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Sample records for molecular structure input

  1. Input-dependent induction of oligonucleotide structural motifs for performing molecular logic.

    PubMed

    Li, Tao; Ackermann, Damian; Hall, Anna M; Famulok, Michael

    2012-02-22

    The K(+)-H(+)-triggered structural conversion of multiple nucleic acid helices involving duplexes, triplexes, G-quadruplexes, and i-motifs is studied by gel electrophoresis, circular dichroism, and thermal denaturation. We employ the structural interconversions for perfoming molecular logic operations, as verified by fluorimetry and colorimetry. Short G-rich and C-rich cDNA and RNA single strands are hybridized to produce four A-form and B-form duplexes. Addition of K(+) triggers the unwinding of the duplexes by inducing the folding of G-rich strands into DNA- or RNA G-quadruplex mono- and multimers, respectively. We found a decrease in pH to have different consequences on the resulting structural output, depending on whether the C-rich strand is DNA or RNA: while the protonated C-rich DNA strand folds into at least two isomers of a stable i-motif structure, the protonated C-rich RNA strand binds a DNA/RNA hybrid duplex to form a Y·RY parallel triplex. When using K(+) and H(+) as external stimuli, or inputs, and the induced G-quadruplexes as reporters, these structural interconversions of nucleic acid helices can be employed for performing logic-gate operations. The signaling mode for detecting these conversions relies on complex formation between DNA or RNA G-quadruplexes (G4) and the cofactor hemin. The G4/hemin complexes catalyze the H(2)O(2)-mediated oxidation of peroxidase substrates, resulting in a fluorescence or color change. Depending on the nature of the respective peroxidase substrate, distinct output signals can be generated, allowing one to operate multiple logic gates such as NOR, INH, or AND.

  2. The energy and momentum input of supernova explosions in structured and ionized molecular clouds

    NASA Astrophysics Data System (ADS)

    Walch, Stefanie; Naab, Thorsten

    2015-08-01

    We investigate the early impact of single and binary supernova (SN) explosions on dense gas clouds with three-dimensional, high-resolution, hydrodynamic simulations. The effect of cloud structure, radiative cooling and ionizing radiation from the progenitor stars on the net input of kinetic energy, fkin = Ekin/ESN, thermal energy, ftherm = Etherm/ESN, and gas momentum, fP = P/PSN, to the interstellar medium (ISM) is tested. For clouds with bar{n} = 100cm^{-3}, the momentum generating Sedov and pressure-driven snowplough phases are terminated early (∝0.01 Myr) and radiative cooling limits the coupling to ftherm ˜ 0.01, fkin ˜ 0.05, and fP ˜ 9, significantly lower than for the case without cooling. For pre-ionized clouds, these numbers are only increased by ˜50 per cent, independent of the cloud structure. This only suffices to accelerate ˜5 per cent of the cloud to radial velocities ≳30 km s-1. A second SN might enhance the coupling efficiencies if delayed past the Sedov phase of the first explosion. Such very low coupling efficiencies cast doubts on many subresolution models for SN feedback, which are, in general, validated a posteriori. Ionizing radiation appears not to significantly enhance the coupling of SNe to the surrounding gas as it drives the ISM into inert dense shells and cold clumps, a process which is unresolved in galaxy-scale simulations. Our results indicate that the momentum input of SNe in ionized, structured clouds is larger (more than a factor of 10) than the corresponding momentum yield of the progenitor's stellar winds.

  3. Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters.

    PubMed

    Róg, Tomasz; Orłowski, Adam; Llorente, Alicia; Skotland, Tore; Sylvänne, Tuulia; Kauhanen, Dimple; Ekroos, Kim; Sandvig, Kirsten; Vattulainen, Ilpo

    2016-06-01

    In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present in these models are: cholesterol (CHOL), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidyl-ethanolamine (SOPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-D-erythro-sphingosyl-phosphatidylcholine (SM24). The bilayers׳ compositions are based on lipidomic studies of PC-3 prostate cancer cells and exosomes discussed in Llorente et al. (2013) [1], showing an increase in the section of long-tail lipid species (SOPS, SOPE, and SM24) in the exosomes. Former knowledge about lipid asymmetry in cell membranes was accounted for in the models, meaning that the model of the inner leaflet is composed of a mixture of PC, PS, PE, and cholesterol, while the extracellular leaflet is composed of SM, PC and cholesterol discussed in Van Meer et al. (2008) [2]. The provided data include lipids׳ topologies, equilibrated structures of asymmetric bilayers, all force field parameters, and input files with parameters describing simulation conditions (md.mdp). The data is associated with the research article "Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner" (Róg et al., 2016) [3].

  4. Minimizing structural vibrations with Input Shaping (TM)

    NASA Technical Reports Server (NTRS)

    Singhose, Bill; Singer, Neil

    1995-01-01

    A new method for commanding machines to move with increased dynamic performance was developed. This method is an enhanced version of input shaping, a patented vibration suppression algorithm. This technique intercepts a command input to a system command that moves the mechanical system with increased performance and reduced residual vibration. This document describes many advanced methods for generating highly optimized shaping sequences which are tuned to particular systems. The shaping sequence is important because it determines the trade off between move/settle time of the system and the insensitivity of the input shaping algorithm to variations or uncertainties in the machine which can be controlled. For example, a system with a 5 Hz resonance that takes 1 second to settle can be improved to settle instantaneously using a 0.2 shaping sequence (thus improving settle time by a factor of 5). This system could vary by plus or minus 15% in its natural frequency and still have no apparent vibration. However, the same system shaped with a 0.3 second shaping sequence could tolerate plus or minus 40% or more variation in natural frequency. This document describes how to generate sequences that maximize performance, sequences that maximize insensitivity, and sequences that trade off between the two. Several software tools are documented and included.

  5. Molecularly Defined Circuitry Reveals Input-Output Segregation in Deep Layers of the Medial Entorhinal Cortex.

    PubMed

    Sürmeli, Gülşen; Marcu, Daniel Cosmin; McClure, Christina; Garden, Derek L F; Pastoll, Hugh; Nolan, Matthew F

    2015-12-02

    Deep layers of the medial entorhinal cortex are considered to relay signals from the hippocampus to other brain structures, but pathways for routing of signals to and from the deep layers are not well established. Delineating these pathways is important for a circuit level understanding of spatial cognition and memory. We find that neurons in layers 5a and 5b have distinct molecular identities, defined by the transcription factors Etv1 and Ctip2, and divergent targets, with extensive intratelencephalic projections originating in layer 5a, but not 5b. This segregation of outputs is mirrored by the organization of glutamatergic input from stellate cells in layer 2 and from the hippocampus, with both preferentially targeting layer 5b over 5a. Our results suggest a molecular and anatomical organization of input-output computations in deep layers of the MEC, reveal precise translaminar microcircuitry, and identify molecularly defined pathways for spatial signals to influence computation in deep layers.

  6. Input clustering and the microscale structure of local circuits

    PubMed Central

    DeBello, William M.; McBride, Thomas J.; Nichols, Grant S.; Pannoni, Katy E.; Sanculi, Daniel; Totten, Douglas J.

    2014-01-01

    The recent development of powerful tools for high-throughput mapping of synaptic networks promises major advances in understanding brain function. One open question is how circuits integrate and store information. Competing models based on random vs. structured connectivity make distinct predictions regarding the dendritic addressing of synaptic inputs. In this article we review recent experimental tests of one of these models, the input clustering hypothesis. Across circuits, brain regions and species, there is growing evidence of a link between synaptic co-activation and dendritic location, although this finding is not universal. The functional implications of input clustering and future challenges are discussed. PMID:25309336

  7. Input Shaping to Reduce Solar Array Structural Vibrations

    NASA Technical Reports Server (NTRS)

    Doherty, Michael J.; Tolson, Robert J.

    1998-01-01

    Structural vibrations induced by actuators can be minimized using input shaping. Input shaping is a feedforward method in which actuator commands are convolved with shaping functions to yield a shaped set of commands. These commands are designed to perform the maneuver while minimizing the residual structural vibration. In this report, input shaping is extended to stepper motor actuators. As a demonstration, an input-shaping technique based on pole-zero cancellation was used to modify the Solar Array Drive Assembly (SADA) actuator commands for the Lewis satellite. A series of impulses were calculated as the ideal SADA output for vibration control. These impulses were then discretized for use by the SADA stepper motor actuator and simulated actuator outputs were used to calculate the structural response. The effectiveness of input shaping is limited by the accuracy of the knowledge of the modal frequencies. Assuming perfect knowledge resulted in significant vibration reduction. Errors of 10% in the modal frequencies caused notably higher levels of vibration. Controller robustness was improved by incorporating additional zeros in the shaping function. The additional zeros did not require increased performance from the actuator. Despite the identification errors, the resulting feedforward controller reduced residual vibrations to the level of the exactly modeled input shaper and well below the baseline cases. These results could be easily applied to many other vibration-sensitive applications involving stepper motor actuators.

  8. Photosensitive film structure with two independent optical inputs

    NASA Astrophysics Data System (ADS)

    Mirsagatov, Sh. A.; Rubinov, V. M.; Sabirov, K.

    The volt-ampere characteristics of nCdS-nCdTe-pCdTe structures in the dark and in white-light illumination were determined in order to test the operation of these structures in the two-input photodetector mode. It is shown that in such structures the photocurrent is controlled by the conductivity modulation of the space-charge region of the p-n junction and the photoconductive layer of cadmium sulfide.

  9. Understanding molecular structure from molecular mechanics.

    PubMed

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  10. Image annotation by input-output structural grouping sparsity.

    PubMed

    Han, Yahong; Wu, Fei; Tian, Qi; Zhuang, Yueting

    2012-06-01

    Automatic image annotation (AIA) is very important to image retrieval and image understanding. Two key issues in AIA are explored in detail in this paper, i.e., structured visual feature selection and the implementation of hierarchical correlated structures among multiple tags to boost the performance of image annotation. This paper simultaneously introduces an input and output structural grouping sparsity into a regularized regression model for image annotation. For input high-dimensional heterogeneous features such as color, texture, and shape, different kinds (groups) of features have different intrinsic discriminative power for the recognition of certain concepts. The proposed structured feature selection by structural grouping sparsity can be used not only to select group-of-features but also to conduct within-group selection. Hierarchical correlations among output labels are well represented by a tree structure, and therefore, the proposed tree-structured grouping sparsity can be used to boost the performance of multitag image annotation. In order to efficiently solve the proposed regression model, we relax the solving process as a framework of the bilayer regression model for multilabel boosting by the selection of heterogeneous features with structural grouping sparsity (Bi-MtBGS). The first-layer regression is to select the discriminative features for each label. The aim of the second-layer regression is to refine the feature selection model learned from the first layer, which can be taken as a multilabel boosting process. Extensive experiments on public benchmark image data sets and real-world image data sets demonstrate that the proposed approach has better performance of multitag image annotation and leads to a quite interpretable model for image understanding.

  11. Long-term variation in above and belowground plant inputs alters soil organic matter biogeochemistry at the molecular-level

    NASA Astrophysics Data System (ADS)

    Simpson, M. J.; Pisani, O.; Lin, L.; Lun, O.; Simpson, A.; Lajtha, K.; Nadelhoffer, K. J.

    2015-12-01

    The long-term fate of soil carbon reserves with global environmental change remains uncertain. Shifts in moisture, altered nutrient cycles, species composition, or rising temperatures may alter the proportions of above and belowground biomass entering soil. However, it is unclear how long-term changes in plant inputs may alter the composition of soil organic matter (SOM) and soil carbon storage. Advanced molecular techniques were used to assess SOM composition in mineral soil horizons (0-10 cm) after 20 years of Detrital Input and Removal Treatment (DIRT) at the Harvard Forest. SOM biomarkers (solvent extraction, base hydrolysis and cupric (II) oxide oxidation) and both solid-state and solution-state nuclear magnetic resonance (NMR) spectroscopy were used to identify changes in SOM composition and stage of degradation. Microbial activity and community composition were assessed using phospholipid fatty acid (PLFA) analysis. Doubling aboveground litter inputs decreased soil carbon content, increased the degradation of labile SOM and enhanced the sequestration of aliphatic compounds in soil. The exclusion of belowground inputs (No roots and No inputs) resulted in a decrease in root-derived components and enhanced the degradation of leaf-derived aliphatic structures (cutin). Cutin-derived SOM has been hypothesized to be recalcitrant but our results show that even this complex biopolymer is susceptible to degradation when inputs entering soil are altered. The PLFA data indicate that changes in soil microbial community structure favored the accelerated processing of specific SOM components with littler manipulation. These results collectively reveal that the quantity and quality of plant litter inputs alters the molecular-level composition of SOM and in some cases, enhances the degradation of recalcitrant SOM. Our study also suggests that increased litterfall is unlikely to enhance soil carbon storage over the long-term in temperate forests.

  12. Combustion inputs into a terrestrial archive over 265 years as evidenced by BPCA molecular markers

    NASA Astrophysics Data System (ADS)

    Hanke, Ulrich M.; Eglinton, Timothy I.; Wiedemeier, Daniel B.; Schmidt, Michael W. I.

    2015-04-01

    Pyrogenic organic matter (PyOM) such as char and soot is produced during the incomplete combustion of biomass and fossil fuel. It is composed of condensed aromatic structures and can resist degradation processes, maybe over long periods of time. Land-use changes, industrial activity and its transport by wind and water affect the fluxes of PyOM from the source to its sedimentary archive. Investigating environmental PyOM with the molecular marker benzene polycarboxylic acid (BPCA) method provides various information about quantity, quality (BPCA distribution pattern) and about its isotopic composition (13C and 14C). Assessing PyOM quality can indicate whether it is mostly combustion condensate (soot) or combustion residue (charcoal) and potentially allow source apportionment. Our study area is the Pettaquamscutt River catchment area (35 km2), Rhode Island, U.S.A. It is located down-wind of industrial areas recording deposition of long-distance atmospheric transport as well as local catchment inputs, both from natural and anthropogenic sources. We investigated 50 samples of a sediment record over a time span of 265 years (1733-1998 AD). Previous investigations provided information on the age of deposition, the content of polycyclic aromatic hydrocarbons (PAH) as well as of the radiocarbon contents of total organic carbon (TOC) and PAH (Lima, 2004). We used the BPCA molecular marker method to quantify and characterize PyOM in the same record. First results show that quantity and quality of PyOM change over 265 years. Our investigation aims at understanding how different sources of PyOM are reflected in terrestrial archives by comparing the results of BPCA with radiocarbon-dated TOC and PAH records. Among other aspects, the PAH record reflects the Great Depression and the 1970s oil embargo in North America. We interpret the BPCA distribution patterns regarding the simultaneous shift of dominant fuels including wood, coal, petroleum and gas. Future work will include

  13. Modeling Recognition Memory Using the Similarity Structure of Natural Input

    ERIC Educational Resources Information Center

    Lacroix, Joyca P. W.; Murre, Jaap M. J.; Postma, Eric O.; van den Herik, H. Jaap

    2006-01-01

    The natural input memory (NAM) model is a new model for recognition memory that operates on natural visual input. A biologically informed perceptual preprocessing method takes local samples (eye fixations) from a natural image and translates these into a feature-vector representation. During recognition, the model compares incoming preprocessed…

  14. Design of two and three input molecular logic gates using non-Watson-Crick base pairing-based molecular beacons.

    PubMed

    Lin, Jia-Hui; Tseng, Wei-Lung

    2014-03-21

    This study presents a single, resettable, and sensitive molecular beacon (MB) used to operate molecular-scale logic gates. The MB consists of a random DNA sequence, a fluorophore at the 5'-end, and a quencher at the 3'-end. The presence of Hg(2+), Ag(+), and coralyne promoted the formation of stable T-Hg(2+)-T, C-Ag(+)-C, and A2-coralyne-A2 coordination in the MB probe, respectively, thereby driving its conformational change. The metal ion or small molecule-mediated coordination of mismatched DNA brought the fluorophore and the quencher into close proximity, resulting in collisional quenching of fluorescence between the two organic dyes. Because thiol can bind Hg(2+) and remove it from the T-Hg(2+)-T-based MB, adding thiol to a solution of the T-Hg(2+)-T-based MB allowed the fluorophore and the quencher to be widely separated. A similar phenomenon was observed when replacing Hg(2+) with Ag(+). Because Ag(+) strongly binds to iodide, cyanide, and cysteine, they were capable of removing Ag(+) from the C-Ag(+)-C-based MB, restoring the fluorescence of the MB. Moreover, the fluorescence of the A2-coralyne-A2-based MB could be switched on by adding polyadenosine. Using these analytes as inputs and the MB as a signal transducer, we successfully developed a series of two-input, three-input, and set-reset logic gates at the molecular level.

  15. Dynamic molecular graphs: "hopping" structures.

    PubMed

    Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María

    2014-05-05

    This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions.

  16. Improved input and output couplers for SC acceleration structure

    SciTech Connect

    Solyak, N.; Gonin, I.; Latina, A.; Lunin, A.; Poloubotko, V.; Yakovlev, V.; /Fermilab

    2009-04-01

    Different couplers are described that allow the reduction of both transverse wake potential and RF kick in the SC acceleration structure of ILC. A simple rotation of the couplers reducing the RF kick and transverse wake kick is discussed for both the main linac and bunch compressors, along with possible limitations of this method. Designs of a coupler unit are presented which preserve axial symmetry of the structure, and provide reduced both the RF kick and transverse wake field.

  17. Neural Microstates Govern Perception of Auditory Input without Rhythmic Structure.

    PubMed

    Henry, Molly J; Herrmann, Björn; Obleser, Jonas

    2016-01-20

    Human perception fluctuates with the phase of neural oscillations in the presence of environmental rhythmic structure by which neural oscillations become entrained. However, in the absence of predictability afforded by rhythmic structure, we hypothesize that the neural dynamical states associated with optimal psychophysical performance are more complex than what has been described previously for rhythmic stimuli. The current electroencephalography study characterized the brain dynamics associated with optimal detection of gaps embedded in narrow-band acoustic noise stimuli lacking low-frequency rhythmic structure. Optimal gap detection was associated with three spectrotemporally distinct delta-governed neural microstates. Individual microstates were characterized by unique instantaneous combinations of neural phase in the delta, theta, and alpha frequency bands. Critically, gap detection was not predictable from local fluctuations in stimulus acoustics. The current results suggest that, in the absence of rhythmic structure to entrain neural oscillations, good performance hinges on complex neural states that vary from moment to moment. Significance statement: Our ability to hear faint sounds fluctuates together with slow brain activity that synchronizes with environmental rhythms. However, it is so far not known how brain activity at different time scales might interact to influence perception when there is no rhythm with which brain activity can synchronize. Here, we used electroencephalography to measure brain activity while participants listened for short silences that interrupted ongoing noise. We examined brain activity in three different frequency bands: delta, theta, and alpha. Participants' ability to detect gaps depended on different numbers of frequency bands--sometimes one, sometimes two, and sometimes three--at different times. Changes in the number of frequency bands that predict perception are a hallmark of a complex neural system.

  18. Learning structure of sensory inputs with synaptic plasticity leads to interference

    PubMed Central

    Chrol-Cannon, Joseph; Jin, Yaochu

    2015-01-01

    Synaptic plasticity is often explored as a form of unsupervised adaptation in cortical microcircuits to learn the structure of complex sensory inputs and thereby improve performance of classification and prediction. The question of whether the specific structure of the input patterns is encoded in the structure of neural networks has been largely neglected. Existing studies that have analyzed input-specific structural adaptation have used simplified, synthetic inputs in contrast to complex and noisy patterns found in real-world sensory data. In this work, input-specific structural changes are analyzed for three empirically derived models of plasticity applied to three temporal sensory classification tasks that include complex, real-world visual and auditory data. Two forms of spike-timing dependent plasticity (STDP) and the Bienenstock-Cooper-Munro (BCM) plasticity rule are used to adapt the recurrent network structure during the training process before performance is tested on the pattern recognition tasks. It is shown that synaptic adaptation is highly sensitive to specific classes of input pattern. However, plasticity does not improve the performance on sensory pattern recognition tasks, partly due to synaptic interference between consecutively presented input samples. The changes in synaptic strength produced by one stimulus are reversed by the presentation of another, thus largely preventing input-specific synaptic changes from being retained in the structure of the network. To solve the problem of interference, we suggest that models of plasticity be extended to restrict neural activity and synaptic modification to a subset of the neural circuit, which is increasingly found to be the case in experimental neuroscience. PMID:26300769

  19. Learning Complex Grammar in the Virtual Classroom: A Comparison of Processing Instruction, Structured Input, Computerized Visual Input Enhancement, and Traditional Instruction

    ERIC Educational Resources Information Center

    Russell, Victoria

    2012-01-01

    This study investigated the effects of processing instruction (PI) and structured input (SI) on the acquisition of the subjunctive in adjectival clauses by 92 second-semester distance learners of Spanish. Computerized visual input enhancement (VIE) was combined with PI and SI in an attempt to increase the salience of the targeted grammatical form…

  20. Synchronization in neuronal oscillator networks with input heterogeneity and arbitrary network structure

    NASA Astrophysics Data System (ADS)

    Davison, Elizabeth; Dey, Biswadip; Leonard, Naomi

    Mathematical studies of synchronization in networks of neuronal oscillators offer insight into neuronal ensemble behavior in the brain. Systematic means to understand how network structure and external input affect synchronization in network models have the potential to improve methods for treating synchronization-related neurological disorders such as epilepsy and Parkinson's disease. To elucidate the complex relationships between network structure, external input, and synchronization, we investigate synchronous firing patterns in arbitrary networks of neuronal oscillators coupled through gap junctions with heterogeneous external inputs. We first apply a passivity-based Lyapunov analysis to undirected networks of homogeneous FitzHugh-Nagumo (FN) oscillators with homogeneous inputs and derive a sufficient condition on coupling strength that guarantees complete synchronization. In biologically relevant regimes, we employ Gronwall's inequality to obtain a bound tighter than those previously reported. We extend both analyses to a homogeneous FN network with heterogeneous inputs and show how cluster synchronization emerges under conditions on the symmetry of the coupling matrix and external inputs. Our results can be generalized to any network of semi-passive oscillators.

  1. Image inputs in Structure-from-Motion Photogrammetry: optimising image greyscaling

    NASA Astrophysics Data System (ADS)

    O'Connor, James; Smith, Mike J.; James, Mike R.

    2016-04-01

    Structure-from-motion (SfM) photogrammetry is an emerging technology receiving much attention within the geoscience community due to its ease of use and the lack of prior information required to build topographic models from images. However, little consideration is given to image inputs considering image sharpness and contrast both have an effect on the quality of photogrammetric outputs. This task is made more challenging across natural image sequences due to the presence of low-contrast surfaces which are often at oblique angles to input images. As most feature detectors operate on a single image channel, monochrome inputs can be pre-processed for input into SfM workflows and relative accuracy measured. In this contribution we process two sets of imagery from both a real world, close range scenario (Constitution Hill, Aberystwyth) and a controlled dataset in laboratory conditions simulating a UAV flight with convergent viewing geometry. With each, we generate greyscale subsets comprised of weighted combinations of the spectral bands of the input images prior to executing SfM workflows. Output point clouds are measured against high-accuracy terrestrial laser scans in order to assess residual error and compare output solutions. When compared with untreated image inputs into a commonly used commercial package (Agisoft Photoscan Pro) we show minor improvements in the accuracy of photogrammetrically derived products.

  2. The stability of input structures in a supply-driven input-output model: A regional analysis

    SciTech Connect

    Allison, T.

    1994-06-01

    Disruptions in the supply of strategic resources or other crucial factor inputs often present significant problems for planners and policymakers. The problem may be particularly significant at the regional level where higher levels of product specialization mean supply restrictions are more likely to affect leading regional industries. To maintain economic stability in the event of a supply restriction, regional planners may therefore need to evaluate the importance of market versus non-market systems for allocating the remaining supply of the disrupted resource to the region`s leading consuming industries. This paper reports on research that has attempted to show that large short term changes on the supply side do not lead to substantial changes in input coefficients and do not therefore mean the abandonment of the concept of the production function as has been suggested (Oosterhaven, 1988). The supply-driven model was tested for six sectors of the economy of Washington State and found to yield new input coefficients whose values were in most cases close approximations of their original values, even with substantial changes in supply. Average coefficient changes from a 50% output reduction in these six sectors were in the vast majority of cases (297 from a total of 315) less than +2.0% of their original values, excluding coefficient changes for the restricted input. Given these small changes, the most important issue for the validity of the supply-driven input-output model may therefore be the empirical question of the extent to which these coefficient changes are acceptable as being within the limits of approximation.

  3. A Bayesian approach to model structural error and input variability in groundwater modeling

    NASA Astrophysics Data System (ADS)

    Xu, T.; Valocchi, A. J.; Lin, Y. F. F.; Liang, F.

    2015-12-01

    Effective water resource management typically relies on numerical models to analyze groundwater flow and solute transport processes. Model structural error (due to simplification and/or misrepresentation of the "true" environmental system) and input forcing variability (which commonly arises since some inputs are uncontrolled or estimated with high uncertainty) are ubiquitous in groundwater models. Calibration that overlooks errors in model structure and input data can lead to biased parameter estimates and compromised predictions. We present a fully Bayesian approach for a complete assessment of uncertainty for spatially distributed groundwater models. The approach explicitly recognizes stochastic input and uses data-driven error models based on nonparametric kernel methods to account for model structural error. We employ exploratory data analysis to assist in specifying informative prior for error models to improve identifiability. The inference is facilitated by an efficient sampling algorithm based on DREAM-ZS and a parameter subspace multiple-try strategy to reduce the required number of forward simulations of the groundwater model. We demonstrate the Bayesian approach through a synthetic case study of surface-ground water interaction under changing pumping conditions. It is found that explicit treatment of errors in model structure and input data (groundwater pumping rate) has substantial impact on the posterior distribution of groundwater model parameters. Using error models reduces predictive bias caused by parameter compensation. In addition, input variability increases parametric and predictive uncertainty. The Bayesian approach allows for a comparison among the contributions from various error sources, which could inform future model improvement and data collection efforts on how to best direct resources towards reducing predictive uncertainty.

  4. Teaching Literary Texts at the Intermediate Level: A Structured Input Approach.

    ERIC Educational Resources Information Center

    Katz, Stacey

    This article proposes a model for sensitizing students to the richness of literary texts based on Lee and VanPatten's (1995) structured input/output approach to teaching foreign languages (FL). It begins by discussing the difficulties and challenges of intermediate-level FL courses, noting that the concept of "bridge courses" may be faulty because…

  5. Continuum electrostatic calculations of the pKa of ionizable residues in an ion channel: dynamic vs. static input structure.

    PubMed

    Aguilella-Arzo, M; Aguilella, V M

    2010-04-01

    We have computed the pK(a)'s of the ionizable residues of a protein ion channel, the Staphylococcus aureus toxin alpha-hemolysin, by using two types of input structures, namely the crystal structure of the heptameric alpha-hemolysin and a set of over four hundred snapshots from a 4.38 ns Molecular Dynamics simulation of the protein inserted in a phospholipid planar bilayer. The comparison of the dynamic picture provided by the Molecular Simulation with the static one based on the X-ray crystal structure of the protein embedded in a lipid membrane allows analyzing the influence of the fluctuations in the protein structure on its ionization properties. We find that the use of the dynamic structure provides interesting information about the sensitivity of the computed pK(a) of a given residue to small changes in the local structure. The calculated pK(a) are consistent with previous indirect estimations obtained from single-channel conductance and selectivity measurements.

  6. Guidance manual for the input of biological information to water-intake-structure design

    SciTech Connect

    Neitzel, D.A.; Simmons, M.A.; McKenzie, D.H.

    1981-12-01

    This manual is intended to provide guidance to the biologist who is asked to provide biological input during the construction or subsequent alteration of a water intake structure. Examples of the types of biological information that might be included in intake design are presented. Procedures for quantifying biological information and defining specific tasks that will generate quantifiable data are discussed. Procedures described apply both to new and modified water intake structures.

  7. Procedure for developing biological input for the design, location, or modification of water-intake structures

    SciTech Connect

    Neitzel, D.A.; McKenzie, D.H.

    1981-12-01

    To minimize adverse impact on aquatic ecosystems resulting from the operation of water intake structures, design engineers must have relevant information on the behavior, physiology and ecology of local fish and shellfish. Identification of stimulus/response relationships and the environmental factors that influence them is the first step in incorporating biological information in the design, location or modification of water intake structures. A procedure is presented in this document for providing biological input to engineers who are designing, locating or modifying a water intake structure. The authors discuss sources of stimuli at water intakes, historical approaches in assessing potential/actual impact and review biological information needed for intake design.

  8. Active control of structurally-coupled sound fields in elastic cylinders by vibrational force inputs

    NASA Technical Reports Server (NTRS)

    Jones, J. D.; Fuller, C. R.

    1990-01-01

    Active control of structurally-coupled sound fields in elastic cylinders is analytically and experimentally studied. The primary (noise) field in the cylinder model is generated by the coupled dynamic response of the shell under loading by a single exterior acoustic source. Control of the interior sound field is achieved by applying vibrational force inputs directly to the shell wall. Action of the point controllers serve to increase the input impedance of select structural modes of the shell which are well-coupled to the interior acoustic cavity, thus substantially reducing sound transmission into the cavity. Spatially-averaged noise reductions in excess of 30 dB are demonstrated for acoustic resonant conditions within the cavity. Twin controller configurations are presented which demonstrate the ability to independently control orthogonal modes of the interior acoustic space. Benefits and drawbacks of this new methodology for noise control are discussed and clearly demonstrated.

  9. Analysis of UHF RFID CMOS rectifier structures and input impedance characteristics

    NASA Astrophysics Data System (ADS)

    Jamali, Behnam; Ranasinghe, Damith C.; Cole, Peter H.

    2005-12-01

    Passive radio frequency identification (RFID) systems deployment efforts are revolutionizing supply chain logistics by providing unprecedented supply chain visibility. The widely used bandwidth of operation in modern systems is the UHF ISM (industrial, scientific, and medical) band. The performance of UHF RFID systems are largely reliant on low power CMOS circuits, efficient power rectification and the ability of RFID label antennas to match to the input impedance of the RFID label IC. This paper examines a new rectifying structure and considers it for its merits in RFID applications while analysing contribution of the rectifying structure to the input impedance of RFID chips as this is an important consideration in impedance matching to an external antenna.

  10. Molecular modeling of nucleic acid structure

    PubMed Central

    Galindo-Murillo, Rodrigo; Bergonzo, Christina

    2013-01-01

    This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. This unit provides an overview of computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, generation of an initial model, and characterization of the overall three-dimensional structure. PMID:18428873

  11. Structural optimisation and input selection of an artificial neural network for river level prediction

    NASA Astrophysics Data System (ADS)

    Leahy, Paul; Kiely, Ger; Corcoran, Gearóid

    2008-06-01

    SummaryAccurate river level prediction, necessary for reliable flood forecasting, is a difficult task due to the complexity and inherent nonlinearity of the catchment hydrological system. Although artificial neural networks (ANNs) offer advantages over mechanistic or conceptual hydrological models for river level prediction, their applicability is limited by the fact that each ANN has to be specifically optimised and trained for a particular prediction problem and suitable input vectors selected. A recently developed novel optimisation algorithm combining properties of simulated annealing and tabu search is used to arrive at an optimal ANN for the prediction of river levels 5 h in advance. The algorithm seeks to minimise the value of a cost function based on the complexity and performance of the ANN. This is done by removing inter-neuron connections and adjusting the weights of the remaining connections. The candidate inputs presented to the algorithm were: current values of river levels at the flood location and two upstream locations; the change in level over the previous 4 h at the flood point, mean sea level pressure (SLP) and the change in SLP over the previous 24 h. The optimisation removed 79% of the network connections and three of the candidate inputs, leaving the current levels at the two upstream locations and at the flood point as the only inputs. The optimised ANN was then trained using the standard backpropagation algorithm. This methodology produces an ANN of greatly reduced complexity albeit with a reduced performance compared to an unoptimised ANN trained with backpropagation only. However, it has the advantage of being generally applicable and represents an improvement over trial and error as a method of ANN structural optimisation and input selection. For this prediction problem, current levels at two upstream locations and at the flood point are the best predictors of the level at the flood point.

  12. Variable input observer for structural health monitoring of high-rate systems

    NASA Astrophysics Data System (ADS)

    Hong, Jonathan; Laflamme, Simon; Cao, Liang; Dodson, Jacob

    2017-02-01

    The development of high-rate structural health monitoring methods is intended to provide damage detection on timescales of 10 µs -10ms where speed of detection is critical to maintain structural integrity. Here, a novel Variable Input Observer (VIO) coupled with an adaptive observer is proposed as a potential solution for complex high-rate problems. The VIO is designed to adapt its input space based on real-time identification of the system's essential dynamics. By selecting appropriate time-delayed coordinates defined by both a time delay and an embedding dimension, the proper input space is chosen which allows more accurate estimations of the current state and a reduction of the convergence rate. The optimal time-delay is estimated based on mutual information, and the embedding dimension is based on false nearest neighbors. A simulation of the VIO is conducted on a two degree-of-freedom system with simulated damage. Results are compared with an adaptive Luenberger observer, a fixed time-delay observer, and a Kalman Filter. Under its preliminary design, the VIO converges significantly faster than the Luenberger and fixed observer. It performed similarly to the Kalman Filter in terms of convergence, but with greater accuracy.

  13. The Molecular Structure of Penicillin

    NASA Astrophysics Data System (ADS)

    Bentley, Ronald

    2004-10-01

    The chemical structure of penicillin was determined between 1942 and 1945 under conditions of secrecy established by the U.S. and U.K. governments. The evidence was not published in the open literature but as a monograph. This complex volume does not present a structure proof that can be readily comprehended by a student. In this article, a basic structural proof for the penicillin molecule is provided, emphasizing the chemical work. The stereochemistry of penicillin is also described, and various rearrangements are considered on the basis of the accepted β-lactam structure.

  14. Inputs of anthropogenic nitrogen influence isotopic composition and trophic structure in SE Australian estuaries.

    PubMed

    Mazumder, Debashish; Saintilan, Neil; Alderson, Brendan; Hollins, Suzanne

    2015-11-15

    Urban development in coastal settings has increased the input of nitrogen into estuaries globally, in many cases changing the composition of estuarine ecosystems. By focussing on three adjacent estuaries with a gradient of anthropogenic N loadings, we used stable isotopes of N and C to test for changes due to increased anthropogenic N input on the structure of some key trophic linkages in estuaries. We found a consistent enrichment in δ(15)N corresponding to increased anthropogenic N at the three ecosystem levels studied: fine benthic organic matter, grazing invertebrate, and planktivorous fish. The degree of enrichment in δ(15)N between fine benthic organic matter and the grapsid crab Parasesarma erythrodactyla was identical across the three sites. The glassfish Ambassis jacksoniensis showed lower levels of enrichment compared to basal food sources at the higher N-loaded sites, suggesting a possible effect of anthropogenic N in decreasing food-chain length in these estuaries.

  15. Stability analysis of large space structure control systems with delayed input

    NASA Technical Reports Server (NTRS)

    Reddy, A. S. S. R.; Bainum, P. M.

    1988-01-01

    Large space structural systems, due to their inherent flexibility and low mass to area ratio, are represented by large dimensional mathematical models. For implementation of the control laws for such systems a finite amount of time is required to evaluate the control signals; and this time delay may cause instability in the closed loop control system that was previously designed without taking the input delay into consideration. The stability analysis of a simple harmonic oscillator representing the equation of a single mode as a function of delay time is analyzed analytically and verified numerically. The effect of inherent damping on the delay is also analyzed. The control problem with delayed input is also formulated in the discrete time domain.

  16. Stability analysis of large space structure control systems with delayed input

    NASA Technical Reports Server (NTRS)

    Reddy, A. S. S. R.; Bainum, Peter M.

    1988-01-01

    Large space structural systems, due to their inherent flexibility and low mass to area ratio, are represented by large dimensional mathematical models. For implementation of the control laws for such systems a finite amount of time is required to evaluate the control signals; and this time delay may cause instability in the closed loop control system that was previously designed without taking the input delay into consideration. The stability analysis of a simple harmonic oscillator representing the equation of a single mode as a function of delay time is treated analytically and verified numerically. The effect of inherent damping on the delay is also analyzed. The control problem with delayed input is also formulated in the discrete time domain.

  17. [Electron microscopy analysis of the structural elements of the vestibular input to nodulus Purkinje's cells in rats exposed to a 9-day space flight].

    PubMed

    Krasnov, I B

    2008-01-01

    Electron microscopy was used to study structural elements of the vestibular afferent input to the cerebellar nodulus Purkinje's cells--terminals of mossy fibers and granular cells in the granular layer and parallel fibers and Purkinje's cell dendrites in the molecular layer in rats decapitated in 2-3 hours and 9 days after the 9-day space flight aboard NASA shuttle Columbia (STS 40, SLS-1 mission). Analysis of the revealed ultrastructural changes on the base of morphofunctional correlations leads to the following conclusions: 1) space flight induced a prolonged reduction in vestibular input to most of the mossy fiber terminals and nodulus Purkinje's cells; 2) within the initial hours of recovery the vestibular input to a part of mossy fiber terminals and granular cells was increasing due to elevation of the sensitivity of vestibular receptors in microgravity; 3) regain of the vestibular input to Purkinje's cells after space flight is hampered by structural, as a result of microgravity effects, and also functional, developing shortly after space flight, impediments, and 4) in 9 d after landing the vestibular input to Purkinje's cells was almost normal. The observed reduction in the vestibular input to the nodulus Purkinje's cells during and after the spaceflight microgravity is presumably the key to the mechanism altering the velocity storage in mammals in microgravity and on return from space flight.

  18. Parallel Readout of Pathway-Specific Inputs to Laminated Brain Structures

    PubMed Central

    Makarova, Julia; Ibarz, José M.; Makarov, Valeri A.; Benito, Nuria; Herreras, Oscar

    2011-01-01

    Local field potentials (LFPs) capture the electrical activity produced by principal cells during integration of converging synaptic inputs from multiple neuronal populations. However, since synaptic currents mix in the extracellular volume, LFPs have complex spatiotemporal structure, making them hard to exploit. Here we propose a biophysical framework to identify and separate LFP-generators. First we use a computational multineuronal model that scales up single cell electrogenesis driven by several synaptic inputs to realistic aggregate LFPs. This approach relies on the fixed but distinct locations of synaptic inputs from different presynaptic populations targeting a laminated brain structure. Thus the LFPs are contributed by several pathway-specific LFP-generators, whose electrical activity is defined by the spatial distribution of synaptic terminals and the time course of synaptic currents initiated in target cells by the corresponding presynaptic population. Then we explore the efficacy of independent component analysis to blindly separate converging sources and reconstruct pathway-specific LFP-generators. This approach can optimally locate synaptic inputs with subcellular accuracy while the reconstructed time course of pathway-specific LFP-generators is reliable in the millisecond scale. We also describe few cases where the non-linear intracellular interaction of strongly overlapping LFP-generators may lead to a significant cross-contamination and the appearance of derivative generators. We show that the approach reliably disentangle ongoing LFPs in the hippocampus into contribution of several LFP-generators. We were able to readout in parallel the pathway-specific presynaptic activity of projection cells in the entorhinal cortex and pyramidal cells in the ipsilateral and contralateral CA3. Thus we provide formal mathematical and experimental support for parallel readout of the activity of converging presynaptic populations in working neuronal circuits from

  19. A new extension of unscented Kalman filter for structural health assessment with unknown input

    NASA Astrophysics Data System (ADS)

    Al-Hussein, Abdullah; Haldar, Achintya

    2014-03-01

    A time-domain nonlinear system identification (SI)-based structural health assessment (SHA) procedure, using Unscented Kalman Filter (UKF) concept, is presented in this paper. It is a two-stage procedure. It integrates an iterative least squares technique and the unscented Kalman filter concept. The authors believe that the integrated procedure significantly improves the basic UKF concept. The procedure can assess the health of a structure using only a limited number of noise-contaminated acceleration time-histories measured only at a small part of a structure and does not need information on input excitation. The structures are represented by finite element models and the location and severity of defect(s) are assessed by tracking the changes in the stiffness properties of individual elements from their expected values. With the help of examples, it is demonstrated that the method is capable of accurately identifying defect-free and defective states of structures. Small and relatively large defects are introduced at different locations in the structure and the capability of the method to detect the health of the structure is examined. It is demonstrated that the accuracy of the method is much better than the other methods currently available for the structural health assessment. It is also superior to the extended Kalman filter. Considering the accuracy and robustness, the procedure can be used as a nondestructive structural health assessment procedure.

  20. The Molecular Structure of Penicillin

    ERIC Educational Resources Information Center

    Bentley, Ronald

    2004-01-01

    Overviews of the observations that constitute a structure proof for penicillin, specifically aimed at the general student population, are presented. Melting points and boiling points were criteria of purity and a crucial tool was microanalysis leading to empirical formulas.

  1. Structured Molecular Gas Reveals Galactic Spiral Arms

    NASA Astrophysics Data System (ADS)

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory 13CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  2. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    SciTech Connect

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  3. Trigeminothalamic barrelette neurons: natural structural side asymmetries and sensory input-dependent plasticity in adult rats.

    PubMed

    Negredo, P; Martin, Y B; Lagares, A; Castro, J; Villacorta, J A; Avendaño, C

    2009-11-10

    In the rodent trigeminal principal nucleus (Pr5) the barrelette thalamic-projecting neurons relay information from individual whiskers to corresponding contralateral thalamic barreloids. Here we investigated the presence of lateral asymmetries in the dendritic trees of these neurons, and the morphometric changes resulting from input-dependent plasticity in young adult rats. After retrograde labeling with dextran amines from the thalamus, neurons were digitally reconstructed with Neurolucida, and metrically and topologically analyzed with NeuroExplorer. The most unexpected and remarkable result was the observation of side-to-side asymmetries in the barrelette neurons of control rats. These asymmetries more significantly involved the number of low-grade trees and the total dendritic length, which were greater on the left side. Chronic global input loss resulting from infraorbital nerve (IoN) transection, or loss of active touch resulting from whisker clipping in the right neutralized, or even reversed, the observed lateral differences. While results after IoN transection have to be interpreted in the context of partial neuron death in this model, profound bilateral changes were found after haptic loss, which is achieved without inflicting any nerve damage. After whisker trimming, neurons on the left side closely resembled neurons on the right in controls, the natural dendritic length asymmetry being reversed mainly by a shortening of the left trees and a more moderate elongation of the right trees. These results demonstrate that dendritic morphometry is both side- and input-dependent, and that unilateral manipulation of the sensory periphery leads to bilateral morphometric changes in second order neurons of the whisker-barrel system. The presence of anatomical asymmetries in neural structures involved in early stages of somatosensory processing could help explain the expression of sensory input-dependent behavioral asymmetries.

  4. ATLAS, an integrated structural analysis and design system. Volume 3: User's manual, input and execution data

    NASA Technical Reports Server (NTRS)

    Dreisbach, R. L. (Editor)

    1979-01-01

    The input data and execution control statements for the ATLAS integrated structural analysis and design system are described. It is operational on the Control Data Corporation (CDC) 6600/CYBER computers in a batch mode or in a time-shared mode via interactive graphic or text terminals. ATLAS is a modular system of computer codes with common executive and data base management components. The system provides an extensive set of general-purpose technical programs with analytical capabilities including stiffness, stress, loads, mass, substructuring, strength design, unsteady aerodynamics, vibration, and flutter analyses. The sequence and mode of execution of selected program modules are controlled via a common user-oriented language.

  5. Structural validation as an input into seismic depth conversion to decrease assigned structural uncertainty

    NASA Astrophysics Data System (ADS)

    Totake, Yukitsugu; Butler, Robert W. H.; Bond, Clare E.

    2017-02-01

    While the interpretation of seismic reflection imagery is powerful and well established for evaluating subsurface structures it is never perfectly accurate. Structural validation techniques are widely used to geometrically test geological interpretations of seismic reflection data. Commonly these techniques are performed on depth sections converted from seismic time-based data using velocity models. Velocity model choices in seismic depth conversion have an impact on the final depth image and hence the structural geometry of interpretations. The impact of these choices in depth conversion on structural validation is rarely examined. Here we explore how multiple versions of a depth section, converted using different velocity models, influence the performance of structural validations for a fold-thrust structure from the deep water Niger Delta. The example illustrates that a range of kinematic models can validate the depth-converted profiles, regardless of the depth conversion choice and are thus poor diagnostic tools. Area-depth-strain (ADS) analysis can constrain the choice both of a kinematic model and the depth conversion, provided the seismic data allow the detachment level and excess areas to be recognised. Incorporation of ADS analysis within an interpretation-depth conversion workflow helps reduce assigned uncertainty in depth conversion, the seismic interpretation, and in the implicit geological model.

  6. Molecular Tracers of Saturated and Polycyclic Aromatic Hydrocarbon Inputs into Central Park Lake, New York City

    PubMed Central

    YAN, BEIZHAN; ABRAJANO, TEOFILO A.; BOPP, RICHARD F.; CHAKY, DAMON A.; BENEDICT, LUCILLE A.; CHILLRUD, STEVEN N.

    2011-01-01

    Saturated hydrocarbons (SH) and polycyclic aromatic hydrocarbons (PAHs) have been quantified in a sediment core obtained from Central Park Lake, New York City. Radionuclides 210Pb and 137Cs were used to assign approximate dates to each individual section in the core. The dating profile based on 210Pb matches very well with the time constraints provided by 137Cs. Radionuclide-derived depositional dates are consistent with temporal information from the petroleum-indicator ratio U/R [the ratio of unresolved complex mixture (UCM) to saturated hydrocarbons in the aliphatic fraction] and the history of fuel use in the NYC area. Ratios of 1,7-dimethylphenanthrane (DMP) to 1,7-DMP plus 2,6-DMP [1,7/(1,7 + 2,6)-DMP], retene to retene plus chrysene [Ret/(Ret + Chy)], and fluoranthene to fluoranthene plus pyrene [Fl/(Fl + Py)] provide additional source discrimination throughout the core. Results show that the ratio U/R is sensitive to petroleum inputs and Ret/(Ret + Chy) is responsive to contributions from softwood combustion, whereas both Fl/(Fl + Py) and 1,7/(1,7 + 2,6)-DMP can be used to discriminate among wood, coal, and petroleum combustion sources. Combined use of these ratios suggests that in New York City, wood combustion dominated 100 years ago, with a shift to coal combustion occurring from the 1900s to the 1950s. Petroleum use began around the 1920s and has dominated since the 1940s. PMID:16201624

  7. Theoretical investigation of the molecular structure of the isoquercitrin molecule

    NASA Astrophysics Data System (ADS)

    Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

    1999-09-01

    Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

  8. Structure and kinematics of molecular jets

    NASA Astrophysics Data System (ADS)

    Snell, R. L.

    1986-04-01

    Observational studies of the structure and kinematics of the supersonic molecular gas in star-forming regions are reviewed. These studies have suggested that the bulk of the high-velocity gas may be ambient-cloud material swept up by a collimated stellar wind. The actual structures of these outflows, however, are poorly understood. One source that may provide a better understanding of molecular outflows is that in the nearby dark cloud LDN 1551. New observations of this outflow are presented and discussed in context of the models proposed by Snell and Schloerb.

  9. On the emergence of molecular structure

    SciTech Connect

    Matyus, Edit; Reiher, Markus; Hutter, Juerg; Mueller-Herold, Ulrich

    2011-05-15

    The structure of (a{sup {+-}},a{sup {+-}},b{sup {+-}})-type Coulombic systems is characterized by the effective ground-state density of the a-type particles, computed via nonrelativistic quantum mechanics without introduction of the Born-Oppenheimer approximation. A structural transition is observed when varying the relative mass of the a- and b-type particles, e.g., between atomic H{sup -} and molecular H{sub 2}{sup +}. The particle-density profile indicates a molecular-type behavior for the positronium ion, Ps{sup -}.

  10. Molecular docking to ensembles of protein structures.

    PubMed

    Knegtel, R M; Kuntz, I D; Oshiro, C M

    1997-02-21

    Until recently, applications of molecular docking assumed that the macromolecular receptor exists in a single, rigid conformation. However, structural studies involving different ligands bound to the same target biomolecule frequently reveal modest but significant conformational changes in the target. In this paper, two related methods for molecular docking are described that utilize information on conformational variability from ensembles of experimental receptor structures. One method combines the information into an "energy-weighted average" of the interaction energy between a ligand and each receptor structure. The other method performs the averaging on a structural level, producing a "geometry-weighted average" of the inter-molecular force field score used in DOCK 3.5. Both methods have been applied in docking small molecules to ensembles of crystal and solution structures, and we show that experimentally determined binding orientations and computed energies of known ligands can be reproduced accurately. The use of composite grids, when conformationally different protein structures are available, yields an improvement in computational speed for database searches in proportion to the number of structures.

  11. Signal processing and damage detection in a frame structure excited by chaotic input force

    NASA Astrophysics Data System (ADS)

    Salvino, Liming W.; Pines, Darryll J.; Todd, Michael D.; Nichols, Jonathan

    2003-07-01

    This paper discusses the development of a general time-frequency data analysis method, the Empirical Mode Decomposition (EMD) and Hilbert Spectrum, and its application to structural health monitoring. The focus of this work is on feature extraction from structural response time series data. This is done by tracking unique characteristics of the adaptive decomposition components and developing a damage index based on previously introduced fundamental relationships connecting the instantaneous phase of a measured time series to the structural mass and stiffness parameters. Damage detection applications are investigated for a laboratory experiment of a simple frame (a model of a multi-story building) where damage is incurred by removing bolts at various locations. The frame is excited by a low dimensional deterministic chaos input as well as by broadband random signal. The time series output of the frame response is then analyzed with the EMD method. The time-frequency features and instantaneous phase relationships are extracted and examined for changes which may occur due to damage. These results are compared to results from other newly developed detection algorithms based on geometric properties of a chaotic attractor. Our results illustrate that the EMD and instantaneous phase detection approach, based on time-frequency analysis along with simple physics-based models, can be used to determine the presence and location of structural damage and permits the development of a reliable damage detection methodology.

  12. Role of FMRFamide in the reproduction of Octopus vulgaris: molecular analysis and effect on visual input.

    PubMed

    Di Cristo, Carlo; Delli Bovi, Pasquale; Di Cosmo, Anna

    2003-10-01

    As a part of continuous research on the neurobiology of the cephalopods in general, and the neuroendocrine control of reproduction in Octopus vulgaris in particular, the presence, the molecular analysis and the effect of FMRFamide on the screening-pigment migration in the visual system have been analysed. FMRFamide immunoreactive fibres are present in the outer plexiform layer of the retina as well as in the plexiform zone of the deep retina. These fibres presumably come from optic and olfactory lobes. We isolated an incomplete Octopus FMRFamide cDNA which encodes an amino terminal truncated precursor containing several FMRFamide-related peptides (FaRPs) showing a high degree of identity with the FaRPs encoded in the precursor of Sepia officinalis, except for the presence of an Rpamide related peptide, present only in cnidarians. Finally, stimulation of isolated retina demonstrated that the effect of this tetrapeptide, coupled with dopamine, is the induction of an extreme adaptation of the retina to the light condition. This situation de facto inhibits sexual maturation. Our results on the effect of FMRFamide on the retina confirm the suggested hypothesis that this peptide plays an inhibitory role on the activity of optic gland.

  13. Vertex centralities in input-output networks reveal the structure of modern economies

    NASA Astrophysics Data System (ADS)

    Blöchl, Florian; Theis, Fabian J.; Vega-Redondo, Fernando; Fisher, Eric O.'N.

    2011-04-01

    Input-output tables describe the flows of goods and services between the sectors of an economy. These tables can be interpreted as weighted directed networks. At the usual level of aggregation, they contain nodes with strong self-loops and are almost completely connected. We derive two measures of node centrality that are well suited for such networks. Both are based on random walks and have interpretations as the propagation of supply shocks through the economy. Random walk centrality reveals the vertices most immediately affected by a shock. Counting betweenness identifies the nodes where a shock lingers longest. The two measures differ in how they treat self-loops. We apply both to data from a wide set of countries and uncover salient characteristics of the structures of these national economies. We further validate our indices by clustering according to sectors’ centralities. This analysis reveals geographical proximity and similar developmental status.

  14. Evaluation of severe accident risks: Quantification of major input parameters. Experts` determination of structural response issues

    SciTech Connect

    Breeding, R.J.; Harper, F.T.; Brown, T.D.; Gregory, J.J.; Payne, A.C.; Gorham, E.D.; Murfin, W.; Amos, C.N.

    1992-03-01

    In support of the Nuclear Regulatory Commission`s (NRC`s) assessment of the risk from severe accidents at commercial nuclear power plants in the US reported in NUREG-1150, the Severe Accident Risk Reduction Program (SAARP) has completed a revised calculation of the risk to the general public from severe accidents at five nuclear power plants: Surry, Sequoyah, Zion, Peach Bottom, and Grand Gulf. The emphasis in this risk analysis was not on determining a ``so-called`` point estimate of risk. Rather, it was to determine the distribution of risk, and to discover the uncertainties that account for the breadth of this distribution. Off-site risk initiation by events, both internal to the power station and external to the power station were assessed. Much of the important input to the logic models was generated by expert panels. This document presents the distributions and the rationale supporting the distributions for the questions posed to the Structural Response Panel.

  15. Students' Understanding of Molecular Structure Representations

    ERIC Educational Resources Information Center

    Ferk, Vesna; Vrtacnik, Margareta; Blejec, Andrej; Gril, Alenka

    2003-01-01

    The purpose of the investigation was to determine the meanings attached by students to the different kinds of molecular structure representations used in chemistry teaching. The students (n = 124) were from primary (aged 13-14 years) and secondary (aged 17-18 years) schools and a university (aged 21-25 years). A computerised "Chemical…

  16. Molecular Association and Structure of Hydrogen Peroxide.

    ERIC Educational Resources Information Center

    Giguere, Paul A.

    1983-01-01

    The statement is sometimes made in textbooks that liquid hydrogen peroxide is more strongly associated than water, evidenced by its higher boiling point and greater heat of vaporization. Discusses these and an additional factor (the nearly double molecular mass of the peroxide), focusing on hydrogen bonds and structure of the molecule. (JN)

  17. Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River

    PubMed Central

    Staley, Christopher; Gould, Trevor J.; Wang, Ping; Phillips, Jane; Cotner, James B.; Sadowsky, Michael J.

    2014-01-01

    Local and regional associations between bacterial communities and nutrient and chemical concentrations were assessed in the Upper Mississippi River in Minnesota to determine if community structure was associated with discrete types of chemical inputs associated with different land cover. Bacterial communities were characterized by Illumina sequencing of the V6 region of 16S rDNA and compared to >40 chemical and nutrient concentrations. Local bacterial community structure was shaped primarily by associations among bacterial orders. However, order abundances were correlated regionally with nutrient and chemical concentrations, and were also related to major land coverage types. Total organic carbon and total dissolved solids were among the primary abiotic factors associated with local community composition and co-varied with land cover. Escherichia coli concentration was poorly related to community composition or nutrient concentrations. Abundances of 14 bacterial orders were related to land coverage type, and seven showed significant differences in abundance (P ≤ 0.046) between forested or anthropogenically-impacted sites. This study identifies specific bacterial orders that were associated with chemicals and nutrients derived from specific land cover types and may be useful in assessing water quality. Results of this study reveal the need to investigate community dynamics at both the local and regional scales and to identify shifts in taxonomic community structure that may be useful in determining sources of pollution in the Upper Mississippi River. PMID:25339945

  18. Spatial structure of the meroplankton community along a Patagonian fjord - The role of changing freshwater inputs

    NASA Astrophysics Data System (ADS)

    Meerhoff, Erika; Tapia, Fabián J.; Castro, Leonardo R.

