01-01

The robust airfoil shape optimization is a direct method for drag reduction over a given range of operating conditions and has three advantages: (1) it prevents severe degradation in the off-design performance by using a smart descent direction in each optimization iteration, (2) it uses a large number of B-spline control points as design variables yet the resulting airfoil shape is fairly smooth, and (3) it allows the user to make a trade-off between the level of optimization and the amount of computing time consumed. The robust optimization method is demonstrated by solving a lift-constrained drag minimization problem for a two-dimensional airfoil in viscous flow with a large number of geometric design variables. Our experience with robust optimization indicates that our strategy produces reasonable airfoil shapes that are similar to the original airfoils, but these new shapes provide drag reduction over the specified range of Mach numbers. We have tested this strategy on a number of advanced airfoil models produced by knowledgeable aerodynamic design team members and found that our strategy produces airfoils better or equal to any designs produced by traditional design methods.

Pancreas and cyst segmentation

NASA Astrophysics Data System (ADS)

Dmitriev, Konstantin; Gutenko, Ievgeniia; Nadeem, Saad; Kaufman, Arie

2016-03-01

Accurate segmentation of abdominal organs from medical images is an essential part of surgical planning and computer-aided disease diagnosis. Many existing algorithms are specialized for the segmentation of healthy organs. Cystic pancreas segmentation is especially challenging due to its low contrast boundaries, variability in shape, location and the stage of the pancreatic cancer. We present a semi-automatic segmentation algorithm for pancreata with cysts. In contrast to existing automatic segmentation approaches for healthy pancreas segmentation which are amenable to atlas/statistical shape approaches, a pancreas with cysts can have even higher variability with respect to the shape of the pancreas due to the size and shape of the cyst(s). Hence, fine results are better attained with semi-automatic steerable approaches. We use a novel combination of random walker and region growing approaches to delineate the boundaries of the pancreas and cysts with respective best Dice coefficients of 85.1% and 86.7%, and respective best volumetric overlap errors of 26.0% and 23.5%. Results show that the proposed algorithm for pancreas and pancreatic cyst segmentation is accurate and stable.

Formation and shape-control of hierarchical cobalt nanostructures using quaternary ammonium salts in aqueous media

PubMed Central

Deshmukh, Ruchi; Mehra, Anurag

2017-01-01

Aggregation and self-assembly are influenced by molecular interactions. With precise control of molecular interactions, in this study, a wide range of nanostructures ranging from zero-dimensional nanospheres to hierarchical nanoplates and spindles have been successfully synthesized at ambient temperature in aqueous solution. The nanostructures reported here are formed by aggregation of spherical seed particles (monomers) in presence of quaternary ammonium salts. Hydroxide ions and a magnetic moment of the monomers are essential to induce shape anisotropy in the nanostructures. The cobalt nanoplates are studied in detail, and a growth mechanism based on collision, aggregation, and crystal consolidation is proposed based on a electron microscopy studies. The growth mechanism is generalized for rods, spindles, and nearly spherical nanostructures, obtained by varying the cation group in the quaternary ammonium hydroxides. Electron diffraction shows different predominant lattice planes on the edge and on the surface of a nanoplate. The study explains, hereto unaddressed, the temporal evolution of complex magnetic nanostructures. These ferromagnetic nanostructures represent an interesting combination of shape anisotropy and magnetic characteristics. PMID:28326240

DNA-linked NanoParticle Lattices with Diamond Symmetry: Stability, Shape and Optical Properties

NASA Astrophysics Data System (ADS)

Emamy, Hamed; Tkachenko, Alexei; Gang, Oleg; Starr, Francis

The linking of nanoparticles (NP) by DNA has been proven to be an effective means to create NP lattices with specific order. Lattices with diamond symmetry are predicted to offer novel photonic properties, but self-assembly of such lattices has proven to be challenging due to the low packing fraction, sensitivity to bond orientation, and local heterogeneity. Recently, we reported an approach to create diamond NP lattices based on the association between anisotropic particles with well-defined tetravalent DNA binding topology and isotropically functionalized NP. Here, we use molecular dynamics simulations to evaluate the Gibbs free energy of these lattices, and thereby determine the stability of these lattices as a function of NP size and DNA stiffness. We also predict the equilibrium shape for the cubic diamond crystallite using the Wulff construction method. Specifically, we predict the equilibrium shape using the surface energy for different crystallographic planes. We evaluate surface energy directly form molecular dynamics simulation, which we correlate with theoretical estimates from the expected number of broken DNA bonds along a facet. Furthermore we study the optical properties of this structure, e.g optical bandgap.

Binding Affinity prediction with Property Encoded Shape Distribution signatures

PubMed Central

Das, Sourav; Krein, Michael P.