    2014-12-01

    Freshwater inputs are major drivers of circulation, hydrographic structure, and productivity patterns along estuarine systems. We assessed the degree to which meroplankton community structure in the Baker/Martinez fjord complex (Chilean Patagonia, 47.5°S) responds to spatial and temporal changes in hydrographic conditions driven by seasonal changes in Baker river outflow. Zooplankton and hydrographic measurements were conducted along the fjord in early spring (October) and late summer (February), when river outflow was minimal and maximal, respectively. Major meroplankton groups found on these surveys were larval barnacles, crabs, bivalves and gastropods. There was a clear change in community structure between October and February, explained by a switch in the numerically dominant group from barnacle to bivalve larvae. This change in community structure was related to changes in hydrographic structure along the fjord, which are mainly associated with seasonal changes in the Baker river outflow. A variance partition analysis showed no significant spatial trend that could account for the variation in meroplankton along the Martinez channel, whereas temporal variability and environmental variables accounted for 36.6% and 27.6% of the variance, respectively. When comparing meroplankton among the Baker and Martinez channels in October, changes in environmental variables explained 44.9% of total variance, whereas spatial variability accounted for 23.5%. Early and late-stage barnacle larvae (i.e. nauplii and cyprids) were more abundant in water with lower temperature, and higher dissolved oxygen and chlorophyll-a concentration, whereas bivalve larvae were more strongly associated to warmer waters. The seasonal shift in numerical dominance, from barnacle larvae in early spring to bivalve larvae in late summer, suggests that reproduction of these groups is triggered by substantially different sets of conditions, both in terms of hydrography and food availability. The

  19. Structural effects in molecular metal halides.

    PubMed

    Hargittai, Magdolna

    2009-03-17

    Metal halides are a relatively large class of inorganic compounds that participate in many industrial processes, from halogen metallurgy to the production of semiconductors. Because most metal halides are ionic crystals at ambient conditions, the term "molecular metal halides" usually refers to vapor-phase species. These gas-phase molecules have a special place in basic research because they exhibit the widest range of chemical bonding from the purely ionic to mostly covalent bonding through to weakly interacting systems. Although our focus is basic research, knowledge of the structural and thermodynamic properties of gas-phase metal halides is also important in industrial processes. In this Account, we review our most recent work on metal halide molecular structures. Our studies are based on electron diffraction and vibrational spectroscopy, and increasingly, we have augmented our experimental work with quantum chemical computations. Using both experimental and computational techniques has enabled us to determine intriguing structural effects with better accuracy than using either technique alone. We loosely group our discussion based on structural effects including "floppiness", relativistic effects, vibronic interactions, and finally, undiscovered molecules with computational thermodynamic stability. Floppiness, or serious "nonrigidity", is a typical characteristic of metal halides and makes their study challenging for both experimentalists and theoreticians. Relativistic effects are mostly responsible for the unique structure of gold and mercury halides. These molecules have shorter-than-expected bonds and often have unusual geometrical configurations. The gold monohalide and mercury dihalide dimers and the molecular-type crystal structure of HgCl(2) are examples. We also examined spin-orbit coupling and the possible effect of the 4f electrons on the structure of lanthanide trihalides. Unexpectedly, we found that the geometry of their dimers depends on the f

  20. Large Woody Debris Input and Its Influence on Channel Structure in Agricultural Lands of Southeast Brazil

    NASA Astrophysics Data System (ADS)

    Paula, Felipe Rossetti De; Ferraz, Silvio Frosini De Barros; Gerhard, Pedro; Vettorazzi, Carlos Alberto; Ferreira, Anderson

    2011-10-01

    Riparian forests are important for the structure and functioning of stream ecosystems, providing structural components such as large woody debris (LWD). Changes in these forests will cause modifications in the LWD input to streams, affecting their structure. In order to assess the influence of riparian forests changes in LWD supply, 15 catchments (third and fourth order) with riparian forests at different conservation levels were selected for sampling. In each catchment we quantified the abundance, volume and diameter of LWD in stream channels; the number, area and volume of pools formed by LWD and basal area and tree diameter of riparian forest. We found that riparian forests were at a secondary successional stage with predominantly young trees (diameter at breast height <10 cm) in all studied streams. Results showed that basal area and diameter of riparian forest differed between the stream groups (forested and non-forested), but tree density did not differ between groups. Differences were also observed in LWD abundance, volume, frequency of LWD pools with subunits and area and volume of LWD pools. LWD diameter, LWD that form pools diameter and frequency of LWD pools without subunits did not differ between stream groups. Regression analyses showed that LWD abundance and volume, and frequency of LWD pools (with and without subunits) were positively related with the proportion of riparian forest. LWD diameter was not correlated to riparian tree diameter. The frequency of LWD pools was correlated to the abundance and volume of LWD, but characteristics of these pools (area and volume) were not correlated to the diameter of LWD that formed the pools. These results show that alterations in riparian forest cause modifications in the LWD abundance and volume in the stream channel, affecting mainly the structural complexity of these ecosystems (reduction in the number and structural characteristics of LWD pools). Our results also demonstrate that riparian forest

  1. 2004 Reversible Associations in Structure & Molecular Biology

    SciTech Connect

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  2. A Multistate Molecular Switch Based on the 6,8-Rearrangement in Bromo-apigeninidin Operated with pH and Host-Guest Inputs.

    PubMed

    Basílio, Nuno; Cruz, Luís; de Freitas, Victor; Pina, Fernando

    2016-07-28

    The equilibrium between 6- and 8-bromo-apigeninidin is quantitatively displaced toward the formation of the former in the presence of cucurbit[7]uril because of the selective recognition of the 6-bromo isomer by the host. This phenomenon permits us to conceive a unidirectional multistate switch addressed with host-guest inputs and enables the reversible activation and deactivation of the 6-/8-bromo-apigeninidin dynamic molecular multistate through coupled host-guest and pH inputs.

  3. Monitoring Soil Carbon Inputs and Changes with Crop Type and Management Practice Using Pyrolysis-Molecular Beam Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Leventhal, J.; Magrini-Bair, K. A.; Hoover, C. M.; Doyle, G. L.; Follett, R. L.; Kimble, J.; Davis, M. F.; Evans, R. J.

    2003-12-01

    With the increasing need to produce more renewable bioenergy products comes the need to assess the impacts of these agricultural cropping practices on soil carbon inputs and changes. In addition, the anticipated increased use of short rotation woody crops for biomass and bioenergy programs requires that we improve our understanding of the effects of management on soil quality and soil organic matter. We have developed an atmospheric pressure rapid pyrolysis technique that can analyze up to 150 samples per day with direct sampling molecular beam mass spectrometry (py-MBMS). The advantage of this technique is that complex biomaterials can be rapidly pyrolyzed and subsequent fragment condensation reduced which provides molecular data for both light and heavy pyrolysis products. Because of the chemical richness of the resultant mass spectra, we use multivariate statistical analysis techniques to provide efficient pattern recognition and identify major pyrolysis products. These products can then be used to characterize soil organic matter content and composition. Preliminary results from 0-5 cm soils cores taken from soils that were cropped with either continuous till or no till sorghum or soybeans show that we can easily distinguish between till and no till regardless of crop type. Analysis of depth increments of forest soils that experienced a chronosequence of wind disturbances showed that we could distinguish depth, location, and recent and older soil organic matter species of the soil cores with this technique. Analysis of well-characterized CRP (Conservation Reserve Program) soils again allowed us to distinguish depth and location and to accurately predict soil microbial biomass contents. We will present these results and discuss their implications for quantitatively assessing the impacts of bioenergy cropping on soil organic matter.

  4. Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure

    DTIC Science & Technology

    2014-08-30

    properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to

  5. Input-based structure-specific proficiency predicts the neural mechanism of adult L2 syntactic processing.

    PubMed

    Deng, Taiping; Zhou, Huixia; Bi, Hong-Yan; Chen, Baoguo

    2015-06-12

    This study used Event-Related Potentials (ERPs) to explore the role of input-based structure-specific proficiency in L2 syntactic processing, using English subject-verb agreement structures as the stimuli. A pre-test/trainings/post-test paradigm of experimental and control groups was employed, and Chinese speakers who learned English as a second language (L2) participated in the experiment. At pre-test, no ERP component related to the subject-verb agreement structures violations was observed in either group. At training session, the experimental group learned the subject-verb agreement structures, while the control group learned other syntactic structures. After two continuously intensive input trainings, at post-test, a significant P600 component related to the subject-verb agreement structures violations was elicited in the experimental group, but not in the control group. These findings suggest that input training improves structure-specific proficiency, which is reflected in the neural mechanism of L2 syntactic processing.

  6. Properties of input-output Hammerstein-bilinear structure with application to an industrial air handling unit

    NASA Astrophysics Data System (ADS)

    Larkowski, T.; Zajic, I.; Burnham, K. J.; Koszalka, L.

    2014-12-01

    When developing mathematical models, especially for control, the practical interest lies in relatively simple extensions of linear structures that offer improved modelling capabilities. In this paper a discrete-time input-output Hammerstein-bilinear structure is introduced and its properties are discussed in detail. It consists of a cascade connection of a static nonlinearity followed by a dynamic bilinear system. By combining advantages of constituent subsystems the Hammerstein-bilinear structure allows for both an input dependant dynamic behaviour (particular property of bilinear systems) and an increased flexibility of the steady-state characteristic (particular property of Hammerstein models) to be obtained simultaneously. Modelling capabilities of such structure are evaluated on an air-handling unit that is a part of an industrial heating, ventilation and air-conditioning system.

  7. Parallel computing structures capable of flexible associations and recognition of fuzzy inputs

    NASA Astrophysics Data System (ADS)

    Hogg, T.; Huberman, B. A.

    1985-10-01

    We experimentally show that computing with attractors leads to fast adaptive behavior in which dynamical associations can be made between different inputs which initially produce sharply distinct outputs. We do so by first defining a set of simple local procedures which allow a computing array to change its state in time so as to produce classical Pavlovian conditioning. We then examine the dynamics of coalescence and dissociation of attractors with a number of quantitative experiments. We also show how such arrays exhibit generalization and differentiation of inputs in their behavior.

  8. Combined Influence of Landscape Composition and Nutrient Inputs on Lake Trophic Structure

    EPA Science Inventory

    The concentration of chlorophyll a is a measure of the biological productivity of a lake and is largely (but not exclusively) determined by available nutrients. As nutrient inputs increase, productivity increases and lakes transition from low trophic state (e.g. oligotrophic) to...

  9. The Roles of Structured Input Activities in Processing Instruction and the Kinds of Knowledge They Promote

    ERIC Educational Resources Information Center

    Marsden, Emma; Chen, Hsin-Ying

    2011-01-01

    This study aimed to isolate the effects of the two input activities in Processing Instruction: referential activities, which force learners to focus on a form and its meaning, and affective activities, which contain exemplars of the target form and require learners to process sentence meaning. One hundred and twenty 12-year-old Taiwanese learners…

  10. Structure and characteristics of landslide input data and consequences on landslide susceptibility assessment and prediction capability

    NASA Astrophysics Data System (ADS)

    Oliveira, S. C.; Zezere, J. L.; Garcia, R. A. C.; Piedade, A.

    2009-04-01

    For the territorial planning and management it is of crucial importance the knowledge of the landslide susceptibility, in order to minimize the physical damages and economic losses associated to a certain instability scenario. Resultant mitigation measures can only be effective if we were able to predict where future landslides will occur. In order to improve the quality of data driven landslide susceptibility assessment, recent research developed worldwide as been focused on some fundamental questions: What is the quality of landslide inventories? What is the most appropriate terrain-unit to adopt? What is the most reliable statistical model? What are the best tools to validate results? In contrast, little attention has been given in the literature to the consequences on the landslide susceptibility assessment resulting from the structure and characteristics of the landslide database. Under the assumption that the conditions that led to slope instability in the past are more likely to generate new instability in the future, the statistically-based landslide susceptibility evaluation for a specific area is based on the spatial correlation between a set of independent, predisposing landslide geo-environmental factors, and the distribution of past landslides, which are considered the dependent variable. Landslides are usually included in the susceptibility models as a single point or as a polygon representing the entire unstable area. The selection of the way landslide information enter into prediction models (point vs polygon) is frequently conditioned by software constrains, and surprisingly, the effects of this choice in landslide susceptibility results has not been made. The purpose of this study is to evaluate the quality of susceptibility results obtained for rotational slides in a 12 km2 test site located at north of Lisbon, Portugal considering: (i) the structure and characteristics of landslide input data; (ii) the capacity of different landslide inventories

  11. Algorithmic dimensionality reduction for molecular structure analysis.

    PubMed

    Brown, W Michael; Martin, Shawn; Pollock, Sara N; Coutsias, Evangelos A; Watson, Jean-Paul

    2008-08-14

    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation--a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation.

  12. Molecular structure of the collagen triple helix.

    PubMed

    Brodsky, Barbara; Persikov, Anton V

    2005-01-01

    The molecular conformation of the collagen triple helix confers strict amino acid sequence constraints, requiring a (Gly-X-Y)(n) repeating pattern and a high content of imino acids. The increasing family of collagens and proteins with collagenous domains shows the collagen triple helix to be a basic motif adaptable to a range of proteins and functions. Its rodlike domain has the potential for various modes of self-association and the capacity to bind receptors, other proteins, GAGs, and nucleic acids. High-resolution crystal structures obtained for collagen model peptides confirm the supercoiled triple helix conformation, and provide new information on hydrogen bonding patterns, hydration, sidechain interactions, and ligand binding. For several peptides, the helix twist was found to be sequence dependent, and such variation in helix twist may serve as recognition features or to orient the triple helix for binding. Mutations in the collagen triple-helix domain lead to a variety of human disorders. The most common mutations are single-base substitutions that lead to the replacement of one Gly residue, breaking the Gly-X-Y repeating pattern. A single Gly substitution destabilizes the triple helix through a local disruption in hydrogen bonding and produces a discontinuity in the register of the helix. Molecular information about the collagen triple helix and the effect of mutations will lead to a better understanding of function and pathology.

  13. Structure and Dynamics of Cellulose Molecular Solutions

    NASA Astrophysics Data System (ADS)

    Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert

    Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.

  14. Effects of switchgrass cultivars and intraspecific differences in root structure on soil carbon inputs and accumulation

    SciTech Connect

    Adkins, Jaron; Jastrow, Julie D.; Morris, Geoffrey P.; Six, Johan; de Graaff, Marie-Anne

    2016-01-01

    Switchgrass (Panicum virgatum L), a cellulosic biofuel feedstock, may promote soil C 21 accumulation compared to annual cropping systems by increasing the amount and retention of 22 root-derived soil C inputs. The aim of this study was to assess how different switchgrass 23 cultivars impact soil C inputs and retention, whether these impacts vary with depth, and whether 24 specific root length (SRL) explains these impacts. We collected soil to a depth of 30 cm from six 25 switchgrass cultivars with root systems ranging from high to low SRL. The cultivars (C4 species) 26 were grown for 27 months on soils previously dominated by C3 plants, allowing us to use the 27 natural difference in 13C isotopic signatures between C3 soils and C4 plants to quantify 28 switchgrass-derived C accumulation. The soil was fractionated into coarse particulate organic 29 matter (CPOM), fine particulate organic matter (FPOM), silt, and clay-sized fractions. We 30 measured total C and plant-derived C in all soil fractions across all depths. The study led to two main results: (1) bulk soil C concentrations beneath switchgrass cultivars varied by 40% in the 0-32 10 cm soil depth and by 70% in the 10-20 cm soil depth, and cultivars with high bulk soil C 33 concentrations tended to have relatively high C concentrations in the mineral soil fractions and 34 relatively low C concentrations in the POM fractions; (2) there were significant differences in 35 switchgrass-derived soil C between cultivars at the 0-10 cm depth, where soil C inputs ranged 36 from 1.2 to 3.2 mg C g-1 dry soil. There was also evidence of a positive correlation between SRL 37 and switchgrass-derived C inputs when one outlier data point was removed. These results 38 indicate that switchgrass cultivars differentially impact mechanisms contributing to soil C accumulation.

  15. Experimental and Theoretical Determination of the Thermomechanical Response of Inelastic Structural Materials to High Energy Thermal Inputs

    DTIC Science & Technology

    1988-12-01

    CLASSIFICATION AUTHORITY 3 . DISTRIBUTION /AVAILABILITY OF REPORT __________________________________ A~PrOyed tOr publIc release, 2o. DECLASSIFICATION...DETERMINATION OF THE THERMOMECHANICAL RESPONSE OF INELASTIC STRUCTURAL MATERIALS TO HIGH ENERGY THERMAL INPUTS 3 Semi-Annual Technical Report Submitted by...D.H. Allen Aerospace Engineering Department and M.S. Pilant Mathematics Department 5Texas A&M University College Station, Texas 77843U 3 to the Air

  16. An Integrated Bayesian Uncertainty Estimator: fusion of Input, Parameter and Model Structural Uncertainty Estimation in Hydrologic Prediction System

    NASA Astrophysics Data System (ADS)

    Ajami, N. K.; Duan, Q.; Sorooshian, S.

    2005-12-01

    To-date single conceptual hydrologic models often applied to interpret physical processes within a watershed. Nevertheless hydrologic models regardless of their sophistication and complexity are simplified representation of the complex, spatially distributed and highly nonlinear real world system. Consequently their hydrologic predictions contain considerable uncertainty from different sources including: hydrometeorological forcing inputs, boundary/initial conditions, model structure, model parameters which need to be accounted for. Thus far the effort has gone to address these sources of uncertainty explicitly, making an implicit assumption that uncertainties from different sources are additive. Nevertheless because of the nonlinear nature of the hydrologic systems, it is not feasible to account for these uncertainties independently. Here we present the Integrated Bayesian Uncertainty Estimator (IBUNE) which accounts for total uncertainties from all major sources: inputs forcing, model structure, model parameters. This algorithm explores multi-model framework to tackle model structural uncertainty while using the Bayesian rules to estimate parameter and input uncertainty within individual models. Three hydrologic models including SACramento Soil Moisture Accounting (SAC-SMA) model, Hydrologic model (HYMOD) and Simple Water Balance (SWB) model were considered within IBUNE framework for this study. The results which are presented for the Leaf River Basin, MS, indicates that IBUNE gives a better quantification of uncertainty through hydrological modeling processes, therefore provide more reliable and less bias prediction with realistic uncertainty boundaries.

  17. Speculations on the molecular structure of eumelanin.

    PubMed

    Swift, J A

    2009-04-01

    Eumelanin is the polymeric black pigment commonly found in hair and skin. Its chemical intractability, to all but vigorous oxidizing agents, has hindered satisfactory understanding of its molecular structure. It is well-established that the immediate precursor to polymerization, indole-5,6-quinone (IQ), is biosynthesized from the amino acid tyrosine. Current views are that the polymer consists of single bond connections between random indole and degraded indole units. In this paper, an alternative chemical scheme for the polymerization of IQ is proposed based upon the original suggestion by Horner in 1949 that a Diels-Alder (D-A) reaction might be involved. The proposed basic chemical scheme for eumelanin formation is that D-A addition occurs specifically between the 2- and 3-positions of one IQ molecule and the 7- and 4- positions respectively of a second IQ molecule, that the ensuing diketo bridge is oxidized to carboxyl groups and that, by decarboxylation and aromatization, a fused indole dimer is produced. It is envisaged that, by further D-A addition of more IQ molecules, oligomers of greater molecular mass are produced. Calculations based on published bond lengths and angles for the indole nucleus show that oligomeric units containing a total of up to 11 fused indoles could be packed into a flat circular disc of 20 A diameter. The discs of the extensively conjugated polymer are envisaged to be stacked above each other by pi-pi interaction and with a spacing of 3.4 A to produce cylindrical units, the mass density of which is calculated to be 1.54 gm cm(-3); approximating with actual physical measurements. The size and shape of the predicted cylinders are in concordance with those observed in atomic force microscope investigations of eumelanin proto-particles. The model is also in agreement with published experimental data that 2/3rds of the carbon dioxide liberated during eumelanin formation derives from positions 5- and 6- of the IQ molecule.

  18. Spatial structure of cone inputs to receptive fields in primate lateral geniculate nucleus

    NASA Astrophysics Data System (ADS)

    Reid, R. Clay; Shapley, Robert M.

    1992-04-01

    HUMAN colour vision depends on three classes of cone photoreceptors, those sensitive to short (S), medium (M) or long (L) wavelengths, and on how signals from these cones are combined by neurons in the retina and brain. Macaque monkey colour vision is similar to human, and the receptive fields of macaque visual neurons have been used as an animal model of human colour processing1. P retinal ganglion cells and parvocellular neurons are colour-selective neurons in macaque retina and lateral geniculate nucleus. Interactions between cone signals feeding into these neurons are still unclear. On the basis of experimental results with chromatic adaptation, excitatory and inhibitory inputs from L and M cones onto P cells (and parvocellular neurons) were thought to be quite specific2,3 (Fig. la). But these experiments with spatially diffuse adaptation did not rule out the 'mixed-surround' hypothesis: that there might be one cone-specific mechanism, the receptive field centre, and a surround mechanism connected to all cone types indiscriminately (Fig. le). Recent work has tended to support the mixed-surround hypothesis4-8. We report here the development of new stimuli to measure spatial maps of the linear L-, M- and S-cone inputs to test the hypothesis definitively. Our measurements contradict the mixed-surround hypothesis and imply cone specificity in both centre and surround.

  19. Molecular structures and intramolecular dynamics of pentahalides

    NASA Astrophysics Data System (ADS)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  20. Filamentary structure in the Orion molecular cloud

    NASA Technical Reports Server (NTRS)

    Bally, J.; Langer, W. D.; Bally, J.; Langer, W. D.; Bally, J.; Langer, W. D.

    1986-01-01

    A large scale 13CO map (containing 33,000 spectra) of the giant molecular cloud located in the southern part of Orion is presented which contains the Orion Nebula, NGC1977, and the LI641 dark cloud complex. The overall structure of the cloud is filamentary, with individual features having a length up to 40 times their width. This morphology may result from the effects of star formation in the region or embedded magnetic fields in the cloud. We suggest a simple picture for the evolution of the Orion-A cloud and the formation of the major filament. A rotating proto-cloud (counter rotating with respect to the galaxy) contians a b-field aligned with the galaxtic plane. The northern protion of this cloud collapsed first, perhaps triggered by the pressure of the Ori I OB association. The magnetic field combined with the anisotropic pressure produced by the OB-association breaks the symmetry of the pancake instability, a filament rather than a disc is produced. The growth of instabilities in the filament formed sub-condensations which are recent sites of star formation.

  1. The Determination of Molecular Structure from Rotational Spectra

    DOE R&D Accomplishments Database

    Laurie, V. W.; Herschbach, D. R.

    1962-07-01

    An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

  2. Damage Identification for Large Span Structure Based on Multiscale Inputs to Artificial Neural Networks

    PubMed Central

    Teng, Jun; Cui, Yan

    2014-01-01

    In structural health monitoring system, little research on the damage identification from different types of sensors applied to large span structure has been done in the field. In fact, it is significant to estimate the whole structural safety if the multitype sensors or multiscale measurements are used in application of structural health monitoring and the damage identification for large span structure. A methodology to combine the local and global measurements in noisy environments based on artificial neural network is proposed in this paper. For a real large span structure, the capacity of the methodology is validated, including the decision on damage placement, the discussions on the number of the sensors, and the optimal parameters for artificial neural networks. Furthermore, the noisy environments in different levels are simulated to demonstrate the robustness and effectiveness of the proposed approach. PMID:24977207

  3. An Integrated Hydrologic Bayesian Multi-Model Combination Framework: Confronting Input, parameter and model structural uncertainty in Hydrologic Prediction

    SciTech Connect

    Ajami, N K; Duan, Q; Sorooshian, S

    2006-05-05

    This paper presents a new technique--Integrated Bayesian Uncertainty Estimator (IBUNE) to account for the major uncertainties of hydrologic rainfall-runoff predictions explicitly. The uncertainties from the input (forcing) data--mainly the precipitation observations and from the model parameters are reduced through a Monte Carlo Markov Chain (MCMC) scheme named Shuffled Complex Evolution Metropolis (SCEM) algorithm which has been extended to include a precipitation error model. Afterwards, the Bayesian Model Averaging (BMA) scheme is employed to further improve the prediction skill and uncertainty estimation using multiple model output. A series of case studies using three rainfall-runoff models to predict the streamflow in the Leaf River basin, Mississippi are used to examine the necessity and usefulness of this technique. The results suggests that ignoring either input forcings error or model structural uncertainty will lead to unrealistic model simulations and their associated uncertainty bounds which does not consistently capture and represent the real-world behavior of the watershed.

  4. Molecular cloning of chicken aggrecan. Structural analyses.

    PubMed Central

    Chandrasekaran, L; Tanzer, M L

    1992-01-01

    The large, aggregating chondroitin sulphate proteoglycan of cartilage, aggrecan, has served as a generic model of proteoglycan structure. Molecular cloning of aggrecans has further defined their amino acid sequences and domain structures. In this study, we have obtained the complete coding sequence of chicken sternal cartilage aggrecan by a combination of cDNA and genomic DNA sequencing. The composite sequence is 6117 bp in length, encoding 1951 amino acids. Comparison of chicken aggrecan protein primary structure with rat, human and bovine aggrecans has disclosed both similarities and differences. The domains which are most highly conserved at 70-80% identity are the N-terminal domains G1 and G2 and the C-terminal domain G3. The chondroitin sulphate domain of chicken aggrecan is smaller than that of rat and human aggrecans and has very distinctive repeat sequences. It has two separate sections, one comprising 12 consecutive Ser-Gly-Glu repeats of 20 amino acids each, adjacent to the other which has 23 discontinuous Ser-Gly-Glu repeats of 10 amino acids each; this latter region, N-terminal to the former one, appears to be unique to chicken aggrecan. The two regions contain a total of 94 potential chondroitin sulphate attachment sites. Genomic comparison shows that, although chicken exons 11-14 are identical in size to the rat and human exons, chicken exon 10 is the smallest of the three species. This is also reflected in the size of its chondroitin sulphate coding region and in the total number of Ser-Gly pairs. The putative keratan sulphate domain shows 31-45% identity with the other species and lacks the repetitive sequences seen in the others. In summary, while the linear arrangement of specific domains of chicken aggrecan is identical to that in the aggrecans of other species, and while there is considerable identity of three separate domains, chicken aggrecan demonstrates unique features, notably in its chondroitin sulphate domain and its keratan sulphate

  5. Structures in Galaxies: Nature versus Nurture. Input from Theory and Simulations

    NASA Astrophysics Data System (ADS)

    Athanassoula, E.

    2010-10-01

    Galaxies, in particular disc galaxies, contain a number of structures and substructures with well defined morphological, photometric and kinematic properties. Considerable theoretical effort has been put into explaining their formation and evolution, both analytically and with numerical simulations. In some theories, structures form during the natural evolution of the galaxy, i.e. they are a result of nature. For others, it is the interaction with other galaxies, or with the intergalactic medium—i.e. nurture—that accounts for a structure. Either way, the existence and properties of these structures reveal important information on the underlying potential of the galaxy, i.e. on the amount and distribution of matter—including the dark matter—in it, and on the evolutionary history of the galaxy. Here, I will briefly review the various formation scenarios and the respective role of nature and nurture in the formation, evolution and properties of the main structures and substructures.

  6. Structure and dynamics of layered molecular assemblies

    NASA Astrophysics Data System (ADS)

    Horne, Jennifer Conrad

    This dissertation focuses on the goal of understanding and controlling layered material properties from a molecular perspective. With this understanding, materials can be synthetically tailored to exhibit predetermined bulk properties. This investigation describes the optical response of a family of metal-phosphonate (MP) monolayers and multilayers, materials that are potentially useful because the films are easy to synthesize and are chemically and thermally stable. MP films have shown potential in a variety of chemical sensing and optical applications, and in this dissertation, the suitability of MP films for optical information storage is explored For this application, the extent of photonic energy transport within and between optically active layers is an important factor in determining the stability and specificity of optical modifications made to a material. Intralayer and interlayer energy transport processes can be studied selectively in MP films because the composition, and thus the properties, of each layer are controlled synthetically. It was determined by fluorescence relaxation dynamics in conjunction with atomic force microscopy (AFM) that the substrate and layer morphologies are key factors in determining the layer optical and physical properties. The initial MP layers in a multilayer are structurally heterogeneous, characterized by randomly distributed islands that are ~50 A in diameter. The population dynamics measured for these layers are non-exponential, chromophore concentration-independent, and identical for two different chromophores. The data is explained in the context of an excitation hopping model in a system where the surface is characterized by islands of aggregated chromophores as well as non-aggregated monomers. Within a MP monolayer, the dynamics are dominated by intra-island excitation hopping. Forster (dipolar) energy transfer between the energetically overlapped chromophores does not play a significant role in determining the

  7. Role of intraglomerular circuits in shaping temporally structured responses to naturalistic inhalation-driven sensory input to the olfactory bulb

    PubMed Central

    Carey, Ryan M.; Sherwood, William Erik; Shipley, Michael T.; Borisyuk, Alla

    2015-01-01

    Olfaction in mammals is a dynamic process driven by the inhalation of air through the nasal cavity. Inhalation determines the temporal structure of sensory neuron responses and shapes the neural dynamics underlying central olfactory processing. Inhalation-linked bursts of activity among olfactory bulb (OB) output neurons [mitral/tufted cells (MCs)] are temporally transformed relative to those of sensory neurons. We investigated how OB circuits shape inhalation-driven dynamics in MCs using a modeling approach that was highly constrained by experimental results. First, we constructed models of canonical OB circuits that included mono- and disynaptic feedforward excitation, recurrent inhibition and feedforward inhibition of the MC. We then used experimental data to drive inputs to the models and to tune parameters; inputs were derived from sensory neuron responses during natural odorant sampling (sniffing) in awake rats, and model output was compared with recordings of MC responses to odorants sampled with the same sniff waveforms. This approach allowed us to identify OB circuit features underlying the temporal transformation of sensory inputs into inhalation-linked patterns of MC spike output. We found that realistic input-output transformations can be achieved independently by multiple circuits, including feedforward inhibition with slow onset and decay kinetics and parallel feedforward MC excitation mediated by external tufted cells. We also found that recurrent and feedforward inhibition had differential impacts on MC firing rates and on inhalation-linked response dynamics. These results highlight the importance of investigating neural circuits in a naturalistic context and provide a framework for further explorations of signal processing by OB networks. PMID:25717156

  8. Role of intraglomerular circuits in shaping temporally structured responses to naturalistic inhalation-driven sensory input to the olfactory bulb.

    PubMed

    Carey, Ryan M; Sherwood, William Erik; Shipley, Michael T; Borisyuk, Alla; Wachowiak, Matt

    2015-05-01

    Olfaction in mammals is a dynamic process driven by the inhalation of air through the nasal cavity. Inhalation determines the temporal structure of sensory neuron responses and shapes the neural dynamics underlying central olfactory processing. Inhalation-linked bursts of activity among olfactory bulb (OB) output neurons [mitral/tufted cells (MCs)] are temporally transformed relative to those of sensory neurons. We investigated how OB circuits shape inhalation-driven dynamics in MCs using a modeling approach that was highly constrained by experimental results. First, we constructed models of canonical OB circuits that included mono- and disynaptic feedforward excitation, recurrent inhibition and feedforward inhibition of the MC. We then used experimental data to drive inputs to the models and to tune parameters; inputs were derived from sensory neuron responses during natural odorant sampling (sniffing) in awake rats, and model output was compared with recordings of MC responses to odorants sampled with the same sniff waveforms. This approach allowed us to identify OB circuit features underlying the temporal transformation of sensory inputs into inhalation-linked patterns of MC spike output. We found that realistic input-output transformations can be achieved independently by multiple circuits, including feedforward inhibition with slow onset and decay kinetics and parallel feedforward MC excitation mediated by external tufted cells. We also found that recurrent and feedforward inhibition had differential impacts on MC firing rates and on inhalation-linked response dynamics. These results highlight the importance of investigating neural circuits in a naturalistic context and provide a framework for further explorations of signal processing by OB networks.

  9. Damage Characterization Method for Structural Health Management Using Reduced Number of Sensor Inputs

    NASA Technical Reports Server (NTRS)

    Krishnamurthy, T.; Hochhalter, Jacob D.; Gallegos, Adam M.

    2012-01-01

    The development of validated multidisciplinary Integrated Vehicle Health Management (IVHM) tools, technologies, and techniques to enable detection, diagnosis, prognosis, and mitigation in the presence of adverse conditions during flight will provide effective solutions to deal with safety related challenges facing next generation aircraft. The adverse conditions include loss of control caused by environmental factors, actuator and sensor faults or failures, and damage conditions. A major concern in these structures is the growth of undetected damage (cracks) due to fatigue and low velocity foreign impacts that can reach a critical size during flight, resulting in loss of control of the aircraft. Hence, development of efficient methodologies to determine the presence, location, and severity of damage in critical structural components is highly important in developing efficient structural health management systems.

  10. Uncertainties in predicting structure-borne sound power input into buildings.

    PubMed

    Gibbs, B M

    2013-05-01

    There has been a steady development of methods of measurement and prediction of structure-borne noise in buildings, particularly over the last two decades. In proposing and evaluating these methods, a major consideration has been the likely trade-off between accuracy and simplicity. Structure-borne sound transmission is a more complicated process than airborne sound transmission, but practitioners seek methods of prediction for the former, which are as straightforward as for the latter. In this paper a description is given of a study of multi-contact sources in buildings. The study concentrates on measurement and calculation procedures for sources and calculation procedures for receiver structures, particularly lightweight building elements. Although the study is not exhaustive, the findings point to the limitations of simplified methods, specifically the uncertainties likely as a result of reducing the data sets and computational effort, and the discrepancies resulting from simplifying assumptions.

  11. Molecular clouds and galactic spiral structure

    NASA Technical Reports Server (NTRS)

    Dame, T. M.

    1984-01-01

    Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide.

  12. A survey of quantitative descriptions of molecular structure.

    PubMed

    Guha, Rajarshi; Willighagen, Egon

    2012-01-01

    Numerical characterization of molecular structure is a first step in many computational analysis of chemical structure data. These numerical representations, termed descriptors, come in many forms, ranging from simple atom counts and invariants of the molecular graph to distribution of properties, such as charge, across a molecular surface. In this article we first present a broad categorization of descriptors and then describe applications and toolkits that can be employed to evaluate them. We highlight a number of issues surrounding molecular descriptor calculations such as versioning and reproducibility and describe how some toolkits have attempted to address these problems.

  13. The optimization of force inputs for active structural acoustic control using a neural network

    NASA Technical Reports Server (NTRS)

    Cabell, R. H.; Lester, H. C.; Silcox, R. J.

    1992-01-01

    This paper investigates the use of a neural network to determine which force actuators, of a multi-actuator array, are best activated in order to achieve structural-acoustic control. The concept is demonstrated using a cylinder/cavity model on which the control forces, produced by piezoelectric actuators, are applied with the objective of reducing the interior noise. A two-layer neural network is employed and the back propagation solution is compared with the results calculated by a conventional, least-squares optimization analysis. The ability of the neural network to accurately and efficiently control actuator activation for interior noise reduction is demonstrated.

  14. Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

    SciTech Connect

    Steenbergen, K. G.; Gaston, N.

    2014-02-14

    Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

  15. Input shaping filter methods for the control of structurally flexible, long-reach manipulators

    SciTech Connect

    Kwon, Dong-Soo; Hwang, Dong-Hwan; Babcock, S.M.; Burks, B.L.

    1993-11-01

    Within the Environmental Restoration and Waste Management Program of the US Department of Energy, the remediation of single-shell radioactive waste storage tanks is one of the areas that challenge state-of-the-art equipment and methods. Concepts that utilize long-reach manipulators are being seriously considered for this task. Due to high payload capacity and high length-to-cross-section ratio requirements, these long-reach manipulator systems are expected to exhibit significant structural flexibility. To avoid structural vibrations during operation, various types of shaping filter methods have been investigated. A robust notch filtering method and an impulse shaping method were used as simulation benchmarks. In addition to that, two very different approaches have been developed and compared. One new approach, referred to as a ``feedforward simulation filter,`` uses imbedded simulation with complete knowledge of the system dynamics. The other approach, ``fuzzy shaping method,`` employs a fuzzy logic method to modify the joint trajectory from the desired end-position trajectory without precise knowledge of the system dynamics.

  16. The computational structural mechanics testbed architecture. Volume 5: The Input-Output Manager DMGASP

    NASA Technical Reports Server (NTRS)

    Felippa, Carlos A.

    1989-01-01

    This is the fifth of a set of five volumes which describe the software architecture for the Computational Structural Mechanics Testbed. Derived from NICE, an integrated software system developed at Lockheed Palo Alto Research Laboratory, the architecture is composed of the command language (CLAMP), the command language interpreter (CLIP), and the data manager (GAL). Volumes 1, 2, and 3 (NASA CR's 178384, 178385, and 178386, respectively) describe CLAMP and CLIP and the CLIP-processor interface. Volumes 4 and 5 (NASA CR's 178387 and 178388, respectively) describe GAL and its low-level I/O. CLAMP, an acronym for Command Language for Applied Mechanics Processors, is designed to control the flow of execution of processors written for NICE. Volume 5 describes the low-level data management component of the NICE software. It is intended only for advanced programmers involved in maintenance of the software.

  17. Who gets credit for input? Demographic and structural status cues in voice recognition.

    PubMed

    Howell, Taeya M; Harrison, David A; Burris, Ethan R; Detert, James R

    2015-11-01

    The authors investigate the employee features that, alongside overall voice expression, affect supervisors' voice recognition. Drawing primarily from status characteristics and network position theories, the authors propose and find in a study of 693 employees from 89 different credit union units that supervisors are more likely to credit those reporting the same amount of voice if the employees have higher ascribed or assigned (by the organization) status--cued by demographic variables such as majority ethnicity and full-time work hours. Further, supervisors are more likely to recognize voice from employees who have higher achieved status--cued by their centrality in informal social structures. The authors also find that even when certain groups of lower status employees speak up more, they cannot compensate for the negative effect of their demographic membership on voice recognition by their boss. The authors underscore how recognition of employee voice by supervisors matters for employees. It carries (mediates) the effects of voice expression and status onto performance evaluations 1 year later, which means that demographic differences in the assignment of credit for voice can serve as an implicit pathway for discrimination.

  18. Glyphosate input modifies microbial community structure in clear and turbid freshwater systems.

    PubMed

    Pizarro, H; Vera, M S; Vinocur, A; Pérez, G; Ferraro, M; Menéndez Helman, R J; Dos Santos Afonso, M

    2016-03-01

    Since it was commercially introduced in 1974, glyphosate has been one of the most commonly used herbicides in agriculture worldwide, and there is growing concern about its adverse effects on the environment. Assuming that glyphosate may increase the organic turbidity of water bodies, we evaluated the effect of a single application of 2.4 ± 0.1 mg l(-1) of glyphosate (technical grade) on freshwater bacterioplankton and phytoplankton (pico, micro, and nanophytoplankton) and on the physical and chemical properties of the water. We used outdoor experimental mesocosms under clear and oligotrophic (phytoplanktonic chlorophyll a = 2.04 μg l(-1); turbidity = 2.0 NTU) and organic turbid and eutrophic (phytoplanktonic chlorophyll a = 50.3 μg l(-1); turbidity = 16.0 NTU) scenarios. Samplings were conducted at the beginning of the experiment and at 1, 8, 19, and 33 days after glyphosate addition. For both typologies, the herbicide affected the abiotic water properties (with a marked increase in total phosphorus), but it did not affect the structure of micro and nanophytoplankton. In clear waters, glyphosate treatment induced a trend toward higher bacteria and picoeukaryotes abundances, while there was a 2 to 2.5-fold increase in picocyanobacteria number. In turbid waters, without picoeukaryotes at the beginning of the experiment, glyphosate decreased bacteria abundance but increased the number of picocyanobacteria, suggesting a direct favorable effect. Moreover, our results show that the impact of the herbicide was observed in microorganisms from both oligo and eutrophic conditions, indicating that the impact would be independent of the trophic status of the water body.

  19. A novel cyanide-selective colorimetric and fluorescent chemosensor: first molecular security keypad lock based on phosphotungstic acid and CN- inputs.

    PubMed

    Tavallali, Hossein; Deilamy-Rad, Gohar; Parhami, Abolfath; Hasanli, Nahid

    2014-02-15

    Rhodamine B (RhB) an available dye has been developed as novel and efficient colorimetric and fluorometric chemosensor for cyanide ions in an absolutely aqueous media. The UV-vis absorption and fluorescent emission titrations experiments have been employed to study the sensing process. RhB could act as an efficient "ON-OFF" fluorescent response for phosphotungstic acid (H3PW12O40 or PTA) based on an ion associate process. Also (RhB(+))3 · PTA(3-) could operate as an "OFF-ON" fluorescent sensor for cyanide anions based on a ligand substitution process. It has been identified as highly sensitive probe for CN(-) which responds at 0.3 and 0.04 μmol L(-1) concentration levels by absorption and fluorescent method respectively. Depending upon the sequence of addition of PTA and CN(-) ions into the solution, RhB could be as a molecular security keypad lock with PTA and CN(-) inputs. The ionic inputs to new fluorophore have been mimicked as a superimposed electronic molecular keypad lock. The results were compared successfully (>96%) with the data of a spectrophotometry approved method (EPA 9014-1) for cyanide ions.

  20. Structures of High Density Molecular Fluids

    SciTech Connect

    Baer, B; Cynn, H; Iota, V; Yoo, C-S

    2002-02-01

    The goal of this proposal is to develop an in-situ probe for high density molecular fluids. We will, therefore, use Coherent Anti-Stokes Raman Spectroscopy (CARS) applied to laser heated samples in a diamond-anvil cell (DAC) to investigate molecular fluids at simultaneous conditions of high temperatures (T > 2000K) and high pressures (P > 10 GPa.) Temperatures sufficient to populate vibrational levels above the ground state will allow the vibrational potential to be mapped by CARS. A system capable of heating and probing these samples will be constructed. Furthermore, the techniques that enable a sample to be sufficiently heated and probed while held at static high pressure in a diamond-anvil-cell will be developed. This will be an in-situ investigation of simple molecules under conditions relevant to the study of detonation chemistry and the Jovain planet interiors using state of the art non-linear spectroscopy, diamond-anvil-cells, and laser heating technology.

  1. Colour Chemistry, Part I, Principles, Colour, and Molecular Structure

    ERIC Educational Resources Information Center

    Hallas, G.

    1975-01-01

    Discusses various topics in color chemistry, including the electromagnetic spectrum, the absorption and reflection of light, additive and subtractive color mixing, and the molecular structure of simple colored substances. (MLH)

  2. Evidence of sewage input to inner shelf sediments in the NE coast of Brazil obtained by molecular markers distribution.

    PubMed

    Carreira, Renato S; Albergaria-Barbosa, Ana Cecília R; Arguelho, Maria L P M; Garcia, Carlos A B

    2015-01-15

    Coprostanol (5β-cholestan-3β-ol) and other fecal steroids were used as markers to trace the input of sewage to the shelf along the coast of Sergipe and Alagoas States, in NE Brazil. Surface sediment samples in shallow regions (<50 m depth) on the shelf were collected adjacent to four fluvial systems, whose drainage basins exhibit distinct levels of human influence. Highest coprostanol concentrations were observed in the area under influence of the Sergipe River (58.6 ± 74.6 ng g(-)(1); maximum of 184.1 ng g(-)(1)), whereas in the Vaza-Barris (18.9 ± 23.6 ng g(-)(1)) and the Piaui/Real (12.3 ± 6.7 ng g(-)(1)) rivers the levels of coprostanol were near the method's limit of detection. Nearby the São Francisco River, the largest in the NE Brazil, coprostanol was virtually absent. The findings of the present study, supported by coprostanol-based diagnostic ratios, revealed that, when sanitation is lacking in the coastal region, even a small-sized river like the Sergipe River can effectively contribute to the export of sewage-derived organic matter to the inner continental shelf in the studied region.

  3. Joint input-response estimation for structural systems based on reduced-order models and vibration data from a limited number of sensors

    NASA Astrophysics Data System (ADS)

    Lourens, E.; Papadimitriou, C.; Gillijns, S.; Reynders, E.; De Roeck, G.; Lombaert, G.

    2012-05-01

    An algorithm is presented for jointly estimating the input and state of a structure from a limited number of acceleration measurements. The algorithm extends an existing joint input-state estimation filter, derived using linear minimum-variance unbiased estimation, to applications in structural dynamics. The filter has the structure of a Kalman filter, except that the true value of the input is replaced by an optimal estimate. No prior information on the dynamic evolution of the input forces is assumed and no regularization is required, permitting online application. The effectiveness and accuracy of the proposed algorithm are demonstrated using data from a numerical cantilever beam example as well as a laboratory experiment on an instrumented steel beam and an in situ experiment on a footbridge.

  4. Instructional Approach to Molecular Electronic Structure Theory

    ERIC Educational Resources Information Center

    Dykstra, Clifford E.; Schaefer, Henry F.

    1977-01-01

    Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

  5. Hygrothermal aging effects on buried molecular structures at epoxy interfaces.

    PubMed

    Myers, John N; Zhang, Chi; Lee, Kang-Wook; Williamson, Jaimal; Chen, Zhan

    2014-01-14

    Interfacial properties such as adhesion are determined by interfacial molecular structures. Adhesive interfaces in microelectronic packages that include organic polymers such as epoxy are susceptible to delamination during accelerated stress testing. Infrared-visible sum frequency generation vibrational spectroscopy (SFG) and attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) were used to study molecular structures at buried epoxy interfaces during hygrothermal aging to relate molecular structural changes at buried interfaces to decreases in macroscopic adhesion strength. SFG peaks associated with strongly hydrogen bonded water were detected at hydrophilic epoxy interfaces. Ordered interfacial water was also correlated to large decreases in interfacial adhesion strength that occurred as a result of hygrothermal aging, which suggests that water diffused to the interface and replaced original hydrogen bond networks. No water peaks were observed at hydrophobic epoxy interfaces, which was correlated with a much smaller decrease in adhesion strength from the same aging process. ATR-FTIR water signals observed in the epoxy bulk were mainly contributed by relatively weakly hydrogen bonded water molecules, which suggests that the bulk and interfacial water structure was different. Changes in interfacial methyl structures were observed regardless of the interfacial hydrophobicity which could be due to water acting as a plasticizer that restructured both the bulk and interfacial molecular structure. This research demonstrates that SFG studies of molecular structural changes at buried epoxy interfaces during hygrothermal aging can contribute to the understanding of moisture-induced failure mechanisms in electronic packages that contain organic adhesives.

  6. Intensity Inhomogeneity Correction of Structural MR Images: A Data-Driven Approach to Define Input Algorithm Parameters

    PubMed Central

    Ganzetti, Marco; Wenderoth, Nicole; Mantini, Dante

    2016-01-01

    Intensity non-uniformity (INU) in magnetic resonance (MR) imaging is a major issue when conducting analyses of brain structural properties. An inaccurate INU correction may result in qualitative and quantitative misinterpretations. Several INU correction methods exist, whose performance largely depend on the specific parameter settings that need to be chosen by the user. Here we addressed the question of how to select the best input parameters for a specific INU correction algorithm. Our investigation was based on the INU correction algorithm implemented in SPM, but this can be in principle extended to any other algorithm requiring the selection of input parameters. We conducted a comprehensive comparison of indirect metrics for the assessment of INU correction performance, namely the coefficient of variation of white matter (CVWM), the coefficient of variation of gray matter (CVGM), and the coefficient of joint variation between white matter and gray matter (CJV). Using simulated MR data, we observed the CJV to be more accurate than CVWM and CVGM, provided that the noise level in the INU-corrected image was controlled by means of spatial smoothing. Based on the CJV, we developed a data-driven approach for selecting INU correction parameters, which could effectively work on actual MR images. To this end, we implemented an enhanced procedure for the definition of white and gray matter masks, based on which the CJV was calculated. Our approach was validated using actual T1-weighted images collected with 1.5 T, 3 T, and 7 T MR scanners. We found that our procedure can reliably assist the selection of valid INU correction algorithm parameters, thereby contributing to an enhanced inhomogeneity correction in MR images. PMID:27014050

  7. Dynamics of phytoplankton community structure in the South China Sea in response to the East Asian aerosol input

    NASA Astrophysics Data System (ADS)

    Guo, C.; Yu, J.; Ho, T.-Y.; Wang, L.; Song, S.; Kong, L.; Liu, H.

    2012-04-01

    Recent studies have demonstrated atmospheric deposition as an important source of bioreactive compounds to the ocean. The South China Sea (SCS), where aerosol loading is among the highest in the world, however, is poorly studied, particularly on the in situ response of phytoplankton community structures to atmospheric deposition. By conducting a series of microcosm bioassays at different hydrographical locations and simulating different aerosol event scales, we observed both positive and negative responses to the input of East Asian (EA) aerosol with high nitrogen (N) and trace metal contents, in terms of biomass, composition and physiological characteristics of phytoplankton communities. High levels of aerosol loading relieved phytoplankton nitrogen and trace metal limitations in SCS, and thus increased total phytoplankton biomass, enhanced their physiological indicators (e.g. photosynthetic efficiency) and shifted phytoplankton assemblages from being dominated by picoplankton to microphytoplanton, especially diatoms. However, under low levels of aerosol loading, the composition shift and biomass accumulation were not apparent, suggesting that the stimulation effects might be counterbalanced by enhanced grazing mortality indicated by increased abundance of protist grazers. Trace metal toxicity of the aerosols might also be the reason for the reduction of picocyanobacteria when amended with high EA aerosols. The magnitude and duration of the deposition event, as well as the hydrographical and trophic conditions of receiving waters are also important factors when predicting the influence of an aerosol deposition event. Our results demonstrated different responses of phytoplankton and microbial food web dynamics to different scales of atmospheric input events in SCS and highlighted the need for achieving an accurate comprehension of atmospheric nutrient on the biogeochemical cycles of the oceans.

  8. Design and microwave test of an ultrawideband input/output structure for sheet beam travelling wave tubes

    NASA Astrophysics Data System (ADS)

    Shu, Guoxiang; Wang, Jianxun; Liu, Guo; Yang, Liya; Luo, Yong; Wang, Shafei

    2015-06-01

    Broadband operation is of great importance for the applications of travelling wave tubes such as high-data communication and wideband radar. An input/output (I/O) structure operating with broadband property plays a significant role to achieve these applications. In this paper, a Y-type branch waveguide (YTBW) coupler and its improvements are proposed and utilized to construct an extremely wideband I/O structure to ensure the broadband operation for sheet beam travelling wave tubes (SB-TWTs). Cascaded reflection resonators are utilized to improve the isolation characteristic and transmission efficiency. Furthermore, to minimize the reflectivity of the port connected with the RF circuit, wave-absorbing material (WAM) is loaded in the resonator. Simulation results for the YTBW loaded with WAM predict an excellent performance with a 50.2% relative bandwidth for port reflectivity under -15 dB, transmission up to -1.5 dB, and meanwhile isolation under -20 dB. In addition, the coupler has a relatively compact configuration and the beam tunnel can be widened, which is beneficial for the propagation of the electrons. A Q-band YTBW loaded with two reflection resonators is fabricated and microwave tested. Vector network analyzer (VNA) measured results have an excellent agreement with our simulation, which verify our theoretical analysis and simulation calculation.

  9. A Direct Design from Input/Output Data of Fault-Tolerant Control System Based on GIMC Structure

    NASA Astrophysics Data System (ADS)

    Sakuishi, Tsubasa; Yubai, Kazuhiro; Hirai, Junji

    This paper deals with a design method of fault-tolerant control system based on Generalized Internal Model Control (GIMC) structure consisting of a standard outer loop feedback controller and an extra inner loop controller. The distinguished feature of GIMC structure is that the controller design for performance and robustness may be done separately. The outer loop controller is designed for nominal performance using some controller synthesis to meet (nominal) control specification, while the inner loop controller is designed to make a trade-off between robustness and performance. This feature is suitable for fault-tolerant control. The outer loop controller is designed for fault-free case, and the inner loop controller for faulty case. In the conventional methods, the inner loop controller is designed to maximize the robust stability margin without information on fault. Therefore, the performance in the faulty case tends to become conservative. In this paper, the inner loop controller is directly designed from experimental data collected from the faulty system. Since the collected data contains information on the fault, conservativeness in the conventional methods is decreased. The inner loop controller is designed by Virtual Reference Feedback Tuning (VRFT). VRFT is a direct design method from input-output data without identifying any models. Since complexity of the controller can be specified by the designer, no complexity reduction has to be required, which becomes advantageous upon implementation. The effectiveness of the proposed design method is confirmed by an experiment.

  10. Design and microwave test of an ultrawideband input/output structure for sheet beam travelling wave tubes

    SciTech Connect

    Shu, Guoxiang; Wang, Jianxun; Liu, Guo; Yang, Liya; Luo, Yong; Wang, Shafei

    2015-06-15

    Broadband operation is of great importance for the applications of travelling wave tubes such as high-data communication and wideband radar. An input/output (I/O) structure operating with broadband property plays a significant role to achieve these applications. In this paper, a Y-type branch waveguide (YTBW) coupler and its improvements are proposed and utilized to construct an extremely wideband I/O structure to ensure the broadband operation for sheet beam travelling wave tubes (SB-TWTs). Cascaded reflection resonators are utilized to improve the isolation characteristic and transmission efficiency. Furthermore, to minimize the reflectivity of the port connected with the RF circuit, wave-absorbing material (WAM) is loaded in the resonator. Simulation results for the YTBW loaded with WAM predict an excellent performance with a 50.2% relative bandwidth for port reflectivity under −15 dB, transmission up to −1.5 dB, and meanwhile isolation under −20 dB. In addition, the coupler has a relatively compact configuration and the beam tunnel can be widened, which is beneficial for the propagation of the electrons. A Q-band YTBW loaded with two reflection resonators is fabricated and microwave tested. Vector network analyzer (VNA) measured results have an excellent agreement with our simulation, which verify our theoretical analysis and simulation calculation.

  11. Design and microwave test of an ultrawideband input/output structure for sheet beam travelling wave tubes.

    PubMed

    Shu, Guoxiang; Wang, Jianxun; Liu, Guo; Yang, Liya; Luo, Yong; Wang, Shafei

    2015-06-01

    Broadband operation is of great importance for the applications of travelling wave tubes such as high-data communication and wideband radar. An input/output (I/O) structure operating with broadband property plays a significant role to achieve these applications. In this paper, a Y-type branch waveguide (YTBW) coupler and its improvements are proposed and utilized to construct an extremely wideband I/O structure to ensure the broadband operation for sheet beam travelling wave tubes (SB-TWTs). Cascaded reflection resonators are utilized to improve the isolation characteristic and transmission efficiency. Furthermore, to minimize the reflectivity of the port connected with the RF circuit, wave-absorbing material (WAM) is loaded in the resonator. Simulation results for the YTBW loaded with WAM predict an excellent performance with a 50.2% relative bandwidth for port reflectivity under -15 dB, transmission up to -1.5 dB, and meanwhile isolation under -20 dB. In addition, the coupler has a relatively compact configuration and the beam tunnel can be widened, which is beneficial for the propagation of the electrons. A Q-band YTBW loaded with two reflection resonators is fabricated and microwave tested. Vector network analyzer (VNA) measured results have an excellent agreement with our simulation, which verify our theoretical analysis and simulation calculation.

  12. Marine Biotoxins: Laboratory Culture and Molecular Structure

    DTIC Science & Technology

    1991-01-21

    toxins that are associated with the human fish intoxication known as ciguatera , ciguatoxin and maitotoxin. of unknown structure at the outset of this...87-C-7210 Appendix A. Bibliography 1. Ciguatera - what we know and what we would like to know. P.J. Scheuer in "Mycotoxins and Phycotoxins 󈨜". (S...Mycotoxins, and Phycotoxins, Tokyo. Japan, August 1988. 2. Third International Conference on Ciguatera , Puerto Rico. April 1990. C. Personnel Receiving Pay

  13. Marine Toxins Origin, Structure, and Molecular Pharmacology

    DTIC Science & Technology

    1990-01-01

    thin-layer chromatography (TLC) were instrumental in the initial isolation and purification processes. Mass spectrometry (MS), infrared spectroscopy ...Frederick, MD 21701-5011 Methods of detection, metabolism, and pathophysiology of the brevetoxins, PbTx-2 and PbTx-3, are summarized. Infrared spectros...1R), circular dichroism (CD), nuclear magnetic resonance spectroscopy (NMR), and X-ray crystal- lography all played important roles in structure

  14. Molecular Eigensolution Symmetry Analysis and Fine Structure

    PubMed Central

    Harter, William G.; Mitchell, Justin C.

    2013-01-01

    Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES). Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES) used in Born–Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v), then applied to families of Oh clusters in SF6 spectra and to extreme clusters. PMID:23344041

  15. Giant Molecular Cloud Structure and Evolution

    NASA Technical Reports Server (NTRS)

    Hollenbach, David (Technical Monitor); Bodenheimer, P. H.

    2003-01-01

    Bodenheimer and Burkert extended earlier calculations of cloud core models to study collapse and fragmentation. The initial condition for an SPH collapse calculation is the density distribution of a Bonnor-Ebert sphere, with near balance between turbulent plus thermal energy and gravitational energy. The main parameter is the turbulent Mach number. For each Mach number several runs are made, each with a different random realization of the initial turbulent velocity field. The turbulence decays on a dynamical time scale, leading the cloud into collapse. The collapse proceeds isothermally until the density has increased to about 10(exp 13) g cm(exp -3). Then heating is included in the dense regions. The nature of the fragmentation is investigated. About 15 different runs have been performed with Mach numbers ranging from 0.3 to 3.5 (the typical value observed in molecular cloud cores is 0.7). The results show a definite trend of increasing multiplicity with increasing Mach number (M), with the number of fragments approximately proportional to (1 + M). In general, this result agrees with that of Fisher, Klein, and McKee who published three cases with an AMR grid code. However our results show that there is a large spread about this curve. For example, for M=0.3 one case resulted in no fragmentation while a second produced three fragments. Thus it is not only the value of M but also the details of the superposition of the various velocity modes that play a critical role in the formation of binaries. Also, the simulations produce a wide range of separations (10-1000 AU) for the multiple systems, in rough agreement with observations. These results are discussed in two conference proceedings.

  16. Ionization probes of molecular structure and chemistry

    SciTech Connect

    Johnson, P.M.

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  17. Syntheses and molecular structures of new cali.

    PubMed

    Attner, J; Radius, U

    2001-01-01

    An unusual disproportionation reaction of the molybdenum(IV) and tungsten(IV) chlorides [MCl4L2] (M=Mo, L=Et2S, Et2O; M=W; L= Et2S) in the presence of p-tBu-calix[4]arene (Cax(OH)4) and triethylamine leads to d0 complexes [(CaxO4)[CaxO2(OH)2]M] (1) and d3 compounds (HNEt3)2[(CaxO4)2M2] (2). Complexes la (M = Mo), 1b (M = W), and the HCl adduct of 2a (M = Mo) have been structurally characterized. Compound 1a represents one of the few examples of a well-characterized molybdenum(VI) hexa-alkoxide complex of the type [Mo(OR)6]. Isolation and structural characterization of the side product [(CaxO4W)[kappa2(O)-kappa1(O)-CaxO3(OH)](CaxO4WCl)] (3) suggests the intermediacy of chloro-containing calix[4]arene complexes in these reaction mixtures. The reaction of 1a with HCI provides [CaxO4MoCl2] (4a), the first well-defined example of a mixed molybdenum(VI) alkoxide halide compound of the general formula [MoClx(OR)6-x].

  18. Microwave spectrum and molecular structure of PNO

    NASA Astrophysics Data System (ADS)

    Okabayashi, Toshiaki; Yamazaki, Emi; Tanimoto, Mitsutoshi

    1999-08-01

    The microwave spectra of P14N16O and its isotopomers P15N16O and P14N18O were observed in a dc glow discharge plasma of a mixture of nitric oxide and hydrogen gases over solid red phosphorus placed on the stainless steel electrode. Rotational transitions of the parent P14N16O species were measured in the ground state as well as in the vibrationally excited ν1 (PN str.), ν2 (bend), and 2ν2 states. The l=0 substate of the 2ν2 state interacts with the ν1 state through a Fermi resonance. The rotational constants determined for the ground states of the three isotopomers yield the substitution structure, rs(PN)=151.6516(87) pm and rs(NO)=119.5025(80) pm.

  19. Connecting the density structure of molecular clouds with star formation

    NASA Astrophysics Data System (ADS)

    Kainulainen, Jouni

    In the current paradigm of turbulence-regulated interstellar medium (ISM), star formation rates of entire galaxies are intricately linked to the density structure of the individual molecular clouds. This density structure is essentially encapsulated in the probability distribution function of volume densities (ρ-PDF), which directly affects the star formation rates predicted by analytic models. Contrasting its fundamental role, the ρ-PDF function has remained virtually unconstrained by observations. I describe in this contribution the recent progress in attaining observational constraints for the column density PDFs (N-PDFs) of molecular clouds that function as a proxy of the ρ-PDFs. Specifically, observational works point towards a universal correlation between the shape of the N-PDFs and star formation activity in molecular clouds. The correlation is in place from the scales of a parsec up to the scales of entire galaxies, making it a fundamental, global link between the ISM structure and star formation.

  20. Molecular structure of vapor-deposited amorphous selenium

    NASA Astrophysics Data System (ADS)

    Goldan, A. H.; Li, C.; Pennycook, S. J.; Schneider, J.; Blom, A.; Zhao, W.

    2016-10-01

    The structure of amorphous selenium is clouded with much uncertainty and contradictory results regarding the dominance of polymeric chains versus monomer rings. The analysis of the diffraction radial distribution functions are inconclusive because of the similarities between the crystalline allotropes of selenium in terms of the coordination number, bond length, bond angle, and dihedral angle. Here, we took a much different approach and probed the molecular symmetry of the thermodynamically unstable amorphous state via analysis of structural phase transformations. We verified the structure of the converted metastable and stable crystalline structures using scanning transmission electron microscopy. In addition, given that no experimental technique can tell us the exact three-dimensional atomic arrangements in glassy semiconductors, we performed molecular-dynamic simulations using a well-established empirical three-body interatomic potential. We developed a true vapor-deposited process for the deposition of selenium molecules onto a substrate using empirical molecular vapor compositions and densities. We prepared both vapor-deposited and melt-quenched samples and showed that the simulated radial distribution functions match very well to experiment. The combination of our experimental and molecular-dynamic analyses shows that the structures of vapor- and melt-quenched glassy/amorphous selenium are quite different, based primarily on rings and chains, respectively, reflecting the predominant structure of the parent phase in its thermodynamic equilibrium.

  1. Reverse engineering chemical structures from molecular descriptors : how many solutions?

    SciTech Connect

    Brown, William Michael; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-06-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

  2. Molecular Evolution, Structure, and Function of Peroxidasins

    PubMed Central

    Soudi, Monika; Zamocky, Marcel; Jakopitsch, Christa; Furtmüller, Paul G; Obinger, Christian

    2012-01-01

    Peroxidasins represent the subfamily 2 of the peroxidase-cyclooxygenase superfamily and are closely related to chordata peroxidases (subfamily 1) and peroxinectins (subfamily 3). They are multidomain proteins containing a heme peroxidase domain with high homology to human lactoperoxidase that mediates one- and two-electron oxidation reactions. Additional domains of the secreted and glycosylated metalloproteins are type C-like immunoglobulin domains, typical leucine-rich repeats, as well as a von Willebrand factor C module. These are typical motifs of extracellular proteins that mediate protein–protein interactions. We have reconstructed the phylogeny of this new family of oxidoreductases and show the presence of four invertebrate clades as well as one vertebrate clade that includes also two different human representatives. The variability of domain assembly in the various clades was analyzed, as was the occurrence of relevant catalytic residues in the peroxidase domain based on the knowledge of catalysis of the mammalian homologues. Finally, the few reports on expression, localization, enzymatic activity, and physiological roles in the model organisms Drosophila melanogaster, Caenorhabditis elegans, and Homo sapiens are critically reviewed. Roles attributed to peroxidasins include antimicrobial defense, extracellular matrix formation, and consolidation at various developmental stages. Many research questions need to be solved in future, including detailed biochemical/physical studies and elucidation of the three dimensional structure of a model peroxidasin as well as the relation and interplay of the domains and the in vivo functions in various organisms including man. PMID:22976969

  3. Importance of Molecular Structure on the Thermophoresis of Binary Mixtures.

    PubMed

    Kumar, Pardeep; Goswami, Debabrata

    2014-12-26

    Using thermal lens spectroscopy, we study the role of molecular structural isomers of butanol on the thermophoresis (or Soret effect) of binary mixtures of methanol in butanol. In this study, we show that the thermal lens signal due to the Soret effect changes its sign for all the different concentrations of binary mixtures of butanol with methanol except for the one containing tertiary-butanol. The magnitude and sign of the Soret coefficients strongly depend on the molecular structure of the isomers of butanol in the binary mixture with methanol. This isomerization dependence is in stark contrast to the expected mass dependence of the Soret effect.

  4. Sampling of Stochastic Input Parameters for Rockfall Calculations and for Structural Response Calculations Under Vibratory Ground Motion

    SciTech Connect

    M. Gross

    2004-09-01

    The purpose of this scientific analysis is to define the sampled values of stochastic (random) input parameters for (1) rockfall calculations in the lithophysal and nonlithophysal zones under vibratory ground motions, and (2) structural response calculations for the drip shield and waste package under vibratory ground motions. This analysis supplies: (1) Sampled values of ground motion time history and synthetic fracture pattern for analysis of rockfall in emplacement drifts in nonlithophysal rock (Section 6.3 of ''Drift Degradation Analysis'', BSC 2004 [DIRS 166107]); (2) Sampled values of ground motion time history and rock mechanical properties category for analysis of rockfall in emplacement drifts in lithophysal rock (Section 6.4 of ''Drift Degradation Analysis'', BSC 2004 [DIRS 166107]); (3) Sampled values of ground motion time history and metal to metal and metal to rock friction coefficient for analysis of waste package and drip shield damage to vibratory motion in ''Structural Calculations of Waste Package Exposed to Vibratory Ground Motion'' (BSC 2004 [DIRS 167083]) and in ''Structural Calculations of Drip Shield Exposed to Vibratory Ground Motion'' (BSC 2003 [DIRS 163425]). The sampled values are indices representing the number of ground motion time histories, number of fracture patterns and rock mass properties categories. These indices are translated into actual values within the respective analysis and model reports or calculations. This report identifies the uncertain parameters and documents the sampled values for these parameters. The sampled values are determined by GoldSim V6.04.007 [DIRS 151202] calculations using appropriate distribution types and parameter ranges. No software development or model development was required for these calculations. The calculation of the sampled values allows parameter uncertainty to be incorporated into the rockfall and structural response calculations that support development of the seismic scenario for the

  5. From non-random molecular structure to life and mind

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1989-01-01

    The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.

  6. ALMA Reveals Internal Structure of Molecular Clouds in the LMC

    NASA Astrophysics Data System (ADS)

    Sawada, T.; Hasegawa, T.; Koda, J.

    2015-12-01

    We carried out high-resolution (0.7 pc) CO J=1-0 mosaic observations of five giant molecular clouds, which cover a wide range of evolutionary stages based on their associations to recent star formation, in the Large Magellanic Cloud with ALMA. The observations revealed a variety of spatial structures of the gas, from faint and diffuse emission to bright and compact structures. The variation of structures, which is similar to that seen in the Milky Way, is quantified by the brightness distribution function (BDF) and brightness distribution index (BDI) established in our prior studies. The structured molecular gas may indicate the readiness for, rather than the outcome of, star formation.

  7. Origin and structure of polar domains in doped molecular crystals

    PubMed Central

    Meirzadeh, E.; Azuri, I.; Qi, Y.; Ehre, D.; Rappe, A. M.; Lahav, M.; Kronik, L.; Lubomirsky, I.

    2016-01-01

    Doping is a primary tool for the modification of the properties of materials. Occlusion of guest molecules in crystals generally reduces their symmetry by the creation of polar domains, which engender polarization and pyroelectricity in the doped crystals. Here we describe a molecular-level determination of the structure of such polar domains, as created by low dopant concentrations (<0.5%). The approach comprises crystal engineering and pyroelectric measurements, together with dispersion-corrected density functional theory and classical molecular dynamics calculations of the doped crystals, using neutron diffraction data of the host at different temperatures. This approach is illustrated using centrosymmetric α-glycine crystals doped with minute amounts of different L-amino acids. The experimentally determined pyroelectric coefficients are explained by the structure and polarization calculations, thus providing strong support for the local and global understanding of how different dopants influence the properties of molecular crystals. PMID:27824050

  8. Molecular structure and elastic properties of thermotropic liquid crystals: integrated molecular dynamics--statistical mechanical theory vs molecular field approach.

    PubMed

    Ilk Capar, M; Nar, A; Ferrarini, A; Frezza, E; Greco, C; Zakharov, A V; Vakulenko, A A

    2013-03-21

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  9. Molecular structure and elastic properties of thermotropic liquid crystals: Integrated molecular dynamics—Statistical mechanical theory vs molecular field approach

    NASA Astrophysics Data System (ADS)

    Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.

    2013-03-01

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  10. Molecular structure of DNA by scanning tunneling microscopy.

    PubMed

    Cricenti, A; Selci, S; Felici, A C; Generosi, R; Gori, E; Djaczenko, W; Chiarotti, G

    1989-09-15

    Uncoated DNA molecules marked with an activated tris(l-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 to 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.

  11. Molecular Structure of DNA by Scanning Tunneling Microscopy

    NASA Astrophysics Data System (ADS)

    Cricenti, A.; Selci, S.; Felici, A. C.; Generosi, R.; Gori, E.; Djaczenko, W.; Chiarotti, G.

    1989-09-01

    Uncoated DNA molecules marked with an activated tris(1-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 and 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.

  12. Connecting molecular structure and exciton diffusion length in rubrene derivatives.

    PubMed

    Mullenbach, Tyler K; McGarry, Kathryn A; Luhman, Wade A; Douglas, Christopher J; Holmes, Russell J

    2013-07-19

    Connecting molecular structure and exciton diffusion length in rubrene derivatives demonstrates how the diffusion length of rubrene can be enhanced through targeted functionalization aiming to enhance self-Förster energy transfer. Functionalization adds steric bulk, forcing the molecules farther apart on average, and leading to increased photoluminescence efficiency. A diffusion length enhancement greater than 50% is realized over unsubstituted rubrene.

  13. Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model

    NASA Astrophysics Data System (ADS)

    Song-Feng, Zhao; Fang, Huang; Guo-Li, Wang; Xiao-Xin, Zhou

    2016-03-01

    We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov-Popov-Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  14. Molecular design for growth of supramolecular membranes with hierarchical structure.

    PubMed

    Zha, R Helen; Velichko, Yuri S; Bitton, Ronit; Stupp, Samuel I

    2016-02-07

    Membranes with hierarchical structure exist in biological systems, and bio-inspired building blocks have been used to grow synthetic analogues in the laboratory through self-assembly. The formation of these synthetic membranes is initiated at the interface of two aqueous solutions, one containing cationic peptide amphiphiles (PA) and the other containing the anionic biopolymer hyaluronic acid (HA). The membrane growth process starts within milliseconds of interface formation and continues over much longer timescales to generate robust membranes with supramolecular PA-HA nanofibers oriented orthogonal to the interface. Computer simulation indicates that formation of these hierarchically structured membranes requires strong interactions between molecular components at early time points in order to generate a diffusion barrier between both solutions. Experimental studies using structurally designed PAs confirm simulation results by showing that only PAs with high ζ potential are able to yield hierarchically structured membranes. Furthermore, the chemical structure of such PAs must incorporate residues that form β-sheets, which facilitates self-assembly of long nanofibers. In contrast, PAs that form low aspect ratio nanostructures interact weakly with HA and yield membranes that exhibit non-fibrous fingering protrusions. Furthermore, experimental results show that increasing HA molecular weight decreases the growth rate of orthogonal nanofibers. This result is supported by simulation results suggesting that the thickness of the interfacial contact layer generated immediately after initiation of self-assembly increases with polymer molecular weight.

  15. Molecular, Functional, and Structural Imaging of Major Depressive Disorder.

    PubMed

    Zhang, Kai; Zhu, Yunqi; Zhu, Yuankai; Wu, Shuang; Liu, Hao; Zhang, Wei; Xu, Caiyun; Zhang, Hong; Hayashi, Takuya; Tian, Mei

    2016-06-01

    Major depressive disorder (MDD) is a significant cause of morbidity and mortality worldwide, correlating with genetic susceptibility and environmental risk factors. Molecular, functional, and structural imaging approaches have been increasingly used to detect neurobiological changes, analyze neurochemical correlates, and parse pathophysiological mechanisms underlying MDD. We reviewed recent neuroimaging publications on MDD in terms of molecular, functional, and structural alterations as detected mainly by magnetic resonance imaging (MRI) and positron emission tomography. Altered structure and function of brain regions involved in the cognitive control of affective state have been demonstrated. An abnormal default mode network, as revealed by resting-state functional MRI, is likely associated with aberrant metabolic and serotonergic function revealed by radionuclide imaging. Further multi-modal investigations are essential to clarify the characteristics of the cortical network and serotonergic system associated with behavioral and genetic variations in MDD.

  16. Insights into molecular structure and digestion rate of oat starch.

    PubMed

    Xu, Jinchuan; Kuang, Qirong; Wang, Kai; Zhou, Sumei; Wang, Shuo; Liu, Xingxun; Wang, Shujun

    2017-04-01

    The in vitro digestibility of oat starch and its relationship with starch molecular structure was investigated. The in vitro digestion results showed that the first-order kinetic constant (k) of oat starches (OS-1 and OS-2) was lower than that of rice starch. The size of amylose chains, amylose content and degree of branching (DB) of amylopectin in oat starch were significantly higher than the corresponding parameters in rice starch. The larger molecular size of oat starch may account for its lower digestion rate. The fine structure of amylopectin showed that oat starch had less chains of DP 6-12 and DP>36, which may explain the small difference in digestion rate between oat and rice starch. The biosynthesis model from oat amylopectin fine structure data suggested a lower starch branching enzyme (SBE) activity and/or a higher starch synthase (SS) activity, which may decrease the DB of oat starch and increase its digestion rate.

  17. Photoelectron Angular Distribution and Molecular Structure in Multiply Charged Anions

    SciTech Connect

    Xing, Xiaopeng; Wang, Xue B.; Wang, Lai S.

    2009-02-12

    Photoelectrons emitted from multiply charged anions (MCAs) carry information of the intramolecular Coulomb repulsion (ICR), which is dependent on molecular structures. Using photoelectron imaging, we observed the effects of ICR on photoelectron angular distributions (PAD) of the three isomers of benzene dicarboxylate dianions C6H4(CO2)22– (o-, m- and p-BDC2–). Photoelectrons were observed to peak along the laser polarization due to the ICR, but the anisotropy was the largest for p-BDC2–, followed by the m- and o-isomer. The observed anisotropy is related to the direction of the ICR or the detailed molecular structures, suggesting that photoelectron imaging may allow structural information to be obtained for complex multiply charged anions.

  18. Molecular and electronic structure of electroactive self-assembled monolayers

    NASA Astrophysics Data System (ADS)

    Méndez De Leo, Lucila P.; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J.

    2013-03-01

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  19. Molecular and electronic structure of electroactive self-assembled monolayers.

    PubMed

    Méndez De Leo, Lucila P; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J

    2013-03-21

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  20. MOLVIE: an interactive visualization environment for molecular structures.

    PubMed

    Sun, Huandong; Li, Ming; Xu, Ying

    2003-05-01

    A Molecular visualization interactive environment (MOLVIE), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of MOLVIE, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html.

  1. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

    PubMed

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

  2. Three-dimensional depth profiling of molecular structures.

    PubMed

    Wucher, A; Cheng, J; Zheng, L; Winograd, N

    2009-04-01

    Molecular time of flight secondary ion mass spectrometry (ToF-SIMS) imaging and cluster ion beam erosion are combined to perform a three-dimensional chemical analysis of molecular films. The resulting dataset allows a number of artifacts inherent in sputter depth profiling to be assessed. These artifacts arise from lateral inhomogeneities of either the erosion rate or the sample itself. Using a test structure based on a trehalose film deposited on Si, we demonstrate that the "local" depth resolution may approach values which are close to the physical limit introduced by the information depth of the (static) ToF-SIMS method itself.

  3. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron

    PubMed Central

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons. PMID:27570482

  4. Structural and functional effects of conventional and low pesticide input crop-protection programs on benthic macroinvertebrate communities in outdoor pond mesocosms.

    PubMed

    Auber, Arnaud; Roucaute, Marc; Togola, Anne; Caquet, Thierry

    2011-11-01

    The impacts of current and alternative wheat crop protection programs were compared in outdoor pond mesocosms in a 10-month long study. Realistic exposure scenarios were built based upon the results of modelling of drift, drainage and runoff of pesticides successively applied under two environmental situations characteristics of drained soils of northern France. Each situation was associated to two crop protection programs ("Conventional" and "Low-input") differing in the nature of pesticides used, number of treatments and application rate. Both programs induced significant direct negative effects on various invertebrate groups. Bifenthrin and cyprodynil were identified as the main responsible for these effects in conventional and low-input program, respectively. Indirect effects were also demonstrated especially following treatments with cyprodynil. Litter breakdown was significantly reduced in all treated mesocosms as the functional consequence of the decrease in the abundance of shredders (asellids, Gammarus pulex) illustrating the link between structural and functional effects of pesticides on macroinvertebrate communities. Recovery was observed for many taxa before the end of the study but not for the most sensitive non mobile taxa such as G. pulex. No influence of the agropedoclimatic situation on the effects was shown, suggesting than the main impacts were associated to inputs from drift. The results confirm that the proposed low-input program was less hazardous than the conventional program but the observed structural and functional impact of the low-input program suggest that further improvement of alternative crop protection programs is still needed.

  5. How Effective Are Affective Activities? Relative Benefits of Two Types of Structured Input Activities as Part of a Computer-Delivered Lesson on the Spanish Subjunctive

    ERIC Educational Resources Information Center

    Henshaw, Florencia

    2012-01-01

    Proponents of Processing Instruction (VanPatten, 2005) claim that learners benefit most when presented with both referential and affective structured input activities. Following a classic pretest-posttest design, the present study investigates the role of these two types of activities on the learning of the Spanish subjunctive. Groups differed…

  6. Biogeochemistry and limnology in Antarctic subglacial weathering: molecular evidence of the linkage between subglacial silica input and primary producers in a perennially ice-covered lake

    NASA Astrophysics Data System (ADS)

    Takano, Yoshinori; Kojima, Hisaya; Takeda, Eriko; Yokoyama, Yusuke; Fukui, Manabu

    2015-12-01

    We report a 6,000 years record of subglacial weathering and biogeochemical processes in two perennially ice-covered glacial lakes at Rundvågshetta, on the Soya Coast of Lützow-Holm Bay, East Antarctica. The two lakes, Lake Maruwan Oike and Lake Maruwan-minami, are located in a channel that drains subglacial water from the base of the East Antarctic ice sheet. Greenish-grayish organic-rich laminations in sediment cores from the lakes indicate continuous primary production affected by the inflow of subglacial meltwater containing relict carbon, nitrogen, sulfur, and other essential nutrients. Biogenic silica, amorphous hydrated silica, and DNA-based molecular signatures of sedimentary facies indicate that diatom assemblages are the dominant primary producers, supported by the input of inorganic silicon (Si) from the subglacial inflow. This study highlights the significance of subglacial water-rock interactions during physical and chemical weathering processes and the importance of such interactions for the supply of bioavailable nutrients.

  7. A fluorescent molecularly-imprinted polymer gate with temperature and pH as inputs for detection of alpha-fetoprotein.

    PubMed

    Karfa, Paramita; Roy, Ekta; Patra, Santanu; Kumar, Deepak; Madhuri, Rashmi; Sharma, Prashant K

    2016-04-15

    In this work, we have reported a new approach on the use of stimuli-responsive molecularly imprinted polymer (MIP) for trace level sensing of alpha-fetoprotein (AFP), which is a well know cancer biomarker. The stimuli-responsive MIP is composed of three components, a thermo-responsive monomer, a pH responsive component (tyrosine derivative) and a highly fluorescent vinyl silane modified carbon dot. The synthesized AFP-imprinted polymer possesses excellent selectivity towards their template molecule and dual-stimuli responsive behavior. Along with this, the imprinted polymer was also explored as 'OR' logic gate with two stimuli (pH and temperature) as inputs. However, the non-imprinted polymers did not have such 'OR' gate property, which confirms the role of template binding. The imprinted polymer was also used for estimation of AFP in the concentration range of 3.96-80.0 ng mL(-1), with limit of detection (LOD) 0.42 ng mL(-1). The role of proposed sensor was successfully exploited for analysis of AFP in real human blood plasma, serum and urine sample.

  8. Solution structures and molecular interactions of selective melanocortin receptor antagonists.

    PubMed

    Lee, Chul-Jin; Yun, Ji-Hye; Lim, Sung-Kil; Lee, Weontae

    2010-12-01

    The solution structures and inter-molecular interaction of the cyclic melanocortin antagonists SHU9119, JKC363, HS014, and HS024 with receptor molecules have been determined by NMR spectroscopy and molecular modeling. While SHU9119 is known as a nonselective antagonist, JKC363, HS014, and HS024 are selective for the melanocortin subtype-4 receptor (MC4R) involved in modulation of food intake. Data from NMR and molecular dynamics suggest that the conformation of the Trp9 sidechain in the three MC4R-selective antagonists is quite different from that of SHU9119. This result strongly supports the concept that the spatial orientation of the hydrophobic aromatic residue is more important for determining selectivity than the presence of a basic, "arginine-like" moiety responsible for biological activity. We propose that the conformation of hydrophobic residues of MCR antagonists is critical for receptor-specific selectivity.

  9. Study of the structuring of pure molecular liquids

    NASA Astrophysics Data System (ADS)

    Letamendia, L.; Duplessix, R.; Nouchi, G.; Vaucamps, C.

    Recent experiments have shown that changes in the slope of specific heat variation as a function of temperature in liquids are not always regular. In this study, the authors consider the possibility that fluid structure can change with temperature, by shifting from one form to another. They study such molecular liquids as benzene, hexafluorobenzene, and quinoleine using Rayleigh-Brillouin and depolarized Rayleigh diffusion, and total intensity diffusion. The authors clearly found anomalies for all collective properties of the medium in the liquids studied, though purely molecular properties were undisturbed. The accidents observed occurred at the same temperatures, whatever the collective or intermolecular property under study. But it took some time (several hours) for them to manifest themselves, which suggests that molecular liquids are characterized by a long thermodynamic equilibrium. Results also show a disturbance in hydrodynamic state at accident temperatures, which are similar to those generated by long spatial correlation processes.

  10. Molecular structures in the charmonium spectrum: the XYZ puzzle

    NASA Astrophysics Data System (ADS)

    Ortega, P. G.; Entem, D. R.; Fernández, F.

    2013-06-01

    We study in the framework of a constituent quark model the possible contributions of molecular structures to the XYZ charmonium-like states. We analyze simultaneously the c\\bar{c} structures and the possible molecular components in the coupled channel formalism. In the 1++ sector two states appear which could be identified with X(3872) and X(3940). The recently confirmed X(3915) state appears as a mixture of c\\bar{c} and D\\bar{D} components as a JPC = 0++ state in agreement with the new measurements. A second broad resonance which may correspond with the so-called Y(3940) state is found with these quantum numbers. In the JPC = 1-- sector we also found significant contributions of the molecular structures which may affect the phenomenology. In particular the study allows us to understand the G(3900) state recently observed in Belle and BaBar. All these resonances together with the prediction of the model of a c\\bar{c} structure for Z(3930) provide a reasonable scenario for the so-called XYZ states with masses near 3.9 GeV.

  11. Improving structure-based function prediction using molecular dynamics

    PubMed Central

    Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.

    2009-01-01

    Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472

  12. Molecular solutes in ionic liquids: a structural perspective.

    PubMed

    Pádua, Agílio A H; Costa Gomes, Margarida F; Canongia Lopes, José N A

    2007-11-01

    Understanding physicochemical properties of ionic liquids is important for their rational use in extractions, reactions, and other applications. Ionic liquids are not simple fluids: their ions are generally asymetric, flexible, with delocalized electrostatic charges, and available in a wide variety. It is difficult to capture their subtle properties with models that are too simplistic. Molecular simulation using atomistic force fields, which describe structures and interactions in detail, is an excellent tool to gain insights into their liquid-state organization, how they solvate different compounds, and what molecular factors determine their properties. The identification of certain ionic liquids as self-organized phases, with aggregated nonpolar and charged domains, provides a new way to interpret the solvation and structure of their mixtures. Many advances are the result of a successful interplay between experiment and modeling, possible in this field where none of the two methodologies had a previous advance.

  13. Molecular modelling of miraculin: Structural analyses and functional hypotheses.

    PubMed

    Paladino, Antonella; Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

    2008-02-29

    Miraculin is a plant protein that displays the peculiar property of modifying taste by swiching sour into a sweet taste. Its monomer is flavourless at all pH as well as at high concentration; the dimer form elicits its taste-modifying activity at acidic pH; a tetrameric form is also reported as active. Two histidine residues, located in exposed regions, are the main responsible of miraculin activity, as demonstrated by mutagenesis studies. Since structural data of miraculin are not available, we have predicted its three-dimensional structure and simulated both its dimer and tetramer forms by comparative modelling and molecular docking techniques. Finally, molecular dynamics simulations at different pH conditions have indicated that at acidic pH the dimer assumes a widely open conformation, in agreement with the hypotheses coming from other studies.

  14. Biogeography of soil organic matter molecular structure across multiple soil size fractions

    NASA Astrophysics Data System (ADS)

    Meier, C. L.; Neff, J.

    2009-12-01

    Recent work suggests that there is a common soil decomposition sequence whereby plant inputs are metabolized into a physiologically constrained set of compounds originating from microbes that may persist in soil over relatively long time-scales. Plant inputs tend to be found in coarse particulate fractions (>180 μm) with relatively fast turnover times, while microbially derived compounds tend to accrue in the finer silt + clay fractions (<53 μm) with relatively long turnover times. To investigate whether a common decomposition sequence exists, we used pyrolysis gas chromatography/mass spectrometry (py-GC/MS) to characterize the molecular structure of soil organic matter (SOM) in three size fractions (590-180 μm, 180-53 μm, and <53 μm), using soils sampled from multiple biomes (alpine tundra, sub-alpine forest, boreal forest, temperate coniferous, temperate deciduous, dry desert/savannah, and tropical forest). We hypothesized that: 1) regardless of biome, fractions >180 μm would be chemically similar, and would be characterized by lignin and other plant-derived compounds; and 2) fractions <53 μm would also be similar across biomes but would be dominated by microbially-derived compounds like polysaccharides. Across all biomes, we found that there was significantly less lignin in <53 μm fractions compared to >180 μm fractions (p<0.0001), providing some support for the idea that plant material is not incorporated into soil C pools with relatively long turnover times. However, a principal components analysis (PCA) showed that the >180 μm coarse particulate fractions also contained compounds associated with microbial origins, indicating that microbial C is not limited to <53 μm size fractions. The PCA also revealed that samples within each of the three size fractions did not cluster together (i.e. they did not share a common molecular structure), but we did note that: 1) cold alpine and sub-alpine sites were unique and chemically similar; and 2) tropical

  15. Nanoparticle Probes for Structural and Functional Photoacoustic Molecular Tomography

    PubMed Central

    Chen, Haobin; Yuan, Zhen; Wu, Changfeng

    2015-01-01

    Nowadays, nanoparticle probes have received extensive attention largely due to its potential biomedical applications in structural, functional, and molecular imaging. In addition, photoacoustic tomography (PAT), a method based on the photoacoustic effect, is widely recognized as a robust modality to evaluate the structure and function of biological tissues with high optical contrast and high acoustic resolution. The combination of PAT with nanoparticle probes holds promises for detecting and imaging diseased tissues or monitoring their treatments with high sensitivity. This review will introduce the recent advances in the emerging field of nanoparticle probes and their preclinical applications in PAT, as well as relevant perspectives on future development. PMID:26609534

  16. FilFinder: Filamentary structure in molecular clouds

    NASA Astrophysics Data System (ADS)

    Koch, Eric W.; Rosolowsky, Erik W.

    2016-08-01

    FilFinder extracts and analyzes filamentary structure in molecular clouds. In particular, it is capable of uniformly extracting structure over a large dynamical range in intensity. It returns the main filament properties: local amplitude and background, width, length, orientation and curvature. FilFinder offers additional tools to, for example, create a filament-only image based on the properties of the radial fits. The resulting mask and skeletons may be saved in FITS format, and property tables may be saved as a CSV, FITS or LaTeX table.

  17. STOCK: Structure mapper and online coarse-graining kit for molecular simulations

    DOE PAGES

    Bevc, Staš; Junghans, Christoph; Praprotnik, Matej

    2015-03-15

    We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be providedmore » by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.« less

  18. STOCK: Structure mapper and online coarse-graining kit for molecular simulations

    SciTech Connect

    Bevc, Staš; Junghans, Christoph; Praprotnik, Matej

    2015-03-15

    We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be provided by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.

  19. Sculpting Molecular Potentials to Design Optimized Materials: The Inverse Design of New Molecular Structures

    DTIC Science & Technology

    2010-05-10

    Miloradovic, A. Persoons, T . Verbiest, M. J . Therien, and K. Clays, "Molecular Symmetry and Solution Phase Structure Interrogated by Hyper-Raleigh...34 Nano Lett., 8, 2814-2818 (2008).  T . V. Duncan, K. Song, S.- T . Hung, I. Miloradovic, A. Persoons, T . Verbiest, M. J . Therien, and K. Clays...Beratan, Weitao Yang, Michael J . Therien, Koen Clays Duke University Office of Research Support Duke University Durham, NC 27705 - REPORT

  20. Molecular structures of amyloid and prion fibrils: consensus versus controversy.

    PubMed

    Tycko, Robert; Wickner, Reed B

    2013-07-16

    Many peptides and proteins self-assemble into amyloid fibrils. Examples include mammalian and fungal prion proteins, polypeptides associated with human amyloid diseases, and proteins that may have biologically functional amyloid states. To understand the propensity for polypeptides to form amyloid fibrils and to facilitate rational design of amyloid inhibitors and imaging agents, it is necessary to elucidate the molecular structures of these fibrils. Although fibril structures were largely mysterious 15 years ago, a considerable body of reliable structural information about amyloid fibril structures now exists, with essential contributions from solid state nuclear magnetic resonance (NMR) measurements. This Account reviews results from our laboratories and discusses several structural issues that have been controversial. In many cases, the amino acid sequences of amyloid fibrils do not uniquely determine their molecular structures. Self-propagating, molecular-level polymorphism complicates the structure determination problem and can lead to apparent disagreements between results from different laboratories, particularly when different laboratories study different polymorphs. For 40-residue β-amyloid (Aβ₁₋₄₀) fibrils associated with Alzheimer's disease, we have developed detailed structural models from solid state NMR and electron microscopy data for two polymorphs. These polymorphs have similar peptide conformations, identical in-register parallel β-sheet organizations, but different overall symmetry. Other polymorphs have also been partially characterized by solid state NMR and appear to have similar structures. In contrast, cryo-electron microscopy studies that use significantly different fibril growth conditions have identified structures that appear (at low resolution) to be different from those examined by solid state NMR. Based on solid state NMR and electron paramagnetic resonance (EPR) measurements, the in-register parallel β-sheet organization

  1. Evaluation of Various Spectral Inputs for Estimation of Forest Biochemical and Structural Properties from Airborne Imaging Spectroscopy Data

    NASA Astrophysics Data System (ADS)

    Homolová, L.; Janoutová, R.; Malenovský, Z.

    2016-06-01

    In this study we evaluated various spectral inputs for retrieval of forest chlorophyll content (Cab) and leaf area index (LAI) from high spectral and spatial resolution airborne imaging spectroscopy data collected for two forest study sites in the Czech Republic (beech forest at Štítná nad Vláří and spruce forest at Bílý Kříž). The retrieval algorithm was based on a machine learning method - support vector regression (SVR). Performance of the four spectral inputs used to train SVR was evaluated: a) all available hyperspectral bands, b) continuum removal (CR) 645 - 710 nm, c) CR 705 - 780 nm, and d) CR 680 - 800 nm. Spectral inputs and corresponding SVR models were first assessed at the level of spectral databases simulated by combined leaf-canopy radiative transfer models PROSPECT and DART. At this stage, SVR models using all spectral inputs provided good performance (RMSE for Cab < 10 μg cm-2 and for LAI < 1.5), with consistently better performance for beech over spruce site. Since application of trained SVRs on airborne hyperspectral images of the spruce site produced unacceptably overestimated values, only the beech site results were analysed. The best performance for the Cab estimation was found for CR bands in range of 645 - 710 nm, whereas CR bands in range of 680 - 800 nm were the most suitable for LAI retrieval. The CR transformation reduced the across-track bidirectional reflectance effect present in airborne images due to large sensor field of view.

  2. Prediction of detonation performance of CHNO and CHNOAl explosives through molecular structure.

    PubMed

    Keshavarz, Mohammad Hossein

    2009-07-30

    A new pathway has been introduced to predict detonation pressure of CHNO and CHNOAl explosives. Although aluminized explosives can have Chapman-Jouguet detonation performance significantly different from those expected from existing thermodynamic computer codes for equilibrium and steady state calculations, new correlation can also be used here. Molecular structures of CHNO and CHNOAl explosives are the only necessary parameters that would be needed in this new scheme. There is no need to use heat of formation or any experimental data. Besides, elemental compositions of CHNO and CHNOAl explosives rather than assumed detonation products are essential input parameters. Predicted detonation pressures for CHNO explosives are compared with experimental data as well as computed results gained by complicated computer code using BKWR and BKWS equations of state so the new method shows the best results. Also, the calculated results for CHNOAl explosives indicate good agreement with the measured data as compared to estimated results of BKWS-EOS using full and partial equilibrium.

  3. Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.

    PubMed

    Romo, Tod D; Leioatts, Nicholas; Grossfield, Alan

    2014-12-15

    LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 140 prebuilt tools, including suites of tools for analyzing simulation convergence, three-dimensional histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only four core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development.

  4. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  5. Structural characterization of polymorphs and molecular complexes of finasteride

    NASA Astrophysics Data System (ADS)

    Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.

    1999-01-01

    The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.

  6. Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.

  7. Biological spectra analysis: Linking biological activity profiles to molecular structure

    PubMed Central

    Fliri, Anton F.; Loging, William T.; Thadeio, Peter F.; Volkmann, Robert A.

    2005-01-01

    Establishing quantitative relationships between molecular structure and broad biological effects has been a longstanding challenge in science. Currently, no method exists for forecasting broad biological activity profiles of medicinal agents even within narrow boundaries of structurally similar molecules. Starting from the premise that biological activity results from the capacity of small organic molecules to modulate the activity of the proteome, we set out to investigate whether descriptor sets could be developed for measuring and quantifying this molecular property. Using a 1,567-compound database, we show that percent inhibition values, determined at single high drug concentration in a battery of in vitro assays representing a cross section of the proteome, provide precise molecular property descriptors that identify the structure of molecules. When broad biological activity of molecules is represented in spectra form, organic molecules can be sorted by quantifying differences between biological spectra. Unlike traditional structure–activity relationship methods, sorting of molecules by using biospectra comparisons does not require knowledge of a molecule's putative drug targets. To illustrate this finding, we selected as starting point the biological activity spectra of clotrimazole and tioconazole because their putative target, lanosterol demethylase (CYP51), was not included in the bioassay array. Spectra similarity obtained through profile similarity measurements and hierarchical clustering provided an unbiased means for establishing quantitative relationships between chemical structures and biological activity spectra. This methodology, which we have termed biological spectra analysis, provides the capability not only of sorting molecules on the basis of biospectra similarity but also of predicting simultaneous interactions of new molecules with multiple proteins. PMID:15625110

  8. Discovering structural alerts for mutagenicity using stable emerging molecular patterns.

    PubMed

    Métivier, Jean-Philippe; Lepailleur, Alban; Buzmakov, Aleksey; Poezevara, Guillaume; Crémilleux, Bruno; Kuznetsov, Sergei O; Le Goff, Jérémie; Napoli, Amedeo; Bureau, Ronan; Cuissart, Bertrand

    2015-05-26

    This study is dedicated to the introduction of a novel method that automatically extracts potential structural alerts from a data set of molecules. These triggering structures can be further used for knowledge discovery and classification purposes. Computation of the structural alerts results from an implementation of a sophisticated workflow that integrates a graph mining tool guided by growth rate and stability. The growth rate is a well-established measurement of contrast between classes. Moreover, the extracted patterns correspond to formal concepts; the most robust patterns, named the stable emerging patterns (SEPs), can then be identified thanks to their stability, a new notion originating from the domain of formal concept analysis. All of these elements are explained in the paper from the point of view of computation. The method was applied to a molecular data set on mutagenicity. The experimental results demonstrate its efficiency: it automatically outputs a manageable number of structural patterns that are strongly related to mutagenicity. Moreover, a part of the resulting structures corresponds to already known structural alerts. Finally, an in-depth chemical analysis relying on these structures demonstrates how the method can initiate promising processes of chemical knowledge discovery.

  9. Heat-induced changes to lipid molecular structure in Vimy flaxseed: Spectral intensity and molecular clustering

    NASA Astrophysics Data System (ADS)

    Yu, Peiqiang; Damiran, Daalkhaijav

    2011-06-01

    Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed ( Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH 3 asymmetric (ca. 2959 cm -1), CH 2 asymmetric (ca. 2928 cm -1), CH 3 symmetric (ca. 2871 cm -1) and CH 2 symmetric (ca. 2954 cm -1) functional groups, lipid carbonyl C dbnd O ester group (ca. 1745 cm -1), lipid unsaturation group (CH attached to C dbnd C) (ca. 3010 cm -1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120 °C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease ( P < 0.05) in the CH 2 asymmetric to CH 3 asymmetric stretching band peak intensity ratios for the flaxseed. There were linear and quadratic effects ( P < 0.05) of the treatment time from 0, 20, 40 and 60 min on the ratios of the CH 2 asymmetric to CH 3 asymmetric stretching vibration intensity. Autoclaving had no significant effect ( P > 0.05) on lipid carbonyl C dbnd O ester group and lipid unsaturation group (CH attached to C dbnd C) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH 3 and CH 2 asymmetric and symmetric region (ca. 2988-2790 cm -1). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study

  10. State of water, molecular structure, and cytotoxicity of silk hydrogels.

    PubMed

    Numata, Keiji; Katashima, Takuya; Sakai, Takamasa

    2011-06-13

    A novel technique was developed to regulate the bulk water content of silk hydrogels by adjusting the concentrations of silk proteins, which is helpful to investigate the effects of the state of water in polymeric hydrogel on its biological functions, such as cytotoxicity. Gelation of the silk hydrogel was induced with ethanol and its gelation behavior was analyzed by rheometry. The silk hydrogels prepared at various silk concentrations were characterized with respect to their water content, molecular and network structures, state of water, mechanical properties, and cytotoxicity to human mesenchymal stem cells. The network structure of silk hydrogel was heterogeneous with β-sheet and fibrillar structures. The influence of the state of water in the silk hydrogel on the cytotoxicity was recognized by means of differential scanning calorimetry and cell proliferation assay, which revealed that the bound water will support cell-adhesion proteins in the cellular matrix to interact with the surface of the silk hydrogels.

  11. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  12. The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

    NASA Astrophysics Data System (ADS)

    Myasnikov, Alexander G.; Afonina, Zhanna A.; Ménétret, Jean-François; Shirokov, Vladimir A.; Spirin, Alexander S.; Klaholz, Bruno P.

    2014-11-01

    During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.

  13. Three decades of structure- and property-based molecular design.

    PubMed

    Müller, Klaus

    2014-01-01

    Roche has pioneered structure- and property-based molecular design to drug discovery. While this is an ongoing development, the past three decades feature key events that have revolutionized the way drug discovery is conducted in Big Pharma industry. It has been a great privilege to have been involved in this transformation process, to have been able to collaborate with, direct, guide, or simply encourage outstanding experts in various disciplines to build and further develop what has become a major pillar of modern small-molecule drug discovery. This article is an account of major events that took place since the early decision of Roche to implement computer-assisted molecular modeling 32 years ago and is devoted to the key players involved. It highlights the internal build-up of structural biology, with protein X-ray structure determination at its core, and the early setup of bioinformatics. It describes the strategic shift to large compound libraries and high-throughput screening with the development of novel compound storage and ultra-high-throughput screening facilities, as well as the strategic return to focused screening of small motif-based compound libraries. These developments were accompanied by the rise of miniaturized parallel compound property analytics which resulted in a major paradigm shift in medicinal chemistry from linear to multi-dimensional lead optimization. The rapid growth of huge collections of property data stimulated the development of various novel data mining concepts with 'matched molecular pair' analysis and novel variants thereof playing crucial roles. As compound properties got more prominent in molecular design, exploration of specific structural motifs for property modulation became a research activity complementary to target-oriented medicinal chemistry. The exploration of oxetane is given as an example. For the sake of brevity, this account cannot detail all further developments that have taken place in each individual area of

  14. Structure of a molecular liquid GeI4

    NASA Astrophysics Data System (ADS)

    Fuchizaki, Kazuhiro; Sakagami, Takahiro; Kohara, Shinji; Mizuno, Akitoshi; Asano, Yuta; Hamaya, Nozomu

    2016-11-01

    A molecular liquid GeI4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge-I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I-I distance definitely shorter than the intramolecular one. The prepeak observed at  ˜1 Å-1 in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak’s height is confirmed by a simulation, in which the molecular size is changed.

  15. Structure-based molecular modeling approaches to GPCR oligomerization.

    PubMed

    Kaczor, Agnieszka A; Selent, Jana; Poso, Antti

    2013-01-01

    Classical structure-based drug design techniques using G-protein-coupled receptors (GPCRs) as targets focus nearly exclusively on binding at the orthosteric site of a single receptor. Dimerization and oligomerization of GPCRs, proposed almost 30 years ago, have, however, crucial relevance for drug design. Targeting these complexes selectively or designing small molecules that affect receptor-receptor interactions might provide new opportunities for novel drug discovery. In order to study the mechanisms and dynamics that rule GPCRs oligomerization, it is essential to understand the dynamic process of receptor-receptor association and to identify regions that are suitable for selective drug binding, which may be determined with experimental methods such as Förster resonance energy transfer (FRET) or Bioluminescence resonance energy transfer (BRET) and computational sequence- and structure-based approaches. The aim of this chapter is to provide a comprehensive description of the structure-based molecular modeling methods for studying GPCR dimerization, that is, protein-protein docking, molecular dynamics, normal mode analysis, and electrostatics studies.

  16. Optical investigation of molecular structure of sophisticated materials for photonics

    NASA Astrophysics Data System (ADS)

    Gnyba, Marcin; Keraenen, Mikko

    2003-10-01

    Permanent development of photonics stimulates a searching for new materials, which have better optical, mechanical and electrical properties. One of the new classes of materials with large application and development potential are hybrid polymers, synthesized in sol-gel technology. Thanks to incorporation of organic components into an in organic network, a combination of advantages of both class of materials became available. Properties of hybrids may be formed in wide range. These materials can be used in photonics to produce planar waveguides, lenses, Bragg gratings and components for integrated optics. Moreover, dielectric layers, coatings and packaging are made from hybrids. Additionally, research to apply them in optical fiber sensors (including bio-sensors) and solid state lasers is underway. However, to obtain a high quality product, a strict control of its molecular structure must be ensured. This is a very difficult task, because of a sophisticated structure of hybrid polymers. To address these problems, optical, non-destructive measurement techniques such as Raman and infrared spectroscopy were used. They are compementary methods, so their simultaneous application, as it was shown in this paper, can significantly increase the amoung of information about molecular structure of materials and process of their synthesis.

  17. Kinetic Effects of Aromatic Molecular Structures on Diffusion Flame Extinction

    SciTech Connect

    Won, Sang Hee; Dooley, S.; Dryer, F. L.; Ju, Yiguang

    2011-01-01

    Kinetic effects of aromatic molecular structures for jet fuel surrogates on the extinction of diffusion flames have been investigated experimentally and numerically in the counterflow configuration for toluene, n-propylbenzene, 1,2,4-trimethylbenzene, and 1,3,5-trimethylbenzene. Quantitative measurement of OH concentration for aromatic fuels was conducted by directly measuring the quenching rate from the emission lifetimes of OH planar laser induced fluorescence (LIF). The kinetic models for toluene and 1,2,4-trimethylbenzene were validated against the measurements of extinction strain rates and LIF measurements. A semi-detailed n-propylbenzene kinetic model was developed and tested. The experimental results showed that the extinction limits are ranked from highest to lowest as n-propylbenzene, toluene, 1,2,4-trimethylbenzene, and 1,3,5-trimethylbenzene. The present models for toluene and n-propylbenzene agree reasonably well with the measurements, whereas the model for 1,2,4-trimethylbenzene under-estimates extinction limits. Kinetic pathways of OH production and consumption were analyzed to investigate the impact of fuel fragmentation on OH formation. It was found that, for fuels with different molecular structures, the fuel decomposition pathways and their propagation into the formation of radical pool play an important role to determine the extinction limits of diffusion flames. Furthermore, OH concentrations were found to be representative of the entire radical pool concentration, the balance between chain branching and propagation/termination reactions and the balance between heat production from the reaction zone and heat losses to the fuel and oxidizer sides. Finally, a proposed “OH index,” was defined to demonstrate a linear correlation between extinction strain rate and OH index and fuel mole fraction, suggesting that the diffusion flame extinctions for the tested aromatic fuels can be determined by the capability of a fuel to establish a radical pool

  18. Bohm's Quantum Potential and the Visualization of Molecular Structure

    NASA Technical Reports Server (NTRS)

    Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.

  19. Structurally Defined Molecular Hypervalent Iodine Catalysts for Intermolecular Enantioselective Reactions

    PubMed Central

    Haubenreisser, Stefan; Wöste, Thorsten H.; Martínez, Claudio; Ishihara, Kazuaki

    2015-01-01

    Abstract Molecular structures of the most prominent chiral non‐racemic hypervalent iodine(III) reagents to date have been elucidated for the first time. The formation of a chirally induced supramolecular scaffold based on a selective hydrogen‐bonding arrangement provides an explanation for the consistently high asymmetric induction with these reagents. As an exploratory example, their scope as chiral catalysts was extended to the enantioselective dioxygenation of alkenes. A series of terminal styrenes are converted into the corresponding vicinal diacetoxylation products under mild conditions and provide the proof of principle for a truly intermolecular asymmetric alkene oxidation under iodine(I/III) catalysis. PMID:26596513

  20. Relationship between antimold activity and molecular structure of cinnamaldehyde analogues.

    PubMed

    Zhang, Yuanyuan; Li, Shujun; Kong, Xianchao

    2013-03-01

    A quantitative structure-activity relationship (QSAR) modeling of the antimold activity of cinnamaldehyde analogues against of Aspergillus niger and Paecilomyces variotii was presented. The molecular descriptors of cinnamaldehyde analogues were calculated by the CODESSA program, and these descriptors were selected by best multi-linear regression method (BMLR). Satisfactory multilinear regression models of Aspergillus niger and Paecilomyces variotii were obtained with R(2)=0.9099 and 0.9444, respectively. The models were also satisfactorily validated using internal validation and leave one out validation. The QSAR models provide the guidance for further synthetic work.

  1. Structural Organization of {pi} Conjugated Highly Luminescent Molecular Material

    SciTech Connect

    Toudic, B.; Limelette, P.; Le Gac, F.; Moreac, A.; Rabiller, P.; Froyer, G.

    2005-11-18

    We report on striking evidence for a room temperature structural phase instability in p-hexaphenyl, inducing a nonplanar conformation of the molecules. Solid state proton NMR and single crystal x-ray diffraction allow the analysis of the organization, the individual dynamics and the involved symmetry breaking. The analysis of Raman spectra above and below room temperature reveals a singular behavior suggesting a modification of the overlap between the electronic wave function induced by the nonplanarity. These results provide a new basis to answer fundamental issues related to molecular and electronic materials and, in particular, luminescent organic devices.

  2. Molecular and electronic structures of cerium and cerium suboxide clusters

    NASA Astrophysics Data System (ADS)

    Kafader, Jared O.; Topolski, Josey E.; Jarrold, Caroline Chick

    2016-10-01

    The anion photoelectron (PE) spectra of Ce2Oy- (y = 1, 2), Ce3Oy- (y = 0-4), Ce4Oy- (y = 0-2), and Ce5Oy- (y = 1, 2) are reported and analyzed with supporting results from density functional theory calculations. The PE spectra all exhibit an intense electronic transition to the neutral ground state, all falling in the range of 0.7 to 1.1 eV electron binding energy, with polarization dependence consistent with detachment from diffuse Ce 6s-based molecular orbitals. There is no monotonic increase in electron affinity with increasing oxidation. A qualitative picture of how electronic structure evolves with an oxidation state emerges from comparison between the spectra and the computational results. The electronic structure of the smallest metallic cluster observed in this study, Ce3, is similar to the bulk structure in terms of atomic orbital occupancy (4f 5d2 6s). Initial cerium cluster oxidation involves largely ionic bond formation via Ce 5d and O 2p orbital overlap (i.e., larger O 2p contribution), with Ce—O—Ce bridge bonding favored over Ce=O terminal bond formation. With subsequent oxidation, the Ce 5d-based molecular orbitals are depleted of electrons, with the highest occupied orbitals described as diffuse Ce 6s based molecular orbitals. In the y ≤ (x + 1) range of oxidation states, each Ce center has a singly occupied non-bonding 4f orbital. The PE spectrum of Ce3O4- is unique in that it exhibits a single nearly vertical transition. The highly symmetric structure predicted computationally is the same structure determined from Ce3O4+ IR predissociation spectra [A. M. Burow et al., Phys. Chem. Chem. Phys. 13, 19393 (2011)], indicating that this structure is stable in -1, 0, and +1 charge states. Spectra of clusters with x ≥ 3 exhibit considerable continuum signal above the ground state transition; the intensity of the continuum signal decreases with increasing oxidation. This feature is likely the result of numerous quasi-bound anion states or two

  3. Influence of Heat Input on the Content of Delta Ferrite in the Structure of 304L Stainless Steel GTA Welded Joints

    NASA Astrophysics Data System (ADS)

    Sejč, Pavol; Kubíček, Rastislav

    2011-12-01

    Welding of austenitic stainless steel has its specific issues, even when the weldability is considered good. The main problems of austenitic stainless steel welding are connected with its metallurgical weldability. The amount of the components presented in the structure of stainless steel welded joint affect its properties, therefore the understanding of the behavior of stainless steel during its welding is important for successful processing and allows the fabricators the possibility to manage the resulting issues. This paper is focused on the influence of heat input on the structural changes in GTA welded joints of austenitic stainless steel designated: ASTM SA TP 304L.

  4. Molecular structure of uranium carbides: isomers of UC3.

    PubMed

    Zalazar, M Fernanda; Rayón, Víctor M; Largo, Antonio

    2013-03-21

    In this article, the most relevant isomers of uranium tricarbide are studied through quantum chemical methods. It is found that the most stable isomer has a fan geometry in which the uranium atom is bonded to a quasilinear C3 unit. Both, a rhombic and a ring CU(C2) structures are found about 104-125 kJ/mol higher in energy. Other possible isomers including linear geometries are located even higher. For each structure, we provide predictions for those molecular properties (vibrational frequencies, IR intensities, dipole moments) that could eventually help in their experimental detection. We also discuss the possible routes for the formation of the different UC3 isomers as well as the bonding situation by means of a topological analysis of the electron density.

  5. Crystal and molecular structures of new enantiopure quinuclidines.

    PubMed

    Kania, Iwona; Stadnicka, Katarzyna; Oleksyn, Barbara J

    2004-03-01

    X-ray crystal structure analysis was performed on single crystals of two diastereomeric enantiopure quinuclidines, (3R,8R)-3-vinyl-8-hydroxymethyl-quinuclidine (quincoridine, QCD) and (3R,8S)-3-vinyl-8-hydroxymethyl-quinuclidine (quincorine, QCI) as their salts with tartaric and p-toluenesulphonate anions, respectively. The molecules of these quinuclidine derivatives are considered here as fragments of the Cinchona alkaloids, quinidine and quinine. A comparison of the conformational features of QCD, QCI, and Cinchona alkaloids in the crystalline state shows that the molecular geometry of the title compounds is similar to that of threo-alkaloids (e.g., R,R isomer of epicinchonine) rather than to quinidine and quinine. The packing of the molecules in both structures is dominated by intermolecular hydrogen bonds.