2010-01-01

We report the use of the molecular signatures known as “Property-Encoded Shape Distributions” (PESD) together with standard Support Vector Machine (SVM) techniques to produce validated models that can predict the binding affinity of a large number of protein ligand complexes. This “PESD-SVM” method uses PESD signatures that encode molecular shapes and property distributions on protein and ligand surfaces as features to build SVM models that require no subjective feature selection. A simple protocol was employed for tuning the SVM models during their development, and the results were compared to SFCscore – a regression-based method that was previously shown to perform better than 14 other scoring functions. Although the PESD-SVM method is based on only two surface property maps, the overall results were comparable. For most complexes with a dominant enthalpic contribution to binding (ΔH/-TΔS > 3), a good correlation between true and predicted affinities was observed. Entropy and solvent were not considered in the present approach and further improvement in accuracy would require accounting for these components rigorously. PMID:20095526

Perchlorate-induced combustion of organic matter with variable molecular weights: Implications for Mars missions

NASA Astrophysics Data System (ADS)

Sephton, Mark A.; Lewis, James M. T.; Watson, Jonathan S.; Montgomery, Wren; Garnier, Carole

2014-11-01

Instruments on the Viking landers and Curiosity rover analyzed samples of Mars and detected carbon dioxide and organic compounds of uncertain origin. Mineral-assisted reactions are leading to uncertainty, particularly those involving perchlorate minerals which thermally decompose to produce chlorine and oxygen which can then react with organic matter to generate organochlorine compounds and carbon dioxide. Although generally considered a problem for interpretation, the release profiles of generated gases can indicate the type of organic matter present. We have performed a set of experiments with perchlorate and organic matter of variable molecular weights. Results indicate that organic susceptibility to thermal degradation and mineral-assisted reactions is related to molecular weight. Low molecular weight organic matter reacts at lower temperatures than its high molecular weight counterparts. The natural occurrence and association of organic matter with differing molecular weights helps to discriminate between contamination (usually low molecular weight organic matter only) and indigenous carbon (commonly low and high molecular weight organic matter together). Our results can be used to provide insights into data returning from Mars.

A new genus of leafhopper subtribe Paraboloponina (Hemiptera: Cicadellidae) with molecular phylogeny of related genera.

PubMed

Meshram, Naresh M; Shashank, Pathour R; Sinha, Twinkle

2017-01-01

A new leafhopper genus Chandra and species Chandra dehradunensis gen. nov., sp. nov. are described, illustrated from India and placed in the subtribe Paraboloponina (Cidadellidae: Deltocephalinae: Drabescini). This genus is closely associated with the genus Parabolopona Webb but differs in shape of the head, placement of antennae, male genitalia and molecular analysis using Histone H3 and COI genes confirmed the difference. The taxonomic and phylogenetic position of Chandra is discussed using morphological characters and preliminary molecular evidence of the new genus and related genus Parabolopona.

Variable Camber Continuous Aerodynamic Control Surfaces and Methods for Active Wing Shaping Control

NASA Technical Reports Server (NTRS)

Nguyen, Nhan T. (Inventor)

2016-01-01

An aerodynamic control apparatus for an air vehicle improves various aerodynamic performance metrics by employing multiple spanwise flap segments that jointly form a continuous or a piecewise continuous trailing edge to minimize drag induced by lift or vortices. At least one of the multiple spanwise flap segments includes a variable camber flap subsystem having multiple chordwise flap segments that may be independently actuated. Some embodiments also employ a continuous leading edge slat system that includes multiple spanwise slat segments, each of which has one or more chordwise slat segment. A method and an apparatus for implementing active control of a wing shape are also described and include the determination of desired lift distribution to determine the improved aerodynamic deflection of the wings. Flap deflections are determined and control signals are generated to actively control the wing shape to approximate the desired deflection.

Investigation of Selectively-Reinforced Metallic Lugs

NASA Technical Reports Server (NTRS)

Farley, Gary L.; Abada, Christopher H.

2007-01-01

An investigation of the effects of material and geometric variables on the response of U-shaped band-reinforced metallic lugs was performed. Variables studied were reinforcement, adhesive and metallic lug mechanical properties, hole diameter, reinforcement and adhesive thickness, and the distance from the hole s center to the end of the lug. Generally, U-shaped band reinforced lugs exhibited superior performance than non-reinforced lugs, that is higher load at the conventional lug design criteria of four percent hole elongation. Depending upon the reinforcement configuration the increase in load may be negligible to 15 or 20 percent. U-shaped band reinforcement increases lug load carrying capability primarily through two mechanisms; increasing the slope of the response curve after the initial knee and restraining overall deformation of the metallic portion of the lug facilitating increased yielding of metallic material between the hole and the edge of the metallic portion of the lug.

Long-Term Time Variability in the X-Ray Pulse Shape of the Crab Nebula Pulsar

NASA Astrophysics Data System (ADS)

Fazio, Giovanni G.

2000-01-01

This is the final performance report for our grant 'Long-Term Time Variability in the X-Ray Pulse Shape of the Crab Nebula Pulsar.' In the first year of this grant, we received the 50,000-second ROSAT (German acronym for X-ray satellite) High Resolution Images (HRI) observation of the Crab Nebula pulsar. We used the data to create a 65-ms-resolution pulse profile and compared it to a similar pulse profile obtained in 1991. No statistically significant differences were found. These results were presented at the January 1998 meeting of the American Astronomical Society. Since then, we have performed more sensitive analyses to search for potential changes in the pulse profile shape between the two data sets. Again, no significant variability was found. In order to augment this long (six-year) baseline data set, we have analyzed archival observations of the Crab Nebula pulsar with the Rossi X-Ray Timing Explorer (RXTE). While these observations have shorter time baselines than the ROSAT data set, their higher signal-to-noise offers similar sensitivity to long-term variability. Again, no significant variations have been found, confirming our ROSAT results. This work was done in collaboration with Prof. Stephen Eikenberry, Cornell University. These analyses will be included in Cornell University graduate student Dae-Sik Moon's doctoral thesis.

Diffusion-weighted magnetic resonance imaging in the characterization of testicular germ cell neoplasms: Effect of ROI methods on apparent diffusion coefficient values and interobserver variability.

PubMed

Tsili, Athina C; Ntorkou, Alexandra; Astrakas, Loukas; Xydis, Vasilis; Tsampalas, Stavros; Sofikitis, Nikolaos; Argyropoulou, Maria I

2017-04-01

To evaluate the difference in apparent diffusion coefficient (ADC) measurements at diffusion-weighted (DW) magnetic resonance imaging of differently shaped regions-of-interest (ROIs) in testicular germ cell neoplasms (TGCNS), the diagnostic ability of differently shaped ROIs in differentiating seminomas from nonseminomatous germ cell neoplasms (NSGCNs) and the interobserver variability. Thirty-three TGCNs were retrospectively evaluated. Patients underwent MR examinations, including DWI on a 1.5-T MR system. Two observers measured mean tumor ADCs using four distinct ROI methods: round, square, freehand and multiple small, round ROIs. The interclass correlation coefficient was analyzed to assess interobserver variability. Statistical analysis was used to compare mean ADC measurements among observers, methods and histologic types. All ROI methods showed excellent interobserver agreement, with excellent correlation (P<0.001). Multiple, small ROIs provided the lower mean ADC in TGCNs. Seminomas had lower mean ADC compared to NSGCNs for each ROI method (P<0.001). Round ROI proved the most accurate method in characterizing TGCNS. Interobserver variability in ADC measurement is excellent, irrespective of the ROI shape. Multiple, small round ROIs and round ROI proved the more accurate methods for ADC measurement in the characterization of TGCNs and in the differentiation between seminomas and NSGCNs, respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative analyses of variability in normal vaginal shape and dimension on MR images

PubMed Central

Luo, Jiajia; Betschart, Cornelia; Ashton-Miller, James A.; DeLancey, John O. L.

2016-01-01

Introduction and hypothesis We present a technique for quantifying inter-individual variability in normal vaginal shape, axis, and dimension, and report findings in healthy women. Methods Eighty women (age: 28~70 years) with normal pelvic organ support underwent supine, multi-planar proton-density MRI. Vaginal width was assessed at five evenly-spaced locations, and vaginal axis, length, and surface area were quantified via ImageJ and MATLAB. Results The mid-sagittal plane angles, relative to the horizontal, of three vaginal axes were 90± 11, 72± 21, and 41± 22° (caudal to cranial, p < 0.001). The mean (± SD) vaginal widths were 17± 5, 24± 4, 30± 7, 41± 9, and 45± 12 mm at the five locations (caudal to cranial, p < 0.001). Mid-sagittal lengths for anterior and posterior vaginal walls were 63± 9 and 98 ± 18 mm respectively. The vaginal surface area was 72 ± 21 cm2 (range: 34 ~ 164 cm2). The coefficient of determination between any demographic variable and any vaginal dimension did not exceed 0.16. Conclusions Large variations in normal vaginal shape, axis, and dimensions were not explained by body size or other demographic variables. This variation has implications for reconstructive surgery, intravaginal and surgical product design, and vaginal drug delivery. PMID:26811115

Elbow joint variability for different hand positions of the round off in gymnastics.