  6. Noninvasive structural, functional, and molecular imaging in drug development.

    PubMed

    Rudin, Markus

    2009-06-01

    Modern drug research is mechanism-based and the development of disease modifying therapies involves the identification of molecular key players in the pathological cascade. Today, noninvasive imaging tools enable the visualization and quantitative assessment of the expression of molecular targets, of their interaction with potential ligands, as well as of the functional consequence of this interaction at a molecular (e.g. activation of signaling cascades), cellular, metabolic, physiological, and morphological level in a temporo-spatially resolved manner. The ability to gather such information from the intact organism with all regulatory processes in place renders imaging highly attractive for the biomedical researcher and for the drug developer in particular. Molecular imaging is potentially capable of providing this information. Today, proof-of-principle has been established that imaging is in fact adding value to the drug discovery and development processes. Numerous studies have used structural and functional imaging readouts to document therapy efficacy, mainly during lead optimization. Similarly, major efforts have been devoted to the development and evaluation of imaging biomarkers that might serve as early readouts for therapy response with the potential of being used in the clinical drug evaluation thereby facilitating translational research. In this contribution, we illustrate the role and potential of imaging in modern drug discovery and development with selected examples. Yet, despite its huge potential the impact of imaging on drug discovery has been modest in the past; potential reasons will be discussed. Nevertheless, noninvasive imaging methods are rapidly evolving and it is beyond doubt that their importance for biomedical research will increase.

  7. Phenol-formaldehyde resins: A quantitative NMR study of molecular structure and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ottenbourgs, Benjamin Tony

    Phenol-formaldehyde (PF) resins have been the subject of this work. 13C liquid-state and solid-state NMR has been used to investigate the molecular structure of mainly novolak and partially of resole resins. 1H wideline in combination with 13C solid-state NMR relaxometry has been applied to study the curing and the molecular dynamics of phenolic resins. It was the intention to provide an insight in the relationship between resin composition, resin structure and subsequent resin properties (by means of the molecular dynamics). An improved 13C liquid-state NMR quantification technique of novolaks in THF-CDCl3 solutions is demonstrated. Full quantitative 13C liquid-state spectra of phenol-formaldehyde resins with high signal- to-noise ratio were obtained by using chromium acetylacetonate under optimized spectral conditions within a few hours spectrometer time. Attached proton test (APT) spectra enabled proper peak assignments in the region with significant overlap. For several novolaks, prepared under different catalytic conditions, the degree of polymerization, degree of branching, number average molecular weight, isomeric distribution, and the number of unreacted ortho and para phenol ring positions was determined with a reduced margin of error, by analyzing and integrating the 13C spectra. The power of 13C solid-state NMR in the analysis of cured PF resins is shown. Particular importance was ascribed to the question of the quantifiability of the experiments when it was desired to measure the degree of conversion by means of a 13C CP/MAS contact time study. The network structure present, and thus also the mechanical properties, is critically dependent upon the final degree of conversion obtained after curing. The degree of conversion, which depended on the cure conditions (cure temperature, cure pressure and cure time), was limited by vitrification as was demonstrated by DSC experiments. Changes in the spin-lattice relaxation time T 1H were observed, providing

  8. The molecular structure of waxy maize starch nanocrystals.

    PubMed

    Angellier-Coussy, Hélène; Putaux, Jean-Luc; Molina-Boisseau, Sonia; Dufresne, Alain; Bertoft, Eric; Perez, Serge

    2009-08-17

    The insoluble residues obtained by submitting amylopectin-rich native starch granules from waxy maize to a mild acid hydrolysis consist of polydisperse platelet nanocrystals that have retained the allomorphic type of the parent granules. The present investigation is a detailed characterization of their molecular composition. Two major groups of dextrins were found in the nanocrystals and were isolated. Each group was then structurally characterized using beta-amylase and debranching enzymes (isoamylase and pullulanase) in combination with anion-exchange chromatography. The chain lengths of the dextrins in both groups corresponded with the thickness of the crystalline lamellae in the starch granules. Only approximately 62 mol% of the group of smaller dextrins with an average degree of polymerization (DP) 12.2 was linear, whereas the rest consisted of branched dextrins. The group of larger dextrins (DP 31.7) apparently only consisted of branched dextrins, several of which were multiply branched molecules. It was shown that many of the branch linkages were resistant to the action of the debranching enzymes. The distribution of branched molecules in the two populations of dextrins suggested that the nanocrystals possessed a regular and principally homogeneous molecular structure.

  9. Anti-cancer chalcones: Structural and molecular target perspectives.

    PubMed

    Mahapatra, Debarshi Kar; Bharti, Sanjay Kumar; Asati, Vivek

    2015-06-15

    Chalcone or (E)-1,3-diphenyl-2-propene-1-one scaffold remained a fascination among researchers in the 21st century due to its simple chemistry, ease of synthesis and a wide variety of promising biological activities. Several natural and (semi) synthetic chalcones have shown anti-cancer activity due to their inhibitory potential against various targets namely ABCG2/P-gp/BCRP, 5α-reductase, aromatase, 17-β-hydroxysteroid dehydrogenase, HDAC/Situin-1, proteasome, VEGF, VEGFR-2 kinase, MMP-2/9, JAK/STAT signaling pathways, CDC25B, tubulin, cathepsin-K, topoisomerase-II, Wnt, NF-κB, B-Raf and mTOR etc. In this review, a comprehensive study on molecular targets/pathways involved in carcinogenesis, mechanism of actions (MOAs), structure activity relationships (SARs) and patents granted have been highlighted. With the knowledge of molecular targets, structural insights and SARs, this review may be helpful for (medicinal) chemists to design more potent, safe, selective and cost effective anti-cancer chalcones.

  10. Structure, molecular evolution, and hydrolytic specificities of largemouth bass pepsins.

    PubMed

    Miura, Yoko; Suzuki-Matsubara, Mieko; Kageyama, Takashi; Moriyama, Akihiko

    2016-02-01

    The nucleotide sequences of largemouth bass pepsinogens (PG1, 2 and 3) were determined after molecular cloning of the respective cDNAs. Encoded PG1, 2 and 3 were classified as fish pepsinogens A1, A2 and C, respectively. Molecular evolutionary analyses show that vertebrate pepsinogens are classified into seven monophyletic groups, i.e. pepsinogens A, F, Y (prochymosins), C, B, and fish pepsinogens A and C. Regarding the primary structures, extensive deletion was obvious in S'1 loop residues in fish pepsin A as well as tetrapod pepsin Y. This deletion resulted in a decrease in hydrophobic residues in the S'1 site. Hydrolytic specificities of bass pepsins A1 and A2 were investigated with a pepsin substrate and its variants. Bass pepsins preferred both hydrophobic/aromatic residues and charged residues at the P'1 sites of substrates, showing the dual character of S'1 sites. Thermodynamic analyses of bass pepsin A2 showed that its activation Gibbs energy change (∆G(‡)) was lower than that of porcine pepsin A. Several sites of bass pepsin A2 moiety were found to be under positive selection, and most of them are located on the surface of the molecule, where they are involved in conformational flexibility. The broad S'1 specificity and flexible structure of bass pepsin A2 are thought to cause its high proteolytic activity.

  11. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca; Heberle, Frederick A; Kucerka, Norbert; Tieleman, D. Peter; Katsaras, John

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  12. Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

    ERIC Educational Resources Information Center

    Murphy, Peter M.

    2007-01-01

    A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

  13. Maintain rigid structures in Verlet based cartesian molecular dynamics simulations.

    PubMed

    Tao, Peng; Wu, Xiongwu; Brooks, Bernard R

    2012-10-07

    An algorithm is presented to maintain rigid structures in Verlet based cartesian molecular dynamics (MD) simulations. After each unconstrained MD step, the coordinates of selected particles are corrected to maintain rigid structures through an iterative procedure of rotation matrix computation. This algorithm, named as SHAPE and implemented in CHARMM program suite, avoids the calculations of Lagrange multipliers, so that the complexity of computation does not increase with the number of particles in a rigid structure. The implementation of this algorithm does not require significant modification of propagation integrator, and can be plugged into any cartesian based MD integration scheme. A unique feature of the SHAPE method is that it is interchangeable with SHAKE for any object that can be constrained as a rigid structure using multiple SHAKE constraints. Unlike SHAKE, the SHAPE method can be applied to large linear (with three or more centers) and planar (with four or more centers) rigid bodies. Numerical tests with four model systems including two proteins demonstrate that the accuracy and reliability of the SHAPE method are comparable to the SHAKE method, but with much more applicability and efficiency.

  14. Electronic and Magnetic Structure of Octahedral Molecular Sieves

    NASA Astrophysics Data System (ADS)

    Morey-Oppenheim, Aimee M.

    The major part of this research consists of magnetic and electronic studies of metal doped cryptomelane-type manganese oxide octahedral molecular sieves (KOMS-2). The second part of this study involves the magnetic characterization of cobalt doped MCM-41 before and after use in the synthesis of single walled carbon nanotubes. Manganese oxides have been used widely as bulk materials in catalysis, chemical sensors, and batteries due to the wide range of possible stable oxidation states. The catalytic function of manganese oxides is further tuned by doping the material with numerous transition metals. It is of particular interest the oxidation states of Mn present after doping. New titrations to determine the oxidation state of Mn were investigated. To further examine the structure of KOMS-2, the magnetic contribution of dopant metals was also examined. The KOMS-2 structure having both diamagnetic and paramagnetic metal ions substitutions was studied. MCM-41 with the incorporation of cobalt into the structure was analyzed for its magnetic properties. The material undergoes significant structural change during the synthesis of single walled carbon nanotubes. It was the focus of this portion of the research to do a complete magnetic profile of both the before and after reaction material.

  15. General theory for multiple input-output perturbations in complex molecular systems. 1. Linear QSPR electronegativity models in physical, organic, and medicinal chemistry.

    PubMed

    González-Díaz, Humberto; Arrasate, Sonia; Gómez-SanJuan, Asier; Sotomayor, Nuria; Lete, Esther; Besada-Porto, Lina; Ruso, Juan M

    2013-01-01

    In general perturbation methods starts with a known exact solution of a problem and add "small" variation terms in order to approach to a solution for a related problem without known exact solution. Perturbation theory has been widely used in almost all areas of science. Bhor's quantum model, Heisenberg's matrix mechanincs, Feyman diagrams, and Poincare's chaos model or "butterfly effect" in complex systems are examples of perturbation theories. On the other hand, the study of Quantitative Structure-Property Relationships (QSPR) in molecular complex systems is an ideal area for the application of perturbation theory. There are several problems with exact experimental solutions (new chemical reactions, physicochemical properties, drug activity and distribution, metabolic networks, etc.) in public databases like CHEMBL. However, in all these cases, we have an even larger list of related problems without known solutions. We need to know the change in all these properties after a perturbation of initial boundary conditions. It means, when we test large sets of similar, but different, compounds and/or chemical reactions under the slightly different conditions (temperature, time, solvents, enzymes, assays, protein targets, tissues, partition systems, organisms, etc.). However, to the best of our knowledge, there is no QSPR general-purpose perturbation theory to solve this problem. In this work, firstly we review general aspects and applications of both perturbation theory and QSPR models. Secondly, we formulate a general-purpose perturbation theory for multiple-boundary QSPR problems. Last, we develop three new QSPR-Perturbation theory models. The first model classify correctly >100,000 pairs of intra-molecular carbolithiations with 75-95% of Accuracy (Ac), Sensitivity (Sn), and Specificity (Sp). The model predicts probabilities of variations in the yield and enantiomeric excess of reactions due to at least one perturbation in boundary conditions (solvent, temperature

  16. Molecular Clouds in the North American and Pelican Nebulae: Structures

    NASA Astrophysics Data System (ADS)

    Zhang, Shaobo; Xu, Ye; Yang, Ji

    2014-03-01

    We present observations of a 4.25 deg2 area toward the North American and Pelican Nebulae in the J = 1-0 transitions of 12CO, 13CO, and C18O. Three molecules show different emission areas with their own distinct structures. These different density tracers reveal several dense clouds with a surface density of over 500 M ⊙ pc-2 and a mean H2 column density of 5.8, 3.4, and 11.9 × 1021 cm-2 for 12CO, 13CO, and C18O, respectively. We obtain a total mass of 5.4 × 104 M ⊙ (12CO), 2.0 × 104 M ⊙ (13CO), and 6.1 × 103 M ⊙ (C18O) in the complex. The distribution of excitation temperature shows two phases of gas: cold gas (~10 K) spreads across the whole cloud; warm gas (>20 K) outlines the edge of the cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud: the Gulf of Mexico, Caribbean Islands and Sea, and Pelican's Beak, Hat, and Neck. The areas of 13CO emission range within 2-10 pc2 with mass of (1-5) × 103 M ⊙ and line width of a few km s-1. The different line properties and signs of star-forming activity indicate they are in different evolutionary stages. Four filamentary structures with complicated velocity features are detected along the dark lane in LDN 935. Furthermore, a total of 611 molecular clumps within the 13CO tracing cloud are identified using the ClumpFind algorithm. The properties of the clumps suggest that most of the clumps are gravitationally bound and at an early stage of evolution with cold and dense molecular gas.

  17. Mathematical analysis of compressive/tensile molecular and nuclear structures

    NASA Astrophysics Data System (ADS)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  18. Molecular, morphological and fossil input data for inferring relationship among viviparous brotulas (Bythitidae) - Resulting in a family status change for Dinematichthyidae.

    PubMed

    Knudsen, Steen Wilhelm; Møller, Peter Rask; Schwarzhans, Werner; Nielsen, Jørgen G

    2016-09-01

    This article comprise the data related to the research article (Møller et al., 2016) [1], and makes it possible to explore and reproduce the topologies that allowed [1] to infer the relationship between the families Bythitidae and Dinematichthyidae. The supplementary data holds nexus-input files for the Bayesian analysis and the '.xml'-input files - with and without nucleotide data - that are used in the fossil-calibrated phylogenetic analysis with a relaxed clock model. The resulting topologies are provided as '.new'-files together with a characters matrix file for traits to trace across the inferred phylogenies.

  19. Harvesting on a stage-structured single population model with mature individuals in a polluted environment and pulse input of environmental toxin.

    PubMed

    Jiao, Jianjun; Yang, Xiaosong; Chen, Lansun

    2009-09-01

    In the natural world, there are many species whose individual members have a life history that they take them with two distinct stages: immaturity and maturity. In particular, we have in mind mammalian populations and some amphibious animals. We improve the assumption of a single population as a whole. It is assumed that the immature individuals and mature individuals are divided by a fixed period. This paper concentrates on the study of a stage-structured single population model with mature individuals in a polluted environment and pulse input of environmental toxin at fixed moments. Furthermore, the mature individuals are harvested continuously. We show that the population goes extinct if the harvesting rate is beyond a critical threshold. Conditions for the extended permanence of the population are also examined. From the biological point of view, it is easy to protect species by controlling the harvesting amount, impulsive period of the exogenous input of toxin and toxin impulsive input amount, etc. Our results provide reasonable tactics for biological resource management.

  20. Structured illumination microscopy for vibrational molecular imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Watanabe, Kozue; Palonpon, Almar F.; Smith, Nicholas I.; Chiu, Liang-da; Kasai, Atsushi; Hashimoto, Hitoshi; Kawata, Satoshi; Fujita, Katsumasa

    2016-09-01

    Raman microscopy is a powerful tool for analytical imaging. The wavelength shift of Raman scattering corresponds to molecular vibrational energy. Therefore, we can access rich chemical information, such as distribution, concentration, and chemical environment of sample molecules. Despite these strengths of Raman microscopy, the spatial resolution has been a limiting factor for many practical applications. In this study, we developed a large-area, high-resolution Raman microscope by utilizing structured illumination microscopy (SIM) to overcome the spatial resolution limit. A structured line-illumination (SLI) Raman microscope was constructed. The structured illumination is introduced along the line direction by the interference of two line-shaped beams. In SIM, the spatial frequency mixing between structured illumination and Raman scattering from the sample allows access to the high spatial frequency information beyond the conventional cut-off. As a result, the FWHM of 40-nm fluorescence particle images showed a clear resolution enhancement in the line direction: 366 nm in LI and 199 nm in SLI microscope. Using the developed microscope, we successfully demonstrated high-resolution Raman imaging of various kinds of specimens, such as few-layer graphene, graphite, mouse brain tissue, and polymer nanoparticles. The high resolution Raman images showed the capability to extract original spectral features from the mixed Raman spectra of a multi-component sample because of the enhanced spatial resolution, which is advantageous in observing complex spectral features. The Raman microscopy technique reported here enables us to see the detailed chemical structures of chemical, biological, and medical samples with a spatial resolution smaller than 200 nm.

  1. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

    SciTech Connect

    Mehere, P.; Robinson, H.; Han, Q.; Lemkul, J. A.; Vavricka, C. J.; Bevan, D. R.; Li, J.

    2010-11-01

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  2. Tyrosine Aminotransferase: Biochemical and Structural Properties and Molecular Dynamics Simulations

    SciTech Connect

    P Mehere; Q Han; J Lemkul; C Vavricka; H Robinson; D Bevan; J Li

    2011-12-31

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  3. Hydration structure of salt solutions from ab initio molecular dynamics

    SciTech Connect

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-07

    The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  4. Hydration structure of salt solutions from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-01

    The solvation structures of Na^+, K^+, and Cl^- ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na^+, K^+, and Cl^-, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  5. Hydration structure of salt solutions from ab initio molecular dynamics.

    PubMed

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L

    2013-01-07

    The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  6. Molecular and structural insight into plasmodium falciparum RIO2 kinase.

    PubMed

    Chouhan, Devendra K; Sharon, Ashoke; Bal, Chandralata

    2013-02-01

    Among approximately 65 kinases of the malarial genome, RIO2 (right open reading frame) kinase belonging to the atypical class of kinase is unique because along with a kinase domain, it has a highly conserved N-terminal winged helix (wHTH) domain. The wHTH domain resembles the wing like domain found in DNA binding proteins and is situated near to the kinase domain. Ligand binding to this domain may reposition the kinase domain leading to inhibition of enzyme function and could be utilized as a novel allosteric site to design inhibitor. In the present study, we have generated a model of RIO2 kinase from Plasmodium falciparum utilizing multiple modeling, simulation approach. A novel putative DNA-binding site is identified for the first time in PfRIO2 kinase to understand the DNA binding events involving wHTH domain and flexible loop. Induced fit DNA docking followed by minimization, molecular dynamics simulation, energetic scoring and binding mode studies are used to reveal the structural basis of PfRIO2-ATP-DNA complex. Ser105 as a potential site of phosphorylation is revealed through the structural studies of ATP binding in PfRIO2. Overall the present study discloses the structural facets of unknown PfRIO2 complex and opens an avenue toward exploration of novel drug target.

  7. Transmission electron microscopy in molecular structural biology: A historical survey.

    PubMed

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented.

  8. Structural and molecular interrogation of intact biological systems

    PubMed Central

    Chung, Kwanghun; Wallace, Jenelle; Kim, Sung-Yon; Kalyanasundaram, Sandhiya; Andalman, Aaron S.; Davidson, Thomas J.; Mirzabekov, Julie J.; Zalocusky, Kelly A.; Mattis, Joanna; Denisin, Aleksandra K.; Pak, Sally; Bernstein, Hannah; Ramakrishnan, Charu; Grosenick, Logan; Gradinaru, Viviana; Deisseroth, Karl

    2014-01-01

    Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease. PMID:23575631

  9. Solving structures of protein complexes by molecular replacement with Phaser

    SciTech Connect

    McCoy, Airlie J.

    2007-01-01

    Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases.

  10. Guiding Molecular Motors with Nano-Imprinted Structures

    NASA Astrophysics Data System (ADS)

    Bunk, Richard; Carlberg, Patrick; Månsson, Alf; Nicholls, Ian A.; Omling, Pär; Sundberg, Mark; Tågerud, Sven; Montelius, Lars

    2005-05-01

    This work, for the first time, demonstrates that nano-imprinted samples, with 100 nm wide polymer lines, can act as guides for molecular motors consisting of motor proteins actin and myosin. The motor protein function was characterized using fluorescence microscopy and compared to actomyosin motility on non-structured nitrocellulose surfaces. Our results open for further use of the nano-imprint technique in the production of disposable chips for bio-nanotechnological applications and miniaturized biological test systems. We discuss how the nano-imprinted motor protein assay system may be optimized and also how it compares to previously tested assay systems involving low-resolution UV-lithography and low throughput but high-resolution electron beam lithography.

  11. The molecular structure of naphthalene by electron diffraction

    NASA Astrophysics Data System (ADS)

    Ketkar, S. N.; Fink, M.

    1981-11-01

    The molecular structure of gaseous naphthalene has been studied by electron diffraction at a nozzle tip temperature of about 25°C. The molecule has D 2h symmetry to within experimental error. The results for the distances ( ra), bond angle and r.m.s. amplitude ( l) are r(CH) = 1.092(6) Å, r(C 9C 1) = 1.422(2) Å, r(C 1C 2) = 1.381(2) Å, r(C 2C 3) = 1.417(4) Å, r(C 10C 9) = 1.412(8) Å, ∠C 10C 9C 1 = 119.5(3)°, ∠CCH = 119.9(7)°, l(CH) = 0.076(6) Å, l(CC) = 0.047(2) Å.

  12. Diffusion and structure in silica liquid: a molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Hung, P. K.; Hong, N. V.; Vinh, L. T.

    2007-11-01

    Diffusion and structure in liquid silica under pressure have been investigated by a molecular dynamics model of 999 atoms with the inter-atomic potentials of van Beest, Kramer and van Santen. The simulation reveals that silica liquid is composed of the species SiO4, SiO5 and SiO6 with a fraction dependent on pressure. The density as well as volume of voids can be expressed as a linear function of the fraction of those species. Low-density liquid is mainly constructed of SiO4 and has a large number of O- and Si-voids and a large void tube. This tube contains most O-voids and is spread over the whole system. The anomalous diffusion behavior is observed and discussed.

  13. Crystal and molecular structure of three biologically active nitroindazoles

    NASA Astrophysics Data System (ADS)

    Cabildo, Pilar; Claramunt, Rosa M.; López, Concepción; García, M. Ángeles; Pérez-Torralba, Marta; Pinilla, Elena; Torres, M. Rosario; Alkorta, Ibon; Elguero, José

    2011-01-01

    3-Bromo-1-methyl-7-nitro-1 H-indazole ( 1), 3-bromo-2-methyl-7-nitro-2 H-indazole ( 2) and 3,7-dinitro-1(2) H-indazole ( 3) have been synthesized and characterized by X-ray diffraction, 13C and 15N NMR spectroscopy in solution and in solid-state. The dihedral angles obtained in the crystal structures are in good agreement with the molecular parameters calculated using DFT B3LYP calculations employing the 6-311++G(d,p) basis set. Compounds 1 and 2 present intermolecular halogen bonds between the bromine and the oxygen atoms of the nitro group and in compound 3 inter- and intramolecular hydrogen bonding exists.

  14. On the interaction structure of linear multi-input feedback control systems. M.S. Thesis; [problem solving, lattices (mathematics)

    NASA Technical Reports Server (NTRS)

    Wong, P. K.

    1975-01-01

    The closely-related problems of designing reliable feedback stabilization strategy and coordinating decentralized feedbacks are considered. Two approaches are taken. A geometric characterization of the structure of control interaction (and its dual) was first attempted and a concept of structural homomorphism developed based on the idea of 'similarity' of interaction pattern. The idea of finding classes of individual feedback maps that do not 'interfere' with the stabilizing action of each other was developed by identifying the structural properties of nondestabilizing and LQ-optimal feedback maps. Some known stability properties of LQ-feedback were generalized and some partial solutions were provided to the reliable stabilization and decentralized feedback coordination problems. A concept of coordination parametrization was introduced, and a scheme for classifying different modes of decentralization (information, control law computation, on-line control implementation) in control systems was developed.

  15. The Impact of Adjacent-Dependencies and Staged-Input on the Learnability of Center-Embedded Hierarchical Structures

    ERIC Educational Resources Information Center

    Lai, Jun; Poletiek, Fenna H.

    2011-01-01

    A theoretical debate in artificial grammar learning (AGL) regards the learnability of hierarchical structures. Recent studies using an A[superscript n]B[superscript n] grammar draw conflicting conclusions ([Bahlmann and Friederici, 2006] and [De Vries et al., 2008]). We argue that 2 conditions crucially affect learning A[superscript…

  16. Molecular structure and exciton dynamics in organic conjugated polymers

    NASA Astrophysics Data System (ADS)

    Thomas, Alan K.

    , quenchable, isolated singlet excitations. The structure of J aggregates which leads to isolated excitations, and the role which inter-chain contact sites play in triplet formation from these singlet excitations is revealed. New structure-function relationships were uncovered in poly (3-alkyl-thienylenevinylene) (P3ATV) derivatives using resonance Raman and photocurrent spectroscopies. Time-dependent spectroscopic theory was used to interpret experimental Raman and absorption spectra that revealed the presence of structural polymorphs. These polymorphs provide an explanation of the spectroscopic evidence without presumption of a deactivating dark state in this unusually non-fluorescence material. Photovoltaic devices constructed from blends of poly (2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT) and PCBM blends were examined using Raman and photocurrent imaging techniques. These techniques were used to identify different packing states in blended thin films and correlate photocurrent production with local order. Intensity modulated spectroscopic techniques (IMPS) were then used to locate regions of non-geminate charge recombination at interfaces between amorphous and crystalline regions in working devices. Next, P3HT/PCBM OPV devices were exposed to ionizing radiation in a vacuum chamber. These devices were characterized before and after exposure, using standardized solar cell tests, Raman imaging, wide-field IMPS, and IMVS spectroscopies. An analysis of the spectroscopic data determined that the donor polymer is highly resistant to radiation damage, and that the degradation of device performance is due to an effect (cross-linking or degradation) within aggregates of the acceptor. This dissertation concludes with an interpretation of the significance of the findings contained herein to organic electronics, followed by a brief outlook for future work in these fields. Potential theories to describe and predict molecular interactions for organic polymers in

  17. Molecular structure of cyclic deoxydiadenylic acid at atomic resolution.

    PubMed

    Frederick, C A; Coll, M; van der Marel, G A; van Boom, J H; Wang, A H

    1988-11-01

    The molecular structure of a small cyclic nucleotide, cyclic deoxydiadenylic acid, has been determined by single-crystal X-ray diffraction analysis and refined to an R factor of 7.8% at 1.0-A resolution. The crystals are in the monoclinic space group C2 with unit cell dimensions of a = 24.511 (3) A, b = 24.785 (3) A, c = 13.743 (3) A, and beta = 94.02 (2) degrees. The structure was solved by the direct methods program SHELXS-86. There are 2 independent cyclic d(ApAp) molecules, 2 hydrated magnesium ions, and 26 water molecules in the asymmetric unit of the unit cell. The two cyclic d(ApAp) molecules have similar conformations within their 12-membered sugar-phosphate backbone ring, but they have quite different appearances due to the different glycosyl torsion angles that make one molecule more compact and the other extended and open. Three of the four deoxyribose rings are in the less common C3'-endo conformation. All four phosphate groups have their phosphodiester torsion angles alpha/zeta in the gauche(+)/gauche(+) conformation. One of the cyclic d(ApAp) molecules associates with another symmetry-related molecule to form a self-intercalated dimer that is a stable structure in solution, as observed in NMR studies. Many interesting intermolecular interactions, including base-base stacking, ribose-base stacking, base pairing, base-phosphate hydrogen bonding, and metal ion-phosphate interactions, are found in the crystal lattice. This structure may be relevant for understanding the conformational potentiality of an endogenous biological regulator of cellulose synthesis, cyclic (GpGp).

  18. Derivatives of Ergot-alkaloids: Molecular structure, physical properties, and structure-activity relationships

    NASA Astrophysics Data System (ADS)

    Ivanova, Bojidarka B.; Spiteller, Michael

    2012-09-01

    A comprehensive screening of fifteen functionalized Ergot-alkaloids, containing bulk aliphatic cyclic substituents at D-ring of the ergoline molecular skeleton was performed, studying their structure-active relationships and model interactions with α2A-adreno-, serotonin (5HT2A) and dopamine D3 (D3A) receptors. The accounted high affinity to the receptors binding loops and unusual bonding situations, joined with the molecular flexibility of the substituents and the presence of proton accepting/donating functional groups in the studied alkaloids, may contribute to further understanding the mechanisms of biological activity in vivo and in predicting their therapeutic potential in central nervous system (CNS), including those related the Schizophrenia. Since the presented correlation between the molecular structure and properties, was based on the comprehensively theoretical computational and experimental physical study on the successfully isolated derivatives, through using routine synthetic pathways in a relatively high yields, marked these derivatives as 'treasure' for further experimental and theoretical studied in areas such as: (a) pharmacological and clinical testing; (b) molecular-drugs design of novel psychoactive substances; (c) development of the analytical protocols for determination of Ergot-alkaloids through a functionalization of the ergoline-skeleton, and more.

  19. Structural and molecular basis of starch viscosity in hexaploid wheat.

    PubMed

    Ral, J-P; Cavanagh, C R; Larroque, O; Regina, A; Morell, M K

    2008-06-11

    Wheat starch is considered to have a low paste viscosity relative to other starches. Consequently, wheat starch is not preferred for many applications as compared to other high paste viscosity starches. Increasing the viscosity of wheat starch is expected to increase the functionality of a range of wheat flour-based products in which the texture is an important aspect of consumer acceptance (e.g., pasta, and instant and yellow alkaline noodles). To understand the molecular basis of starch viscosity, we have undertaken a comprehensive structural and rheological analysis of starches from a genetically diverse set of wheat genotypes, which revealed significant variation in starch traits including starch granule protein content, starch-associated lipid content and composition, phosphate content, and the structures of the amylose and amylopectin fractions. Statistical analysis highlighted the association between amylopectin chains of 18-25 glucose residues and starch pasting properties. Principal component analysis also identified an association between monoesterified phosphate and starch pasting properties in wheat despite the low starch-phosphate level in wheat as compared to tuber starches. We also found a strong negative correlation between the phosphate ester content and the starch content in flour. Previously observed associations between internal starch granule fatty acids and the swelling peak time and pasting temperature have been confirmed. This study has highlighted a range of parameters associated with increased starch viscosity that could be used in prebreeding/breeding programs to modify wheat starch pasting properties.

  20. Structural and electronic properties of Diisopropylammonium bromide molecular ferroelectric crystal

    NASA Astrophysics Data System (ADS)

    Alsaad, A.; Qattan, I. A.; Ahmad, A. A.; Al-Aqtash, N.; Sabirianov, R. F.

    2015-10-01

    We report the results of ab-initio calculations based on Generalized Gradient Approximation (GGA) and hybrid functional (HSE06) of electronic band structure, density of states and partial density of states to get a deep insight into structural and electronic properties of P21 ferroelectric phase of Diisopropylammonium Bromide molecular crystal (DIPAB). We found that the optical band gap of the polar phase of DIPAB is ∼ 5 eV confirming it as a good dielectric. Examination of the density of states and partial density of states reveal that the valence band maximum is mainly composed of bromine 4p orbitals and the conduction band minimum is dominated by carbon 2p, carbon 2s, and nitrogen 2s orbitals. A unique aspect of P21 ferroelectric phase is the permanent dipole within the material. We found that P21 DIPAB has a spontaneous polarization of 22.64 consistent with recent findings which make it good candidate for the creation of ferroelectric tunneling junctions (FTJs) which have the potential to be used as memory devices.

  1. Molecular Structures and Interactions in the Yeast Kinetochore

    PubMed Central

    Cho, U.-S.; Corbett, K.D.; Al-Bassam, J.; Bellizzi, J.J.; De Wulf, P.; Espelin, C.W.; Miranda, J.J.; Simons, K.; Wei, R.R.; Sorger, P.K.; Harrison, S.C.

    2011-01-01

    Kinetochores are the elaborate protein assemblies that attach chromosomes to spindle microtubules in mitosis and meiosis. The kinetochores of point-centromere yeast appear to represent an elementary module, which repeats a number of times in kinetochores assembled on regional centromeres. Structural analyses of the discrete protein subcomplexes that make up the budding-yeast kinetochore have begun to reveal principles of kinetochore architecture and to uncover molecular mechanisms underlying functions such as transmission of tension and establishment and maintenance of bipolar attachment. The centromeric DNA is probably wrapped into a compact organization, not only by a conserved, centromeric nucleosome, but also by interactions among various other DNA-bound kinetochore components. The rod-like, heterotetrameric Ndc80 complex, roughly 600 Å long, appears to extend from the DNA-proximal assembly to the plus end of a microtubule, to which one end of the complex is known to bind. Ongoing structural studies will clarify the roles of a number of other well-defined complexes. PMID:21467141

  2. Bonding and structure in dense multi-component molecular mixtures

    SciTech Connect

    Meyer, Edmund R.; Ticknor, Christopher; Bethkenhagen, Mandy; Hamel, Sebastien; Redmer, Ronald; Kress, Joel D.; Collins, Lee A.

    2015-10-30

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systems engendered by variations in the concentration ratios. As a result, a basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.

  3. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    PubMed

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  4. Chitosan Molecular Structure as a Function of N-Acetylation

    SciTech Connect

    Franca, Eduardo F.; Freitas, Luiz C.; Lins, Roberto D.

    2011-07-01

    Molecular dynamics simulations have been carried out to characterize the structure and solubility of chitosan nanoparticle-like structures as a function of the deacetylation level (0, 40, 60, and 100%) and the spatial distribution of the N-acetyl groups in the particles. The polysaccharide chains of highly N-deacetylated particles where the N-acetyl groups are uniformly distributed present a high flexibility and preference for the relaxed two-fold helix and five-fold helix motifs. When these groups are confined to a given region of the particle, the chains adopt preferentially a two-fold helix with f and w values close to crystalline chitin. Nanoparticles with up to 40% acetylation are moderately soluble, forming stable aggregates when the N-acetyl groups are unevenly distributed. Systems with 60% or higher N-acetylation levels are insoluble and present similar degrees of swelling regardless the distribution of their N-acetyl groups. Overall particle solvation is highly affected by electrostatic forces resulting from the degree of acetylation. The water mobility and orientation around the polysaccharide chains affects the stability of the intramolecular O3- HO3(n) ... O5(n+ 1) hydrogen bond, which in turn controls particle aggregation.

  5. Bonding and structure in dense multi-component molecular mixtures

    DOE PAGES

    Meyer, Edmund R.; Ticknor, Christopher; Bethkenhagen, Mandy; ...

    2015-10-30

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systemsmore » engendered by variations in the concentration ratios. As a result, a basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.« less

  6. Molecular structure of tetramethylgermane from gas electron diffraction

    NASA Astrophysics Data System (ADS)

    Csákvári, Éva; Rozsondai, Béla; Hargittai, István

    1991-05-01

    The molecular structure of Ge(CH 3) 4 has been determined from gas-phase electron diffraction augmented by a normal coordinate analysis. Assuming tetrahedral symmetry for the germanium bond configuration, the following structural parameters are found: rg(GeC) = 1.958 ± 0.004 Å, rg(CH) = 1.111 ± 0.003 Å and ∠(GeCH) = 110.7 ± 0.2° ( R=4.0%). The methyl torsional barrier V 0 is estimated to be 1.3 kJ mol -1 on the basis of an effective angle of torsion 23.0 ± 1.5°, from the staggered form, yielded directly by the analysis. The GeC bond length of Ge(CH 3) 4 is the same, within experimental error, as that of Ge(C 6H 5) 4 and is in agreement with the prediction of a modified Schomaker-Stevenson relationship.

  7. Magnetic Field Structure in Molecular Clouds by Polarization Measurements

    NASA Astrophysics Data System (ADS)

    Chen, W. P.; Su, B. H.; Eswaraiah, C.; Pandey, A. K.; Wang, C. W.; Lai, S. P.; Tamura, M.; Sato, S.

    2015-03-01

    We report on a program to delineate magnetic field structure inside molecular clouds by optical and infrared polarization observations. An ordered magnetic field inside a dense cloud may efficiently align the spinning dust grains to cause a detectable level of optical and near-infrared polarization of otherwise unpolarized background starlight due to dichroic extinction. The near-infrared polarization data were taken by SIRPOL mounted on IRSF in SAAO. Here we present the SIRPOL results in RCW 57, for which the magnetic field is oriented along the cloud filaments, and in Carina Nebula, for which no intrinsic polarization is detected in the turbulent environment. We further describe TRIPOL, a compact and efficient polarimer to acquire polarized images simultaneously at g', r', and i' bands, which is recently developed at Nagoya University for adaption to small-aperture telescopes. We show how optical observations probe the translucent outer parts of a cloud, and when combining with infrared observations probing the dense parts, and with millimeter and submillimeter observations to sutdy the central embedded protostar, if there is one, would yield the magnetic field structure on different length scales in the star-formation process.

  8. Molecular clouds in the North American and Pelican Nebulae: structures

    SciTech Connect

    Zhang, Shaobo; Xu, Ye; Yang, Ji

    2014-03-01

    We present observations of a 4.25 deg{sup 2} area toward the North American and Pelican Nebulae in the J = 1-0 transitions of {sup 12}CO, {sup 13}CO, and C{sup 18}O. Three molecules show different emission areas with their own distinct structures. These different density tracers reveal several dense clouds with a surface density of over 500 M {sub ☉} pc{sup –2} and a mean H{sub 2} column density of 5.8, 3.4, and 11.9 × 10{sup 21} cm{sup –2} for {sup 12}CO, {sup 13}CO, and C{sup 18}O, respectively. We obtain a total mass of 5.4 × 10{sup 4} M {sub ☉} ({sup 12}CO), 2.0 × 10{sup 4} M {sub ☉} ({sup 13}CO), and 6.1 × 10{sup 3} M {sub ☉} (C{sup 18}O) in the complex. The distribution of excitation temperature shows two phases of gas: cold gas (∼10 K) spreads across the whole cloud; warm gas (>20 K) outlines the edge of the cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud: the Gulf of Mexico, Caribbean Islands and Sea, and Pelican's Beak, Hat, and Neck. The areas of {sup 13}CO emission range within 2-10 pc{sup 2} with mass of (1-5) × 10{sup 3} M {sub ☉} and line width of a few km s{sup –1}. The different line properties and signs of star-forming activity indicate they are in different evolutionary stages. Four filamentary structures with complicated velocity features are detected along the dark lane in LDN 935. Furthermore, a total of 611 molecular clumps within the {sup 13}CO tracing cloud are identified using the ClumpFind algorithm. The properties of the clumps suggest that most of the clumps are gravitationally bound and at an early stage of evolution with cold and dense molecular gas.

  9. Structure and function of natural sulphide-oxidizing microbial mats under dynamic input of light and chemical energy

    PubMed Central

    Klatt, Judith M; Meyer, Steffi; Häusler, Stefan; Macalady, Jennifer L; de Beer, Dirk; Polerecky, Lubos

    2016-01-01

    We studied the interaction between phototrophic and chemolithoautotrophic sulphide-oxidizing microorganisms in natural microbial mats forming in sulphidic streams. The structure of these mats varied between two end-members: one characterized by a layer dominated by large sulphur-oxidizing bacteria (SOB; mostly Beggiatoa-like) on top of a cyanobacterial layer (B/C mats) and the other with an inverted structure (C/B mats). C/B mats formed where the availability of oxygen from the water column was limited (<5 μm). Aerobic chemolithotrophic activity of the SOB depended entirely on oxygen produced locally by cyanobacteria during high light conditions. In contrast, B/C mats formed at locations where oxygen in the water column was comparatively abundant (>45 μM) and continuously present. Here SOB were independent of the photosynthetic activity of cyanobacteria and outcompeted the cyanobacteria in the uppermost layer of the mat where energy sources for both functional groups were concentrated. Outcompetition of photosynthetic microbes in the presence of light was facilitated by the decoupling of aerobic chemolithotrophy and oxygenic phototrophy. Remarkably, the B/C mats conserved much less energy than the C/B mats, although similar amounts of light and chemical energy were available. Thus ecosystems do not necessarily develop towards optimal energy usage. Our data suggest that, when two independent sources of energy are available, the structure and activity of microbial communities is primarily determined by the continuous rather than the intermittent energy source, even if the time-integrated energy flux of the intermittent energy source is greater. PMID:26405833

  10. Structure and function of natural sulphide-oxidizing microbial mats under dynamic input of light and chemical energy.

    PubMed

    Klatt, Judith M; Meyer, Steffi; Häusler, Stefan; Macalady, Jennifer L; de Beer, Dirk; Polerecky, Lubos

    2016-04-01

    We studied the interaction between phototrophic and chemolithoautotrophic sulphide-oxidizing microorganisms in natural microbial mats forming in sulphidic streams. The structure of these mats varied between two end-members: one characterized by a layer dominated by large sulphur-oxidizing bacteria (SOB; mostly Beggiatoa-like) on top of a cyanobacterial layer (B/C mats) and the other with an inverted structure (C/B mats). C/B mats formed where the availability of oxygen from the water column was limited (<5 μm). Aerobic chemolithotrophic activity of the SOB depended entirely on oxygen produced locally by cyanobacteria during high light conditions. In contrast, B/C mats formed at locations where oxygen in the water column was comparatively abundant (>45 μM) and continuously present. Here SOB were independent of the photosynthetic activity of cyanobacteria and outcompeted the cyanobacteria in the uppermost layer of the mat where energy sources for both functional groups were concentrated. Outcompetition of photosynthetic microbes in the presence of light was facilitated by the decoupling of aerobic chemolithotrophy and oxygenic phototrophy. Remarkably, the B/C mats conserved much less energy than the C/B mats, although similar amounts of light and chemical energy were available. Thus ecosystems do not necessarily develop towards optimal energy usage. Our data suggest that, when two independent sources of energy are available, the structure and activity of microbial communities is primarily determined by the continuous rather than the intermittent energy source, even if the time-integrated energy flux of the intermittent energy source is greater.

  11. Ab initio study of structural and mechanical property of solid molecular hydrogens

    NASA Astrophysics Data System (ADS)

    Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

    2015-06-01

    Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

  12. Synchrotron-based and globar-sourced molecular (micro)spectroscopy contributions to advances in new hulless barley (with structure alteration) research on molecular structure, molecular nutrition, and nutrient delivery.

    PubMed

    Yang, Ling; Yu, Peiqiang

    2017-01-02

    This paper aimed to review synchrotron-based and globar-sourced molecular infrared (micro)spectroscopy contributions to advances in new hulless barley (with structure alteration) research on molecular structure, molecular nutrition, and nutrient delivery in ruminants. It reviewed recent progress in barley varieties, its utilization for animal and human, inherent structure features and chemical make-up, evaluation and research methodology, breeding progress, rumen degradation, and intestinal digestion. The emphasis of this review was focused on the effect of alteration of carbohydrate traits of newly developed hulless barley on molecular structure changes and nutrient delivery and quantification of the relationship between molecular structure features and changes and truly absorbed nutrient supply to ruminants. This review provides an insight into how inherent structure changes on a molecular basis affect nutrient utilization and availability in ruminants.

  13. Prediction of molecular properties including symmetry from quantum-based molecular structural formulas, VIF.

    PubMed

    Alia, Joseph D; Vlaisavljevich, Bess; Abbot, Matthew; Warneke, Hallie; Mastin, Tyson

    2008-10-09

    Structurally covariant valency interaction formulas, VIF, gain chemical significance by comparison with resonance structures and natural bond orbital, NBO, bonding schemes and at the same time allow for additional prediction such as symmetry of ring systems and destabilization of electron pairs with respect to reference energy of -1/2 Eh. Comparisons are based on three chemical interpretations of Sinanoğlu's theory of structural covariance: (1) sets of structurally covariant quantum structural formulas, VIF, are interpreted as the same quantum operator represented in linearly related basis frames; (2) structurally covariant VIF pictures are interpreted as sets of molecular species with similar energy; and (3) the same VIF picture can be interpreted as different quantum operators, one-electron density or Hamiltonian; for example. According to these three interpretations, bond pair, lone pair, and free radical electrons understood in terms of a localized orbital representation are recognized as having energies above, below, or equal to a predetermined reference, frequently-1/2 Eh. The probable position of electron pairs and radical electrons is predicted. The selectivity of concerted ring closures in allyl anion and cation is described. Symmetries of conjugated ring systems are predicted according to their numbers of pi-electrons and spin-multiplicity. The pi-distortivity of benzene is predicted.The 3c/2e- H-bridging bonds in diborane are derived in a natural way according to the notion that the bridging bonds will have delocalizing interactions between them consistent with results of the NBO method. Key chemical bonding motifs are described using VIF. These include 2c/1e-, 2c/2e-, 2c/3e-, 3c/2e-, 3c/3e-,3c/4e-, 4n antiaromatic, and 4n+2 aromatic bonding systems. Some common organic functional groups are represented as VIF pictures and because these pictures can be interpreted simultaneously as one-electron density and Hamiltonian operators, the valence shell

  14. Evaluation of models for developing biological input for the design and location of water-intake structures

    SciTech Connect

    Simmons, M.A.; McKenzie, D.H.

    1981-12-01

    An approach for assessing multiple stimulus/response relations between fish and water intake structures is presented in this report. The approach stresses stimulus/response relations influencing fish and shellfish distribution and is made up of two methods. The first places emphasis on spatial and temperal distributions of populations; information is presented in the form of a non-predictive model, which allows for organizing information and documenting review processes. The second approach encompasses functional relationships between environmental and biological stimuli and responses of organisms. By using the two methods together, functional relationships can be evaluated to define the distribution of a fish or shellfish species. This information can then be used to resolve questions relating to impingement and entrainment.

  15. Quantitative structure-property relationships for predicting Henry's law constant from molecular structure.

    PubMed

    Dearden, John C; Schüürmann, Gerrit

    2003-08-01

    Various models are available for the prediction of Henry's law constant (H) or the air-water partition coefficient (Kaw), its dimensionless counterpart. Incremental methods are based on structural features such as atom types, bond types, and local structural environments; other regression models employ physicochemical properties, structural descriptors such as connectivity indices, and descriptors reflecting the electronic structure. There are also methods to calculate H from the ratio of vapor pressure (p(v)) and water solubility (S(w)) that in turn can be estimated from molecular structure, and quantum chemical continuum-solvation models to predict H via the solvation-free energy (deltaG(s)). This review is confined to methods that calculate H from molecular structure without experimental information and covers more than 40 methods published in the last 26 years. For a subset of eight incremental methods and four continuum-solvation models, a comparative analysis of their prediction performance is made using a test set of 700 compounds that includes a significant number of more complex and drug-like chemical structures. The results reveal substantial differences in the application range as well as in the prediction capability, a general decrease in prediction performance with decreasing H, and surprisingly large individual prediction errors, which are particularly striking for some quantum chemical schemes. The overall best-performing method appears to be the bond contribution method as implemented in the HENRYWIN software package, yielding a predictive squared correlation coefficient (q2) of 0.87 and a standard error of 1.03 log units for the test set.

  16. Crystal and molecular structure of the antimalarial agent enpiroline.

    PubMed Central

    Karle, J M; Karle, I L

    1989-01-01

    To identify common spatial and structural features of amino alcohol antimalarial agents with the eventual goal of designing more effective drugs and a better understanding of the mechanism of action of this class of antimalarial agents, the three-dimensional crystal and molecular structure of enpiroline, a new antimalarial agent active against chloroquine-resistant Plasmodium falciparum, was determined by X-ray crystallography and compared with the crystal structures of the cinchona alkaloids and of the new antimalarial agent WR 194,965. The aromatic rings of the phenyl-pyridine ring system of enpiroline are twisted from each other by approximately 18 degrees. The intramolecular aliphatic N-O distance in enpiroline was 2.80 A (1 A = 0.1 nm), which is close to the N-O distance found in the antimalarial cinchona alkaloids. Enpiroline contains both an intramolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms and an intermolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms of two neighboring molecules. One enantiomer of enpiroline superimposed best with quinine, and the other enantiomer of enpiroline superimposed best with quinidine, suggesting that both enantiomers of enpiroline possess antimalarial activity. Since a common feature of the crystal structures of the amino alcohol antimalarial agents is the formation of intermolecular hydrogen bonds, the common spatial direction of hydrogen bond formation indicates the potential ability of these antimalarial agents to bind to a common receptor site. The crystallographic parameters were as follows: C19H18F6N5O; Mr = 404.3; symmetry of unit cell, monoclinic; space group, P2(1)/a; parameters of unit cell---a = 9.454 +/- 0.004 A, b = 18.908 +/- 0.008 A, c = 10.300 +/- 0.004 A, and beta = 96.55 +/- 0.03 degrees: V (volume of unit cell) = 1829.2 A3; Z (number of molecules per unit cell) = 4; Dchi (calculated density) = 1.46 g cm-3; source of radiation, CuK alpha (lambda = 1.54178 A); mu

  17. Molecular Population Genetic Structure in the Piping Plover

    USGS Publications Warehouse

    Miller, Mark P.; Haig, Susan M.; Gratto-Trevor, Cheri L.; Mullins, Thomas D.

    2009-01-01

    The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect

  18. Pervasive small-scale structure in molecular clouds

    NASA Technical Reports Server (NTRS)

    Martin, B.; Lada, E.

    1986-01-01

    An unbiased CO survey of molecular cloud cores was completed, and the profiles were analyzed within the context of a model for emission from clumpy clouds. It was found that all sources observed contain a significant amount of structure that is not resolved with our 2.3-arcmin beam, and that the parameters which describe the degree of clumping span a remarkably narrow range of the possible values. We studied two separate samples of cloud cores: a large sample of warm cores from the Massachusetts-Stony Brook 12CO survey of the first galactic quadrant, and a sample of cool cores in the Taurus dark clouds chosen primarily on the basis of H2CO emission. We observed all sources in the 1-0 transition of 12CO and 13CO with the 5-m telescope of the Millimeter Wave Observatory. The 12CO/13CO ratios can be explained if there is unresolved structure giving rise to significant variations of opacity across the beam. Our model cloud consists of a large number of identical clumps distributed randomly in the beam. These clumps have velocity widths v small compared to the width of the observed profile, which is determined by the relative motion of the clumps. The entire cloud is isothermal and in local thermodynamic equilibrium. With these assumptions the intensity and linewidth ratios depend on three parameters: the abundance ratio; the peak 13CO opacity through a single clump, tau(0); and the average number of clumps on a line of sight N. Small tau(0) and large N correspond to the microturbulent limit, which is indistinguishable from a uniform gas distribution. In the other extreme, large tau(0) and snall N, at a given velocity at most one clump contributes to the profile on each line of sight. A figure is presented which shows the model parameters which reproduce the measured intensity and linewidth ratios for the sample of warm cores, assuming an abundance ratio of 75.

  19. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

    PubMed Central

    de Steenhuijsen Piters, Wouter A. A.

    2016-01-01

    ABSTRACT The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. PMID:26838716

  20. Automatic molecular structure perception for the universal force field.

    PubMed

    Artemova, Svetlana; Jaillet, Léonard; Redon, Stephane

    2016-05-15

    The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well-adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self-contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience (http://www.samson-connect.net). We validate both the automatic perception method and the UFF implementation on a series of benchmarks.

  1. Modeling Carbon and Hydrocarbon Molecular Structures in EZTB

    NASA Technical Reports Server (NTRS)

    Lee, Seungwon; vonAllmen, Paul

    2007-01-01

    A software module that models the electronic and mechanical aspects of hydrocarbon molecules and carbon molecular structures on the basis of first principles has been written for incorporation into, and execution within, the Easy (Modular) Tight-Binding (EZTB) software infrastructure, which is summarized briefly in the immediately preceding article. Of particular interest, this module can model carbon crystals and nanotubes characterized by various coordinates and containing defects, without need to adjust parameters of the physical model. The module has been used to study the changes in electronic properties of carbon nanotubes, caused by bending of the nanotubes, for potential utility as the basis of a nonvolatile, electriccharge- free memory devices. For example, in one application of the module, it was found that an initially 50-nmlong carbon, (10,10)-chirality nanotube, which is a metallic conductor when straight, becomes a semiconductor with an energy gap of .3 meV when bent to a lateral displacement of 4 nm at the middle.

  2. Death Associated Protein Kinases: Molecular Structure and Brain Injury

    PubMed Central

    Nair, Syam; Hagberg, Henrik; Krishnamurthy, Rajanikant; Thornton, Claire; Mallard, Carina

    2013-01-01

    Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk) family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1. PMID:23880846

  3. Death associated protein kinases: molecular structure and brain injury.

    PubMed

    Nair, Syam; Hagberg, Henrik; Krishnamurthy, Rajanikant; Thornton, Claire; Mallard, Carina

    2013-07-04

    Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk) family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1.

  4. Molecular structures of fructans from Agave tequilana Weber var. azul.

    PubMed

    Lopez, Mercedes G; Mancilla-Margalli, Norma A; Mendoza-Diaz, Guillermo

    2003-12-31

    Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought.

  5. Structural basis for the antifolding activity of a molecular chaperone

    PubMed Central

    Huang, Chengdong; Rossi, Paolo; Saio, Tomohide; Kalodimos, Charalampos G.

    2016-01-01

    Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase (PhoA) and maltose binding protein (MBP) captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of the non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone. PMID:27501151

  6. Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution

    SciTech Connect

    Franca, Eduardo D.; Lins, Roberto D.; Freitas, Luiz C.; Straatsma, t. P.

    2008-11-08

    Molecular dynamics simulations have been used to characterize the structure of chitin and chitosan fibers in aqueous solutions. Chitin fibers, whether isolated or in the form of a β-chitin nanoparticle, adopt the so-called 2-fold helix with Φ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)•••O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)•••O5(n+1) hydrogen bond, which is affect by the water exchange around the O3-HO3 hydroxyl group.

  7. The Influence of Molecular Cooling in Pregalactic Structure Formation

    NASA Astrophysics Data System (ADS)

    Stancil, P. C.; Abel, T.; Lepp, S.; Dalgarno, A.

    1999-12-01

    The detailed chemistry and cooling in collapsing primordial clouds will be presented for total baryonic densities up to 106 cm-3. The model consists of 160 reactions of 23 species including H2, HD, HeH+, and LiH, and accounts for 8 different cooling and heating mechanisms. The hydrodynamic evolution of the gas is modeled under the assumptions of free-fall, isothermal, and isobaric collapse as well as for the central regions of 105 M⊙ objects in hierarchical scenarios. The latter being drawn from three-dimensional cosmological hydrodynamical simulations. The dominant processes in the reaction network are identified and a minimal model that accurately predicts the full chemistry will be presented. It is found that radiative cooling due to collisional excitation of HD can lower the temperature in a primordial cloud below that reachable through H2 cooling alone. Further, the temperature evolution is influenced by the choice of the adopted H2 radiative cooling function. Implications for globular cluster and primordial star formation, as well as structure formation on small scales and the importance of molecular cooling in general will be discussed. The work of P.C.S. was supported by the DoE ORNL LDRD Seed Money Fund. T.A. acknowledges support from NSF Grant ASC--9318185. The work of S.L. and A.D. was supported by NSF Cooperative Agreement OSR-9353227 and Astronomical Sciences Grant AST-93-01099, respectively.

  8. Structural basis for the antifolding activity of a molecular chaperone

    NASA Astrophysics Data System (ADS)

    Huang, Chengdong; Rossi, Paolo; Saio, Tomohide; Kalodimos, Charalampos G.

    2016-09-01

    Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase and maltose-binding protein captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone.