PubMed

Farana, Roman; Irwin, Gareth; Jandacka, Daniel; Uchytil, Jaroslav; Mullineaux, David R

2015-02-01

The aim of the present study was to conduct within-gymnast analyses of biological movement variability in impact forces, elbow joint kinematics and kinetics of expert gymnasts in the execution of the round-off with different hand positions. Six international level female gymnasts performed 10 trials of the round-off from a hurdle step to a back-handspring using two hand potions: parallel and T-shape. Two force plates were used to determine ground reaction forces. Eight infrared cameras were employed to collect the kinematic data automatically. Within gymnast variability was calculated using biological coefficient of variation (BCV) discretely for ground reaction force, kinematic and kinetic measures. Variability of the continuous data was quantified using coefficient of multiple correlations (CMC). Group BCV and CMC were calculated and T-test with effect size statistics determined differences between the variability of the two techniques examined in this study. The major observation was a higher level of biological variability in the elbow joint abduction angle and adduction moment of force in the T-shaped hand position. This finding may lead to a reduced repetitive abduction stress and thus protect the elbow joint from overload. Knowledge of the differences in biological variability can inform clinicians and practitioners with effective skill selection. Copyright © 2014 Elsevier B.V. All rights reserved.

HIV-1 Genetic Variability in Cuba and Implications for Transmission and Clinical Progression.

PubMed

Blanco, Madeline; Machado, Liuber Y; Díaz, Héctor; Ruiz, Nancy; Romay, Dania; Silva, Eladio

2015-10-01

INTRODUCTION Serological and molecular HIV-1 studies in Cuba have shown very low prevalence of seropositivity, but an increasing genetic diversity attributable to introduction of many HIV-1 variants from different areas, exchange of such variants among HIV-positive people with several coinciding routes of infection and other epidemiologic risk factors in the seropositive population. The high HIV-1 genetic variability observed in Cuba has possible implications for transmission and clinical progression. OBJECTIVE Study genetic variability for the HIV-1 env, gag and pol structural genes in Cuba; determine the prevalence of B and non-B subtypes according to epidemiologic and behavioral variables and determine whether a relationship exists between genetic variability and transmissibility, and between genetic variability and clinical disease progression in people living with HIV/AIDS. METHODS Using two molecular assays (heteroduplex mobility assay and nucleic acid sequencing), structural genes were characterized in 590 people with HIV-1 (480 men and 110 women), accounting for 3.4% of seropositive individuals in Cuba as of December 31, 2013. Nonrandom sampling, proportional to HIV prevalence by province, was conducted. Relationships between molecular results and viral factors, host characteristics, and patients' clinical, epidemiologic and behavioral variables were studied for molecular epidemiology, transmission, and progression analyses. RESULTS Molecular analysis of the three HIV-1 structural genes classified 297 samples as subtype B (50.3%), 269 as non-B subtypes (45.6%) and 24 were not typeable. Subtype B prevailed overall and in men, mainly in those who have sex with men. Non-B subtypes were prevalent in women and heterosexual men, showing multiple circulating variants and recombinant forms. Sexual transmission was the predominant form of infection for all. B and non-B subtypes were encountered throughout Cuba. No association was found between subtypes and transmission or clinical progression, although the proportion of deaths was higher for subtype B. Among those who died during the study period, there were no differences between subtypes in the mean time from HIV or AIDS diagnosis to death. CONCLUSIONS Our results suggest that B and non-B HIV-1 subtypes found in Cuba do not differ in transmissibility and in clinical disease progression. KEYWORDS HIV-1, AIDS, molecular epidemiology, transmissibility, clinical progression, subtypes, circulating recombinant forms, pathogenesis, Cuba.

Probabilistic modeling of anatomical variability using a low dimensional parameterization of diffeomorphisms.

PubMed

Zhang, Miaomiao; Wells, William M; Golland, Polina

2017-10-01

We present an efficient probabilistic model of anatomical variability in a linear space of initial velocities of diffeomorphic transformations and demonstrate its benefits in clinical studies of brain anatomy. To overcome the computational challenges of the high dimensional deformation-based descriptors, we develop a latent variable model for principal geodesic analysis (PGA) based on a low dimensional shape descriptor that effectively captures the intrinsic variability in a population. We define a novel shape prior that explicitly represents principal modes as a multivariate complex Gaussian distribution on the initial velocities in a bandlimited space. We demonstrate the performance of our model on a set of 3D brain MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Our model yields a more compact representation of group variation at substantially lower computational cost than the state-of-the-art method such as tangent space PCA (TPCA) and probabilistic principal geodesic analysis (PPGA) that operate in the high dimensional image space. Copyright © 2017 Elsevier B.V. All rights reserved.