  9. Investigating molecular structures: Rapidly examining molecular fingerprints through fast passage broadband fourier transform microwave spectroscopy

    NASA Astrophysics Data System (ADS)

    Grubbs, Garry Smith Smitty, II

    Microwave spectroscopy is a gas phase technique typically geared toward measuring the rotational transitions of molecules. The information contained in this type of spectroscopy pertains to a molecules structure, both geometric and electronic, which give insight into a molecule's chemistry. Typically this type of spectroscopy is high resolution, but narrowband ≤1 MHz in frequency. This is achieved by tuning a cavity, exciting a molecule with electromagnetic radiation in the microwave region, turning the electromagnetic radiation off, and measuring a signal from the molecular relaxation in the form of a free induction decay (FID). The FID is then Fourier transformed to give a frequency of the transition. "Fast passage" is defined as a sweeping of frequencies through a transition at a time much shorter (≤10 mus) than the molecular relaxation (≈100 mus). Recent advancements in technology have allowed for the creation of these fast frequency sweeps, known as "chirps", which allow for broadband capabilities. This work presents the design, construction, and implementation of one such novel, high-resolution microwave spectrometer with broadband capabilities. The manuscript also provides the theory, technique, and motivations behind building of such an instrument. In this manuscript it is demonstrated that, although a gas phase technique, solids, liquids, and transient species may be studied with the spectrometer with high sensitivity, making it a viable option for many molecules wanting to be rotationally studied. The spectrometer has a relative correct intensity feature that, when coupled with theory, may ease the difficulty in transition assignment and facilitate dynamic chemical studies of the experiment. Molecules studied on this spectrometer have, in turn, been analyzed and assigned using common rotational spectroscopic analysis. Detailed theory on the analysis of these molecules has been provided. Structural parameters such as rotational constants and

  10. Chemical input multiplicity facilitates arithmetical processing.

    PubMed

    Margulies, David; Melman, Galina; Felder, Clifford E; Arad-Yellin, Rina; Shanzer, Abraham

    2004-12-01

    We describe the design and function of a molecular logic system, by which a combinatorial recognition of the input signals is utilized to efficiently process chemically encoded information. Each chemical input can target simultaneously multiple domains on the same molecular platform, resulting in a unique combination of chemical states, each with its characteristic fluorescence output. Simple alteration of the input reagents changes the emitted logic pattern and enables it to perform different algebraic operations between two bits, solely in the fluorescence mode. This system exhibits parallelism in both its chemical inputs and light outputs.

  11. A Structural and Molecular Approach for the Study Biomarkers

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  12. How Molecular Structure Affects Mechanical Properties of an Advanced Polymer

    NASA Technical Reports Server (NTRS)

    Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.; Hinkley, Jeffrey A.

    2000-01-01

    density was performed over a range of temperatures below the glass transition temperature. The physical characterization, elastic properties and notched tensile strength all as a function of molecular weight and test temperature were determined. For the uncrosslinked SI material, it was shown that notched tensile strength is a strong function of both temperature and molecular weight, whereas stiffness is only a strong function of temperature. For the crosslinked PETI-SI material, it was shown that the effect of crosslinking significantly enhances the mechanical performance of the low molecular weight material; comparable to that exhibited by the high molecular weight material.

  13. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    SciTech Connect

    Nagaoka, Masataka

    2015-12-31

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  14. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    NASA Astrophysics Data System (ADS)

    Nagaoka, Masataka

    2015-12-01

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical `atomistic' molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  15. Fast metabolite identification with Input Output Kernel Regression

    PubMed Central

    Brouard, Céline; Shen, Huibin; Dührkop, Kai; d'Alché-Buc, Florence; Böcker, Sebastian; Rousu, Juho

    2016-01-01

    Motivation: An important problematic of metabolomics is to identify metabolites using tandem mass spectrometry data. Machine learning methods have been proposed recently to solve this problem by predicting molecular fingerprint vectors and matching these fingerprints against existing molecular structure databases. In this work we propose to address the metabolite identification problem using a structured output prediction approach. This type of approach is not limited to vector output space and can handle structured output space such as the molecule space. Results: We use the Input Output Kernel Regression method to learn the mapping between tandem mass spectra and molecular structures. The principle of this method is to encode the similarities in the input (spectra) space and the similarities in the output (molecule) space using two kernel functions. This method approximates the spectra-molecule mapping in two phases. The first phase corresponds to a regression problem from the input space to the feature space associated to the output kernel. The second phase is a preimage problem, consisting in mapping back the predicted output feature vectors to the molecule space. We show that our approach achieves state-of-the-art accuracy in metabolite identification. Moreover, our method has the advantage of decreasing the running times for the training step and the test step by several orders of magnitude over the preceding methods. Availability and implementation: Contact: celine.brouard@aalto.fi Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307628

  16. A Structural and Molecular Approach for the Study Biomarkers

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  17. Habitat management affects soil chemistry and allochthonous organic inputs mediating microbial structure and exo-enzyme activity in Wadden Sea salt-marsh soils

    NASA Astrophysics Data System (ADS)

    Mueller, Peter; Granse, Dirk; Thi Do, Hai; Weingartner, Magdalena; Nolte, Stefanie; Hoth, Stefan; Jensen, Kai

    2016-04-01

    The Wadden Sea (WS) region is Europe's largest wetland and home to approximately 20% of its salt marsh area. Mainland salt marshes of the WS are anthropogenically influenced systems and have traditionally been used for livestock grazing in wide parts. After foundation of WS National Parks in the late 1980s and early 1990s, artificial drainage has been abandoned; however, livestock grazing is still common in many areas of the National Parks and is under ongoing discussion as a habitat-management practice. While studies so far focused on effects of livestock grazing on biodiversity, little is known about how biogeochemical processes, element cycling, and particularly carbon sequestration are affected. Here, we present data from a recent field study focusing on grazing effects on soil properties, microbial exo-enzyme activity, microbial abundance and structure. Exo-enzyme activity was studied conducting digestive enzyme assays for various enzymes involved in C- and N cycling. Microbial abundance and structure was assessed measuring specific gene abundance of fungi and bacteria using quantitative PCR. Soil compaction induced by grazing led to higher bulk density and decreases in soil redox (∆ >100 mV). Soil pH was significantly lower in grazed parts. Further, the proportion of allochthonous organic matter (marine input) was significantly smaller in grazed vs. ungrazed sites, likely caused by a higher sediment trapping capacity of the taller vegetation in the ungrazed sites. Grazing induced changes in bulk density, pH and redox resulted in reduced activity of enzymes involved in microbial C acquisition; however, there was no grazing effect on enzymes involved in N acquisition. While changes in pH, bulk density or redox did not affect microbial abundance and structure, the relative amount of marine organic matter significantly reduced the relative abundance of fungi (F:B ratio). We conclude that livestock grazing directly affects microbial exo-enzyme activity, thus

  18. Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development.

    PubMed

    Chen, Zhen; Wilmanns, Matthias; Zeng, An-Ping

    2010-10-01

    The future of industrial biotechnology requires efficient development of highly productive and robust strains of microorganisms. Present praxis of strain development cannot adequately fulfill this requirement, primarily owing to the inability to control reactions precisely at a molecular level, or to predict reliably the behavior of cells upon perturbation. Recent developments in two areas of biology are changing the situation rapidly: structural biology has revealed details about enzymes and associated bioreactions at an atomic level; and synthetic biology has provided tools to design and assemble precisely controllable modules for re-programming cellular metabolic circuitry. However, because of different emphases, to date, these two areas have developed separately. A linkage between them is desirable to harness their concerted potential. We therefore propose structural synthetic biotechnology as a new field in biotechnology, specifically for application to the development of industrial microbial strains.

  19. Sensitivity of simulated global-scale freshwater fluxes and storages to input data, hydrological model structure, human water use and calibration

    NASA Astrophysics Data System (ADS)

    Müller Schmied, H.; Eisner, S.; Franz, D.; Wattenbach, M.; Portmann, F. T.; Flörke, M.; Döll, P.

    2014-09-01

    Global-scale assessments of freshwater fluxes and storages by hydrological models under historic climate conditions are subject to a variety of uncertainties. Using the global hydrological model WaterGAP (Water - Global Assessment and Prognosis) 2.2, we investigated the sensitivity of simulated freshwater fluxes and water storage variations to five major sources of uncertainty: climate forcing, land cover input, model structure/refinements, consideration of human water use and calibration (or no calibration) against observed mean river discharge. In a modeling experiment, five variants of the standard version of WaterGAP 2.2 were generated that differed from the standard version only regarding the investigated source of uncertainty. The basin-specific calibration approach for WaterGAP was found to have the largest effect on grid cell fluxes as well as on global AET (actual evapotranspiration) and discharge into oceans for the period 1971-2000. Regarding grid cell fluxes, climate forcing ranks second before land cover input. Global water storage trends are most sensitive to model refinements (mainly modeling of groundwater depletion) and consideration of human water use. The best fit to observed time series of monthly river discharge or discharge seasonality is obtained with the standard WaterGAP 2.2 model version which is calibrated and driven by daily reanalysis-based WFD/WFDEI (combination of Watch Forcing Data based on ERA40 and Watch Forcing Data based on ERA-Interim) climate data. Discharge computed by a calibrated model version using monthly CRU TS (Climate Research Unit time-series) 3.2 and GPCC (Global Precipitation Climatology Center) v6 climate input reduced the fit to observed discharge for most stations. Taking into account uncertainties of climate and land cover data, global 1971-2000 discharge into oceans and inland sinks ranges between 40 000 and 42 000 km3 yr-1. Global actual evapotranspiration, with 70 000 km3 yr-1, is rather unaffected by climate

  20. Chemical biology at the crossroads of molecular structure and mechanism.

    PubMed

    Doudna, Jennifer A

    2005-11-01

    Chemical insight into biological function is the holy grail of structural biology. Small molecules are central players as building blocks, effectors and probes of macromolecular structure and function.

  1. Determination of the experimental equilibrium structure of solid nitromethane using path-integral molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Reilly, Anthony M.; Habershon, Scott; Morrison, Carole A.; Rankin, David W. H.

    2010-03-01

    Path-integral molecular dynamics (PIMD) simulations with an empirical interaction potential have been used to determine the experimental equilibrium structure of solid nitromethane at 4.2 and 15 K. By comparing the time-averaged molecular structure determined in a PIMD simulation to the calculated minimum-energy (zero-temperature) molecular structure, we have derived structural corrections that describe the effects of thermal motion. These corrections were subsequently used to determine the equilibrium structure of nitromethane from the experimental time-averaged structure. We find that the corrections to the intramolecular and intermolecular bond distances, as well as to the torsion angles, are quite significant, particularly for those atoms participating in the anharmonic motion of the methyl group. Our results demonstrate that simple harmonic models of thermal motion may not be sufficiently accurate, even at low temperatures, while molecular simulations employing more realistic potential-energy surfaces can provide important insight into the role and magnitude of anharmonic atomic motions.

  2. Effect of valence of lanthanide ion and molecular symmetry in polyoxotungstoborate on the molecular structure and spectrochemical properties

    NASA Astrophysics Data System (ADS)

    Iijima, Jun; Naruke, Haruo

    2017-01-01

    The compound K9(NH4)H[CeIV(α-BW11O39)(W5O18)]·16H2O (1) was successfully isolated and structurally characterized. The structural investigation revealed that 1 displayed a less molecular distortion, whereas Ln3+-analogs exhibited a large molecular distortion. IR spectroscopy demonstrated that the spectral patterns of 1 and Ce3+-analog were depending on each valence of Ce (IV/III). 11B-NMR spectroscopy showed that a decrease in site symmetry of B atom in the polyoxotungstoborate was related with an increase in a half width of NMR peak. There is a difference in molecular distortion between 1 and Ce3+-analog, but they have similar large half widths because of the same site symmetry of B atom. The 4f electron in Ce atom exhibited less effect on the chemical shift.

  3. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    SciTech Connect

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  4. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.

    PubMed

    Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-01

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  5. Designing π-stacked molecular structures to control heat transport through molecular junctions

    SciTech Connect

    Kiršanskas, Gediminas; Li, Qian; Solomon, Gemma C.; Flensberg, Karsten; Leijnse, Martin

    2014-12-08

    We propose and analyze a way of using π stacking to design molecular junctions that either enhance or suppress a phononic heat current, but at the same time remain conductors for an electric current. Such functionality is highly desirable in thermoelectric energy converters, as well as in other electronic components where heat dissipation should be minimized or maximized. We suggest a molecular design consisting of two masses coupled to each other with one mass coupled to each lead. By having a small coupling (spring constant) between the masses, it is possible to either reduce or perhaps more surprisingly enhance the phonon conductance. We investigate a simple model system to identify optimal parameter regimes and then use first principle calculations to extract model parameters for a number of specific molecular realizations, confirming that our proposal can indeed be realized using standard molecular building blocks.

  6. Multi-molecular markers and metals as tracers of organic matter inputs and contamination status from an Environmental Protection Area in the SW Atlantic (Laranjeiras Bay, Brazil).

    PubMed

    Martins, César C; Bícego, Marcia C; Figueira, Rubens C L; Angelli, José Lourenço F; Combi, Tatiane; Gallice, Wellington C; Mansur, Andressa V; Nardes, Emanoela; Rocha, Marília L; Wisnieski, Edna; Ceschim, Liziane M M; Ribeiro, Andreza P

    2012-02-15

    The sources and concentrations of aliphatic hydrocarbons (AHs) and polycyclic aromatic hydrocarbons (PAHs), faecal and biogenic sterols, and trace metals at 10 sampling sites located in Laranjeiras Bay, a large Environmental Protection Area in the southern Atlantic region of Brazil, were determined to assess the sources of organic matter and the contamination status of estuarine sediments. Organic compounds were determined by GC-FID and GC-MS, and ICP-OES was used to evaluate trace metals. The total AHs concentration ranged from 0.28 to 8.19 μg g(-1), and n-C(29) and n-C(31) alkanes were predominant, indicating significant inputs from higher terrestrial plants. Unresolved complex mixtures (UCM) were not detected at any site, suggesting that the study area was not significantly contaminated by fossil fuels. The total PAH concentration varied from 3.85 to 89.2 ng g(-1). The ratio between selected PAH isomers showed that combustion of biomass, coal, and petroleum is the main source of PAHs in the study area. The concentrations of the faecal sterols coprostanol and epicoprostanol were below the detection limits, suggesting that sewage was not a significant contributor to sedimentary organic matter. The concentrations of the trace metals (As, Cr, Cu, Ni, Pb and Zn) were low, except near sites located at the mouths of rivers that discharge into the study area and near urbanised regions (Paranaguá city and the adjoining harbour). In general, the concentrations of PAHs were below the threshold effect concentrations (TEL) levels. Although the As, Cr and Ni concentrations were above the TEL levels, the study area can be considered as preserved from human activities.

  7. Molecular structure of amino alcohols on aluminum surface

    NASA Astrophysics Data System (ADS)

    Masoud, M. S.; Awad, M. K.; Ali, Alaa E.; El-Tahawy, M. M. T.

    2014-04-01

    Quantum chemical calculations were applied on monoethanolamine (MEA), diethanolamine (DEA) and triethanolamine (TEA) as corrosion inhibitors for aluminum exterior using ab initio Møller-Plesset (MP2) and Density Function Theory (DFT-B3LYP) at 6-311++G(d,p) ground set. Quantum chemical parameters such as the maximum employed molecular orbital energy (EHOMO), the minimum unemployed molecular orbital energy (ELUMO), energy disparity (ΔE), dipole moment (μ), sum of the total negative charge (TNC), molecular volume (MV), electronegativity (χ), chemical potential (Pi), global hardness (η), softness (σ) and the fraction of electrons transferred (ΔN), were calculated. Further calculations were done to explore the effects of inhibitors and solvent. Furthermore, the inhibitors’ interactions with the metal exterior were studied by applying COMPASS method. R2 values showed good correlations between the corrosion inhibitors’ effectiveness and several quantum parameters.

  8. The Link between Fluid Flow, Structure and Hydrothermal Inputs in Central Chile: An Interdisciplinary Approach for Low-Enthalpy Andean Hydrogeothermal Modeling

    NASA Astrophysics Data System (ADS)

    Arancibia, G.; Daniele, L.; Navarro, L.; Astudillo, F.; Vázquez, M.; Morata, D.

    2014-12-01

    The interaction between fault zones and hydrogeological domains are an open challenge and require the understanding of the complex relationship between structure, fluid flow and hydrothermal transport and processes. Faults stimulate hydraulic conductivity when acting as conduit, but it can also be a barrier by mineral precipitation and comminution. Structural heterogeneity of fractured lithology induces a flow partition within the aquifer system creating preferential flows paths and some fracture connectivity. We propose an interdisciplinary approach from hydrogeological and structural point of view, in a low-enthalpy aquifer system in the central valley of Central Chile, where several low-temperature thermal springs are spatially related to regional long-lived fault zone (Pocuro Fault Zone). Pocuro Fault zone is a kilometric NS-striking steeply dipping fault zone, with at least 50 km long. Metric wide fault core includes gouge and cataclastic rocks, whereas decametric damage zone consists of intensely fractured and hydrothermal altered Meso-Cenozoic volcanic and volcaniclastic host rocks, crossed by centimetric to milimetric subvertical NE-striking veins. Preliminary results of vein infill clays minerals and zeolites from damage zone, suggest P-T conditions interpreted as an exhumed fossil high-temperature (120º-230ºC) geothermal system. Currently, only low-temperature thermal springs are discharging with different geochemical patterns (bicarbonate to chlorine and sulphate dominant ions) and a homogeneous temperature range (20º-25ºC). This is an interesting study case, to better understand the permeability evolution of geothermal system and the link between internal fault architecture, hydrogeology and hydrothermal inputs.

  9. Molecular analysis of neocortical layer structure in the ferret

    PubMed Central

    Rowell, Joanna J.; Mallik, Atul K.; Dugas-Ford, Jennifer; Ragsdale, Clifton W.

    2010-01-01

    Molecular markers that distinguish specific layers of rodent neocortex are increasingly employed to study cortical development and the physiology of cortical circuits. The extent to which these markers represent general features of neocortical cell type identity across mammals is, however, unknown. To assess the conservation of layer markers more broadly, we isolated orthologs for fifteen layer-enriched genes in the ferret, a carnivore with a large, gyrencephalic brain, and analyzed their patterns of neocortical gene expression. Our major findings are: (1) Many but not all layer markers tested show similar patterns of layer-specific gene expression between mouse and ferret cortex, supporting the view that layer-specific cell type identity is conserved at a molecular level across mammalian superorders; (2) Our panel of deep layer markers (ER81/ETV1, SULF2, PCP4, FEZF2/ZNF312, CACNA1H, KCNN2/SK2, SYT6, FOXP2, CTGF) provides molecular evidence that the specific stratifications of layer 5 and 6 into 5a, 5b, 6a and 6b are also conserved between rodents and carnivores. (3) Variations in layer-specific gene expression are more pronounced across areas of ferret cortex than between homologous areas of mouse and ferret cortex; (4) This variation of area gene expression was clearest with the superficial layer markers studied (SERPINE2, MDGA1, CUX1, UNC5D, RORB/NR1F2, EAG2/KCNH5). Most dramatically, the layer 4 markers RORB and EAG2 disclosed a molecular sublamination to ferret visual cortex and demonstrated a molecular dissociation among the so-called agranular areas of the neocortex. Our findings establish molecular markers as a powerful complement to cytoarchitecture for neocortical layer and cell-type comparisons across mammals. PMID:20575059

  10. Attosecond time-resolved imaging of molecular structure by photoelectron holography.

    PubMed

    Bian, Xue-Bin; Bandrauk, André D

    2012-06-29

    Dynamic imaging of the molecular structure of H(2)(+) is investigated by attosecond photoelectron holography. The interference between direct (reference) and backward rescattered (signal) photoelectrons in attosecond photoelectron holography reveals the birth time of both channels and the spatial information of molecular structure. This is confirmed by simulations with a semiclassical model and numerical solutions of the corresponding time-dependent Schrödinger equation, suggesting an attosecond time-resolved way of imaging molecular structure obtained from laser induced rescattering of ionized electrons. It is shown that both short and long rescattered electron trajectories can be imaged from the momentum distribution.

  11. An estimation of the input conductivity characteristic of some resistive (percolation) structures composed of elements having a two-term polynomial characteristic

    NASA Astrophysics Data System (ADS)

    Gluskin, Emanuel

    2007-07-01

    A specific circuit connection is suggested for the calculation of the input conductivity (current caused by voltage) characteristic i in= F( v in) of a 1-port named “ f-circuit”, composed of similar conductors described by conductive characteristic of the type f( v)= D mv m+D nv n. It is assumed that such circuit models can be relevant to the theory of percolation structures [S.W. Kenkel, J.P. Straley, Percolation theory of nonlinear circuit elements, Phys. Rev. Lett. 49(11)(1982)767-770; J.P. Straley, S.W. Kenkel, Percolation theory for nonlinear conductors, Phys. Rev. B 29(11)(1984)6299-6305; R. Rammal, A.-M.S. Trembley, Resistance noise in nonlinear resistor networks, Phys. Rev. Lett. 58(4)(1987)415-418; Ch.P. Hatsell, A quasi-power theorem for bulk conductors: comments on Rheoencephalography, IEEE Trans. Biomed. Eng. 38(7)(1991)665-669; L. Venkataraman, Y.S. Hong, P. Kim, Electron transport in a multichannel one-dimensional conductor: molybdenum selenide nanowires, Phys. Rev. Lett 96(076601)(2006)076601-1-076601-4; A.A. Snarskii, K.V. Slipchenko, A.A. Sevryukov, Critical behavior in two-phase, highly inhomogeneous composites, J. Exp. Theor. Phy. 89(4)(1999)788-799; A.A. Snarskii, M. Zhenirovskiy, Effective conductivity of non-linear composites, Physica B 322(2002)84-91], in a state not far from the percolation threshold, even though the main result seems to be sufficiently interesting by itself and one can expect that other interesting applications for such conductive structures will be found. The f-circuit is constructed here from two power-law “ α-circuits”, f( v)∼ vα, of the same topology [E. Gluskin, One-ports composed of power-law resistors, IEEE Trans. CAS-II 51(9)(2004)464-467], but having different α. In this construction, named “ f-connection”, the respective nodes of the α-circuits are short-circuited, and the respective branches become connected in parallel, which causes f(.) to be an additive function; thus f( v)= D mv m+D nv n is

  12. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    NASA Astrophysics Data System (ADS)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  13. An integrated evaluation of molecular marker indices and linear alkylbenzenes (LABs) to measure sewage input in a subtropical estuary (Babitonga Bay, Brazil).

    PubMed

    Martins, César C; Cabral, Ana Caroline; Barbosa-Cintra, Scheyla C T; Dauner, Ana Lúcia L; Souza, Fernanda M

    2014-05-01

    Babitonga Bay is a South Atlantic estuary with significant ecological function; it is part of the last remaining areas of mangrove communities in the Southern Hemisphere. The aim of this study was to determine the spatial distribution of the faecal sterols and linear alkylbenzenes (LABs) in surface sediments and to perform an integrated evaluation of several molecular marker indices to assess the sewage contamination status in the study area. The highest observed concentrations of faecal sterols (coprostanol + epicoprostanol) and LABs were 6.65 μg g(-1) and 413.3 ng g(-1), respectively. Several faecal sterol indices were calculated and correlated with coprostanol levels; these analyses showed that the index limits presented in the current literature could underestimate the sewage contamination in this study area. For the overall estuarine system, a low sewage impact may be assumed based on the low total mass inventories calculated for coprostanol (between 1.4% and 4.8%).

  14. Molecular and crystal structures of noble gas compounds

    NASA Astrophysics Data System (ADS)

    Nabiev, Sh Sh; Sokolov (deceased, V. B.; Chaivanov, B. B.

    2014-12-01

    Data on the structures of xenon and krypton compounds in various physical states are analyzed and generalized. The structures of simple, coordination, polymeric and clathrate-like compounds of these elements with various types of bonds are considered. Characteristic features of their vibrational spectra are discussed in relation to structural transformations caused by cation-anion interactions, structurally non-rigid intramolecular rearrangements and other factors. The bibliography includes 332 references.

  15. Supersonic turbulence and structure of interstellar molecular clouds.

    PubMed

    Boldyrev, Stanislav; Nordlund, Ake; Padoan, Paolo

    2002-07-15

    The interstellar medium provides a unique laboratory for highly supersonic, driven hydrodynamic turbulence. We propose a theory of such turbulence, test it by numerical simulations, and use the results to explain observational scaling properties of interstellar molecular clouds, the regions where stars are born.

  16. Molecular structure of the number 21 chromosome and Down syndrome

    SciTech Connect

    Smith, G.F.

    1985-01-01

    This book contains 19 papers. Some of the titles are: The Biology of Down Syndrome, Human Chromosome Analysis, Expression of Genes on Human Chromosome 21, Comparative Gene Mapping of Human Chromosome 21 and Mouse Chromosome 16, and Relating Molecular Specificity to Normal and Abnormal Brain Development.

  17. Study on molecular structural characteristics of tea polysaccharide.

    PubMed

    Guo, Li; Du, Xianfeng; Lan, Jing; Liang, Qin

    2010-08-01

    Tea polysaccharide (TPS) is attracting more attention gradually due to its particular biological properties. However, molecular characteristics of TPS are unclear since appropriate method is still absent. So, study on the molecular characteristics of TPS was carried out by high-performance size-exclusion chromatography (HPSEC), multi-angle laser light scattering (MALLS) and viscosimetry. The results showed that the molar masses of TPS ranged from 2.287 x 10(5) to 2.762 x 10(5)gmol(-1), the RMS radii distributed from 132.1 to 145.9 nm, and M(w)/M(n) is 1.028. The Mark-Houwink equation was established as [eta]=0.5423 M(w)(0.5379), and the intrinsic viscosity and molecular chain parameters were as follows: [eta]=1.007 dL g(-1), k(H)=0.845, k(K)=0.387, alpha=0.5379, K=0.5423. In addition, based on the slope of the RMS radius versus molar mass conformational plot being 0.24+/-0.00, we suggest that the molecular morphology of TPS is a homogeneous and spherical polymer with branch in solution.

  18. Structural properties and interaction energies affecting drug design. An approach combining molecular simulations, statistics, interaction energies and neural networks.

    PubMed

    Ioannidis, Dimitris; Papadopoulos, Georgios E; Anastassopoulos, Georgios; Kortsaris, Alexandros; Anagnostopoulos, Konstantinos

    2015-06-01

    In order to elucidate some basic principles for protein-ligand interactions, a subset of 87 structures of human proteins with their ligands was obtained from the PDB databank. After a short molecular dynamics simulation (to ensure structure stability), a variety of interaction energies and structural parameters were extracted. Linear regression was performed to determine which of these parameters have a potentially significant contribution to the protein-ligand interaction. The parameters exhibiting relatively high correlation coefficients were selected. Important factors seem to be the number of ligand atoms, the ratio of N, O and S atoms to total ligand atoms, the hydrophobic/polar aminoacid ratio and the ratio of cavity size to the sum of ligand plus water atoms in the cavity. An important factor also seems to be the immobile water molecules in the cavity. Nine of these parameters were used as known inputs to train a neural network in the prediction of seven other. Eight structures were left out of the training to test the quality of the predictions. After optimization of the neural network, the predictions were fairly accurate given the relatively small number of structures, especially in the prediction of the number of nitrogen and sulfur atoms of the ligand.

  19. Direction-of-arrival estimation for co-located multiple-input multiple-output radar using structural sparsity Bayesian learning

    NASA Astrophysics Data System (ADS)

    Wen, Fang-Qing; Zhang, Gong; Ben, De

    2015-11-01

    This paper addresses the direction of arrival (DOA) estimation problem for the co-located multiple-input multiple-output (MIMO) radar with random arrays. The spatially distributed sparsity of the targets in the background makes compressive sensing (CS) desirable for DOA estimation. A spatial CS framework is presented, which links the DOA estimation problem to support recovery from a known over-complete dictionary. A modified statistical model is developed to accurately represent the intra-block correlation of the received signal. A structural sparsity Bayesian learning algorithm is proposed for the sparse recovery problem. The proposed algorithm, which exploits intra-signal correlation, is capable being applied to limited data support and low signal-to-noise ratio (SNR) scene. Furthermore, the proposed algorithm has less computation load compared to the classical Bayesian algorithm. Simulation results show that the proposed algorithm has a more accurate DOA estimation than the traditional multiple signal classification (MUSIC) algorithm and other CS recovery algorithms. Project supported by the National Natural Science Foundation of China (Grant Nos. 61071163, 61271327, and 61471191), the Funding for Outstanding Doctoral Dissertation in Nanjing University of Aeronautics and Astronautics, China (Grant No. BCXJ14-08), the Funding of Innovation Program for Graduate Education of Jiangsu Province, China (Grant No. KYLX 0277), the Fundamental Research Funds for the Central Universities, China (Grant No. 3082015NP2015504), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PADA), China.

  20. [Cajal bodies and histone locus bodies: molecular structure and function].

    PubMed

    Khodiuchenko, T A; Krasikova, A V

    2014-01-01

    The review provides modern classification of evolutionarily conserved coilin-containing nuclear bodies of somatic and germ cells that is based on the characteristic features of their molecular composition and the nature of their functions. The main differences between Cajal bodies and histone locus bodies, which are involved in the biogenesis of small nuclear spliceosomal and nucleolar RNAs and in the 3'-end processing of histone precursor messenger RNA, respectively, are considered. It is shown that a significant contribution to the investigation of the diversity of coilin-containing bodies was made by the studies on the architecture of the RNA processing machinery in oocyte nuclei in a number of model organisms. The characteristics features of the molecular composition of coilin-containing bodies in the nuclei of growing oocytes (the so-called germinal vesicles) of vertebrates, including amphibians and birds, are described.

  1. Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations.

    PubMed

    Fang, Jiansong; Pang, Xiaocong; Wu, Ping; Yan, Rong; Gao, Li; Li, Chao; Lian, Wenwen; Wang, Qi; Liu, Ai-lin; Du, Guan-hua

    2016-05-01

    A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2)) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives.

  2. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    SciTech Connect

    Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J.

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  3. [Structural and molecular origin of information recording/reading].

    PubMed

    Kuzurman, P A; Arkhipova, G V

    2002-01-01

    On the basis of experimental data on the thermoinduced state of water dispersions of natural and synthetic phospholipids in the presence of nootropic agents, a new phenomenological molecular mechanism of information recording/reading was proposed. The mechanism is based on the polymorphism of membrane lipids. A new approach, to the problem of memory was suggested, which considers memory as an information data bank and separates this concept from the concept of the mechanisms of information recording/reading.

  4. MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

    EPA Science Inventory

    Abstract
    One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

  5. ONTOGENETIC ALTERATIONS IN MOLECULAR AND STRUCTURAL CORRELATES OF DENDRITIC GROWTH FOLLOWING DEVELOPMENTAL EXPOSURE TO POLYCHLORINATED BIPHENYLS.

    EPA Science Inventory

    This is the first report showing both molecular and structural changes in brain following developmental exposure to a neurotoxicant. It is known that perinatal exposure to a neurotoxicant, polychlorinated biphenyls (PCBs), is associated with decreased IQ scores, impaired learnin...

  6. Ultra-low-molecular-weight heparins: precise structural features impacting specific anticoagulant activities.

    PubMed

    Lima, Marcelo A; Viskov, Christian; Herman, Frederic; Gray, Angel L; de Farias, Eduardo H C; Cavalheiro, Renan P; Sassaki, Guilherme L; Hoppensteadt, Debra; Fareed, Jawed; Nader, Helena B

    2013-03-01

    Ultra-low-molecular-weight heparins (ULMWHs) with better efficacy and safety ratios are under development; however, there are few structural data available. The main structural features and molecular weight of ULMWHs were studied and compared to enoxaparin. Their monosaccharide composition and average molecular weights were determined and preparations studied by nuclear magnetic resonance spectroscopy, scanning ultraviolet spectroscopy, circular dichroism and gel permeation chromatography. In general, ULMWHs presented higher 3-O-sulphated glucosamine and unsaturated uronic acid residues, the latter being comparable with their higher degree of depolymerisation. The analysis showed that ULMWHs are structurally related to LMWHs; however, their monosaccharide/oligosaccharide compositions and average molecular weights differed considerably explaining their different anticoagulant activities. The results relate structural features to activity, assisting the development of new and improved therapeutic agents, based on depolymerised heparin, for the prophylaxis and treatment of thrombotic disorders.

  7. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    EPA Science Inventory

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  8. Molecular structures and functional relationships in clostridial neurotoxins.

    PubMed

    Swaminathan, Subramanyam

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.

  9. Molecular Structures and Functional Relationships in Clostridial Neurotoxins

    SciTech Connect

    Swaminathan S.

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.

  10. Molecular Structure and Transport Dynamics in Perfluoro Sulfonyl Imide Membranes

    SciTech Connect

    Idupulapati, Nagesh B.; Devanathan, Ramaswami; Dupuis, Michel

    2011-05-25

    We report a detailed and comprehensive analysis of the nanostructure, transport dynamics of water and hydronium and water percolation in hydrated perfluoro sulfonyl imides (PFSI), a polymer considered for proton transport in PEM fuel cells, using classical molecular dynamics simulations. The dynamical changes are related to the changes in the membrane nanostructure. Water network percolation threshold, the level at which a consistent spanning water network starts to develop in the membrane, lies between hydration level (λ) 6 and 7. The higher acidity of the sulfonyl imide acid group of PFSI compared to Nafion reported in our earlier ab initio study, translates into more free hydronium ions at low hydration levels. Nevertheless, the calculated diffusion coefficients of the H3O+ ions and H2O molecules as a function the hydration level were observed to be almost the same as that of Nafion, indicating similar conductivity and consistent with the experimental observations. This research was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory, a U.S. Department of Energy (DOE) national scientific user facility located at the Pacific Northwest National Laboratory (PNNL). This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  11. From electron microscopy to molecular cell biology, molecular genetics and structural biology: intracellular transport and kinesin superfamily proteins, KIFs: genes, structure, dynamics and functions.

    PubMed

    Hirokawa, Nobutaka

    2011-01-01

    Cells transport and sort various proteins and lipids following synthesis as distinct types of membranous organelles and protein complexes to the correct destination at appropriate velocities. This intracellular transport is fundamental for cell morphogenesis, survival and functioning not only in highly polarized neurons but also in all types of cells in general. By developing quick-freeze electron microscopy (EM), new filamentous structures associated with cytoskeletons are uncovered. The characterization of chemical structures and functions of these new filamentous structures led us to discover kinesin superfamily molecular motors, KIFs. In this review, I discuss the identification of these new structures and characterization of their functions using molecular cell biology and molecular genetics. KIFs not only play significant roles by transporting various cargoes along microtubule rails, but also play unexpected fundamental roles on various important physiological processes such as learning and memory, brain wiring, development of central nervous system and peripheral nervous system, activity-dependent neuronal survival, development of early embryo, left-right determination of our body and tumourigenesis. Furthermore, by combining single-molecule biophysics with structural biology such as cryo-electrom microscopy and X-ray crystallography, atomic structures of KIF1A motor protein of almost all states during ATP hydrolysis have been determined and a common mechanism of motility has been proposed. Thus, this type of studies could be a good example of really integrative multidisciplinary life science in the twenty-first century.

  12. Input-state approach to Boolean networks.

    PubMed

    Cheng, Daizhan

    2009-03-01

    This paper investigates the structure of Boolean networks via input-state structure. Using the algebraic form proposed by the author, the logic-based input-state dynamics of Boolean networks, called the Boolean control networks, is converted into an algebraic discrete-time dynamic system. Then the structure of cycles of Boolean control systems is obtained as compounded cycles. Using the obtained input-state description, the structure of Boolean networks is investigated, and their attractors are revealed as nested compounded cycles, called rolling gears. This structure explains why small cycles mainly decide the behaviors of cellular networks. Some illustrative examples are presented.

  13. VAMMPIRE: a matched molecular pairs database for structure-based drug design and optimization.

    PubMed

    Weber, Julia; Achenbach, Janosch; Moser, Daniel; Proschak, Ewgenij

    2013-06-27

    Structure-based optimization to improve the affinity of a lead compound is an established approach in drug discovery. Knowledge-based databases holding molecular replacements can be supportive in the optimization process. We introduce a strategy to relate the substitution effect within matched molecular pairs (MMPs) to the atom environment within the cocrystallized protein-ligand complex. Virtually Aligned Matched Molecular Pairs Including Receptor Environment (VAMMPIRE) database and the supplementary web interface ( http://vammpire.pharmchem.uni-frankfurt.de ) provide valuable information for structure-based lead optimization.

  14. Molecular structure of the coalescence of liquid interfaces

    NASA Technical Reports Server (NTRS)

    Koplik, Joel; Banavar, Jayanth R.

    1992-01-01

    When two bodies of liquid merge, their interfaces must also rupture and rearrange into one. Virtually no information is available concerning the small-scale dynamics of this process. Molecular dynamics simulations of coalescence in systems of about 10,000 Lennard-Jones particles have been performed, arranged so as to mimic laboratory experiments on dense liquids. The coalescence event begins when molecules near the boundary of one liquid body thermally fluctuate into the range of attraction of the other, forming a string of mutually attracting molecules. These molecules gradually thicken into a tendril, which continues to thicken as the bodies smoothly combine in a zipper-like merger.

  15. Protein structure in context: The molecular landscape of angiogenesis

    PubMed Central

    Span, Elise A.; Goodsell, David S.; Ramchandran, Ramani; Franzen, Margaret; Herman, Timothy; Sem, Daniel S.

    2014-01-01

    A team of students, educators, and researchers has developed new materials to teach cell signaling within its cellular context. Two non-traditional modalities are employed: physical models, to explore the atomic details of several of the proteins in the angiogenesis signaling cascade, and illustrations of the proteins in their cellular environment, to give an intuitive understanding of the cellular context of the pathway. The experiences of the team underscore the utility of these types of materials as an effective mode for fostering students’ understanding of the molecular world, and the scientific method used to define it. PMID:23868376

  16. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement.

    PubMed

    García-Iriepa, Cristina; Gueye, Moussa; Léonard, Jérémie; Martínez-López, David; Campos, Pedro J; Frutos, Luis Manuel; Sampedro, Diego; Marazzi, Marco

    2016-03-07

    In spite of considerable interest in the design of molecular switches towards photo-controllable (bio)materials, few studies focused on the major influence of the surrounding environment on the switch photoreactivities. We present a combined experimental and computational study of a retinal-like molecular switch linked to a peptide, elucidating the effects on the photoreactivity and on the α-helix secondary structure. Temperature-dependent, femtosecond UV-vis transient absorption spectroscopy and high-level hybrid quantum mechanics/molecular mechanics methods were applied to describe the photoisomerization process and the subsequent peptide rearrangement. It was found that the conformational heterogeneity of the ground state peptide controls the excited state potential energy surface and the thermally activated population decay. Still, a reversible α-helix to α-hairpin conformational change is predicted, paving the way for a fine photocontrol of different secondary structure elements, hence (bio)molecular functions, using retinal-inspired molecular switches.

  17. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    SciTech Connect

    Marcia, Marco Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-11-01

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

  18. High input impedance amplifier

    NASA Technical Reports Server (NTRS)

    Kleinberg, Leonard L.

    1995-01-01

    High input impedance amplifiers are provided which reduce the input impedance solely to a capacitive reactance, or, in a somewhat more complex design, provide an extremely high essentially infinite, capacitive reactance. In one embodiment, where the input impedance is reduced in essence, to solely a capacitive reactance, an operational amplifier in a follower configuration is driven at its non-inverting input and a resistor with a predetermined magnitude is connected between the inverting and non-inverting inputs. A second embodiment eliminates the capacitance from the input by adding a second stage to the first embodiment. The second stage is a second operational amplifier in a non-inverting gain-stage configuration where the output of the first follower stage drives the non-inverting input of the second stage and the output of the second stage is fed back to the non-inverting input of the first stage through a capacitor of a predetermined magnitude. These amplifiers, while generally useful, are very useful as sensor buffer amplifiers that may eliminate significant sources of error.

  19. MDS MIC Catalog Inputs

    NASA Technical Reports Server (NTRS)

    Johnson-Throop, Kathy A.; Vowell, C. W.; Smith, Byron; Darcy, Jeannette

    2006-01-01

    This viewgraph presentation reviews the inputs to the MDS Medical Information Communique (MIC) catalog. The purpose of the group is to provide input for updating the MDS MIC Catalog and to request that MMOP assign Action Item to other working groups and FSs to support the MITWG Process for developing MIC-DDs.

  20. Talking Speech Input.

    ERIC Educational Resources Information Center

    Berliss-Vincent, Jane; Whitford, Gigi

    2002-01-01

    This article presents both the factors involved in successful speech input use and the potential barriers that may suggest that other access technologies could be more appropriate for a given individual. Speech input options that are available are reviewed and strategies for optimizing use of speech recognition technology are discussed. (Contains…

  1. The Molecular Structure of the Liquid Ordered Phase

    NASA Astrophysics Data System (ADS)

    Lyman, Edward

    2014-03-01

    Molecular dynamics simulations reveal substructures within the liquid-ordered phase of lipid bilayers. These substructures, identified in a 10 μsec all-atom trajectory of liquid-ordered/liquid-disordered coexistence (Lo/Ld) , are composed of saturated hydrocarbon chains packed with local hexagonal order, and separated by interstitial regions enriched in cholesterol and unsaturated chains. Lipid hydrocarbon chain order parameters calculated from the Lo phase are in excellent agreement with 2H NMR measurements; the local hexagonal packing is also consistent with 1H-MAS NMR spectra of the Lo phase, NMR diffusion experiments, and small angle X-ray- and neutron scattering. The balance of cholesterol-rich to local hexagonal order is proposed to control the partitioning of membrane components into the Lo regions. The latter have been frequently associated with formation of so-called rafts, platforms in the plasma membranes of cells that facilitate interaction between components of signaling pathways.

  2. Molecular structure, functionality and applications of oxidized starches: A review.

    PubMed

    Vanier, Nathan Levien; El Halal, Shanise Lisie Mello; Dias, Alvaro Renato Guerra; da Rosa Zavareze, Elessandra

    2017-04-15

    During oxidation, the hydroxyl groups of starch molecules are first oxidized to carbonyl groups, then to carboxyl groups. The contents of the carbonyl and carboxyl groups in a starch molecule therefore indicate the extent of starch oxidation. The mechanisms of starch oxidation with different oxidizing agents, including sodium hypochlorite, hydrogen peroxide, ozone and sodium periodate, are described in this review. The effects of these oxidizing agents on the molecular, physicochemical, thermal, pasting and morphological properties of starch are described as well. In addition, the main industrial applications of oxidized starches are presented. The present review is important for understanding the effects of oxidation on starch properties, and this information may facilitate the development of novel oxidized starches for both food and non-food applications.

  3. Microwave spectrum, molecular structure, and quadrupole coupling of vinyl chloroformate

    NASA Astrophysics Data System (ADS)

    Bimler, Jonathan; Broadbent, Stacy; Utzat, Karissa A.; Bohn, Robert K.; Restrepo, Albeiro; Harvey Michels, H.; True, Nancy S.

    2012-09-01

    Vinyl chloroformate is confirmed to have the planar structure reported in an earlier study [1]. Our study uses much higher resolution microwave rotational spectra and ab initio calculations have been extended to a higher level. Naturally abundant isotopologs with single substitution of 37Cl, 13C, and 18O isotopes have also been measured and a substitution structure obtained. The quadrupole coupling constants of the 35Cl and 37Cl isotopologs have been determined. The potential energy profiles of internal rotation about the Odbnd Csbnd Osbnd C and Csbnd Osbnd Cdbnd C dihedral angles have been calculated.

  4. Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

    PubMed

    Ivanciuc, Ovidiu

    2013-06-01

    Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

  5. The molecular structural features controlling stickiness in cooked rice, a major palatability determinant.

    PubMed

    Li, Hongyan; Fitzgerald, Melissa A; Prakash, Sangeeta; Nicholson, Timothy M; Gilbert, Robert G

    2017-03-06

    The stickiness of cooked rice is important for eating quality and consumer acceptance. The first molecular understanding of stickiness is obtained from leaching and molecular structural characteristics during cooking. Starch is a highly branched glucose polymer. We find (i) the molecular size of leached amylopectin is 30 times smaller than that of native amylopectin while (ii) that of leached amylose is 5 times smaller than that of native amylose, (iii) the chain-length distribution (CLD: the number of monomer units in a chain on the branched polymer) of leached amylopectin is similar to native amylopectin while (iv) the CLD of leached amylose is much narrower than that of the native amylose, and (v) mainly amylopectin, not amylose, leaches out of the granule and rice kernel during cooking. Stickiness is found to increase with decreasing amylose content in the whole grain, and, in the leachate, with increasing total amount of amylopectin, the proportion of short amylopectin chains, and amylopectin molecular size. Molecular adhesion mechanisms are put forward to explain this result. This molecular structural mechanism provides a new tool for rice breeders to select cultivars with desirable palatability by quantifying the components and molecular structure of leached starch.

  6. The molecular structural features controlling stickiness in cooked rice, a major palatability determinant

    PubMed Central

    Li, Hongyan; Fitzgerald, Melissa A.; Prakash, Sangeeta; Nicholson, Timothy M.; Gilbert, Robert G.

    2017-01-01

    The stickiness of cooked rice is important for eating quality and consumer acceptance. The first molecular understanding of stickiness is obtained from leaching and molecular structural characteristics during cooking. Starch is a highly branched glucose polymer. We find (i) the molecular size of leached amylopectin is 30 times smaller than that of native amylopectin while (ii) that of leached amylose is 5 times smaller than that of native amylose, (iii) the chain-length distribution (CLD: the number of monomer units in a chain on the branched polymer) of leached amylopectin is similar to native amylopectin while (iv) the CLD of leached amylose is much narrower than that of the native amylose, and (v) mainly amylopectin, not amylose, leaches out of the granule and rice kernel during cooking. Stickiness is found to increase with decreasing amylose content in the whole grain, and, in the leachate, with increasing total amount of amylopectin, the proportion of short amylopectin chains, and amylopectin molecular size. Molecular adhesion mechanisms are put forward to explain this result. This molecular structural mechanism provides a new tool for rice breeders to select cultivars with desirable palatability by quantifying the components and molecular structure of leached starch. PMID:28262830

  7. The molecular structural features controlling stickiness in cooked rice, a major palatability determinant

    NASA Astrophysics Data System (ADS)

    Li, Hongyan; Fitzgerald, Melissa A.; Prakash, Sangeeta; Nicholson, Timothy M.; Gilbert, Robert G.

    2017-03-01

    The stickiness of cooked rice is important for eating quality and consumer acceptance. The first molecular understanding of stickiness is obtained from leaching and molecular structural characteristics during cooking. Starch is a highly branched glucose polymer. We find (i) the molecular size of leached amylopectin is 30 times smaller than that of native amylopectin while (ii) that of leached amylose is 5 times smaller than that of native amylose, (iii) the chain-length distribution (CLD: the number of monomer units in a chain on the branched polymer) of leached amylopectin is similar to native amylopectin while (iv) the CLD of leached amylose is much narrower than that of the native amylose, and (v) mainly amylopectin, not amylose, leaches out of the granule and rice kernel during cooking. Stickiness is found to increase with decreasing amylose content in the whole grain, and, in the leachate, with increasing total amount of amylopectin, the proportion of short amylopectin chains, and amylopectin molecular size. Molecular adhesion mechanisms are put forward to explain this result. This molecular structural mechanism provides a new tool for rice breeders to select cultivars with desirable palatability by quantifying the components and molecular structure of leached starch.

  8. Molecular cloning of the 8000-base thyroglobulin structural gene.

    PubMed

    Christophe, D; Mercken, L; Brocas, H; Pohl, V; Vassart, G

    1982-03-01

    Bovine thyroglobulin mRNA was reverse-transcribed into full-length double-stranded cDNA. The existence of three HindIII restriction endonuclease sites in the 8000-base thyroglobulin structural gene had allowed the easy cloning of the two internal HindIII fragments [Christophe et al. (1980) Eur. J. Biochem. 111, 419-423]. In the present study, the central portion of the structural gene was cloned in Escherichia coli as two individual recombinant plasmids containing 2000-base-pair and 4700-base-pair segments located respectively 5' and 3' relative to the unique BamHI site of the cDNA. BamHI linkers were added to the double-stranded cDNA and, following restriction with HindIII, selective cloning of the 5' (2600-base-pair) and 3' (1000-base-pair) terminal HindIII fragments was achieved by inserting them between the HindIII and BamHI sites of the plasmid pBR322. Partial sequencing of the 1000-base-pair 3'-terminal fragment demonstrated the presence of an A-A-U-A-A-A sequence in the mRNA 14 bases upstream from a poly(A) tract corresponding to the 3' end of the mRNA. Together, the four clones represent about 99% of the thyroglobulin structural gene and provide the starting material for the determination of thyroglobulin primary structure.

  9. Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry.

    PubMed

    Reading, Eamonn; Munoz-Muriedas, Jordi; Roberts, Andrew D; Dear, Gordon J; Robinson, Carol V; Beaumont, Claire

    2016-02-16

    Ion mobility-mass spectrometry (IM-MS) in combination with molecular modeling offers the potential for small molecule structural isomer identification by measurement of their gas phase collision cross sections (CCSs). Successful application of this approach to drug metabolite identification would facilitate resource reduction, including animal usage, and may benefit other areas of pharmaceutical structural characterization including impurity profiling and degradation chemistry. However, the conformational behavior of drug molecules and their metabolites in the gas phase is poorly understood. Here the gas phase conformational space of drug and drug-like molecules has been investigated as well as the influence of protonation and adduct formation on the conformations of drug metabolite structural isomers. The use of CCSs, measured from IM-MS and molecular modeling information, for the structural identification of drug metabolites has also been critically assessed. Detection of structural isomers of drug metabolites using IM-MS is demonstrated and, in addition, a molecular modeling approach has been developed offering rapid conformational searching and energy assessment of candidate structures which agree with experimental CCSs. Here it is illustrated that isomers must possess markedly dissimilar CCS values for structural differentiation, the existence and extent of CCS differences being ionization state and molecule dependent. The results present that IM-MS and molecular modeling can inform on the identity of drug metabolites and highlight the limitations of this approach in differentiating structural isomers.

  10. The Scent of Roses and beyond: Molecular Structures, Analysis, and Practical Applications of Odorants

    ERIC Educational Resources Information Center

    Mannschreck, Albrecht; von Angerer, Erwin

    2011-01-01

    A few odorous compounds found in roses are chosen to arouse the reader's interest in their molecular structures. This article differs from some similar reports on odorants mainly by combining the structural description with the presentation of the following types of isomers: constitutional isomers, enantiomers, and diastereomers. The preparation…

  11. Teaching the Structure of Immunoglobulins by Molecular Visualization and SDS-PAGE Analysis

    ERIC Educational Resources Information Center

    Rižner, Tea Lanišnik

    2014-01-01

    This laboratory class combines molecular visualization and laboratory experimentation to teach the structure of the immunoglobulins (Ig). In the first part of the class, the three-dimensional structures of the human IgG and IgM molecules available through the RCSB PDB database are visualized using freely available software. In the second part, IgG…

  12. Relationships between molecular structure and chromosomal aberrations in virto human lymphocytes induced by substituted nitrobenzenes

    SciTech Connect

    Huang, Q.G.; Kong, L.R.; Liu, Y.B.; Wang, L.S.

    1996-12-31

    Most nitrated aromatics are genotoxic, some structure-activity relationship (SAR) studies have been done about their mutagenicity, but most studies are concerned with the nitrated polycyclic aromatic hydrocarbons. This report studied the substituted nitrobenzenes and the relationship between molecular structure and genotoxicity of these compounds. 8 refs., 1 tab.

  13. Photoexcited State Molecular Structures in Solution Studied by Pump-Probe XAFS

    NASA Astrophysics Data System (ADS)

    Chen, Lin

    2002-03-01

    The photoexcitation causes displacement of electron densities within or among molecules, which consequently leads to nuclear movements. Such nuclear displacements often occur in transient states with short lifetimes. Knowing transient molecular structures during photochemical reactions is important for understanding fundamental aspects of solar energy conversion and storage. Fast x-ray techniques provide direct probes for these transient structures. Using x-ray pulses from the Advanced Photon Source at Argonne, a laser pulse pump, x-ray pulse probe XAFS technique has been developed to capture transient molecular structures in disordered media with nanosecond time resolution. We have carried out several pump-probe XAFS measurements on 1)identifying a transient molecular structure of the photodissociation product of nickel-tetraphenylporphyrin with piperidine axial ligands (NiTPP-L2); 2)determination of the MLCT state structure of Bis(2,9-dimethyl-1,10-phenanthroline) Copper(I) [Cu(I)(dmp)2]+, and 3) triplet state molecular structures of metalloporphyrins. These studies not only prove the feasibility of the technique, but also gain structural information that otherwise will not be available. Future studies include probing transient structures in electron donor-acceptor complexes and optical polarization selected XAFS (OPS-XAFS) using the same technique with a 100-ps time resolution. This work is supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, U. S. Department of Energy, under contract W-31-109-Eng-38.

  14. Guided folding takes a start from the molecular imprinting of structured epitopes.

    PubMed

    Cenci, L; Guella, G; Andreetto, E; Ambrosi, E; Anesi, A; Bossi, A M

    2016-08-25

    A biomimetic route towards assisted folding was explored. Molecularly imprinted polymeric nanoparticles (MIP NPs), i.e. biomimetics with entailed molecular recognition properties made by a template assisted synthesis, were prepared to target a structured epitope: the cystine containing peptide CC9ox, which corresponds to the apical portion of the β-hairpin hormone Hepcidin-25. The structural selection was achieved by the MIP NPs; moreover, the MIP NPs demonstrated favouring the folding of the linear random peptide (CC9red) into the structured one (CC9ox), anticipating the future role of the MIP NPs as in situ nanomachines to counteract folding defects.

  15. The observation of correlated velocity structures in a translucent molecular cloud and implications for turbulence

    NASA Technical Reports Server (NTRS)

    Magnani, L.; Larosa, T. N.; Shore, S. N.

    1993-01-01

    We present a formaldehyde map of the translucent high-latitude molecular cloud MBM 16. The molecular gas traced by the H2CO is located in spatially distinct large structures that exhibit velocity coherence on a scale of 0.5 pc. These structures are not pressure-confined and are probably not self-gravitating. They may be transient structures. If so, we suggest that they are produced by shear flows whose scale length is of order the size of the cloud.

  16. First principles investigations of electronic structure and transport properties of graphitic structures and single molecular junctions

    NASA Astrophysics Data System (ADS)

    Owens, Jonathan R.

    properties of the IV curves of single molecule nano-junctions. Specifically, these systems consist of a zinc-porphyrin molecule coupled between two gold electrodes, i.e., a nano-gap. The first observation we want to explain is the asymmetric nature of the experimental IV curve for this porphyrin system, where the IV curve is skewed heavily to the negative bias region. Using a plane-wave DFT calculation, we present the density of states of the porphyrin molecule (both in the presence and absence of the electrodes) and indeed see highly delocalized states (as confirmed by site-projection of the DOS) only in the negative bias region, meaning that the channels with high transmission probability reside there, in agreement with experimental observation. The next problem studied pertains to observed switching in an experimentally-measured IV curve, this time of a longer zinc porphyrin molecule, still within a gold nano-gap. The switching behavior is observed only at 300K, not at 4.2K. The temperature-dependance of this problem renders our previous toolset of DFT calculations void; DFT is a ground-state theory. Instead, we employ a density functional-based tight-binding (DFTB) approach in a molecular dynamics simulation. Basically, the structural configuration evaluated at each time step is based on a tight-binding electronic structure calculation, instead of a typical MD force field. Trajectories are presented at varying temperatures and electric field strengths. Indeed, we observe a conformation of the porphyrin molecule between two configurations of the dihedral angle of the central nitrogen ring, ±15. {o} at 300K, but not 4.2K. These confirmations are equally likely, i.e., the structure assumes these configurations an equal number of teams, meaning the average structure has an angle of 0. {o}. After computing the DOS of all three aforementioned configurations (0. {text{o}} and ±15. {text{o}}), we indeed see a difference between the DOS curves at ±15. {text{o}} (which are

  17. Molecular dynamics study of grain boundary structure and properties at high temperatures

    NASA Astrophysics Data System (ADS)

    Fensin, Saryu Jindal

    This thesis reports research involving the development and application of atomistic simulation methods to study the effects of high homologous temperatures on the structural, thermodynamic, kinetic and mechanical properties of grain boundaries in metals. Our interest in these properties is due to the role they play in governing the evolution of microstructure and deformation of metals during solidification processing. The interest in developing more predictive models for the formation of solidification defects highlights a need to better understand the thermodynamic driving forces underlying grain-boundary premelting and the mobility and shear strength of these interfaces at high temperatures. In this work we study two different elemental systems, namely Ni and Cu, and consider a variety of grain boundary structures characterized by different misorientation angles, twist/tilt character and zero-temperature energies. A method to calculate the disjoining potential from molecular dynamics (MD) is developed and applied to grain boundaries in Ni. The disjoining potential characterizes the variation in grain-boundary free energy as a function of the width of a premelted interfacial layer. The MD method for the calculation of this property is applied to grain boundaries that display continuous premelting transitions, as well as a boundary characterized by a disordered atomic structure displaying a finite interfacial width at the melting temperature. The disjoining potential represents an important input property to larger scale models of solidification and grain coalescence. We further develop analysis methods to characterize the change in the atomic structure of an asymmetric tilt grain boundary in elemental Cu as a function of temperature. This boundary is characterized by a potential-energy surface with multiple minima as a function of the relative translation of the grains parallel to the interface plane. The more complex structure of this boundary, relative to the

  18. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    SciTech Connect

    Eisenberg, David S.

    2008-07-15

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  19. Molecular and supra-molecular structure of waxy starches developed from cassava (Manihot esculenta Crantz).

    PubMed

    Rolland-Sabaté, Agnès; Sanchez, Teresa; Buléon, Alain; Colonna, Paul; Ceballos, Hernan; Zhao, Shan-Shan; Zhang, Peng; Dufour, Dominique

    2013-02-15

    The aim of this work was to characterize the amylopectin of low amylose content cassava starches obtained from transgenesis comparatively with a natural waxy cassava starch (WXN) discovered recently in CIAT (International Center for Tropical Agriculture). Macromolecular features, starch granule morphology, crystallinity and thermal properties of these starches were determined. M¯(w) of amylopectin from the transgenic varieties are lower than WXN. Branched and debranched chain distributions analyses revealed slight differences in the branching degree and structure of these amylopectins, principally on DP 6-9 and DP>37. For the first time, a deep structural characterization of a series of transgenic lines of waxy cassava was carried out and the link between structural features and the mutated gene expression approached. The transgenesis allows to silenced partially or totally the GBSSI, without changing deeply the starch granule ultrastructure and allows to produce clones with similar amylopectin as parental cassava clone.

  20. Colonization and community structure of arbuscular mycorrhizal fungi in maize roots at different depths in the soil profile respond differently to phosphorus inputs on a long-term experimental site.

    PubMed

    Wang, Chao; White, Philip J; Li, Chunjian

    2016-12-30

    Effects of soil depth and plant growth stages on arbuscular mycorrhizal fungal (AMF) colonization and community structure in maize roots and their potential contribution to host plant phosphorus (P) nutrition under different P-fertilizer inputs were studied. Research was conducted on a long-term field experiment over 3 years. AMF colonization was assessed by AM colonization rate and arbuscule abundances and their potential contribution to host P nutrition by intensity of fungal alkaline phosphatase (ALP)/acid phosphatase (ACP) activities and expressions of ZmPht1;6 and ZmCCD8a in roots from the topsoil and subsoil layer at different growth stages. AMF community structure was determined by specific amplification of 18S rDNA. Increasing P inputs up to 75-100 kg ha(-1) yr(-1) increased shoot biomass and P content but decreased AMF colonization and interactions between AMF and roots. AM colonization rate, intensity of fungal ACP/ALP activities, and expression of ZmPht1;6 in roots from the subsoil were greater than those from topsoil at elongation and silking but not at the dough stage when plants received adequate or excessive P inputs. Neither P input nor soil depth influenced the number of AMF operational taxonomic units (OTUs) present in roots, but P-fertilizer input, in particular, influenced community composition and relative AMF abundance. In conclusion, although increasing P inputs reduce AMF colonization and influence AMF community structure, AMF can potentially contribute to plant P nutrition even in well-fertilized soils, depending on the soil layer in which roots are located and the growth stage of host plants.

  1. Molecular structures of porphyrin-quinone models for electron transfer

    SciTech Connect

    Fajer, J.; Barkigia, K.M.; Melamed, D.; Sweet, R.M.; Kurreck, H.; Gersdorff, J. von; Plato, M.; Rohland, H.C.; Elger, G.; Moebius, K.

    1996-08-15

    Synthetic porphyrin-quinone complexes are commonly used to mimic electron transport in photosynthetic reaction centers and to probe the effects of energetics, distances, and relative orientations on rates of electron transfer between donor-acceptor couples. The structures of two such models have been determined by X-ray diffraction. The redox pairs consist of a zinc porphyrin covalently linked to benzoquinone in cis and trans configurations via a cyclohexanediyl bridge. The crystallographic studies were undertaken to provide a structural foundation for the extensive body of experimental and theoretical results that exists for these compounds in both the ground and photoinduced charge-separated states. The results validate conclusions reached from theoretical calculations, EPR and two-dimensional NMR results for these states. 15 refs., 6 figs., 2 tabs.

  2. Laboratory spectra of C60 and related molecular structures

    NASA Technical Reports Server (NTRS)

    Janca, J.; Solc, M.; Vetesnik, M.

    1994-01-01

    The electronic spectra of fullerene structures in high frequency discharge are studied in the plasma chemistry laboratory of the Faculty of Science of Masaryk University in Brno. The ultraviolet and visual spectra are investigated in order to be compared with the diffuse interstellar bands and interpreted within the theory of quantum mechanics. The preliminary results of the study are presented here in the form of a poster.

  3. Structure of molecular liquids: hard rod-disk mixtures.

    PubMed

    Cheung, David L; Anton, Lucian; Allen, Michael P; Masters, Andrew J

    2008-01-01

    The structure of hard rod-disk mixtures is studied using Monte Carlo simulations and integral equation theory, for a range of densities in the isotropic phase. By extension of methods used in single component fluids, the pair correlation functions of the molecules are calculated and comparisons between simulation and integral equation theory, using a number of different closure relations, are made. Comparison is also made for thermodynamic data and phase behavior.

  4. Rattlesnake Neurotoxin Structure, Mechanism of Action, Immunology and Molecular Biology

    DTIC Science & Technology

    1992-09-10

    Revised 1985). For the protection of human subjects, the investigator(s) adhered to policies of applicable Federal Law 45 CFR 46. condurting research...trial crystallization studies. Sequencing of the basic subunit of Mojave toxin was also proposed in this application , to facilitate our x-ray structural...hydroxysuccinimidyl-4-azidobenzoate ( HSAB ), to synaptosomes and synaptosomal membranes yielded bands on SDS-PAGE migrating at 102kD, equating to a 88kD

  5. Molecular Analyses Reveal Unexpected Genetic Structure in Iberian Ibex Populations

    PubMed Central

    Pérez, Jesús M.; Soriguer, Ramón C.; Granados, José E.

    2017-01-01

    Background Genetic differentiation in historically connected populations could be the result of genetic drift or adaptation, two processes that imply a need for differing strategies in population management. The aim of our study was to use neutral genetic markers to characterize C. pyrenaica populations genetically and examine results in terms of (i) demographic history, (ii) subspecific classification and (iii) the implications for the management of Iberian ibex. Methodology/Principal Findings We used 30 neutral microsatellite markers from 333 Iberian ibex to explore genetic diversity in the three main Iberian ibex populations in Spain corresponding to the two persisting subspecies (victoria and hispanica). Our molecular analyses detected recent genetic bottlenecks in all the studied populations, a finding that coincides with the documented demographic decline in C. pyrenaica in recent decades. Genetic divergence between the two C. pyrenaica subspecies (hispanica and victoriae) was substantial (FST between 0.39 and 0.47). Unexpectedly, we found similarly high genetic differentiation between two populations (Sierra Nevada and Maestrazgo) belonging to the subspecies hispanica. The genetic pattern identified in our study could be the result of strong genetic drift due to the severe genetic bottlenecks in the studied populations, caused in turn by the progressive destruction of natural habitat, disease epidemics and/or uncontrolled hunting. Conclusions Previous Capra pyrenaica conservation decision-making was based on the clear distinction between the two subspecies (victoriae and hispanica); yet our paper raises questions about the usefulness for conservation plans of the distinction between these subspecies. PMID:28135293

  6. Molecular structure and transport dynamics in perfluoro sulfonyl imide membranes.

    PubMed

    Idupulapati, Nagesh; Devanathan, Ram; Dupuis, Michel

    2011-06-15

    We report a detailed and comprehensive analysis from classical molecular dynamics simulations of the nanostructure of a model of hydrated perfluoro sulfonyl imide (PFSI) membrane, a polymeric system of interest as a proton conductor in polymer electrolyte membrane fuel cells. We also report on the transport dynamics of water and hydronium ions, and water network percolation in this system. We find that the water network percolation threshold for PFSI, i.e. the threshold at which a consistent spanning water network starts to develop in the membrane, is found to occur between hydration levels (λ) 6 and 7. The higher acidity of the sulfonyl imide acid group of PFSI compared to the sulfonic acid group in Nafion, as computationally characterized in our earlier ab initio study (Idupulapati et al 2010 J. Phys. Chem. A 114 6904-12), results in a larger fraction of 'free' hydronium ions at low hydration levels in PFSI compared to Nafion. However, the calculated diffusion coefficients of the H(3)O(+) ions and H(2)O molecules as a function the hydration level are observed to be almost the same as that of Nafion, indicating similar conductivity and consistent with experimental data.

  7. Quantitative structure-hydrophobicity relationships of molecular fragments and beyond.

    PubMed

    Zou, Jian-Wei; Huang, Meilan; Huang, Jian-Xiang; Hu, Gui-Xiang; Jiang, Yong-Jun

    2016-03-01

    Quantitative structure-property relationship (QSPR) models were firstly established for the hydrophobic substituent constant (πX) using the theoretical descriptors derived solely from electrostatic potentials (EPSs) at the substituent atoms. The descriptors introduced are found to be related to hydrogen-bond basicity, hydrogen-bond acidity, cavity, or dipolarity/polarizability terms in linear solvation energy relationship, which endows the models good interpretability. The predictive capabilities of the models constructed were also verified by rigorous Monte Carlo cross-validation. Then, eight groups of meta- or para-disubstituted benzenes and one group of substituted pyridines were investigated. QSPR models for individual systems were achieved with the ESP-derived descriptors. Additionally, two QSPR models were also established for Rekker's fragment constants (foct), which is a secondary-treatment quantity and reflects average contribution of the fragment to logP. It has been demonstrated that the descriptors derived from ESPs at the fragments, can be well used to quantitatively express the relationship between fragment structures and their hydrophobic properties, regardless of the attached parent structure or the valence state. Finally, the relations of Hammett σ constant and ESP quantities were explored. It implies that σ and π, which are essential in classic QSAR and represent different type of contributions to biological activities, are also complementary in interaction site.

  8. Structure and photochromic properties of molybdenum-containing silica gels obtained by molecular-lamination method

    SciTech Connect

    Belotserkovskaya, N.G.; Dobychin, D.P.; Pak, V.N.

    1992-05-10

    The structure and physicochemical properties of molybdenum-containing silica gels obtained by molecular lamination have been studied quite extensively. Up to the present, however, no studies have been made of the influence of the pore structure of the original silica gel on the structure and properties of molybdenum-containing silica gels (MSG). The problem is quite important, since molybdenum silicas obtained by molecular lamination may find applications in catalysis and as sensors of UV radiation. In either case, the structure of the support is not a factor to be ignored. Here, the authors are reporting on an investigation of the structure of MSG materials with different pore structures and their susceptibility to reduction of the Mo(VI) oxide groupings when exposed to UV radiation. 16 refs., 2 figs., 2 tabs.

  9. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    SciTech Connect

    Yu,P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  10. A circumstellar molecular gas structure associated with the massive young star Cepheus A-HW 2

    NASA Technical Reports Server (NTRS)

    Torrelles, Jose M.; Rodriguez, Luis F.; Canto, Jorge; Ho, Paul T. P.

    1993-01-01

    We report the detection via VLA-D observations of ammonia of a circumstellar high-density molecular gas structure toward the massive young star related to the object Cepheus A-HW 2, a firm candidate for the powering source of the high-velocity molecular outflow in the region. We suggest that the circumstellar molecular gas structure could be related to the circumstellar disk previously suggested from infrared, H2O, and OH maser observations. We consider as a plausible scenario that the double radio continuum source of HW 2 could represent the ionized inner part of the circumstellar disk, in the same way as proposed to explain the double radio source in L1551. The observed motions in the circumstellar molecular gas can be produced by bound motions (e.g., infall or rotation) around a central mass of about 10-20 solar masses (B0.5 V star or earlier).

  11. Charge-distribution effect of imaging molecular structure by high-order above-threshold ionization

    SciTech Connect

    Wang Bingbing; Fu Panming; Guo Yingchun; Zhang Bin; Zhao Zengxiu; Yan Zongchao

    2010-10-15

    Using a triatomic molecular model, we show that the interference pattern in the high-order above-threshold ionization (HATI) spectrum depends dramatically on the charge distribution of the molecular ion. Therefore the charge distribution can be considered a crucial factor for imaging a molecular geometric structure. Based on this study, a general destructive interference formula for each above-threshold ionization channel is obtained for a polyatomic molecule concerning the positions and charge values of each nuclei. Comparisons are made for the HATI spectra of CO{sub 2}, O{sub 2}, NO{sub 2}, and N{sub 2}. These results may shed light on imaging complex molecular structure by the HATI spectrum.

  12. Structural, magnetic and optical properties of two concomitant molecular crystals

    NASA Astrophysics Data System (ADS)

    Silva, Manuela Ramos; Milne, Bruce; Coutinho, Joana T.; Pereira, Laura C. J.; Martín-Ramos, Pablo; Pereira da Silva, Pedro S.; Martín-Gil, Jesús

    2016-03-01

    A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Cu(II) ions assemble in alternating chains with Cu … Cu distances of 2.5685(4) and 3.1760(4) Å. The temperature dependence of the magnetic susceptibility reveals an antiferromagnetic interaction between the paddle-wheel copper centers with an exchange of -300 cm-1. The exchange integral was also determined by quantum chemical ab-initio calculations, using polarised and unpolarised basis sets reproducing well the experimental value. The second harmonic generation efficiency of a concomitantly crystallized material was evaluated and was found to be comparable to urea.

  13. Crystal and molecular structure of barley alpha-amylase.

    PubMed

    Kadziola, A; Abe, J; Svensson, B; Haser, R

    1994-05-27

    The three-dimensional structure of barley malt alpha-amylase (isoform AMY2-2) was determined by multiple isomorphous replacement using three heavy-atom derivatives and solvent flattening. The model was refined using a combination of simulated annealing and conventional restrained least-squares crystallographic refinement to an R-factor of 0.153 based on 18,303 independent reflections with F(o) > sigma(F(o)) between 10 and 2.8 A resolution, with root-mean-square deviations of 0.016 A and 3.3 degrees from ideal bond lengths and bond angles, respectively. The final model consists of 403 amino acid residues, three calcium ions and 153 water molecules. The polypeptide chain folds into three domains: a central domain forming a (beta alpha)8-barrel of 286 residues, with a protruding irregular structured loop domain of 64 residues (domain B) connecting strand beta 3 and helix alpha 3 of the barrel, and a C-terminal domain of 53 residues forming a five stranded anti-parallel beta-sheet. Unlike the previously known alpha-amylase structures, AMY2-2 contains three Ca2+ binding sites co-ordinated by seven or eight oxygen atoms from carboxylate groups, main-chain carbonyl atoms and water molecules, all calcium ions being bound to domain B and therefore essential for the structural integrity of that domain. Two of the Ca2+ sites are located only 7.0 A apart with one Asp residue serving as ligand for both. One Ca2+ site located at about 20 A from the other two was found to be exchangeable with Eu3+. By homology with other alpha-amylases, some important active site residues are identified as Asp179, Glu204 and Asp289, and are situated at the C-terminal end of the central beta-barrel. A starch granule binding site, previously identified as Trp276 and Trp277, is situated on alpha-helix 6 in the central (beta alpha)8-barrel, at the surface of the enzyme. This binding site region is associated with a considerable disruption of the (beta alpha)8-barrel 8-fold symmetry.

  14. The liquid structure of tetrachloroethene: Molecular dynamics simulations and reverse Monte Carlo modeling with interatomic potentials

    NASA Astrophysics Data System (ADS)

    Gereben, Orsolya; Pusztai, László

    2013-10-01

    The liquid structure of tetrachloroethene has been investigated on the basis of measured neutron and X-ray scattering structure factors, applying molecular dynamics simulations and reverse Monte Carlo (RMC) modeling with flexible molecules and interatomic potentials. As no complete all-atom force field parameter set could be found for this planar molecule, the closest matching all-atom Optimized Potentials for Liquid Simulations (OPLS-AA) intra-molecular parameter set was improved by equilibrium bond length and angle parameters coming from electron diffraction experiments [I. L. Karle and J. Karle, J. Chem. Phys. 20, 63 (1952)]. In addition, four different intra-molecular charge distribution sets were tried, so in total, eight different molecular dynamics simulations were performed. The best parameter set was selected by calculating the mean square difference between the calculated total structure factors and the corresponding experimental data. The best parameter set proved to be the one that uses the electron diffraction based intra-molecular parameters and the charges qC = 0.1 and qCl = -0.05. The structure was further successfully refined by applying RMC computer modeling with flexible molecules that were kept together by interatomic potentials. Correlation functions concerning the orientation of molecular axes and planes were also determined. They reveal that the molecules closest to each other exclusively prefer the parallel orientation of both the molecular axes and planes. Molecules forming the first maximum of the center-center distribution have a preference for <30° and >60° axis orientation and >60° molecular plane arrangement. A second coordination sphere at ˜11 Å and a very small third one at ˜16 Å can be found as well, without preference for any axis or plane orientation.

  15. DFT study of the effect of substitution on the molecular structure of copper phthalocyanine

    NASA Astrophysics Data System (ADS)

    Kaur, Prabhjot; Sachdeva, Ritika; Singh, Sukhwinder; Saini, G. S. S.

    2016-05-01

    To study the effect of sulfonic acid group as substituent on the molecular structure of an organic compound copper Phthalocyanine, the optimized geometry, mulliken charges, energies and dipole momemts of copper phthalocyanine and copper phthalocyaninetetrasulfonic acid tetra sodium salt have been investigated using density functional theory. Also to predict the change in reactive sites after substitution, molecular electrostatic potential maps for both the molecules have been calculated.

  16. The Molecular and Morphologic Structures That Make Saltatory Conduction Possible in Peripheral Nerve.

    PubMed

    Carroll, Steven L

    2017-03-14

    Saltatory conduction is the process by which action potentials are rapidly and efficiently propagated along myelinated axons. In the peripheral nervous system, saltatory conduction is made possible by a series of morphologically and molecularly distinct subdomains in both axons and their associated myelinating Schwann cells. This review briefly summarizes current knowledge on the molecular structure and physiology of the node of Ranvier and adjacent regions of the axoglial unit in peripheral nerve.

  17. A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders.

    PubMed

    Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

    2016-10-07

    In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

  18. A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders

    NASA Astrophysics Data System (ADS)

    Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

    2016-10-01

    In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

  19. Molecular and crystal structure of anhydrous zirconium perchlorate

    SciTech Connect

    Genkina, E.A.; Babaeva, V.P.; Rosolovskii, V.Ya.

    1985-08-01

    An x-ray diffraction investigation (diffractometer, Mo K..cap alpha.., graphite monochromator, omega scan technique, Theta less than or equal to 30/sup 0/, 1060 reflections, least-squares method in the anisotropic approximation to R = 0.058) of anhydrous zirconium perchlorate has been carried out. The crystals of Zr(Cl0/sub 4/)/sub 4/ are monoclinic: ..cap alpha.. = 12.899(3), b = 13.188(7), c = 7.937(3) A, ..gamma.. = 107.91/sup 0/, Z = 4, space group Bb. The structure has an island character and is built up from isolated Zr(ClO/sub 4/)/sub 4/ molecules. The Zr atom is surrounded by eight O atoms in four bidentate perchlorato groups. The Zr-O distances lie in the range from 2.13 to 2.23 A, averaging 2.19 A. The eight-vertex polyhedron around Zr is the mmmm steroisomer of a dodecahedron. The centers of the perchlorato groups are located at the vertices of flattened tetrahedron. The ClO/sub 4/ groups have a distorted tetrahedral structure, and the mean length of the Cl-O/sub b/ bonds (1.50 A) is 0.11 A greater than the mean length of the Cl-O/sub t/ bonds, pointing out the essentially covalent character of the bonds of the perchlorato groups with the central Zr atom.

  20. Molecular determinants of staphylococcal biofilm dispersal and structuring

    PubMed Central

    Le, Katherine Y.; Dastgheyb, Sana; Ho, Trung V.; Otto, Michael

    2014-01-01

    Staphylococci are frequently implicated in human infections, and continue to pose a therapeutic dilemma due to their ability to form deeply seated microbial communities, known as biofilms, on the surfaces of implanted medical devices and host tissues. Biofilm development has been proposed to occur in three stages: (1) attachment, (2) proliferation/structuring, and (3) detachment/dispersal. Although research within the last several decades has implicated multiple molecules in the roles as effectors of staphylococcal biofilm proliferation/structuring and detachment/dispersal, to date, only phenol soluble modulins (PSMs) have been consistently demonstrated to serve in this role under both in vitro and in vivo settings. PSMs are regulated directly through a density-dependent manner by the accessory gene regulator (Agr) system. They disrupt the non-covalent forces holding the biofilm extracellular matrix together, which is necessary for the formation of channels, a process essential for the delivery of nutrients to deeper biofilm layers, and for dispersal/dissemination of clusters of biofilm to distal organs in acute infection. Given their relevance in both acute and chronic biofilm-associated infections, the Agr system and the psm genes hold promise as potential therapeutic targets. PMID:25505739

  1. Current and emerging opportunities for molecular simulations in structure-based drug design

    PubMed Central

    Michel, Julien

    2014-01-01

    An overview of the current capabilities and limitations of molecular simulation of biomolecular complexes in the context of computer-aided drug design is provided. Steady improvements in computer hardware coupled with more refined representations of energetics are leading to a new appreciation of the driving forces of molecular recognition. Molecular simulations are poised to more frequently guide the interpretation of biophysical measurements of biomolecular complexes. Ligand design strategies emerge from detailed analyses of computed structural ensembles. The feasibility of routine applications to ligand optimization problems hinges upon successful extensive large scale validation studies and the development of protocols to intelligently automate computations. PMID:24469595

  2. Structural and dipolar fluctuations in liquid water: A Car-Parrinello molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Skarmoutsos, Ioannis; Masia, Marco; Guardia, Elvira

    2016-03-01

    A Car-Parrinello molecular dynamics simulation was performed to investigate the local tetrahedral order, molecular dipole fluctuations and their interrelation with hydrogen bonding in liquid water. Water molecules were classified in three types, exhibiting low, intermediate and high tetrahedral order. Transitions from low to high tetrahedrally ordered structures take place only through transitions to the intermediate state. The molecular dipole moments depend strongly on the tetrahedral order and hydrogen bonding. The average dipole moment of water molecules with a strong tetrahedral order around them comes in excellent agreement with previous estimations of the dipole moment of ice Ih molecules.

  3. Exploring Molecular and Mechanical Gradients in Structural Bioscaffolds†

    PubMed Central

    Waite, J. Herbert; Lichtenegger, Helga C.; Stucky, Galen D.; Hansma, Paul

    2007-01-01

    Most organisms consist of a functionally adaptive assemblage of hard and soft tissues. Despite the obvious advantages of reinforcing soft protoplasm with a hard scaffold, such composites can lead to tremendous mechanical stresses where the two meet. Although little is known about how nature relieves these stresses, it is generally agreed that fundamental insights about molecular adaptation at hard/soft interfaces could profoundly influence how we think about biomaterials. Based on two noncellular tissues, mussel byssus and polychaete jaws, recent studies suggest that one natural strategy to minimize interfacial stresses between adjoining stiff and soft tissue appears to be the creation of a “fuzzy” boundary, which avoids abrupt changes in mechanical properties. Instead there is a gradual mechanical change that accompanies the transcendence from stiff to soft and vice versa. In byssal threads, the biochemical medium for achieving such a gradual mechanical change involves the elegant use of collagen-based self-assembling block copolymers. There are three distinct diblock copolymer types in which one block is always collagenous, whereas the other can be either elastin-like (soft), amorphous polyglycine (intermediate), or silk-like (stiff). Gradients of these are made by an incrementally titrated expression of the three proteins in secretory cells the titration phenotype of which is linked to their location. Thus, reflecting exactly the composition of each thread, the distal cells secrete primarily the silk– and polyglycine–collagen diblocks, whereas the proximal cells secrete the elastin– and polyglycine–collagen diblocks. Those cells in between exhibit gradations of collagens with silk or elastin blocks. Spontaneous self-assembly appears to be by pH triggered metal binding by histidine (HIS)-rich sequences at both the amino and carboxy termini of the diblocks. In the polychaete jaws, HIS-rich sequences are expanded into a major block domain. Histidine

  4. Molecular tools for investigating ANME community structure and function

    SciTech Connect

    Hallam, Steven J.; Page, Antoine P.; Constan, Lea; Song, Young C.; Norbeck, Angela D.; Brewer, Heather M.; Pasa-Tolic, Ljiljana

    2011-05-20

    Methane production and consumption in anaerobic marine sediments 1 is catalyzed by a series of reversible tetramethanopterin (H4MPT)-linked C1 transfer reactions. Although many of these reactions are conserved between one-carbon compound utilizing microorganisms, two remain diagnostic for archaeal methane metabolism. These include reactions catalyzed by N5-methyltetrahydromethanopterin: coenzyme M methyltransferase and methyl coenzyme M reductase. The latter enzyme is central to C-H bond formation and cleavage underlying methanogenic and reverse methanogenic phenotypes. Here we describe a set of novel tools for the detection and functional analysis of H4MPT-linked C1 transfer reactions mediated by uncultivated anaerobic methane oxidizing archaea (ANME). These tools include polymerase chain reaction primers targeting ANME methyl coenzyme M reductase subunit A subgroups and protein extraction methods from marine sediments compatible with high-resolution mass spectrometry for profiling population structure and functional dynamics. [910, 1,043

  5. Molecular Structure and Reactivity in the Pyrolysis of Aldehydes

    NASA Astrophysics Data System (ADS)

    Sias, Eric; Cole, Sarah; Sowards, John; Warner, Brian; Wright, Emily; McCunn, Laura R.

    2016-06-01

    The effect of alkyl chain structure on pyrolysis mechanisms has been investigated in a series of aldehydes. Isovaleraldehyde, CH_3CH(CH_3)CH_2CHO, and pivaldehyde, (CH_3)_3CCHO, were subject to thermal decomposition in a resistively heated SiC tubular reactor at 800-1200 °C. Matrix-isolation FTIR spectroscopy was used to identify pyrolysis products. Carbon monoxide and isobutene were major products from each of the aldehydes, which is consistent with what is known from previous studies of unbranched alkyl-chain aldehydes. Other products observed include vinyl alcohol, propene, acetylene, and ethylene, revealing complexities to be considered in the pyrolysis of large, branched-chain aldehydes.

  6. Crystal and molecular structure of sodium paratungstate 26 hydrate

    SciTech Connect

    Cruywagen, J.J.; Nassibemi, L.R.; Niven, M.L.; Vander Merwe, I.F.

    1986-08-01

    On standing, an acid solution of tungstate yields single crystals of the paratungstate salt Na/sub 10/(H/sub 2/W/sub 12/O/sub 42/ /SUB sd/ /SUP ./ 26H/sub 2/O. The space group is P1, (No. 2), a 11.811(2), b = 12.486(2), c = 12.206(2) A, ..cap alpha.. = 82.29(1), ..beta.. = 115.12(1), ..gamma.. = 113.76(1) /sup 0/, V = 1485.6 A/sup 3/, Z = 1. The structure was solved by direct methods and refined to R = 0.0397, R /SUB w/ = 0.0403 (w = (sigma/sup 2/F)/sup -1/). The 12 WO/sub 6/ octahedra (shared edges and vertices) are distorted from regular geometry; one of the sodium ions exhibits disorder and there is extensive hydrogen bonding between the water molecules and the oxygens of the paratungstate anion.

  7. Searching molecular structure databases with tandem mass spectra using CSI:FingerID

    PubMed Central

    Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian

    2015-01-01

    Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. We present a method for searching molecular structure databases using tandem MS data of small molecules. Our method computes a fragmentation tree that best explains the fragmentation spectrum of an unknown molecule. We use the fragmentation tree to predict the molecular structure fingerprint of the unknown compound using machine learning. This fingerprint is then used to search a molecular structure database such as PubChem. Our method is shown to improve on the competing methods for computational metabolite identification by a considerable margin. PMID:26392543

  8. Molecular dynamics of protein kinase-inhibitor complexes: a valid structural information.

    PubMed

    Caballero, Julio; Alzate-Morales, Jans H

    2012-01-01

    Protein kinases (PKs) are key components of protein phosphorylation based signaling networks in eukaryotic cells. They have been identified as being implicated in many diseases. High-resolution X-ray crystallographic data exist for many PKs and, in many cases, these structures are co-complexed with inhibitors. Although this valuable information confirms the precise structure of PKs and their complexes, it ignores the dynamic movements of the structures which are relevant to explain the affinities and selectivity of the ligands, to characterize the thermodynamics of the solvated complexes, and to derive predictive models. Atomistic molecular dynamics (MD) simulations present a convenient way to study PK-inhibitor complexes and have been increasingly used in recent years in structure-based drug design. MD is a very useful computational method and a great counterpart for experimentalists, which helps them to derive important additional molecular information. That enables them to follow and understand structure and dynamics of protein-ligand systems with extreme molecular detail on scales where motion of individual atoms can be tracked. MD can be used to sample dynamic molecular processes, and can be complemented with more advanced computational methods (e.g., free energy calculations, structure-activity relationship analysis). This review focuses on the most commonly applications to study PK-inhibitor complexes using MD simulations. Our aim is that researchers working in the design of PK inhibitors be aware of the benefits of this powerful tool in the design of potent and selective PK inhibitors.

  9. Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics.

    PubMed Central

    Woolf, T B

    1997-01-01

    Understanding the role of the lipid bilayer in membrane protein structure and dynamics is needed for tertiary structure determination methods. However, the molecular details are not well understood. Molecular dynamics computer calculations can provide insight into these molecular details of protein:lipid interactions. This paper reports on 10 simulations of individual alpha-helices in explicit lipid bilayers. The 10 helices were selected from the bacteriorhodopsin structure as representative alpha-helical membrane folding components. The bilayer is constructed of dimyristoyl phosphatidylcholine molecules. The only major difference between simulations is the primary sequence of the alpha-helix. The results show dramatic differences in motional behavior between alpha-helices. For example, helix A has much smaller root-mean-squared deviations than does helix D. This can be understood in terms of the presence of aromatic residues at the interface for helix A that are not present in helix D. Additional motions are possible for the helices that contain proline side chains relative to other amino acids. The results thus provide insight into the types of motion and the average structures possible for helices within the bilayer setting and demonstrate the strength of molecular simulations in providing molecular details that are not directly visualized in experiments. Images FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 Figure 6 PMID:9370432

  10. Hierarchical QSAR technology based on the Simplex representation of molecular structure

    NASA Astrophysics Data System (ADS)

    Kuz'min, V. E.; Artemenko, A. G.; Muratov, E. N.

    2008-06-01

    This article is about the hierarchical quantitative structure-activity relationship technology (HiT QSAR) based on the Simplex representation of molecular structure (SiRMS) and its application for different QSAR/QSP(property)R tasks. The essence of this technology is a sequential solution (with the use of the information obtained on the previous steps) to the QSAR problem by the series of enhanced models of molecular structure description [from one dimensional (1D) to four dimensional (4D)]. It is a system of permanently improved solutions. In the SiRMS approach, every molecule is represented as a system of different simplexes (tetratomic fragments with fixed composition, structure, chirality and symmetry). The level of simplex descriptors detailing increases consecutively from the 1D to 4D representation of the molecular structure. The advantages of the approach reported here are the absence of "molecular alignment" problems, consideration of different physical-chemical properties of atoms (e.g. charge, lipophilicity, etc.), the high adequacy and good interpretability of obtained models and clear ways for molecular design. The efficiency of the HiT QSAR approach is demonstrated by comparing it with the most popular modern QSAR approaches on two representative examination sets. The examples of successful application of the HiT QSAR for various QSAR/QSPR investigations on the different levels (1D-4D) of the molecular structure description are also highlighted. The reliability of developed QSAR models as predictive virtual screening tools and their ability to serve as the base of directed drug design was validated by subsequent synthetic and biological experiments, among others. The HiT QSAR is realized as a complex of computer programs known as HiT QSAR software that also includes a powerful statistical block and a number of useful utilities.

  11. Molecular Structure of Aggregated Amyloid-β: Insights from Solid State Nuclear Magnetic Resonance

    PubMed Central

    Tycko, Robert

    2016-01-01

    Amyloid-β (Aβ) peptides aggregate to form polymorphic amyloid fibrils and a variety of intermediate assemblies, including oligomers and protofibrils, both in vitro and in human brain tissue. Since the beginning of the 21st century, considerable progress has been made on characterization of the molecular structures of Aβ aggregates. Full molecular structural models that are based primarily on data from solid state nuclear magnetic resonance measurements have been developed for several in vitro Aβ fibrils and one metastable protofibril. Partial structural characterization of other aggregation intermediates has been achieved. One full structural model for fibrils derived from brain tissue has also been reported. Future work is likely to focus on additional structures from brain tissue and on further clarification of nonfibrillar Aβ aggregates. PMID:27481836

  12. A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

    PubMed

    Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

    2017-04-04

    Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology.

  13. Molecular structure and liquid-crystalline characteristics of chitosan phenylcarbamate.

    PubMed

    Kuse, Yasunori; Asahina, Daisuke; Nishio, Yoshiyuki

    2009-01-12

    Chitosan phenylcarbamate (CtsPC) samples were synthesized to have different degrees of substitution (DS) ranging from approximately 2.7 to approximately 3.7, and the lyotropic liquid crystallinity was mainly characterized by spectrophotometry. The products of DS>2.8 formed a cholesteric type of mesophase in concentrated solutions of >44 wt % with polar aprotic solvents such as N,N-dimethylformamide (DMF), N,N-dimethylacetamide (DMAc), and dimethyl sulfoxide (DMSO), and some of the solutions imparted vivid colorations because of selective visible light reflection. The cholesteric helical pitch increased with increasing temperature and with decreasing polymer concentration, but the helical sense remained left-handed under the adopted measurement conditions. It was also found that the helical pitch increased in proportion to the increment of DS, whereas an average degree of phenylcarbamoyl polyaddition in the side chains (DPs) rather affected the pitch distribution measuring an orderliness in the cholesteric structure. With a small increase in DPs (e.g., from 1.01 to 1.04), the cholesteric orderliness decreased and the temperature sensitivity of the pitch turned sluggish. Wide-angle X-ray diffractometry was also used for evaluating the distance and azimuth difference between adjacent nematic thin layers in the cholesteric mesophase.

  14. Microwave Spectroscopy and Molecular Structure of Isonitrosyl Hydroxide (hoon)

    NASA Astrophysics Data System (ADS)

    Crabtree, Kyle N.; Talipov, Marat R.; O'Connor, Gerard; Martinez, Oscar, Jr.; Khursan, Sergey L.; McCarthy, Michael C.

    2014-06-01

    Nitrous acid (HONO) is an important member of the atmospheric nitrogen cycle whose chemistry involves a variety of gas-phase, photochemical, and heterogeneous processes. Among its formation pathways in the atmosphere is the ternary association of hydroxyl (OH) with nitric oxide (NO), but the formation of the isonitrosyl hydroxide (HOON) isomer has largely been ignored owing to early theoretical studies that questioned its stability. Guided by new high-level ab initio calculations, we have detected the rotational spectrum of trans-HOON in an electrical discharge of a dilute mixture of NO and water vapor by a combination of Fourier transform microwave spectroscopy and double resonance methods. No evidence for the cis isomer was found in any of our spectroscopic surveys between 15.4--17.0 GHz. A semi-experimental equilibrium structure for trans-HOON has been derived to high precision from isotopic substitution (DOON, H18OON, HO18ON, HOO15N) along with zero-point vibrational corrections calculated at the CCSD(T)/aug-cc-pVTZ level of theory. Most notably, the central O--O bond in trans-HOON is found to be 1.9149 ± 0.0005 Å in length, which is the longest known O--O bond in a molecule (nearly 20% longer than the analogous bond in the HOOO radical).

  15. Crystal and mol-ecular structure of aflatrem.

    PubMed

    Lenta, Bruno N; Ngatchou, Jules; Kenfack, Patrice T; Neumann, Beate; Stammler, Hans-Georg; Sewald, Norbert

    2015-11-01

    The crystal structure of the title compound, C32H39NO4, confirms the absolute configuration of the seven chiral centres in the mol-ecule. The molecule has a 1,1-dimethylprop-2-enyl substituent on the indole nucleus and this nucleus shares one edge with the five-membered ring which is, in turn, connected to a sequence of three edge-shared fused rings. The skeleton is completed by the 7,7-trimethyl-6,8-dioxabi-cyclo-[3.2.1]oct-3-en-2-one group connected to the terminal cyclohexene ring. The two cyclohexane rings adopt chair and half-chair conformations, while in the dioxabi-cyclo-[3.2.1]oct-3-en-2-one unit, the six-membered ring has a half-chair conformation. The indole system of the mol-ecule exhibits a tilt of 2.02 (1)° between its two rings. In the crystal, O-H⋯O hydrogen bonds connect mol-ecules into chains along [010]. Weak N-H⋯π inter-actions connect these chains, forming sheets parallel to (10-1).

  16. Modification of LDPE molecular structure by gamma irradiation for bioapplications

    NASA Astrophysics Data System (ADS)

    Ferreira, L. M.; Falcão, A. N.; Gil, M. H.

    2005-07-01

    The surface properties of low-density polyethylene (LDPE) can be modified by the grafting of 2-hydroxyethyl methacrylate (HEMA). This was done aiming at the production of new materials suitable for bioapplications. Samples with different monomer concentrations were prepared from LDPE particles by gamma irradiation, following different irradiation protocols, including irradiation in presence and absence of air. The samples were characterized by thermal analysis techniques (DSC and TGA) and by Fourier transform infrared spectroscopy (FTIR). The results obtained show a decrease in the crystallinity of the supporting matrix for copolymers with high yields of grafting. However, the new materials prepared maintain good structural order resulting from the protective effect of polyHEMA grafted onto LDPE backbone. These effects can improve the diffusion of other species deeper inside the matrix and increase the material hydrophilicity. The studies performed made possible the selection of experimental protocols adequate for the production of new copolymeric materials with high grafting yield. These were used in the production of new LDPE films with enhanced hydrophilic properties.

  17. Computational nanochemistry study of the molecular structure and properties of ethambutol.

    PubMed

    Salgado-Morán, Guillermo; Ruiz-Nieto, Samuel; Gerli-Candia, Lorena; Flores-Holguín, Norma; Favila-Pérez, Alejandra; Glossman-Mitnik, Daniel

    2013-09-01

    The M06 family of density functionals was employed to calculate the molecular structure and properties of the ethambutol molecule. Besides determination of molecular structures, UV-vis spectra were computed using TD-DFT in the presence of a solvent and the results compared with available experimental data. The chemical reactivity descriptors were calculated through conceptual DFT. The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to Fukui function indices. A comparison between the descriptors calculated through vertical energy values and those arising from Koopmans' theorem approximation were performed in order to check the validity of the latter procedure.

  18. Spectroscopic study of molecular structure, antioxidant activity and biological effects of metal hydroxyflavonol complexes

    NASA Astrophysics Data System (ADS)

    Samsonowicz, Mariola; Regulska, Ewa

    2017-02-01

    Flavonols with varied hydroxyl substitution can act as strong antioxidants. Thanks to their ability to chelate metals as well as to donate hydrogen atoms they have capacity to scavenge free radicals. Their metal complexes are often more active in comparison with free ligands. They exhibit interesting biological properties, e.g. anticancer, antiphlogistic and antibacterial. The relationship between molecular structure and their biological properties was intensively studied using spectroscopic methods (UV-Vis, IR, Raman, NMR, ESI-MS). The aim of this paper is review on spectroscopic analyses of molecular structure and biological activity of hydroxyflavonol metal complexes.

  19. Modulated structure and molecular dissociation of solid chlorine at high pressures

    NASA Astrophysics Data System (ADS)

    Li, Peifang; Gao, Guoying; Ma, Yanming

    2012-08-01

    Among diatomic molecular halogen solids, high pressure structures of solid chlorine (Cl2) remain elusive and least studied. We here report first-principles structural search on solid Cl2 at high pressures through our developed particle-swarm optimization algorithm. We successfully reproduced the known molecular Cmca phase (phase I) at low pressure and found that it remains stable up to a high pressure 142 GPa. At 150 GPa, our structural searches identified several energetically competitive, structurally similar, and modulated structures. Analysis of the structural results and their similarity with those in solid Br2 and I2, it was suggested that solid Cl2 adopts an incommensurate modulated structure with a modulation wave close to 2/7 in a narrow pressure range 142-157 GPa. Eventually, our simulations at >157 GPa were able to predict the molecular dissociation of solid Cl2 into monatomic phases having body centered orthorhombic (bco) and face-centered cubic (fcc) structures, respectively. One unique monatomic structural feature of solid Cl2 is the absence of intermediate body centered tetragonal (bct) structure during the bco → fcc transition, which however has been observed or theoretically predicted in solid Br2 and I2. Electron-phonon coupling calculations revealed that solid Cl2 becomes superconductors within bco and fcc phases possessing a highest superconducting temperature of 13.03 K at 380 GPa. We further probed the molecular Cmca → incommensurate phase transition mechanism and found that the softening of the Ag vibrational (rotational) Raman mode in the Cmca phase might be the driving force to initiate the transition.

  20. The anharmonic force field and equilibrium molecular structure of ketene

    NASA Astrophysics Data System (ADS)

    East, Allan L. L.; Allen, Wesley D.; Klippenstein, Stephen J.

    1995-06-01

    A comprehensive anharmonic vibrational analysis of isotopic ketenes has been performed on the basis of a complete ab initio quartic force field constructed by means of second-order Møller-Plesset perturbation theory (MP2) and the coupled-cluster singles and doubles (CCSD) approach, augmented for structural optimizations by a contribution for connected triple excitations [CCSD(T)]. The atomic-orbital basis sets of the study entailed C,O(10s6p/5s4p) and H(6s/4s) spaces multiply polarized in the valence region to give QZ(2d,2p) and QZ(2d1f,2p1d) sets. An iterative anharmonic vibrational refinement of a limited set of quadratic scaling parameters on 27 fundamentals of H2CCO, HDCCO, D2CCO, and H2C13CO generates a final quartic force field which reproduces the empirical νi data with an average absolute error of only 1.1 cm-1. This force field yields a complete and self-consistent set of Coriolis (ζij), vibrational anharmonic (χij), vibration-rotation interaction (αi), and quartic and sextic centrifugal distortion constants, providing a critical assessment of the assorted spectroscopic constants determined over many years and also facilitating future computations of vibrational state densities for detailed tests of unimolecular dissociation theories. The harmonic frequencies ascertained for H2CCO (in cm-1), with associated anharmonicities in parentheses, are ω1(a1)=3202.2(-129.2), ω2(a1)=2197.2(-44.4), ω3(a1)=1415.2(-25.9), ω4(a1)=1146.0(-29.7), ω5(b1)=581.9(+7.1), ω6(b1)=502.6(+26.3), ω7(b2)=3308.2(-141.3), ω8(b2)=996.0(-17.9), and ω9(b2)=433.6(+5.0). The large positive anharmonicity for the ν6(b1) C=C=O bending mode, which is principally a Coriolis effect, warrants continued investigation. Explicit first-order treatments of the strong Fermi interactions within the (ν4,2ν5,ν5+ν6,2ν6) manifold reveal resonance shifts for ν4(H2CCO, HDCCO, D2CCO) of (-12.1, -10.0, +12.2) cm-1, in order. The experimental assignments for this Fermi tetrad are confirmed to

  1. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

    PubMed Central

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-01-01

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

  2. Molecular structure and dynamics in bacterial mercury resistance

    SciTech Connect

    Johs, Alexander; Shi, Liang; Miller, Susan M; Summers, Anne O; Liang, Liyuan

    2008-01-01

    Bacteria participate significantly in mercury transformation in natural and industrial environments. Previous studies have shown that bacterial mercury resistance is mediated by the mer operon, typically located on transposons or plasmids. It encodes specific genes that facilitate uptake of mercury species, cleavage of organomercurials, and reduction of Hg(II) to Hg(0). Expression of mer operon genes is regulated by MerR, a metal-responsive regulator protein on the level of transcription. In vitro studies have shown that MerR forms a non-transcribing pre-initiation complex with RNA polymerase and the promoter DNA. Binding of Hg(II) induces conformational changes in MerR and other components of the complex resulting in the transcription of mer operon genes. As part of ongoing investigations on allosteric conformational changes induced by Hg(II) in dimeric MerR, and the implications on the binding of RNA polymerase to the promoter of the mer operon, we applied small angle scattering to study the regulatory mechanism of MerR in the presence and absence of Hg(II). Our results show that in the presence of Hg(II) the MerR dimer undergoes a significant reorientation from a compact state to a conformation revealing two distinct domains. Bacterial reduction of Hg(II) can also occur at concentrations too low to induce mer operon functions. Dissimilatory metal reducing bacteria, such as Shewanella and Geobacter are able to reduce Hg(II) in the presence of mineral oxides. This process has been linked to the activity of outer membrane multiheme cytochromes. We isolated and purified a decaheme outer membrane cytochrome OmcA from Shewanella oneidensis MR-1 and characterized its envelope shape in solution by small angle x-ray scattering. Structural features were identified and compared to homology models. These results show that OmcA is an elongated macromolecule consisting of separate modules, which may be connected by flexible linkers.

  3. Molecular Structures of Isolevuglandin-Protein Cross-Links.

    PubMed

    Bi, Wenzhao; Jang, Geeng-Fu; Zhang, Lei; Crabb, John W; Laird, James; Linetsky, Mikhail; Salomon, Robert G

    2016-10-17

    Isolevuglandins (isoLGs) are stereo and structurally isomeric γ-ketoaldehydes produced through free radical-induced oxidation of arachidonates. Some isoLG isomers are also generated through enzymatic cyclooxygenation. Post-translational modification of proteins by isoLGs is associated with loss-of-function, cross-linking and aggregation. We now report that a low level of modification by one or two molecules of isoLG has a profound effect on the activity of a multi subunit protease, calpain-1. Modification of one or two key lysyl residues apparently suffices to abolish catalytic activity. Covalent modification of calpain-1 led to intersubunit cross-linking. Hetero- and homo-oligomers of the catalytic and regulatory subunits of calpain-1 were detected by SDS-PAGE with Western blotting. N-Acetyl-glycyl-lysine methyl ester and β-amyloid(11-17) peptide EVHHQKL were used as models for characterizing the cross-linking of protein lysyl residues resulting from adduction of iso[4]LGE2. Aminal, bispyrrole, and trispyrrole cross-links of these two peptides were identified and fully characterized by mass spectrometry. Aminal and bispyrrole dimers were both detected. Furthermore, a complex mixture of derivatives of the bispyrrole cross-link containing one or more additional atoms of oxygen was found. Interesting differences are evident in the predominant cross-link type generated in the reaction of iso[4]LGE2 with these peptides. More aminal cross-links versus bispyrrole are formed during the reaction of the dipeptide with iso[4]LGE2. In contrast, more bispyrrole versus aminal cross-links are formed during the reaction of EVHHQKL with iso[4]LGE2. It is tempting to speculate that the EVHHQKL peptide-pyrrole modification forms noncovalent aggregates that favor the production of covalent bispyrrole cross-links because β-amyloid(11-17) tends to spontaneously oligomerize.

  4. Structure enhancement methodology using theory and experiment: gas-phase molecular structures using a dynamic interaction between electron diffraction, molecular mechanics, and ab initio data.

    PubMed

    Kafka, Graeme R; Masters, Sarah L; Rankin, David W H

    2007-07-05

    A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).

  5. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    PubMed

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.

  6. Assessing protein conformational sampling and structural stability via de novo design and molecular dynamics simulations.

    PubMed

    Cunha, Keila C; Rusu, Victor H; Viana, Isabelle F T; Marques, Ernesto T A; Dhalia, Rafael; Lins, Roberto D

    2015-06-01

    Molecular dynamics and de novo techniques, associated to quality parameter sets, have excelled at determining the structure of small proteins with high accuracy. To achieve a detailed description of protein conformations, these methods must critically assess the thermodynamic features of the molecular ensembles. Here, a comparison of the conformational ensemble generated by molecular dynamics and de novo techniques were carried out for six Top7-based proteins carrying gp41 HIV-1 epitopes. The native Top7, a highly stable computationally designed protein, was used as benchmark. Structural stability, flexibility, and secondary structure content were assessed. The consistency of the latter was compared to experimental circular dichroism spectra for all proteins. While both methods are capable to identify the stable from unstable chimeric proteins, the sampled conformational space and flexibility differ significantly in both methods. Molecular dynamics simulations seem to better describe secondary structure content and identify regions responsible for conformational instability. The de novo method, as implemented in Rosetta-a prime tool for protein design, overestimates secondary structure content. On the other hand, its empirical energy function is capable to predict the threshold for protein stability.

  7. Using Molecular Replacement Phasing to Study the Structure and Function of RNA.

    PubMed

    Marcia, Marco

    2016-01-01

    In recent years a wide variety of RNA molecules regulating fundamental cellular processes has been discovered. Therefore, RNA structure determination is experiencing a boost and many more RNA structures are likely to be determined in the years to come. The broader availability of experimentally determined RNA structures implies that molecular replacement (MR) will be used more and more frequently as a method for phasing future crystallographic structures. In this report we describe various aspects relative to RNA structure determination by MR. First, we describe how to select and create MR search models for nucleic acids. Second, we describe how to perform MR searches on RNA using available crystallographic software. Finally, we describe how to refine and interpret the successful MR solutions. These protocols are applicable to determine novel RNA structures as well as to establish structural-functional relationships on existing RNA structures.

  8. Input and Input Processing in Second Language Acquisition.

    ERIC Educational Resources Information Center

    Alcon, Eva

    1998-01-01

    Analyzes second-language learners' processing of linguistic data within the target language, focusing on input and intake in second-language acquisition and factors and cognitive processes that affect input processing. Input factors include input simplification, input enhancement, and interactional modifications. Individual learner differences…

  9. Profiling of the molecular weight and structural isomer abundance of macroalgae-derived phlorotannins.

    PubMed

    Heffernan, Natalie; Brunton, Nigel P; FitzGerald, Richard J; Smyth, Thomas J

    2015-01-16

    Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4-12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

  10. Input Decimated Ensembles

    NASA Technical Reports Server (NTRS)

    Tumer, Kagan; Oza, Nikunj C.; Clancy, Daniel (Technical Monitor)

    2001-01-01

    Using an ensemble of classifiers instead of a single classifier has been shown to improve generalization performance in many pattern recognition problems. However, the extent of such improvement depends greatly on the amount of correlation among the errors of the base classifiers. Therefore, reducing those correlations while keeping the classifiers' performance levels high is an important area of research. In this article, we explore input decimation (ID), a method which selects feature subsets for their ability to discriminate among the classes and uses them to decouple the base classifiers. We provide a summary of the theoretical benefits of correlation reduction, along with results of our method on two underwater sonar data sets, three benchmarks from the Probenl/UCI repositories, and two synthetic data sets. The results indicate that input decimated ensembles (IDEs) outperform ensembles whose base classifiers use all the input features; randomly selected subsets of features; and features created using principal components analysis, on a wide range of domains.

  11. Evolving molecular cloud structure and the column density probability distribution function

    NASA Astrophysics Data System (ADS)

    Ward, Rachel L.; Wadsley, James; Sills, Alison

    2014-12-01

    The structure of molecular clouds can be characterized with the probability distribution function (PDF) of the mass surface density. In particular, the properties of the distribution can reveal the nature of the turbulence and star formation present inside the molecular cloud. In this paper, we explore how these structural characteristics evolve with time and also how they relate to various cloud properties as measured from a sample of synthetic column density maps of molecular clouds. We find that, as a cloud evolves, the peak of its column density PDF will shift to surface densities below the observational threshold for detection, resulting in an underlying lognormal distribution which has been effectively lost at late times. Our results explain why certain observations of actively star-forming, dynamically older clouds, such as the Orion molecular cloud, do not appear to have any evidence of a lognormal distribution in their column density PDFs. We also study the evolution of the slope and deviation point of the power-law tails for our sample of simulated clouds and show that both properties trend towards constant values, thus linking the column density structure of the molecular cloud to the surface density threshold for star formation.

  12. Molecular dynamics simulations of soliton-like structures in a dusty plasma medium

    SciTech Connect

    Tiwari, Sanat Kumar Das, Amita; Sen, Abhijit; Kaw, Predhiman

    2015-03-15

    The existence and evolution of soliton-like structures in a dusty plasma medium are investigated in a first principles approach using molecular dynamic (MD) simulations of particles interacting via a Yukawa potential. These localized structures are found to exist in both weakly and strongly coupled regimes with their structures becoming sharper as the correlation effects between the dust particles get stronger. A surprising result, compared to fluid simulations, is the existence of rarefactive soliton-like structures in our non-dissipative system, a feature that arises from the charge conjugation symmetry property of the Yukawa fluid. Our simulation findings closely resemble many diverse experimental results reported in the past.

  13. The Vertex Version of Weighted Wiener Number for Bicyclic Molecular Structures

    PubMed Central

    Gao, Wei; Wang, Weifan

    2015-01-01

    Graphs are used to model chemical compounds and drugs. In the graphs, each vertex represents an atom of molecule and edges between the corresponding vertices are used to represent covalent bounds between atoms. We call such a graph, which is derived from a chemical compound, a molecular graph. Evidence shows that the vertex-weighted Wiener number, which is defined over this molecular graph, is strongly correlated to both the melting point and boiling point of the compounds. In this paper, we report the extremal vertex-weighted Wiener number of bicyclic molecular graph in terms of molecular structural analysis and graph transformations. The promising prospects of the application for the chemical and pharmacy engineering are illustrated by theoretical results achieved in this paper. PMID:26640513

  14. Determination of molecular-ion structures through the use of accelerated beams

    SciTech Connect

    Gemmell, D.S.

    1987-01-01

    In this talk we report on recent research on molecular-ion structures using fast molecular-ion beams provided by Argonne's 5-MV Dynamitron accelerator. The method has become known as the ''Coulomb-explosion'' technique. When molecular-ion projectiles travelling at velocities of a few percent of the velocity of light strike a foil, the electrons that bind the molecular projectiles are almost always totally stripped off within the first few Angstroms of penetration into the solid target. This leaves a cluster of bare (or nearly bare) nuclei which separate rapidly as a result of their mutual Coulomb repulsion. This violent dissociation process in which the initial electrostatic potential energy is converted into kinetic energy of relative motion in the center-of-mass, has been termed a ''Coulomb explosion.'' 4 refs., 2 figs.

  15. Molecular structure and dynamical properties of niosome bilayers with and without cholesterol incorporation: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Ritwiset, Aksornnarong; Krongsuk, Sriprajak; Johns, Jeffrey Roy

    2016-09-01

    Niosomes are non-ionic surfactant vesicles having a bilayer structure formed by self-assembly of hydrated surfactants, usually with cholesterol incorporation. Stability and mechanical properties of niosomes strongly depend on type of non-ionic surfactants and compositions used. In this study we present the structural and dynamical properties of niosome bilayers composed of sorbitan monostearate (Span60) with 0% and 50% cholesterol compositions which are investigated by using molecular dynamics simulations. The simulations reveal that niosome bilayer without cholesterol prefer to form in the gel phase with a higher order structure, while in the presence of cholesterol the bilayer exhibits more fluidity having a less ordered structure. The niosome bilayer with 50% cholesterol inclusion shows an increase of area per lipid (∼11%) and thickness (∼39%) compared with the niosome bilayer without cholesterol. The Span60 tailgroup orientation of the niosome bilayers without cholesterol exhibits more tilt (34.5o ± 0.5) than that of the bilayer with 50% cholesterol (15.4o ± 0.8). Additionally, our results show that the addition of cholesterol to the bilayer causes the higher in lateral and transverse diffusion, as well as an increase in the hydrogen bond number between Span60 and water. Such characteristics not only enhance the niosome stability but also increase the fluidity, which are necessary for the niosomal drug delivery.