Drag coefficient Variability and Thermospheric models

NASA Astrophysics Data System (ADS)

Moe, Kenneth

Satellite drag coefficients depend upon a variety of factors: The shape of the satellite, its altitude, the eccentricity of its orbit, the temperature and mean molecular mass of the ambient atmosphere, and the time in the sunspot cycle. At altitudes where the mean free path of the atmospheric molecules is large compared to the dimensions of the satellite, the drag coefficients can be determined from the theory of free-molecule flow. The dependence on altitude is caused by the concentration of atomic oxygen which plays an important role by its ability to adsorb on the satellite surface and thereby affect the energy loss of molecules striking the surface. The eccentricity of the orbit determines the satellite velocity at perigee, and therefore the energy of the incident molecules relative to the energy of adsorption of atomic oxygen atoms on the surface. The temperature of the ambient atmosphere determines the extent to which the random thermal motion of the molecules influences the momentum transfer to the satellite. The time in the sunspot cycle affects the ambient temperature as well as the concentration of atomic oxygen at a particular altitude. Tables and graphs will be used to illustrate the variability of drag coefficients. Before there were any measurements of gas-surface interactions in orbit, Izakov and Cook independently made an excellent estimate that the drag coefficient of satellites of compact shape would be 2.2. That numerical value, independent of altitude, was used by Jacchia to construct his model from the early measurements of satellite drag. Consequently, there is an altitude dependent bias in the model. From the sparce orbital experiments that have been done, we know that the molecules which strike satellite surfaces rebound in a diffuse angular distribution with an energy loss given by the energy accommodation coefficient. As more evidence accumulates on the energy loss, more realistic drag coefficients are being calculated. These improved drag coefficients help evaluate the biases in present models. Moreover, they make possible the derivation of accurate densities from accelerometer measurements.

Statistical Shape Modeling for Cavopulmonary Assist Device Development: Variability of Vascular Graft Geometry and Implications for Hemodynamics.

PubMed

Bruse, Jan L; Giusti, Giuliano; Baker, Catriona; Cervi, Elena; Hsia, Tain-Yen; Taylor, Andrew M; Schievano, Silvia

2017-06-01

Patients born with a single functional ventricle typically undergo three-staged surgical palliation in the first years of life, with the last stage realizing a cross-like total cavopulmonary connection (TCPC) of superior and inferior vena cavas (SVC and IVC) with both left and right pulmonary arteries, allowing all deoxygenated blood to flow passively back to the lungs (Fontan circulation). Even though within the past decades more patients survive into adulthood, the connection comes at the prize of deficiencies such as chronic systemic venous hypertension and low cardiac output, which ultimately may lead to Fontan failure. Many studies have suggested that the TCPC's inherent insufficiencies might be addressed by adding a cavopulmonary assist device (CPAD) to provide the necessary pressure boost. While many device concepts are being explored, few take into account the complex cardiac anatomy typically associated with TCPCs. In this study, we focus on the extra cardiac conduit vascular graft connecting IVC and pulmonary arteries as one possible landing zone for a CPAD and describe its geometric variability in a cohort of 18 patients that had their TCPC realized with a 20mm vascular graft. We report traditional morphometric parameters and apply statistical shape modeling to determine the main contributors of graft shape variability. Such information may prove useful when designing CPADs that are adapted to the challenging anatomical boundaries in Fontan patients. We further compute the anatomical mean 3D graft shape (template graft) as a representative of key shape features of our cohort and prove this template graft to be a significantly better approximation of population and individual patient's hemodynamics than a commonly used simplified tube geometry. We therefore conclude that statistical shape modeling results can provide better models of geometric and hemodynamic boundary conditions associated with complex cardiac anatomy, which in turn may impact on improved cardiac device development.

A method for assessment of the shape of the proximal femur and its relationship to osteoporotic hip fracture.

PubMed

Gregory, J S; Testi, D; Stewart, A; Undrill, P E; Reid, D M; Aspden, R M

2004-01-01

The shape of the proximal femur has been demonstrated to be important in the occurrence of fractures of the femoral neck. Unfortunately, multiple geometric measurements frequently used to describe this shape are highly correlated. A new method, active shape modeling (ASM) has been developed to quantify the morphology of the femur. This describes the shape in terms of orthogonal modes of variation that, consequently, are all independent. To test this method, digitized standard pelvic radiographs were obtained from 26 women who had suffered a hip fracture and compared with images from 24 age-matched controls with no fracture. All subjects also had their bone mineral density (BMD) measured at five sites using dual-energy X-ray absorptiometry. An ASM was developed and principal components analysis used to identify the modes which best described the shape. Discriminant analysis was used to determine which variable, or combination of variables, was best able to discriminate between the groups. ASM alone correctly identified 74% of the individuals and placed them in the appropriate group. Only one of the BMD values (Ward's triangle) achieved a higher value (82%). A combination of Ward's triangle BMD and ASM improved the accuracy to 90%. Geometric variables used in this study were weaker, correctly classifying less than 60% of the study group. Logistic regression showed that after adjustment for age, body mass index, and BMD, the ASM data was still independently associated with hip fracture (odds ratio (OR)=1.83, 95% confidence interval 1.08 to 3.11). The odds ratio was calculated relative to a 10% increase in the probability of belonging to the fracture group. Though these initial results were obtained from a limited data set, this study shows that ASM may be a powerful method to help identify individuals at risk of a hip fracture in the future.

Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC protein.

PubMed

Leong, Siew Wen; Lim, Theam Soon; Ismail, Asma; Choong, Yee Siew

2018-05-01

With the development of de novo binders for protein targets from non-related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking "disembodied" amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural protein-antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen-based detection agents for typhoid diagnostics. Copyright © 2017 John Wiley & Sons, Ltd.

A systematic overview of Descolea (Agaricales) in the Nothofagaceae forests of Patagonia.

PubMed

Kuhar, Francisco; Smith, Matthew E; Mujic, Alija; Truong, Camille; Nouhra, Eduardo

2017-10-01

The descolea clade includes species of ectomycorrhizal basidiomycetes in the genera Descolea, Setchelliogaster, Descomyces, and Timgrovea that are known primarily from the Southern Hemisphere. Taxa in this group produce basidiomes that range in morphology from typical epigeous mushrooms (Descolea) and secotioid taxa (Setchelliogaster) to fully gasteroid species (Descomyces and Timgrovea). High intraspecific morphological variation has been reported in several species within this clade, suggesting that careful morphological and molecular studies are needed to refine species concepts. Molecular analyses of fresh Patagonian collections in conjunction with taxonomic studies have confirmed high variability in key morphological features, including overall sporocarp form, spore shape and dimensions, universal veil remnants, and cuticle configuration. Based on our synthesis, we emend the genus Descolea to include sequestrate species. We describe the new sequestrate taxon Descolea inferna sp. nov. from Nothofagaceae forests in Patagonia and we propose Cortinarius squamatus as a synonym of our new combination Descolea brunnea. We also formalize the identity of Descolea pallida as a synonym of Descolea antarctica and provide new specimens of Cortinarius archeuretus, a species that has not been encountered since the original discovery during the expeditions of Roland Thaxter in 1905-1906. Here we re-describe and transfer this species to Descolea as D. archeureta. We also discuss diagnostic features that can be used to delimitate the four known South American taxa in the descolea clade. Copyright © 2017 British Mycological Society. All rights reserved.

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

PubMed Central

Lasker, Keren; Förster, Friedrich; Bohn, Stefan; Walzthoeni, Thomas; Villa, Elizabeth; Unverdorben, Pia; Beck, Florian; Aebersold, Ruedi; Sali, Andrej; Baumeister, Wolfgang

2012-01-01

The 26S proteasome is at the executive end of the ubiquitin-proteasome pathway for the controlled degradation of intracellular proteins. While the structure of its 20S core particle (CP) has been determined by X-ray crystallography, the structure of the 19S regulatory particle (RP), which recruits substrates, unfolds them, and translocates them to the CP for degradation, has remained elusive. Here, we describe the molecular architecture of the 26S holocomplex determined by an integrative approach based on data from cryoelectron microscopy, X-ray crystallography, residue-specific chemical cross-linking, and several proteomics techniques. The “lid” of the RP (consisting of Rpn3/5/6/7/8/9/11/12) is organized in a modular fashion. Rpn3/5/6/7/9/12 form a horseshoe-shaped heterohexamer, which connects to the CP and roofs the AAA-ATPase module, positioning the Rpn8/Rpn11 heterodimer close to its mouth. Rpn2 is rigid, supporting the lid, while Rpn1 is conformationally variable, positioned at the periphery of the ATPase ring. The ubiquitin receptors Rpn10 and Rpn13 are located in the distal part of the RP, indicating that they were recruited to the complex late in its evolution. The modular structure of the 26S proteasome provides insights into the sequence of events prior to the degradation of ubiquitylated substrates. PMID:22307589

Echinococcus equinus and Echinococcus granulosus sensu stricto from the United Kingdom: genetic diversity and haplotypic variation.