  16. Crystal structure and molecular dynamics studies of L-amino acid oxidase from Bothrops atrox.

    PubMed

    Feliciano, Patricia R; Rustiguel, Joane K; Soares, Ricardo O S; Sampaio, Suely V; Cristina Nonato, M

    2017-03-15

    L-amino acid oxidases (LAAOs) are dimeric flavoproteins that catalyze the deamination of L-amino acid to α-keto acid, producing ammonia and hydrogen peroxide. In this study, we report the crystal structure and molecular dynamics simulations of LAAO from the venom of Bothrops atrox (BatroxLAAO). BatroxLAAO presents several biological and pharmacological properties with promising biomedical applications. BatroxLAAO structure contains the highly conserved structural pattern of LAAOs comprising a FAD-binding domain, substrate-binding domain and helical domain, and a dimeric arrangement that can be stabilized by zinc. Also, molecular dynamics results show an asymmetric behavior, and a direct communication between FAD- and substrate-binding domains of counterpart subunits. These findings shed light on the structural role of dimerization to catalytic mechanism of SV-LAAOs.

  17. Structure and behavior of human α-thrombin upon ligand recognition: thermodynamic and molecular dynamics studies.

    PubMed

    Silva, Vivian de Almeira; Cargnelutti, Maria Thereza; Giesel, Guilherme M; Palmieri, Leonardo C; Monteiro, Robson Q; Verli, Hugo; Lima, Luis Mauricio T R

    2011-01-01

    Thrombin is a serine proteinase that plays a fundamental role in coagulation. In this study, we address the effects of ligand site recognition by alpha-thrombin on conformation and energetics in solution. Active site occupation induces large changes in secondary structure content in thrombin as shown by circular dichroism. Thrombin-D-Phe-Pro-Arg-chloromethyl ketone (PPACK) exhibits enhanced equilibrium and kinetic stability compared to free thrombin, whose difference is rooted in the unfolding step. Small-angle X-ray scattering (SAXS) measurements in solution reveal an overall similarity in the molecular envelope of thrombin and thrombin-PPACK, which differs from the crystal structure of thrombin. Molecular dynamics simulations performed with thrombin lead to different conformations than the one observed in the crystal structure. These data shed light on the diversity of thrombin conformers not previously observed in crystal structures with distinguished catalytic and conformational behaviors, which might have direct implications on novel strategies to design direct thrombin inhibitors.

  18. Molecular structure and the EPR calculation of the gas phase succinonitrile molecule

    NASA Astrophysics Data System (ADS)

    Kepceoǧlu, A.; Kılıç, H. Ş.; Dereli, Ö.

    2017-02-01

    Succinonitrile (i.e. butanedinitrile) is a colorless nitrile compound that can be used in the gel polymer batteries as a solid-state solvent electrolytes and has a plastic crystal structure. Prior to the molecular structure calculation of the succinonitrile molecule, the conformer analysis were calculated by using semi empirical method PM3 core type Hamiltonian and eight different conformer structures were determined. Molecular structure with energy related properties of these conformers having the lowest energy was calculated by using DFT (B3LYP) methods with 6-311++G(d,p) basis set. Possible radicals, can be formed experimentally, were modeled in this study. EPR parameters of these model radicals were calculated and then compared with that obtained experimentally.

  19. Search for Length Dependent Stable Structures of Polyglutamaine Proteins with Replica Exchange Molecular Dynamic

    NASA Astrophysics Data System (ADS)

    Kluber, Alexander; Hayre, Robert; Cox, Daniel

    2012-02-01

    Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.

  20. Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Whitfield, T. W.; Crain, J.; Martyna, G. J.

    2006-03-01

    In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.

  1. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    PubMed Central

    Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-01-01

    Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts. PMID:24189228

  2. De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation

    PubMed Central

    Maffeo, Christopher; Yoo, Jejoong; Aksimentiev, Aleksei

    2016-01-01

    The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Here we demonstrate a computational method that allows the equilibrium structure of a large, complex DNA origami object to be determined to atomic resolution. Through direct comparison with the results of cryo-electron microscopy, we demonstrate de novo reconstruction of a 4.7 megadalton pointer structure by means of fully atomistic molecular dynamics simulations. Furthermore, we show that elastic network-guided simulations performed without solvent can yield similar accuracy at a fraction of the computational cost, making this method an attractive approach for prototyping and validation of self-assembled DNA nanostructures. PMID:26980283

  3. Computational characterization of the molecular structure and properties of Dye 7 for organic photovoltaics.

    PubMed

    Baldenebro-López, Jesús; Castorena-González, José; Flores-Holguin, Norma; Calderón-Guillén, Joel; Glossman-Mitnik, Daniel

    2012-03-01

    Organic dyes have great potential for its use in solar cells. In this recent work, the molecular structure and properties of Dye 7 were obtained using density functional theory (DFT) and different levels of calculation. Upon comparing the molecular structure and the ultraviolet visible spectrum with experimental data reported in the literature, it was found that the M05-2X/6-31G(d) level of calculation gave the best approximation. Once the appropriate methodology had been obtained, the molecule was characterized by obtaining the infrared spectrum, dipole moment, total energy, isotropic polarizability, molecular orbital energies, free energy of solvation in different solvents, and the chemical reactivity sites using the condensed Fukui functions.

  4. CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

    PubMed Central

    2011-01-01

    CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. Annotations are enclosed in curly braces and anchored to an atomic node or at the end of the molecular graph depending on the annotation type. CurlySMILES includes predefined annotations for stereogenicity, electron delocalization charges, extra-molecular interactions and connectivity, surface attachment, solutions, and crystal structures and allows extensions for domain-specific annotations. CurlySMILES provides a shorthand format to encode molecules with repetitive substructural parts or motifs such as monomer units in macromolecules and amino acids in peptide chains. CurlySMILES further accommodates special formats for non-molecular materials that are commonly denoted by composition of atoms or substructures rather than complete atom connectivity. PMID:21214931

  5. Molecular structure of poly(methyl methacrylate) surface II: Effect of stereoregularity examined through all-atom molecular dynamics.

    PubMed

    Jha, Kshitij C; Zhu, He; Dhinojwala, Ali; Tsige, Mesfin

    2014-11-04

    Utilizing all-atom molecular dynamics (MD), we have analyzed the effect of tacticity and temperature on the surface structure of poly(methyl methacrylate) (PMMA) at the polymer-vacuum interface. We quantify these effects primarily through orientation, measured as the tilt with respect to the surface normal, and the surface number densities of the α-methyl, ester-methyl, carbonyl, and backbone methylene groups. Molecular structure on the surface is a complex interplay between orientation and number densities and is challenging to capture through sum frequency generation (SFG) spectroscopy alone. Independent quantification of the number density and orientation of chemical groups through all-atom MD presents a comprehensive model of stereoregular PMMA on the surface. SFG analysis presented in part I of this joint publication measures the orientation of molecules that are in agreement with MD results. We observe the ester-methyl groups as preferentially oriented, irrespective of tacticity, followed by the α-methyl and carbonyl groups. SFG spectroscopy also points to ester-methyl being dominant on the surface. The backbone methylene groups show a very broad angular distribution, centered along the surface plane. The surface number density ratios of ester-methyl to α-methyl groups show syndiotactic PMMA having the lowest value. Isotactic PMMA has the highest ratios of ester- to α-methyl. These subtle trends in the relative angular orientation and number densities that influence the variation of surface structure with tacticity are highlighted in this article. A more planar conformation of the syndiotactic PMMA along the surface (x-y plane) can be visualized through the trajectories from all-atom MD. Results from conformation tensor calculations for chains with any of their segments contributing to the surface validate the visual observation.

  6. Optimization of large amorphous silicon and silica structures for molecular dynamics simulations of energetic impacts

    NASA Astrophysics Data System (ADS)

    Samela, Juha; Norris, Scott A.; Nordlund, Kai; Aziz, Michael J.

    2011-07-01

    A practical method to create optimized amorphous silicon and silica structures for molecular dynamics simulations is developed and tested. The method is based on the Wooten, Winer, and Weaire algorithm and combination of small optimized blocks to larger structures. The method makes possible to perform simulations of either very large cluster hypervelocity impacts on amorphous targets or small displacements induced by low energy ion impacts in silicon.

  7. From Molecular Structure to Global Processes : NMR Spectroscopy in Analytical/Environmental Chemistry

    NASA Astrophysics Data System (ADS)

    Simpson, A.

    2009-04-01

    NMR Spectroscopy is arguably the most powerful tool to elucidate structure and probe molecular interactions. A range of NMR approaches will be introduced with emphasis on addressing and understanding structure and reactivity of soil organic matter at the molecular level. The presentation will be split into three main sections. The first section will look at evidence from advanced NMR based approaches that when considered synergistically describes the major structural components in soil organic matter. Multidimensional NMR spectroscopy (1-3D NMR), automated pattern matching, spectral simulations, diffusion NMR and hybrid-diffusion NMR will be introduced in context of molecular structure. Finally the structural components in soil will be contrasted to those found in aquatic dissolved organic matter. Secondly molecular interactions of natural organic matter will be considered. Advanced structural studies have provided detailed spectral assignments which in turn permit the reactivity of various soil components to be elucidated. Aggregation and self-association of soil and dissolved organic matter will be discussed along with the structural components likely responsible for aggregation/colloid formation. Interactions of soil organic matter with anthropogenic chemicals will also be considered and NMR techniques based on "Saturation Transfer Difference" introduced. These techniques are extremely powerful and can be used to both; describe mechanistically how anthropogenic chemicals sorb to whole soils and identify the structural components (lignin, protein, cellulose, etc..) that are responsible for the binding/sorption in soil. In the last section, the "big questions" and challenges facing the field will be considered along with some novel experimental NMR based approaches that should, in future, assist in providing answers to these questions.

  8. Conformation of the umifenovir cation in the molecular and crystal structures of four carboxylic acid salts

    NASA Astrophysics Data System (ADS)

    Orola, Liana; Sarcevica, Inese; Kons, Artis; Actins, Andris; Veidis, Mikelis V.

    2014-01-01

    The umifenovir salts of maleic, salicylic, glutaric, and gentisic acid as well as the chloroform solvate of the salicylate were prepared. Single crystals of the five compounds were obtained and their molecular and crystal structures determined by X-ray diffraction. In each structure the conformation of phenyl ring with respect to the indole group of the umifenovir moiety is different. The water solubility and melting points of the studied umifenovir salts have been determined.

  9. Molecular Modeling of Rigid-Rod Polymers Structures Dominated by Electrostatic Interactions

    DTIC Science & Technology

    2005-11-01

    the structure in solutions of PBO in strong acids . The role of the dielectric properties of the medium ( dielectric constant) and counterions. 1...morphology which the polymer adopts. We propose to undertake a molecular modeling study of the effect of strong acids on the structure and properties of PBO...methane sulphonic and chlorine sulphonic acids [5], (protons are connected with oxygen atoms as well). Besides we have considered also patially protonated

  10. Input transformation by dendritic spines of pyramidal neurons

    PubMed Central

    Araya, Roberto

    2014-01-01

    In the mammalian brain, most inputs received by a neuron are formed on the dendritic tree. In the neocortex, the dendrites of pyramidal neurons are covered by thousands of tiny protrusions known as dendritic spines, which are the major recipient sites for excitatory synaptic information in the brain. Their peculiar morphology, with a small head connected to the dendritic shaft by a slender neck, has inspired decades of theoretical and more recently experimental work in an attempt to understand how excitatory synaptic inputs are processed, stored and integrated in pyramidal neurons. Advances in electrophysiological, optical and genetic tools are now enabling us to unravel the biophysical and molecular mechanisms controlling spine function in health and disease. Here I highlight relevant findings, challenges and hypotheses on spine function, with an emphasis on the electrical properties of spines and on how these affect the storage and integration of excitatory synaptic inputs in pyramidal neurons. In an attempt to make sense of the published data, I propose that the raison d'etre for dendritic spines lies in their ability to undergo activity-dependent structural and molecular changes that can modify synaptic strength, and hence alter the gain of the linearly integrated sub-threshold depolarizations in pyramidal neuron dendrites before the generation of a dendritic spike. PMID:25520626

  11. 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…

  12. The History of Molecular Structure Determination Viewed through the Nobel Prizes.

    ERIC Educational Resources Information Center

    Jensen, William P.; Palenik, Gus J.; Suh, Il-Hwan

    2003-01-01

    Discusses the importance of complex molecular structures. Emphasizes their individual significance through examination of the Nobel Prizes of the 20th century. Highlights prizes awarded to Conrad Rontgen, Francis H.C. Crick, James D. Watson, Maurice H.F. Wilkins, and others. (SOE)

  13. Development and Assessment of a Molecular Structure and Properties Learning Progression

    ERIC Educational Resources Information Center

    Cooper, Melanie M.; Underwood, Sonia M.; Hilley, Caleb Z.; Klymkowsky, Michael W.

    2012-01-01

    Previously, we found that: (i) many students were unable to construct representations of simple molecular structures; (ii) a majority of students fail to make the important connection between these representations and macroscopic properties of the material; and (iii) they were unable to decode the information contained in such representations.…

  14. 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…

  15. Structure and Function: Insights into Bioinorganic Systems from Molecular Mechanics Calculations

    NASA Astrophysics Data System (ADS)

    Marques, Helder M.; Egan, Timothy J.; de Villiers, Katherine A.

    The use of empirical force field methods for modeling important systems in bioinorganic chemistry, including the cobalt corrins (derivatives of vitamin B12) and the iron porphyrins, is described. Particular attention is given to the use of molecular dynamics and simulated annealing calculations in exploring the solution structures of corrin, and those of likely complexes between the ferriprotoporphyrin-IX and the arylmethanol antimalarials.

  16. Looking beyond Lewis Structures: A General Chemistry Molecular Modeling Experiment Focusing on Physical Properties and Geometry

    ERIC Educational Resources Information Center

    Linenberger, Kimberly J.; Cole, Renee S.; Sarkar, Somnath

    2011-01-01

    We present a guided-inquiry experiment using Spartan Student Version, ready to be adapted and implemented into a general chemistry laboratory course. The experiment provides students an experience with Spartan Molecular Modeling software while discovering the relationships between the structure and properties of molecules. Topics discussed within…

  17. Structural Order in Water: Comparison between the Spectral Analysis of Raman Data and Molecular Dynamics Results

    NASA Astrophysics Data System (ADS)

    Faginas Lago, N.; Paolantoni, M.; Laganá, A.; Alberti, M.

    2007-12-01

    We utilize molecular dynamics calculations performed using the DL_POLY suite of programs to test the validity of two popular water interaction models and to better understand the structural order of its liquid phase by comparing calculated properties with the Raman spectrum.

  18. Molecular Docking of Enzyme Inhibitors: A Computational Tool for Structure-Based Drug Design

    ERIC Educational Resources Information Center

    Rudnitskaya, Aleksandra; Torok, Bela; Torok, Marianna

    2010-01-01

    Molecular docking is a frequently used method in structure-based rational drug design. It is used for evaluating the complex formation of small ligands with large biomolecules, predicting the strength of the bonding forces and finding the best geometrical arrangements. The major goal of this advanced undergraduate biochemistry laboratory exercise…

  19. Biological and Molecular Structure Analyses of the Controls on Soil Organic Matter Dynamics.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A combination of biological analysis, such as incubation and microbial biomass determination, 13C and 14C tracers, soil fractionation, and matrix analysis (LF, POM, silt, and clay) with molecular structure analysis (py-MBMS) on long-term sites with a C3 ' C4 crop switch provided the tools for determ...

  20. Well-ordered monolayers of alkali-doped coronene and picene: Molecular arrangements and electronic structures

    SciTech Connect

    Yano, M.; Endo, M.; Hasegawa, Y.; Okada, R.; Yamada, Y. Sasaki, M.

    2014-07-21

    Adsorptions of alkali metals (such as K and Li) on monolayers of coronene and picene realize the formation of ordered phases, which serve as well-defined model systems for metal-intercalated aromatic superconductors. Upon alkali-doping of the monolayers of coronene and picene, scanning tunneling microscopy and X-ray absorption spectroscopy revealed the rearrangement of the entire molecular layer. The K-induced reconstruction of both monolayers resulted in the formation of a structure with a herringbone-like arrangement of molecules, suggesting the intercalation of alkali metals between molecular planes. Upon reconstruction, a shift in both the vacuum level and core levels of coronene was observed as a result of a charge transfer from alkali metals to coronene. In addition, a new density of states near the Fermi level was formed in both the doped coronene and the doped picene monolayers. This characteristic electronic feature of the ordered monolayer has been also reported in the multilayer picene films, ensuring that the present monolayer can model the properties of the metal-intercalated aromatic hydrocarbons. It is suggested that the electronic structure near the Fermi level is sensitive to the molecular arrangement, and that both the strict control and determinations of the molecular structure in the doped phase should be important for the determination of the electronic structure of these materials.

  1. Photoinduced self-structured surface pattern on a molecular azo glass film: structure-property relationship and wavelength correlation.

    PubMed

    Wang, Xiaolin; Yin, Jianjun; Wang, Xiaogong

    2011-10-18

    In this study, three series of star-shaped molecular azo glasses were synthesized, and self-structured surface pattern formation on the azo compound films was studied by laser irradiation at different wavelengths. The molecular azo glasses were synthesized from three core precursors (Tr-AN, Tr-35AN, Tr-H35AN), which were prepared by ring-opening reactions between 1,3,5-triglycidyl isocyanurate and corresponding aniline derivatives. The star-shaped azo compounds were obtained through azo-coupling reactions between the core precursors and diazonium salts of 4-chloroaniline, 4-aminobenzonitrile, and 4-nitroaniline, respectively. By using the two-step reaction scheme, three series of azo compounds with different structures were obtained. The core precursors and azo compounds were characterized by using (1)H NMR, FT-IR, UV-vis, mass spectrometry, and thermal analyses. The self-structured surface pattern formation on films of the azo compounds was studied by irradiating the azo compound films with a normal-incident laser beam at different wavelengths (488, 532, and 589 nm). The results show that the photoinduced surface pattern formation behavior is closely related to the structure of the azo compounds, excitation wavelength, and light polarization conditions. The absorption band position of the π-π* transition is mainly determined by the electron-withdrawing groups on the azo chromophores. When the excitation wavelength is between λ(max) and the band tail at the longer wavelength side, the self-structured surface patterns can be more efficiently induced to form on the films. The 3,5-dimethyl substitution on azo chromophores inhibits the surface pattern formation for certain excitation wavelengths. Increasing molecular interaction also shows an effect of restraining the surface pattern formation. The irradiations with linearly and circularly polarized light cause significant differences in the alignment manner of the pillarlike structures and their saturated height.

  2. Structure of the thermolabile mutant aldolase B, A149P: molecular basis of hereditary fructose intolerance.

    PubMed

    Malay, Ali D; Allen, Karen N; Tolan, Dean R

    2005-03-18

    Hereditary fructose intolerance (HFI) is a potentially lethal inborn error in metabolism caused by mutations in the aldolase B gene, which is critical for gluconeogenesis and fructose metabolism. The most common mutation, which accounts for 53% of HFI alleles identified worldwide, results in substitution of Pro for Ala at position 149. Structural and functional investigations of human aldolase B with the A149P substitution (AP-aldolase) have shown that the mutation leads to losses in thermal stability, quaternary structure, and activity. X-ray crystallography is used to reveal the structural basis of these perturbations. Crystals of AP-aldolase are grown at two temperatures (4 degrees C and 18 degrees C), and the structure solved to 3.0 angstroms resolution, using the wild-type structure as the phasing model. The structures reveal that the single residue substitution, A149P, causes molecular disorder around the site of mutation (residues 148-159), which is propagated to three adjacent beta-strand and loop regions (residues 110-129, 189-199, 235-242). Disorder in the 110-129-loop region, which comprises one subunit-subunit interface, provides an explanation for the disrupted quaternary structure and thermal instability. Greater structural perturbation, particularly at a Glu189-Arg148 salt bridge in the active-site architecture, is observed in the structure determined at 18 degrees C, which could explain the temperature-dependent loss in activity. The disorder revealed in these structures is far greater than that predicted by homology modeling and underscores the difficulties in predicting perturbations of protein structure and function by homology modeling alone. The AP-aldolase structure reveals the molecular basis of a hereditary disease and represents one of only a few structures known for mutant proteins at the root of the thousands of other inherited disorders.

  3. IR spectrum simulation of molecular structure model of Shendong coal vitrinite by using quantum chemistry method.

    PubMed

    Jia, Jian-Bo; Wang, Ying; Li, Feng-Hai; Yi, Gui-Yun; Zeng, Fan-Gui; Guo, Hong-Yu

    2014-01-01

    The structure of coal needs to be understood from a molecular point of view for clean, effective and high value-added utilization of coal. In the literature, molecular structure model of Shendong coal vitrinite (SV) was established by the authors on the basis of experimental results of ultimate analysis and 13C NMR, and the calculated 13C NMR spectrum of SV model was consistent with the experimental spectrum. In order to further verify the accuracy of SV structure model established by the authors, the infrared spectrum of SV structure model was calculated using quantum chemistry semi-empirical VAMP in this thesis. The results showed that the peak shape of calculated IR spectrum of SV structure model was similar to the experiment's, but the wave number of calculated IR spectrum was obviously higher than that of experimental spectrum. According to the calculated results for model compounds by using the same method, calculated vibrational frequency was higher than that of experiment for the same functional groups. Hence, the calculated IR spectrum should be corrected. After correction the calculated IR spectrum of SV structure model matched well with the experimental spectrum. In other words, the SV structure model can truly reflect the structure characteristics of SV.

  4. Theoretical Study of Donor - Spacer - Acceptor Structure Molecule for Molecular Rectifier

    NASA Astrophysics Data System (ADS)

    Mizuseki, Hiroshi; Kenji, Niimura; Belosludov, Rodion; Farajian, Amir; Kawazoe, Yoshiyuki

    2003-03-01

    Recently, the molecular electronics has attracted strong attention as a ``post-silicone technology'' to establish a future nanoscale electronic devices. To realize this molecular device, unimolecular rectifiering function is one of the most important constituents in nanotechnology [C. Majumder, H. Mizuseki, and Y. Kawazoe, Molecular Scale Rectifier: Theoretical Study, J. Phys. Chem. A, 105 (2001) 9454-9459.]. In the present study, the geometric and electronic structure of alkyl derivative C37H50N4O4 (PNX) molecule, (donor - spacer - acceptor), a leading candidate of molecular rectifying device, has been investigated theoretically using ab initio quantum mechanical calculation. The results suggest that in such donor-acceptor molecular complexes, while the lowest unoccupied orbital concentrates on the acceptor subunit, the highest occupied molecular orbital is localized on the donor subunit. The approximate potential differences for optimized PNX molecule have been estimated at the B3PW91/6-311g++(d,p) level of theory, which achieves quite good agreement with experimentally reported results. This study was performed through Special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government.

  5. Molecular dynamics simulations of H2 adsorption in tetramethyl ammonium lithium phthalocyanine crystalline structures.

    PubMed

    Lamonte, Kevin; Gómez Gualdrón, Diego A; Cabrales-Navarro, Fredy A; Scanlon, Lawrence G; Sandi, Giselle; Feld, William; Balbuena, Perla B

    2008-12-11

    Tetramethyl ammonium lithium phthalocyanine is explored as a potential material for storage of molecular hydrogen. Density functional theory calculations are used to investigate the molecular structure and the dimer conformation. Additional scans performed to determine the interactions of a H2 molecule located at various distances from the molecular sites are used to generate a simple force field including dipole-induced-dipole interactions. This force field is employed in molecular dynamics simulations to calculate adsorption isotherms at various pressures. The regions of strongest adsorption are quantified as functions of temperature, pressure, and separation between molecules in the adsorbent phase, and compared to the regions of strongest binding energy as given by the proposed force field. It is found that the total adsorption could not be predicted only from the spatial distribution of the strongest binding energies; the available volume is the other contributing factor even if the volume includes regions of much lower binding energy. The results suggest that the complex anion is primarily involved in the adsorption process with molecular hydrogen, whereas the cation serves to provide access for hydrogen adsorption in both sides of the anion molecular plane, and spacing between the planes.

  6. [Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

    PubMed

    Abaturov, L V; Nosova, N G

    2013-01-01

    The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the

  7. Molecular genetic structure-function analysis of translation initiation factor eIF5B.

    PubMed

    Shin, Byung-Sik; Dever, Thomas E

    2007-01-01

    Recently, significant progress has been made in obtaining three-dimensional (3-D) structures of the factors that promote translation initiation, elongation, and termination. These structures, when interpreted in light of previous biochemical characterizations of the factors, provide significant insight into the function of the factors and the molecular mechanism of specific steps in the translation process. In addition, genetic analyses in yeast have helped elucidate the in vivo roles of the factors in various steps of the translation pathway. We have combined these two approaches and use molecular genetic studies to define the structure-function properties of translation initiation factors in the yeast Saccharomyces cerevisiae. In this chapter, we describe our multistep approach in which we first characterize a site-directed mutant of the factor of interest using in vivo and in vitro assays of protein synthesis. Next, we subject the mutant gene to random mutagenesis and screen for second-site mutations that restore the factor's function in vivo. Following biochemical and in vivo characterization of the suppressor mutant, we interpret the results in light of the 3-D structure of the factor to define the structure-function properties of the factor and to provide new molecular insights into the mechanism of translation.

  8. Using solvents with different molecular sizes to investigate the structure of Antheraea pernyi silk.

    PubMed

    Wang, Yu; Porter, David; Shao, Zhengzhong

    2013-11-11

    The interaction between silk and polar solvents of different molecular size can be an important tool for understanding the structural features of natural silk; in particular, the disordered regions associated with the key property of mechanical toughness. In this work, we investigate the transitions induced in the tensile performance and structure of as-reeled Antheraea pernyi silks from different silkworms by a range of solvents that can only soften the protein chains in the amorphous regions. The results indicate that polar solvents with different molecular sizes affect the silk to different degrees, and silks with slightly different structures display significantly different tensile performance in the same solvent. The solvent molecular size is quantitatively correlated with the accessible volume in the amorphous regions before and after the yield point, which suggests that the volume accessible to the solvent molecules decreases as the solvent radius increases. Moreover, silks with more ordered structure (less free volume) in the amorphous regions are less sensitive to solvents than those with more disordered structures. However, silks with higher free volume have higher toughness due to the greater strain to failure.

  9. Structural characterization of interfacial n-octanol and 3-octanol using molecular dynamic simulations.

    PubMed

    Napoleon, Raeanne L; Moore, Preston B

    2006-03-02

    Structurally isomeric octanol interfacial systems, water/vapor, 3-octanol/vapor, n-octanol/vapor, 3-octanol/water, and n-octanol/water are investigated at 298 K using molecular dynamics simulation techniques. The present study is intended to investigate strongly associated liquid/liquid interfaces and probe the atomistic structure of these interfaces. The octanol and water molecules were initially placed randomly into a box and were equilibrated using constant pressure techniques to minimize bias within the initial conditions as well as to fully sample the structural conformations of the interface. An interface formed via phase separation during equilibration and resulted in a slab geometry with a molecularly sharp interface. However, some water molecules remained within the octanol phase with a mole fraction of 0.12 after equilibration. The resulting "wet" octanol interfaces were analyzed using density profiles and orientational order parameters. Our results support the hypothesis of an ordered interface only 1 or 2 molecular layers deep before bulk properties are reached for both the 3-octanol and water systems. However, in contrast to most other interfacial systems studied by molecular dynamics simulations, the n-octanol interface extends for several molecular layers. The octanol hydroxyl groups form a hydrogen-bonding network with water which orders the surface molecules toward a preferred direction and produces a hydrophilic/hydrophobic layering. The ordered n-octanol produces an oscillating low-high density of oxygen atoms out of phase with a high-low density of carbon atoms, consistent with an oscillating dielectric. In contrast, the isomeric 3-octanol has only a single carbon-rich layer directly proximal to the interface, which is a result of the different molecular topology. Both 3-octanol and n-octanol roughen the water interface with respect to the water/vapor interface. The "wet" octanol phases, in the octanol/water systems reach bulk properties in a

  10. Ultra-spatial synchrotron radiation for imaging molecular chemical structure: Applications in plant and animal studies

    DOE PAGES

    Yu, Peiqiang

    2007-01-01

    Synchrotron-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical features and make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced synchrotron technique to the study of plant and animal tissues' inherent structure at a cellular or subcellular level. In this article, a novel approach was introduced to show the potential of themore » newly developed, advanced synchrotron-based analytical technology, which can be used to reveal molecular structural-chemical features of various plant and animal tissues.« less

  11. Chemically directing d-block heterometallics to nanocrystal surfaces as molecular beacons of surface structure

    SciTech Connect

    Rosen, Evelyn L.; Gilmore, Keith; Sawvel, April M.; Hammack, Aaron T.; Doris, Sean E.; Aloni, Shaul; Altoe, Virginia; Nordlund, Dennis; Weng, Tsu -Chien; Sokaras, Dimosthenis; Cohen, Bruce E.; Urban, Jeffrey J.; Ogletree, D. Frank; Milliron, Delia J.; Prendergast, David; Helms, Brett A.

    2015-07-28

    Our understanding of structure and bonding in nanoscale materials is incomplete without knowledge of their surface structure. Needed are better surveying capabilities responsive not only to different atoms at the surface, but also their respective coordination environments. We report here that d-block organometallics, when placed at nanocrystal surfaces through heterometallic bonds, serve as molecular beacons broadcasting local surface structure in atomic detail. This unique ability stems from their elemental specificity and the sensitivity of their d-orbital level alignment to local coordination environment, which can be assessed spectroscopically. Re-surfacing cadmium and lead chalcogenide nanocrystals with iron- or ruthenium-based molecular beacons is readily accomplished with trimethylsilylated cyclopentadienyl metal carbonyls. For PbSe nanocrystals with iron-based beacons, we show how core-level X-ray spectroscopies and DFT calculations enrich our understanding of both charge and atomic reorganization at the surface when beacons are bound.

  12. Structures and stabilities of diacetylene-expanded polyhedranes by quantum mechanics and molecular mechanics.

    PubMed

    Jarowski, Peter D; Diederich, François; Houk, Kendall N

    2005-03-04

    The structures, heats of formation, and strain energies of diacetylene (buta-1,3-diynediyl) expanded molecules have been computed with ab initio and molecular mechanics calculations. Expanded cubane, prismane, tetrahedrane, and expanded monocyclics and bicyclics were optimized at the HF/6-31G(d) and B3LYP/6-31G(d) levels. The heats of formation of these systems were obtained from isodesmic equations at the HF/6-31G(d) level. Heats of formation were also calculated from Benson group equivalents. The strain energies of these expanded molecules were estimated by several independent methods. An adapted MM3 molecular mechanics force field, specifically parametrized to treat conjugated acetylene units, was employed for one measure of strain energy and as an additional method for structural analysis. Expanded dodecahedrane and icosahedrane were calculated by this method. Expanded molecules were considered structurally in the context of their potential material applications.

  13. Novel aldehyde and thiosemicarbazone derivatives: Synthesis, spectroscopic characterization, structural studies and molecular docking studies

    NASA Astrophysics Data System (ADS)

    Karakurt, Tuncay; Tahtaci, Hakan; Subasi, Nuriye Tuna; Er, Mustafa; Ağar, Erbil

    2016-12-01

    In this study our purpose is that, synthesis and characterization of compounds containing the aldehyde and thiosemicarbazone groups and comparison of the theoretical results with the experimental results. The structures of all synthesized compounds were elucidated by IR, 1H NMR, 13C NMR, elemental analyses techniques. The structure of compound (4) (C9H8N4O2S) was also elucidated by X-ray diffraction analysis. In addition, the theoretical IR spectrum, 1H NMR and 13C NMR chemical shift values, frontier molecular orbital values (FMO) of these molecules were analyzed by using Becke-3- Lee-Yang-Parr (B3LYP) method with LanL2DZ basis set. Finally, molecular docking studies were performed on synthesized compounds using the 4DKI beta-lactam protein structure to determine the potential binding mode of inhibitors.

  14. Molecular Dynamics Study of Carbon Nanotubes/Polyamide Reverse Osmosis Membranes: Polymerization, Structure, and Hydration.

    PubMed

    Araki, Takumi; Cruz-Silva, Rodolfo; Tejima, Syogo; Takeuchi, Kenji; Hayashi, Takuya; Inukai, Shigeki; Noguchi, Toru; Tanioka, Akihiko; Kawaguchi, Takeyuki; Terrones, Mauricio; Endo, Morinobu

    2015-11-11

    Carbon nanotubes/polyamide (PA) nanocomposite thin films have become very attractive as reverse osmosis (RO) membranes. In this work, we used molecular dynamics to simulate the influence of single walled carbon nanotubes (SWCNTs) in the polyamide molecular structure as a model case of a carbon nanotubes/polyamide nanocomposite RO membrane. It was found that the addition of SWCNTs decreases the pore size of the composite membrane and increases the Na and Cl ion rejection. Analysis of the radial distribution function of water confined in the pores of the membranes shows that SWCNT+PA nanocomposite membranes also exhibit smaller clusters of water molecules within the membrane, thus suggesting a dense membrane structure (SWCNT+PA composite membranes were 3.9% denser than bare PA). The results provide new insights into the fabrication of novel membranes reinforced with tubular structures for enhanced desalination performance.

  15. Structural and dynamic properties of calcium aluminosilicate melts: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Bouhadja, M.; Jakse, N.; Pasturel, A.

    2013-06-01

    The structural and dynamic properties of calcium aluminosilicate (CaO-Al2O3)1-x(SiO2)x melts with low silica content, namely, along the concentration ratio R = 1 are studied by classical molecular dynamics. An empirical potential has been developed here on the basis of our previous ab initio molecular dynamics. The new potential gives a description of the structural as well as the dynamics with a good accuracy. The self-intermediate scattering function and associated α-relaxation times are analyzed within the mode-coupling theory. Our results indicate a decrease of the fragility whose structural origin is a reduction of the number of fivefold coordinated Al atoms and non-bridging oxygen.

  16. Chemically directing d-block heterometallics to nanocrystal surfaces as molecular beacons of surface structure

    DOE PAGES

    Rosen, Evelyn L.; Gilmore, Keith; Sawvel, April M.; ...

    2015-07-28

    Our understanding of structure and bonding in nanoscale materials is incomplete without knowledge of their surface structure. Needed are better surveying capabilities responsive not only to different atoms at the surface, but also their respective coordination environments. We report here that d-block organometallics, when placed at nanocrystal surfaces through heterometallic bonds, serve as molecular beacons broadcasting local surface structure in atomic detail. This unique ability stems from their elemental specificity and the sensitivity of their d-orbital level alignment to local coordination environment, which can be assessed spectroscopically. Re-surfacing cadmium and lead chalcogenide nanocrystals with iron- or ruthenium-based molecular beacons ismore » readily accomplished with trimethylsilylated cyclopentadienyl metal carbonyls. For PbSe nanocrystals with iron-based beacons, we show how core-level X-ray spectroscopies and DFT calculations enrich our understanding of both charge and atomic reorganization at the surface when beacons are bound.« less

  17. Correlating Molecular Structures with Transport Dynamics in High-Efficiency Small-Molecule Organic Photovoltaics.

    PubMed

    Peng, Jiajun; Chen, Yani; Wu, Xiaohan; Zhang, Qian; Kan, Bin; Chen, Xiaoqing; Chen, Yongsheng; Huang, Jia; Liang, Ziqi

    2015-06-24

    Efficient charge transport is a key step toward high efficiency in small-molecule organic photovoltaics. Here we applied time-of-flight and organic field-effect transistor to complementarily study the influences of molecular structure, trap states, and molecular orientation on charge transport of small-molecule DRCN7T (D1) and its analogue DERHD7T (D2). It is revealed that, despite the subtle difference of the chemical structures, D1 exhibits higher charge mobility, the absence of shallow traps, and better photosensitivity than D2. Moreover, charge transport is favored in the out-of-plane structure within D1-based organic solar cells, while D2 prefers in-plane charge transport.

  18. Establishing whether the structural feature controlling the mechanical properties of starch films is molecular or crystalline.

    PubMed

    Li, Ming; Xie, Fengwei; Hasjim, Jovin; Witt, Torsten; Halley, Peter J; Gilbert, Robert G

    2015-03-06

    The effects of molecular and crystalline structures on the tensile mechanical properties of thermoplastic starch (TPS) films from waxy, normal, and high-amylose maize were investigated. Starch structural variations were obtained through extrusion and hydrothermal treatment (HTT). The molecular and crystalline structures were characterized using size-exclusion chromatography and X-ray diffractometry, respectively. TPS from high-amylose maize showed higher elongation at break and tensile strength than those from normal maize and waxy maize starches when processed with 40% plasticizer. Within the same amylose content, the mechanical properties were not affected by amylopectin molecular size or the crystallinity of TPS prior to HTT. This lack of correlation between the molecular size, crystallinity and mechanical properties may be due to the dominant effect of the plasticizer on the mechanical properties. Further crystallization of normal maize TPS by HTT increased the tensile strength and Young's modulus, while decreasing the elongation at break. The results suggest that the crystallinity from the remaining ungelatinized starch granules has less significant effect on the mechanical properties than that resulting from starch recrystallization, possibly due to a stronger network from leached-out amylose surrounding the remaining starch granules.

  19. Kinked structures of isolated nicotinic receptor M2 helices: a molecular dynamics study.

    PubMed

    Sankararamakrishnan, R; Samsom, M S

    1994-12-01

    The pore-lining M2 helix of the nicotinic acetylcholine receptor exhibits a pronounced kink when the corresponding ion channel is in a closed conformation [N. Unwin (1993) Journal of Molecular Biology, Vol. 229, pp. 1101-1124]. We have performed molecular dynamics simulations of isolated 22-residue M2 helices in order to identify a possible molecular origin of this kink. In order to sample a wide range of conformational space, a simulated annealing protocol was used to generate five initial M2 helix structures, each of which was subsequently used as the basis of 300 ps MD simulations. Two helix sequences (M2 alpha and M2 delta) were studied in this manner, resulting in a total of ten 300 ps trajectories. Kinked helices present in the trajectories were identified and energy minimized to yield a total of five different stable kinked structures. For comparison, a similar molecular dynamics simulation of a Leu23 helix yielded no stable kinked structures. In four of the five kinked helices, the kink was stabilized by H bonds between the helix backbone and polar side-chain atoms. Comparison with data from the literature on site-directed mutagenesis of M2 residues suggests that such polar side-chain to main-chain H bonds may also contribute to kinking of M2 helices in the intact channel protein.

  20. Mechanically interlocked daisy-chain-like structures as multidimensional molecular muscles

    NASA Astrophysics Data System (ADS)

    Chang, Jia-Cheng; Tseng, Shin-Han; Lai, Chien-Chen; Liu, Yi-Hung; Peng, Shie-Ming; Chiu, Sheng-Hsien

    2016-09-01

    Daisy chains (DCs) are garlands of flowers that can be worn as bracelets and necklaces. As a result of their beautiful interlocked structures and possible muscle-like motions, cyclic molecular DCs ([cn]DCs, where n is the number of repeating units) have long been attractive synthetic targets for supramolecular chemists. Herein we report artificial molecular muscles that—unlike one-dimensional (1D) biological muscles—contract and stretch in 2D or 3D. These systems have the structures of [c3]- and [c4]DCs with subcomponents that operate as molecular switches, powered through the addition or removal of Zn2+ ions to impart muscle-like behaviour. We assembled these [c3]- and [c4]DCs selectively by exploiting structural rigidity, coordination geometries and bond rotational barriers that disfavoured the formation of smaller homologues. The switching phenomena of our [c3]- and [c4]DCs resulted in the contracted molecular muscles stretching by approximately 23 and 36%, respectively, comparable to the value (27%) for linear biological muscles.

  1. Reconstruction of three-dimensional molecular structure from diffraction of laser-aligned molecules

    PubMed Central

    Yang, Jie; Makhija, Varun; Kumarappan, Vinod; Centurion, Martin

    2014-01-01

    Diffraction from laser-aligned molecules has been proposed as a method for determining 3-D molecular structures in the gas phase. However, existing structural retrieval algorithms are limited by the imperfect alignment in experiments and the rotational averaging in 1-D alignment. Here, we demonstrate a two-step reconstruction comprising a genetic algorithm that corrects for the imperfect alignment followed by an iterative phase retrieval method in cylindrical coordinates. The algorithm was tested with simulated diffraction patterns. We show that the full 3-D structure of trifluorotoluene, an asymmetric-top molecule, can be reconstructed with atomic resolution. PMID:26798781

  2. Demonstration of molecular beam epitaxy and a semiconducting band structure for I-Mn-V compounds

    SciTech Connect

    Jungwirth, T.; Novak, V.; Cukr, M.; Zemek, J.; Marti, X.; Horodyska, P.; Nemec, P.; Holy, V.; Maca, F.; Shick, A. B.; Masek, J.; Kuzel, P.; Nemec, I.; Gallagher, B. L.; Campion, R. P.; Foxon, C. T.; Wunderlich, J.

    2011-01-15

    Our ab initio theory calculations predict a semiconducting band structure of I-Mn-V compounds. We demonstrate on LiMnAs that high-quality materials with group-I alkali metals in the crystal structure can be grown by molecular beam epitaxy. Optical measurements on the LiMnAs epilayers are consistent with the theoretical electronic structure. Our calculations also reproduce earlier reports of high antiferromagnetic ordering temperature and predict large, spin-orbit-coupling-induced magnetic anisotropy effects. We propose a strategy for employing antiferromagnetic semiconductors in high-temperature semiconductor spintronics.

  3. Structural and spectral characterizations of C1C2 channelrhodopsin and its mutants by molecular simulations

    NASA Astrophysics Data System (ADS)

    Kamiya, Motoshi; Kato, Hideaki E.; Ishitani, Ryuichiro; Nureki, Osamu; Hayashi, Shigehiko

    2013-01-01

    Molecular dynamics (MD) simulations and excitation energy calculations of C1C2 chimera channelrhodopsin, a light-gated ion channel protein utilized as a biotechnological tool for optogenetics, based on a protein structure determined recently by X-ray crystallography were performed to investigate its structural and spectral properties. The MD simulations showed stability of hydrogen-bonds responsible for the channel gating observed in the crystallographic structural model. Analysis of electrostatic contribution of the surrounding protein groups to the absorption energy proposes several site-specific mutations that shift absorption maxima significantly, and provides a clear and controlled guide for engineering design of color variant proteins utilized in optogenetics.

  4. Atomic structure evolution during solidification of liquid niobium from ab initio molecular dynamics simulations

    SciTech Connect

    Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.

    2013-12-12

    Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt–Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.

  5. The cluster structure of dilute aqueous-alcoholic solutions and molecular light scattering in them

    NASA Astrophysics Data System (ADS)

    Malomuzh, N. P.; Slinchak, E. L.

    2007-11-01

    The structures, equations of state, and character of fluctuations of dilute water-glycerol solutions are discussed. Two or three glycerol and about ten water molecules were found to form a fairly stable molecular complex. We call this complex elementary cluster (pseudoparticle). In a certain region of state parameters, the system could be considered a solution of pseudoparticles (clusters). Its properties were modeled by the van der Waals equation. The character of interactions between clusters was analyzed. An anomalous increase in concentration and molecular light scattering fluctuations was caused by the approach to the solution “pseudospinodal.” The experimental data were found to be in quite satisfactory agreement with theoretical estimates.

  6. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    PubMed Central

    Hao, Yajiang; Inhester, Ludger; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-01-01

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging. PMID:26798806

  7. THE ROTATING MOLECULAR STRUCTURES AND THE IONIZED OUTFLOW ASSOCIATED WITH IRAS 16547-4247

    SciTech Connect

    Franco-Hernandez, Ramiro; Moran, James M.; RodrIguez, Luis F.; Garay, Guido

    2009-08-20

    We present Very Large Array 1.3 cm radio continuum and water maser observations as well as Submillimeter Array SO{sub 2} (226.300 GHz) and 1.3 mm dust continuum observations toward the massive star formation region IRAS 16547-4247. We find evidence of multiple sources in the central part of the region. There is evidence of a rotating structure associated with the most massive of these sources, traced at small scales ({approx}50 AU) by the water masers. At large scales ({approx}1000 AU), we find a velocity gradient in the SO{sub 2} molecular emission with a barely resolved structure that can be modeled as a rotating ring or two separate objects. The velocity gradients of the masers and of the molecular emission have the same sense and may trace the same structure at different size scales. The position angles of the structures associated with the velocity gradients are roughly perpendicular to the outflow axis observed in radio continuum and several molecular tracers. We estimate the mass of the most massive central source to be around 30 solar masses from the velocity gradient in the water maser emission. The main source of error in this estimate is the radius of the rotating structure. We also find water masers that are associated with the large-scale molecular outflow of the system, as well as water masers that are associated with other sources in the region. Our results suggest that the formation of this source, one of the most luminous protostars or protostellar clusters known, is taking place with the presence of ionized jets and disk-like structures.

  8. Probing the evolution of molecular cloud structure. II. From chaos to confinement

    NASA Astrophysics Data System (ADS)

    Kainulainen, J.; Beuther, H.; Banerjee, R.; Federrath, C.; Henning, T.

    2011-06-01

    We present an analysis of the large-scale molecular cloud structure and of the stability of clumpy structures in nearby molecular clouds. In our recent work, we identified a structural transition in molecular clouds by studying the probability distributions of their gas column densities. In this paper, we further examine the nature of this transition. The transition takes place at the visual extinction of A_V^tail = 2{-4} mag, or equivalently, at Σtail ≈ 40-80 M⊙ pc-2. The clumps identified above this limit have wide ranges of masses and sizes, but a remarkably constant mean volume density of overline{n ≈ 10^3} cm-3. This is 5-10 times higher than the density of the medium surrounding the clumps. By examining the stability of the clumps, we show that they are gravitationally unbound entities, and that the external pressure from the parental molecular cloud is a significant source of confining pressure for them. Then, the structural transition at A_V^tail may be linked to a transition between this population and the surrounding medium. The star-formation rates in the clouds correlate strongly with the total mass in the clumps, i.e., with the mass above A_V^tail, and drops abruptly below that threshold. These results imply that the formation of pressure-confined clumps introduces a prerequisite for star formation. Furthermore, they give a physically motivated explanation for the recently reported relation between the star-formation rates and the amount of dense material in molecular clouds. Likewise, they give rise to a natural threshold for star formation at A_V^tail.

  9. Molecular simulation studies of the structure of phosphorylcholine self-assembled monolayers

    NASA Astrophysics Data System (ADS)

    Zheng, Jie; He, Yi; Chen, Shengfu; Li, Lingyan; Bernards, Matthew T.; Jiang, Shaoyi

    2006-11-01

    We report a study of the structure of phosphorylcholine self-assembled monolayers (PC-SAMs) on Au(111) surfaces using both molecular mechanics (MM) and molecular dynamics (MD) simulation techniques. The lattice structure (i.e., packing densities and patterns) of the PC chains was determined first, by examining the packing energies of different structures by MM simulations in an implicit solvent. The chain orientation (i.e., antiparallel and parallel arrangements of the PC head groups) was then evaluated. The initial azimuthal angles of the PC chains were also adjusted to ensure that the optimal lattice structure was found. Finally, the two most probable lattice structures were solvated with explicit water molecules and their energies were compared after 1.5ns of MD simulations to verify the optimal structures obtained from MM. We found that the optimal lattice structure of the PC-SAM corresponds to a √7×√7 R19° lattice structure (i.e., surface coverage of 50.4Å2/molecule) with a parallel arrangement of the head groups. The corresponding thickness of the optimal PC-SAM is 13.4Å which is in agreement with that from experiments. The head groups of the PC chains are aligned on the surface in such a way that their dipole components are minimized. The P →N vector of the head groups forms an angle of 82° with respect to the surface normal. The tilt direction of molecular chains was observed to be towards their next nearest neighbor.

  10. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

    PubMed

    Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Dror, Ron O; Shaw, David E

    2012-08-01

    Accurate computational prediction of protein structure represents a longstanding challenge in molecular biology and structure-based drug design. Although homology modeling techniques are widely used to produce low-resolution models, refining these models to high resolution has proven difficult. With long enough simulations and sufficiently accurate force fields, molecular dynamics (MD) simulations should in principle allow such refinement, but efforts to refine homology models using MD have for the most part yielded disappointing results. It has thus far been unclear whether MD-based refinement is limited primarily by accessible simulation timescales, force field accuracy, or both. Here, we examine MD as a technique for homology model refinement using all-atom simulations, each at least 100 μs long-more than 100 times longer than previous refinement simulations-and a physics-based force field that was recently shown to successfully fold a structurally diverse set of fast-folding proteins. In MD simulations of 24 proteins chosen from the refinement category of recent Critical Assessment of Structure Prediction (CASP) experiments, we find that in most cases, simulations initiated from homology models drift away from the native structure. Comparison with simulations initiated from the native structure suggests that force field accuracy is the primary factor limiting MD-based refinement. This problem can be mitigated to some extent by restricting sampling to the neighborhood of the initial model, leading to structural improvement that, while limited, is roughly comparable to the leading alternative methods.

  11. Dynamic Structural Changes in a Molecular Zeolite-Supported Iridium Catalyst for Ethene Hydrogenation

    SciTech Connect

    Uzun, Alper; Gates, Bruce C.

    2009-11-16

    The structure of a catalyst often changes as a result of changes in the reactive environment during operation. Examples include changes in bulk phases, extended surface structures, and nanoparticle morphologies; now we report real-time characterization of changes in the structure of a working supported catalyst at the molecular level. Time-resolved extended X-ray absorption fine structure (EXAFS) data demonstrate the reversible interconversion of mononuclear iridium complexes and tetrairidium clusters inside zeolite Y cages, with the structure controlled by the C{sub 2}H{sub 4}/H{sub 2} ratio during ethene hydrogenation at 353 K. The data demonstrate break-up of tetrairidium clusters into mononuclear complexes indicated by a decrease in the Ir-Ir coordination number in ethene-rich feed. When the feed composition was switched to first equimolar and then to a H{sub 2}-rich (C{sub 2}H{sub 4}/H{sub 2} = 0.3) feed, the EXAFS spectra show the reformation of tetrairidium clusters as the Ir-Ir coordination number increased again. When the feed composition was cycled from ethene-rich to H{sub 2}-rich, the predominant species in the catalyst cycled accordingly. Evidence confirming the structural change is provided by IR spectra of iridium carbonyls formed by probing of the catalyst with CO. The data are the first showing how to tune the structure of a solid catalyst at the molecular scale by choice of the reactant composition.

  12. A tetraphenylethylene core-based 3D structure small molecular acceptor enabling efficient non-fullerene organic solar cells.

    PubMed

    Liu, Yuhang; Mu, Cheng; Jiang, Kui; Zhao, Jingbo; Li, Yunke; Zhang, Lu; Li, Zhengke; Lai, Joshua Yuk Lin; Hu, Huawei; Ma, Tingxuan; Hu, Rongrong; Yu, Demei; Huang, Xuhui; Tang, Ben Zhong; Yan, He

    2015-02-01

    A tetraphenylethylene core-based small molecular acceptor with a unique 3D molecular structure is developed. Bulk-heterojunction blend films with a small feature size (≈20 nm) are obtained, which lead to non-fullerene organic solar cells (OSCs) with 5.5% power conversion efficiency. The work provides a new molecular design approach to efficient non-fullerene OSCs based on 3D-structured small-molecule acceptors.

  13. Molecular modeling of phosphorylation sites in proteins using a database of local structure segments.

    PubMed

    Plewczynski, Dariusz; Jaroszewski, Lukasz; Godzik, Adam; Kloczkowski, Andrzej; Rychlewski, Leszek

    2005-11-01

    A new bioinformatics tool for molecular modeling of the local structure around phosphorylation sites in proteins has been developed. Our method is based on a library of short sequence and structure motifs. The basic structural elements to be predicted are local structure segments (LSSs). This enables us to avoid the problem of non-exact local description of structures, caused by either diversity in the structural context, or uncertainties in prediction methods. We have developed a library of LSSs and a profile--profile-matching algorithm that predicts local structures of proteins from their sequence information. Our fragment library prediction method is publicly available on a server (FRAGlib), at http://ffas.ljcrf.edu/Servers/frag.html . The algorithm has been applied successfully to the characterization of local structure around phosphorylation sites in proteins. Our computational predictions of sequence and structure preferences around phosphorylated residues have been confirmed by phosphorylation experiments for PKA and PKC kinases. The quality of predictions has been evaluated with several independent statistical tests. We have observed a significant improvement in the accuracy of predictions by incorporating structural information into the description of the neighborhood of the phosphorylated site. Our results strongly suggest that sequence information ought to be supplemented with additional structural context information (predicted with our segment similarity method) for more successful predictions of phosphorylation sites in proteins.

  14. CH5M3D: an HTML5 program for creating 3D molecular structures

    PubMed Central

    2013-01-01

    Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

  15. Structural distortions in molecular-based quantum cellular automata: a minimal model based study.

    PubMed

    Bonilla, Alejandro Santana; Gutierrez, Rafael; Sandonas, Leonardo Medrano; Nozaki, Daijiro; Bramanti, Alessandro Paolo; Cuniberti, Gianaurelio

    2014-09-07

    Molecular-based quantum cellular automata (m-QCA), as an extension of quantum-dot QCAs, offer a novel alternative in which binary information can be encoded in the molecular charge configuration of a cell and propagated via nearest-neighbor Coulombic cell-cell interactions. Appropriate functionality of m-QCAs involves a complex relationship between quantum mechanical effects, such as electron transfer processes within the molecular building blocks, and electrostatic interactions between cells. The influence of structural distortions of single m-QCA are addressed in this paper within a minimal model using an diabatic-to-adiabatic transformation. We show that even small changes of the classical square geometry between driver and target cells, such as those induced by distance variations or shape distortions, can make cells respond to interactions in a far less symmetric fashion, modifying and potentially impairing the expected computational behavior of the m-QCA.

  16. Molecular structure and spectral (FT-IR, Raman) investigations of 3-aminocoumarin

    NASA Astrophysics Data System (ADS)

    Dereli, Ömer

    2016-05-01

    The molecular structure of 3-Aminocoumarin was determined by conformational analysis. Conformational space was scanned by conformer distribution option of Spartan 08 program package using Merck Molecular Force Field (MMFF) method. Then obtained conformers were optimized by B3LYP/6-311++ G( d, p) and B3LYP/6-311 G( d, p) levels of Density Functional Theory. As a result of these calculations, only one conformer was determined. Vibrational frequencies of this conformer were calculated by Gaussian 03 program package using the same levels of geometry optimizations. The FT-IR and Raman spectra of 3-Aminocoumarin were recorded and compared with the calculated values. Consequently, a good agreement between experimental and the calculated values were founded. Molecular electrostatic potentials (MEPs), HOMO-LUMO energies, thermodynamic properties and Mulliken atomic charges were also covered in this study.

  17. Molecular early main group metal hydrides: synthetic challenge, structures and applications.

    PubMed

    Harder, Sjoerd

    2012-11-25

    Within the general area of early main group metal chemistry, the controlled synthesis of well-defined metal hydride complexes is a rapidly developing research field. As group 1 and 2 metal complexes are generally highly dynamic and lattice energies for their [MH](∞) and [MH(2)](∞) salts are high, the synthesis of well-defined soluble hydride complexes is an obvious challenge. Access to molecular early main group metal hydrides, however, is rewarding: these hydrocarbon-soluble metal hydrides are highly reactive, have found use in early main group metal catalysis and are potentially also valuable molecular model systems for polar metal hydrides as a hydrogen storage material. The article focusses specifically on alkali and alkaline-earth metal hydride complexes and discusses the synthetic challenge, molecular structures, reactivity and applications.

  18. Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.

    PubMed

    Koromyslova, Anna D; Chugunov, Anton O; Efremov, Roman G

    2014-04-28

    Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them--protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.

  19. Metal ion mediated molecularly imprinted polymer for selective capturing antibiotics containing beta-diketone structure.