PubMed

Boufana, Belgees; Lett, Wai San; Lahmar, Samia; Buishi, Imad; Bodell, Anthony J; Varcasia, Antonio; Casulli, Adriano; Beeching, Nicholas J; Campbell, Fiona; Terlizzo, Monica; McManus, Donald P; Craig, Philip S

2015-02-01

Cystic echinococcosis is endemic in Europe including the United Kingdom. However, information on the molecular epidemiology of Echinococcus spp. from the United Kingdom is limited. Echinococcus isolates from intermediate and definitive animal hosts as well as from human cystic echinococcosis cases were analysed to determine species and genotypes within these hosts. Echinococcus equinus was identified from horse hydatid isolates, cysts retrieved from captive UK mammals and copro-DNA of foxhounds and farm dogs. Echinococcus granulosus sensu stricto (s.s.) was identified from hydatid cysts of sheep and cattle as well as in DNA extracted from farm dog and foxhound faecal samples, and from four human cystic echinococcosis isolates, including the first known molecular confirmation of E. granulosus s.s. infection in a Welsh sheep farmer. Low genetic variability for E. equinus from various hosts and from different geographical locations was detected using the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), indicating the presence of a dominant haplotype (EQUK01). In contrast, greater haplotypic variation was observed for E. granulosus s.s. cox1 sequences. The haplotype network showed a star-shaped network with a centrally placed main haplotype (EgUK01) that had been reported from other world regions. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Molecular Characterization and Chromosomal Distribution of Galileo, Kepler and Newton, Three Foldback Transposable Elements of the Drosophila buzzatii Species Complex

PubMed Central

Casals, Ferran; Cáceres, Mario; Manfrin, Maura Helena; González, Josefa; Ruiz, Alfredo

2005-01-01

Galileo is a foldback transposable element that has been implicated in the generation of two polymorphic chromosomal inversions in Drosophila buzzatii. Analysis of the inversion breakpoints led to the discovery of two additional elements, called Kepler and Newton, sharing sequence and structural similarities with Galileo. Here, we describe in detail the molecular structure of these three elements, on the basis of the 13 copies found at the inversion breakpoints plus 10 additional copies isolated during this work. Similarly to the foldback elements described in other organisms, these elements have long inverted terminal repeats, which in the case of Galileo possess a complex structure and display a high degree of internal variability between copies. A phylogenetic tree built with their shared sequences shows that the three elements are closely related and diverged ∼10 million years ago. We have also analyzed the abundance and chromosomal distribution of these elements in D. buzzatii and other species of the repleta group by Southern analysis and in situ hybridization. Overall, the results suggest that these foldback elements are present in all the buzzatti complex species and may have played an important role in shaping their genomes. In addition, we show that recombination rate is the main factor determining the chromosomal distribution of these elements. PMID:15695364

Receptor-driven, multimodal mapping of the human amygdala.

PubMed

Kedo, Olga; Zilles, Karl; Palomero-Gallagher, Nicola; Schleicher, Axel; Mohlberg, Hartmut; Bludau, Sebastian; Amunts, Katrin

2018-05-01

The human amygdala consists of subdivisions contributing to various functions. However, principles of structural organization at the cellular and molecular level are not well understood. Thus, we re-analyzed the cytoarchitecture of the amygdala and generated cytoarchitectonic probabilistic maps of ten subdivisions in stereotaxic space based on novel workflows and mapping tools. This parcellation was then used as a basis for analyzing the receptor expression for 15 receptor types. Receptor fingerprints, i.e., the characteristic balance between densities of all receptor types, were generated in each subdivision to comprehensively visualize differences and similarities in receptor architecture between the subdivisions. Fingerprints of the central and medial nuclei and the anterior amygdaloid area were highly similar. Fingerprints of the lateral, basolateral and basomedial nuclei were also similar to each other, while those of the remaining nuclei were distinct in shape. Similarities were further investigated by a hierarchical cluster analysis: a two-cluster solution subdivided the phylogenetically older part (central, medial nuclei, anterior amygdaloid area) from the remaining parts of the amygdala. A more fine-grained three-cluster solution replicated our previous parcellation including a laterobasal, superficial and centromedial group. Furthermore, it helped to better characterize the paralaminar nucleus with a molecular organization in-between the laterobasal and the superficial group. The multimodal cyto- and receptor-architectonic analysis of the human amygdala provides new insights into its microstructural organization, intersubject variability, localization in stereotaxic space and principles of receptor-based neurochemical differences.

Software Reviews.

ERIC Educational Resources Information Center

Wulfson, Stephen, Ed.

1987-01-01

Reviews seven computer software programs that can be used in science education programs. Describes courseware which deals with muscles and bones, terminology, classifying animals without backbones, molecular structures, drugs, genetics, and shaping the earth's surface. (TW)

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

Rueegsegger, Michael B.; Bach Cuadra, Meritxell; Pica, Alessia

Purpose: Ocular anatomy and radiation-associated toxicities provide unique challenges for external beam radiation therapy. For treatment planning, precise modeling of organs at risk and tumor volume are crucial. Development of a precise eye model and automatic adaptation of this model to patients' anatomy remain problematic because of organ shape variability. This work introduces the application of a 3-dimensional (3D) statistical shape model as a novel method for precise eye modeling for external beam radiation therapy of intraocular tumors. Methods and Materials: Manual and automatic segmentations were compared for 17 patients, based on head computed tomography (CT) volume scans. A 3Dmore » statistical shape model of the cornea, lens, and sclera as well as of the optic disc position was developed. Furthermore, an active shape model was built to enable automatic fitting of the eye model to CT slice stacks. Cross-validation was performed based on leave-one-out tests for all training shapes by measuring dice coefficients and mean segmentation errors between automatic segmentation and manual segmentation by an expert. Results: Cross-validation revealed a dice similarity of 95% {+-} 2% for the sclera and cornea and 91% {+-} 2% for the lens. Overall, mean segmentation error was found to be 0.3 {+-} 0.1 mm. Average segmentation time was 14 {+-} 2 s on a standard personal computer. Conclusions: Our results show that the solution presented outperforms state-of-the-art methods in terms of accuracy, reliability, and robustness. Moreover, the eye model shape as well as its variability is learned from a training set rather than by making shape assumptions (eg, as with the spherical or elliptical model). Therefore, the model appears to be capable of modeling nonspherically and nonelliptically shaped eyes.« less

Head-and-face shape variations of U.S. civilian workers

PubMed Central

Zhuang, Ziqing; Shu, Chang; Xi, Pengcheng; Bergman, Michael; Joseph, Michael

2016-01-01

The objective of this study was to quantify head-and-face shape variations of U.S. civilian workers using modern methods of shape analysis. The purpose of this study was based on previously highlighted changes in U.S. civilian worker head-and-face shape over the last few decades – touting the need for new and better fitting respirators – as well as the study's usefulness in designing more effective personal protective equipment (PPE) – specifically in the field of respirator design. The raw scan three-dimensional (3D) data for 1169 subjects were parameterized using geometry processing techniques. This process allowed the individual scans to be put in correspondence with each other in such a way that statistical shape analysis could be performed on a dense set of 3D points. This process also cleaned up the original scan data such that the noise was reduced and holes were filled in. The next step, statistical analysis of the variability of the head-and-face shape in the 3D database, was conducted using Principal Component Analysis (PCA) techniques. Through these analyses, it was shown that the space of the head-and-face shape was spanned by a small number of basis vectors. Less than 50 components explained more than 90% of the variability. Furthermore, the main mode of variations could be visualized through animating the shape changes along the PCA axes with computer software in executable form for Windows XP. The results from this study in turn could feed back into respirator design to achieve safer, more efficient product style and sizing. Future study is needed to determine the overall utility of the point cloud-based approach for the quantification of facial morphology variation and its relationship to respirator performance. PMID:23399025

Head-and-face shape variations of U.S. civilian workers.

PubMed

Zhuang, Ziqing; Shu, Chang; Xi, Pengcheng; Bergman, Michael; Joseph, Michael

2013-09-01

The objective of this study was to quantify head-and-face shape variations of U.S. civilian workers using modern methods of shape analysis. The purpose of this study was based on previously highlighted changes in U.S. civilian worker head-and-face shape over the last few decades - touting the need for new and better fitting respirators - as well as the study's usefulness in designing more effective personal protective equipment (PPE) - specifically in the field of respirator design. The raw scan three-dimensional (3D) data for 1169 subjects were parameterized using geometry processing techniques. This process allowed the individual scans to be put in correspondence with each other in such a way that statistical shape analysis could be performed on a dense set of 3D points. This process also cleaned up the original scan data such that the noise was reduced and holes were filled in. The next step, statistical analysis of the variability of the head-and-face shape in the 3D database, was conducted using Principal Component Analysis (PCA) techniques. Through these analyses, it was shown that the space of the head-and-face shape was spanned by a small number of basis vectors. Less than 50 components explained more than 90% of the variability. Furthermore, the main mode of variations could be visualized through animating the shape changes along the PCA axes with computer software in executable form for Windows XP. The results from this study in turn could feed back into respirator design to achieve safer, more efficient product style and sizing. Future study is needed to determine the overall utility of the point cloud-based approach for the quantification of facial morphology variation and its relationship to respirator performance. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.