    PubMed

    Qu, Shanshan; Wang, Xiaobo; Tong, Changlun; Wu, Jianmin

    2010-12-24

    A new molecularly imprinted polymer (MIP) targeting to quinolones (Qs) and tetracyclines (TCs) was synthesized using itaconic acid (ITA) and ciprofloxacin (CIP) as a functional monomer and template molecule, respectively. Factors affecting the overall performance of MIP were investigated, and the results showed that Fe(3+) ion play a vital role in the formation of MIP with high molecular imprinting effect. Meanwhile, the chelating ability of monomer, species of template molecule, as well as the molar ratio of monomer and template also contribute to the performance of the obtained MIP. Cyclic voltammetry verified that, with the participation of Fe(3+) ions, a ternary complex of ITA-Fe(3+)-CIP could be formed before polymerization. Compared with conventional MIP prepared from commonly used monomer, methacrylic acid (MAA), the new MIP show significantly enhanced molecular imprinting effect and higher capacity for specific adsorption of target compounds as revealed by static and dynamic binding experiments. The MIP was successfully used as solid-phase extraction (SPE) adsorbent for enriching a broad spectrum of antibiotics containing beta-diketone structure from surface water sample. HPLC detection showed that high recovery rate (78.6-113.6%) was found in these spiked antibiotics, whereas recovery rate for the non structurally related drugs, epinephrine (EP) and dopamine (DOPA), was very low (4.7-7.6%) on the MIP cartridges. The results demonstrate that the MIP prepared by the strategy proposed in this work, could specifically target to a series of structurally related antibiotics containing beta-diketone structure.

  20. Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA.

    PubMed

    Sidhu, Navdeep S; Schreiber, Kathrin; Pröpper, Kevin; Becker, Stefan; Usón, Isabel; Sheldrick, George M; Gärtner, Jutta; Krätzner, Ralph; Steinfeld, Robert

    2014-05-01

    Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.

  1. Applications of Systematic Molecular Scaffold Enumeration to Enrich Structure-Activity Relationship Information.

    PubMed

    Mok, N Yi; Brown, Nathan

    2017-01-23

    Establishing structure-activity relationships (SARs) in hit identification during early stage drug discovery is important in accelerating hit confirmation and expansion. We describe the development of EnCore, a systematic molecular scaffold enumeration protocol using single atom mutations, to enhance the application of objective scaffold definitions and to enrich SAR information from analysis of high-throughput screening output. A list of 43 literature medicinal chemistry compound series, each containing a minimum of 100 compounds, published in the Journal of Medicinal Chemistry was collated to validate the protocol. Analysis using the top representative Level 1 scaffolds this list of literature compound series demonstrated that EnCore could mimic the scaffold exploration conducted when establishing SAR. When EnCore was applied to analyze an HTS library containing over 200 000 compounds, we observed that over 70% of the molecular scaffolds matched extant scaffolds within the library after enumeration. In particular, over 60% of the singleton scaffolds with only one representative compound were found to have structurally related compounds after enumeration. These results illustrate the potential of EnCore to enrich SAR information. A case study using literature cyclooxygenase-2 inhibitors further demonstrates the advantage of EnCore application in establishing SAR from structurally related scaffolds. EnCore complements literature enumeration methods in enabling changes to the physicochemical properties of molecular scaffolds and structural modifications to aliphatic rings and linkers. The enumerated scaffold clusters generated would constitute a comprehensive collection of scaffolds for scaffold morphing and hopping.

  2. Structural studies of a vasorelaxant lectin from Dioclea reflexa Hook seeds: Crystal structure, molecular docking and dynamics.

    PubMed

    Pinto-Junior, Vanir Reis; Osterne, Vinicius José Silva; Santiago, Mayara Queiroz; Correia, Jorge Luis Almeida; Pereira-Junior, Francisco Nascimento; Leal, Rodrigo Bainy; Pereira, Maria Gonçalves; Chicas, Larissa Silva; Nagano, Celso Shiniti; Rocha, Bruno Anderson Matias; Silva-Filho, José Caetano; Ferreira, Wandemberg Paiva; Rocha, Cíntia Renata Costa; Nascimento, Kyria Santiago; Assreuy, Ana Maria Sampaio; Cavada, Benildo Sousa

    2017-05-01

    The three-dimensional structure of Dioclea reflexa seed lectin (DrfL) was studied in detail by a combination of X-ray crystallography, molecular docking and molecular dynamics. DrfL was purified by affinity chromatography using Sephadex G-50 matrix. Its primary structure was obtained by mass spectrometry, and crystals belonging to orthorhombic space group P212121 were grown by the vapor diffusion method at 293K. The crystal structure was solved at 1.765Å and was very similar to that of other lectins from the same subtribe. The structure presented Rfactor and Rfree of 21.69% and 24.89%, respectively, with no residues in nonallowed regions of Ramachandran plot. Similar to other Diocleinae lectins, DrfL was capable of relaxing aortic rings via NO induction, with CRD participation, albeit with low intensity (32%). In silico analysis results demonstrated that DrfL could strongly interact with complex N-glycans, components of blood vessel glycoconjugates. Despite the high similarity among Diocleinae lectins, it was also reported that each lectin has unique CRD properties that influence carbohydrate binding, resulting in different biological effects presented by these molecules.

  3. Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

    SciTech Connect

    Sidhu, Navdeep S.; Schreiber, Kathrin; Pröpper, Kevin; Becker, Stefan; Usón, Isabel; Sheldrick, George M.; Gärtner, Jutta; Krätzner, Ralph Steinfeld, Robert

    2014-05-01

    Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.

  4. Molecular dynamics simulation of the structure and dynamics of 5-HT3 serotonin receptor

    NASA Astrophysics Data System (ADS)

    Antonov, M. Yu.; Popinako, A. V.; Prokopiev, G. A.

    2016-10-01

    In this work, we investigated structure, dynamics and ion transportation in transmembrane domain of the 5-HT3 serotonin receptor. High-resolution (0.35 nm) structure of the 5-HT3 receptor in complex with stabilizing nanobodies was determined by protein crystallography in 2014 (Protein data bank (PDB) code 4PIR). Transmembrane domain of the structure was prepared in complex with explicit membrane environment (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC)) and solvent (TIP3P water model). Molecular dynamics protocols for simulation and stabilization of the transmembrane domain of the 5-HT3 receptor model were developed and 60 ns simulation of the structure was conducted in order to explore structural parameters of the system. We estimated the mean force profile for Na+ ions using umbrella sampling method.

  5. Selective Refinement and Molecular Dynamics Ranking Selection of Near-native Protein Structures

    NASA Astrophysics Data System (ADS)

    Zhang, Jiong; Zhang, Jingfen; Xu, Dong; Shang, Yi; Kosztin, Ioan

    2014-03-01

    In recent years in silico protein structure prediction reached a level where a variety of servers can generate large pools of near-native structures. However, the identification and further refinement of the best structures from the pool of decoys remain problematic. To address these issues, we have developed a selective refinement protocol (SRP), and a molecular dynamics (MD) simulation based ranking method (MDR). In SRP the refinement of structures is accomplished by using the relax mode of the Rosetta software package, subject to specific constraints determined by the type and complexity of the target. The final best models are selected with MDR by testing their relative stability against gradual heating during all atom MD simulations. We have implemented the selective refinement protocol and the MDR method in Mufold-MD, our fully automated protein structure prediction server. Mufold-MD was one of the top servers in the CASP10 competition.

  6. Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy.

    PubMed

    Punjani, Ali; Brubaker, Marcus A; Fleet, David J

    2017-04-01

    Discovering the 3D atomic-resolution structure of molecules such as proteins and viruses is one of the foremost research problems in biology and medicine. Electron Cryomicroscopy (cryo-EM) is a promising vision-based technique for structure estimation which attempts to reconstruct 3D atomic structures from a large set of 2D transmission electron microscope images. This paper presents a new Bayesian framework for cryo-EM structure estimation that builds on modern stochastic optimization techniques to allow one to scale to very large datasets. We also introduce a novel Monte-Carlo technique that reduces the cost of evaluating the objective function during optimization by over five orders of magnitude. The net result is an approach capable of estimating 3D molecular structure from large-scale datasets in about a day on a single CPU workstation.

  7. DFT study of the molecular and crystal structure and vibrational analysis of cisplatin.

    PubMed

    Georgieva, I; Trendafilova, N; Dodoff, N; Kovacheva, D

    2017-04-05

    DFT and periodic-DFT (PAW-PBE method, code VASP) calculations have been performed to study the structural and vibrational characteristics of cis-diamminedichloroplatinum(II) (cisplatin) at molecular and outside molecular level. To estimate the effect of the intermolecular interactions in crystal on the structural and vibrational properties of cisplatin, three theoretical models are considered in the present study: monomer (isolated molecule), hydrogen bonded dimer and periodic solid state structures. The work focused on the role of the theoretical models for correct modeling and prediction of geometrical and vibrational parameters of cisplatin. It has been found that the elaborate three-dimensional intermolecular hydrogen bonding network in the crystalline cisplatin significantly influences the structural and vibrational pattern of cisplatin and therefore the isolated cisplatin molecule is not the correct computational model regardless of the theoretical level used. To account for the whole intermolecular hydrogen bonding network in direction of both a and c axis and for more reliable calculations of structural and vibrational parameters periodic DFT calculations were carried out in the full crystalline periodic environment with the known lattice parameters for each cisplatin polymorph phase. The model calculations performed both at molecular level and for the periodic structures of alpha and beta cisplatin polymorph forms revealed the decisive role of the extended theoretical model for reliable prediction of the structural and vibrational characteristics of cisplatin. The powder diffraction pattern and the calculated IR and Raman spectra predicted beta polymorph form of our cisplatin sample freshly synthesized for the purposes of the present study using the Dhara's method. The various rotamers realized in the polymorph forms of cisplatin were explained by the low population of the large number of rotamers in solution as well as with the high rotamer

  8. Self-structured surface patterns on molecular azo glass films induced by laser light irradiation.

    PubMed

    Yin, Jianjun; Ye, Gang; Wang, Xiaogong

    2010-05-04

    In this work, formation of photoinduced self-structured surface pattern and its correlation with chromophoric structures were studied by using a series of star-shaped azo compounds, which exist as stable molecular glass at room temperature. For the synthesis, a star-shaped precursor (Tr-AN) was prepared by a ring-open reaction between 1, 3, 5-triglycidyl isocyanurate and N-methylaniline. The star-shaped azo compounds were then synthesized through azo-coupling reactions between the precursor and diazonium salts of 4-nitroaniline, 2-methyl-4-nitroaniline, and 4-aminobenzonitrile, respectively. Through these steps, three azo compounds were obtained to bear different donor-acceptor type azo chromophores at the peripheral positions. The formation of the photoinduced self-structured patterns was investigated by irradiating solid thin films of the molecular azo glass with a uniform laser beam (532 nm, 200 mW/cm(2)) at normal incidence. For comparison, formation of surface-relief-gratings (SRGs) was also investigated by exposing the thin films to an interference pattern of the laser beams (532 nm, 80 mW/cm(2)). The results show that SRGs can be inscribed on the films of all three star-shaped azo compounds, but self-structured surface patterns is only observed on film of the azo compound containing 4-cyanoazobenzene moieties (Tr-AZ-CN) under the same irradiation condition. The electron-withdrawing groups, which control the absorption band position, show a significant influence on both the self-structured pattern formation and SRG inscription rate. Under proper experimental conditions, both self-structured surface pattern and SRG can simultaneously be observed on the Tr-AZ-CN films. The observations can lead to a deeper understanding of the photoinduced effects, especially their correlation with molecular structures.

  9. DFT study of the molecular and crystal structure and vibrational analysis of cisplatin

    NASA Astrophysics Data System (ADS)

    Georgieva, I.; Trendafilova, N.; Dodoff, N.; Kovacheva, D.

    2017-04-01

    DFT and periodic-DFT (PAW-PBE method, code VASP) calculations have been performed to study the structural and vibrational characteristics of cis-diamminedichloroplatinum(II) (cisplatin) at molecular and outside molecular level. To estimate the effect of the intermolecular interactions in crystal on the structural and vibrational properties of cisplatin, three theoretical models are considered in the present study: monomer (isolated molecule), hydrogen bonded dimer and periodic solid state structures. The work focused on the role of the theoretical models for correct modeling and prediction of geometrical and vibrational parameters of cisplatin. It has been found that the elaborate three-dimensional intermolecular hydrogen bonding network in the crystalline cisplatin significantly influences the structural and vibrational pattern of cisplatin and therefore the isolated cisplatin molecule is not the correct computational model regardless of the theoretical level used. To account for the whole intermolecular hydrogen bonding network in direction of both a and c axis and for more reliable calculations of structural and vibrational parameters periodic DFT calculations were carried out in the full crystalline periodic environment with the known lattice parameters for each cisplatin polymorph phase. The model calculations performed both at molecular level and for the periodic structures of alpha and beta cisplatin polymorph forms revealed the decisive role of the extended theoretical model for reliable prediction of the structural and vibrational characteristics of cisplatin. The powder diffraction pattern and the calculated IR and Raman spectra predicted beta polymorph form of our cisplatin sample freshly synthesized for the purposes of the present study using the Dhara's method. The various rotamers realized in the polymorph forms of cisplatin were explained by the low population of the large number of rotamers in solution as well as with the high rotamer

  10. Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair

    PubMed Central

    Zhang, Yuchen; Alsop, Richard J.; Soomro, Asfia; Yang, Fei-Chi

    2015-01-01

    The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3–90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers. PMID:26557428

  11. Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair.

    PubMed

    Zhang, Yuchen; Alsop, Richard J; Soomro, Asfia; Yang, Fei-Chi; Rheinstädter, Maikel C

    2015-01-01

    The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3-90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.

  12. Molecular modelling of structure and deformation mechanisms of auxetic behaviour in the α-quartz structures

    NASA Astrophysics Data System (ADS)

    Yao, Yong Tao; Alderson, Andrew; Alderson, Kim Lesley

    2011-11-01

    Force field based simulation has been employed to predict the deformation mechanisms of auxetic nano-materials having tetrahedral framework. The structure of α-quartz was studied in detail for subjecting to uniaxial loading along the Z direction. The cooperative dilation and rotation of tetrahedra acting concurrently were demonstrated to be the main deformation mechanism of α-quartz, confirming previous analytical model. Slight tetrahedral distortion also existed for undeformed and deformed structure.

  13. Molecular modelling of structure and deformation mechanisms of auxetic behaviour in the α-quartz structures

    NASA Astrophysics Data System (ADS)

    Yao, Yong Tao; Alderson, Andrew; Alderson, Kim Lesley

    2012-04-01

    Force field based simulation has been employed to predict the deformation mechanisms of auxetic nano-materials having tetrahedral framework. The structure of α-quartz was studied in detail for subjecting to uniaxial loading along the Z direction. The cooperative dilation and rotation of tetrahedra acting concurrently were demonstrated to be the main deformation mechanism of α-quartz, confirming previous analytical model. Slight tetrahedral distortion also existed for undeformed and deformed structure.

  14. Photophysical and electrochemical properties, and molecular structures of organic dyes for dye-sensitized solar cells.

    PubMed

    Ooyama, Yousuke; Harima, Yutaka

    2012-12-21

    Dye-sensitized solar cells (DSSCs) based on organic dyes adsorbed on oxide semiconductor electrodes, such as TiO(2), ZnO, or NiO, which have emerged as a new generation of sustainable photovoltaic devices, have attracted much attention from chemists, physicists, and engineers because of enormous scientific interest in not only their construction and operational principles, but also in their high incident-solar-light-to-electricity conversion efficiency and low cost of production. To develop high-performance DSSCs, it is important to create efficient organic dye sensitizers, which should be optimized for the photophysical and electrochemical properties of the dyes themselves, with molecular structures that provide good light-harvesting features, good electron communication between the dye and semiconductor electrode and between the dye and electrolyte, and to control the molecular orientation and arrangement of the dyes on a semiconductor surface. The aim of this Review is not to make a list of a number of organic dye sensitizers developed so far, but to provide a new direction in the epoch-making molecular design of organic dyes for high photovoltaic performance and long-term stability of DSSCs, based on the accumulated knowledge of their photophysical and electrochemical properties, and molecular structures of the organic dye sensitizers developed so far.

  15. Molecular structure of yeast RNA polymerase III: demonstration of the tripartite transcriptive system in lower eukaryotes.

    PubMed Central

    Valenzuela, P; Hager, G L; Weinberg, F; Rutter, W J

    1976-01-01

    Homogeneous RNA polymerase III (RNA nucleotidyltransferase III) has been obtained from yeast. The subunit composition of the enzyme was examined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The enzyme is composed of 12 putative subunits with molecular weights 160,000, 128,000, 82,000, 41,000, 40,500, 37,000, 34,000, 28,000, 24,000, 20,000, 14,500, and 11,000. The high-molecular-weight subunits and several of the smaller subunits of yeast RNA polymerase III are clearly different from those of enzymes I and II, indicating a distinct molecular structure. However, the molecular weights of some of the small subunits (41,000, 28,000, 24,000, and 14,500) appear to be identical to those of polymerases I and II. Thus, it is possible that the three classes of enzymes in yeast have some common subunits. As in other eukaryotes, yeast polymerase II is inhibited by relatively low concentrations of alpha-amanitin; however, contrary to what has been found in higher eukaryotes, yeast polymerase III is resistant (up to 2 mg/ml) to alpha-amanitin, while yeast polymerase I is sensitive to high concentrations of the drug (50% inhibition at 0.3 mg/ml). These results establish the existence of RNA polymerase III in yeast and provide a structural basis for the discrimination of the three functional polymerases in eukaryotes. Images PMID:772675

  16. Application of molecular dynamics simulations for structural studies of carbon nanotubes.

    PubMed

    Bródka, A; Kołoczek, J; Burian, A

    2007-01-01

    Molecular dynamics studies based on the Brenner-Tersoff second-generation reactive empirical bond order potential and the Lennard-Jones carbon-carbon potential for intra- and inter-layer interactions have been performed for carbon nanotubes. These potentials reproduce reasonably the carbon-carbon distances and inter-layer spacing. The structure factors and the reduced radial distribution functions computed from the cartesian coordinates, resulting from energy minimisation and molecular dynamics simulations at 2 K and 300 K have been obtained for two models of two- and five-wall carbon nanotubes containing defects in the form of five and seven membered carbon rings. The results of computations have been compared with experimental data obtained from neutron and X-ray diffraction. The energy relaxation and the molecular dynamics simulations at 2 K and 300 K with appropriate values of the Debye-Waller factor lead practically to the same results which are in a good agreement with the experimental data indicating that molecular dynamics reproduce all structure features of the investigated carbon nanotubes together with thermal oscillations. Possible applications of this approach for other carbon nanotubes and related materials have been also discussed.

  17. Functional Proteomic And Structural Insights Into Molecular Recognition in the Nitrilase Family Enzymes

    SciTech Connect

    Barglow, K.T.; Saikatendu, K.; Bracey, M.H.; Huey, R.; Morris, G.M.; Olson, A.J.; Stevens, R.C.; Cravatt, B.F.

    2009-05-11

    Nitrilases are a large and diverse family of nonpeptidic C-N hydrolases. The mammalian genome encodes eight nitrilase enzymes, several of which remain poorly characterized. Prominent among these are nitrilase-1 (Nit1) and nitrilase-2 (Nit2), which, despite having been shown to exert effects on cell growth and possibly serving as tumor suppressor genes, are without known substrates or selective inhibitors. In previous studies, we identified several nitrilases, including Nit1 and Nit2, as targets for dipeptide-chloroacetamide activity-based proteomics probes. Here, we have used these probes, in combination with high-resolution crystallography and molecular modeling, to systematically map the active site of Nit2 and identify residues involved in molecular recognition. We report the 1.4 {angstrom} crystal structure of mouse Nit2 and use this structure to identify residues that discriminate probe labeling between the Nit1 and Nit2 enzymes. Interestingly, some of these residues are conserved across all vertebrate Nit2 enzymes and, conversely, not found in any vertebrate Nit1 enzymes, suggesting that they are key discriminators of molecular recognition between these otherwise highly homologous enzymes. Our findings thus point to a limited set of active site residues that establish distinct patterns of molecular recognition among nitrilases and provide chemical probes to selectively perturb the function of these enzymes in biological systems.

  18. Raman spectroscopy as an advanced structural nanoprobe for conjugated molecular semiconductors

    NASA Astrophysics Data System (ADS)

    Wood, Sebastian; Razzell Hollis, Joseph; Kim, Ji-Seon

    2017-02-01

    Raman spectroscopy has emerged as a powerful and important characterisation tool for probing molecular semiconducting materials. The useful optoelectronic properties of these materials arise from the delocalised π-electron density in the conjugated core of the molecule, which also results in large Raman scattering cross-sections and a strong coupling between its electronic states and vibrational modes. For this reason, Raman spectroscopy offers a unique insight into the properties of molecular semiconductors, including: chemical structure, molecular conformation, molecular orientation, and fundamental photo- and electro-chemical processes—all of which are critically important to the performance of a wide range of optical and electronic organic semiconductor devices. Experimentally, Raman spectroscopy is non-intrusive, non-destructive, and requires no special sample preparation, and so is suitable for a wide range of in situ measurements, which are particularly relevant to issues of thermal and photochemical stability. Here we review the development of the family of Raman spectroscopic techniques, which have been applied to the study of conjugated molecular semiconductors. We consider the suitability of each technique for particular circumstances, and the unique insights it can offer, with a particular focus on the significance of these measurements for the continuing development of stable, high performance organic electronic devices.

  19. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of mannitol.

    PubMed

    Moorthi, P P; Gunasekaran, S; Swaminathan, S; Ramkumaar, G R

    2015-02-25

    A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of mannitol. The FT-IR and FT-Raman spectra of mannitol were recorded in the solid phase. The molecular geometry, vibrational frequencies, thermodynamic functions and atomic charges of mannitol in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking cc-pVDZ basis set. The complete vibrational assignments were performed on the basis of Total Energy Distribution (TED) of the vibrational modes. The UV absorption spectra of the title compound dissolved in water. Natural bond orbital analysis has been carried out to explain the charge transfer or delocalization of charge due to the intra-molecular interactions. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO methods. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of mannitol are calculated using B3LYP/cc-pVDZ and HF/cc-pVDZ methods on the finite-field approach. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP) have been investigated using theoretical calculations, the calculated HOMO and LUMO energies shows that the charge transfer within the molecule.

  20. Univariate and multivariate molecular spectral analyses of lipid related molecular structural components in relation to nutrient profile in feed and food mixtures

    NASA Astrophysics Data System (ADS)

    Abeysekara, Saman; Damiran, Daalkhaijav; Yu, Peiqiang

    2013-02-01

    The objectives of this study were (i) to determine lipid related molecular structures components (functional groups) in feed combination of cereal grain (barley, Hordeum vulgare) and wheat (Triticum aestivum) based dried distillers grain solubles (wheat DDGSs) from bioethanol processing at five different combination ratios using univariate and multivariate molecular spectral analyses with infrared Fourier transform molecular spectroscopy, and (ii) to correlate lipid-related molecular-functional structure spectral profile to nutrient profiles. The spectral intensity of (i) CH3 asymmetric, CH2 asymmetric, CH3 symmetric and CH2 symmetric groups, (ii) unsaturation (Cdbnd C) group, and (iii) carbonyl ester (Cdbnd O) group were determined. Spectral differences of functional groups were detected by hierarchical cluster analysis (HCA) and principal components analysis (PCA). The results showed that the combination treatments significantly inflicted modifications (P < 0.05) in nutrient profile and lipid related molecular spectral intensity (CH2 asymmetric stretching peak height, CH2 symmetric stretching peak height, ratio of CH2 to CH3 symmetric stretching peak intensity, and carbonyl peak area). Ratio of CH2 to CH3 symmetric stretching peak intensity, and carbonyl peak significantly correlated with nutrient profiles. Both PCA and HCA differentiated lipid-related spectrum. In conclusion, the changes of lipid molecular structure spectral profiles through feed combination could be detected using molecular spectroscopy. These changes were associated with nutrient profiles and functionality.

  1. Validity boundary of orbital-free molecular dynamics method corresponding to thermal ionization of shell structure

    NASA Astrophysics Data System (ADS)

    Gao, Chang; Zhang, Shen; Kang, Wei; Wang, Cong; Zhang, Ping; He, X. T.

    2016-11-01

    With 6LiD as an example, we show that the applicable region of the orbital-free molecular dynamics (OFMD) method in a large temperature range is determined by the thermal ionization process of bound electrons in shell structures. The validity boundary of the OFMD method is defined roughly by the balance point of the average thermal energy of an electron and the ionization energy of the lowest localized electronic state. This theoretical proposition is based on the observation that the deviation of the OFMD method originates from its less accurate description to the charge density in partially ionized shells, as compared with the results of the extended first-principles molecular dynamics method, which well reproduces the charge density of shell structures.

  2. Regularizing the molecular potential in electronic structure calculations. II. Many-body methods

    SciTech Connect

    Bischoff, Florian A.

    2014-11-14

    In Paper I of this series [F. A. Bischoff, “Regularizing the molecular potential in electronic structure calculations. I. SCF methods,” J. Chem. Phys. 141, 184105 (2014)] a regularized molecular Hamilton operator for electronic structure calculations was derived and its properties in SCF calculations were studied. The regularization was achieved using a correlation factor that models the electron-nuclear cusp. In the present study we extend the regularization to correlated methods, in particular the exact solution of the two-electron problem, as well as second-order many body perturbation theory. The nuclear and electronic correlation factors lead to computations with a smaller memory footprint because the singularities are removed from the working equations, which allows coarser grid resolution while maintaining the precision. Numerical examples are given.

  3. Synthesis of a specified, silica molecular sieve by using computationally predicted organic structure-directing agents.

    PubMed

    Schmidt, Joel E; Deem, Michael W; Davis, Mark E

    2014-08-04

    Crystalline molecular sieves are used in numerous applications, where the properties exploited for each technology are the direct consequence of structural features. New materials are typically discovered by trial and error, and in many cases, organic structure-directing agents (OSDAs) are used to direct their formation. Here, we report the first successful synthesis of a specified molecular sieve through the use of an OSDA that was predicted from a recently developed computational method that constructs chemically synthesizable OSDAs. Pentamethylimidazolium is computationally predicted to have the largest stabilization energy in the STW framework, and is experimentally shown to strongly direct the synthesis of pure-silica STW. Other OSDAs with lower stabilization energies did not form STW. The general method demonstrated here to create STW may lead to new, simpler OSDAs for existing frameworks and provide a way to predict OSDAs for desired, theoretical frameworks.

  4. Characteristic Features of Molecular Structure and Packing of Organopolysilanes with Asymmetric Side Chains

    NASA Astrophysics Data System (ADS)

    Furukawa, Shoji; Ohta, Hidetaka

    2005-01-01

    The molecular structure and packing of poly(methyl ethyl silane), [(CH3)Si(C2H5)]n, and poly(methyl n-propyl silane), [(CH3)Si(C3H7)]n, have been examined by the X-ray diffraction method. For poly(methyl ethyl silane), several configurations are possible for the arrangement of the C2H5 group, whereas the C3H7 groups stretch along one equivalent direction for poly(methyl n-propyl silane). In both cases, the molecular structure and packing are mostly determined by the intramolecular steric hindrance and van der Waals interaction between side chains, which is the same as that of polysilanes with symmetric side chains.

  5. Effect of fuel molecular structure on soot formation in gas turbine engines

    NASA Technical Reports Server (NTRS)

    Naegeli, D. W.; Moses, C. A.

    1980-01-01

    A high-pressure research combustor operating over a wide range of burner inlet conditions was used to determine the effects of fuel molecular structure on soot formation. Six test fuels with equal hydrogen content (12.8 percent) were blended to stress different molecular components and final boiling points. The fuels containing high concentrations (20 percent) of poly-cyclic aromatics and partially saturated polycyclic structures such as tetralin, produced more soot than would be expected from a hydrogen content correlation for typical petroleum based fuels. However, fuels containing naphthenes, such as decalin, agreed with the hydrogen content correlation. The contribution of polycylic aromatics to soot formation was equivalent to a reduction in fuel hydrogen content of about 1%. The fuel sensitivity to soot formation due to the polycyclic aromatic contribution decreased as burner inlet pressure and fuel/air ratio increased.

  6. Computational Study of the Structure and Mechanical Properties of the Molecular Crystal RDX

    DTIC Science & Technology

    2011-01-01

    structure and affect the physiological absorption of advanced pharmaceutical ingredients and the decomposition of high explosives. Report...physiological absorption of advanced pharmaceutical ingredients and the decomposition of high explosives. This work used molecular dynamics to study the...l’Energie Atomique Centre d’Etudes de Vajours, Sevran, France. 221 [35] Yoo, C., Cynn, H., Howard, W. M., and Holmes, N. (1998). Equations of

  7. Synthesis, structures, and physical properties of aromatic molecular-bowl hydrocarbons.

    PubMed

    Wu, Yao-Ting; Siegel, Jay S

    2014-01-01

    This chapter summarizes the synthesis, physical properties, structure, and crystal packing of buckybowls. Buckybowls exemplify an intermediate class of polynuclear aromatic compounds between the closed-shell fullerenes and the flat extended arrays of graphene. These warped sheets can be seen as fragments of fullerenes or the end cap of single-walled carbon nanotubes; and, their curvature endows them with physical properties distinct from flat polynuclear hydrocarbons, which opens up unique possibilities for molecular bowls in various organic materials applications.

  8. Structural and energy properties of interstitial molecular hydrogen in single-crystal silicon

    SciTech Connect

    Melnikov, V. V.

    2015-06-15

    The structural and energy characteristics of interstitial molecular hydrogen in single-crystal silicon are theoretically studied. The dependence of the potential energy of the system on the position and orientation of the interstitial defect is investigated, and the mechanism of interaction of a hydrogen molecule with a silicon crystal is considered. A three-dimensional model is employed to calculate the energy spectrum of H{sub 2} in Si, and the obtained dispersion law is analyzed.

  9. CHIH-DFT determination of the molecular structure and IR and UV spectra of solanidine.

    PubMed

    Glossman-Mitnik, Daniel

    2007-01-01

    Solanidine is the steroidal aglycon of some potato glycoalkaloids and a very important precursor for the synthesis of hormones and some pharmacologically active compounds. In this work, we make use of a new chemistry model within Density Functional Theory, called CHIH-DFT, to calculate the molecular structure of solanidine, as well to predict its infrared and ultraviolet spectra. The calculated values are compared with the experimental data available for this molecule as a means of validation of our proposed chemistry model.

  10. Cluster molecular orbital description of the electronic structures of mixed-valence iron oxides and silicates

    USGS Publications Warehouse

    Sherman, David M.

    1986-01-01

    A molecular orbital description, based on spin-unrestricted X??-scattered wave calculations, is given for the electronic structures of mixed valence iron oxides and silicates. The cluster calculations show that electron hopping and optical intervalence charge-transger result from weak FeFe bonding across shared edges of FeO6 coordination polyhedra. In agreement with Zener's double exchange model, FeFe bonding is found to stabilize ferromagnetic coupling between Fe2+ and Fe3+ cations. ?? 1986.

  11. Molecular orbital calculations on atomic structures of Si-based covalent amorphous ceramics

    SciTech Connect

    Matsunaga, K.; Matsubara, H.

    1999-07-01

    The authors have performed ab-initio Hartree-Fock molecular orbital calculations of local atomic structures and chemical bonding states in Si-N covalent amorphous ceramics. Solute elements such as boron, carbon and oxygen were considered in the Si-N network, and the bonding characteristics around the solute elements were analyzed. When a nitrogen atom is substituted by a carbon atom, it was found that Si-C bonds reinforce the Si-N network due to strong covalency.

  12. Canopy Research Network seeks input

    NASA Astrophysics Data System (ADS)

    In July 1993, the Canopy Research Network was established with a 2-year planning grant from the National Science Foundation to bring together forest canopy researchers, quantitative scientists, and computer specialists to establish methods for collecting, storing, analyzing, interpreting, and displaying three-dimensional data that relate to tree crowns and forest canopies. The CRN is now soliciting input from scientists in other fields who may have developed techniques and software to help obtain answers to questions that concern the complex three-dimensional structure of tree crowns and forest canopies. Over the next 3 years, the CRN plans to compile an array of research questions and issues requiring information on canopy structure, examine useful information models and software tools already in use in allied fields, and develop conceptual models and recommendations for the types and format of information and analyses necessary to answer research questions posed by canopy researchers.

  13. Relationships between the structure of natural organic matter and its reactivity towards molecular ozone and hydroxyl radicals

    USGS Publications Warehouse

    Westerhoff, P.; Aiken, G.; Amy, G.; Debroux, J.

    1999-01-01

    Oxidation reaction rate parameters for molecular ozone (O3) and hydroxyl (HO) radicals with a variety of hydrophobic organic acids (HOAs) isolated from different geographic locations were determined from batch ozonation studies. Rate parameter values, obtained under equivalent dissolved organic carbon concentrations in both the presence and absence of non-NOM HO radical scavengers, varied as a function of NOM structure. First-order rate constants for O3 consumption (k(O3)) averaged 8.8 x 10-3 s-1, ranging from 3.9 x 10-3 s-1 for a groundwater HOA to > 16 x 10-3 s-1 for river HOAs with large terrestrial carbon inputs. The average second-order rate constant (k(HO,DOC) between HO radicals and NOM was 3.6 x 108 l (mol C)-1 s-1; a mass of 12 g C per mole C was used in all calculations. Specific ultraviolet absorbance (SUVA) at 254 or 280 nm of the HOAs correlated well (r > 0.9) with O3 consumption rate parameters, implying that organic ??-electrons strongly and selectively influence oxidative reactivity. HO radical reactions with NOM were less selective, although correlation between k(HO,DOC) and SUVA existed. Other physical-chemical properties of NOM, such as aromatic and aliphatic carbon content from 13C-NMR spectroscopy, proved less sensitive for predicting oxidation reactivity than SUVA. The implication of this study is that the structural nature of NOM varies temporally and spatially in a water source, and both the nature and amount of NOM will influence oxidation rates.

  14. Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

    PubMed Central

    Mendez, Derek; Watkins, Herschel; Qiao, Shenglan; Raines, Kevin S.; Lane, Thomas J.; Schenk, Gundolf; Nelson, Garrett; Subramanian, Ganesh; Tono, Kensuke; Joti, Yasumasa; Yabashi, Makina; Ratner, Daniel; Doniach, Sebastian

    2016-01-01

    During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlined for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. It is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules. PMID:27840681

  15. Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

    DOE PAGES

    Mendez, Derek; Watkins, Herschel; Qiao, Shenglan; ...

    2016-09-26

    During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlinedmore » for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. Finally, it is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules.« less

  16. Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

    SciTech Connect

    Mendez, Derek; Watkins, Herschel; Qiao, Shenglan; Raines, Kevin S.; Lane, Thomas J.; Schenk, Gundolf; Nelson, Garrett; Subramanian, Ganesh; Tono, Kensuke; Joti, Yasumasa; Yabashi, Makina; Ratner, Daniel; Doniach, Sebastian

    2016-09-26

    During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlined for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. Finally, it is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules.

  17. Teaching the structure of immunoglobulins by molecular visualization and SDS-PAGE analysis.

    PubMed

    Rižner, Tea Lanišnik

    2014-01-01

    This laboratory class combines molecular visualization and laboratory experimentation to teach the structure of the immunoglobulins (Ig). In the first part of the class, the three-dimensional structures of the human IgG and IgM molecules available through the RCSB PDB database are visualized using freely available software. In the second part, IgG and IgM are studied using electrophoretic methods. Through SDS-PAGE analysis under reducing conditions, the students determine the number and molecular masses of the polypeptide chains, while through SDS-PAGE under nonreducing conditions, the students assess the oligomerization of these Ig molecules. The aims of this class are to expand upon the knowledge and understanding of the Ig structure that the students have gained from classroom lectures. The combination of this molecular visualization of the Ig molecules and the SDS-PAGE experimentation ensures variety in the teaching techniques, while the implication of the Ig molecules in human disease promotes interest for biomedical students.

  18. Roles of water in protein structure and function studied by molecular liquid theory.

    PubMed

    Imai, Takashi

    2009-01-01

    The roles of water in the structure and function of proteins have not been completely elucidated. Although molecular simulation has been widely used for the investigation of protein structure and function, it is not always useful for elucidating the roles of water because the effect of water ranges from atomic to thermodynamic level. The three-dimensional reference interaction site model (3D-RISM) theory, which is a statistical-mechanical theory of molecular liquids, can yield the solvation structure at the atomic level and calculate the thermodynamic quantities from the intermolecular potentials. In the last few years, the author and coworkers have succeeded in applying the 3D-RISM theory to protein aqueous solution systems and demonstrated that the theory is useful for investigating the roles of water. This article reviews some of the recent applications and findings, which are concerned with molecular recognition by protein, protein folding, and the partial molar volume of protein which is related to the pressure effect on protein.

  19. On the molecular electron structure of three phosphinine-containing macrocycles.

    PubMed

    Ferro, V R; López, R; Omar, S; de la Vega, J M García

    2007-04-15

    A broad set of structural models and theoretical methods has been successfully used for studying both the molecular electron structure of the silacalix[3]phosphinine and the changes of the macrocycle core under the conditions that frequently correspond to its complexes with metals. The macrocycle core of the silacalix[3]phosphinine and its neutral derivatives are strongly deviated from the main molecular plane. The phosphorous electron lone pairs and the pi-cloud of the phosphinine units give the main contribution to the electron valence structure in the silacalix[3]phosphinine and also in its both oxidized and reduced derivatives. Although the electron lone pairs of the P atoms tend to be strongly repulsive, they are either totally or partially extended above all the fragment of the phosphorous atoms depending on geometrical factors or even strongly coupled with the pi-cloud of the phosphinine units. Electronic processes that take away part of the electron density from the macrocyle favor both its planar configuration and the asymmetric distribution of the valence electrons in the silacalix[3]phosphinine and its derivatives. The limit condition to this effect is the appearance of a new in-plane sigma molecular orbital between the P atoms of two neighboring phosphinine units.

  20. Partially collapsed cristobalite structure in the non molecular phase V in CO2

    PubMed Central

    Santoro, Mario; Gorelli, Federico A.; Bini, Roberto; Haines, Julien; Cambon, Olivier; Levelut, Claire; Montoya, Javier A.; Scandolo, Sandro

    2012-01-01

    Non molecular CO2 has been an important subject of study in high pressure physics and chemistry for the past decade opening up a unique area of carbon chemistry. The phase diagram of CO2 includes several non molecular phases above 30 GPa. Among these, the first discovered was CO2-V which appeared silica-like. Theoretical studies suggested that the structure of CO2-V is related to that of β-cristobalite with tetrahedral carbon coordination similar to silicon in SiO2, but reported experimental structural studies have been controversial. We have investigated CO2-V obtained from molecular CO2 at 40–50 GPa and T > 1500 K using synchrotron X-ray diffraction, optical spectroscopy, and computer simulations. The structure refined by the Rietveld method is a partially collapsed variant of SiO2 β-cristobalite, space group , in which the CO4 tetrahedra are tilted by 38.4° about the c-axis. The existence of CO4 tetrahedra (average O-C-O angle of 109.5°) is thus confirmed. The results add to the knowledge of carbon chemistry with mineral phases similar to SiO2 and potential implications for Earth and planetary interiors. PMID:22431594

  1. Effects of molecular structure on microscopic heat transport in chain polymer liquids

    SciTech Connect

    Matsubara, Hiroki Kikugawa, Gota; Ohara, Taku; Bessho, Takeshi; Yamashita, Seiji

    2015-04-28

    In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T{sub c}) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

  2. Micromachined silicon acoustic delay line with 3D-printed micro linkers and tapered input for improved structural stability and acoustic directivity

    NASA Astrophysics Data System (ADS)

    Cho, Y.; Kumar, A.; Xu, S.; Zou, J.

    2016-10-01

    Recent studies have shown that micromachined silicon acoustic delay lines can provide a promising solution to achieve real-time photoacoustic tomography without the need for complex transducer arrays and data acquisition electronics. To achieve deeper imaging depth and wider field of view, a longer delay time and therefore delay length are required. However, as the length of the delay line increases, it becomes more vulnerable to structural instability due to reduced mechanical stiffness. In this paper, we report the design, fabrication, and testing of a new silicon acoustic delay line enhanced with 3D printed polymer micro linker structures. First, mechanical deformation of the silicon acoustic delay line (with and without linker structures) under gravity was simulated by using finite element method. Second, the acoustic crosstalk and acoustic attenuation caused by the polymer micro linker structures were evaluated with both numerical simulation and ultrasound transmission testing. The result shows that the use of the polymer micro linker structures significantly improves the structural stability of the silicon acoustic delay lines without creating additional acoustic attenuation and crosstalk. In addition, the improvement of the acoustic acceptance angle of the silicon acoustic delay lines was also investigated to better suppress the reception of unwanted ultrasound signals outside of the imaging plane. These two improvements are expected to provide an effective solution to eliminate current limitations on the achievable acoustic delay time and out-of-plane imaging resolution of micromachined silicon acoustic delay line arrays.

  3. A molecular dynamics study on the structural and electronic properties of two-dimensional icosahedral B12 cluster based structures

    NASA Astrophysics Data System (ADS)

    Kah, Cherno Baba; Yu, M.; Jayanthi, C. S.; Wu, S. Y.

    2014-03-01

    Our previous study on one-dimensional icosahedral B12 cluster (α-B12) based chain [Bulletin of APS Annual Meeting, p265 (2013)] and ring structures has prompted us to study the two-dimensional (2D) α-B12 based structures. Recently, we have carried out a systematic molecular dynamics study on the structural stabilities and electronic properties of the 2D α-B12 based structures using the SCED-LCAO method [PRB 74, 15540 (2006)]. We have considered several types of symmetry for these 2D structures such as δ3, δ4, δ6 (flat triangular), and α' types. We have found that the optimized structures are energetically in the order of δ6 < α' < δ3 < δ4 which is different from the energy order of α'< δ6 < δ4 < δ3 found in the 2D boron monolayer sheets [ACS Nano 6, 7443 (2012)]. A detailed discussion of this study will be presented. The first author acknowledges the McSweeny Fellowship for supporting his research in this work.

  4. Structural analysis of desheptapeptide(B24-B30) insulin by molecular replacement.

    PubMed

    Sujin, B; Dianlin, X; Jiping, Z; Wenrui, C; Dongcai, L

    1998-06-01

    Desheptapeptide (B24-B30) insulin (DHPI), a virtually inactive insulin analog, has been crystallized in space group P2, 2, 2, with two DHPI molecules in an asymmetric unit. The orientatin and positions of the molecules were determind by molecular replacement. and a structural model was built at 0.3 nm resolution. The current model shows that the two DMHI monomers are related by a non-crystallographic 2-fold axis, nearly parallel to the crystallographicc axis. This structural feature complicated the determination of the orientation of the local 2-fold axis, which was later confirmed by analysing the diffraction data of DHPI crystals.

  5. On the vibration of double-walled carbon nanotubes using molecular structural and cylindrical shell models

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Rouhi, S.; Aryayi, M.

    2016-01-01

    The vibrational behavior of double-walled carbon nanotubes is studied by the use of the molecular structural and cylindrical shell models. The spring elements are employed to model the van der Waals interaction. The effects of different parameters such as geometry, chirality, atomic structure and end constraint on the vibration of nanotubes are investigated. Besides, the results of two aforementioned approaches are compared. It is indicated that by increasing the nanotube side length and radius, the computationally efficient cylindrical shell model gives rational results.

  6. Extracting elements of molecular structure from the all-particle wave function

    SciTech Connect

    Matyus, Edit; Reiher, Markus; Hutter, Juerg; Mueller-Herold, Ulrich

    2011-11-28

    Structural information is extracted from the all-particle (non-Born-Oppenheimer) wave function by calculating radial and angular densities derived from n-particle densities. As a result, one- and two-dimensional motifs of classical molecular structure can be recognized in quantum mechanics. Numerical examples are presented for three- (H{sup -}, Ps{sup -}, H{sub 2}{sup +}), four- (Ps{sub 2}, H{sub 2}), and five-particle (H{sub 2}D{sup +}) systems.

  7. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

    PubMed Central

    šponer, Jiří; Cang, Xiaohui; Cheatham, Thomas E.

    2013-01-01

    The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids. PMID:22525788

  8. Structural transformations from point to extended defects in silicon: A molecular dynamics study

    SciTech Connect

    Marques, Luis A.; Pelaz, Lourdes; Santos, Ivan; Lopez, Pedro; Aboy, Maria

    2008-11-15

    We use classical molecular dynamics simulation techniques to study how point defects aggregate to form extended defects in silicon. We have found that <110> chains of alternating interstitials and bond defects, a generalization of the Si di-interstitial structure, are metastable at room temperature but spontaneously transform into (311) defects when annealed at higher temperatures. Obtained atomic configurations and energetics are in good agreement with experiments and previous theoretical calculations. We have found a (311) structural unit which consists of two interstitial chains along <110> but arranged differently with respect to the known (311) units.

  9. Spatially resolved dynamic structure factor of finite systems from molecular dynamics simulations

    SciTech Connect

    Raitza, Thomas; Roepke, Gerd; Reinholz, Heidi; Morozov, Igor

    2011-09-15

    The dynamical response of metallic clusters up to 10{sup 3} atoms is investigated using the restricted molecular dynamics simulations scheme. Exemplarily, a sodium like material is considered. Correlation functions are evaluated to investigate the spatial structure of collective electron excitations and the optical response of laser-excited clusters. In particular, the spectrum of bilocal correlation functions shows resonances representing different modes of collective excitations inside the nano plasma. The spatial structure, the resonance energy, and the width of the eigenmodes have been investigated for various values of electron density, temperature, cluster size, and ionization degree. Comparison with bulk properties is performed and the dispersion relation of collective excitations is discussed.

  10. Molecular dynamics simulations of the structure evolutions of Cu-Zr metallic glasses under irradiation

    NASA Astrophysics Data System (ADS)

    Lang, Lin; Tian, Zean; Xiao, Shifang; Deng, Huiqiu; Ao, Bingyun; Chen, Piheng; Hu, Wangyu

    2017-02-01

    Molecular dynamics simulations have been performed to investigate the structural evolution of Cu64.5Zr35.5 metallic glasses under irradiation. The largest standard cluster analysis (LSCA) method was used to quantify the microstructure within the collision cascade regions. It is found that the majority of clusters within the collision cascade regions are full and defective icosahedrons. Not only the smaller structures (common neighbor subcluster) but also primary clusters greatly changed during the collision cascades; while most of these radiation damages self-recover quickly in the following quench states. These findings indicate the Cu-Zr metallic glasses have excellent irradiation-resistance properties.

  11. Molecular Structure, Function, and Dynamics of Clathrin-Mediated Membrane Traffic

    PubMed Central

    Kirchhausen, Tom; Owen, David; Harrison, Stephen C.

    2014-01-01

    Clathrin is a molecular scaffold for vesicular uptake of cargo at the plasma membrane, where its assembly into cage-like lattices underlies the clathrin-coated pits of classical endocytosis. This review describes the structures of clathrin, major cargo adaptors, and other proteins that participate in forming a clathrin-coated pit, loading its contents, pinching off the membrane as a lattice-enclosed vesicle, and recycling the components. It integrates as much of the structural information as possible at the time of writing into a sketch of the principal steps in coated-pit and coated-vesicle formation. PMID:24789820

  12. Molecular and crystal structure of 2-{( E)-[(4-Methylphenyl)imino]methyl}-4-nitrophenol: A redetermination

    NASA Astrophysics Data System (ADS)

    Kaynar, Nihal Kan; Tanak, Hasan; Şahin, Songul; Dege, Necmi; Ağar, Erbil; Yavuz, Metin

    2016-03-01

    The crystal structure of the title compound, C14H12N2O3, was recently determined as a mixture of its neutral (OH containing) and zwitterionic (NH containing) forms, in a 0.60 (4): 0.40 (4) ratio using the X-ray determination. In this study, the title compound has been characterized by FT-IR and X-ray diffraction. The redetermination showed that the title compound has only enol (OH) form because of lack of the NH stretching vibration in FT-IR spectrum. In addition, the molecular structure and tautomerism of the title compound have been discussed.

  13. Molecular dynamics approach to water structure of HII mesophase of monoolein

    NASA Astrophysics Data System (ADS)

    Kolev, Vesselin; Ivanova, Anela; Madjarova, Galia; Aserin, Abraham; Garti, Nissim

    2012-02-01

    The goal of the present work is to study theoretically the structure of water inside the water cylinder of the inverse hexagonal mesophase (HII) of glyceryl monooleate (monoolein, GMO), using the method of molecular dynamics. To simplify the computational model, a fixed structure of the GMO tube is maintained. The non-standard cylindrical geometry of the system required the development and application of a novel method for obtaining the starting distribution of water molecules. A predictor-corrector schema is employed for generation of the initial density of water. Molecular dynamics calculations are performed at constant volume and temperature (NVT ensemble) with 1D periodic boundary conditions applied. During the simulations the lipid structure is kept fixed, while the dynamics of water is unrestrained. Distribution of hydrogen bonds and density as well as radial distribution of water molecules across the water cylinder show the presence of water structure deep in the cylinder (about 6 Å below the GMO heads). The obtained results may help understanding the role of water structure in the processes of insertion of external molecules inside the GMO/water system. The present work has a semi-quantitative character and it should be considered as the initial stage of more comprehensive future theoretical studies.

  14. Structure and functional features of olive pollen pectin methylesterase using homology modeling and molecular docking methods.

    PubMed

    Jimenez-Lopez, Jose C; Kotchoni, Simeon O; Rodríguez-García, María I; Alché, Juan D

    2012-12-01

    Pectin methylesterases (PMEs), a multigene family of proteins with multiple differentially regulated isoforms, are key enzymes implicated in the carbohydrates (pectin) metabolism of cell walls. Olive pollen PME has been identified as a new allergen (Ole e 11) of potential relevance in allergy amelioration, since it exhibits high prevalence among atopic patients. In this work, the structural and functional characterization of two olive pollen PME isoforms and their comparison with other PME plants was performed by using different approaches: (1) the physicochemical properties and functional-regulatory motifs characterization, (2) primary sequence analysis, 2D and 3D comparative structural features study, (3) conservation and evolutionary analysis, (4) catalytic activity and regulation based on molecular docking analysis of a homologue PME inhibitor, and (5) B-cell epitopes prediction by sequence and structural based methods and protein-protein interaction tools, while T-cell epitopes by inhibitory concentration and binding score methods. Our results indicate that the structural differences and low conservation of residues, together with differences in physicochemical and posttranslational motifs might be a mechanism for PME isovariants generation, regulation, and differential surface epitopes generation. Olive PMEs perform a processive catalytic mechanism, and a differential molecular interaction with specific PME inhibitor, opening new possibilities for PME activity regulation. Despite the common function of PMEs, differential features found in this study will lead to a better understanding of the structural and functional characterization of plant PMEs and help to improve the component-resolving diagnosis and immunotherapy of olive pollen allergy by epitopes identification.

  15. Molecular basis of classic galactosemia from the structure of human galactose 1-phosphate uridylyltransferase.

    PubMed

    McCorvie, Thomas J; Kopec, Jolanta; Pey, Angel L; Fitzpatrick, Fiona; Patel, Dipali; Chalk, Rod; Shrestha, Leela; Yue, Wyatt W

    2016-06-01

    Classic galactosemia is a potentially lethal disease caused by the dysfunction of galactose 1-phosphate uridylyltransferase (GALT). Over 300 disease-associated GALT mutations have been reported, with the majority being missense changes, although a better understanding of their underlying molecular effects has been hindered by the lack of structural information for the human enzyme. Here, we present the 1.9 Å resolution crystal structure of human GALT (hGALT) ternary complex, revealing a homodimer arrangement that contains a covalent uridylylated intermediate and glucose-1-phosphate in the active site, as well as a structural zinc-binding site, per monomer. hGALT reveals significant structural differences from bacterial GALT homologues in metal ligation and dimer interactions, and therefore is a zbetter model for understanding the molecular consequences of disease mutations. Both uridylylation and zinc binding influence the stability and aggregation tendency of hGALT. This has implications for disease-associated variants where p.Gln188Arg, the most commonly detected, increases the rate of aggregation in the absence of zinc likely due to its reduced ability to form the uridylylated intermediate. As such our structure serves as a template in the future design of pharmacological chaperone therapies and opens new concepts about the roles of metal binding and activity in protein misfolding by disease-associated mutants.

  16. In-silico bonding schemes to encode chemical bonds involving sharing of electrons in molecular structures.

    PubMed

    Punnaivanam, Sankar; Sathiadhas, Jerome Pastal Raj; Panneerselvam, Vinoth

    2016-05-01

    Encoding of covalent and coordinate covalent bonds in molecular structures using ground state valence electronic configuration is achieved. The bonding due to electron sharing in the molecular structures is described with five fundamental bonding categories viz. uPair-uPair, lPair-uPair, uPair-lPair, vPair-lPair, and lPair-lPair. The involvement of lone pair electrons and the vacant electron orbitals in chemical bonding are explained with bonding schemes namely "target vacant promotion", "source vacant promotion", "target pairing promotion", "source pairing promotion", "source cation promotion", "source pairing double bond", "target vacant occupation", and "double pairing promotion" schemes. The bonding schemes are verified with a chemical structure editor. The bonding in the structures like ylides, PCl5, SF6, IF7, N-Oxides, BF4(-), AlCl4(-) etc. are explained and encoded unambiguously. The encoding of bonding in the structures of various organic compounds, transition metals compounds, coordination complexes and metal carbonyls is accomplished.

  17. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

    PubMed

    Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

    2016-05-01

    Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.

  18. A reassessment of the molecular structure-functional relationships of the inhaled general anaesthetics.

    PubMed

    Halsey, M J

    1984-01-01

    The importance of structure-activity relationships in the inhaled general anaesthetic agents may have been underestimated in the elucidation of the central and peripheral mechanisms of general anaesthesia. It is true that there is no single spatial arrangement of atoms in a molecule that is essential for anaesthetic activity; the "anesthesiophore", as it was termed, is a myth. However, the chemical structure of a compound is directly related to its physical properties which in turn are one of the major determinants in the molecular mechanisms. Second, chemical structures are the major factors in the physical, chemical and biological stability of the anaesthetics; in particular the electron distributions, bond densities and net atomic charges determine the extent and mode of biotransformation. Some of the evidence for the importance of structure in the anesthetic "side effects" on circulation, respiration and neuroelectric irritability is presented. An example of the detailed structural-molecular studies is provided by the nuclear magnetic resonance investigations of anaesthetic conformational perturbations of haemoglobin which we have used as a model system for elucidating the ground rules of anaesthetic-protein interactions.

  19. Molecular basis of classic galactosemia from the structure of human galactose 1-phosphate uridylyltransferase

    PubMed Central

    McCorvie, Thomas J.; Kopec, Jolanta; Pey, Angel L.; Fitzpatrick, Fiona; Patel, Dipali; Chalk, Rod; Shrestha, Leela; Yue, Wyatt W.

    2016-01-01

    Classic galactosemia is a potentially lethal disease caused by the dysfunction of galactose 1-phosphate uridylyltransferase (GALT). Over 300 disease-associated GALT mutations have been reported, with the majority being missense changes, although a better understanding of their underlying molecular effects has been hindered by the lack of structural information for the human enzyme. Here, we present the 1.9 Å resolution crystal structure of human GALT (hGALT) ternary complex, revealing a homodimer arrangement that contains a covalent uridylylated intermediate and glucose-1-phosphate in the active site, as well as a structural zinc-binding site, per monomer. hGALT reveals significant structural differences from bacterial GALT homologues in metal ligation and dimer interactions, and therefore is a zbetter model for understanding the molecular consequences of disease mutations. Both uridylylation and zinc binding influence the stability and aggregation tendency of hGALT. This has implications for disease-associated variants where p.Gln188Arg, the most commonly detected, increases the rate of aggregation in the absence of zinc likely due to its reduced ability to form the uridylylated intermediate. As such our structure serves as a template in the future design of pharmacological chaperone therapies and opens new concepts about the roles of metal binding and activity in protein misfolding by disease-associated mutants. PMID:27005423

  20. Molecular dynamics simulations on local structure and diffusion in liquid Ti x Al 1- x alloys

    NASA Astrophysics Data System (ADS)

    Xia, J. H.; Liu, C. S.; Cheng, Z. F.; Shi, D. P.

    2011-10-01

    The microscopic structure and dynamics of liquid Ti xAl 1- x alloys together with pure liquid Ti and Al metals were investigated by means of molecular dynamics simulations. This work gives the structural properties, including pair-correlation function, bond-angle distribution function, HA and Voronoi indices, and their composition dependence. The dynamical properties have also been studied. The calculated pair-correlation function, bond-angle distribution function, and HA and Voronoi indices suggest that the stoichiometric composition Ti 0.75Al 0.25 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum diffusion coefficient at this composition. These results indicate that the mobility of atoms strongly depends on their atomic local structure.